sptdesk.bib

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@ARTICLE{abe1994,
  author = {Abe, T and Early, A and Siegert, F and Weijer, C and Williams, J},
  title = {Patterns of cell movement within the Dictyostelium slug revealed
	by cell type-specific, surface labeling of living cells.},
  journal = {Cell},
  year = {1994},
  volume = {77},
  pages = {687-699},
  endnotereftype = {Journal Article},
  keywords = {locomotion motility locomotion motility multicellular stage pseudoplasmodium
	slug migration differentiation / dedifferentiation / cell-type regulation
	/ cell choice / cell fate},
  shorttitle = {Patterns of cell movement within the Dictyostelium slug revealed by
	cell type-specific, surface labeling of living cells.}
}

@ARTICLE{Acton2002,
  author = {Acton, S. T. and Wethmar, K. and Ley, K.},
  title = {Automatic tracking of rolling leukocytes in vivo},
  journal = {Microvasc Res},
  year = {2002},
  volume = {63},
  pages = {139-48},
  number = {1},
  month = {Jan},
  note = {21624400 0026-2862 Journal Article},
  abstract = {The analysis of instantaneous and average rolling leukocyte velocity
	is crucial to the study of inflammatory disease. In order to record
	features associated with leukocyte rolling, the leukocyte position
	must be tracked, typically by manual observation. Automated tracking
	of leukocytes is possible for in vitro studies, but not for recordings
	resulting from intravital experiments. Therefore, we have designed
	and implemented an image processing system for automated tracking
	of rolling leukocytes in vivo. The novel image processing techniques
	used in the tracking system successfully address the four major problems
	associated with tracking cells in vivo: background movement, severe
	image noise and clutter, cell deformation and contrast change, and
	occlusion of the target cell by other structures. We have tested
	the system in two experimental protocols in which leukocyte rolling
	is observed in venules of the mouse cremaster muscle with and without
	TNF-alpha treatment. The automated tracking system was validated
	by comparing automatically generated displacement and velocity data
	with data from the same recordings collected manually. The root mean
	squared error between the computed displacements and the manually
	measured displacements was less than 12% of the average displacement
	in TNF-alpha-treated venules. The average velocity error was also
	less than 12%. For untreated venules, the computed and measured displacements
	and velocities had an RMSE of less than 8%. The automated tracking
	system allows one, for the first time, to reliably track rolling
	leukocytes in vivo, thus eliminating possible investigator bias and
	increasing throughput.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11749081},
  endnotereftype = {Journal Article},
  keywords = {Animal Cell Movement Cells, Cultured Contrast Media/pharmacology Image
	Processing, Computer-Assisted/*methods Leukocytes/*metabolism Mice
	Mice, Inbred C57BL Microscopy, Video/*methods Models, Statistical
	Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Tumor
	Necrosis Factor/metabolism/pharmacology},
  shorttitle = {Automatic tracking of rolling leukocytes in vivo},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11749081}
}

@ARTICLE{Anand2003,
  author = {Anand, M. and McFarland, A. R. and Rajagopal, K. R.},
  title = {Gas mixing for achieving suitable conditions for single point aerosol
	sampling in a straight tube: experimental and numerical results},
  journal = {Health Phys},
  year = {2003},
  volume = {84},
  pages = {82-91},
  number = {1},
  month = {Jan},
  note = {22386141 0017-9078 Journal Article},
  abstract = {Experimental measurements of velocity and tracer gas concentration
	are taken in a straight tube to evaluate the effectiveness of mixing
	in achieving conditions as required by ANSI N13.1-1999 for single
	point extractive sampling from stacks and ducts of nuclear facilities.
	Mixing is evaluated for inlet turbulent intensities of 1.5%, 10%,
	and 20%, achieved by introducing various bi-plane grids, and for
	conditions generated by a commercial static gas mixer. The data obtained
	(at Reynolds number = 15,000) highlight the importance of inlet turbulence
	intensity in the process of turbulent dispersion of a dilute gas.
	The gas mixer does not introduce significant pressure losses and
	unlike bi-plane grids, the turbulence downstream of the mixer is
	not homogenous. A judicious choice of the release location that uses
	the large scale eddies and inhomogeneity of the turbulence ensures
	that the specified ANSI N13.1-1999 criteria are attained within 7
	diameters downstream of the duct inlet. This is significantly more
	effective than a bi-plane grid where even with 20% inlet intensity
	the criteria are met only at 21 diameters downstream. The predictions
	of a proposed semi-empirical correlation match favorably with data.
	For example, at 18 diameters downstream with inlet intensities of
	1.5% and 10%, the predicted coefficients of variation (COVs) of 150%
	and 65% are close to the actual values of 154% and 50%; where the
	COV of a set of measurements is the ratio of the standard deviation
	of the set to its mean value. The corresponding results obtained
	using commercially available software are 141% and 12%. Results from
	a particle-tracking model show good qualitative trends, but they
	should not be used to determine compliance with the requirements
	of the ANSI standard.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12498520},
  endnotereftype = {Journal Article},
  keywords = {Aerosols Equipment Design Gases/*analysis *Nuclear Reactors Radiation
	Monitoring/instrumentation/*methods Support, Non-U.S. Gov't},
  shorttitle = {Gas mixing for achieving suitable conditions for single point aerosol
	sampling in a straight tube: experimental and numerical results},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12498520}
}

@ARTICLE{cmaderson1992,
  author = {Anderson, C. M. and Georgiou, G. N. and Morrison, I. E. and Stevenson,
	G. V. and Cherry, R. J.},
  title = {Tracking of cell surface receptors by fluorescence digital imaging
	microscopy using a charge-coupled device camera. Low-density lipoprotein
	and influenza virus receptor mobility at 4 degrees C},
  journal = {J Cell Sci},
  year = {1992},
  volume = {101 ( Pt 2)},
  pages = {415-25},
  month = {Feb},
  note = {92332618 0021-9533 Journal Article},
  abstract = {A fluorescence imaging system, based on using a cooled slow-scan CCD
	camera, has been developed for tracking receptors on the surfaces
	of living cells. The technique is applicable to receptors for particles
	such as lipoproteins and viruses that can be labeled with a few tens
	of fluorophores. The positions of single particles in each image
	are determined to within 25 nm by fitting the fluorescence distribution
	to a two-dimensional Gaussian function. This procedure also provides
	an accurate measure of intensity, which is used as a tag for automated
	tracking of particles from frame to frame. The method is applied
	to an investigation of the mobility of receptors for LDL and influenza
	virus particles on human dermal fibroblasts at 4 degrees C. In contrast
	to previous studies by FRAP (fluorescence recovery after photo-bleaching),
	it is found that receptors have a low but measurable mobility at
	4 degrees C. Analysis of individual particle tracks indicates that
	whilst some receptors undergo random diffusion, others undergo directed
	motion (flow) or diffusion restricted to a domain. A procedure is
	proposed for subdividing receptors according to their different types
	of motion and hence determining their motional parameters. The finding
	that receptors are not completely immobilised at 4 degrees C is significant
	for studies of receptor distributions performed at this temperature.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1629253},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport Cell Membrane/metabolism/*ultrastructure Cold
	Diffusion Fibroblasts/ultrastructure Human Image Processing, Computer-Assisted/*methods
	Microscopy, Fluorescence/*methods Models, Statistical Orthomyxoviridae
	Receptors, LDL/*metabolism/ultrastructure Receptors, Virus/*metabolism/ultrastructure
	Support, Non-U.S. Gov't},
  shorttitle = {Tracking of cell surface receptors by fluorescence digital imaging
	microscopy using a charge-coupled device camera. Low-density lipoprotein
	and influenza virus receptor mobility at 4 degrees C},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1629253}
}

@ARTICLE{Apgar2000BJ.pdf,
  author = {Apgar, J. and Tseng, Y. and Fedorov, E. and Herwig, M. B. and Almo,
	S. C. and Wirtz, D.},
  title = {Multiple-particle tracking measurements of heterogeneities in solutions
	of actin filaments and actin bundles},
  journal = {Biophys J},
  year = {2000},
  volume = {79},
  pages = {1095-106},
  number = {2},
  month = {Aug},
  note = {20380705 0006-3495 Journal Article},
  abstract = {One of the central functions of actin cytoskeleton is to provide the
	mechanical support required for the establishment and maintenance
	of cell morphology. The mechanical properties of actin filament assemblies
	are a consequence of both the available polymer concentration and
	the actin regulatory proteins that direct the formation of higher
	order structures. By monitoring the displacement of well-dispersed
	microspheres via fluorescence microscopy, we probe the degree of
	spatial heterogeneity of F-actin gels and networks in vitro. We compare
	the distribution of the time-dependent mean-square displacement (MSD)
	of polystyrene microspheres imbedded in low- and high-concentration
	F-actin solutions, in the presence and absence of the F-actin-bundling
	protein fascin. The MSD distribution of a 2. 6-microM F-actin solution
	is symmetric and its standard deviation is similar to that of a homogeneous
	solution of glycerol of similar zero-shear viscosity. However, increasing
	actin concentration renders the MSD distribution wide and asymmetric,
	an effect enhanced by fascin. Quantitative changes in the shape of
	the MSD distribution correlate qualitatively with the presence of
	large heterogeneities in F-actin solutions produced by increased
	filament concentration and the presence of actin bundles, as detected
	by confocal microscopy. Multiple-particle tracking offers a new,
	quantitative method to characterize the organization of biopolymers
	in solution.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10920039},
  endnotereftype = {Journal Article},
  keywords = {Actins/*chemistry/physiology/*ultrastructure Animal Chickens Cytoskeleton/physiology
	Microscopy, Confocal/methods Microscopy, Fluorescence/methods Microspheres
	Models, Molecular Muscle, Skeletal/physiology Protein Conformation
	Solutions Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S.
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Multiple-particle tracking measurements of heterogeneities in solutions
	of actin filaments and actin bundles},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10920039}
}

@ARTICLE{Arnheiter1984,
  author = {Arnheiter, H. and Dubois-Dalcq, M. and Lazzarini, R. A.},
  title = {Direct visualization of protein transport and processing in the living
	cell by microinjection of specific antibodies},
  journal = {Cell},
  year = {1984},
  volume = {39},
  pages = {99-109},
  number = {1},
  month = {Nov},
  note = {0092-8674 (Print) Journal Article},
  abstract = {We have prepared polyclonal antibodies to the cytoplasmic portion
	of the envelope glycoprotein G of vesicular stomatitis virus (VSV)
	by using synthetic peptides corresponding to either the 22 or 11
	ultimate carboxy-terminal residues of the G as immunogens. When antibodies
	to the 22 residue peptide are microinjected into monolayer baby hamster
	kidney cells before or shortly after infection with wild-type VSV,
	G protein accumulates in large intracellular patches and little G
	is observed in the Golgi complex or at the cell surface. In contrast,
	when antibodies to the 11 residue peptide are injected, no such patches
	are observed and G protein is seen colocalized with the injected
	antibody at the endoplasmic reticulum, in the Golgi complex, in transport
	vesicles, and at the plasma membrane. Microinjection of these antibodies
	does not disturb the pathway or kinetics of G-protein transport.
	In cells infected with a temperature-sensitive mutant of VSV, 045,
	the glycoprotein accumulates in the endoplasmic reticulum at 39.8
	degrees C, but rapidly moves through the Golgi apparatus and then
	to the cell surface after a temperature shift-down to 32 degrees
	C. Using rhodamine-coupled antibodies to the 11 residue peptide,
	a microscope stage equipped for precise temperature control, and
	a silicon intensifier target video camera, we can visualize by video
	light microscopy the synchronized exocytotic transport of the G protein
	directly in the living cell.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6091920},
  endnotereftype = {Journal Article},
  keywords = {Animals *Antibodies Cell Line Cricetinae Fluorescent Antibody Technique
	Kidney Kinetics Microinjections Microscopy, Electron Mutation Subcellular
	Fractions/metabolism/ultrastructure Vesicular stomatitis-Indiana
	virus/*genetics Video Recording Viral Envelope Proteins/analysis/*metabolism},
  shorttitle = {Direct visualization of protein transport and processing in the living
	cell by microinjection of specific antibodies},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6091920}
}

@ARTICLE{Awasthi1994,
  author = {Awasthi, V and Doolittle, KW and Parulkar, G and McNally, JG},
  title = {Cell tracking using a distributed algorithm for 3-D image segmentation},
  journal = {Bioimaging},
  year = {1994},
  volume = {2},
  pages = {98-112},
  abstract = {We have developed and tested an automated method for simultaneous
	3-D tracking of numerous, fluorescently-tagged cells. The procedure
	uses multiple thresholding to segment individual cells at a starting
	timepoint, and then iteratively applies a template-matching algorithm
	to locate a particular cell's position at subsequent timepoints.
	To speed up the method, we have developed a distributed implementation
	in which template matching is carried out in parallel on several
	different server machines. The distributed implementation showed
	a monotonic decrease in response time with increasing number of servers
	(up to 15 tested), demonstrating that the tracking algorithm is well
	suited to parallelization, and that nearly real-time performance
	could be expected on a parallel processor. Of four different template
	matching statistics tested for 3-D tracking of amoebae from the cellular
	slime mould Dictyostelium discoideum, we found that the automated
	procedure performed best when using a correlation statistic for matching.
	Using this statistic, the method achieved a 98.5% success rate in
	correctly identifying a cell from one time point to the next. This
	method is now being used regularly for 3-D tracking of normal and
	mutant cells of D. discoideum, and as such provides a means to quantify
	the motion of many cells within a three-dimensional tissue mass.},
  endnotereftype = {Journal Article},
  keywords = {3-D microscopy; cell tracking; image segmentation; Dictyostelium},
  shorttitle = {Cell tracking using a distributed algorithm for 3-D image segmentation}
}

@ARTICLE{Axelrod1976,
  author = {Axelrod, D. and Koppel, D. E. and Schlessinger, J. and Elson, E.
	and Webb, W. W.},
  title = {Mobility measurement by analysis of fluorescence photobleaching recovery
	kinetics},
  journal = {Biophys J},
  year = {1976},
  volume = {16},
  pages = {1055-69},
  number = {9},
  month = {Sep},
  note = {0006-3495 Journal Article},
  abstract = {Fluorescence photobleaching recovery (FPR) denotes a method for measuring
	two-dimensional lateral mobility of fluorescent particles, for example,
	the motion of fluorescently labeled molecules in approximately 10
	mum2 regions of a single cell surface. A small spot on the fluorescent
	surface is photobleached by a brief exposure to an intense focused
	laser beam, and the subsequent recovery of the fluorescence is monitored
	by the same, but attenuated, laser beam. Recovery occurs by replenishment
	of intact fluorophore in the bleached spot by lateral transport from
	the surrounding surface. We present the theoretical basis and some
	practical guidelines for simple, rigorous analysis of FPR experiments.
	Information obtainable from FPR experiments includes: (a) identification
	of transport process type, i.e. the admixture of random diffusion
	and uniform directed flow; (b) determination of the absolute mobility
	coefficient, i.e. the diffusion constant and/or flow velocity; and
	(c) the fraction of total fluorophore which is mobile. To illustrate
	the experimental method and to verify the theory for diffusion, we
	describe some model experiments on aqueous solutions of rhodamine
	6G.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=786399},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport *Cytological Techniques Diffusion *Fluorescence
	*Lasers Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Mobility measurement by analysis of fluorescence photobleaching recovery
	kinetics},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=786399}
}

@ARTICLE{Barron1994,
  author = {Barron, J.L. and Fleet, D.J. and Beauchemin, S.S.},
  title = {Performance of optical flow techniques},
  journal = {Intern J Comput Vis},
  year = {1994},
  volume = {12},
  pages = {43-77},
  endnotereftype = {Journal Article},
  shorttitle = {Performance of optical flow techniques}
}

@ARTICLE{Barron1997,
  author = {Barron, J.L. and Liptay, L.},
  title = {Measuring 3D plant growth using optical flow},
  journal = {Bioimaging},
  year = {1997},
  volume = {5},
  pages = {82-86},
  endnotereftype = {Journal Article},
  shorttitle = {Measuring 3D plant growth using optical flow}
}

@ARTICLE{Bausch1999,
  author = {Bausch, A. R. and Moller, W. and Sackmann, E.},
  title = {Measurement of local viscoelasticity and forces in living cells by
	magnetic tweezers},
  journal = {Biophys J},
  year = {1999},
  volume = {76},
  pages = {573-9},
  number = {1 Pt 1},
  month = {Jan},
  note = {99093419 0006-3495 Journal Article},
  abstract = {We measured the viscoelastic properties of the cytoplasm of J774 macrophages
	with a recently developed microrheometer. Ferromagnetic beads (1.3
	microm in diameter) were used to determine the local viscoelastic
	moduli. Step-force pulses were applied to the magnetic beads and
	the displacement was observed by single particle tracking. By analyzing
	the creep response curves in terms of a triphasic mechanical equivalent
	circuit, we measured the shear elastic modulus, the effective viscosities,
	and the strain relaxation time. The values of the shear modulus vary
	by more than an order of magnitude within the cell population (range,
	20-735 Pa; average, 343 Pa) and by a factor of 2 within single cells.
	The effective viscosity of the cytoplasm exhibits a relatively sharp
	distribution about an average of eta = 210 Pa s (+/- 143 Pa s). We
	measured the displacement field generated by the local forces by
	observing the induced motion of nonmagnetic beads. Even at distances
	of the order of 1 microm, no induced motion was seen, suggesting
	that the cytoplasm is composed of clusters of densely packed and
	cross-linked filaments separated by soft regions. In another series
	of experiments we analyzed the magnetophoretic motion of the ferromagnetic
	beads at a constant magnetic force. Measuring the bead velocity parallel
	and perpendicular to the applied force showed that local active forces
	on the beads varied from 50 to 900 pN.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9876170},
  endnotereftype = {Journal Article},
  keywords = {Animal Biophysics Cell Line Colloids Cytoplasm/*physiology Elasticity
	Ferric Compounds Mice Rheology/*methods Support, Non-U.S. Gov't Viscosity},
  shorttitle = {Measurement of local viscoelasticity and forces in living cells by
	magnetic tweezers},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9876170}
}

@ARTICLE{Beauchemin1995,
  author = {Beauchemin, S. S. and Barron, J. L.},
  title = {The computation of optical flow},
  journal = {ACM Computing Surveys},
  year = {1995},
  volume = {27},
  pages = {433-467},
  endnotereftype = {Journal Article},
  shorttitle = {The computation of optical flow}
}

@INCOLLECTION{Becker1996,
  author = {Becker, P.},
  title = {Quantitative Fluorescence Measurements},
  booktitle = {Fluorescence imaging Spectroscopy \& Microscopy},
  publisher = {John Wiley \& Sons},
  year = {1996},
  editor = {Hermann, B.},
  endnotereftype = {Book Section},
  shorttitle = {Quantitative Fluorescence Measurements}
}

@ARTICLE{Ben-Tekaya2005,
  author = {Ben-Tekaya, H. and Miura, K. and Pepperkok, R. and Hauri, H. P.},
  title = {Live imaging of bidirectional traffic from the ERGIC},
  journal = {J Cell Sci},
  year = {2005},
  volume = {118},
  pages = {357-67},
  number = {Pt 2},
  month = {Jan 15},
  note = {0021-9533 Journal Article},
  abstract = {The endoplasmic reticulum-Golgi intermediate compartment (ERGIC) defined
	by the cycling lectin ERGIC-53 consists of tubulovesicular clusters,
	but it is unknown if these membranes are transport vehicles or stationary
	entities. Here, we show by live imaging that GFP-ERGIC-53 mainly
	localizes to long-lived stationary and some short-lived highly mobile
	elements. Unlike the anterograde marker VSV-G-GFP, GFP-ERGIC-53 does
	not vectorially move to the Golgi upon exit from the ERGIC, as assessed
	by a novel quantitative vector field method. Dual-color imaging of
	GFP-ERGIC-53 and a secretory protein (signal-sequence-tagged dsRed)
	reveals that the stationary elements are sites of repeated sorting
	of retrograde and anterograde cargo, and are interconnected by highly
	mobile elements. These results suggest that the ERGIC is stationary
	and not simply a collection of mobile carriers that mediate protein
	traffic from endoplasmic reticulum to Golgi.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15632110},
  endnotereftype = {Journal Article},
  shorttitle = {Live imaging of bidirectional traffic from the ERGIC},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15632110}
}

@BOOK{bergbook1993,
  title = {Random Walk in Biology},
  publisher = {Princeton University Press},
  year = {1993},
  author = {Berg, H},
  address = {Princeton},
  endnotereftype = {Book},
  shorttitle = {Random Walk in Biology}
}

@ARTICLE{Bergman1999,
  author = {Bergman, A. J. and Zygourakis, K.},
  title = {Migration of lymphocytes on fibronectin-coated surfaces: temporal
	evolution of migratory parameters},
  journal = {Biomaterials},
  year = {1999},
  volume = {20},
  pages = {2235-44},
  number = {23-24},
  month = {Dec},
  note = {0142-9612 Journal Article},
  abstract = {Lymphocytes typically interact with implanted biomaterials through
	adsorbed exogenous proteins. To provide a more complete characterization
	of these interactions, analysis of lymphocyte migration on adsorbed
	extracellular matrix proteins must accompany the commonly performed
	adhesion studies. We report here a comparison of the migratory and
	adhesion behavior of Jurkat cells (a T lymphoblastoid cell line)
	on tissue culture treated and untreated polystyrene surfaces coated
	with various concentrations of fibronectin. The average speed of
	cell locomotion showed a biphasic response to substrate adhesiveness
	for cells migrating on untreated polystyrene and a monotonic decrease
	for cells migrating on tissue culture-treated polystyrene. A modified
	approach to the persistent random walk model was implemented to determine
	the time dependence of cell migration parameters. The random motility
	coefficient showed significant increases with time when cells migrated
	on tissue culture-treated polystyrene surfaces, while it remained
	relatively constant for experiments with untreated polystyrene plates.
	Finally, a cell migration computer model was developed to verify
	our modified persistent random walk analysis. Simulation results
	suggest that our experimental data were consistent with temporally
	increasing random motility coefficients.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10614930},
  endnotereftype = {Journal Article},
  keywords = {Adsorption Algorithms Cell Adhesion Cell Culture Techniques *Cell
	Movement Fibronectins/*metabolism Humans Jurkat Cells Lymphocytes/*cytology/metabolism
	Models, Biological Polystyrenes/metabolism Research Support, U.S.
	Gov't, Non-P.H.S. Stress, Mechanical Time Factors},
  shorttitle = {Migration of lymphocytes on fibronectin-coated surfaces: temporal
	evolution of migratory parameters},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10614930}
}

@ARTICLE{AmerChemicalSoc,
  author = {Bernard, A. and Delamarche, E. and Schmid, H. and Michel, B. and
	Bosshard, H. R. and Biebuyck, H.},
  title = {Printing patterns of proteins},
  journal = {Langmuir},
  year = {1998},
  volume = {14},
  pages = {2225-2229},
  number = {9},
  month = {APR 28},
  note = {Times Cited: 182 Letter English Cited References Count: 16 Zl025},
  abstract = {Microcontact printing of proteins proves to be an excellent means
	of directly patterning biomolecules on solid substrates. Monolayer
	quantities of protein equilibrated on the surface of a hydrophobic,
	elastomeric stamp are immobilized there to rinses with buffer. These
	biomolecules can nevertheless transfer with > 99% efficiency from
	the stamp to a substrate after just 1 s of contact. This capability
	allows the simple creation of functional patterns of proteins at
	scales that involve the placement of < 1000 molecules in well-defined
	locations on a surface. The method is suited for the transfer of
	proteins of many different types onto hydrophilic or hydrophobic
	substrates.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000073391300001},
  endnotereftype = {Journal Article},
  keywords = {self-assembled monolayers arrays gold immobilization surfaces},
  shorttitle = {Printing patterns of proteins},
  url = {<Go to ISI>://000073391300001}
}

@ARTICLE{Bernard2000,
  author = {Bernard, A. and Renault, J. P. and Michel, B. and Bosshard, H. R.
	and Delamarche, E.},
  title = {Microcontact Printing of Proteins},
  journal = {Advanced Materials},
  year = {2000},
  volume = {12},
  pages = {1071-1078},
  number = {14},
  note = {printout},
  endnotereftype = {Journal Article},
  shorttitle = {Microcontact Printing of Proteins}
}

@ARTICLE{Blocker1998,
  author = {Blocker, A. and Griffiths, G. and Olivo, J. C. and Hyman, A. A. and
	Severin, F. F.},
  title = {A role for microtubule dynamics in phagosome movement},
  journal = {J Cell Sci},
  year = {1998},
  volume = {111 ( Pt 3)},
  pages = {303-12},
  month = {Feb},
  note = {0021-9533 (Print) Journal Article},
  abstract = {We have shown previously that intracellular phagosome movement requires
	microtubules. Here we provide evidence that within cells phagosomes
	display two different kinds of microtubule-based movements in approximately
	equal proportions. The first type occurs predominantly in the cell
	periphery, often shortly after the phagosome is formed, and at speeds
	below 0.1 microm/second. The second is faster (0.2-1.5 micron/second)
	and occurs mainly after phagosomes have reached the cell interior.
	Treating cells with nanomolar concentrations of taxol or nocodazole
	alters microtubule dynamics without affecting either total polymer
	mass or microtubule organisation. Such treatments slow the accumulation
	of phagosomes in the perinuclear region and reduce the number of
	slow movements by up to 50% without affecting the frequency of fast
	movements. This suggests that a proportion of slow movements are
	mediated by microtubule dynamics while fast movements are powered
	by microtubule motors. In macrophages, interphase microtubules radiate
	from the microtubule organising centre with their plus-end towards
	the cell periphery. To understand the behaviour of 'early' phagosomes
	at the cell periphery we investigated their ability to bind microtubule
	plus-ends in vitro. We show that early phagosomes have a strong preference
	for microtubule plus-ends, whereas 'late' phagosomes do not, and
	that plus-end affinity requires the presence of microtubule-associated
	proteins within cytosol. We suggest that phagosomes can bind to the
	plus-ends of dynamic microtubules and move by following their shrinkage
	or growth.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9427679},
  endnotereftype = {Journal Article},
  keywords = {Actins/physiology Animals Cell Line Mice Microtubule-Associated Proteins/physiology
	Microtubules/*physiology Movement Phagosomes/*physiology Rats Research
	Support, Non-U.S. Gov't},
  shorttitle = {A role for microtubule dynamics in phagosome movement},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9427679}
}

@ARTICLE{Blocker1997,
  author = {Blocker, A. and Severin, F. F. and Burkhardt, J. K. and Bingham,
	J. B. and Yu, H. and Olivo, J. C. and Schroer, T. A. and Hyman, A.
	A. and Griffiths, G.},
  title = {Molecular requirements for bi-directional movement of phagosomes
	along microtubules},
  journal = {J Cell Biol},
  year = {1997},
  volume = {137},
  pages = {113-29},
  number = {1},
  month = {Apr 7},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Microtubules facilitate the maturation of phagosomes by favoring their
	interactions with endocytic compartments. Here, we show that phagosomes
	move within cells along tracks of several microns centrifugally and
	centripetally in a pH- and microtubule-dependent manner. Phagosome
	movement was reconstituted in vitro and required energy, cytosol
	and membrane proteins of this organelle. The activity or presence
	of these phagosome proteins was regulated as the organelle matured,
	with "late" phagosomes moving threefold more frequently than "early"
	ones. The majority of moving phagosomes were minus-end directed;
	the remainder moved towards microtubule plus-ends and a small subset
	moved bi-directionally. Minus-end movement showed pharmacological
	characteristics expected for dyneins, was inhibited by immunodepletion
	of cytoplasmic dynein and could be restored by addition of cytoplasmic
	dynein. Plus-end movement displayed pharmacological properties of
	kinesin, was inhibited partially by immunodepletion of kinesin and
	fully by addition of an anti-kinesin IgG. Immunodepletion of dynactin,
	a dynein-activating complex, inhibited only minus-end directed motility.
	Evidence is provided for a dynactin-associated kinase required for
	dynein-mediated vesicle transport. Movement in both directions was
	inhibited by peptide fragments from kinectin (a putative kinesin
	membrane receptor), derived from the region to which a motility-blocking
	antibody binds. Polypeptide subunits from these microtubule-based
	motility factors were detected on phagosomes by immunoblotting or
	immunoelectron microscopy. This is the first study using a single
	in vitro system that describes the roles played by kinesin, kinectin,
	cytoplasmic dynein, and dynactin in the microtubule-mediated movement
	of a purified membrane organelle.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9105041},
  endnotereftype = {Journal Article},
  keywords = {Adenosine Triphosphate/pharmacology Animals Biological Transport/physiology
	Cells, Cultured/chemistry/metabolism/ultrastructure Cytosol/chemistry/enzymology
	Dynein ATPase/metabolism Hydrogen-Ion Concentration Kidney/cytology
	Kinesin/metabolism Latex Macrophages/cytology/metabolism/ultrastructure
	Membrane Proteins/metabolism Mice Microspheres Microtubule-Associated
	Proteins/metabolism Microtubules/*metabolism Phagosomes/chemistry/drug
	effects/*metabolism Phosphotransferases/metabolism Rats Receptors,
	Cell Surface/metabolism Research Support, Non-U.S. Gov't},
  shorttitle = {Molecular requirements for bi-directional movement of phagosomes along
	microtubules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9105041}
}

@ARTICLE{Blocker1996,
  author = {Blocker, A. and Severin, F. F. and Habermann, A. and Hyman, A. A.
	and Griffiths, G. and Burkhardt, J. K.},
  title = {Microtubule-associated protein-dependent binding of phagosomes to
	microtubules},
  journal = {J Biol Chem},
  year = {1996},
  volume = {271},
  pages = {3803-11},
  number = {7},
  month = {Feb 16},
  note = {0021-9258 (Print) Journal Article},
  abstract = {In macrophages, phagosome movement is microtubule-dependent. Microtubules
	are a prerequisite for phagosome maturation because they facilitate
	interactions between phagosomes and organelles of the endocytic pathway.
	We have established an in vitro assay that measures the binding of
	purified phagosomes to microtubules. This binding depends on the
	presence of membrane proteins, most likely integral to the surface
	of phagosomes, and on macrophage cytosol. The cytosolic binding factor
	can interact with microtubules prior to the addition of phagosomes
	to the assay, suggesting that it is a microtubule-associated protein
	(MAP). Consistent with this, depletion of MAPs from the cytosol by
	microtubule affinity removes all binding activity. Microtubule motor
	proteins show no binding activity, whereas a crude MAP preparation
	is sufficient to support binding and to restore full binding activity
	to MAP-depleted cytosol. We show that the activating MAP factor is
	a heat-sensitive protein(s) that migrates at around 150 kDa by gel
	filtration.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8631997},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Fractionation Cell Line Cytosol/metabolism/ultrastructure
	Endocytosis Horseradish Peroxidase Intracellular Membranes/metabolism/ultrastructure
	Kinetics Macrophages Membrane Fusion Membrane Proteins/isolation
	& purification/metabolism Microtubule-Associated Proteins/isolation
	& purification/*metabolism Microtubules/*metabolism/ultrastructure
	Phagosomes/*metabolism/ultrastructure Research Support, Non-U.S.
	Gov't},
  shorttitle = {Microtubule-associated protein-dependent binding of phagosomes to
	microtubules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8631997}
}

@ARTICLE{Bodnar2003,
  author = {Bodnar, A. and Bacso, Z. and Jenei, A. and Jovin, T. M. and Edidin,
	M. and Damjanovich, S. and Matko, J.},
  title = {Class I HLA oligomerization at the surface of B cells is controlled
	by exogenous beta(2)-microglobulin: implications in activation of
	cytotoxic T lymphocytes},
  journal = {Int Immunol},
  year = {2003},
  volume = {15},
  pages = {331-9},
  number = {3},
  month = {Mar},
  note = {22505480 0953-8178 Journal Article},
  abstract = {Submicroscopic molecular clusters (oligomers) of class I HLA have
	been detected by physical techniques [e.g. fluorescence resonance
	energy transfer (FRET) and single particle tracking of molecular
	diffusion] at the surface of various activated and transformed human
	cells, including B lymphocytes. Here, the sensitivity of this homotypic
	association to exogenous beta(2)-microglobulin (beta(2)m) and the
	role of free heavy chains (FHC) in class I HLA oligomerization were
	investigated on a B lymphoblastoid cell line, JY. Scanning near-field
	optical microscopy and FRET data both demonstrated that FHC and class
	I HLA heterodimers are co-clustered at the cell surface. Culturing
	the cells with excess beta(2)m resulted in a reduced co-clustering
	and decreased molecular homotypic association, as assessed by FRET.
	The decreased HLA clustering on JY target cells (antigen-presenting
	cells) was accompanied with their reduced susceptibility to specific
	lysis by allospecific CD8(+) cytotoxic T lymphocytes (CTL). JY B
	cells with reduced HLA clustering also provoked significantly weaker
	T cell activation signals, such as lower expression of CD69 activation
	marker and lower magnitude of TCR down-regulation, than did the untreated
	B cells. These results together suggest that the actual level of
	beta(2)m available at the cell surface can control CTL activation
	and the subsequent cytotoxic effector function through regulation
	of the homotypic HLA-I association. This might be especially important
	in some inflammatory and autoimmune diseases where elevated serum
	beta(2)m levels are reported.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12618477},
  endnotereftype = {Journal Article},
  shorttitle = {Class I HLA oligomerization at the surface of B cells is controlled
	by exogenous beta(2)-microglobulin: implications in activation of
	cytotoxic T lymphocytes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12618477}
}

@ARTICLE{BolteJM2006,
  author = {S. Bolte and F. P. Cordeli{\`e}res},
  title = {A guided tour into subcellular colocalization analysis in light microscopy.},
  journal = {J Microsc},
  year = {2006},
  volume = {224},
  pages = {213--232},
  number = {Pt 3},
  month = {Dec},
  abstract = {It is generally accepted that the functional compartmentalization
	of eukaryotic cells is reflected by the differential occurrence of
	proteins in their compartments. The location and physiological function
	of a protein are closely related; local information of a protein
	is thus crucial to understanding its role in biological processes.
	The visualization of proteins residing on intracellular structures
	by fluorescence microscopy has become a routine approach in cell
	biology and is increasingly used to assess their colocalization with
	well-characterized markers. However, image-analysis methods for colocalization
	studies are a field of contention and enigma. We have therefore undertaken
	to review the most currently used colocalization analysis methods,
	introducing the basic optical concepts important for image acquisition
	and subsequent analysis. We provide a summary of practical tips for
	image acquisition and treatment that should precede proper colocalization
	analysis. Furthermore, we discuss the application and feasibility
	of colocalization tools for various biological colocalization situations
	and discuss their respective strengths and weaknesses. We have created
	a novel toolbox for subcellular colocalization analysis under ImageJ,
	named JACoP, that integrates current global statistic methods and
	a novel object-based approach.},
  bdsk-url-1 = {http://dx.doi.org/10.1111/j.1365-2818.2006.01706.x},
  doi = {10.1111/j.1365-2818.2006.01706.x},
  institution = {Plateforme d'Imagerie et de Biologie Cellulaire, IFR 87 la Plante
	et son Environnement, Institut des Sciences du V{\'e}g{\'e}tal, Avenue
	de la Terrasse, 91198 Gif-sur-Yvette Cedex, France. Susanne.Bolte@isv.cnrs-gif.fr},
  language = {eng},
  medline-pst = {ppublish},
  owner = {Kota},
  pii = {JMI1706},
  pmid = {17210054},
  timestamp = {2011.03.10},
  url = {http://dx.doi.org/10.1111/j.1365-2818.2006.01706.x}
}

@ARTICLE{Borgdorff2002,
  author = {Borgdorff, A. J. and Choquet, D.},
  title = {Regulation of AMPA receptor lateral movements},
  journal = {Nature},
  year = {2002},
  volume = {417},
  pages = {649-53},
  number = {6889},
  month = {Jun 6},
  note = {22045973 0028-0836 Journal Article},
  abstract = {An essential feature in the modulation of the efficacy of synaptic
	transmission is rapid changes in the number of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole
	propionic acid) receptors at post-synaptic sites on neurons. Regulation
	of receptor endo- and exocytosis has been shown to be involved in
	this process. Whether regulated lateral diffusion of receptors in
	the plasma membrane also participates in receptor exchange to and
	from post-synaptic sites remains unknown. We analysed the lateral
	mobility of native AMPA receptors containing the glutamate receptor
	subunit GluR2 in rat cultured hippocampal neurons, using single-particle
	tracking and video microscopy. Here we show that AMPA receptors alternate
	within seconds between rapid diffusive and stationary behaviour.
	During maturation of neurons, stationary periods increase in frequency
	and length, often in spatial correlation with synaptic sites. Raising
	intracellular calcium, a central element in synaptic plasticity,
	triggers rapid receptor immobilization and local accumulation on
	the neuronal surface. We suggest that calcium influx prevents AMPA
	receptors from diffusing, and that lateral receptor diffusion to
	and from synaptic sites acts in the rapid and controlled regulation
	of receptor numbers at synapses.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12050666},
  endnotereftype = {Journal Article},
  keywords = {Animal Calcium/metabolism Cell Differentiation Cells, Cultured Diffusion
	Hippocampus/cytology Kinetics Microscopy, Video Neurons/cytology/*metabolism
	Photolysis Protein Subunits Protein Transport Rats Receptors, AMPA/*metabolism
	Support, Non-U.S. Gov't Synapses/*metabolism},
  shorttitle = {Regulation of AMPA receptor lateral movements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12050666}
}

@ARTICLE{Borisy2000,
  author = {Borisy, G.G. and Svitkina, T.M.},
  title = {Actin machinery: Pushing the envelope},
  journal = {Curr. Opin. Cell Biol.},
  year = {2000},
  volume = {12},
  pages = {104-112},
  endnotereftype = {Journal Article},
  shorttitle = {Actin machinery: Pushing the envelope}
}

@ARTICLE{Bornfleth1999,
  author = {Bornfleth, H. and Edelmann, P. and Zink, D. and Cremer, T. and Cremer,
	C.},
  title = {Quantitative motion analysis of subchromosomal foci in living cells
	using four-dimensional microscopy},
  journal = {Biophys J},
  year = {1999},
  volume = {77},
  pages = {2871-86},
  number = {5},
  month = {Nov},
  note = {0 0006-3495 Journal article},
  abstract = {The motion of subchromosomal foci and of whole chromosome territories
	in live human cell nuclei was investigated in four-dimensional space-time
	images. Visualization of subchromosomal foci was achieved by incorporating
	Cy3-dUTP into the nuclear DNA of two different cell types after microinjection.
	A subsequent segregation of the labeled cell nuclei led to the presence
	of only a few labeled chromosome territories on a background of nonlabeled
	chromatin (. Hum. Genet. 102:241-251). This procedure yielded many
	distinct signals in a given cell nucleus. Motion analysis in four-dimensional
	space-time images was performed using single-particle tracking and
	a statistical approach to the detection of a possible directional
	motion of foci relative to the center of mass of a chromosome territory.
	The accuracy of the analysis was tested using simulated data sets
	that closely mirrored the experimental setup and using microparticles
	of known size. Application of the analysis tools to experimental
	data showed that mutual diffusion-like movements between foci located
	on different chromosomes were more pronounced than inside the territories.
	In the time range observed, movements of individual foci could best
	be described by a random diffusion process. The statistical test
	for joint directed motion of several foci inside chromosome territories
	revealed that foci occasionally switched from random to directional
	motion inside the territories.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=0010545385},
  endnotereftype = {Journal Article},
  shorttitle = {Quantitative motion analysis of subchromosomal foci in living cells
	using four-dimensional microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=0010545385}
}

@ARTICLE{Branch1998,
  author = {Branch, D. W. and Corey, J. M. and Weyhenmeyer, J. A. and Brewer,
	G. J. and Wheeler, B. C.},
  title = {Microstamp patterns of biomolecules for high-resolution neuronal
	networks},
  journal = {Med Biol Eng Comput},
  year = {1998},
  volume = {36},
  pages = {135-41},
  number = {1},
  month = {Jan},
  note = {0140-0118 (Print) Journal Article Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't,
	P.H.S.},
  abstract = {A microstamping technique has been developed for high-resolution patterning
	of proteins on glass substrates for the localisation of neurons and
	their axons and dendrites. The patterning process uses a microfabricated
	polydimethylsiloxane stamp with micrometer length features to transfer
	multiple types of biomolecules to silane-derivatised substrates,
	using glutaraldehyde as a homobifunctional linker. To test the efficacy
	of the procedure, substrates are compared in which poly-d-lysine
	(PDL) was physisorbed and patterned by photoresist with those stamped
	with PDL. Fluorescein isothiocyanate labelled poly-l-lysine was used
	to verify the presence and uniformity of the patterns on the glass
	substrates. As a biological assay, B104 neuroblastoma cells were
	plated on stamped and physisorbed glass coverslips. Pattern compliance
	was determined as the percentage of cells on the pattern 8 h after
	plating. Results indicate that the stamping and photoresist patterning
	procedure are equivalent. Substrates stamped with PDL had an average
	pattern compliance of 52.6 +/- 4.4%, compared to 54.6 +/- 8.1% for
	physisorbed substrates. Measures of background avoidance were also
	equivalent. As the procedure permits successive stamping of multiple
	proteins, each with its own micropattern, it should be very useful
	for defining complex substrates to assist in cell patterning and
	other cell guidance studies.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9614762},
  endnotereftype = {Journal Article},
  keywords = {Cells, Cultured Cytology/*instrumentation Humans Nerve Net Neuroblastoma
	Tumor Cells, Cultured},
  shorttitle = {Microstamp patterns of biomolecules for high-resolution neuronal networks},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9614762}
}

@ARTICLE{Branch2001,
  author = {Branch, D. W. and Wheeler, B. C. and Brewer, G. J. and Leckband,
	D. E.},
  title = {Long-term stability of grafted polyethylene glycol surfaces for use
	with microstamped substrates in neuronal cell culture},
  journal = {Biomaterials},
  year = {2001},
  volume = {22},
  pages = {1035-47},
  number = {10},
  month = {May},
  note = {0142-9612 (Print) Journal Article Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, P.H.S.},
  abstract = {Crucial to long-term stability of neuronal micropatterns is functional
	retention of the underlying substratum while exposed to cell culture
	conditions. We report on the ability of covalently bound PEG films
	in long-term cell culture to continually retard protein adhesion
	and cell growth. PDMS microstamps were used to create poly-d-lysine
	(PDL) substrates permissive to cell attachment and growth, and polyethylene
	glycol (PEG) substrates were used to minimize protein and cell adhesion.
	Film thickness was measured using null ellipsometry and atomic force
	microscopy (AFM). Organosilane film structure was examined using
	Fourier transform infrared (FT-IR) spectroscopy. Long-term film stability
	in cell culture conditions was tested by immersion in 0.1 M sodium
	phosphate buffer pH 7.4 for up to one month. Null ellipsometry and
	water contact measurements indicated that organosilane films were
	stable up to one month, whereas the PEG film thickness declined rapidly
	after day 25. Hippocampal cells plated at 200 cells/mm2 on uniform
	PEG substrates gave a steady increase in biofilm thickness on PEG
	films throughout the culture, possibly from proteins of neuronal
	origin. We found that all the layers in the cross-linking procedure
	were stable in cell culture conditions, with the exception of PEG,
	which degraded after day 25.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11352085},
  endnotereftype = {Journal Article},
  keywords = {Animals *Biocompatible Materials Cell Adhesion Cell Division Cells,
	Cultured Cross-Linking Reagents Drug Stability Materials Testing
	Microscopy, Atomic Force Neurons/*cytology *Polyethylene Glycols
	Rats Silicon Spectroscopy, Fourier Transform Infrared Surface Properties
	Water},
  shorttitle = {Long-term stability of grafted polyethylene glycol surfaces for use
	with microstamped substrates in neuronal cell culture},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11352085}
}

@ARTICLE{Branch2000,
  author = {Branch, D. W. and Wheeler, B. C. and Brewer, G. J. and Leckband,
	D. E.},
  title = {Long-term maintenance of patterns of hippocampal pyramidal cells
	on substrates of polyethylene glycol and microstamped polylysine},
  journal = {IEEE Trans Biomed Eng},
  year = {2000},
  volume = {47},
  pages = {290-300},
  number = {3},
  month = {Mar},
  note = {0018-9294 (Print) Journal Article Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, P.H.S.},
  abstract = {For neurons to attach and remain in precise micropatterns for weeks
	in culture, background molecules that remain nonpermissive for extended
	culture durations need to be identified. Nonpermissive background
	molecules of either polyethylene glycol (PEG) or the amino acid serine
	(C3H7NO3) were evaluated. The foreground regions were microstamped
	with 3-, 5-, or 10-micron lines of poly-D-lysine (PDL), which promotes
	neural attachment and growth. After 29 days in culture the foreground
	compliance, or the fraction of all live somata which rested on the
	desired PDL surface, averaged 86% for serine and 90% for PEG, with
	only a small decline. The background compliance, or the fraction
	of square areas in the pattern background which were free of neurite
	extension, declined from highs of 40% and 55% (midculture) to 5.5%
	and 12% (29 days) for serine and PEG, respectively. Images of the
	cultures suggest that PEG is significantly more effective as a nonpermissive
	substrate. We conclude that these materials, especially PEG, are
	adequate for the maintenance of long-term patterned cultures of neurons.
	We believe that this is the first report of high-quality long-term
	patterning of cultured neurons.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10743770},
  endnotereftype = {Journal Article},
  keywords = {Adsorption Animals *Biocompatible Materials Biosensing Techniques
	Cell Culture Techniques/*methods Cells, Cultured Compliance Glass/chemistry
	Hippocampus/*cytology/embryology/physiology Microscopy, Fluorescence
	Molecular Weight Neurites/physiology *Polyethylene Glycols/chemistry/pharmacokinetics
	*Polylysine Pyramidal Cells/*cytology/physiology Rats Serine/metabolism
	Silanes/chemistry Surface Properties},
  shorttitle = {Long-term maintenance of patterns of hippocampal pyramidal cells on
	substrates of polyethylene glycol and microstamped polylysine},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10743770}
}

@ARTICLE{Breen1994,
  author = {Breen, E J and Williams, K L},
  title = {Optical flow analysis of the ventral cellular layer of the migrating
	Dictyostelium discoideum slug.},
  journal = {Microbiol. UK},
  year = {1994},
  volume = {140},
  pages = {1241-1252},
  endnotereftype = {Journal Article},
  keywords = {locomotion motility locomotion motility shadowing / rotary shadowing
	computer programs / modeling / mathematics},
  shorttitle = {Optical flow analysis of the ventral cellular layer of the migrating
	Dictyostelium discoideum slug.}
}

@ARTICLE{Brock2003,
  author = {Brock, A. and Chang, E. and Ho, C. C. and LeDuc, P. and Jiang, X.
	and Whitesides, G. M. and Ingber, D. E.},
  title = {Geometric determinants of directional cell motility revealed using
	microcontact printing},
  journal = {Langmuir},
  year = {2003},
  volume = {19},
  pages = {1611-7},
  number = {5},
  month = {Mar 4},
  note = {0743-7463 (Print) Journal Article},
  abstract = {Mammalian cells redirect their movement in response to changes in
	the physical properties of their extracellular matrix (ECM) adhesive
	scaffolds, including changes in available substrate area, shape,
	or flexibility. Yet, little is known about the cell's ability to
	discriminate between different types of spatial signals. Here we
	utilize a soft-lithography-based, microcontact printing technology
	in combination with automated computerized image analysis to explore
	the relationship between ECM geometry and directional motility. When
	fibroblast cells were cultured on fibronectin-coated adhesive islands
	with the same area (900 micrometers2) but different geometric forms
	(square, triangle, pentagon, hexagon, trapezoid, various parallelograms)
	and aspect ratios, cells preferentially extended new lamellipodia
	from their corners. In addition, by imposing these simple geometric
	constraints through ECM, cells were directed to deposit new fibronectin
	fibrils in these same corner regions. These data indicate that mammalian
	cells can sense edges within ECM patterns that exhibit a wide range
	of angularity and that they use these spatial cues to guide where
	they will deposit ECM and extend new motile processes during the
	process of directional migration.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14674434},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion Cell Movement/*physiology Cell Size Cells, Cultured
	Extracellular Matrix/physiology/*ultrastructure Fibroblasts/*physiology/ultrastructure
	Fibronectins/*physiology Focal Adhesions/physiology *Image Processing,
	Computer-Assisted Mice NIH 3T3 Cells Pseudopodia/*physiology Research
	Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Geometric determinants of directional cell motility revealed using
	microcontact printing},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14674434}
}

@ARTICLE{Broday2002,
  author = {Broday, D. M.},
  title = {Motion of nanobeads proximate to plasma membranes during single particle
	tracking},
  journal = {Bull Math Biol},
  year = {2002},
  volume = {64},
  pages = {531-63},
  number = {3},
  month = {May},
  note = {22089675 0092-8240 Journal Article},
  abstract = {Drag and torque on nanobeads translating within the pericellular layer
	while attached to glycolipids of the plasma membrane are calculated
	by a novel hydrodynamic model. The model considers a bead that translates
	proximate to a rigid planar interface that separates two distinct
	Brinkman media. The hydrodynamic resistance is calculated numerically
	by a modified boundary integral equation formulation, where the pertinent
	boundary conditions result in a hybrid system of Fredholm integrals
	of the first and second kinds. The hydrodynamic resistance on the
	translating bead is calculated for different combinations of the
	Brinkman screening lengths in the two layers, and for different viscosity
	ratios. Depending on the bead-membrane separation and on the hydrodynamic
	properties of both the plasma membrane and the pericellular layer,
	the drag on the bead may be affected by the properties of the plasma
	membrane. The Stokes-Einstein relation is applied for calculating
	the diffusivity of probes (colloidal gold nanobeads attached to glycolipids)
	in the plasma membrane. This approach provides an alternative way
	for the interpretation of in vitro observations during single particle
	tracking procedure, and predicts new properties of the plasma membrane
	structure.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12094408},
  endnotereftype = {Journal Article},
  keywords = {Cell Membrane/*physiology Glycolipids/physiology Gold Colloid *Models,
	Biological Numerical Analysis, Computer-Assisted Rheology},
  shorttitle = {Motion of nanobeads proximate to plasma membranes during single particle
	tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12094408}
}

@ARTICLE{Broday2000,
  author = {Broday, D. M.},
  title = {Diffusion of clusters of transmembrane proteins as a model of focal
	adhesion remodeling},
  journal = {Bull Math Biol},
  year = {2000},
  volume = {62},
  pages = {891-924},
  number = {5},
  month = {Sep},
  note = {20470089 0092-8240 Journal Article},
  abstract = {Focal adhesions play a major role in maintaining the cell shape and
	motility, and in regulating numerous cellular processes. Observations
	suggest that the functioning of focal adhesions is possible due to
	their dynamic nature, yet the mechanisms that govern their motion
	are not well understood. This study addresses the process of focal
	adhesion remodeling using two distinct theoretical approaches. Namely,
	adhesion sites are modeled as clusters of integrins that are either
	bound to cytoskeletal elements or dissociated and temporarily free
	of any attachments. In the first approach effects of cluster size
	and permeability on the diffusion of mobile adhesion structures are
	studied using Brinkman's effective medium approach. Diffusion coefficients
	calculated by this hydrodynamic model significantly decrease with
	the increase in contact area (the effective size of the focal adhesion).
	In the second approach focal adhesions are modeled as clusters of
	transmembrane proteins tightly connected to the cytoskeleton, but
	still capable of motion. The remodeling of these clusters is coupled
	to the deformation of the cytoskeleton by means of equating energies
	at the end states of a reversible elastodynamic interaction. Due
	to large uncertainty of the plasma membrane and the cytoskeleton
	properties, predicted diffusion coefficients vary within several
	orders of magnitude. However, a reasonable set of parameters for
	each model yields diffusion coefficients that compare favorably with
	those measured by single-particle tracking (SPT), fluorescence recovery
	after photobleaching (FRAP), and fluorescence digital imaging (FDI).
	The estimated Young's modulus of the stress fibers is also in good
	agreement with measurements. To assess the relevance of the models
	to focal adhesion remodeling and to improve their predictions, further
	data on the morphology of focal adhesions and on properties of the
	plasma membrane and the cytoskeleton are required.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11016089},
  endnotereftype = {Journal Article},
  keywords = {Cell Adhesion/*physiology Cell Membrane/physiology Cytoskeleton/physiology
	Human Integrins/physiology Membrane Proteins/*physiology *Models,
	Biological Models, Theoretical},
  shorttitle = {Diffusion of clusters of transmembrane proteins as a model of focal
	adhesion remodeling},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11016089}
}

@ARTICLE{Brown2000,
  author = {Brown, F. L. and Leitner, D. M. and McCammon, J. A. and Wilson, K.
	R.},
  title = {Lateral diffusion of membrane proteins in the presence of static
	and dynamic corrals: suggestions for appropriate observables},
  journal = {Biophys J},
  year = {2000},
  volume = {78},
  pages = {2257-69},
  number = {5},
  month = {May},
  note = {20241858 0006-3495 Journal Article},
  abstract = {We consider the possibility of inferring the nature of cytoskeletal
	interaction with transmembrane proteins via optical experiments such
	as single-particle tracking (SPT) and near-field scanning optical
	microscopy (NSOM). In particular, we demonstrate that it may be possible
	to differentiate between static and dynamic barriers to diffusion
	by examining the time-dependent variance and higher moments of protein
	population inside cytoskeletal "corrals." Simulations modeling Band
	3 diffusion on the surface of erythrocytes provide a concrete demonstration
	that these statistical tools might prove useful in the study of biological
	systems.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10777724},
  endnotereftype = {Journal Article},
  keywords = {Anion Exchange Protein 1, Erythrocyte/chemistry/metabolism Biophysics
	Cytoskeleton/chemistry/metabolism Diffusion Erythrocyte Membrane/chemistry/metabolism
	Membrane Fluidity Membrane Proteins/chemistry/*metabolism Models,
	Biological Optics Support, U.S. Gov't, Non-P.H.S.},
  shorttitle = {Lateral diffusion of membrane proteins in the presence of static and
	dynamic corrals: suggestions for appropriate observables},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10777724}
}

@ARTICLE{Bulinski2001,
  author = {Bulinski, J. C. and Odde, D. J. and Howell, B. J. and Salmon, T.
	D. and Waterman-Storer, C. M.},
  title = {Rapid dynamics of the microtubule binding of ensconsin in vivo},
  journal = {J Cell Sci},
  year = {2001},
  volume = {114},
  pages = {3885-97},
  number = {Pt 21},
  month = {Nov},
  note = {0021-9533 Journal Article},
  abstract = {Microtubule-associated proteins (MAPs) are proteins that reversibly
	bind to and regulate microtubule dynamics and functions in vivo.
	We examined the dynamics of binding of a MAP called ensconsin (E-MAP-115)
	to microtubules in vivo. We used 5xGFP-EMTB, a construct in which
	the microtubule-binding domain of ensconsin (EMTB) is fused to five
	copies of green fluorescent protein (GFP), as a reporter molecule
	amenable to the use of fluorescent speckle microscopy. Fluorescent
	speckle microscopy (FSM) sequences and kymograph analyses showed
	rapid dynamics of speckles comprised of 5xGFP-EMTB in untreated cells.
	By contrast, in detergent-lysed cytoskeletons, speckles were not
	dynamic. Since detergent-lysed cytoskeletons differ from living cells
	in that they lack both ATP and dynamic microtubules, we used azide
	treatment to substantially reduce the level of ATP in living cells
	and we used Taxol to halt microtubule dynamics. Both treatments slowed
	the dynamics of 5xGFP-EMTB speckles observed by FSM. We also used
	fluorescence recovery after photobleaching (FRAP) to quantify the
	half-time of binding and dissociation of the 5xGFP-EMTB chimera and
	to compare this half-time to that of the full-length MAP molecule.
	In untreated cells, the t(g) of either 5xGFP-EMTB or full-length
	GFP-ensconsin was similarly rapid (approximately 4 seconds), while
	in ATP-reduced and Taxol-treated cells, t(g) was increased to 210
	seconds and 40 seconds, respectively. In detergent-extracted cells
	no recovery was seen. Consistent with the rapid dynamics of 5xGFP-EMTB
	measured with fluorescent speckle microscopy and FRAP, we estimated
	that the affinity of the MAP for microtubules is approximately 40
	microM in untreated living cells, compared with approximately 1 microM
	in vitro. However, K(D,app) was not significantly changed in the
	presence of azide and was increased to 110 microM in the presence
	of Taxol. To test whether changes in the phosphorylation state of
	cellular proteins might be responsible for altering the dynamics
	of ensconsin binding, we used FSM to monitor staurosporine-treated
	cells. Staurosporine treatment substantially halted dynamics of 5xGFP-EMTB
	speckles along MTs. Our results show that ensconsin is highly dynamic
	in its association with microtubules, and its microtubule association
	can be altered by in vivo phosphorylation events.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11719555},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cercopithecus aethiops Genes, Reporter Green Fluorescent
	Proteins Luminescent Proteins/genetics/metabolism Microscopy, Fluorescence/methods
	Microtubule-Associated Proteins/genetics/*metabolism Microtubules/*metabolism
	Protein Binding Protein Processing, Post-Translational Recombinant
	Fusion Proteins/genetics/metabolism Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, P.H.S. Time Factors Tyrosine/metabolism},
  shorttitle = {Rapid dynamics of the microtubule binding of ensconsin in vivo},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11719555}
}

@ARTICLE{Cai2003,
  author = {Cai, H. and Richter, C. P. and Chadwick, R. S.},
  title = {Motion analysis in the hemicochlea},
  journal = {Biophys J},
  year = {2003},
  volume = {85},
  pages = {1929-37},
  number = {3},
  month = {Sep},
  note = {22824780 0006-3495 Journal Article},
  abstract = {Optical flow techniques are often used to estimate velocity fields
	to represent motion in successive video images. Usually the method
	is mathematically ill-posed, because the single scalar equation representing
	the conservation of local intensity contains more than one unknown
	velocity component. Instead of regularizing the problem using optimization
	techniques, we formulate a well-posed problem for the gerbil hemicochlea
	preparation by introducing an in-plane incompressibility constraint,
	and then show that local brightness is also conserved. We solve the
	resulting system using a Lagrangian description of the conservation
	equations. With this approach, the displacement of isointensity contours
	on sequential images determines the normal component of velocity
	of an area element, while the tangential component is computed from
	the local constant area constraint. We have validated our method
	using pairs of images generated from our calculations of the vibrational
	deformation in a cross section of the organ of Corti and tectorial
	membrane in the mammalian cochlea, and quantified the superior performance
	of our method when complex artificial motion is applied to a noisy
	image obtained from the hemicochlea preparation. The micromechanics
	of the organ of Corti and the tectorial membrane is then analyzed
	by our new method.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12944305},
  endnotereftype = {Journal Article},
  shorttitle = {Motion analysis in the hemicochlea},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12944305}
}

@ARTICLE{calssonBJ2002,
  author = {Carlsson, A. E. and Shah, A. D. and Elking, D. and Karpova, T. S.
	and Cooper, J. A.},
  title = {Quantitative analysis of actin patch movement in yeast},
  journal = {Biophys J},
  year = {2002},
  volume = {82},
  pages = {2333-43},
  number = {5},
  month = {May},
  note = {21961476 0006-3495 Journal Article},
  abstract = {To investigate the mechanism of cortical actin patch movement in yeast,
	we implement a method for computer tracking the motion of the patches.
	Digital images from fluorescence microscope movies of living cells
	are fed into an image-processing program, which generates two-dimensional
	patch coordinates in the plane of focus for each movie frame via
	an algorithm based on detection of rapid intensity variations. The
	patch coordinates in neighboring frames are connected by a minimum-distance
	algorithm. The method is used to analyze control cells and cells
	treated with the actin-depolymerizing agent latrunculin. The motion
	of the patches in both cases, as analyzed by mean-square patch displacements,
	is found to be a random walk on average, with a much lower diffusion
	coefficient for the latrunculin-treated cells. The mean-squared patch
	travel distances for all of the latrunculin-treated cells are lower
	than those for all of the control cells. The patches move independently
	of one another. We develop a quantitative criterion for the presence
	of directed motion, and show that numerous patches in the control
	cells display directed motion to a very high degree of certainty.
	A small number of patches in the latrunculin-treated cells display
	directed motion.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11964224},
  endnotereftype = {Journal Article},
  keywords = {Actins/*physiology Computer Simulation Genes, Reporter Kinetics Luminescent
	Proteins/analysis/genetics Movement Saccharomyces cerevisiae/*physiology
	Support, U.S. Gov't, P.H.S. Time Factors Transfection},
  shorttitle = {Quantitative analysis of actin patch movement in yeast},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11964224}
}

@ARTICLE{Chada2003,
  author = {Chada, S. R. and Hollenbeck, P. J.},
  title = {Mitochondrial movement and positioning in axons: the role of growth
	factor signaling},
  journal = {J Exp Biol},
  year = {2003},
  volume = {206},
  pages = {1985-92},
  number = {Pt 12},
  month = {Jun},
  note = {0022-0949 (Print) Journal Article Review},
  abstract = {The extreme length of axonal processes requires that aerobic ATP production
	and Ca(2+) homeostasis are non-uniformly organized in the cytoplasm.
	As a result, the transport and positioning of mitochondria along
	axons is essential for neuronal homeostasis. Mitochondria undergo
	rapid but intermittent transport in both the anterograde and retrograde
	directions in axons. We have shown that in chick embryonic sensory
	neurons, the transport of mitochondria responds to physiological
	changes in the cell and, particularly, to growth cone activity. When
	an axon is actively elongating, mitochondria move preferentially
	anterograde and then become stationary, accumulating in the region
	of the active growth cone. When axonal elongation ceases, mitochondria
	in the distal axon resume movement but undergo net retrograde transport
	and become uniformly distributed along the axon. This redistribution
	of mitochondria is achieved in two ways: there is a transition between
	motile and stationary mitochondria and a large up- and downregulation
	of their anterograde, but not retrograde, motor activity. Mitochondrial
	transport does not respond to the experimentally induced elongation
	of axons in the absence of an active growth cone, implying that signals
	from the active growth cone regulate transport. To determine the
	nature of these signals, we have focally stimulated the shafts of
	sensory axons in culture with nerve growth factor (NGF) covalently
	conjugated to polystyrene beads. We find that mitochondria accumulate
	at regions of focal NGF stimulation. This response is specific to
	mitochondria and does not result from general disruption of the cytoskeleton
	in the region of stimulation. Disruption of the phosphoinositide
	3-kinase (PI 3-kinase) pathway, one of the signaling pathways downstream
	from NGF-receptor binding, completely eliminates NGF effects on mitochondrial
	behavior in axons. We propose that mitochondrial transport and/or
	docking are regulated in part via NGF/TrkA/PI 3-kinase signaling.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12756280},
  endnotereftype = {Journal Article},
  keywords = {1-Phosphatidylinositol 3-Kinase/metabolism Animals Chick Embryo Growth
	Cones/*metabolism/physiology Immunohistochemistry Microscopy, Fluorescence
	Mitochondria/*physiology Nerve Growth Factor/*metabolism Receptor,
	trkA/metabolism Research Support, U.S. Gov't, P.H.S. Signal Transduction/*physiology},
  shorttitle = {Mitochondrial movement and positioning in axons: the role of growth
	factor signaling},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12756280}
}

@ARTICLE{cheezumBJ2001,
  author = {Cheezum, M. K. and Walker, W. F. and Guilford, W. H.},
  title = {Quantitative comparison of algorithms for tracking single fluorescent
	particles},
  journal = {Biophys J},
  year = {2001},
  volume = {81},
  pages = {2378-88},
  number = {4},
  month = {Oct},
  note = {21450444 0006-3495 Journal Article},
  abstract = {Single particle tracking has seen numerous applications in biophysics,
	ranging from the diffusion of proteins in cell membranes to the movement
	of molecular motors. A plethora of computer algorithms have been
	developed to monitor the sub-pixel displacement of fluorescent objects
	between successive video frames, and some have been claimed to have
	"nanometer" resolution. To date, there has been no rigorous comparison
	of these algorithms under realistic conditions. In this paper, we
	quantitatively compare specific implementations of four commonly
	used tracking algorithms: cross-correlation, sum-absolute difference,
	centroid, and direct Gaussian fit. Images of fluorescent objects
	ranging in size from point sources to 5 microm were computer generated
	with known sub-pixel displacements. Realistic noise was added and
	the above four algorithms were compared for accuracy and precision.
	We found that cross-correlation is the most accurate algorithm for
	large particles. However, for point sources, direct Gaussian fit
	to the intensity distribution is the superior algorithm in terms
	of both accuracy and precision, and is the most robust at low signal-to-noise.
	Most significantly, all four algorithms fail as the signal-to-noise
	ratio approaches 4. We judge direct Gaussian fit to be the best algorithm
	when tracking single fluorophores, where the signal-to-noise is frequently
	near 4.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11566807},
  endnotereftype = {Journal Article},
  keywords = {*Algorithms Analysis of Variance Comparative Study *Computer Simulation
	Fluorescence *Image Processing, Computer-Assisted *Models, Theoretical
	Motion Particle Size Statistics Support, U.S. Gov't, P.H.S.},
  shorttitle = {Quantitative comparison of algorithms for tracking single fluorescent
	particles},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11566807}
}

@ARTICLE{Chen1999,
  author = {Chen, C. S. and Brangwynne, C. and Ingber, D. E.},
  title = {Pictures in cell biology: squaring up to the cell-shape debate},
  journal = {Trends Cell Biol},
  year = {1999},
  volume = {9},
  pages = {283},
  number = {7},
  month = {Jul},
  note = {0962-8924 Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10438233},
  endnotereftype = {Journal Article},
  keywords = {Actins/ultrastructure Animals Capillaries Cattle *Cell Size Cytoskeleton/ultrastructure
	Endothelium, Vascular/*cytology Photography},
  shorttitle = {Pictures in cell biology: squaring up to the cell-shape debate},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10438233}
}

@ARTICLE{Chen1999a,
  author = {Chen, C. S. and Ingber, D. E.},
  title = {Tensegrity and mechanoregulation: from skeleton to cytoskeleton},
  journal = {Osteoarthritis Cartilage},
  year = {1999},
  volume = {7},
  pages = {81-94},
  number = {1},
  month = {Jan},
  note = {1063-4584 Journal Article Review},
  abstract = {OBJECTIVE: To elucidate how mechanical stresses that are applied to
	the whole organism are transmitted to individual cells and transduced
	into a biochemical response. DESIGN: In this article, we describe
	fundamental design principles that are used to stabilize the musculoskeletal
	system at many different size scales and show that these design features
	are embodied in one particular form of architecture that is known
	as tensegrity. RESULTS: Tensegrity structures are characterized by
	use of continuous tension and local compression; architecture, prestress
	(internal stress prior to application of external force), and triangulation
	play the most critical roles in terms of determining their mechanical
	stability. In living organisms, use of a hierarchy of tensegrity
	networks both optimizes structural efficiency and provides a mechanism
	to mechanically couple the parts with the whole: mechanical stresses
	applied at the macroscale result in structural rearrangements at
	the cell and molecular level. CONCLUSION: Due to use of tensegrity
	architecture, mechanical stress is concentrated and focused on signal
	transducing molecules that physically associate with cell surface
	molecules that anchor cells to extracellular matrix, such as integrins,
	and with load-bearing elements within the internal cytoskeleton and
	nucleus. Mechanochemical transduction may then proceed through local
	stress-dependent changes in molecular mechanics, thermodynamics,
	and kinetics within the cell. In this manner, the entire cellular
	response to stress may be orchestrated and tuned by altering the
	prestress in the cell, just as changing muscular tone can alter mechanical
	stability and structural coordination throughout the whole musculoskeletal
	system.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10367017},
  endnotereftype = {Journal Article},
  keywords = {Biomechanics Cytoskeleton/*physiology Humans *Musculoskeletal Physiology
	Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't,
	P.H.S. Signal Transduction/physiology Stress, Mechanical},
  shorttitle = {Tensegrity and mechanoregulation: from skeleton to cytoskeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10367017}
}

@ARTICLE{Chen1998,
  author = {Chen, C. S. and Mrksich, M. and Huang, S. and Whitesides, G. M. and
	Ingber, D. E.},
  title = {Micropatterned surfaces for control of cell shape, position, and
	function},
  journal = {Biotechnol Prog},
  year = {1998},
  volume = {14},
  pages = {356-63},
  number = {3},
  month = {May-Jun},
  note = {8756-7938 Journal Article},
  abstract = {The control of cell position and function is a fundamental focus in
	the development of applications ranging from cellular biosensors
	to tissue engineering. Using microcontact printing of self-assembled
	monolayers (SAMs) of alkanethiolates on gold, we manufactured substrates
	that contained micrometer-scale islands of extracellular matrix (ECM)
	separated by nonadhesive regions such that the pattern of islands
	determined the distribution and position of bovine and human endothelial
	cells. In addition, the size and geometry of the islands were shown
	to control cell shape. Traditional approaches to modulate cell shape,
	either by attaching suspended cells to microbeads of different sizes
	or by plating cells on substrates coated with different densities
	of ECM, suggested that cell shape may play an important role in control
	of apoptosis as well as growth. Data are presented which show how
	micropatterned substrates were used to definitively test this hypothesis.
	Progressively restricting bovine and human endothelial cell extension
	by culturing cells on smaller and smaller micropatterned adhesive
	islands regulated a transition from growth to apoptosis on a single
	continuum of cell spreading, thus confirming the central role of
	cell shape in cell function. The micropatterning technology is therefore
	essential not only for construction of biosurface devices but also
	for the investigation of the fundamental biology of cell-ECM interactions.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9622515},
  endnotereftype = {Journal Article},
  keywords = {Animals Apoptosis Bioreactors Biosensing Techniques Cattle Cell Division
	*Cell Physiology Cells, Cultured Humans Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Micropatterned surfaces for control of cell shape, position, and function},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9622515}
}

@ARTICLE{Chen1997,
  author = {Chen, C. S. and Mrksich, M. and Huang, S. and Whitesides, G. M. and
	Ingber, D. E.},
  title = {Geometric control of cell life and death},
  journal = {Science},
  year = {1997},
  volume = {276},
  pages = {1425-8},
  number = {5317},
  month = {May 30},
  note = {0036-8075 Journal Article},
  abstract = {Human and bovine capillary endothelial cells were switched from growth
	to apoptosis by using micropatterned substrates that contained extracellular
	matrix-coated adhesive islands of decreasing size to progressively
	restrict cell extension. Cell spreading also was varied while maintaining
	the total cell-matrix contact area constant by changing the spacing
	between multiple focal adhesion-sized islands. Cell shape was found
	to govern whether individual cells grow or die, regardless of the
	type of matrix protein or antibody to integrin used to mediate adhesion.
	Local geometric control of cell growth and viability may therefore
	represent a fundamental mechanism for developmental regulation within
	the tissue microenvironment.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9162012},
  endnotereftype = {Journal Article},
  keywords = {Animals Antigens, CD29/physiology Apoptosis/*physiology Cattle Cell
	Adhesion/physiology Cell Division/*physiology Cell Size/*physiology
	Cells, Cultured Endothelium, Vascular/*cytology/physiology Extracellular
	Matrix/physiology Fibronectins/physiology Humans Integrins/physiology
	Ligands Research Support, Non-U.S. Gov't Research Support, U.S. Gov't,
	Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Vitronectin/physiology},
  shorttitle = {Geometric control of cell life and death},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9162012}
}

@ARTICLE{Chen2000,
  author = {Chen, C. S. and Ostuni, E. and Whitesides, G. M. and Ingber, D. E.},
  title = {Using self-assembled monolayers to pattern ECM proteins and cells
	on substrates},
  journal = {Methods Mol Biol},
  year = {2000},
  volume = {139},
  pages = {209-19},
  note = {1064-3745 Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10840789},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion Extracellular Matrix Proteins/*metabolism Research
	Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.
	Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Using self-assembled monolayers to pattern ECM proteins and cells
	on substrates},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10840789}
}

@ARTICLE{Chen2004,
  author = {Chen, C. S. and Tan, J. and Tien, J.},
  title = {Mechanotransduction at cell-matrix and cell-cell contacts},
  journal = {Annu Rev Biomed Eng},
  year = {2004},
  volume = {6},
  pages = {275-302},
  note = {1523-9829 (Print) Journal Article Review},
  abstract = {Mechanical forces play an important role in the organization, growth,
	maturation, and function of living tissues. At the cellular level,
	many of the biological responses to external forces originate at
	two types of specialized microscale structures: focal adhesions that
	link cells to their surrounding extracellular matrix and adherens
	junctions that link adjacent cells. Transmission of forces from outside
	the cell through cell-matrix and cell-cell contacts appears to control
	the maturation or disassembly of these adhesions and initiates intracellular
	signaling cascades that ultimately alter many cellular behaviors.
	In response to externally applied forces, cells actively rearrange
	the organization and contractile activity of the cytoskeleton and
	redistribute their intracellular forces. Recent studies suggest that
	the localized concentration of these cytoskeletal tensions at adhesions
	is also a major mediator of mechanical signaling. This review summarizes
	the role of mechanical forces in the formation, stabilization, and
	dissociation of focal adhesions and adherens junctions and outlines
	how integration of signals from these adhesions over the entire cell
	body affects how a cell responds to its mechanical environment. This
	review also describes advanced optical, lithographic, and computational
	techniques for the study of mechanotransduction.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15255771},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion *Cell Communication Cytoskeleton/metabolism
	Extracellular Matrix/*metabolism Focal Adhesions Humans Integrins
	Stress, Mechanical},
  shorttitle = {Mechanotransduction at cell-matrix and cell-cell contacts},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15255771}
}

@ARTICLE{Chen2003,
  author = {Chen, D. T. and Weeks, E. R. and Crocker, J. C. and Islam, M. F.
	and Verma, R. and Gruber, J. and Levine, A. J. and Lubensky, T. C.
	and Yodh, A. G.},
  title = {Rheological microscopy: local mechanical properties from microrheology},
  journal = {Phys Rev Lett},
  year = {2003},
  volume = {90},
  pages = {108301},
  number = {10},
  month = {Mar 14},
  note = {0031-9007 Journal Article},
  abstract = {We demonstrate how tracer microrheology methods can be extended to
	study submicron scale variations in the viscoelastic response of
	soft materials; in particular, a semidilute solution of lambda-DNA.
	The polymer concentration is depleted near the surfaces of the tracer
	particles, within a distance comparable to the polymer correlation
	length. The rheology of this microscopic layer alters the tracers'
	motion and can be precisely quantified using one- and two-point microrheology.
	Interestingly, we found this mechanically distinct layer to be twice
	as thick as the layer of depleted concentration, likely due to solvent
	drainage through the locally perturbed polymer structure.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12689039},
  endnotereftype = {Journal Article},
  keywords = {Bacteriophage lambda/genetics DNA, Viral/*chemistry Elasticity Fluorescent
	Dyes/chemistry Microscopy/*methods *Models, Chemical Polystyrenes/*chemistry
	Research Support, U.S. Gov't, Non-P.H.S. Rheology/*methods Rhodamines/chemistry
	Viscosity},
  shorttitle = {Rheological microscopy: local mechanical properties from microrheology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12689039}
}

@ARTICLE{Cherry1994,
  author = {Cherry, R. J. and Georgiou, G. N. and Morrison, I. E.},
  title = {New insights into the structure of cell membranes from single particle
	tracking experiments},
  journal = {Biochem Soc Trans},
  year = {1994},
  volume = {22},
  pages = {781-4},
  number = {3},
  month = {Aug},
  note = {95121726 0300-5127 Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7821684},
  endnotereftype = {Journal Article},
  keywords = {Cell Membrane/chemistry Diffusion Fibroblasts/chemistry Fluorescent
	Dyes Human Lipoproteins, LDL/chemistry Membrane Proteins/*chemistry
	Molecular Structure Receptors, Virus/chemistry Support, Non-U.S.
	Gov't},
  shorttitle = {New insights into the structure of cell membranes from single particle
	tracking experiments},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7821684}
}

@ARTICLE{Cherry1998,
  author = {Cherry, R. J. and Smith, P. R. and Morrison, I. E. and Fernandez,
	N.},
  title = {Mobility of cell surface receptors: a re-evaluation},
  journal = {FEBS Lett},
  year = {1998},
  volume = {430},
  pages = {88-91},
  number = {1-2},
  month = {Jun 23},
  note = {98341740 0014-5793 Journal Article Review Review, Tutorial},
  abstract = {It has long been known from fluorescence recovery after photobleaching
	experiments that the mobility of most cell surface receptors is much
	smaller than expected for free diffusion of proteins in a fluid lipid
	bilayer. Single-particle tracking experiments are currently revealing
	the complexity of the constraints to free diffusion. Evidence has
	been obtained for several different processes: domain-limited diffusion,
	temporary confinement and anomalous diffusion. The type of motion
	exhibited by a given receptor will profoundly influence the rate
	of any functional process which requires movement in the plane of
	the membrane. In particular, anomalous diffusion greatly reduces
	the distance travelled by a receptor on a time scale of minutes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9678600},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Evaluation Studies Fluorescence Human Receptors, Cell Surface/*metabolism/physiology
	Support, Non-U.S. Gov't},
  shorttitle = {Mobility of cell surface receptors: a re-evaluation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9678600}
}

@ARTICLE{Clow1999,
  author = {Clow, P A and McNally, J G},
  title = {In vivo observations of myosin II dynamics support a role in rear
	retraction.},
  journal = {Mol. Biol. Cell},
  year = {1999},
  volume = {10},
  pages = {1309-1323},
  endnotereftype = {Journal Article},
  keywords = {myosin II microscopy video microscopy cytoskeleton motility cell movement},
  shorttitle = {In vivo observations of myosin II dynamics support a role in rear
	retraction.}
}

@ARTICLE{Cognet2003,
  author = {Cognet, L. and Tardin, C. and Boyer, D. and Choquet, D. and Tamarat,
	P. and Lounis, B.},
  title = {Single metallic nanoparticle imaging for protein detection in cells},
  journal = {Proc Natl Acad Sci U S A},
  year = {2003},
  volume = {100},
  pages = {11350-5},
  number = {20},
  month = {Sep 30},
  note = {22882875 0027-8424 Journal Article},
  abstract = {We performed a visualization of membrane proteins labeled with 10-nm
	gold nanoparticles in cells, using an all-optical method based on
	photothermal interference contrast. The high sensitivity of the method
	and the stability of the signals allows 3D imaging of individual
	nanoparticles without the drawbacks of photobleaching and blinking
	inherent to fluorescent markers. A simple analytical model is derived
	to account for the measurements of the signal amplitude and the spatial
	resolution. The photothermal interference contrast method provides
	an efficient, reproducible, and promising way to visualize low amounts
	of proteins in cells by optical means.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=13679586},
  endnotereftype = {Journal Article},
  shorttitle = {Single metallic nanoparticle imaging for protein detection in cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=13679586}
}

@ARTICLE{Cohen1993,
  author = {Cohen, L.D. and Cohen, I.},
  title = {Finite-Element Methods for Active Contour Models and Balloons for
	2-D and 3-D Images},
  journal = {IEEE Trans Pattern Anal Machine Intell},
  year = {1993},
  volume = {15},
  pages = {1131-1147},
  number = {11},
  endnotereftype = {Journal Article},
  shorttitle = {Finite-Element Methods for Active Contour Models and Balloons for
	2-D and 3-D Images}
}

@MISC{Collins2005,
  author = {Collins, T.},
  title = {Online Manual for the WCIF-ImageJ collection},
  year = {2005},
  bdsk-url-1 = {http://www.uhnresearch.ca/facilities/wcif/imagej/},
  endnotereftype = {Electronic Source},
  shorttitle = {Online Manual for the WCIF-ImageJ collection},
  url = {http://www.uhnresearch.ca/facilities/wcif/imagej/}
}

@ARTICLE{Cooper1990,
  author = {Cooper, M. S. and Cornell-Bell, A. H. and Chernjavsky, A. and Dani,
	J. W. and Smith, S. J.},
  title = {Tubulovesicular processes emerge from trans-Golgi cisternae, extend
	along microtubules, and interlink adjacent trans-golgi elements into
	a reticulum},
  journal = {Cell},
  year = {1990},
  volume = {61},
  pages = {135-45},
  number = {1},
  month = {Apr 6},
  note = {0092-8674 (Print) Journal Article},
  abstract = {Morphological dynamics and membrane transport within the living Golgi
	apparatus of astrocytes labeled with NBD-ceramide were imaged using
	both electronically enhanced fluorescence video and laser confocal
	microscopy. In time-lapse recordings, continuous tubulovesicular
	processes are observed to emerge from trans-Golgi elements and extend
	along microtubules at average rates of 0.4 microns/s. In addition,
	discrete fluorescent particles are observed to emerge from the trans-Golgi
	and subsequently migrate along microtubules at comparable velocities.
	Frequently, tubulovesicular processes form stable connections that
	interlink adjacent trans-Golgi elements into an extensive reticulum.
	Laser photobleaching-recovery experiments reveal that tubulovesicular
	processes can provide direct pathways for the diffusion of membrane
	lipids between joined trans-Golgi elements. These results suggest
	that microtubule-based transport and membrane fusion can operate
	to interconnect certain cisternal membranes of adjacent Golgi elements
	within the cell.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2180583},
  endnotereftype = {Journal Article},
  keywords = {Animals Animals, Newborn Astrocytes/cytology/*ultrastructure Cells,
	Cultured Fluorescent Antibody Technique Fluorescent Dyes Golgi Apparatus/*ultrastructure
	Hippocampus/cytology Lasers Microscopy/methods Microscopy, Fluorescence
	Microtubules/*ultrastructure Organelles/*ultrastructure Pyramidal
	Tracts/cytology Rats Research Support, Non-U.S. Gov't Research Support,
	U.S. Gov't, P.H.S. Time Factors Tubulin/analysis Video Recording},
  shorttitle = {Tubulovesicular processes emerge from trans-Golgi cisternae, extend
	along microtubules, and interlink adjacent trans-golgi elements into
	a reticulum},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2180583}
}

@MANUAL{Cordelieres2004,
  title = {Manual Tracking},
  author = {Cordelieres, Fabrice},
  year = {2004},
  bdsk-url-1 = {http://rsb.info.nih.gov/ij/plugins/manual-tracking.html},
  endnotereftype = {Computer Program},
  shorttitle = {Manual Tracking},
  url = {http://rsb.info.nih.gov/ij/plugins/manual-tracking.html}
}

@INCOLLECTION{Cox1999,
  author = {Cox, G.C.},
  title = {Measurements in the Confocal Microscope},
  booktitle = {Confocal Microscopy Methods and Protocols},
  publisher = {Humana Press},
  year = {1999},
  editor = {Paddok, S.W.},
  address = {Totowa, NJ},
  endnotereftype = {Book Section},
  shorttitle = {Measurements in the Confocal Microscope}
}

@ARTICLE{Craig2001,
  author = {Craig, A. M. and Lichtman, J. W.},
  title = {Getting a bead on receptor movements},
  journal = {Nat Neurosci},
  year = {2001},
  volume = {4},
  pages = {219-20},
  number = {3},
  month = {Mar},
  note = {21127795 1097-6256 Comment Journal Article Review Review, Tutorial},
  abstract = {Studies of populations of receptor proteins suggest that their number
	and location are highly regulated. Single-particle tracking of glycine
	receptors now reveals the direct movement of receptors between different
	clusters of the anchoring protein gephyrin.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11224530},
  endnotereftype = {Journal Article},
  keywords = {Animal Human *Microspheres Neurons/*metabolism Receptors, Glycine/*metabolism
	Synaptic Membranes/*metabolism},
  shorttitle = {Getting a bead on receptor movements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11224530}
}

@MISC{cromey2007,
  author = {Cromey, DW},
  title = {Digital Imaging: Ethics.},
  year = {2007},
  bdsk-url-1 = {http://swehsc.pharmacy.arizona.edu/exppath/},
  owner = {Kota},
  timestamp = {2011.03.10},
  url = {http://swehsc.pharmacy.arizona.edu/exppath/}
}

@ARTICLE{Csucs2003,
  author = {Csucs, G. and Michel, R. and Lussi, J. W. and Textor, M. and Danuser,
	G.},
  title = {Microcontact printing of novel co-polymers in combination with proteins
	for cell-biological applications},
  journal = {Biomaterials},
  year = {2003},
  volume = {24},
  pages = {1713-20},
  number = {10},
  month = {May},
  note = {0142-9612 (Print) Journal Article},
  abstract = {Microcontact printing (microcP) is a cost effective and simple method
	to create chemically micropatterned surfaces for cell biological
	applications. We have combined the technique with the spontaneous
	molecular assembly of a polycationic PEG-grafted copolymer, poly-L-lysine-g-poly(ethylene
	glycol) (PLL-g-PEG). PLL-g-PEG with omega-functionalized PEG chains
	was print-transferred onto tissue culture polystyrene (TCPS) or glass
	substrates, resulting in patterns with a lateral resolution down
	to 1 microm. Subsequently, dipping in an aqueous solution of non-functionalized
	PLL-g-PEG was used to backfill the non-printed regions of the surface,
	rendering them highly protein and thus cell resistant. In a second
	approach, proteins were stamped and a PLL-g-PEG backfill was applied
	for passivation of the bare surface regions. Printing of peptide(RGD)-functionalized
	PLL-g-PEG or proteins combined with a subsequent PLL-g-PEG backfill
	can be applied to a wide variety of substrate materials with negatively
	charged surfaces such as TCPS, glass and many metal oxides. We have
	tested the printed surfaces with human foreskin fibroblasts for cell
	adhesion and long-term performance and with fish epidermal keratocytes
	for cell motility and short-time behaviour. Both cell types reacted
	selectively to the surface micropatterns. Fibroblasts adhered to
	the printed (adhesive) regions only, where they remained attached
	up to at least 1 week and were even able to proliferate. Keratocyte
	spreading and motility were also directed by the geometry of the
	underlying patterns. The results prove that microcP in conjunction
	with the use of PLL-g-PEG and its derivatives provides a simple and
	robust alternative to previously reported micropatterning methods
	for future cell biological and biotechnological applications.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12593952},
  endnotereftype = {Journal Article},
  keywords = {Animals Biocompatible Materials/*chemistry Biotechnology Cell Adhesion
	Cell Movement Cells, Cultured Humans Materials Testing Microscopy,
	Fluorescence Polyethylene Glycols/*chemistry Polylysine/*analogs
	& derivatives/*chemistry Research Support, Non-U.S. Gov't Spectrum
	Analysis Surface Properties X-Rays},
  shorttitle = {Microcontact printing of novel co-polymers in combination with proteins
	for cell-biological applications},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12593952}
}

@ARTICLE{Cuvelier2007,
  author = {Cuvelier, D. and Thery, M. and Chu, Y. S. and Dufour, S. and Thiery,
	J. P. and Bornens, M. and Nassoy, P. and Mahadevan, L.},
  title = {The universal dynamics of cell spreading},
  journal = {Curr Biol},
  year = {2007},
  volume = {17},
  pages = {694-9},
  number = {8},
  month = {Apr 17},
  note = {0960-9822 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Cell adhesion and motility depend strongly on the interactions between
	cells and extracellular matrix (ECM) substrates. When plated onto
	artificial adhesive surfaces, cells first flatten and deform extensively
	as they spread. At the molecular level, the interaction of membrane-based
	integrins with the ECM has been shown to initiate a complex cascade
	of signaling events [1], which subsequently triggers cellular morphological
	changes and results in the generation of contractile forces [2].
	Here, we focus on the early stages of cell spreading and probe their
	dynamics by quantitative visualization and biochemical manipulation
	with a variety of cell types and adhesive surfaces, adhesion receptors,
	and cytoskeleton-altering drugs. We find that the dynamics of adhesion
	follows a universal power-law behavior. This is in sharp contrast
	with the common belief that spreading is regulated by either the
	diffusion of adhesion receptors toward the growing adhesive patch
	[3-5] or by actin polymerization [6-8]. To explain this, we propose
	a simple quantitative and predictive theory that models cells as
	viscous adhesive cortical shells enclosing a less viscous interior.
	Thus, although cell spreading is driven by well-identified biomolecular
	interactions, it is dynamically limited by its mesoscopic structure
	and material properties.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17379524},
  endnotereftype = {Journal Article},
  shorttitle = {The universal dynamics of cell spreading},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17379524}
}

@ARTICLE{Dahm2001,
  author = {Dahm, T. and White, J. and Grill, S. and Fullekrug, J. and Stelzer,
	E. H.},
  title = {Quantitative ER <--> Golgi transport kinetics and protein separation
	upon Golgi exit revealed by vesicular integral membrane protein 36
	dynamics in live cells},
  journal = {Mol Biol Cell},
  year = {2001},
  volume = {12},
  pages = {1481-98},
  number = {5},
  month = {May},
  note = {21260035 1059-1524 Journal Article},
  abstract = {To quantitatively investigate the trafficking of the transmembrane
	lectin VIP36 and its relation to cargo-containing transport carriers
	(TCs), we analyzed a C-terminal fluorescent-protein (FP) fusion,
	VIP36-SP-FP. When expressed at moderate levels, VIP36-SP-FP localized
	to the endoplasmic reticulum, Golgi apparatus, and intermediate transport
	structures, and colocalized with epitope-tagged VIP36. Temperature
	shift and pharmacological experiments indicated VIP36-SP-FP recycled
	in the early secretory pathway, exhibiting trafficking representative
	of a class of transmembrane cargo receptors, including the closely
	related lectin ERGIC53. VIP36-SP-FP trafficking structures comprised
	tubules and globular elements, which translocated in a saltatory
	manner. Simultaneous visualization of anterograde secretory cargo
	and VIP36-SP-FP indicated that the globular structures were pre-Golgi
	carriers, and that VIP36-SP-FP segregated from cargo within the Golgi
	and was not included in post-Golgi TCs. Organelle-specific bleach
	experiments directly measured the exchange of VIP36-SP-FP between
	the Golgi and endoplasmic reticulum (ER). Fitting a two-compartment
	model to the recovery data predicted first order rate constants of
	1.22 +/- 0.44%/min for ER --> Golgi, and 7.68 +/- 1.94%/min for Golgi
	--> ER transport, revealing a half-time of 113 +/- 70 min for leaving
	the ER and 1.67 +/- 0.45 min for leaving the Golgi, and accounting
	for the measured steady-state distribution of VIP36-SP-FP (13% Golgi/87%
	ER). Perturbing transport with AlF(4)(-) treatment altered VIP36-SP-GFP
	distribution and changed the rate constants. The parameters of the
	model suggest that relatively small differences in the first order
	rate constants, perhaps manifested in subtle differences in the tendency
	to enter distinct TCs, result in large differences in the steady-state
	localization of secretory components.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11359937},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Markers Brefeldin A/pharmacology COS Cells Carrier
	Proteins/*metabolism Cycloheximide/pharmacology Endoplasmic Reticulum/*metabolism
	Golgi Apparatus/*metabolism Human Kinetics Luminescent Proteins/metabolism
	Membrane Proteins/*metabolism Microscopy, Confocal Microscopy, Video
	Protein Synthesis Inhibitors/pharmacology *Protein Transport/drug
	effects Recombinant Fusion Proteins/genetics/metabolism Secretory
	Vesicles/chemistry/*metabolism Time Factors},
  shorttitle = {Quantitative ER <--> Golgi transport kinetics and protein separation
	upon Golgi exit revealed by vesicular integral membrane protein 36
	dynamics in live cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11359937}
}

@ARTICLE{Daumas2003,
  author = {Daumas, F. and Destainville, N. and Millot, C. and Lopez, A. and
	Dean, D. and Salome, L.},
  title = {Confined diffusion without fences of a g-protein-coupled receptor
	as revealed by single particle tracking},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {356-66},
  number = {1},
  month = {Jan},
  note = {22411885 0006-3495 Evaluation Studies Journal Article Validation
	Studies},
  abstract = {Single particle tracking is a powerful tool for probing the organization
	and dynamics of the plasma membrane constituents. We used this technique
	to study the micro -opioid receptor belonging to the large family
	of the G-protein-coupled receptors involved with other partners in
	a signal transduction pathway. The specific labeling of the receptor
	coupled to a T7-tag at its N-terminus, stably expressed in fibroblastic
	cells, was achieved by colloidal gold coupled to a monoclonal anti
	T7-tag antibody. The lateral movements of the particles were followed
	by nanovideomicroscopy at 40 ms time resolution during 2 min with
	a spatial precision of 15 nm. The receptors were found to have either
	a slow or directed diffusion mode (10%) or a walking confined diffusion
	mode (90%) composed of a long-term random diffusion and a short-term
	confined diffusion, and corresponding to a diffusion confined within
	a domain that itself diffuses. The results indicate that the confinement
	is due to an effective harmonic potential generated by long-range
	attraction between the membrane proteins. A simple model for interacting
	membrane proteins diffusion is proposed that explains the variations
	with the domain size of the short-term and long-term diffusion coefficients.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12524289},
  endnotereftype = {Journal Article},
  keywords = {Bacteriophage T7/chemistry Cell Line Cell Membrane/chemistry/physiology/*ultrastructure
	Comparative Study Diffusion Fibroblasts/chemistry/physiology/ultrastructure
	GTP-Binding Protein Regulators/chemistry/physiology/ultrastructure
	GTP-Binding Proteins/chemistry/physiology/ultrastructure Gold Colloid/chemistry
	Kidney/chemistry/physiology/ultrastructure Microscopy, Video/instrumentation/*methods
	Microspheres Models, Biological Models, Chemical *Motion Nanotechnology/instrumentation/*methods
	Particle Size Receptors, Cell Surface/chemistry/physiology/ultrastructure
	Receptors, Opioid, mu/*chemistry/deficiency/physiology/*ultrastructure
	Signal Transduction/physiology Staining and Labeling/methods Support,
	Non-U.S. Gov't},
  shorttitle = {Confined diffusion without fences of a g-protein-coupled receptor
	as revealed by single particle tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12524289}
}

@ARTICLE{Daumas2002,
  author = {Daumas, F. and Mazarguil, H. and Millot, C. and Lopez, A. and Salome,
	L.},
  title = {Probing functionalized gold colloids for single particle tracking
	experiments},
  journal = {Biochem Biophys Res Commun},
  year = {2002},
  volume = {295},
  pages = {610-5},
  number = {3},
  month = {Jul 19},
  note = {22094606 0006-291x Journal Article},
  abstract = {Functionalized submicroscopic particles are currently used to label
	proteins or lipids at the surface of living cells for single particle
	tracking experiments. In many cases, it can be of crucial importance
	for the particle to be anchored to a single molecule. We have addressed
	this question for the labeling at the plasma membrane of NRK cells
	of the mu-opioid receptor bearing a T7 epitope at the N-terminus.
	Using biophysical methods we were able to prepare quasi-monovalent
	anti-T7 antibody conjugated gold colloids (40 nm diameter) leading
	to stable and specific binding to the receptor. The rational method,
	we report here, can be extended to design customized probes for the
	labeling of various tagged molecules.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12099682},
  endnotereftype = {Journal Article},
  keywords = {Animal Binding Sites Cell Line Cell Membrane/ultrastructure *Colloids
	*Gold/chemistry Hydrogen-Ion Concentration Immunoglobulin Fragments
	Isoelectric Point Kinetics Lipids Microscopy/*methods Rats Receptors,
	Opioid, mu/metabolism Sodium/pharmacology Surface Plasmon Resonance
	Time Factors Transfection},
  shorttitle = {Probing functionalized gold colloids for single particle tracking
	experiments},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12099682}
}

@ARTICLE{Dayel1999,
  author = {Dayel, M. J. and Hom, E. F. and Verkman, A. S.},
  title = {Diffusion of green fluorescent protein in the aqueous-phase lumen
	of endoplasmic reticulum},
  journal = {Biophys J},
  year = {1999},
  volume = {76},
  pages = {2843-51},
  number = {5},
  month = {May},
  note = {0006-3495 Journal Article},
  abstract = {The endoplasmic reticulum (ER) is the major compartment for the processing
	and quality control of newly synthesized proteins. Green fluorescent
	protein (GFP) was used as a noninvasive probe to determine the viscous
	properties of the aqueous lumen of the ER. GFP was targeted to the
	ER lumen of CHO cells by transient transfection with cDNA encoding
	GFP (S65T/F64L mutant) with a C-terminus KDEL retention sequence
	and upstream prolactin secretory sequence. Repeated laser illumination
	of a fixed 2-micrometers diameter spot resulted in complete bleaching
	of ER-associated GFP throughout the cell, indicating a continuous
	ER lumen. A residual amount (<1%) of GFP-KDEL was perinuclear and
	noncontiguous with the ER, presumably within a pre- or cis-Golgi
	compartment involved in KDEL-substrate retention. Quantitative spot
	photobleaching with a single brief bleach pulse indicated that GFP
	was fully mobile with a t1/2 for fluorescence recovery of 88 +/-
	5 ms (SE; 60x lens) and 143 +/- 8 ms (40x). Fluorescence recovery
	was abolished by paraformaldehyde except for a small component of
	reversible photobleaching with t1/2 of 3 ms. For comparison, the
	t1/2 for photobleaching of GFP in cytoplasm was 14 +/- 2 ms (60x)
	and 24 +/- 1 ms (40x). Utilizing a mathematical model that accounted
	for ER reticular geometry, a GFP diffusion coefficient of 0.5-1 x
	10(-7) cm2/s was computed, 9-18-fold less than that in water and
	3-6-fold less than that in cytoplasm. By frequency-domain microfluorimetry,
	the GFP rotational correlation time was measured to be 39 +/- 8 ns,
	approximately 2-fold greater than that in water but comparable to
	that in the cytoplasm. Fluorescence recovery after photobleaching
	using a 40x lens was measured (at 23 degrees C unless otherwise indicated)
	for several potential effectors of ER structure and/or lumen environment:
	t1/2 values (in ms) were 143 +/- 8 (control), 100 +/- 13 (37 degrees
	C), 53 +/- 13 (brefeldin A), and 139 +/- 6 (dithiothreitol). These
	results indicate moderately slowed GFP diffusion in a continuous
	ER lumen.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10233100},
  endnotereftype = {Journal Article},
  keywords = {Animals Biophysics CHO Cells Cell Compartmentation Diffusion Endoplasmic
	Reticulum/*metabolism Fluorescence Polarization Green Fluorescent
	Proteins Hamsters Luminescent Proteins/genetics/*metabolism Oligopeptides/genetics
	Protein Processing, Post-Translational Protein Sorting Signals/genetics
	Recombinant Fusion Proteins/genetics/metabolism Research Support,
	Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Transfection
	Water},
  shorttitle = {Diffusion of green fluorescent protein in the aqueous-phase lumen
	of endoplasmic reticulum},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10233100}
}

@ARTICLE{DeBrabander1988,
  author = {De Brabander, M. and Nuydens, R. and Geerts, H. and Hopkins, C. R.},
  title = {Dynamic behavior of the transferrin receptor followed in living epidermoid
	carcinoma (A431) cells with nanovid microscopy},
  journal = {Cell Motil Cytoskeleton},
  year = {1988},
  volume = {9},
  pages = {30-47},
  number = {1},
  note = {88184685 0886-1544 Journal Article},
  abstract = {Transferrin receptors labeled with the B3/25 monoclonal antibody-gold
	complexes were followed in living A431 cells by using video-enhanced
	contrast microscopy. Initially, the antibody-gold complexes bind
	to receptors which are freely mobile on the upper cell surface; they
	then become trapped at the inner margins of the peripheral lamellae
	and internalize. During endocytosis discrete gold-loaded vesicular
	elements first appear, and then, as they fuse, a heterogenous peripheral
	endosomal compartment forms. The endosomes from this compartment
	then begin to migrate centripetally through the cytoplasm in a saltatory
	way so that within 15 min gold label accumulates in a juxtanuclear
	endosome compartment. This compartment, which consists mainly of
	multivesicular bodies, is thus formed by the influx and retention
	of peripheral endosomal elements and their continued fusion in the
	juxtanuclear area. Although their overall migration is inward, saltating
	endosomes frequently reverse their direction of movement. As label
	builds up in the juxtanuclear area, small vesicles containing gold
	label continuously pinch off from the larger elements and migrate
	toward the cell periphery. Experiments with nocodazole and sodium
	azide show that the saltatory movements, the accumulation and retention
	of endosomes in the juxtanuclear area, and the separation of vesicles
	from endosomes are driven by a microtubule-associated, ATP-dependent,
	motility-generating mechanism. Analysis of the movements shows that
	although each individual vesicle saltation can occur unpredictably
	toward the centre or the periphery of the cell, a net centripetal
	flux is observed. Moreover, it is evident that the probability of
	migration toward and maintenance in the juxtanuclear area is related
	to the diameter of the vesicles. We propose a mechanism by which
	bidirectional saltation along microtubules forming a radial network
	may be instrumental in the selective concentration of large endosomes
	in the juxtanuclear area while small vesicles are left free to return
	to the periphery. This process may be responsible for the sorting
	of receptors and ligands destined either for intracellular degradation
	in juxtanuclear lysosomes or, alternatively, for recycling to the
	plasma membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2895685},
  endnotereftype = {Journal Article},
  keywords = {Alkaloids/pharmacology Azides/pharmacology Benzimidazoles/pharmacology
	Carcinoma, Squamous Cell Cell Line Cell Membrane/metabolism/ultrastructure
	Human Microscopy, Electron Microscopy, Phase-Contrast Microtubules/metabolism/ultrastructure
	Nocodazole Organoids/metabolism/ultrastructure Paclitaxel Receptors,
	Transferrin/drug effects/*metabolism Sodium Azide Support, Non-U.S.
	Gov't},
  shorttitle = {Dynamic behavior of the transferrin receptor followed in living epidermoid
	carcinoma (A431) cells with nanovid microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2895685}
}

@ARTICLE{Deacon2003,
  author = {Deacon, S. W. and Serpinskaya, A. S. and Vaughan, P. S. and Lopez
	Fanarraga, M. and Vernos, I. and Vaughan, K. T. and Gelfand, V. I.},
  title = {Dynactin is required for bidirectional organelle transport},
  journal = {J Cell Biol},
  year = {2003},
  volume = {160},
  pages = {297-301},
  number = {3},
  month = {Feb 3},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Kinesin II is a heterotrimeric plus end-directed microtubule motor
	responsible for the anterograde movement of organelles in various
	cell types. Despite substantial literature concerning the types of
	organelles that kinesin II transports, the question of how this motor
	associates with cargo organelles remains unanswered. To address this
	question, we have used Xenopus laevis melanophores as a model system.
	Through analysis of kinesin II-mediated melanosome motility, we have
	determined that the dynactin complex, known as an anchor for cytoplasmic
	dynein, also links kinesin II to organelles. Biochemical data demonstrates
	that the putative cargo-binding subunit of Xenopus kinesin II, Xenopus
	kinesin II-associated protein (XKAP), binds directly to the p150Glued
	subunit of dynactin. This interaction occurs through aa 530-793 of
	XKAP and aa 600-811 of p150Glued. These results reveal that dynactin
	is required for transport activity of microtubule motors of opposite
	polarity, cytoplasmic dynein and kinesin II, and may provide a new
	mechanism to coordinate their activities.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12551954},
  endnotereftype = {Journal Article},
  keywords = {Animals Binding, Competitive/physiology *Caenorhabditis elegans Proteins
	Calcium-Binding Proteins/*metabolism Cells, Cultured Kinesin/metabolism
	Macromolecular Substances Melanophores/*metabolism Melanosomes/metabolism
	Microtubule-Associated Proteins/*metabolism Models, Biological Muscle
	Proteins/*metabolism Organelles/*metabolism Protein Binding/physiology
	Protein Transport/*physiology Research Support, Non-U.S. Gov't Research
	Support, U.S. Gov't, P.H.S. Xenopus Proteins Xenopus laevis},
  shorttitle = {Dynactin is required for bidirectional organelle transport},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12551954}
}

@ARTICLE{Denoth2002,
  author = {Denoth, J. and Stussi, E. and Csucs, G. and Danuser, G.},
  title = {Single muscle fiber contraction is dictated by inter-sarcomere dynamics},
  journal = {J Theor Biol},
  year = {2002},
  volume = {216},
  pages = {101-22},
  number = {1},
  month = {May 7},
  note = {0022-5193 (Print) Journal Article},
  abstract = {This paper presents first results from a study where we developed
	a generic framework for analysing inter-sarcomere dynamics. Our objective
	is to find an accurate description of a muscle as a linear motor
	composed of parallel and series coupled subunits. The quality of
	theoretical models can be tested through their ability to predict
	experimental observations. With the current method we have found
	rigorous mathematical explanations for mechanisms such as sarcomere
	popping, extra tension and homogenization. These phenomena have been
	observed for many years in single fibers experiments, yet have never
	been completely understood in terms of a mechanical model. Now they
	can be explained on a theoretical basis. Interestingly, rather simplistic
	descriptions of each of the various molecular components in the sarcomere
	(actin-myosin cross-bridges, titin and contributions from passive
	elastic components) are sufficient to predict these behaviors. The
	complexity of a real muscle fiber is addressed through rigorous coupling
	of the single component models in a system of differential equations.
	We examine the properties of the differential equations, based on
	a down-stripped model, which permits the derivation of analytical
	solutions. They suggest that the contraction characteristics of inter-connected
	sarcomeres are essentially dictated by the initial distribution of
	the sarcomeres on the force-length curve and their starting velocities.
	The complete model is applied to show the complexity of inter-sarcomere
	dynamics of activated fibers in stretch-release experiments with
	either external force or length control. Seemingly contradictory
	and unexpected observations from single fiber experiments, which
	have hitherto been discussed with the argument of uncontrollable
	biological variability, turn out to be a consistent set of possible
	fiber responses. They result from a convolution of multiple relatively
	simple rules each of them defining a certain characteristics of the
	single sarcomere.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12076131},
  endnotereftype = {Journal Article},
  keywords = {Animals Models, Biological *Muscle Contraction Muscle Fibers/*physiology
	Sarcomeres/*physiology},
  shorttitle = {Single muscle fiber contraction is dictated by inter-sarcomere dynamics},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12076131}
}

@ARTICLE{Dietrich2002,
  author = {Dietrich, C. and Yang, B. and Fujiwara, T. and Kusumi, A. and Jacobson,
	K.},
  title = {Relationship of lipid rafts to transient confinement zones detected
	by single particle tracking},
  journal = {Biophys J},
  year = {2002},
  volume = {82},
  pages = {274-84},
  number = {1 Pt 1},
  month = {Jan},
  note = {21621642 0006-3495 Journal Article},
  abstract = {We examined the physical and chemical characteristics of transient
	confinement zones (TCZs) that are detected in single particle trajectories
	of molecules moving within the membrane of C3H 10T1/2 murine fibroblasts
	and their relationship to "rafts." We studied the lateral movement
	of different membrane molecules thought to partition to varying degrees
	into or out of the putative lipid domains known as rafts. We found
	that lipid analogs spend significantly less time in TCZs compared
	with Thy-1, a glycosylphosphatidylinositol-anchored protein, and
	GM1, a glycosphingolipid. For Thy-1, we found that zone abundance
	was markedly reduced by cholesterol extraction, suggesting that a
	major source of the observed temporary confinement is related to
	the presence of raft domains. More detailed analysis of particle
	trajectories reveals that zones can be revisited even tens of seconds
	after the original escape and that diffusion within the zones is
	reduced by a factor of approximately 2, consistent with the zone
	being a cholesterol-rich liquid-ordered phase. Surprisingly, transient
	confinement was not strongly temperature dependent. Overall, our
	data demonstrate that there are raft-related domains present in certain
	regions of the plasma membrane of C3H cells, which can persist for
	tens of seconds.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751315},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, Thy-1/chemistry Biotinylation Cell Line Fibroblasts
	G(M1) Ganglioside/metabolism Glycosylphosphatidylinositols/metabolism
	Kinetics Membrane Lipids/*chemistry/metabolism Membrane Microdomains/*chemistry/physiology
	Mice Microscopy, Video Protein Conformation Support, Non-U.S. Gov't
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Relationship of lipid rafts to transient confinement zones detected
	by single particle tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751315}
}

@ARTICLE{Doolittle1995,
  author = {Doolittle, K W and Reddy, I and McNally, J G},
  title = {3D analysis of cell movement during normal and myosin-II-null cell
	morphogenesis in Dictyostelium.},
  journal = {Dev. Biol.},
  year = {1995},
  volume = {167},
  pages = {118-129},
  endnotereftype = {Journal Article},
  keywords = {morphogenetic movement mutant mutagenesis REMI pattern formation morphogenesis
	development myosin microscopy / video / photography},
  shorttitle = {3D analysis of cell movement during normal and myosin-II-null cell
	morphogenesis in Dictyostelium.}
}

@ARTICLE{Dormann2002,
  author = {Dormann, D. and Libotte, T. and Weijer, C. J. and Bretschneider,
	T.},
  title = {Simultaneous quantification of cell motility and protein-membrane-association
	using active contours},
  journal = {Cell Motil Cytoskeleton},
  year = {2002},
  volume = {52},
  pages = {221-30},
  number = {4},
  month = {Aug},
  note = {22105498 0886-1544 Journal Article},
  abstract = {We present a new method for the quantification of dynamic changes
	in fluorescence intensities at the cell membrane of moving cells.
	It is based on an active contour method for cell-edge detection,
	which allows tracking of changes in cell shape and position. Fluorescence
	intensities at specific cortical subregions can be followed in space
	and time and correlated with cell motility. The translocation of
	two GFP tagged proteins (CRAC and GRP1) from the cytosol to the membrane
	in response to stimulation with the chemoattractant cAMP during chemotaxis
	of Dictyostelium cells and studies of the spatio-temporal dynamics
	of this process exemplify the method: We show that the translocation
	can be correlated with motility parameters and that quantitative
	differences in the rate of association and dissociation from the
	membrane can be observed for the two PH domain containing proteins.
	The analysis of periodic CRAC translocation to the leading edge of
	a cell responding to natural cAMP waves in a mound demonstrates the
	power of this approach. It is not only capable of tracking the outline
	of cells within aggregates in front of a noisy background, but furthermore
	allows the construction of spatio-temporal polar plots, capturing
	the dynamics of the protein distribution at the cell membrane within
	the cells' moving co-ordinate system. Compilation of data by means
	of normalised polar plots is suggested as a future tool, which promises
	the so-far impossible practicability of extensive statistical studies
	and automated comparison of complex spatio-temporal protein distribution
	patterns.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12112136},
  endnotereftype = {Journal Article},
  keywords = {Algorithms Animal Cell Aggregation Cell Membrane/*metabolism Cell
	Size Chemotactic Factors/metabolism *Chemotaxis Computer Simulation
	Cyclic AMP/metabolism Dictyostelium/cytology/*physiology Luminescent
	Proteins/genetics/metabolism Microscopy, Fluorescence *Models, Biological
	Protein Transport Protozoan Proteins/genetics/metabolism Receptors,
	Cytoplasmic and Nuclear/genetics/metabolism Recombinant Fusion Proteins/genetics/metabolism
	Support, Non-U.S. Gov't},
  shorttitle = {Simultaneous quantification of cell motility and protein-membrane-association
	using active contours},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12112136}
}

@ARTICLE{Dunn1987,
  author = {Dunn, G. A. and Brown, A. F.},
  title = {A unified approach to analysing cell motility},
  journal = {J Cell Sci Suppl},
  year = {1987},
  volume = {8},
  pages = {81-102},
  note = {0269-3518 Journal Article},
  abstract = {The quantitative analysis of cell motility in culture has several
	important functions. First, it gives a concise and accurate description
	of the motile process and can detect subtle differences in motility
	due to different genetic makeup or experimental conditions. Second,
	its objectivity means that results can be communicated precisely
	and used unambiguously to test hypotheses about motility. Third,
	it may be used to derive a mathematical model with the same statistical
	properties as the motile process and thus elucidate the mechanism
	of motility. In this paper, we introduce a general procedure for
	analysing cell motility in a wide variety of circumstances. We describe
	a pilot project for the analysis of simple geometrical data obtained
	from randomly moving fibroblasts. Finally, as an example, we show
	how an analysis of the translocation of the fibroblasts can lead
	to insights into the mechanism of motility that are arguably not
	obtainable by any other approach.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3503898},
  endnotereftype = {Journal Article},
  keywords = {Animals *Cell Movement Cells, Cultured Chick Embryo *Computer Simulation
	Fibroblasts/physiology *Models, Biological Myocardium/cytology Research
	Support, Non-U.S. Gov't},
  shorttitle = {A unified approach to analysing cell motility},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3503898}
}

@ARTICLE{Eils2003,
  author = {Eils, R. and Athale, C.},
  title = {Computational imaging in cell biology},
  journal = {J Cell Biol},
  year = {2003},
  volume = {161},
  pages = {477-81},
  number = {3},
  month = {May 12},
  note = {22628151 0021-9525 Journal Article Review Review, Tutorial},
  abstract = {Microscopy of cells has changed dramatically since its early days
	in the mid-seventeenth century. Image analysis has concurrently evolved
	from measurements of hand drawings and still photographs to computational
	methods that (semi-) automatically quantify objects, distances, concentrations,
	and velocities of cells and subcellular structures. Today's imaging
	technologies generate a wealth of data that requires visualization
	and multi-dimensional and quantitative image analysis as prerequisites
	to turning qualitative data into quantitative values. Such quantitative
	data provide the basis for mathematical modeling of protein kinetics
	and biochemical signaling networks that, in turn, open the way toward
	a quantitative view of cell biology. Here, we will review technologies
	for analyzing and reconstructing dynamic structures and processes
	in the living cell. We will present live-cell studies that would
	have been impossible without computational imaging. These applications
	illustrate the potential of computational imaging to enhance our
	knowledge of the dynamics of cellular structures and processes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12743101},
  endnotereftype = {Journal Article},
  keywords = {Animal Cell Compartmentation/physiology Cell Nucleus Structures/metabolism/ultrastructure
	Computational Biology/*methods/trends Eukaryotic Cells/metabolism/*ultrastructure
	Human Image Processing, Computer-Assisted/*methods/trends Intracellular
	Membranes/metabolism/ultrastructure Microscopy/*methods/trends Organelles/metabolism/ultrastructure},
  shorttitle = {Computational imaging in cell biology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12743101}
}

@ARTICLE{Elbert1998,
  author = {Elbert, D. L. and Hubbell, J. A.},
  title = {Self-assembly and steric stabilization at heterogeneous, biological
	surfaces using adsorbing block copolymers},
  journal = {Chem Biol},
  year = {1998},
  volume = {5},
  pages = {177-83},
  number = {3},
  month = {Mar},
  note = {1074-5521 Journal Article},
  abstract = {BACKGROUND: We present the synthesis, characterization and initial
	structure-function analysis of a new class of bioactive agent that
	allows the application of techniques from colloid science to biological
	surfaces. Stable colloidal suspensions can be generated by immobilizing
	a dense brush of soluble polymer at the colloidal surface, creating
	a zone protected against the adhesion of approaching particles, a
	phenomenon termed polymeric steric stabilization. This is often accomplished
	for aqueous colloidal dispersions using adsorbing block copolymers.
	We demonstrate that water-soluble block copolymers can be designed
	to adsorb onto heterogeneous biological surfaces and block cell-cell
	and cell-surface adhesion, using polymer compositions and architectures
	that are quite different from surfactants used for stabilizing nonbiological
	colloidal dispersions. RESULTS: Comb copolymers were synthesized
	having polycationic backbones (poly-L-lysine, PLL), serving as the
	anchor for binding to the net negatively charged biological surfaces,
	grafted with water-soluble polynonionic chains (polyethylene glycol,
	PEG), to block biological recognition, producing PLL-graft-PEG copolymers.
	Specific copolymers were found to sterically stabilize red blood
	cells from lectin-induced hemagglutination and fibroblasts from adhesion
	to fibronectin-coated surfaces. The polymer design principles, which
	appear to be unique for adsorption to heterogeneous biological surfaces,
	require the use of very high molecular weight comb copolymers, perhaps
	because anionic sites are non-uniformly distributed on biological
	surfaces, and the ability of larger copolymers to span between highly
	anionic sites. CONCLUSIONS: Water-soluble copolymers were produced
	that can block recognition at biological surfaces, on the basis of
	nonspecific physicochemical phenomena rather than specific biochemical
	interactions.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9545428},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion/drug effects Erythrocytes/drug effects Fibroblasts/drug
	effects Hemagglutination Tests Human Polyethylene Glycols/*chemistry/pharmacology
	Rats Wheat Germ Agglutinins/antagonists & inhibitors/pharmacology},
  shorttitle = {Self-assembly and steric stabilization at heterogeneous, biological
	surfaces using adsorbing block copolymers},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9545428}
}

@ARTICLE{Ellenberg1997,
  author = {Ellenberg, J. and Siggia, E. D. and Moreira, J. E. and Smith, C.
	L. and Presley, J. F. and Worman, H. J. and Lippincott-Schwartz,
	J.},
  title = {Nuclear membrane dynamics and reassembly in living cells: targeting
	of an inner nuclear membrane protein in interphase and mitosis},
  journal = {J Cell Biol},
  year = {1997},
  volume = {138},
  pages = {1193-206},
  number = {6},
  month = {Sep 22},
  note = {0021-9525 Journal Article},
  abstract = {The mechanisms of localization and retention of membrane proteins
	in the inner nuclear membrane and the fate of this membrane system
	during mitosis were studied in living cells using the inner nuclear
	membrane protein, lamin B receptor, fused to green fluorescent protein
	(LBR-GFP). Photobleaching techniques revealed the majority of LBR-GFP
	to be completely immobilized in the nuclear envelope (NE) of interphase
	cells, suggesting a tight binding to heterochromatin and/or lamins.
	A subpopulation of LBR-GFP within ER membranes, by contrast, was
	entirely mobile and diffused rapidly and freely (D = 0. 41 +/- 0.1
	microm2/s). High resolution confocal time-lapse imaging in mitotic
	cells revealed LBR-GFP redistributing into the interconnected ER
	membrane system in prometaphase, exhibiting the same high mobility
	and diffusion constant as observed in interphase ER membranes. LBR-GFP
	rapidly diffused across the cell within the membrane network defined
	by the ER, suggesting the integrity of the ER was maintained in mitosis,
	with little or no fragmentation and vesiculation. At the end of mitosis,
	nuclear membrane reformation coincided with immobilization of LBR-GFP
	in ER elements at contact sites with chromatin. LBR-GFP-containing
	ER membranes then wrapped around chromatin over the course of 2-3
	min, quickly and efficiently compartmentalizing nuclear material.
	Expansion of the NE followed over the course of 30-80 min. Thus,
	selective changes in lateral mobility of LBR-GFP within the ER/NE
	membrane system form the basis for its localization to the inner
	nuclear membrane during interphase. Such changes, rather than vesiculation
	mechanisms, also underlie the redistribution of this molecule during
	NE disassembly and reformation in mitosis.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9298976},
  endnotereftype = {Journal Article},
  keywords = {Animals COS Cells DNA/analysis Endoplasmic Reticulum/chemistry/metabolism/ultrastructure
	Fluorescent Dyes Gene Expression/physiology Green Fluorescent Proteins
	Interphase/*physiology Kinetics Luminescent Proteins Microscopy,
	Electron Mitosis/*physiology Nuclear Envelope/*chemistry/*metabolism/ultrastructure
	Receptors, Cytoplasmic and Nuclear/*analysis/genetics/metabolism
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Nuclear membrane dynamics and reassembly in living cells: targeting
	of an inner nuclear membrane protein in interphase and mitosis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9298976}
}

@ARTICLE{Endler2003,
  author = {Endler, E. E. and Duca, K. A. and Nealey, P. F. and Whitesides, G.
	M. and Yin, J.},
  title = {Propagation of viruses on micropatterned host cells},
  journal = {Biotechnol Bioeng},
  year = {2003},
  volume = {81},
  pages = {719-25},
  number = {6},
  month = {Mar 20},
  note = {0006-3592 (Print) Journal Article},
  abstract = {We have developed a technique to characterize the in vitro propagation
	of viruses. Microcontact printing was used to generate linear arrays
	of alkanethiols on gold surfaces, which served as substrates for
	the patterned culture of baby hamster kidney (BHK-21) cells. Vesicular
	stomatitis virus (VSV) was added to unpatterned cell reservoirs adjacent
	to the patterned cells and incubated, setting in motion a continuously
	advancing viral infection into the patterned cells. At different
	incubation times, multiple arrays were chemically fixed to stop the
	viral propagation. Viral propagation distances into the patterned
	cells were determined by indirect immunofluorescent labeling and
	visualization of the VSV surface glycoprotein (G). The infection
	spread at approximately 50 microm/h in the 140-microm lines. Moreover,
	different temporal stages of the infection process were simultaneously
	visualized along individual lines. These stages included initiation
	of infection, based on G protein expression; cell-cell fusion, based
	on virus-induced clustering of cell nuclei; and cytoskeletal degradation,
	based on localized release of cells from the surface. This work sets
	a foundation for parallel, high-throughput characterization of viral
	and cellular processes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12529886},
  endnotereftype = {Journal Article},
  keywords = {Animals Animals, Newborn Cell Adhesion/physiology Cell Movement/physiology
	Cells, Cultured Cells, Immobilized/cytology/physiology Cricetinae
	Kidney/*cytology/physiology/*virology Membrane Glycoproteins/metabolism
	Membranes, Artificial Microscopy, Fluorescence/instrumentation/methods
	Molecular Probe Techniques Motion Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, Non-P.H.S. Rhabdoviridae Infections/*pathology/physiopathology
	Vesicular stomatitis-Indiana virus/growth & development/isolation
	& purification/*physiology/*ultrastructure Viral Envelope Proteins/metabolism
	Viral Proteins/metabolism Virus Cultivation/methods},
  shorttitle = {Propagation of viruses on micropatterned host cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12529886}
}

@ARTICLE{Endler2005,
  author = {Endler, E. E. and Nealey, P. F. and Yin, J.},
  title = {Fidelity of micropatterned cell cultures},
  journal = {J Biomed Mater Res A},
  year = {2005},
  volume = {74},
  pages = {92-103},
  number = {1},
  month = {Jul 1},
  note = {1549-3296 (Print) Journal Article},
  abstract = {Methods that enable the culture of micropatterned cells may help advance
	our fundamental understanding of cell-cell and cell-surface interactions,
	while facilitating the development and implementation of cell-based
	biological assays. However, the long-term stability of the cell patterns
	can limit the time scales over which such methods can be informative.
	Here we used self-assembling monolayers (SAMs) to localize the adsorption
	of baby hamster kidney (BHK-21) cells as well as cells from a murine
	astrocytoma-derived cell line (delayed brain tumor) in linear arrays.
	We tested the effects of surface chemistries, fibronectin pre-treatments,
	array dimensions, and cell types on pattern fidelity. Changes in
	patterns were monitored by phase-contrast microscopy up to 96 h post-plating,
	followed by digital imaging, and these changes were quantified by
	measuring an "intrusion distance" or the average distance cells extend
	beyond the initial adhesive/non-adhesive boundary. Loss of pattern
	boundaries involved different mechanisms for different cells. Treatment
	of patterned surfaces with fibronectin prior to plating of cells
	tended to promote earlier loss of pattern fidelity, and the extent
	of pattern loss was further augmented for SAMs formed using hydrophobic
	monolayers. Finally, reduction of gap spacing between adjacent cell
	arrays promoted pattern loss.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15920741},
  endnotereftype = {Journal Article},
  keywords = {Adsorption Animals Astrocytoma Brain Neoplasms Cell Culture Techniques/*methods
	Cell Line Cell Line, Tumor Cells, Cultured/*ultrastructure Cricetinae
	Fibronectins/chemistry Image Processing, Computer-Assisted Kidney/cytology
	Mice Microscopy, Phase-Contrast Proteins/chemistry Research Support,
	U.S. Gov't, Non-P.H.S. Surface Properties},
  shorttitle = {Fidelity of micropatterned cell cultures},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15920741}
}

@ARTICLE{Even-Ram2005,
  author = {Even-Ram, S. and Yamada, K. M.},
  title = {Cell migration in 3D matrix},
  journal = {Curr Opin Cell Biol},
  year = {2005},
  volume = {17},
  pages = {524-32},
  number = {5},
  month = {Oct},
  note = {0955-0674 (Print) Journal Article Review},
  abstract = {The ability of cells to migrate within the extracellular matrix and
	to remodel it depends as much on the physical and biochemical characteristics
	of a particular matrix as on cellular properties. Analyzing the different
	modes of migration of cells in matrices, and how cells switch between
	these modes, is vital for understanding a variety of physiological
	and pathological processes. Recent work provides new insights, but
	also raises some debates about the mechanisms and regulation of cell
	migration in three-dimensional matrices.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16112853},
  endnotereftype = {Journal Article},
  keywords = {Animals Basement Membrane/metabolism/physiology Cell Movement/*physiology
	Extracellular Matrix/metabolism/*physiology Humans *Models, Biological
	Monomeric GTP-Binding Proteins/metabolism/physiology Signal Transduction/physiology},
  shorttitle = {Cell migration in 3D matrix},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16112853}
}

@ARTICLE{Feder1996,
  author = {Feder, T. J. and Brust-Mascher, I. and Slattery, J. P. and Baird,
	B. and Webb, W. W.},
  title = {Constrained diffusion or immobile fraction on cell surfaces: a new
	interpretation},
  journal = {Biophys J},
  year = {1996},
  volume = {70},
  pages = {2767-73},
  number = {6},
  month = {Jun},
  note = {96363754 0006-3495 Journal Article},
  abstract = {Protein lateral mobility in cell membranes is generally measured using
	fluorescence photobleaching recovery (FPR). Since the development
	of this technique, the data have been interpreted by assuming free
	Brownian diffusion of cell surface receptors in two dimensions, an
	interpretation that requires that a subset of the diffusing species
	remains immobile. The origin of this so-called immobile fraction
	remains a mystery. In FPR, the motions of thousands of particles
	are inherently averaged, inevitably masking the details of individual
	motions. Recently, tracking of individual cell surface receptors
	has identified several distinct types of motion (Gross and Webb,
	1988; Ghosh and Webb, 1988, 1990, 1994; Kusumi et al. 1993; Qian
	et al. 1991; Slattery, 1995), thereby calling into question the classical
	interpretation of FPR data as free Brownian motion of a limited mobile
	fraction. We have measured the motion of fluorescently labeled immunoglobulin
	E complexed to high affinity receptors (Fc epsilon RI) on rat basophilic
	leukemia cells using both single particle tracking and FPR. As in
	previous studies, our tracking results show that individual receptors
	may diffuse freely, or may exhibit restricted, time-dependent (anomalous)
	diffusion. Accordingly, we have analyzed FPR data by a new model
	to take this varied motion into account, and we show that the immobile
	fraction may be due to particles moving with the anomalous subdiffusion
	associated with restricted lateral mobility. Anomalous subdiffusion
	denotes random molecular motion in which the mean square displacements
	grow as a power law in time with a fractional positive exponent less
	than one. These findings call for a new model of cell membrane structure.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8744314},
  endnotereftype = {Journal Article},
  keywords = {Animal Biophysics Cell Line Cell Membrane/*chemistry/*metabolism Comparative
	Study Diffusion Fluorescent Dyes Membrane Lipids/chemistry/metabolism
	Membrane Proteins/chemistry/metabolism Models, Biological Rats Receptors,
	Cell Surface/metabolism Receptors, IgE/chemistry/metabolism Support,
	U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.},
  shorttitle = {Constrained diffusion or immobile fraction on cell surfaces: a new
	interpretation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8744314}
}

@ARTICLE{Feneberg2001,
  author = {Feneberg, W. and Westphal, M. and Sackmann, E.},
  title = {Dictyostelium cells' cytoplasm as an active viscoplastic body},
  journal = {Eur Biophys J},
  year = {2001},
  volume = {30},
  pages = {284-94},
  number = {4},
  month = {Aug},
  note = {21430129 0175-7571 Journal Article},
  abstract = {We applied a recently developed microrheology technique based on colloidal
	magnetic tweezers to measure local viscoelastic moduli and active
	forces in cells of Dictyostelium discoideum. The active transport
	of nonmagnetic beads taken up by phagocytosis was analyzed by single
	particle tracking, which allowed us to measure the length of straight
	steps and the corresponding velocities of the movements. The motion
	consists of a superposition of nearly straight long-range steps (step
	length in the micrometer range) and local random walks (step widths
	about 0.1 microm). The velocities for the former type of motion range
	from 1 to 3 microm/s. They decrease with increasing bead size and
	are attributed to rapid active transport along microtubuli. The short-range
	local motions exhibit velocities of less than 0.5 microm/s and reflect
	the internal dynamics of the cytoplasm. Viscoelastic response curves
	were measured by application of force pulses with amplitudes varying
	between 50 pN and 400 pN. Analysis of the response curves in terms
	of mechanical equivalent circuits yielded cytoplasmic viscosities
	varying between 10 and 350 Pa s. Simultaneous analysis of the response
	curves and of the bead trajectories showed that the motion of the
	beads is determined by the local yield stress within the cytoplasmic
	scaffold and cisternae, which varies between sigma = 30 Pa and 250
	Pa. The motion of intracellular particles is interpreted in terms
	of viscoplastic behavior and the apparent viscosity is a measure
	of the reciprocal rate of bond breakage within the cytoplasmatic
	network. The viscoelastic moduli are interpreted as dynamic quantities
	which depend sensitively on the amplitude of the forces, and the
	rate of bond breakage is determined by the Arrhenius-Kramers law
	with the activation energy being reduced by the work performed by
	the applied force. In agreement with previous work, we provide evidence
	that the myosin II-deficient cells exhibit higher yield stresses,
	suggesting that the function of myosin II as a cross-linker is taken
	over by the other (non-active) cross-linkers.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11548131},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Transport, Active Biophysics Cytoplasm/*physiology
	Dictyostelium/genetics/*physiology Elasticity Ferric Compounds Latex
	Magnetics Mutation Myosin Type II/genetics/physiology Particle Size
	Phagocytosis Rheology/*instrumentation/methods Support, Non-U.S.
	Gov't Viscosity},
  shorttitle = {Dictyostelium cells' cytoplasm as an active viscoplastic body},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11548131}
}

@ARTICLE{Fink2007,
  author = {Fink, J. and Thery, M. and Azioune, A. and Dupont, R. and Chatelain,
	F. and Bornens, M. and Piel, M.},
  title = {Comparative study and improvement of current cell micro-patterning
	techniques},
  journal = {Lab Chip},
  year = {2007},
  volume = {7},
  pages = {672-80},
  number = {6},
  month = {Jun},
  note = {1473-0197 (Print) Journal Article},
  abstract = {The original micropatterning technique on gold, although very efficient,
	is not accessible to most biology labs and is not compatible with
	their techniques for image acquisition. Other solutions have been
	developed on silanized glass coverslips. These methods are still
	hardly accessible to biology labs and do not provide sufficient reproducibility
	to become incorporated in routine biological protocols. Here, we
	analyzed cell behavior on micro-patterns produced by various alternative
	techniques. Distinct cell types displayed different behavior on micropatterns,
	while some were easily constrained by the patterns others escaped
	or ripped off the patterned adhesion molecules. We report methods
	to overcome some of these limitations on glass coverslips and on
	plastic dishes which are compatible with our experimental biological
	applications. Finally, we present a new method based on UV crosslinking
	of adhesion proteins with benzophenone to easily and rapidly produce
	highly reproducible micropatterns without the use of a microfabricated
	elastomeric stamp.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17538708},
  endnotereftype = {Journal Article},
  shorttitle = {Comparative study and improvement of current cell micro-patterning
	techniques},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17538708}
}

@ARTICLE{Finzi2001,
  author = {Finzi, L. and Galajda, P. and Garab, G.},
  title = {Labeling phosphorylated LHCII with microspheres for tracking studies
	and force measurements},
  journal = {J Photochem Photobiol B},
  year = {2001},
  volume = {65},
  pages = {1-4},
  number = {1},
  month = {Dec 1},
  note = {21615318 1011-1344 Journal Article},
  abstract = {We report a method to selectively label phosphorylated, membrane proteins
	with microscopic particles. This technology is particularly useful
	in single particle studies. In such studies, the particles may serve
	to visualize protein diffusion and/or as 'handles' to study the force
	of interaction between the labeled protein and the membrane matrix.
	In the latter kind of experiments, forces can be applied and measured
	by calibrated optical tweezers. Optical tweezers were used in this
	work to test the strength of the particle labeling. Labeling a single
	protein with a particle produces a long-lived, distinct tag and is
	particularly useful for proteins in photosynthetic membranes, which
	contain endogenous fluorophores that would render single fluorescent
	proteins difficult to detect.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11747998},
  endnotereftype = {Journal Article},
  keywords = {Chloroplasts/metabolism Microspheres Phosphorylation Photosynthetic
	Reaction Center, Plant/*metabolism Spinach/metabolism Staining and
	Labeling/methods Support, Non-U.S. Gov't Thylakoids/metabolism},
  shorttitle = {Labeling phosphorylated LHCII with microspheres for tracking studies
	and force measurements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11747998}
}

@ARTICLE{Fishkind1996,
  author = {Fishkind, D. J. and Silverman, J. D. and Wang, Y. L.},
  title = {Function of spindle microtubules in directing cortical movement and
	actin filament organization in dividing cultured cells},
  journal = {J Cell Sci},
  year = {1996},
  volume = {109 ( Pt 8)},
  pages = {2041-51},
  month = {Aug},
  note = {97009395 0021-9533 Journal Article},
  abstract = {The mitotic spindle has long been recognized to play an essential
	role in determining the position of the cleavage furrow during cell
	division, however little is known about the mechanisms involved in
	this process. One attractive hypothesis is that signals from the
	spindle may function to induce reorganization of cortical structures
	and transport of actin filaments to the equator during cytokinesis.
	While an important idea, few experiments have directly tested this
	model. In the present study, we have used a variety of experimental
	approaches to identify microtubule-dependent effects on key cortical
	events during normal cell cleavage, including cortical flow, reorientation
	of actin filaments, and formation of the contractile apparatus. Single-particle
	tracking experiments showed that the microtubule disrupting drug
	nocodazole induces an inhibition of the movements of cell surface
	receptors following anaphase onset, while the microtubule stabilizing
	drug taxol causes profound changes in the overall pattern of receptor
	movements. These effects were accompanied by a related set of changes
	in the organization of the actin cytoskeleton. In nocodazole-treated
	cells, the three-dimensional organization of cortical actin filaments
	appeared less ordered than in controls. Measurements with fluorescence-detected
	linear dichroism indicated a decrease in the alignment of filaments
	along the spindle axis. In contrast, actin filaments in taxol-treated
	cells showed an increased alignment along the equator on both the
	ventral and dorsal cortical surfaces, mirroring the redistribution
	pattern of surface receptors. Together, these experiments show that
	spindle microtubules are involved in directing bipolar flow of surface
	receptors and reorganization of actin filaments during cell division,
	thus acting as a stimulus for positioning cortical cytoskeletal components
	and organizing the contractile apparatus of dividing tissue culture
	cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8856500},
  endnotereftype = {Journal Article},
  keywords = {Actins/*ultrastructure Anaphase Animal Cell Division Cells, Cultured
	Kidney/cytology/drug effects Microtubules/*physiology Mitosis Mitotic
	Spindle Apparatus/*physiology Nocodazole/pharmacology Paclitaxel/pharmacology
	Rats Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.},
  shorttitle = {Function of spindle microtubules in directing cortical movement and
	actin filament organization in dividing cultured cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8856500}
}

@ARTICLE{Fleet1990,
  author = {Fleet, DJ and Jepson, AD},
  title = {Computation of component image velocity from local phase information},
  journal = {Intern J Comput Vis},
  year = {1990},
  volume = {5},
  pages = {77-104},
  endnotereftype = {Journal Article},
  shorttitle = {Computation of component image velocity from local phase information}
}

@ARTICLE{Folch2000,
  author = {Folch, A. and Jo, B. H. and Hurtado, O. and Beebe, D. J. and Toner,
	M.},
  title = {Microfabricated elastomeric stencils for micropatterning cell cultures},
  journal = {J Biomed Mater Res},
  year = {2000},
  volume = {52},
  pages = {346-53},
  number = {2},
  month = {Nov},
  note = {0021-9304 (Print) Journal Article},
  abstract = {Here we present an inexpensive method to fabricate microscopic cellular
	cultures, which does not require any surface modification of the
	substrate prior to cell seeding. The method utilizes a reusable elastomeric
	stencil (i.e., a membrane containing thru holes) which seals spontaneously
	against the surface. The stencil is applied to the cell-culture substrate
	before seeding. During seeding, the stencil prevents the substrate
	from being exposed to the cell suspension except on the hole areas.
	After cells are allowed to attach and the stencil is peeled off,
	cellular islands with a shape similar to the holes remain on the
	cell-culture substrate. This solvent-free method can be combined
	with a wide range of substrates (including biocompatible polymers,
	homogeneous or nonplanar surfaces, microelectronic chips, and gels),
	biomolecules, and virtually any adherent cell type.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10951374},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion Cell Culture Techniques/*instrumentation *Coated
	Materials, Biocompatible *Dimethylpolysiloxanes Fibroblasts Humans
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
	*Silicones},
  shorttitle = {Microfabricated elastomeric stencils for micropatterning cell cultures},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10951374}
}

@ARTICLE{Folch2000a,
  author = {Folch, A. and Toner, M.},
  title = {Microengineering of cellular interactions},
  journal = {Annu Rev Biomed Eng},
  year = {2000},
  volume = {2},
  pages = {227-56},
  note = {1523-9829 (Print) Journal Article Review},
  abstract = {Tissue function is modulated by an intricate architecture of cells
	and biomolecules on a micrometer scale. Until now, in vitro cellular
	interactions were mainly studied by random seeding over homogeneous
	substrates. Although this strategy has led to important discoveries,
	it is clearly a nonoptimal analog of the in vivo scenario. With the
	incorporation--and adaptation--of microfabrication technology into
	biology, it is now possible to design surfaces that reproduce some
	of the aspects of that architecture. This article reviews past research
	on the engineering of cell-substrate, cell-cell, and cell-medium
	interactions on the micrometer scale.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11701512},
  endnotereftype = {Journal Article},
  keywords = {Animals Biocompatible Materials Biomedical Engineering Cell Adhesion/physiology
	Cell Communication/*physiology Culture Media Extracellular Matrix
	Proteins/physiology Humans Surface Properties},
  shorttitle = {Microengineering of cellular interactions},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11701512}
}

@ARTICLE{Friedl2001,
  author = {Friedl, P. and Borgmann, S. and Brocker, E. B.},
  title = {Amoeboid leukocyte crawling through extracellular matrix: lessons
	from the Dictyostelium paradigm of cell movement},
  journal = {J Leukoc Biol},
  year = {2001},
  volume = {70},
  pages = {491-509},
  number = {4},
  month = {Oct},
  note = {0741-5400 (Print) Journal Article Review},
  abstract = {Cell movement within three-dimensional tissues is a cycling multistep
	process that requires the integration of complex biochemical and
	biophysical cell functions. Different cells solve this challenge
	differently, which leads to differences in migration strategies.
	Migration principles established for leukocytes share many characteristics
	with those described for ameba of the lower eukaryote Dictyostelium
	discoideum. The hallmarks of amoeboid movement include a simple polarized
	shape, dynamic pseudopod protrusion and retraction, flexible oscillatory
	shape changes, and rapid low-affinity crawling. Amoeboid crawling
	includes haptokinetic adhesion-dependent as well as biophysical migration
	mechanisms on or within many structurally and functionally different
	substrates. We describe central aspects of amoeboid movement in leukocytes
	and the implications for leukocyte crawling and positioning strategies
	within interstitial tissues.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11590185},
  endnotereftype = {Journal Article},
  keywords = {Actins/metabolism Animals Cell Adhesion *Cell Movement Cell Size *Chemotaxis,
	Leukocyte Cytoskeleton/physiology/ultrastructure Dictyostelium/cytology/growth
	& development/*physiology Extracellular Matrix/metabolism Leukocytes/*physiology
	*Models, Biological Receptors, Leukocyte-Adhesion/physiology Research
	Support, Non-U.S. Gov't Signal Transduction},
  shorttitle = {Amoeboid leukocyte crawling through extracellular matrix: lessons
	from the Dictyostelium paradigm of cell movement},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11590185}
}

@ARTICLE{Friedl2004,
  author = {Friedl, P. and Brocker, E. B.},
  title = {Reconstructing leukocyte migration in 3D extracellular matrix by
	time-lapse videomicroscopy and computer-assisted tracking},
  journal = {Methods Mol Biol},
  year = {2004},
  volume = {239},
  pages = {77-90},
  note = {1064-3745 (Print) Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14573911},
  endnotereftype = {Journal Article},
  keywords = {CD4-Positive T-Lymphocytes/physiology CD8-Positive T-Lymphocytes/physiology
	Cell Culture Techniques/instrumentation Cell Movement/*physiology
	Collagen Data Interpretation, Statistical Extracellular Matrix/*physiology
	Humans In Vitro Leukocytes/*physiology Microscopy, Video/*methods/statistics
	& numerical data Research Support, Non-U.S. Gov't},
  shorttitle = {Reconstructing leukocyte migration in 3D extracellular matrix by time-lapse
	videomicroscopy and computer-assisted tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14573911}
}

@ARTICLE{Friedl2002,
  author = {Friedl, P. and Brocker, E. B.},
  title = {TCR triggering on the move: diversity of T-cell interactions with
	antigen-presenting cells},
  journal = {Immunol Rev},
  year = {2002},
  volume = {186},
  pages = {83-9},
  month = {Aug},
  note = {0105-2896 (Print) Journal Article Review},
  abstract = {Polarized T cells are mobile cells optimized for migration, receptor
	scanning, and signaling. When in contact with antigen-presenting
	cells (APCs), polarized T cells can develop a spectrum of biophysical
	interaction modes ranging from adhesive sticking to dynamic crawling.
	Both static and dynamic contacts support sustained triggering of
	the T-cell receptor (TCR), leading to signal induction, T blast formation,
	and proliferation. In dynamic interactions, T cells crawl across
	the surface of the APC at speeds of 2-6 micro m/min and simultaneously
	establish an asymmetric tight yet mobile junction plane, representing
	a dynamic immunological synapse. In dynamic synapses three functional
	compartments of the polarized T cell are in close contact with the
	APC surface, i.e. leading edge, cell body and uropod. Through its
	mobility, the asymmetric junction is topographically suited for receptor
	scanning and engagement at the leading edge, retrograde receptor
	movement along the junction, and exit from the uropod. Herein we
	develop a model on scanning encounters between T cells and APCs that
	includes the simultaneous engagement of T-cell leading edge and uropod
	and implicates a serial receptor triggering mode in cell-cell recognition.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12234364},
  endnotereftype = {Journal Article},
  keywords = {Animals Antigen-Presenting Cells/*immunology Cell Movement/immunology
	Humans Lymphocyte Activation/*immunology Receptors, Antigen, T-Cell/*immunology
	Research Support, Non-U.S. Gov't Signal Transduction/*immunology
	T-Lymphocytes/*immunology},
  shorttitle = {TCR triggering on the move: diversity of T-cell interactions with
	antigen-presenting cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12234364}
}

@ARTICLE{Friedl2000,
  author = {Friedl, P. and Brocker, E. B.},
  title = {T cell migration in three-dimensional extracellular matrix: guidance
	by polarity and sensations},
  journal = {Dev Immunol},
  year = {2000},
  volume = {7},
  pages = {249-66},
  number = {2-4},
  note = {1044-6672 (Print) Journal Article Review},
  abstract = {The locomotion of T lymphocytes within 3-D extracellular matrix (ECM)
	is a highly dynamic and flexible process following the principles
	of ameboid movement. Ameboid motility is characterized by a polarized
	yet simple cell shape allowing high speed, rapid directional oscillations,
	and low affinity interactions to the substrate that are coupled to
	a low degree of cytoskeletal organization lacking discrete focal
	contacts. At the onset of T cell migration, a default program, here
	described as migration-associated polarization, is initiated, resulting
	in the polar redistribution of cell surface receptors and cytoskeletal
	elements. Polarization involves protein cycling either to the leading
	edge (i.e. LFA-1, CD45RO, chemokine receptors, focal adhesion kinase),
	to a central polarizing compartment (MTOC, PKC, MARCKS), or into
	the uropod (CD44, CD43, ICAM-1 and -3, beta1 integrins). The function
	of such compartment formation may be important in chemotactic response,
	scanning of encountered cells, and a flexible and adaptive interaction
	with the ECM itself. Due to the simple shape and a diffusely organized
	cytoskeleton, the interactions to the surrounding extracellular matrix
	are rapid and reversible and appear to allow a broad spectrum of
	molecular migration strategies. These range from (1) adhesive and
	haptokinetic following i.e. chemokine-induced motility across 2-D
	surfaces to (2) largely integrin-independent migration predominantly
	guided by shape change and morphological flexibility, as seen in
	3-D type I collagen matrices. Their prominent capacity to rapidly
	adapt to a given structural environment coupled to contact guidance
	mechanisms set T cell locomotion apart from slow, focal contact-dependent
	and more adhesive migration strategies established by fibroblast-like
	cells and cell clusters. It is therefore likely that, within the
	tissues, besides chemotactic or haptotactic gradients, the preformed
	matrix structure has an important impact on T cell trafficking and
	positioning in health and disease.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11097216},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Movement Cell Polarity Extracellular Matrix/*physiology
	Humans Research Support, Non-U.S. Gov't T-Lymphocytes/*physiology},
  shorttitle = {T cell migration in three-dimensional extracellular matrix: guidance
	by polarity and sensations},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11097216}
}

@ARTICLE{Friedl2000a,
  author = {Friedl, P. and Brocker, E. B.},
  title = {The biology of cell locomotion within three-dimensional extracellular
	matrix},
  journal = {Cell Mol Life Sci},
  year = {2000},
  volume = {57},
  pages = {41-64},
  number = {1},
  month = {Jan 20},
  note = {1420-682X (Print) Journal Article Review},
  abstract = {Cell migration in three-dimensional (3-D) extracellular matrix (ECM)
	is not a uniform event but rather comprises a modular spectrum of
	interdependent biophysical and biochemical cell functions. Haptokinetic
	cell migration across two-dimensional (2-D) surfaces consists of
	at least three processes: (i) the protrusion of the leading edge
	for adhesive cell-substratum interactions is followed by (ii) contraction
	of the cell body and (iii) detachment of the trailing edge. In cells
	of flattened morphology migrating slowly across 2-D substrate, contact-dependent
	clustering of adhesion receptors including integrins results in focal
	contact and stress fiber formation. While haptokinetic migration
	is predominantly a function of adhesion and deadhesion events lacking
	spatial barriers towards the advancing cell body, the biophysics
	of the tissues require a set of cellular strategies to overcome matrix
	resistance. Matrix barriers force the cells to adapt their morphology
	and change shape and/or enzymatically degrade ECM components, either
	by contact-dependent proteolysis or by protease secretion. In 3-D
	ECM, in contrast to 2-D substrate, the cell shape is mostly bipolar
	and the cytoskeletal organization is less stringent, frequently lacking
	discrete focal contacts and stress fibers. Morphologically large
	spindle-shaped cells (i.e., fibroblasts, endothelial cells, and many
	tumor cells) of high integrin expression and strong cytoskeletal
	contractility utilize integrin-dependent migration strategies that
	are coupled to the capacity to reorganize ECM. In contrast, a more
	dynamic ameboid migration type employed by smaller cells expressing
	low levels of integrins (i.e., T lymphocytes, dendritic cells, some
	tumor cells) is characterized by largely integrin-independent interaction
	strategies and flexible morphological adaptation to preformed fiber
	strands, without structurally changing matrix architecture. In tumor
	invasion and angiogenesis, migration mechanisms further comprise
	the migration of entire cell clusters or strands maintaining stringent
	cell-cell adhesion and communication while migrating. Lastly, cellular
	interactions, enzyme and cytokine secretion, and tissue remodeling
	provided by reactive stroma cells (i.e. fibroblasts and macrophages)
	contribute to cell migration. In conclusion, depending on the cellular
	composition and tissue context of migration, diverse cellular and
	molecular migration strategies can be developed by different cell
	types.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10949580},
  endnotereftype = {Journal Article},
  keywords = {Animals Antigens, CD44/metabolism Cell Adhesion *Cell Movement Cell
	Size Collagen/metabolism Extracellular Matrix/*metabolism Humans
	Integrins/metabolism Membranes/metabolism Neoplasm Invasiveness/pathology
	Neoplasms/metabolism/pathology Research Support, Non-U.S. Gov't},
  shorttitle = {The biology of cell locomotion within three-dimensional extracellular
	matrix},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10949580}
}

@ARTICLE{Friedl1998,
  author = {Friedl, P. and Brocker, E. B. and Zanker, K. S.},
  title = {Integrins, cell matrix interactions and cell migration strategies:
	fundamental differences in leukocytes and tumor cells},
  journal = {Cell Adhes Commun},
  year = {1998},
  volume = {6},
  pages = {225-36},
  number = {2-3},
  note = {1061-5385 (Print) Journal Article Review},
  abstract = {The principles determining the migration of different cell types may
	results from their differences in origin, size and shape, function
	of adhesion receptors, and environmental factors, including the extracellular
	matrix. Polarized leukocytes (T lymphocytes and dendritic cells)
	migrating in three-dimensional collagen lattices are small developing
	a highly dynamic leading edge and a trailing uropod, whereas invasive
	melanoma cells are larger, highly polarized and less dynamic. In
	contrast to leukocyte, tumor cells may additionally develop migrating
	cell clusters maintaining intense cell-cell interaction and cluster
	polarity. Leukocytes show a speed-oriented, oscillating and directionally
	unpredictable path profile strongly guided by matrix fibers, while
	melanoma cells and migrating cell clusters exhibit slow yet highly
	directional migration. Whereas leukocytes form short-lived interactions
	with collagen fibers in complete absence of tissue remodeling, melanoma
	cells and neoplastic cell clusters reorganize the matrix via profound
	pulling at attachment sites, limited fiber disruption upon detachment,
	and the shedding of cell surface determinants. Using blocking anti-integrin
	antibodies, tumor cell migration and migration-associated matrix
	reorganization were shown to be dependent on beta 1 integrin-mediated
	adhesion, whereas migrating T cells cannot be inhibited by a panel
	of anti-beta 1-, beta 2-, beta 3-, and alpha-integrin antibodies,
	either alone or in combination. Consequently, migrating melanoma
	cells use focal adhesions of integrins coclustered with cytoskeletal
	components at contacts with collagen fibers. T cells, however, lack
	typical focal adhesions, redistribute beta 1 integrins to the uropod
	and the focal adhesion kinase to the leading edge. In conclusion,
	an adhesion-dependent and reorganizing migration type employed by
	melanoma cells may be distinct from largely integrin-independent
	and non-reorganizing migration strategies used by leukocytes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9823473},
  endnotereftype = {Journal Article},
  keywords = {Cell Movement/*physiology Dendritic Cells/chemistry/cytology Extracellular
	Matrix/chemistry/physiology Humans Integrins/*physiology Melanoma/*chemistry
	Neoplasm Circulating Cells/*chemistry Research Support, Non-U.S.
	Gov't T-Lymphocytes/chemistry/*cytology},
  shorttitle = {Integrins, cell matrix interactions and cell migration strategies:
	fundamental differences in leukocytes and tumor cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9823473}
}

@ARTICLE{Friedl1998a,
  author = {Friedl, P. and Zanker, K. S. and Brocker, E. B.},
  title = {Cell migration strategies in 3-D extracellular matrix: differences
	in morphology, cell matrix interactions, and integrin function},
  journal = {Microsc Res Tech},
  year = {1998},
  volume = {43},
  pages = {369-78},
  number = {5},
  month = {Dec 1},
  note = {1059-910X (Print) Journal Article},
  abstract = {Cell migration in extracellular matrix is a complex process of adhesion
	and deadhesion events combined with cellular strategies to overcome
	the biophysical resistance imposed by three-dimensionally interconnected
	matrix ligands. Using a 3-D collagen matrix migration model in combination
	with computer-assisted cell tracking for reconstruction of migration
	paths and confocal microscopy, we investigated molecular principles
	governing cell-matrix interactions and migration of different cell
	types. Highly invasive MV3 melanoma cells and fibroblasts are large
	and highly polarized cells migrating at low speed (0.1-0.5 microm/min)
	and at high directional persistence. MV3 melanoma cells utilize adhesive
	migration strategies as characterized by high beta1 integrin surface
	expression, beta1 integrin clustering at interactions with matrix
	fibers, and beta1 integrin-mediated adhesion for force generation
	and migration. In contrast, T lymphocytes and dendritic cells are
	highly mobile cells of lower beta1 integrin expression migrating
	at 10- to 40-fold higher velocities, and directionally unpredictable
	path profiles. This migration occurs in the absence of focal adhesions
	and largely independent of beta1 integrin-mediated adhesion. Whereas
	cell-matrix interactions of migrating tumor cells result in traction
	and reorientation of collagen fibers, partial matrix degradation,
	and pore formation, leukocytes form transient and short-lived interactions
	with the collagen lacking structural proteolysis and matrix remodeling.
	In conclusion, the 3-D extracellular matrix provides a spatially
	complex and biomechanically demanding substrate for cell migration,
	thereby differing from cell migration across planar ligands. Highly
	adhesive and integrin-dependent migration strategies detected in
	morphologically large and slowly migrating cells may result in reorganization
	of the extracellular matrix, whereas leukocytes favor largely integrin-independent,
	rapid, and flexible migration strategies lacking typical focal adhesions
	and structural matrix remodeling.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9858334},
  endnotereftype = {Journal Article},
  keywords = {Cell Adhesion/physiology Cell Line Cell Movement/*physiology Collagen/physiology
	Comparative Study Computer Simulation Dendritic Cells/physiology
	Extracellular Matrix/*physiology Fibroblasts/physiology Flow Cytometry
	Integrins/*metabolism Microscopy, Electron Microscopy, Fluorescence
	Microscopy, Video Research Support, Non-U.S. Gov't T-Lymphocytes/physiology},
  shorttitle = {Cell migration strategies in 3-D extracellular matrix: differences
	in morphology, cell matrix interactions, and integrin function},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9858334}
}

@ARTICLE{Geerts1987,
  author = {H. Geerts and M. De Brabander and R. Nuydens and S. Geuens and M.
	Moeremans and J. De Mey and P. Hollenbeck},
  title = {Nanovid tracking: a new automatic method for the study of mobility
	in living cells based on colloidal gold and video microscopy.},
  journal = {Biophys J},
  year = {1987},
  volume = {52},
  pages = {775--782},
  number = {5},
  month = {Nov},
  abstract = {We describe a new automatic technique for the study of intracellular
	mobility. It is based on the visualization of colloidal gold particles
	by video-enhanced contrast light microscopy (nanometer video microscopy)
	combined with modern tracking algorithms and image processing hardware.
	The approach can be used for determining the complete statistics
	of saltatory motility of a large number of individual moving markers.
	Complete distributions of jump time, jump velocity, stop time, and
	orientation can be generated. We also show that this method allows
	one to study the characteristics of random motion in the cytoplasm
	of living cells or on cell membranes. The concept is illustrated
	by two studies. First we present the motility of colloidal gold in
	an in vitro system of microtubules and a protein extract containing
	a kinesin-like factor. The algorithm is thoroughly tested by manual
	tracking of the videotapes. The second study involves the motion
	of gold particles microinjected in the cytoplasm of PTK-2 cells.
	Here the results are compared to a study using the spreading of colloidal
	gold particles after microinjection.},
  bdsk-url-1 = {http://dx.doi.org/10.1016/S0006-3495(87)83271-X},
  doi = {10.1016/S0006-3495(87)83271-X},
  institution = {Department of Life Sciences, Janssen Pharmaceutica Research Laboratories,
	Beerse, Belgium.},
  keywords = {Animals; Autoanalysis; Cell Line; Cell Movement; Gold; Microscopy,
	methods; Video Recording},
  language = {eng},
  medline-pst = {ppublish},
  owner = {Kota},
  pii = {S0006-3495(87)83271-X},
  pmid = {3427186},
  timestamp = {2011.03.10},
  url = {http://dx.doi.org/10.1016/S0006-3495(87)83271-X}
}

@ARTICLE{Geiger1995,
  author = {Geiger, D. and Gupta, A. and Costa, L.A. and Vlontzos, J.},
  title = {Dynamic Programming for Detecting, Tracking, and Matching Deformable
	Contours},
  journal = {IEEE Trans Pattern Anal Machine Intell},
  year = {1995},
  volume = {17},
  pages = {294-302},
  number = {3},
  endnotereftype = {Journal Article},
  shorttitle = {Dynamic Programming for Detecting, Tracking, and Matching Deformable
	Contours}
}

@ARTICLE{gellesNAT1988,
  author = {Gelles, J. and Schnapp, B. J. and Sheetz, M. P.},
  title = {Tracking kinesin-driven movements with nanometre-scale precision},
  journal = {Nature},
  year = {1988},
  volume = {331},
  pages = {450-3},
  number = {6155},
  month = {Feb 4},
  note = {88122616 0028-0836 Journal Article},
  abstract = {Several enzyme complexes drive cellular movements by coupling free
	energy-liberating chemical reactions to the production of mechanical
	work. A key goal in the study of these systems is to characterize
	at the molecular level mechanical events associated with individual
	reaction steps in the catalytic cycles of single enzyme molecules.
	Ideally, one would like to measure movements driven by single (or
	a few) enzyme molecules with sufficient temporal resolution and spatial
	precision that these events can be directly observed. Kinesin, a
	force-generating ATPase involved in microtubule-based intracellular
	organelle transport, will drive the unidirectional movement of microscopic
	plastic beads along microtubules in vitro. Under certain conditions,
	a few (less than or equal to 10) kinesin molecules may be sufficient
	to drive either bead movement or organelle transport. Here we describe
	a method for determining precise positional information from light-microscope
	images. The method is applied to measure kinesin-driven bead movements
	in vitro with a precision of 1-2 nm. Our measurements reveal basic
	mechanical features of kinesin-driven movements along the microtubule
	lattice, and place significant constraints on possible molecular
	mechanisms of movement.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3123999},
  endnotereftype = {Journal Article},
  keywords = {Adenosine Triphosphate/metabolism Kinesin Microtubules/metabolism
	Nerve Tissue Proteins/*physiology Support, Non-U.S. Gov't Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Tracking kinesin-driven movements with nanometre-scale precision},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3123999}
}

@ARTICLE{ghoshBJ1994,
  author = {Ghosh, R. N. and Webb, W. W.},
  title = {Automated detection and tracking of individual and clustered cell
	surface low density lipoprotein receptor molecules},
  journal = {Biophys J},
  year = {1994},
  volume = {66},
  pages = {1301-18},
  number = {5},
  month = {May},
  note = {94339330 0006-3495 Journal Article},
  abstract = {We have developed a technique to detect, recognize, and track each
	individual low density lipoprotein receptor (LDL-R) molecule and
	small receptor clusters on the surface of human skin fibroblasts.
	Molecular recognition and high precision (30 nm) simultaneous automatic
	tracking of all of the individual receptors in the cell surface population
	utilize quantitative time-lapse low light level digital video fluorescence
	microscopy analyzed by purpose-designed algorithms executed on an
	image processing work station. The LDL-Rs are labeled with the biologically
	active, fluorescent LDL derivative dil-LDL. Individual LDL-Rs and
	unresolved small clusters are identified by measuring the fluorescence
	power radiated by the sub-resolution fluorescent spots in the image;
	identification of single particles is ascertained by four independent
	techniques. An automated tracking routine was developed to track
	simultaneously, and without user intervention, a multitude of fluorescent
	particles through a sequence of hundreds of time-lapse image frames.
	The limitations on tracking precision were found to depend on the
	signal-to-noise ratio of the tracked particle image and mechanical
	drift of the microscope system. We describe the methods involved
	in (i) time-lapse acquisition of the low-light level images, (ii)
	simultaneous automated tracking of the fluorescent diffraction limited
	punctate images, (iii) localizing particles with high precision and
	limitations, and (iv) detecting and identifying single and clustered
	LDL-Rs. These methods are generally applicable and provide a powerful
	tool to visualize and measure dynamics and interactions of individual
	integral membrane proteins on living cell surfaces.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8061186},
  endnotereftype = {Journal Article},
  keywords = {Algorithms Biophysics Carbocyanines Cell Line Cell Membrane/metabolism
	Computer Simulation Diffusion Fibroblasts/metabolism Fluorescent
	Dyes Human Image Processing, Computer-Assisted Lipoproteins, LDL/metabolism
	Microscopy, Fluorescence Models, Biological Receptor Aggregation
	Receptors, LDL/*metabolism Skin/metabolism Support, Non-U.S. Gov't
	Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.},
  shorttitle = {Automated detection and tracking of individual and clustered cell
	surface low density lipoprotein receptor molecules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8061186}
}

@ARTICLE{Giachetti2000,
  author = {Giachetti, A},
  title = {Matching techniques to compute image motion},
  journal = {IVC},
  year = {2000},
  volume = {18},
  pages = {247},
  number = {3},
  month = {260},
  endnotereftype = {Journal Article},
  shorttitle = {Matching techniques to compute image motion}
}

@ARTICLE{Glick2002,
  author = {Glick, B. S.},
  title = {Can the Golgi form de novo?},
  journal = {Nat Rev Mol Cell Biol},
  year = {2002},
  volume = {3},
  pages = {615-9},
  number = {8},
  month = {Aug},
  note = {1471-0072 Journal Article},
  abstract = {Does the Golgi apparatus proliferate by adding new material to a permanent
	template, or do Golgi structures form de novo by a process of self-organization?
	Recent work suggests that the Golgi is capable of forming de novo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12154372},
  endnotereftype = {Journal Article},
  keywords = {Endoplasmic Reticulum/metabolism Golgi Apparatus/*physiology Models,
	Biological Saccharomyces cerevisiae/cytology/metabolism Secretory
	Vesicles},
  shorttitle = {Can the Golgi form de novo?},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12154372}
}

@ARTICLE{Glick1998,
  author = {Glick, B. S. and Malhotra, V.},
  title = {The curious status of the Golgi apparatus},
  journal = {Cell},
  year = {1998},
  volume = {95},
  pages = {883-9},
  number = {7},
  month = {Dec 23},
  note = {0092-8674 Comment Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9875843},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport Cell Division Golgi Apparatus/*metabolism/ultrastructure
	Intracellular Membranes/metabolism Models, Biological Organelles/*metabolism
	Proteins/*metabolism},
  shorttitle = {The curious status of the Golgi apparatus},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9875843}
}

@ARTICLE{Grabham2000,
  author = {Grabham, P. W. and Foley, M. and Umeojiako, A. and Goldberg, D. J.},
  title = {Nerve growth factor stimulates coupling of beta1 integrin to distinct
	transport mechanisms in the filopodia of growth cones},
  journal = {J Cell Sci},
  year = {2000},
  volume = {113 ( Pt 17)},
  pages = {3003-12},
  month = {Sep},
  note = {20394004 0021-9533 Journal Article},
  abstract = {The cycling of membrane receptors for substrate-bound proteins via
	their interaction with the actin cytoskeleton at the leading edge
	of growth cones and other motile cells is important for neurite outgrowth
	and cell migration. Receptor delivered to the leading edge binds
	to its ligand, which induces coupling of the receptor to a rearward
	flowing network of actin filaments. This coupling is thought to facilitate
	advance. We show here that a soluble growth factor stimulates this
	cycling. We have used single particle tracking to monitor the effects
	of nerve growth factor (NGF) on the movements of beta1 integrin in
	the plane of the plasma membrane of the filopodia of growth cones.
	Beta1 integrin was visualized by its binding of 0.2 microm beads
	coated with a monoclonal Ab directed against an extracellular epitope
	distant from the binding site for extracellular matrix ligands. The
	beads were observed by video microscopy. Beads coated with a low
	concentration of antibody, and therefore bound to unliganded receptor
	with little cross-linking, showed an increase in both diffusion and
	directed forward transport in response to NGF. Transport had a net
	velocity of 37 microm/minute and was characterized by brief periods
	of sustained forward excursions with a velocity of 75-150 microm/minute.
	There was a 2-fold increase in the number of beads accumulated at
	the tips of filopodia after 10 minutes, indicating that NGF enhanced
	the delivery of beta1 integrin to the periphery. Forward transport
	was dependent on an intact actin cytoskeleton and myosin ATPase,
	since treatment with cytochalasin D or the myosin ATPase inhibitor
	butanedione monoxime inhibited the transport but not the diffusion
	of receptors. NGF also greatly increased the steady rearward migration
	of beads coated with a high density of (&bgr;)1 integrin antibody,
	indicating that coupling of cross-linked receptor to the retrograde
	flow of actin is also enhanced. The rate of the retrograde flow of
	actin was unaffected by NGF. These studies show that a soluble factor
	can stimulate the coupling of a receptor for substrate-bound factor
	to two actomyosin-based transport mechanisms and thus facilitate
	the response of the growth cone to the substrate-bound factor by
	increasing cycling of the receptor at the periphery.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10934039},
  endnotereftype = {Journal Article},
  keywords = {Actins/antagonists & inhibitors/physiology Animal Antibodies, Monoclonal/metabolism
	Antigens, CD29/drug effects/*metabolism Biological Transport Cell
	Membrane/metabolism Cells, Cultured Chick Embryo Diffusion Ganglia,
	Sympathetic/cytology/drug effects/*metabolism Growth Cones/*metabolism
	Microscopy, Video Microspheres Movement/drug effects Myosins/antagonists
	& inhibitors/physiology Nerve Growth Factor/*pharmacology Pseudopodia/*metabolism
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Nerve growth factor stimulates coupling of beta1 integrin to distinct
	transport mechanisms in the filopodia of growth cones},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10934039}
}

@ARTICLE{Grabher2007,
  author = {Grabher, C. and Cliffe, A. and Miura, K. and Hayflick, J. and Pepperkok,
	R. and Rorth, P. and Wittbrodt, J.},
  title = {Birth and life of tissue macrophages and their migration in embryogenesis
	and inflammation in medaka},
  journal = {J Leukoc Biol},
  year = {2007},
  volume = {81},
  pages = {263-71},
  number = {1},
  month = {Jan},
  note = {0741-5400 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Macrophages detecting and migrating toward sites of injury and infection
	represent one of the first steps in an immune response. Here we directly
	image macrophage birth and migration in vivo in transgenic medaka
	fish. Macrophages are born as frequently dividing, immotile cells
	with spherical morphology that differentiate into flat, highly motile
	cells. They retain mitotic activity while spreading over the entire
	body. Cells follow restricted paths not only in directed migration,
	but also during patrolling. Along those paths the macrophages rapidly
	patrol the tissue and respond to wounding and bacterial infection
	from long distances. Upon injury they increase their speed and migratory
	persistence. Specifically targeting PI3-kinase isoforms efficiently
	blocks the wounding response and results in a distinct inhibition
	of cell motility and chemotaxis. Our study provides in situ insights
	into the properties of immature and migratory macrophages and presents
	a unique model to further test modulating compounds in vivo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17046968},
  endnotereftype = {Journal Article},
  keywords = {1-Phosphatidylinositol 3-Kinase/metabolism Animals Animals, Genetically
	Modified *Chemotaxis Embryonic Development/*physiology Inflammation/*metabolism
	Leukocytes/metabolism Macrophages/*physiology Oryzias/*immunology
	Signal Transduction},
  shorttitle = {Birth and life of tissue macrophages and their migration in embryogenesis
	and inflammation in medaka},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17046968}
}

@ARTICLE{Greber2006,
  author = {Greber, U. F. and Way, M.},
  title = {A superhighway to virus infection},
  journal = {Cell},
  year = {2006},
  volume = {124},
  pages = {741-54},
  number = {4},
  month = {Feb 24},
  note = {0092-8674 (Print) Journal Article Review},
  abstract = {Microtubule-mediated transport of macromolecules and organelles (also
	known as "cargo") is essential for cells to function. Deficiencies
	in cytoplasmic transport are frequently associated with severe diseases
	and syndromes. Cytoplasmic transport also provides viruses with the
	means to reach their site of replication and is the route for newly
	assembled progeny to leave the infected cell. This parasitic relationship
	of viruses with the host cytoskeleton provides an excellent basis
	for cell biologists to unlock the secrets of cytoplasmic transport
	and unravel mechanisms of disease. Recent advances in live cell imaging
	and computational tracking of fluorescently labeled viruses are now
	revealing how complex the movements of single viruses are in infected
	cells. This review focuses on microtubule-based motility of viruses
	and highlights the mechanisms regulating cytoplasmic transport.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16497585},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport, Active Cell Movement Dynein ATPase/physiology
	Humans Kinesin/physiology Microtubules/*physiology Models, Biological
	Models, Theoretical Molecular Motor Proteins Movement Signal Transduction
	*Viral Physiology Virus Activation Virus Diseases/*virology *Virus
	Replication},
  shorttitle = {A superhighway to virus infection},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16497585}
}

@ARTICLE{Grinnell2003,
  author = {Grinnell, F.},
  title = {Fibroblast biology in three-dimensional collagen matrices},
  journal = {Trends Cell Biol},
  year = {2003},
  volume = {13},
  pages = {264-9},
  number = {5},
  month = {May},
  note = {0962-8924 (Print) Journal Article Review},
  abstract = {Research on fibroblast biology in three-dimensional collagen matrices
	offers new opportunities to understand the reciprocal and adaptive
	interactions that occur between cells and surrounding matrix in a
	tissue-like environment. Such interactions are integral to the regulation
	of connective tissue morphogenesis and dynamics that characterizes
	tissue homeostasis and wound repair. During fibroblast-collagen matrix
	remodeling, mechanical signals from the remodeled matrix feed back
	to modulate cell behavior in an iterative process. As mechanical
	loading (tension) within the matrix increases, the mechanisms used
	by cells to remodel the matrix change. Fibroblasts in matrices that
	are under tension or relaxed respond differently to growth factor
	stimulation, and switching between mechanically loaded and unloaded
	conditions influences whether cells acquire proliferative/biosynthetic
	active or quiescent/resting phenotypes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12742170},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion Collagen/*chemistry Dendrites/metabolism Fibroblasts/*metabolism
	Humans Models, Biological Phenotype Research Support, U.S. Gov't,
	P.H.S. Wound Healing},
  shorttitle = {Fibroblast biology in three-dimensional collagen matrices},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12742170}
}

@ARTICLE{Grinnell1986,
  author = {Grinnell, F.},
  title = {Focal adhesion sites and the removal of substratum-bound fibronectin},
  journal = {J Cell Biol},
  year = {1986},
  volume = {103},
  pages = {2697-706},
  number = {6 Pt 2},
  month = {Dec},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Fibronectin was not removed from the substratum beneath focal adhesion
	sites when fibroblasts spread in serum-free medium on adsorbed fibronectin
	substrata, or when fibroblasts spread in serum-containing medium
	on covalently cross-linked fibronectin substrata. Under these conditions,
	there was colocalization between 140-kD fibronectin receptors and
	focal adhesion sites. It was concluded that removal of adsorbed fibronectin
	from beneath focal adhesion sites was a mechanical process that required
	serum. The effect of serum was nonspecific since serum could be replaced
	by equivalent concentrations of serum albumin, ovalbumin, or gamma
	globulins. Quantitative measurements indicated that the presence
	of proteins in the incubation medium weakens the interaction of fibronectin
	with the substratum, thereby allowing the adsorbed protein to be
	removed from the substratum at sites of high stress. After removing
	fibronectin from the substratum, cells reorganized this material
	into patches and fibrils beneath cells, and the reorganized fibronectin
	colocalized with fibronectin receptors. Some of the patches of fibronectin
	were phagocytosed. The fibronectin fibrils were observed to be in
	register with actin filament bundles and sometimes translocated to
	the upper cell surfaces. It is proposed that removal of fibronectin
	from beneath focal adhesion sites is an example of how cells can
	modify their extracellular matrices through contractile activity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2947902},
  endnotereftype = {Journal Article},
  keywords = {Actins/metabolism Blood Proteins/metabolism *Cell Adhesion Cells,
	Cultured Culture Media Extracellular Matrix/metabolism Fibroblasts/*physiology
	Fibronectins/*physiology Fluorescent Antibody Technique Humans Receptors,
	Fibronectin Receptors, Immunologic/*metabolism Research Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Focal adhesion sites and the removal of substratum-bound fibronectin},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2947902}
}

@ARTICLE{Grooth1985,
  author = {de Grooth, B. G. and Geerken, T. H. and Greve, J.},
  title = {The cytodisk: a cytometer based upon a new principle of cell alignment},
  journal = {Cytometry},
  year = {1985},
  volume = {6},
  pages = {226-33},
  number = {3},
  month = {May},
  note = {85203273 0196-4763 Journal Article},
  abstract = {A new method is described for one-dimensional alignment of small particles
	such as biological cells. A drop of the particle suspension is spread
	out on a flat disk or plate equipped with V-shaped grooves such as
	are present on a gramophone disk. After drying, the particles are
	located on the bottom of the grooves and are thus aligned in a one-dimensional
	array. The new alignment procedure is demonstrated with a suspension
	of fluorescent polystyrene microspheres (diameter 3.8 microns) and
	a suspension of the unicellular algae chlorella vulgaris (diameter
	about 3 microns). It appears that the alignment of cells and spheres
	is very good. When using microspheres, more than 95% of the particles
	in the grooves are located within +/- 2 microns of the centre line
	of the groove. Based upon this cell-alignment principle, a new cytometer,
	named the cytodisk, is proposed. The proposed system has a number
	of advantages over the flow cytometer, among which is the unique
	ability of relocating a previously measured cell for further measurement
	or visual examination. A prototype of a cytodisk, developed for initial
	test measurements, was built in our laboratory. The apparatus, constructed
	from a record player and ordinary long-playing records, uses a simple
	mechanical tracking system and a single optical fiber for fluorescence
	excitation and detection. With this apparatus it is demonstrated
	that a cytodisk can indeed perform quite well: A histogram of fluorescing
	microspheres could be measured with a coefficient of variation of
	4.1%. The performance of this prototype is limited by the quality
	of the mechanical tracking system and the optical system used.(ABSTRACT
	TRUNCATED AT 250 WORDS)},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3996137},
  endnotereftype = {Journal Article},
  keywords = {Chlorella/cytology Flow Cytometry/*instrumentation/methods Microspheres},
  shorttitle = {The cytodisk: a cytometer based upon a new principle of cell alignment},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3996137}
}

@ARTICLE{Gross2002,
  author = {Gross, S. P. and Welte, M. A. and Block, S. M. and Wieschaus, E.
	F.},
  title = {Coordination of opposite-polarity microtubule motors},
  journal = {J Cell Biol},
  year = {2002},
  volume = {156},
  pages = {715-24},
  number = {4},
  month = {Feb 18},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Many cargoes move bidirectionally, frequently reversing course between
	plus- and minus-end microtubule travel. For such cargoes, the extent
	and importance of interactions between the opposite-polarity motors
	is unknown. In this paper we test whether opposite-polarity motors
	on lipid droplets in Drosophila embryos are coordinated and avoid
	interfering with each other's activity, or whether they engage in
	a tug of war. To this end we impaired the minus-end transport machinery
	using dynein and dynactin mutations, and then investigated whether
	plus-end motion was improved or disrupted. We observe a surprisingly
	severe impairment of plus-end motion due to these alterations of
	minus-end motor activity. These observations are consistent with
	a coordination hypothesis, but cannot be easily explained with a
	tug of war model. Our measurements indicate that dynactin plays a
	crucial role in the coordination of plus- and minus-end-directed
	motors. Specifically, we propose that dynactin enables dynein to
	participate efficiently in bidirectional transport, increasing its
	ability to stay "on" during minus-end motion and keeping it "off"
	during plus-end motion.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11854311},
  endnotereftype = {Journal Article},
  keywords = {Animals Drosophila melanogaster/embryology Dynein ATPase/genetics/*metabolism
	Female Male Microtubule-Associated Proteins/genetics/*metabolism
	Microtubules/*metabolism Research Support, Non-U.S. Gov't Research
	Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Coordination of opposite-polarity microtubule motors},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11854311}
}

@ARTICLE{Gross2000,
  author = {Gross, S. P. and Welte, M. A. and Block, S. M. and Wieschaus, E.
	F.},
  title = {Dynein-mediated cargo transport in vivo. A switch controls travel
	distance},
  journal = {J Cell Biol},
  year = {2000},
  volume = {148},
  pages = {945-56},
  number = {5},
  month = {Mar 6},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Cytoplasmic dynein is a microtubule-based motor with diverse cellular
	roles. Here, we use mutations in the dynein heavy chain gene to impair
	the motor's function, and employ biophysical measurements to demonstrate
	that cytoplasmic dynein is responsible for the minus end motion of
	bidirectionally moving lipid droplets in early Drosophila embryos.
	This analysis yields an estimate for the force that a single cytoplasmic
	dynein exerts in vivo (1.1 pN). It also allows us to quantitate dynein-mediated
	cargo motion in vivo, providing a framework for investigating how
	dynein's activity is controlled. We identify three distinct travel
	states whose general features also characterize plus end motion.
	These states are preserved in different developmental stages. We
	had previously provided evidence that for each travel direction,
	single droplets are moved by multiple motors of the same type (Welte
	et al. 1998). Droplet travel distances (runs) are much shorter than
	expected for multiple motors based on in vitro estimates of cytoplasmic
	dynein processivity. Therefore, we propose the existence of a process
	that ends runs before the motors fall off the microtubules. We find
	that this process acts with a constant probability per unit distance,
	and is typically coupled to a switch in travel direction. A process
	with similar properties governs plus end motion, and its regulation
	controls the net direction of transport.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10704445},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport/genetics/physiology Cytoplasm/metabolism
	Drosophila Dynein ATPase/genetics/*physiology Embryo, Nonmammalian
	*Lipid Metabolism Microtubules/*physiology Models, Biological Molecular
	Motors/physiology Mutagenesis, Site-Directed Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S. Time Factors},
  shorttitle = {Dynein-mediated cargo transport in vivo. A switch controls travel
	distance},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10704445}
}

@ARTICLE{Gunzer2000,
  author = {Gunzer, M. and Friedl, P. and Niggemann, B. and Brocker, E. B. and
	Kampgen, E. and Zanker, K. S.},
  title = {Migration of dendritic cells within 3-D collagen lattices is dependent
	on tissue origin, state of maturation, and matrix structure and is
	maintained by proinflammatory cytokines},
  journal = {J Leukoc Biol},
  year = {2000},
  volume = {67},
  pages = {622-9},
  number = {5},
  month = {May},
  note = {0741-5400 (Print) Journal Article},
  abstract = {The function of dendritic cells (DC) depends on active migration through
	three-dimensional (3-D) extracellular matrices. We have analyzed
	the migration of murine DC from different tissue origins within 3-D
	collagen lattices through the use of time-lapse videomicroscopy and
	single-cell tracking. Directly after incorporation, 50-90% of DC
	from the spleen (spDC) and Langerhans cells freshly isolated from
	the epidermis (fLC) displayed active motility in these matrices.
	Whereas mature spDC showed multilateral pseudopod dynamics as well
	as fast and heterogeneous migration, immature fLC displayed a spherical
	shape with faint membrane processes and very homogenous, slow migration
	characteristics. In the absence of external stimuli, migration of
	both, spDC and fLC, vanished after >36 h due to cell death. Maintaining
	fLC viability by external granulocyte-macrophage colony-stimulating
	factor or tumor necrosis factor alpha prolonged migration up to 5
	days. During this period fLC transformed into mature cells with large
	dendrites, thereby developing a heterogeneous migration pattern more
	similar to spDC. In randomly polymerized collagen matrices cell paths
	were without preferential orientation. In contrast, in artificially
	aligned lattices directional paths in accordance with the forced
	fiber orientation were observed. Thus, migration is an inherent property
	of DC, largely influenced by tissue origin, degree of maturity, and
	the 3-D structure of the environment.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10811001},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cell Movement/drug effects/physiology Cell Survival
	Collagen/drug effects/*physiology/ultrastructure Cytokines/*pharmacology
	Dendritic Cells/cytology/drug effects/*immunology Epidermis/cytology/immunology
	Extracellular Matrix/drug effects/*physiology/ultrastructure Female
	Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology Langerhans
	Cells/cytology/drug effects/*immunology Macrophages, Peritoneal/cytology/drug
	effects/*immunology Male Mice Mice, Inbred BALB C Microscopy, Confocal
	Microscopy, Video Research Support, Non-U.S. Gov't Spleen/immunology
	Tumor Necrosis Factor-alpha/pharmacology},
  shorttitle = {Migration of dendritic cells within 3-D collagen lattices is dependent
	on tissue origin, state of maturation, and matrix structure and is
	maintained by proinflammatory cytokines},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10811001}
}

@ARTICLE{Gunzer1997,
  author = {Gunzer, M. and Kampgen, E. and Brocker, E. B. and Zanker, K. S. and
	Friedl, P.},
  title = {Migration of dendritic cells in 3D-collagen lattices. Visualisation
	of dynamic interactions with the substratum and the distribution
	of surface structures via a novel confocal reflection imaging technique},
  journal = {Adv Exp Med Biol},
  year = {1997},
  volume = {417},
  pages = {97-103},
  note = {0065-2598 (Print) Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9286344},
  endnotereftype = {Journal Article},
  keywords = {Animals Antigens, Surface/metabolism *Cell Movement Collagen Dendritic
	Cells/immunology/*physiology Histocompatibility Antigens Class II/metabolism
	In Vitro Langerhans Cells/immunology/physiology Mice Mice, Inbred
	BALB C Microscopy, Confocal/methods Surface Properties},
  shorttitle = {Migration of dendritic cells in 3D-collagen lattices. Visualisation
	of dynamic interactions with the substratum and the distribution
	of surface structures via a novel confocal reflection imaging technique},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9286344}
}

@ARTICLE{Gunzer2000a,
  author = {Gunzer, M. and Schafer, A. and Borgmann, S. and Grabbe, S. and Zanker,
	K. S. and Brocker, E. B. and Kampgen, E. and Friedl, P.},
  title = {Antigen presentation in extracellular matrix: interactions of T cells
	with dendritic cells are dynamic, short lived, and sequential},
  journal = {Immunity},
  year = {2000},
  volume = {13},
  pages = {323-32},
  number = {3},
  month = {Sep},
  note = {1074-7613 (Print) Journal Article},
  abstract = {Cognate interactions of naive T cells with antigen-presenting dendritic
	cells require physical cell-cell contacts leading to signal induction
	and T cell activation. Using a three-dimensional collagen matrix
	videomicroscopy model for ovalbumin peptide-specific activation of
	murine and oxidative mitogenesis of human T cells, we show that T
	cells maintain vigorous migration upon cognate interactions to DC
	(dendritic cell), continuously crawl across the DC surface, and rapidly
	detach (median within 6-12 min). These dynamic and short-lived encounters
	favor sequential contacts with the same or other DC and trigger calcium
	influx, upregulation of activation markers, T blast formation, and
	proliferation. We conclude that a tissue environment supports the
	accumulation of sequential signals, implicating a numeric or "digital"
	control mechanism for an ongoing primary immune response.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11021530},
  endnotereftype = {Journal Article},
  keywords = {Animals Antigen Presentation/*immunology Antigen-Presenting Cells/cytology/immunology/metabolism
	Bone Marrow Cells/cytology/immunology/metabolism Calcium Signaling/immunology
	Cell Adhesion/immunology Cell Aggregation/immunology Cell Communication/*immunology
	Cell Movement/immunology Cells, Cultured Collagen/immunology Dendritic
	Cells/cytology/*immunology/metabolism Extracellular Matrix/*immunology/*metabolism
	Humans Lymphocyte Activation/immunology Mice Mice, Inbred BALB C
	Mice, Transgenic Microscopy, Video Oxidation-Reduction Research Support,
	Non-U.S. Gov't T-Lymphocytes/cytology/*immunology/metabolism Time
	Factors},
  shorttitle = {Antigen presentation in extracellular matrix: interactions of T cells
	with dendritic cells are dynamic, short lived, and sequential},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11021530}
}

@ARTICLE{Hamilton2009,
  author = {Hamilton, N.},
  title = {Quantification and its applications in fluorescent microscopy imaging},
  journal = {Traffic},
  year = {2009},
  volume = {10},
  pages = {951-61},
  number = {8},
  month = {Aug},
  note = {1600-0854 (Electronic) Journal Article Review},
  abstract = {Fluorescent microscope imaging technologies have developed at a rapid
	pace in recent years. High-throughput 2D fluorescent imaging platforms
	are now in wide use and are being applied on a proteome wide scale.
	Multiple fluorophore 3D imaging of live cells is being used to give
	detailed localization and subcellular structure information. Further,
	2D and 3D video microscopy are giving important insights into the
	dynamics of protein localization and transport. In parallel with
	these developments, significant research has gone into developing
	new methodologies for quantifying and extracting meaning from the
	imaging data. Here we outline and give entry points to the literature
	on approaches to quantification such as segmentation, tracking, automated
	classification and data visualization. Particular attention is paid
	to the distinction between and application of concrete quantification
	measures such as number of objects in a cell, and abstract measures
	such as texture.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19500318},
  endnotereftype = {Journal Article},
  keywords = {Cells/cytology/metabolism Image Processing, Computer-Assisted/*methods
	Imaging, Three-Dimensional/instrumentation/*methods Microscopy, Fluorescence/instrumentation/*methods
	Models, Biological Proteins/chemistry/metabolism Software Time Factors},
  shorttitle = {Quantification and its applications in fluorescent microscopy imaging},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19500318}
}

@ARTICLE{Hashimoto1988,
  author = {Hashimoto, Y. and Shinozaki, N.},
  title = {Measurement of cytoplasmic viscosity by fluorescence polarization
	in phytohemagglutinin-stimulated and unstimulated human peripheral
	lymphocytes},
  journal = {J Histochem Cytochem},
  year = {1988},
  volume = {36},
  pages = {609-13},
  number = {6},
  month = {Jun},
  note = {0022-1554 Journal Article},
  abstract = {We have developed an improved technique of fluorescence polarization
	for measurement of the cytoplasmic viscosity of human peripheral
	lymphocytes. When measured using this improved method, the mean value
	of fluorescence polarization in lymphocytes from 20 healthy donors
	was 0.190 +/- 0.005. The mean value of fluorescence polarization
	as percent of control after stimulation of lymphocytes with phytohemagglutinin
	(PHA) was 83.6 +/- 3.8%. We discuss here optimal conditions for PHA
	stimulation of lymphocytes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3367046},
  endnotereftype = {Journal Article},
  keywords = {Cytoplasm/*physiology Fluorescence Polarization Humans In Vitro *Lymphocyte
	Activation Phytohemagglutinins/pharmacology Viscosity},
  shorttitle = {Measurement of cytoplasmic viscosity by fluorescence polarization
	in phytohemagglutinin-stimulated and unstimulated human peripheral
	lymphocytes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3367046}
}

@INCOLLECTION{Haussecker1999,
  author = {Haussecker, H. and Spies, H.},
  title = {Motion},
  booktitle = {Handbook of Computer Vision adn Applications},
  publisher = {Academic Press},
  year = {1999},
  editor = {Jﾃ､hne, B. and Haussecker, H. and Geissler, P.},
  volume = {2},
  pages = {310-396},
  address = {San Diego},
  endnotereftype = {Book Section},
  shorttitle = {Motion}
}

@ARTICLE{Hayden1988,
  author = {Hayden, J. H.},
  title = {Microtubule-associated organelle and vesicle transport in fibroblasts},
  journal = {Cell Motil Cytoskeleton},
  year = {1988},
  volume = {10},
  pages = {255-62},
  number = {1-2},
  note = {0886-1544 (Print) Journal Article},
  abstract = {Allen Video-enhanced contrast/differential interference contrast (AVEC-DIC)
	microscopy was used in conjunction with video intensification immunofluorescence
	microscopy to demonstrate that organelles and vesicle (particles)
	can move in either direction along microtubular linear elements in
	fibroblasts [Hayden et al., 1983]. Since it is not possible to determine
	the number of microtubules making up a linear element with light
	microscopy alone, AVEC-DIC microscopy was used in conjunction with
	whole-mount electron microscopy to show bidirectional transport along
	a single microtubule [Hayden and Allen, 1984]. These studies demonstrate
	that the structural polarity of the microtubule does not determine
	the direction of particle motion, and since dynein is an asymetric
	molecule, a simple microtubule-dynein-particle hypothesis cannot
	explain bidirectional transport along a single microtubule. Very
	little is known about regulation of particle transport in most cell
	types. Human embryonic lung fibroblasts grown on glass coverslips
	were serum-deprived for 24 hours and re-fed with serumless medium;
	the particle translocations/5 minutes were then determined. The cells
	were then re-fed with either serumless medium, serum-containing medium,
	or serumless medium containing some bioactive factor, and the particle
	translocations/5 minutes were again determined for the same cells.
	Medium containing 10% fetal bovine serum inhibited particle translocation
	by 51.8%. Of the bioactive factors tested, only vasopressin produced
	a significant reduction in particle translocations (38%). This suggests
	that protein kinase C or calcium/calmodulin kinase could be involved
	in regulating particle transport.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3180246},
  endnotereftype = {Journal Article},
  keywords = {Cells, Cultured Fibroblasts/*cytology/ultrastructure Humans Microscopy,
	Electron Microscopy, Fluorescence Microscopy, Interference Microtubules/*ultrastructure
	*Organelles Research Support, Non-U.S. Gov't Research Support, U.S.
	Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Video Recording},
  shorttitle = {Microtubule-associated organelle and vesicle transport in fibroblasts},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3180246}
}

@ARTICLE{Hayden1984,
  author = {Hayden, J. H. and Allen, R. D.},
  title = {Detection of single microtubules in living cells: particle transport
	can occur in both directions along the same microtubule},
  journal = {J Cell Biol},
  year = {1984},
  volume = {99},
  pages = {1785-93},
  number = {5},
  month = {Nov},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Video-enhanced contrast/differential interference-contrast microscopy
	was used in conjunction with whole mount electron microscopy to study
	particle transport along linear elements in fibroblasts. Keratocytes
	from the corneal stroma of Rana pipiens were grown on gold indicator
	grids and examined with video microscopy. Video records were taken
	of the linear elements and associated particle transport until lysis
	and/or fixation of the cells was completed. The preparations were
	then processed for whole mount electron microscopy. By combining
	these two methods, we demonstrated that linear elements detected
	in the living cell could be identified as single microtubules, and
	that filaments as small as 10 nm could be detected in lysed and fixed
	cells. The visibility of different cytoplasmic structures changed
	after lysis with many more cellular components becoming visible.
	Microtubules became more difficult to detect after lysis while bundles
	of microfilaments became more prominent. All particle translocations
	were observed to take place along linear elements composed of one
	or more microtubules. Furthermore, particles were observed to translocate
	in one or both directions on the same microtubule.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6333427},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport Cornea/*ultrastructure Cytoskeleton/ultrastructure
	Microscopy/methods Microscopy, Electron Microtubules/*metabolism/ultrastructure
	Rana pipiens Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Detection of single microtubules in living cells: particle transport
	can occur in both directions along the same microtubule},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6333427}
}

@ARTICLE{Heeger1988,
  author = {Heeger, DJ},
  title = {Optical flow using spatiotemporal filters},
  journal = {Intern J Comput Vis},
  year = {1988},
  volume = {1},
  pages = {279-302},
  endnotereftype = {Journal Article},
  shorttitle = {Optical flow using spatiotemporal filters}
}

@ARTICLE{Hegerfeldt2002,
  author = {Hegerfeldt, Y. and Tusch, M. and Brocker, E. B. and Friedl, P.},
  title = {Collective cell movement in primary melanoma explants: plasticity
	of cell-cell interaction, beta1-integrin function, and migration
	strategies},
  journal = {Cancer Res},
  year = {2002},
  volume = {62},
  pages = {2125-30},
  number = {7},
  month = {Apr 1},
  note = {0008-5472 (Print) Journal Article},
  abstract = {Collective cell movement represents an efficient dissemination strategy
	in neoplastic epithelial and mesenchymal cancer. In primary melanoma
	explants cultured in three-dimensional collagen lattices, invasive
	migration of multicellular clusters was dependent on the function
	of beta1 integrins, as shown by preferential beta1-integrin expression
	and clustering in a subset of promigratory cells at the leading edge
	("guiding cells") and the abrogation of multicellular migration by
	adhesion-perturbing anti-beta1-integrin antibody. Interference with
	beta1-integrin function induced complex changes in cluster polarity
	and cohesion, including development of two or several opposing leading
	edges, cluster disruption, and the detachment of individual cells
	followed by beta1-integrin-independent "amoeboid" crawling and dissemination.
	The conversion from beta1-integrin-dependent collective movement
	to beta1-integrin-independent single-cell motility suggests efficient
	cellular and molecular plasticity in tumor cell migration strategies.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11929834},
  endnotereftype = {Journal Article},
  keywords = {Antigens, CD29/*physiology Cell Adhesion/physiology Cell Communication/*physiology
	Cell Movement/*physiology Humans Melanoma/*pathology Research Support,
	Non-U.S. Gov't},
  shorttitle = {Collective cell movement in primary melanoma explants: plasticity
	of cell-cell interaction, beta1-integrin function, and migration
	strategies},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11929834}
}

@ARTICLE{Helfer2001,
  author = {Helfer, E. and Harlepp, S. and Bourdieu, L. and Robert, J. and MacKintosh,
	F. C. and Chatenay, D.},
  title = {Viscoelastic properties of actin-coated membranes},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  year = {2001},
  volume = {63},
  pages = {021904},
  number = {2 Pt 1},
  month = {Feb},
  note = {21206580 1539-3755 Journal Article},
  abstract = {In living cells, cytoskeletal filaments interact with the plasma membrane
	to form structures that play a key role in cell shape and mechanical
	properties. To study the interaction between these basic components,
	we designed an in vitro self-assembled network of actin filaments
	attached to the outer surface of giant unilamellar vesicles. Optical
	tweezers and single-particle tracking experiments are used to study
	the rich dynamics of these actin-coated membranes (ACM). We show
	that microrheology studies can be carried out on such an individual
	microscopic object. The principle of the experiment consists in measuring
	the thermally excited position fluctuations of a probe bead attached
	biochemically to the membrane. We propose a model that relates the
	power spectrum of these thermal fluctuations to the viscoelastic
	properties of the membrane. The presence of the actin network modifies
	strongly the membrane dynamics with respect to a fluid, lipid bilayer
	one. It induces first a finite (omega=0) two-dimensional (2D) shear
	modulus G(0)(2D) approximately 0.5 to 5 microN/m in the membrane
	plane. Moreover, the frequency dependence at high frequency of the
	shear modulus [G(')(2D)(f ) approximately f(0.85+/-0.07)] and of
	the bending modulus (kappa(ACM)(f) approximately f(0.55+/-0.21))
	demonstrate the viscoelastic behavior of the composite membrane.
	These results are consistent with a common exponent of 0.75 for both
	moduli as expected from our model and from prior measurements on
	actin solutions.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11308515},
  endnotereftype = {Journal Article},
  shorttitle = {Viscoelastic properties of actin-coated membranes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11308515}
}

@ARTICLE{Helfer2000,
  author = {Helfer, E. and Harlepp, S. and Bourdieu, L. and Robert, J. and MacKintosh,
	F. C. and Chatenay, D.},
  title = {Microrheology of biopolymer-membrane complexes},
  journal = {Phys Rev Lett},
  year = {2000},
  volume = {85},
  pages = {457-60},
  number = {2},
  month = {Jul 10},
  note = {20447140 0031-9007 Journal Article},
  abstract = {We create tailored microstructures, consisting of complexes of lipid
	membranes with self-assembled biopolymer shells, to study the fundamental
	properties and interactions of these basic components of living cells.
	We measure the mechanical response of these artificial structures
	at the micrometer scale, using optical tweezers and single-particle
	tracking. These systems exhibit rich dynamics that illustrate the
	viscoelastic character of the quasi-two-dimensional biopolymer network.
	We present a theoretical model relating the rheological properties
	of these membranes to the observed dynamics.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10991307},
  endnotereftype = {Journal Article},
  keywords = {Actins/*chemistry Biopolymers/*chemistry Cell Membrane/*chemistry
	Elasticity Lasers Lipid Bilayers *Models, Chemical Rheology Support,
	Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S.},
  shorttitle = {Microrheology of biopolymer-membrane complexes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10991307}
}

@ARTICLE{Hibino2003,
  author = {Hibino, K. and Watanabe, T. M. and Kozuka, J. and Iwane, A. H. and
	Okada, T. and Kataoka, T. and Yanagida, T. and Sako, Y.},
  title = {Single- and multiple-molecule dynamics of the signaling from H-Ras
	to cRaf-1 visualized on the plasma membrane of living cells},
  journal = {Chemphyschem},
  year = {2003},
  volume = {4},
  pages = {748-53},
  number = {7},
  month = {Jul 14},
  note = {1439-4235 Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12901307},
  endnotereftype = {Journal Article},
  keywords = {Cell Membrane/*enzymology/metabolism Epidermal Growth Factor/pharmacology
	Female Hela Cells Human *MAP Kinase Signaling System Microfilaments/drug
	effects Microscopy, Fluorescence Protein Transport Proto-Oncogene
	Protein p21(ras)/*metabolism Proto-Oncogene Proteins c-raf/*metabolism},
  shorttitle = {Single- and multiple-molecule dynamics of the signaling from H-Ras
	to cRaf-1 visualized on the plasma membrane of living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12901307}
}

@ARTICLE{Hicks1995,
  author = {Hicks, B. W. and Angelides, K. J.},
  title = {Tracking movements of lipids and Thy1 molecules in the plasmalemma
	of living fibroblasts by fluorescence video microscopy with nanometer
	scale precision},
  journal = {J Membr Biol},
  year = {1995},
  volume = {144},
  pages = {231-44},
  number = {3},
  month = {Apr},
  note = {95387382 0022-2631 Journal Article},
  abstract = {The lateral diffusion of 100 nm fluorescent latex microspheres (FS)
	bound to either N-biotinyl-phosphatidyl-ethanolamine or the glycosylphosphatidylinositol-linked
	protein Thy1 were monitored in the plasmalemma of primary rat fibroblasts
	by single particle tracking of FS centroids from digital fluorescence
	micrographs. A silicon intensified target camera was found to be
	superior to slow scan cooled CCD and intensified interline transfer
	CCD cameras for monitoring lateral diffusion of rapidly moving FS
	with nanometer level precision. To estimate the maximum tracking
	precision, a 4 sec-sequence comprising 120 images of FS fixed to
	a cover glass was obtained. The mean distance of the centroids from
	the origin was 7.5 +/- 0.4 nm, and no centroids were beyond 16 nm
	from the origin. The SIT camera was then used to track FS attached
	to lipids and Thy1 molecules on the surface of fibroblasts. The lateral
	diffusion of lipid-bound FS was unconstrained, and the ensemble averaged
	diffusion coefficient was 0.80 x 10(-9) cm2/sec. Thy1-bound FS existed
	in two mobility populations, both of which demonstrated constrained
	mobility. The rapidly moving population, comprising 61% of the total,
	had an ensemble diffusion coefficient of 6.1 x 10(-10) cm2/sec, and
	appeared to be restricted to domains with a mean length of about
	700 nm. The slowly moving population, comprising about 39% of the
	total, had a diffusion coefficient of 5.7 x 10(-12) cm2/sec. These
	results demonstrate that nanovid can be extended to the realm of
	fluorescence microscopy and support previous studies indicating that
	while the lateral mobilities of at least some lipids are not constrained
	to small domains by barriers to lateral diffusion in the fibroblast
	plasmalemma, a peripheral membrane protein which is bound only by
	a lipid anchor can be prevented from diffusing freely.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7658460},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, Thy-1/immunology/*metabolism Biotin/metabolism Cell
	Membrane/*metabolism Cells, Cultured Diffusion Fibroblasts/metabolism/ultrastructure
	Fluorescent Dyes/metabolism Image Processing, Computer-Assisted Membrane
	Fluidity *Microscopy, Fluorescence *Microscopy, Video Phosphatidylethanolamines/*metabolism
	Rats Support, U.S. Gov't, P.H.S. Time Factors},
  shorttitle = {Tracking movements of lipids and Thy1 molecules in the plasmalemma
	of living fibroblasts by fluorescence video microscopy with nanometer
	scale precision},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7658460}
}

@ARTICLE{hirschbergJCB1998,
  author = {Hirschberg, K. and Miller, C. M. and Ellenberg, J. and Presley, J.
	F. and Siggia, E. D. and Phair, R. D. and Lippincott-Schwartz, J.},
  title = {Kinetic analysis of secretory protein traffic and characterization
	of golgi to plasma membrane transport intermediates in living cells},
  journal = {J Cell Biol},
  year = {1998},
  volume = {143},
  pages = {1485-503},
  number = {6},
  month = {Dec 14},
  note = {99069477 0021-9525 Journal Article},
  abstract = {Quantitative time-lapse imaging data of single cells expressing the
	transmembrane protein, vesicular stomatitis virus ts045 G protein
	fused to green fluorescent protein (VSVG-GFP), were used for kinetic
	modeling of protein traffic through the various compartments of the
	secretory pathway. A series of first order rate laws was sufficient
	to accurately describe VSVG-GFP transport, and provided compartment
	residence times and rate constants for transport into and out of
	the Golgi complex and delivery to the plasma membrane. For ER to
	Golgi transport the mean rate constant (i.e., the fraction of VSVG-GFP
	moved per unit of time) was 2.8% per min, for Golgi to plasma membrane
	transport it was 3.0% per min, and for transport from the plasma
	membrane to a degradative site it was 0.25% per min. Because these
	rate constants did not change as the concentration of VSVG-GFP in
	different compartments went from high (early in the experiment) to
	low (late in the experiment), secretory transport machinery was never
	saturated during the experiments. The processes of budding, translocation,
	and fusion of post-Golgi transport intermediates carrying VSVG- GFP
	to the plasma membrane were also analyzed using quantitative imaging
	techniques. Large pleiomorphic tubular structures, rather than small
	vesicles, were found to be the primary vehicles for Golgi to plasma
	membrane transport of VSVG-GFP. These structures budded as entire
	domains from the Golgi complex and underwent dynamic shape changes
	as they moved along microtubule tracks to the cell periphery. They
	carried up to 10,000 VSVG-GFP molecules and had a mean life time
	in COS cells of 3.8 min. In addition, they fused with the plasma
	membrane without intersecting other membrane transport pathways in
	the cell. These properties suggest that the post-Golgi intermediates
	represent a unique transport organelle for conveying large quantities
	of protein cargo from the Golgi complex directly to the plasma membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9852146},
  endnotereftype = {Journal Article},
  keywords = {Aluminum Compounds/pharmacology Animal Biological Transport COS Cells
	Cell Membrane/drug effects/*metabolism/ultrastructure Cytochalasin
	B/pharmacology Fluorides/pharmacology Golgi Apparatus/drug effects/*metabolism/ultrastructure
	Kinetics Luminescent Proteins/metabolism Models, Biological Nocodazole/pharmacology
	Recombinant Fusion Proteins/metabolism Support, Non-U.S. Gov't Time
	Factors Transfection Vesicular stomatitis-Indiana virus/genetics
	Viral Envelope Proteins/genetics/*metabolism},
  shorttitle = {Kinetic analysis of secretory protein traffic and characterization
	of golgi to plasma membrane transport intermediates in living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9852146}
}

@ARTICLE{Hirschberg1999,
  author = {Hirschberg, K. and Presley, J. and Phair, R. and Lippincott-Schwartz,
	J.},
  title = {5 analysis of secretory protein trafficking within living cells},
  journal = {J Histochem Cytochem},
  year = {1999},
  volume = {47},
  pages = {1644},
  number = {12},
  month = {Dec},
  note = {0022-1554 (Print) Journal article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10567452},
  endnotereftype = {Journal Article},
  shorttitle = {5 analysis of secretory protein trafficking within living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10567452}
}

@ARTICLE{Hollenbeck1996,
  author = {Hollenbeck, P. J.},
  title = {The pattern and mechanism of mitochondrial transport in axons},
  journal = {Front Biosci},
  year = {1996},
  volume = {1},
  pages = {d91-102},
  month = {Jul 1},
  note = {1093-4715 (Electronic) Journal Article Review},
  abstract = {Mitochondria in nerve axons display motility behavior that is as distinctive
	as their metabolic function. Unlike many other classes of organelles,
	mitochondria undergo net movement that is the sum of movements in
	both the anterograde and retrograde directions, and their net velocity
	is strongly influenced by their recruitment between stationary and
	motile states. They recently became the first specific class of organelle
	shown to be capable of moving along either microtubule or F-actin
	tracks in the axon, indicating that they probably use a diversity
	of molecular motors. Although we still know relatively little about
	how the movement of specific classes of axonal organelles is coordinated
	with their function in the neuron, in the case of mitochondria it
	is at least clear that their transport delivers them to regions of
	the neuron where ATP consumption is likely to be high, and disperses
	them when local energy needs change. In addition, although mitochondria
	contain both anterograde and retrograde motor activities, the modulation
	of their motility necessary to achieve these redistributions seems
	to rely largely upon regulation of the anterograde motor activity
	alone. A further element in the regulation of their motility and
	distribution is the apparent "docking" of mitochondria to microtubules
	or neurofilaments, a phenomenon which may serve to stabilize their
	distribution once regulated motility has moved them to appropriate
	sites. This review considers the current state of knowledge in these
	areas with an emphasis on the pattern of regulation of motility and
	how it underlies the role of mitochondria as the aerobic ATP source
	of the neuron.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9159217},
  endnotereftype = {Journal Article},
  keywords = {Adenosine Triphosphate/metabolism Animals Axonal Transport Axons/*metabolism
	Cytoskeleton/metabolism Humans Microfilaments/metabolism Microtubules/metabolism
	Mitochondria/*metabolism Neurofilament Proteins/metabolism Research
	Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {The pattern and mechanism of mitochondrial transport in axons},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9159217}
}

@ARTICLE{Hollenbeck1993,
  author = {Hollenbeck, P. J.},
  title = {Products of endocytosis and autophagy are retrieved from axons by
	regulated retrograde organelle transport},
  journal = {J Cell Biol},
  year = {1993},
  volume = {121},
  pages = {305-15},
  number = {2},
  month = {Apr},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Cellular homeostasis in neurons requires that the synthesis and anterograde
	axonal transport of protein and membrane be balanced by their degradation
	and retrograde transport. To address the nature and regulation of
	retrograde transport in cultured sympathetic neurons, I analyzed
	the behavior, composition, and ultrastructure of a class of large,
	phase-dense organelles whose movement has been shown to be influenced
	by axonal growth (Hollenbeck, P. J., and D. Bray. 1987. J. Cell Biol.
	105:2827-2835). In actively elongating axons these organelles underwent
	both anterograde and retrograde movements, giving rise to inefficient
	net retrograde transport. This could be shifted to more efficient,
	higher volume retrograde transport by halting axonal outgrowth, or
	conversely shifted to less efficient retrograde transport with a
	larger anterograde component by increasing the intracellular cyclic
	AMP concentration. When neurons were loaded with Texas red-dextran
	by trituration, autophagy cleared the label from an even distribution
	throughout the neuronal cytosol to a punctate, presumably lysosomal,
	distribution in the cell body within 72 h. During this process, 100%
	of the phase-dense organelles were fluorescent, showing that they
	contained material sequestered from the cytosol and indicating that
	they conveyed this material to the cell body. When 29 examples of
	this class of organelle were identified by light microscopy and then
	relocated using correlative electron microscopy, they had a relatively
	constant ultrastructure consisting of a bilamellar or multilamellar
	boundary membrane and cytoplasmic contents, characteristic of autophagic
	vacuoles. When neurons took up Lucifer yellow, FITC-dextran, or Texas
	red-ovalbumin from the medium via endocytosis at the growth cone,
	100% of the phase-dense organelles became fluorescent, demonstrating
	that they also contain products of endocytosis. Furthermore, pulse-chase
	experiments with fluorescent endocytic tracers confirmed that these
	organelles are formed in the most distal region of the axon and undergo
	net retrograde transport. Quantitative ratiometric imaging with endocytosed
	8-hydroxypyrene-1,3,6-trisulfonic acid showed that the mean pH of
	their lumena was 7.05. These results indicate that the endocytic
	and autophagic pathways merge in the distal axon, resulting in a
	class of predegradative organelles that undergo regulated transport
	back to the cell body.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7682217},
  endnotereftype = {Journal Article},
  keywords = {Animals Autophagy *Axonal Transport/drug effects Cells, Cultured/metabolism/ultrastructure
	Chick Embryo Endocytosis Forskolin/pharmacology Ganglia, Sympathetic/embryology/*metabolism/ultrastructure
	Neurons/*metabolism/ultrastructure Organelles/metabolism/ultrastructure
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Products of endocytosis and autophagy are retrieved from axons by
	regulated retrograde organelle transport},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7682217}
}

@ARTICLE{Hooper1999,
  author = {Hooper, N. M.},
  title = {Detergent-insoluble glycosphingolipid/cholesterol-rich membrane domains,
	lipid rafts and caveolae (review)},
  journal = {Mol Membr Biol},
  year = {1999},
  volume = {16},
  pages = {145-56},
  number = {2},
  month = {Apr-Jun},
  note = {99346533 0968-7688 Journal Article Review Review, Academic},
  abstract = {Within the cell membrane glycosphingolipids and cholesterol cluster
	together in distinct domains or lipid rafts, along with glycosyl-phosphatidylinositol
	(GPI)-anchored proteins in the outer leaflet and acylated proteins
	in the inner leaflet of the bilayer. These lipid rafts are characterized
	by insolubility in detergents such as Triton X-100 at 4 degrees C.
	Studies on model membrane systems have shown that the clustering
	of glycosphingolipids and GPI-anchored proteins in lipid rafts is
	an intrinsic property of the acyl chains of these membrane components,
	and that detergent extraction does not artefactually induce clustering.
	Cholesterol is not required for clustering in model membranes but
	does enhance this process. Single particle tracking, chemical cross-linking,
	fluorescence resonance energy transfer and immunofluorescence microscopy
	have been used to directly visualize lipid rafts in membranes. The
	sizes of the rafts observed in these studies range from 70-370 nm,
	and depletion of cellular cholesterol levels disrupts the rafts.
	Caveolae, flask-shaped invaginations of the plasma membrane, that
	contain the coat protein caveolin, are also enriched in cholesterol
	and glycosphingolipids. Although caveolae are also insoluble in Triton
	X-100, more selective isolation procedures indicate that caveolae
	do not equate with detergent-insoluble lipid rafts. Numerous proteins
	involved in cell signalling have been identified in caveolae, suggesting
	that these structures may function as signal transduction centres.
	Depletion of membrane cholesterol with cholesterol binding drugs
	or by blocking cellular cholesterol biosynthesis disrupts the formation
	and function of both lipid rafts and caveolae, indicating that these
	membrane domains are involved in a range of biological processes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10417979},
  endnotereftype = {Journal Article},
  keywords = {Animal Cell Membrane/metabolism/physiology Cholesterol/*metabolism/physiology
	Detergents Glycosphingolipids/*metabolism Human *Lipid Bilayers Models,
	Biological Octoxynol Solubility Support, Non-U.S. Gov't},
  shorttitle = {Detergent-insoluble glycosphingolipid/cholesterol-rich membrane domains,
	lipid rafts and caveolae (review)},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10417979}
}

@ARTICLE{Horn1981,
  author = {Horn, B.K.P. and Schunck, B.G.},
  title = {Determining Optical Flow},
  journal = {Artificial Intelligence},
  year = {1981},
  volume = {17},
  pages = {185-203},
  note = {HornSchunck1981.pdf},
  endnotereftype = {Journal Article},
  shorttitle = {Determining Optical Flow}
}

@ARTICLE{Huang2001,
  author = {Huang, N. P. and Michel, R. and Voros, J. and Textor, M. and Hofer,
	R. and Rossi, A. and Elbert, E. L. and Hubbell, J. A. and Spencer,
	N. D.},
  title = {Poly(L-lysine)-g-poly(ehtylene glycol) Layers on Metal Oxide Surfaces:
	Surface-Analytical Characterization and Resistance to Serum and Fibrinogen
	Adsorption},
  journal = {Langmuir},
  year = {2001},
  volume = {17},
  pages = {489-498},
  endnotereftype = {Journal Article},
  keywords = {PLL PEG},
  shorttitle = {Poly(L-lysine)-g-poly(ehtylene glycol) Layers on Metal Oxide Surfaces:
	Surface-Analytical Characterization and Resistance to Serum and Fibrinogen
	Adsorption}
}

@ARTICLE{Hui2007,
  author = {Hui, E. E. and Bhatia, S. N.},
  title = {Micromechanical control of cell-cell interactions},
  journal = {Proc Natl Acad Sci U S A},
  year = {2007},
  volume = {104},
  pages = {5722-6},
  number = {14},
  month = {Apr 3},
  note = {0027-8424 (Print) Journal Article Research Support, N.I.H., Extramural
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.},
  abstract = {The development and function of living tissues depends largely on
	interactions between cells that can vary in both time and space;
	however, temporal control of cell-cell interaction is experimentally
	challenging. By using a micromachined silicon substrate with moving
	parts, we demonstrate the dynamic regulation of cell-cell interactions
	via direct manipulation of adherent cells with micrometer-scale precision.
	We thereby achieve mechanical control of both tissue composition
	and spatial organization. As a case study, we demonstrate the utility
	of this tool in deconstructing the dynamics of intercellular communication
	between hepatocytes and supportive stromal cells in coculture. Our
	findings indicate that the maintenance of the hepatocellular phenotype
	by stroma requires direct contact for a limited time ( approximately
	hours) followed by a sustained soluble signal that has an effective
	range of <400 microm. This platform enables investigation of dynamic
	cell-cell interaction in a multitude of applications, spanning embryogenesis,
	homeostasis, and pathogenic processes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17389399},
  endnotereftype = {Journal Article},
  shorttitle = {Micromechanical control of cell-cell interactions},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17389399}
}

@ARTICLE{Huisken2004,
  author = {Huisken, J. and Swoger, J. and Del Bene, F. and Wittbrodt, J. and
	Stelzer, E. H.},
  title = {Optical sectioning deep inside live embryos by selective plane illumination
	microscopy},
  journal = {Science},
  year = {2004},
  volume = {305},
  pages = {1007-9},
  number = {5686},
  month = {Aug 13},
  note = {1095-9203 Journal Article},
  abstract = {Large, living biological specimens present challenges to existing
	optical imaging techniques because of their absorptive and scattering
	properties. We developed selective plane illumination microscopy
	(SPIM) to generate multidimensional images of samples up to a few
	millimeters in size. The system combines two-dimensional illumination
	with orthogonal camera-based detection to achieve high-resolution,
	optically sectioned imaging throughout the sample, with minimal photodamage
	and at speeds capable of capturing transient biological phenomena.
	We used SPIM to visualize all muscles in vivo in the transgenic Medaka
	line Arnie, which expresses green fluorescent protein in muscle tissue.
	We also demonstrate that SPIM can be applied to visualize the embryogenesis
	of the relatively opaque Drosophila melanogaster in vivo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15310904},
  endnotereftype = {Journal Article},
  keywords = {Anatomy, Cross-Sectional Animals Animals, Genetically Modified Drosophila
	melanogaster/*embryology Embryo, Nonmammalian/*anatomy & histology/cytology
	Embryonic Development Green Fluorescent Proteins Heart/*embryology
	*Image Processing, Computer-Assisted *Imaging, Three-Dimensional
	Lasers Light Luminescent Proteins/analysis Microscopy, Fluorescence/*methods
	Morphogenesis Oryzias/*embryology},
  shorttitle = {Optical sectioning deep inside live embryos by selective plane illumination
	microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15310904}
}

@ARTICLE{Ingber2006,
  author = {Ingber, D. E.},
  title = {Mechanical control of tissue morphogenesis during embryological development},
  journal = {Int J Dev Biol},
  year = {2006},
  volume = {50},
  pages = {255-66},
  number = {2-3},
  note = {0214-6282 (Print) Journal Article},
  abstract = {Twenty years ago, we proposed a model of developmental control based
	on tensegrity architecture, in which tissue pattern formation in
	the embryo is controlled through mechanical interactions between
	cells and extracellular matrix (ECM) which place the tissue in a
	state of isometric tension (prestress). The model proposed that local
	changes in the mechanical compliance of the ECM, for example, due
	to regional variations in basement membrane degradation beneath growing
	epithelium, may result in local stretching of the ECM and associated
	adherent cells, much like a "run-in-a-stocking". Cell growth and
	function would be controlled locally though physical distortion of
	the associated cells, or changes in cytoskeletal tension. Importantly,
	experimental studies have demonstrated that cultured cells can be
	switched between different fates, including growth, differentiation,
	apoptosis, directional motility and different stem cell lineages,
	by modulating cell shape. Experiments in whole embryonic organ rudiments
	also have confirmed the tight correlation between basement membrane
	thinning, cell tension generation and new bud and branch formation
	during tissue morphogenesis and that this process can be inhibited
	or accelerated by dissipating or enhancing cytoskeletal tension,
	respectively. Taken together, this work confirms that mechanical
	forces generated in the cytoskeleton of individual cells and exerted
	on ECM scaffolds, play a critical role in the sculpting of the embryo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16479493},
  endnotereftype = {Journal Article},
  shorttitle = {Mechanical control of tissue morphogenesis during embryological development},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16479493}
}

@ARTICLE{Ingber2003,
  author = {Ingber, D. E.},
  title = {Tensegrity II. How structural networks influence cellular information
	processing networks},
  journal = {J Cell Sci},
  year = {2003},
  volume = {116},
  pages = {1397-408},
  number = {Pt 8},
  month = {Apr 15},
  note = {0021-9533 Journal Article Review Review, Tutorial},
  abstract = {The major challenge in biology today is biocomplexity: the need to
	explain how cell and tissue behaviors emerge from collective interactions
	within complex molecular networks. Part I of this two-part article,
	described a mechanical model of cell structure based on tensegrity
	architecture that explains how the mechanical behavior of the cell
	emerges from physical interactions among the different molecular
	filament systems that form the cytoskeleton. Recent work shows that
	the cytoskeleton also orients much of the cell's metabolic and signal
	transduction machinery and that mechanical distortion of cells and
	the cytoskeleton through cell surface integrin receptors can profoundly
	affect cell behavior. In particular, gradual variations in this single
	physical control parameter (cell shape distortion) can switch cells
	between distinct gene programs (e.g. growth, differentiation and
	apoptosis), and this process can be viewed as a biological phase
	transition. Part II of this article covers how combined use of tensegrity
	and solid-state mechanochemistry by cells may mediate mechanotransduction
	and facilitate integration of chemical and physical signals that
	are responsible for control of cell behavior. In addition, it examines
	how cell structural networks affect gene and protein signaling networks
	to produce characteristic phenotypes and cell fate transitions during
	tissue development.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12640025},
  endnotereftype = {Journal Article},
  keywords = {Animals Apoptosis/physiology Cell Adhesion/physiology Cell Differentiation/physiology
	Cell Division/physiology Cytoskeleton/*physiology Extracellular Matrix/physiology
	Humans Integrins/physiology Mechanotransduction, Cellular/physiology
	Models, Biological Research Support, Non-U.S. Gov't Research Support,
	U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Signal
	Transduction/*physiology},
  shorttitle = {Tensegrity II. How structural networks influence cellular information
	processing networks},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12640025}
}

@ARTICLE{Ingber2003a,
  author = {Ingber, D. E.},
  title = {Tensegrity I. Cell structure and hierarchical systems biology},
  journal = {J Cell Sci},
  year = {2003},
  volume = {116},
  pages = {1157-73},
  number = {Pt 7},
  month = {Apr 1},
  note = {0021-9533 Journal Article Review},
  abstract = {In 1993, a Commentary in this journal described how a simple mechanical
	model of cell structure based on tensegrity architecture can help
	to explain how cell shape, movement and cytoskeletal mechanics are
	controlled, as well as how cells sense and respond to mechanical
	forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model
	can now be revisited and placed in context of new advances in our
	understanding of cell structure, biological networks and mechanoregulation
	that have been made over the past decade. Recent work provides strong
	evidence to support the use of tensegrity by cells, and mathematical
	formulations of the model predict many aspects of cell behavior.
	In addition, development of the tensegrity theory and its translation
	into mathematical terms are beginning to allow us to define the relationship
	between mechanics and biochemistry at the molecular level and to
	attack the larger problem of biological complexity. Part I of this
	two-part article covers the evidence for cellular tensegrity at the
	molecular level and describes how this building system may provide
	a structural basis for the hierarchical organization of living systems--from
	molecule to organism. Part II, which focuses on how these structural
	networks influence information processing networks, appears in the
	next issue.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12615960},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Size/physiology Cytoskeleton/*physiology/ultrastructure
	Eukaryotic Cells/*physiology/ultrastructure Humans Microfilaments/physiology
	Microtubules/physiology Models, Biological Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S. Stress, Mechanical Tensile Strength/physiology},
  shorttitle = {Tensegrity I. Cell structure and hierarchical systems biology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12615960}
}

@ARTICLE{Ingber2003b,
  author = {Ingber, D. E.},
  title = {Mechanobiology and diseases of mechanotransduction},
  journal = {Ann Med},
  year = {2003},
  volume = {35},
  pages = {564-77},
  number = {8},
  note = {0785-3890 Journal Article Review},
  abstract = {The current focus of medicine on molecular genetics ignores the physical
	basis of disease even though many of the problems that lead to pain
	and morbidity, and bring patients to the doctor's office, result
	from changes in tissue structure or mechanics. The main goal of this
	article is therefore to help integrate mechanics into our understanding
	of the molecular basis of disease. This article first reviews the
	key roles that physical forces, extracellular matrix and cell structure
	play in the control of normal development, as well as in the maintenance
	of tissue form and function. Recent insights into cellular mechanotransduction--the
	molecular mechanism by which cells sense and respond to mechanical
	stress--also are described. Re-evaluation of human pathophysiology
	in this context reveals that a wide range of diseases included within
	virtually all fields of medicine and surgery share a common feature:
	their etiology or clinical presentation results from abnormal mechanotransduction.
	This process may be altered by changes in cell mechanics, variations
	in extracellular matrix structure, or by deregulation of the molecular
	mechanisms by which cells sense mechanical signals and convert them
	into a chemical or electrical response. Molecules that mediate mechanotransduction,
	including extracellular matrix molecules, transmembrane integrin
	receptors, cytoskeletal structures and associated signal transduction
	components, may therefore represent targets for therapeutic intervention
	in a variety of diseases. Insights into the mechanical basis of tissue
	regulation also may lead to development of improved medical devices,
	engineered tissues, and biologically-inspired materials for tissue
	repair and reconstruction.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14708967},
  endnotereftype = {Journal Article},
  keywords = {Biology/*methods Biomechanics Clinical Medicine/*methods Humans *Mechanotransduction,
	Cellular Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S. Stress, Mechanical},
  shorttitle = {Mechanobiology and diseases of mechanotransduction},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14708967}
}

@ARTICLE{Inoue2003,
  author = {Inoue, A. and Okabe, S.},
  title = {The dynamic organization of postsynaptic proteins: translocating
	molecules regulate synaptic function},
  journal = {Curr Opin Neurobiol},
  year = {2003},
  volume = {13},
  pages = {332-40},
  number = {3},
  month = {Jun},
  note = {22733525 0959-4388 Journal Article Review Review Literature},
  abstract = {Physiological roles for postsynaptic molecules in synaptogenesis and
	plasticity are under intense investigation. Recent imaging experiments,
	including GFP-based and single-particle tracking strategies, reveal
	rapid movement of synaptic components to and from the postsynaptic
	sites. Furthermore, specific patterns of neuronal activity and/or
	activation of specific transmitter receptors trigger selective translocation
	of postsynaptic components. These emerging dynamic properties of
	synaptic specializations add another layer of complexity to the signaling
	mechanisms of CNS synapses.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12850218},
  endnotereftype = {Journal Article},
  keywords = {Animal Human Presynaptic Terminals/chemistry/metabolism Proteins/*chemistry/*metabolism
	Receptors, Glutamate/chemistry/metabolism Support, Non-U.S. Gov't
	Synapses/*chemistry/*metabolism},
  shorttitle = {The dynamic organization of postsynaptic proteins: translocating molecules
	regulate synaptic function},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12850218}
}

@ARTICLE{Ishikawa2003,
  author = {Ishikawa, J. and Okano, J. and Ohki, K. and Amagai, A. and Maeda,
	Y. and Miyata, H.},
  title = {Phagocytosis of Dictyostelium discoideum studied by the particle-tracking
	method},
  journal = {Exp Cell Res},
  year = {2003},
  volume = {288},
  pages = {268-76},
  number = {2},
  month = {Aug 15},
  note = {22796561 0014-4827 Journal Article},
  abstract = {Single phagocytic events of cellular slime mold Dictyostelium discoideum
	were studied by the method of particle tracking. A 2-microm polystyrene
	bead, which had been covalently coated with folate, was attached
	to the advancing edge of a Dictyostelium ameba with the aid of an
	optical trap. The bead was transported backward on the cell surface.
	Forty-five percent of the transported beads were internalized. The
	bead motion was analyzed by determining every 33 ms the x-y coordinate
	of the centroid of the phase-contrast image of the bead. The x(t)
	and y(t) traces were smoothed over 1 s and the difference between
	the smoothed (x(t) and y(t)) and the original traces, delta(x) identical
	with x(t) - x(t) and delta(y) identical with y(t) - y(t), were calculated,
	which represented relatively rapid components of the bead motion.
	The plot of delta(2) = (delta(x)(2) + delta(y)(2)) against time could
	be divided into three phases on the basis of the variance of delta(2).
	Comparison of the plot with the video sequence indicated that the
	first phase corresponded to the transport, the second phase to the
	internalization, and the third phase to the postinternalization process
	(intracellular movement). Cytochalasin A at 5 microM completely inhibited
	phagocytosis without affecting the binding of bead to the cell surface,
	indicating the importance of actin cytoskeleton in all the phases.
	At 1 microM cytochalasin A the variance of the postinternalization
	process decreased, and the duration of the transport phase increased.
	At 0.25 microM cytochalasin A the duration of the internalization
	phase exhibited a significant increase, but other parameters did
	not change appreciably. The complex and differential effects of cytochalasin
	A on the parameters characterizing the three phases in the phagocytic
	process indicate that various aspects of actin dynamics are involved
	in the individual process of phagocytosis.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12915118},
  endnotereftype = {Journal Article},
  shorttitle = {Phagocytosis of Dictyostelium discoideum studied by the particle-tracking
	method},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12915118}
}

@BOOK{Jacquez1972,
  title = {Compartmental analysis in biology and medicine},
  publisher = {Elsevier},
  year = {1972},
  author = {Jacquez, J.A.},
  endnotereftype = {Book},
  shorttitle = {Compartmental analysis in biology and medicine}
}

@ARTICLE{Jiang2004,
  author = {Jiang, X. and Bruzewicz, D. A. and Thant, M. M. and Whitesides, G.
	M.},
  title = {Palladium as a substrate for self-assembled monolayers used in biotechnology},
  journal = {Anal Chem},
  year = {2004},
  volume = {76},
  pages = {6116-21},
  number = {20},
  month = {Oct 15},
  note = {0003-2700 (Print) Journal Article},
  abstract = {This paper describes self-assembled monolayers (SAMs) on palladium
	that resist the nonspecific adsorption of proteins and the adhesion
	of mammalian cells. These SAMs form when thin films of palladium
	are exposed to solutions of alkanethiol with the general structure
	HS(CH(2))(m)()(OCH(2)CH(2))(n)()OH (m = 2, 11; n = 3, 6, 7). Ellipsometry
	and surface plasmon resonance spectroscopy (using a palladium-on-gold
	substrate) showed that these SAMs resist adsorption of all proteins
	present in bovine serum. Microislands of SAMs of octadecanethiol
	on palladium allowed patterned adhesion and growth of mammalian cells
	(in a "sea" of oligo(ethyleneglycol)-terminated SAM). The oligo(ethyleneglycol)-terminated
	SAM resisted the invasion of cells for over four weeks under standard
	conditions of cell culture; similar SAMs on gold remained patterned
	for only two weeks.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15481961},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animals *Biotechnology Cell Line Humans Mice Palladium/*chemistry
	Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't,
	P.H.S. Surface Plasmon Resonance},
  shorttitle = {Palladium as a substrate for self-assembled monolayers used in biotechnology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15481961}
}

@ARTICLE{Jiang2005,
  author = {Jiang, X. and Bruzewicz, D. A. and Wong, A. P. and Piel, M. and Whitesides,
	G. M.},
  title = {Directing cell migration with asymmetric micropatterns},
  journal = {Proc Natl Acad Sci U S A},
  year = {2005},
  volume = {102},
  pages = {975-8},
  number = {4},
  month = {Jan 25},
  note = {0027-8424 (Print) Journal Article},
  abstract = {This report shows that the direction of polarization of attached mammalian
	cells determines the direction in which they move. Surfaces micropatterned
	with appropriately functionalized self-assembled monolayers constrain
	individual cells to asymmetric geometries (for example, a teardrop);
	these geometries polarize the morphology of the cell. After electrochemical
	desorption of the self-assembled monolayers removes these constraints
	and allows the cells to move across the surface, they move toward
	their blunt ends.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15653772},
  endnotereftype = {Journal Article},
  keywords = {Animals COS Cells Cell Communication *Cell Movement Cell Polarity
	Humans Mice NIH 3T3 Cells Research Support, Non-U.S. Gov't Research
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Directing cell migration with asymmetric micropatterns},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15653772}
}

@ARTICLE{Jin2002,
  author = {Jin, T. and Li, J.},
  title = {Dynamitin controls Beta 2 integrin avidity by modulating cytoskeletal
	constraint on integrin molecules},
  journal = {J Biol Chem},
  year = {2002},
  volume = {277},
  pages = {32963-9},
  number = {36},
  month = {Sep 6},
  note = {22194336 0021-9258 Journal Article},
  abstract = {Dynamitin, a subunit of the microtubule-dependent motor complex, was
	implicated in cell adhesion by binding to MacMARCKS (Macrophage-enriched
	myristoylated alanine-rice C kinase substrate). However, how dynamitin
	is involved in cell adhesion is unclear despite the fact that both
	MacMARCKS and microtubules regulate beta(2) integrin activation.
	We report that dynamitin regulates beta(2) integrin avidity toward
	iC3b by modulating the lateral mobility of beta(2) integrin molecules.
	Using the single particle tracking method, we found that integrin
	molecular mobility in cells expressing the fusion protein CFP (cyan
	fluorescent protein)-dynamitin or CFP-MB (the MacMARCKS binding domain
	peptide of dynamitin) increased 6-fold over the control cells, suggesting
	that disturbing dynamitin function dramatically altered the cytoskeletal
	constraint on beta(2) integrin molecules. Further mechanistic studies
	revealed that overexpression of dynamitin stimulated the phosphorylation
	of endogenous MacMARCKS protein, which lead to the enhanced tyrosine
	phosphorylation of paxillin. This effect of dynamitin correlates
	with the observation that higher concentration of PKC inhibitor is
	required to block beta(2) integrin mobility in dynamitin-expressing
	cells. Although dynamitin acts at the point of MacMARCKS phosphorylation,
	it is upstream of RhoA, because its effect was blocked by RhoA inhibitor.
	Thus, we conclude that dynamitin is a part of the cytoskeletal constraint
	that locks beta(2) integrin in the inactive form.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12082093},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, CD18/*metabolism Cell Line Cytoskeletal Proteins/metabolism
	Cytoskeleton/*metabolism Enzyme Inhibitors/pharmacology Human Integrins/*metabolism
	Ligands Luminescent Proteins/metabolism Membrane Proteins/*metabolism
	Mice Microscopy, Fluorescence Microscopy, Video Microtubule-Associated
	Proteins/*physiology Microtubules/metabolism Phosphoproteins/metabolism
	Phosphorylation Plasmids/metabolism Protein Binding Protein Kinase
	C/metabolism Recombinant Fusion Proteins/metabolism Staurosporine/pharmacology
	Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S. Time Factors
	Transfection Tyrosine/metabolism rhoA GTP-Binding Protein/metabolism},
  shorttitle = {Dynamitin controls Beta 2 integrin avidity by modulating cytoskeletal
	constraint on integrin molecules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12082093}
}

@ARTICLE{Jones1996,
  author = {Jones, J. D. and Luby-Phelps, K.},
  title = {Tracer diffusion through F-actin: effect of filament length and cross-linking},
  journal = {Biophys J},
  year = {1996},
  volume = {71},
  pages = {2742-50},
  number = {5},
  month = {Nov},
  note = {0006-3495 Journal Article},
  abstract = {We have determined diffusion coefficients for small (50- to 70-nm
	diameter) fluorescein-thiocarbamoyl-labeled Ficoll tracers through
	F-actin as a function of filament length and cross-linking. fx45
	was used to regulate filament length and avidin/biotinylated actin
	or ABP-280 was used to prepare cross-linked actin gels. We found
	that tracer diffusion was generally independent of filament length
	in agreement with theoretical predictions for diffusion through solutions
	of rods. However, in some experiments diffusion was slower through
	short (< or = 1.0 micron) filaments, although this result was not
	consistently reproducible. Measured diffusion coefficients through
	unregulated F-actin and filaments of lengths > 1.0 micron were more
	rapid than predicted by theory for tracer diffusion through rigid,
	random networks, which was consistent with some degree of actin bundling.
	Avidin-induced cross-linking of biotinylated F-actin did not affect
	diffusion through unregulated F-actin, but in cases where diffusion
	was slower through short filaments this cross-linking method resulted
	in enhanced tracer diffusion rates indistinguishable from unregulated
	F-actin. This finding, in conjunction with increased turbidity of
	1.0-micron filaments upon avidin cross-linking, indicated that this
	cross-linking method induces F-actin bundling. By contrast, ABP-280
	cross-linking retarded diffusion through unregulated F-actin and
	decreased turbidity. Tracer diffusion under these conditions was
	well approximated by the diffusion theory. Both cross-linking procedures
	resulted in gel formation as determined by falling ball viscometry.
	These results demonstrate that network microscopic geometry is dependent
	on the cross-linking method, although both methods markedly increase
	F-actin macroscopic viscosity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8913611},
  endnotereftype = {Journal Article},
  keywords = {Actins/*chemistry Animals Avidin/chemistry Biotin/chemistry Diffusion
	Ficoll/chemistry Fluorescein Fluoresceins/chemistry/diagnostic use
	Gels Macromolecular Substances Microfilament Proteins/chemistry Microfilaments/chemistry
	Nephelometry and Turbidimetry Protein Binding Rabbits Scattering,
	Radiation Viscosity},
  shorttitle = {Tracer diffusion through F-actin: effect of filament length and cross-linking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8913611}
}

@ARTICLE{Kandere-Grzybowska2005,
  author = {Kandere-Grzybowska, K. and Campbell, C. and Komarova, Y. and Grzybowski,
	B. A. and Borisy, G. G.},
  title = {Molecular dynamics imaging in micropatterned living cells},
  journal = {Nat Methods},
  year = {2005},
  volume = {2},
  pages = {739-41},
  number = {10},
  month = {Oct},
  note = {1548-7091 (Print) Journal Article},
  abstract = {Micropatterning approaches using self-assembled monolayers of alkyl
	thiols on gold are not optimal for important imaging modalities in
	cell biology because of absorption of light and scattering of electrons
	by the gold layer. We report here an anisotropic solid microetching
	(ASOMIC) procedure that overcomes these limitations. The method allows
	molecular dynamics imaging by wide-field and total internal reflection
	fluorescence (TIRF) microscopy of living mammalian cells and correlative
	platinum replica electron microscopy.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16179919},
  endnotereftype = {Journal Article},
  keywords = {Animals Cytoskeleton/*ultrastructure Gold/*chemistry *Microscopy,
	Electron *Microscopy, Fluorescence Platinum/*chemistry *Replica Techniques
	Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, P.H.S. Sulfhydryl Compounds/chemistry},
  shorttitle = {Molecular dynamics imaging in micropatterned living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16179919}
}

@ARTICLE{Kano2000,
  author = {Kano, F. and Sako, Y. and Tagaya, M. and Yanagida, T. and Murata,
	M.},
  title = {Reconstitution of brefeldin A-induced golgi tubulation and fusion
	with the endoplasmic reticulum in semi-intact chinese hamster ovary
	cells},
  journal = {Mol Biol Cell},
  year = {2000},
  volume = {11},
  pages = {3073-87},
  number = {9},
  month = {Sep},
  note = {1059-1524 Journal Article},
  abstract = {The fungal metabolite brefeldin A (BFA) induces the disassembly of
	the Golgi complex in mammalian cells. The drug seems to accentuate
	tubule formation and causes the subsequent fusion with the endoplasmic
	reticulum (ER). To investigate the biochemical requirements and kinetics
	of BFA-induced Golgi disassembly, we have reconstituted the process
	of green fluorescent protein-tagged Golgi complex disassembly in
	streptolysin O-permeabilized semi-intact Chinese hamster ovary cells.
	For quantitative analysis of the morphological changes to the Golgi
	complex in semi-intact cells, we developed a novel morphometric analysis.
	Based on this analysis, we have dissected the BFA-induced Golgi disassembly
	process biochemically into two processes, Golgi tubule formation
	and fusion with the ER, and found that the formation is induced by
	only ATP and the residual factors in the cells and that the subsequent
	fusion is mediated in an N-ethylmaleimide-sensitive factor-dependent
	manner via Golgi tubules. Tubulation occurs by two pathways that
	depend on either microtubule integrity or exogenously added cytosol.
	In the presence of GTPgammaS, coat protein I inhibited the Golgi
	tubule fusion with the ER but showed no apparent effect on tubulation.
	Additionally, we analyzed the kinetics of tubulation and fusion independently
	in nocodazole-treated and -untreated semi-intact cells and found
	that tubulation is a rate-limiting step of the Golgi disassembly.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10982401},
  endnotereftype = {Journal Article},
  keywords = {Animals Brefeldin A/*pharmacology CHO Cells Coat Protein Complex I/metabolism
	Cytosol/physiology Endoplasmic Reticulum/drug effects/physiology/*ultrastructure
	Genes, Reporter Golgi Apparatus/drug effects/physiology/*ultrastructure
	Guanosine 5'-O-(3-Thiotriphosphate)/pharmacology Hamsters Kinetics
	Luminescent Proteins/analysis Membrane Fusion/*drug effects Microtubules/drug
	effects/physiology/*ultrastructure Recombinant Fusion Proteins/analysis
	Support, Non-U.S. Gov't Transfection},
  shorttitle = {Reconstitution of brefeldin A-induced golgi tubulation and fusion
	with the endoplasmic reticulum in semi-intact chinese hamster ovary
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10982401}
}

@ARTICLE{Kao1994,
  author = {Kao, H. P. and Verkman, A. S.},
  title = {Tracking of single fluorescent particles in three dimensions: use
	of cylindrical optics to encode particle position},
  journal = {Biophys J},
  year = {1994},
  volume = {67},
  pages = {1291-300},
  number = {3},
  month = {Sep},
  note = {95111068 0006-3495 Journal Article},
  abstract = {We present a novel optical technique for three-dimensional tracking
	of single fluorescent particles using a modified epifluorescence
	microscope containing a weak cylindrical lens in the detection optics
	and a microstepper-controlled fine focus. Images of small, fluorescent
	particles were circular in focus but ellipsoidal above and below
	focus; the major axis of the ellipsoid shifted by 90 degrees in going
	through focus. Particle z position was determined from the image
	shape and orientation by applying a peak detection algorithm to image
	projections along the x and y axes; x, y position was determined
	from the centroid of the particle image. Typical spatial resolution
	was 12 nm along the optical axis and 5 nm in the image plane with
	a maximum sampling rate of 3-4 Hz. The method was applied to track
	fluorescent particles in artificial solutions and living cells. In
	a solution of viscosity 30 cP, the mean squared distance (MSD) traveled
	by a 264 nm diameter rhodamine-labeled bead was linear with time
	to 20 s. The measured diffusion coefficient, 0.0558 +/- 0.001 micron2/s
	(SE, n = 4), agreed with the theoretical value of 0.0556 micron2/s.
	Statistical variability of MSD curves for a freely diffusing bead
	was in quantitative agreement with Monte Carlo simulations of three-dimensional
	random walks. In a porous glass matrix, the MSD data was curvilinear
	and showed reduced bead diffusion. In cytoplasm of Swiss 3T3 fibroblasts,
	bead diffusion was restricted. The water permeability in individual
	Chinese Hamster Ovary cells was measured from the z movement of a
	fluorescent bead fixed at the cell surface in response osmotic gradients;
	water permeability was increased by > threefold in cells expressing
	CHIP28 water channels. The simplicity and precision of this tracking
	method may be useful to quantify the complex trajectories of fluorescent
	particles in living cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7811944},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animal Biophysics Computer Simulation Diffusion *Fluorescence
	Intracellular Fluid/physiology Mice *Motion Movement/physiology *Optics
	Particle Size Solutions Support, U.S. Gov't, P.H.S. Water},
  shorttitle = {Tracking of single fluorescent particles in three dimensions: use
	of cylindrical optics to encode particle position},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7811944}
}

@ARTICLE{Kass1987,
  author = {Kass, M and Witkin, A and Terzopoulos, D},
  title = {Snakes: Active Contour Models},
  journal = {Int. J. Computer Vision},
  year = {1987},
  volume = {1},
  pages = {321-331},
  endnotereftype = {Journal Article},
  shorttitle = {Snakes: Active Contour Models}
}

@ARTICLE{Kearney1987,
  author = {Kearney, J.K. and Thompson, W.B. and Boley, D.L.},
  title = {Optical flow estimation: An error analysis of gradient-based methods
	with local optimisation},
  journal = {IEEE Trans. on Pattern Analysis andMachine Intelligence},
  year = {1987},
  volume = {9},
  pages = {229-244},
  number = {2},
  note = {http://citeseer.ist.psu.edu/context/96627/0},
  endnotereftype = {Journal Article},
  shorttitle = {Optical flow estimation: An error analysis of gradient-based methods
	with local optimisation}
}

@ARTICLE{Klausner1992,
  author = {Klausner, R. D. and Donaldson, J. G. and Lippincott-Schwartz, J.},
  title = {Brefeldin A: insights into the control of membrane traffic and organelle
	structure},
  journal = {J Cell Biol},
  year = {1992},
  volume = {116},
  pages = {1071-80},
  number = {5},
  month = {Mar},
  note = {0021-9525 Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1740466},
  endnotereftype = {Journal Article},
  keywords = {Animals Brefeldin A Cell Compartmentation Cyclopentanes/*pharmacology
	Endoplasmic Reticulum/drug effects Golgi Apparatus/drug effects Intracellular
	Membranes/drug effects/*metabolism Organelles/drug effects/*ultrastructure},
  shorttitle = {Brefeldin A: insights into the control of membrane traffic and organelle
	structure},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1740466}
}

@ARTICLE{Kreitzer2000,
  author = {Kreitzer, G. and Marmorstein, A. and Okamoto, P. and Vallee, R. and
	Rodriguez-Boulan, E.},
  title = {Kinesin and dynamin are required for post-Golgi transport of a plasma-membrane
	protein},
  journal = {Nat Cell Biol},
  year = {2000},
  volume = {2},
  pages = {125-7},
  number = {2},
  month = {Feb},
  note = {1465-7392 (Print) Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10655593},
  endnotereftype = {Journal Article},
  keywords = {Animals Antibodies/pharmacology Biological Transport Cell Membrane/*metabolism
	Cell Polarity Cells, Cultured Dogs Dynamins GTP Phosphohydrolases/*metabolism
	Golgi Apparatus/*metabolism Kidney/cytology Kinesin/*metabolism Microtubules/drug
	effects Receptors, Nerve Growth Factor/*metabolism Research Support,
	Non-U.S. Gov't},
  shorttitle = {Kinesin and dynamin are required for post-Golgi transport of a plasma-membrane
	protein},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10655593}
}

@ARTICLE{Kucik1996,
  author = {Kucik, D. F. and Dustin, M. L. and Miller, J. M. and Brown, E. J.},
  title = {Adhesion-activating phorbol ester increases the mobility of leukocyte
	integrin LFA-1 in cultured lymphocytes},
  journal = {J Clin Invest},
  year = {1996},
  volume = {97},
  pages = {2139-44},
  number = {9},
  month = {May 1},
  note = {96209348 0021-9738 Journal Article},
  abstract = {Lymphocytes activate adhesion to intracellular adhesion mlecule 1
	(ICAM-1) via leukocyte function associated antigen 1 (LFA-1), their
	major beta 2 integrin, in response to PMA (phorbol 12-myristate 13-acetate)
	without an increase in the number of receptors expressed. The molecular
	details of the mechanism are unknown. To determine the effect of
	PMA activation on LFA-1 movement within the plasma membrane, we used
	the single particle tracking technique to measure the diffusion rate
	of LFA-1 molecules on EBV-transformed B cells before and after PMA
	activation. Diffusion of LFA-1 on unactivated cells was restricted
	compared to CR1 (CD35), another transmembrane protein of equivalent
	size. PMA caused a 10-fold increase in the diffusion rate of LFA-1
	without any effect on CD35. The increased LFA-1 motion induced by
	PMA was random, not directed, indicating that it was due to a release
	of constraints rather than the application of forces. The diffusion
	rates of LFA-1 are consistent with cytoskeletal attachment before
	and free diffusion after PMA. Cytochalasin D led to an equivalent
	increase in mobility and, at low doses, stimulated adhesion, implying
	that the nonadhesive state of LFA-1 is actively maintained by the
	lymphocyte cytoskeleton.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621804},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport Carcinogens/*pharmacology Cell Adhesion/drug
	effects Cell Membrane/*metabolism/ultrastructure Cytoskeleton/metabolism/ultrastructure
	Human Lymphocyte Function-Associated Antigen-1/metabolism/*ultrastructure
	Lymphocytes/*cytology/metabolism/ultrastructure Phorbol Esters/*pharmacology
	Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.},
  shorttitle = {Adhesion-activating phorbol ester increases the mobility of leukocyte
	integrin LFA-1 in cultured lymphocytes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621804}
}

@ARTICLE{Kucik1999,
  author = {Kucik, D. F. and Elson, E. L. and Sheetz, M. P.},
  title = {Weak dependence of mobility of membrane protein aggregates on aggregate
	size supports a viscous model of retardation of diffusion},
  journal = {Biophys J},
  year = {1999},
  volume = {76},
  pages = {314-22},
  number = {1 Pt 1},
  month = {Jan},
  note = {99093392 0006-3495 Journal Article},
  abstract = {Proteins in plasma membranes diffuse more slowly than proteins inserted
	into artificial lipid bilayers. On a long-range scale (>250 nm),
	submembrane barriers, or skeleton fences that hinder long-range diffusion
	and create confinement zones, have been described. Even within such
	confinement zones, however, diffusion of proteins is much slower
	than predicted by the viscosity of the lipid. The cause of this slowing
	of diffusion on the micro scale has not been determined and is the
	focus of this paper. One way to approach this question is to determine
	the dependence of particle motion on particle size. Some current
	models predict that the diffusion coefficient of a membrane protein
	aggregate will depend strongly on its size, while others do not.
	We have measured the diffusion coefficients of membrane glycoprotein
	aggregates linked together by concanavalin A molecules bound to beads
	of various sizes, and also the diffusion coefficients of individual
	concanavalin A binding proteins. The measurements demonstrate at
	most a weak dependence of diffusion coefficient on aggregate size.
	This finding supports retardation by viscous effects, and is not
	consistent with models involving direct interaction of diffusing
	proteins with cytoskeletal elements.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9876143},
  endnotereftype = {Journal Article},
  keywords = {Animal Biophysics Cell Membrane/chemistry/metabolism/ultrastructure
	Cells, Cultured Diffusion Goldfish In Vitro Macromolecular Systems
	Membrane Glycoproteins/*chemistry/*metabolism Microscopy, Electron
	Models, Biological Protein Binding Support, U.S. Gov't, Non-P.H.S.
	Support, U.S. Gov't, P.H.S. Viscosity},
  shorttitle = {Weak dependence of mobility of membrane protein aggregates on aggregate
	size supports a viscous model of retardation of diffusion},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9876143}
}

@ARTICLE{Kucik1990,
  author = {Kucik, D. F. and Elson, E. L. and Sheetz, M. P.},
  title = {Cell migration does not produce membrane flow},
  journal = {J Cell Biol},
  year = {1990},
  volume = {111},
  pages = {1617-22},
  number = {4},
  month = {Oct},
  note = {91009494 0021-9525 Journal Article},
  abstract = {We have previously reported that rearward migration of surface particles
	on slowly moving cells is not driven by membrane flow (Sheetz, M.
	P., S. Turney, H. Qian, and E. L. Elson. 1989. Nature (Lond.). 340:284-288)
	and recent photobleaching measurements have ruled out any rapid rearward
	lipid flow (Lee, J., M. Gustafsson, D. E. Magnussen, and K. Jacobson.
	1990. Science (Wash. DC.) 247:1229-1233). It was not possible, however,
	to conclude from those studies that a slower or tank-tread membrane
	lipid flow does not occur. Therefore, we have used the technology
	of single particle tracking to examine the movements of diffusing
	particles on rapidly locomoting fish keratocytes where the membrane
	current is likely to be greatest. The keratocytes had a smooth lamellipodial
	surface on which bound Con A-coated gold particles were observed
	either to track toward the nuclear region (velocity of 0.35 +/- 0.15
	micron/s) or to diffuse randomly (apparent diffusion coefficient
	of [3.5 +/- 2.0] x 10(-10) cm2/s). We detected no systematic drift
	relative to the cell edge of particles undergoing random diffusion
	even after the cell had moved many micrometers. The average net particle
	displacement was 0.01 +/- 2.7% of the cell displacement. These results
	strongly suggest that neither the motions of membrane proteins driven
	by the cytoskeleton nor other possible factors produce a bulk flow
	of membrane lipid.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2211827},
  endnotereftype = {Journal Article},
  keywords = {Animal Biomechanics Cell Membrane/*physiology Cell Movement/*physiology
	Diffusion Goldfish Keratinocytes/metabolism Membrane Lipids/metabolism
	Models, Biological Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.},
  shorttitle = {Cell migration does not produce membrane flow},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2211827}
}

@ARTICLE{Kucik1990a,
  author = {Kucik, D. F. and Elson, E. L. and Sheetz, M. P.},
  title = {Cell migration does not produce membrane flow},
  journal = {J Cell Biol},
  year = {1990},
  volume = {111},
  pages = {1617-22},
  number = {4},
  month = {Oct},
  note = {91009494 0021-9525 Journal Article},
  abstract = {We have previously reported that rearward migration of surface particles
	on slowly moving cells is not driven by membrane flow (Sheetz, M.
	P., S. Turney, H. Qian, and E. L. Elson. 1989. Nature (Lond.). 340:284-288)
	and recent photobleaching measurements have ruled out any rapid rearward
	lipid flow (Lee, J., M. Gustafsson, D. E. Magnussen, and K. Jacobson.
	1990. Science (Wash. DC.) 247:1229-1233). It was not possible, however,
	to conclude from those studies that a slower or tank-tread membrane
	lipid flow does not occur. Therefore, we have used the technology
	of single particle tracking to examine the movements of diffusing
	particles on rapidly locomoting fish keratocytes where the membrane
	current is likely to be greatest. The keratocytes had a smooth lamellipodial
	surface on which bound Con A-coated gold particles were observed
	either to track toward the nuclear region (velocity of 0.35 +/- 0.15
	micron/s) or to diffuse randomly (apparent diffusion coefficient
	of [3.5 +/- 2.0] x 10(-10) cm2/s). We detected no systematic drift
	relative to the cell edge of particles undergoing random diffusion
	even after the cell had moved many micrometers. The average net particle
	displacement was 0.01 +/- 2.7% of the cell displacement. These results
	strongly suggest that neither the motions of membrane proteins driven
	by the cytoskeleton nor other possible factors produce a bulk flow
	of membrane lipid.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2211827},
  endnotereftype = {Journal Article},
  keywords = {Animal Biomechanics Cell Membrane/*physiology Cell Movement/*physiology
	Diffusion Goldfish Keratinocytes/metabolism Membrane Lipids/metabolism
	Models, Biological Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.},
  shorttitle = {Cell migration does not produce membrane flow},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2211827}
}

@ARTICLE{Kucik1989,
  author = {Kucik, D. F. and Elson, E. L. and Sheetz, M. P.},
  title = {Forward transport of glycoproteins on leading lamellipodia in locomoting
	cells},
  journal = {Nature},
  year = {1989},
  volume = {340},
  pages = {315-7},
  number = {6231},
  month = {Jul 27},
  note = {89314158 0028-0836 Journal Article},
  abstract = {In several types of locomoting cells, active rearward transport of
	particles on the cell surface has been observed and correlated with
	motility. No forward transport of particles has previously been reported,
	however. Here we report rapid forward transport of concanavalin A-coated
	gold particles on the dorsal surfaces of lamellipodia of fish epidermal
	keratocytes. These movements are active, not diffusive, and more
	rapid than either rearward particle transport or the rate of cell
	locomotion. We observed forward transport in migrating, but not in
	stationary cells, and could block the movement by treatment with
	cytochalasin D. These studies demonstrate for the first time that
	small numbers of glycoproteins can be actively transported on the
	surface of the cell to the front of the lamellipodium. We suggest
	that this mechanism transports proteins involved in cell locomotion,
	such as proteins necessary for adhesion, and could also produce an
	extensile force.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2473406},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Transport/drug effects *Cell Movement/drug effects
	Concanavalin A Cytochalasin D Cytochalasins/pharmacology Cytoplasm/metabolism/physiology
	Diffusion Epidermis/cytology Gold Goldfish In Vitro Keratin Membrane
	Glycoproteins/*metabolism Probability Support, Non-U.S. Gov't Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Forward transport of glycoproteins on leading lamellipodia in locomoting
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2473406}
}

@ARTICLE{Kucik1991,
  author = {Kucik, D. F. and Kuo, S. C. and Elson, E. L. and Sheetz, M. P.},
  title = {Preferential attachment of membrane glycoproteins to the cytoskeleton
	at the leading edge of lamella},
  journal = {J Cell Biol},
  year = {1991},
  volume = {114},
  pages = {1029-36},
  number = {5},
  month = {Sep},
  note = {91340827 0021-9525 Journal Article},
  abstract = {The active forward movement of cells is often associated with the
	rearward transport of particles over the surfaces of their lamellae.
	Unlike the rest of the lamella, we found that the leading edge (within
	0.5 microns of the cell boundary) is specialized for rearward transport
	of membrane-bound particles, such as Con A-coated latex microspheres.
	Using a single-beam optical gradient trap (optical tweezers) to apply
	restraining forces to particles, we can capture, move and release
	particles at will. When first bound on the central lamellar surface,
	Con A-coated particles would diffuse randomly; when such bound particles
	were brought to the leading edge of the lamella with the optical
	tweezers, they were often transported rearward. As in our previous
	studies, particle transport occurred with a concurrent decrease in
	apparent diffusion coefficient, consistent with attachment to the
	cytoskeleton. For particles at the leading edge of the lamella, weak
	attachment to the cytoskeleton and transport occurred with a half-time
	of 3 s; equivalent particles elsewhere on the lamella showed no detectable
	attachment when monitored for several minutes. Particles held on
	the cell surface by the laser trap attached more strongly to the
	cytoskeleton with time. These particles could escape a trapping force
	of 0.7 X 10(-6) dyne after 18 +/- 14 (sd) s at the leading edge,
	and after 64 +/- 34 (SD) s elsewhere on the lamella. Fluorescent
	succinylated Con A staining showed no corresponding concentration
	of general glycoproteins at the leading edge, but cytochalasin D-resistant
	filamentous actin was found at the leading edge. Our results have
	implications for cell motility: if the forces used for rearward particle
	transport were applied to a rigid substratum, cells would move forward.
	Such a mechanism would be most efficient if the leading edge of the
	cell contained preferential sites for attachment and transport.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1874785},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Transport Cell Compartmentation *Cell Movement Concanavalin
	A/metabolism Cytoskeleton/*metabolism Goldfish Keratinocytes/metabolism/*ultrastructure
	Membrane Glycoproteins/*metabolism Microscopy, Fluorescence Protein
	Binding Receptors, Concanavalin A/metabolism Support, Non-U.S. Gov't
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Preferential attachment of membrane glycoproteins to the cytoskeleton
	at the leading edge of lamella},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1874785}
}

@ARTICLE{Kucik2001,
  author = {Kucik, D. F. and O'Toole, T. E. and Zheleznyak, A. and Busettini,
	D. K. and Brown, E. J.},
  title = {Activation-enhanced alpha(IIb)beta(3)-integrin-cytoskeleton interactions
	outside of focal contacts require the alpha-subunit},
  journal = {Mol Biol Cell},
  year = {2001},
  volume = {12},
  pages = {1509-18},
  number = {5},
  month = {May},
  note = {21260037 1059-1524 Journal Article},
  abstract = {Integrins link the cell's cytoskeleton to the extracellular matrix,
	as well as to receptors on other cells. These links occur not only
	at focal contacts but also at smaller integrin-containing protein
	complexes outside of focal contacts. We previously demonstrated the
	importance of focal contact-independent integrin-cytoskeleton interactions
	of beta(2) integrins: activation of adhesion resulted from a release
	of integrins from cytoskeletal constraints. To determine whether
	changes in integrin-cytoskeleton interactions were related to activation
	of the integrin, we used single particle tracking to examine focal
	contact-independent cytoskeletal associations of alpha(IIb)beta(3)-integrin,
	in which activation results in a large conformational change. Direct
	activation of alpha(IIb)beta(3) by mutation did not mimic activation
	of lymphocytes with phorbol ester, because it enhanced integrin-cytoskeleton
	interactions, whereas activation of lymphocytes decreased them. Using
	additional integrin mutants, we found that both alpha- and beta-cytoplasmic
	domains were required for these links. This suggests that 1) both
	beta(2)- and beta(3)-integrins interact with the cytoskeleton outside
	of focal contacts; 2) activation of a cell and activation of an integrin
	are distinct processes, and both can affect integrin-cytoskeleton
	interactions; and 3) the role of the alpha-subunit in integrin-cytoskeleton
	interactions in at least some circumstances is more direct than generally
	supposed.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11359939},
  endnotereftype = {Journal Article},
  keywords = {Amino Acid Motifs Amino Acid Sequence Animal CHO Cells Cytoskeleton/*metabolism
	Diffusion Focal Adhesions/metabolism Hamsters Ligands Microspheres
	Models, Biological Molecular Sequence Data Mutation Platelet Glycoprotein
	GPIIb-IIIa Complex/chemistry/genetics/*metabolism Protein Binding
	*Protein Conformation Protein Structure, Tertiary *Protein Subunits
	Support, U.S. Gov't, Non-P.H.S.},
  shorttitle = {Activation-enhanced alpha(IIb)beta(3)-integrin-cytoskeleton interactions
	outside of focal contacts require the alpha-subunit},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11359939}
}

@ARTICLE{Kues2001,
  author = {Kues, T. and Dickmanns, A. and Luhrmann, R. and Peters, R. and Kubitscheck,
	U.},
  title = {High intranuclear mobility and dynamic clustering of the splicing
	factor U1 snRNP observed by single particle tracking},
  journal = {Proc Natl Acad Sci U S A},
  year = {2001},
  volume = {98},
  pages = {12021-6},
  number = {21},
  month = {Oct 9},
  note = {21477426 0027-8424 Journal Article},
  abstract = {Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are components
	of the splicing machinery that removes introns from precursor mRNA.
	Like other splicing factors, U snRNPs are diffusely distributed throughout
	the nucleus and, in addition, are concentrated in distinct nuclear
	substructures referred to as speckles. We have examined the intranuclear
	distribution and mobility of the splicing factor U1 snRNP on a single-molecule
	level. Isolated U1 snRNPs were fluorescently labeled and incubated
	with digitonin-permeabilized 3T3 cells in the presence of Xenopus
	egg extract. By confocal microscopy, U1 snRNPs were found to be imported
	into nuclei, yielding a speckled intranuclear distribution. Employing
	a laser video-microscope optimized for high sensitivity and high
	speed, single U1 snRNPs were visualized and tracked at a spatial
	precision of 35 nm and a time resolution of 30 ms. The single-particle
	data revealed that U1 snRNPs occurred in small clusters that colocalized
	with speckles. In the clusters, U1 snRNPs resided for a mean decay
	time of 84 ms before leaving the optical slice in the direction of
	the optical axis, which corresponded to a mean effective diffusion
	coefficient of 1 microm(2)/s. An analysis of the trajectories of
	single U1 snRNPs revealed that at least three kinetic classes of
	low, medium, and high mobility were present. Moreover, the mean square
	displacements of these fractions were virtually independent of time,
	suggesting arrays of binding sites. The results substantiate the
	view that nuclear speckles are not rigid structures but highly dynamic
	domains characterized by a rapid turnover of U1 snRNPs and other
	splicing factors.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11593012},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animal Carbocyanines Cell Nucleus/*metabolism Fluorescent
	Dyes Hydrazines Mice RNA Splicing Ribonucleoprotein, U1 Small Nuclear/*metabolism
	Support, Non-U.S. Gov't},
  shorttitle = {High intranuclear mobility and dynamic clustering of the splicing
	factor U1 snRNP observed by single particle tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11593012}
}

@MANUAL{Kuhn2001,
  title = {MultiTracker},
  author = {Kuhn, Jeffrey},
  year = {2001},
  bdsk-url-1 = {http://rsb.info.nih.gov/ij/plugins/multitracker.html},
  endnotereftype = {Journal Article},
  shorttitle = {MultiTracker},
  url = {http://rsb.info.nih.gov/ij/plugins/multitracker.html}
}

@ARTICLE{AmerChemicalSoc,
  author = {Kumar, A. and Biebuyck, H. A. and Whitesides, G. M.},
  title = {Patterning Self-Assembled Monolayers - Applications in Materials
	Science},
  journal = {Langmuir},
  year = {1994},
  volume = {10},
  pages = {1498-1511},
  number = {5},
  month = {MAY},
  note = {Times Cited: 578 Article English Cited References Count: 41 Nn491},
  abstract = {This paper describes an experimentally simple technique, based on
	stamping or contact printing, to pattern the adsorption of alkanethiolates
	on surfaces of gold, on scales from 0.2 to 100 mum, and illustrates
	the use of these patterned surfaces. An elastomeric stamp, fabricated
	from poly(dimethylsiloxane)(PDMS), was used to deliver alkanethiol
	to predetermined regions of the surface of an evaporated gold film.
	With this technique, organic surfaces patterned with well-defined
	regions exhibiting different chemical and physical properties have
	been produced. This technique was used to pattern the adsorption
	of single and multiple SAMs on a single substrate. This method of
	preparing patterned surfaces has been used in a variety of applications,
	including the preparation of well-defined, heterogeneous substrates
	for scanning probe microscopies, the formation of microelectrodes,
	the formation of microstructures of silicon, the preparation of substrates
	for the study of condensation figures, and the preparation of substrates
	for patterned formation of microcrystals.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://A1994NN49100031},
  endnotereftype = {Journal Article},
  keywords = {mechanical-properties crystalline silicon alkaline-solutions breath
	figures gold thiols growth films alkanethiols surfaces},
  shorttitle = {Patterning Self-Assembled Monolayers - Applications in Materials Science},
  url = {<Go to ISI>://A1994NN49100031}
}

@ARTICLE{Kuo1991,
  author = {Kuo, S. C. and Gelles, J. and Steuer, E. and Sheetz, M. P.},
  title = {A model for kinesin movement from nanometer-level movements of kinesin
	and cytoplasmic dynein and force measurements},
  journal = {J Cell Sci Suppl},
  year = {1991},
  volume = {14},
  pages = {135-8},
  note = {91358541 0269-3518 Journal Article},
  abstract = {Our detailed measurements of the movements of kinesin- and dynein-coated
	latex beads have revealed several important features of the motors
	which underlie basic mechanical aspects of the mechanisms of motor
	movements. Kinesin-coated beads will move along the paths of individual
	microtubule protofilaments with high fidelity and will pause at 4
	nm intervals along the microtubule axis under low ATP conditions.
	In contrast, cytoplasmic dynein-coated beads move laterally across
	many protofilaments as they travel along the microtubule, without
	any regular pauses, suggesting that the movements of kinesin-coated
	beads are not an artefact of the method. These kinesin bead movements
	suggest a model for kinesin movement in which the two heads walk
	along an individual protofilament in a hand-over-hand fashion. A
	free head would only be able to bind to the next forward tubulin
	subunit on the protofilament and its binding would pull off the trailing
	head to start the cycle again. This model is consistent with the
	observed cooperativity between the heads and with the movement by
	single dimeric molecules. Several testable predictions of the model
	are that kinesin should be able to bind to both alpha and beta tubulin
	and that the length of the neck region of the molecule should control
	the off-axis motility. In this article, we describe the technology
	for measuring nanometer-level movements and the force generated by
	the kinesin molecule.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1832166},
  endnotereftype = {Journal Article},
  keywords = {Adenosinetriphosphatase/*physiology Calibration Cytoplasm/physiology
	Dynein ATPase/*physiology Electronics Image Processing, Computer-Assisted
	Kinesin Kinetics Models, Biological Optics Photomicrography Videotape
	Recording},
  shorttitle = {A model for kinesin movement from nanometer-level movements of kinesin
	and cytoplasmic dynein and force measurements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1832166}
}

@ARTICLE{Kural2005,
  author = {Kural, C. and Kim, H. and Syed, S. and Goshima, G. and Gelfand, V.
	I. and Selvin, P. R.},
  title = {Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated
	movement?},
  journal = {Science},
  year = {2005},
  volume = {308},
  pages = {1469-72},
  number = {5727},
  month = {Jun 3},
  note = {1095-9203 (Electronic) Journal Article},
  abstract = {We used fluorescence imaging with one nanometer accuracy (FIONA) to
	analyze organelle movement by conventional kinesin and cytoplasmic
	dynein in a cell. We located a green fluorescence protein (GFP)-tagged
	peroxisome in cultured Drosophila S2 cells to within 1.5 nanometers
	in 1.1 milliseconds, a 400-fold improvement in temporal resolution,
	sufficient to determine the average step size to be approximately
	8 nanometers for both dynein and kinesin. Furthermore, we found that
	dynein and kinesin do not work against each other in vivo during
	peroxisome transport. Rather, multiple kinesins or multiple dyneins
	work together, producing up to 10 times the in vitro speed.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15817813},
  endnotereftype = {Journal Article},
  keywords = {Animals *Biological Transport Cell Line Drosophila Dynein ATPase/*physiology
	Fluorescence Green Fluorescent Proteins Kinesin/*physiology Molecular
	Motors/*physiology Peroxisomes/*metabolism Research Support, N.I.H.,
	Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated
	movement?},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15817813}
}

@ARTICLE{Kusumi1997,
  author = {Kusumi, A. and Sako, Y.},
  title = {[Two-photon excitation fluorescence microscopy]},
  journal = {Tanpakushitsu Kakusan Koso},
  year = {1997},
  volume = {42},
  pages = {1151-3},
  number = {7 Suppl},
  month = {May},
  note = {0039-9450 Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9170942},
  endnotereftype = {Journal Article},
  keywords = {*Microscopy, Fluorescence/instrumentation/methods},
  shorttitle = {[Two-photon excitation fluorescence microscopy]},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9170942}
}

@ARTICLE{Kusumi1996,
  author = {Kusumi, A. and Sako, Y.},
  title = {Cell surface organization by the membrane skeleton},
  journal = {Curr Opin Cell Biol},
  year = {1996},
  volume = {8},
  pages = {566-74},
  number = {4},
  month = {Aug},
  note = {0955-0674 Journal Article Review Review, Tutorial},
  abstract = {Single-particle tracking and laser tweezers have facilitated the observation
	of the mechanics of molecular interactions in the plasma membrane
	of living cells at the level of single (or a few) molecules at nanometer/piconewton
	precision. These techniques have recently revealed that the membrane
	skeleton provides both confining and binding effects on the movement
	of membrane proteins, and that it can play a pivotal role in the
	molecular organization of the plasma membrane, especially in the
	formation of special membrane domains.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8791449},
  endnotereftype = {Journal Article},
  keywords = {Biomechanics Cell Compartmentation Cell Membrane/*physiology/ultrastructure
	Cytological Techniques Cytoskeleton/*physiology Diffusion Elasticity
	Lasers Membrane Proteins/*metabolism Models, Biological Motion},
  shorttitle = {Cell surface organization by the membrane skeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8791449}
}

@ARTICLE{Kusumi1996a,
  author = {Kusumi, A. and Sako, Y.},
  title = {Cell surface organization by the membrane skeleton},
  journal = {Curr Opin Cell Biol},
  year = {1996},
  volume = {8},
  pages = {566-74},
  number = {4},
  month = {Aug},
  note = {96386280 0955-0674 Journal Article Review Review, Tutorial},
  abstract = {Single-particle tracking and laser tweezers have facilitated the observation
	of the mechanics of molecular interactions in the plasma membrane
	of living cells at the level of single (or a few) molecules at nanometer/piconewton
	precision. These techniques have recently revealed that the membrane
	skeleton provides both confining and binding effects on the movement
	of membrane proteins, and that it can play a pivotal role in the
	molecular organization of the plasma membrane, especially in the
	formation of special membrane domains.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8791449},
  endnotereftype = {Journal Article},
  keywords = {Biomechanics Cell Compartmentation Cell Membrane/*physiology/ultrastructure
	Cytological Techniques Cytoskeleton/*physiology Diffusion Elasticity
	Lasers Membrane Proteins/*metabolism Models, Biological Motion},
  shorttitle = {Cell surface organization by the membrane skeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8791449}
}

@ARTICLE{Kusumi1998,
  author = {Kusumi, A. and Sako, Y. and Fujiwara, T. and Tomishige, M.},
  title = {Application of laser tweezers to studies of the fences and tethers
	of the membrane skeleton that regulate the movements of plasma membrane
	proteins},
  journal = {Methods Cell Biol},
  year = {1998},
  volume = {55},
  pages = {173-94},
  note = {0091-679x Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9352517},
  endnotereftype = {Journal Article},
  keywords = {Animals Calibration Cell Membrane/*physiology Human *Lasers Membrane
	Proteins/*physiology Micromanipulation/instrumentation/*methods Microscopy/instrumentation/methods
	Receptors, Cell Surface/metabolism},
  shorttitle = {Application of laser tweezers to studies of the fences and tethers
	of the membrane skeleton that regulate the movements of plasma membrane
	proteins},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9352517}
}

@ARTICLE{kusumiBJ1993,
  author = {Kusumi, A. and Sako, Y. and Yamamoto, M.},
  title = {Confined lateral diffusion of membrane receptors as studied by single
	particle tracking (nanovid microscopy). Effects of calcium-induced
	differentiation in cultured epithelial cells},
  journal = {Biophys J},
  year = {1993},
  volume = {65},
  pages = {2021-40},
  number = {5},
  month = {Nov},
  note = {94128889 0006-3495 Journal Article},
  abstract = {The movements of E-cadherin, epidermal growth factor receptor, and
	transferrin receptor in the plasma membrane of a cultured mouse keratinocyte
	cell line were studied using both single particle tracking (SPT;
	nanovid microscopy) and fluorescence photobleaching recovery (FPR).
	In the SPT technique, the receptor molecules are labeled with 40
	nm-phi colloidal gold particles, and their movements are followed
	by video-enhanced differential interference contrast microscopy at
	a temporal resolution of 33 ms and at a nanometer-level spatial precision.
	The trajectories of the receptor molecules obtained by SPT were analyzed
	by developing a method that is based on the plot of the mean-square
	displacement against time. Four characteristic types of motion were
	observed: (a) stationary mode, in which the microscopic diffusion
	coefficient is less than 4.6 x 10(-12) cm2/s; (b) simple Brownian
	diffusion mode; (c) directed diffusion mode, in which unidirectional
	movements are superimposed on random motion; and (d) confined diffusion
	mode, in which particles undergoing Brownian diffusion (microscopic
	diffusion coefficient between 4.6 x 10(-12) and 1 x 10(-9) cm2/s)
	are confined within a limited area, probably by the membrane-associated
	cytoskeleton network. Comparison of these data obtained by SPT with
	those obtained by FPR suggests that the plasma membrane is compartmentalized
	into many small domains 300-600 nm in diameter (0.04-0.24 microns2
	in area), in which receptor molecules are confined in the time scale
	of 3-30 s, and that the long-range diffusion observed by FPR can
	occur by successive movements of the receptors to adjacent compartments.
	Calcium-induced differentiation decreases the sum of the percentages
	of molecules in the directed diffusion and the stationary modes outside
	of the cell-cell contact regions on the cell surface (which is proposed
	to be the percentage of E-cadherin bound to the cytoskeleton/membrane-skeleton),
	from approximately 60% to 8% (low- and high-calcium mediums, respectively).},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8298032},
  endnotereftype = {Journal Article},
  keywords = {Animal Biophysics Cadherins/metabolism Calcium/pharmacology Cell Differentiation/drug
	effects Cell Line Cell Membrane/drug effects/metabolism Diffusion
	Fluorescence Gold Colloid Keratinocytes/cytology/drug effects/*metabolism
	Membrane Proteins/metabolism Mice Microscopy, Interference Models,
	Biological Photochemistry Receptor, Epidermal Growth Factor/metabolism
	Receptors, Cell Surface/*metabolism Receptors, Transferrin/metabolism},
  shorttitle = {Confined lateral diffusion of membrane receptors as studied by single
	particle tracking (nanovid microscopy). Effects of calcium-induced
	differentiation in cultured epithelial cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8298032}
}

@ARTICLE{Kusumi1991,
  author = {Kusumi, A. and Tsuji, A. and Murata, M. and Sako, Y. and Yoshizawa,
	A. C. and Kagiwada, S. and Hayakawa, T. and Ohnishi, S.},
  title = {Development of a streak-camera-based time-resolved microscope fluorimeter
	and its application to studies of membrane fusion in single cells},
  journal = {Biochemistry},
  year = {1991},
  volume = {30},
  pages = {6517-27},
  number = {26},
  month = {Jul 2},
  note = {0006-2960 Journal Article},
  abstract = {A time-resolved microscope fluorimeter based on a synchroscan streak
	camera and a fast pulsed laser system has been developed to measure
	the fluorescence lifetime decay under the fluorescence microscope.
	This system allows one to measure the nanosecond fluorescence lifetimes
	of fluorophores in a small spot (0.8-6.3 microns diameter) in single
	cultured cells under a fluorescence microscope, while the cells are
	being viewed under a high-power objective lens. A signal acquisition
	time between a second and a minute was usually sufficient to obtain
	fluorescence decay curves with good quality for 10(3)-10(5) fluorophores
	localized in 1 microns 2 domain. A signal-to-noise ratio better than
	30 was obtained for approximately 30,000 fluorescein-labeled band
	3 molecules in a 2 microns 2 region in a single human erythrocyte
	ghost after signal accumulation for 30 s. The measured lifetimes
	for a variety of fluorescent probes attached to proteins in solution
	and lipids in liposomes showed a good agreement with those measured
	in a cuvette under standard conditions by time-correlated single
	photon counting. With the development of this instrument, microscope
	fluorimetry has become a practical, straightforward, quantitative
	technique for investigation of molecular processes in single cells
	in culture. Time-resolved microscope fluorimetry has been applied
	to observe fusion of liposomes in vitro and that of endosomes in
	single cells by monitoring resonance energy transfer. Inspection
	of individual liposomes and endosomes revealed the extent of fusion
	for each vesicle. Since the use of time-resolved microscope fluorimetry
	eliminates the need for subcellular fractionation or the complex
	correction procedures in steady-state microfluorimetry, it greatly
	simplifies the assay for endosome fusion in vivo. The results showed
	that extensive fusion of sequentially formed endosomes takes place
	all over the cell matrix in cultured cells. This suggests that extensive
	fusion with incoming endosomes takes place in many endosomal compartments,
	possibly sorting organelles, or that the early endosomes fuse with
	the preexisting network of tubular cisternae of the endosomal compartment
	at many points in the network. It is concluded that time-resolved
	microscope fluorimetry is a powerful noninvasive technique for studies
	of in situ biochemistry and biophysics using cells and tissues.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2054350},
  endnotereftype = {Journal Article},
  keywords = {Animals Anion Exchange Protein 1, Erythrocyte/*analysis Cell Line
	Erythrocyte Membrane/*physiology/ultrastructure Fluorescent Dyes
	Human Liposomes *Membrane Fusion Mice Microscopy, Fluorescence/*instrumentation/methods
	Naphthalenesulfonates Organelles/*physiology/ultrastructure Serum
	Albumin, Bovine/chemistry Support, Non-U.S. Gov't Support, U.S. Gov't,
	P.H.S.},
  shorttitle = {Development of a streak-camera-based time-resolved microscope fluorimeter
	and its application to studies of membrane fusion in single cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2054350}
}

@INCOLLECTION{Lakowicz1999,
  author = {Lakowicz, J.R.},
  title = {Principles of fluorescence spectroscopy},
  publisher = {Kluwer Academic/Plenum Publishers},
  year = {1999},
  address = {New York},
  edition = {2nd},
  endnotereftype = {Book Section},
  shorttitle = {Principles of fluorescence spectroscopy}
}

@ARTICLE{Lambert2002,
  author = {Lambert, M. and Choquet, D. and Mege, R. M.},
  title = {Dynamics of ligand-induced, Rac1-dependent anchoring of cadherins
	to the actin cytoskeleton},
  journal = {J Cell Biol},
  year = {2002},
  volume = {157},
  pages = {469-79},
  number = {3},
  month = {Apr 29},
  note = {21977640 0021-9525 Journal Article},
  abstract = {Cadherin receptors are key morphoregulatory molecules during development.
	To dissect their mode of action, we developed an approach based on
	the use of myogenic C2 cells and beads coated with an Ncad-Fc ligand,
	allowing us to mimic cadherin-mediated adhesion. We used optical
	tweezers and video microscopy to investigate the dynamics of N-cadherin
	anchoring within the very first seconds of bead-cell contact. The
	analysis of the bead movement by single-particle tracking indicated
	that N-cadherin molecules were freely diffusive in the first few
	seconds after bead binding. The beads rapidly became diffusion-restricted
	and underwent an oriented rearward movement as a result of N-cadherin
	anchoring to the actin cytoskeleton. The kinetics of anchoring were
	dependent on ligand density, suggesting that it was an inducible
	process triggered by active cadherin recruitment. This anchoring
	was inhibited by the dominant negative form of Rac1, but not that
	of Cdc42. The Rac1 mutant had no effect on cell contact formation
	or cadherin-catenin complex recruitment, but did inhibit actin recruitment.
	Our results suggest that cadherin anchoring to the actin cytoskeleton
	is an adhesion-triggered, Rac1-regulated process enabling the transduction
	of mechanical forces across the cell membrane; they uncover novel
	aspects of the action of cadherins in cell sorting, cell migration,
	and growth cone navigation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11970959},
  endnotereftype = {Journal Article},
  keywords = {Actins/*metabolism Animal Cadherins/genetics/*metabolism *Cell Adhesion/drug
	effects Cell Line Chickens Cytoskeleton/*metabolism Immunoglobulins,
	Fc/genetics/metabolism Kinetics Ligands Lovastatin/pharmacology Mice
	Microspheres Recombinant Fusion Proteins/genetics/metabolism Support,
	Non-U.S. Gov't cdc42 GTP-Binding Protein/metabolism rac1 GTP-Binding
	Protein/*physiology},
  shorttitle = {Dynamics of ligand-induced, Rac1-dependent anchoring of cadherins
	to the actin cytoskeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11970959}
}

@ARTICLE{Lang1986,
  author = {Lang, I. and Scholz, M. and Peters, R.},
  title = {Molecular mobility and nucleocytoplasmic flux in hepatoma cells},
  journal = {J Cell Biol},
  year = {1986},
  volume = {102},
  pages = {1183-90},
  number = {4},
  month = {Apr},
  note = {0021-9525 Journal Article},
  abstract = {Fluorescence microphotolysis (photobleaching) was used to measure,
	in single polyethylene glycol-induced polykaryons of hepatoma tissue
	culture cells, nucleocytoplasmic flux and intracellular mobility
	for a series of dextrans ranging in molecular mass from 3 to 150
	kD and for bovine serum albumin. For the dextrans, the cytoplasmic
	and the nucleoplasmic translational diffusion coefficients amounted
	to approximately 9 and approximately 15%, respectively, of the value
	in dilute buffer. The diffusion coefficients depended inversely on
	molecular radius, suggesting that diffusion was dominated by viscosity
	effects. By application of the Stokes-Einstein equation, cytoplasmic
	and nucleoplasmic viscosities were derived to be 6.6 and 8.1 cP,
	respectively, at 23 degrees C. Between 10 and 37 degrees C nucleoplasmic
	diffusion coefficients increased by approximately 45-85%, whereas
	cytoplasmic diffusion coefficients were virtually independent of
	temperature. In contrast to that of the dextrans, diffusion of bovine
	serum albumin was more restricted. In the cytoplasm the diffusion
	coefficient was approximately 1.5% of the value in dilute buffer;
	in the nucleus albumin was largely immobile. This indicated that
	albumin mobility is dominated by association with immobile cellular
	structures. Nucleocytoplasmic flux of dextrans depended inversely
	on molecular mass with an exclusion limit between 17 and 41 kD. This
	agrees with previous measurements on primary hepatocytes (Peters,
	R., 1984, EMBO [Eur. Mol. Biol. Organ.] J. 3:1831-1836), suggesting
	that in both cell types the nuclear envelope has properties of a
	molecular sieve with a functional pore radius of approximately 55
	A.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2420804},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cell Nucleus/*ultrastructure Cytoplasm/ultrastructure
	Dextrans/diagnostic use Liver Neoplasms, Experimental/*ultrastructure
	Microscopy, Fluorescence Nuclear Envelope/ultrastructure Rats Research
	Support, Non-U.S. Gov't},
  shorttitle = {Molecular mobility and nucleocytoplasmic flux in hepatoma cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2420804}
}

@ARTICLE{Lepock1983,
  author = {Lepock, J. R. and Cheng, K. H. and Campbell, S. D. and Kruuv, J.},
  title = {Rotational diffusion of TEMPONE in the cytoplasm of Chinese hamster
	lung cells},
  journal = {Biophys J},
  year = {1983},
  volume = {44},
  pages = {405-12},
  number = {3},
  month = {Dec},
  note = {0006-3495 Journal Article},
  abstract = {The correlation time for rotational diffusion (tau R) of 2,2,6,6-tetramethyl-4-piperidone-N-oxide
	(TEMPONE) in Chinese hamster lung (V79) cells has been measured.
	For these cells in an isosmotic solution at 20 degrees C, tau R =
	4.18 X 10(-11) s, approximately 3.6 times greater than tau R = 1.17
	X 10(-11) s in water. The relationship between tau R and viscosity
	was investigated in a number of glycerol-water (0-50%) and sucrose-water
	(20-40%) solutions and a constant Stokes-Einstein volume of 44 A3
	was found for TEMPONE in solutions of less than 20% glycerol and
	sucrose. This gives an average shear viscosity (for rotation of a
	small molecule) of 0.038 poise for the cytoplasm. When nonsecular
	terms were used in the calculation of tau R, the activation energies
	for rotation of TEMPONE in the above solutions correlated well with
	the activation energies for shear viscosity. The viscosity increases
	as the cell is shrunk in hypertonic solutions. It also increases
	with decreasing temperature with an activation energy of 3.7 kcal/mol,
	about the same as the activation energy for the viscosity of pure
	water. The rotational correlation times were carefully calculated
	considering inhomogeneous line broadening, non-Lorentzian line shapes,
	the need for accurate tensor values and nonsecular terms.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6318842},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cell Survival/drug effects Cricetulus Cyclic N-Oxides/*diagnostic
	use Cytoplasm/*metabolism Diffusion Electron Spin Resonance Spectroscopy
	Hamsters Lung/*metabolism Rotation *Spin Labels Triacetoneamine-N-Oxyl/*diagnostic
	use Viscosity},
  shorttitle = {Rotational diffusion of TEMPONE in the cytoplasm of Chinese hamster
	lung cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6318842}
}

@ARTICLE{Leymarie1993,
  author = {Leymarie, F. and Levine, M.D.},
  title = {Tracking Deformable Objects in the Plane Using an Active Contour
	Model},
  journal = {IEEE Trans Pattern Anal Machine Intell},
  year = {1993},
  volume = {15},
  pages = {617-634},
  number = {6},
  endnotereftype = {Journal Article},
  shorttitle = {Tracking Deformable Objects in the Plane Using an Active Contour Model}
}

@ARTICLE{Li2003,
  author = {Li, N. and Tourovskaia, A. and Folch, A.},
  title = {Biology on a chip: microfabrication for studying the behavior of
	cultured cells},
  journal = {Crit Rev Biomed Eng},
  year = {2003},
  volume = {31},
  pages = {423-88},
  number = {5-6},
  note = {0278-940X (Print) Journal Article Review},
  abstract = {The ability to culture cells in vitro has revolutionized hypothesis
	testing in basic cell and molecular biology research and has become
	a standard methodology in drug screening and toxicology assays. However,
	the traditional cell culture methodology--consisting essentially
	of the immersion of a large population of cells in a homogeneous
	fluid medium--has become increasingly limiting, both from a fundamental
	point of view (cells in vivo are surrounded by complex spatiotemporal
	microenvironments) and from a practical perspective (scaling up the
	number of fluid handling steps and cell manipulations for high-throughput
	studies in vitro is prohibitively expensive). Microfabrication technologies
	have enabled researchers to design, with micrometer control, the
	biochemical composition and topology of the substrate, the medium
	composition, as well as the type of neighboring cells surrounding
	the microenvironment of the cell. In addition, microtechnology is
	conceptually well suited for the development of fast, low-cost in
	vitro systems that allow for high-throughput culturing and analysis
	of cells under large numbers of conditions. Here we review a variety
	of applications of microfabrication in cell culture studies, with
	an emphasis on the biology of various cell types.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15139302},
  endnotereftype = {Journal Article},
  keywords = {Animals Biosensing Techniques/*instrumentation/methods Cell Adhesion/physiology
	Cell Culture Techniques/*instrumentation/methods *Cell Physiology
	Equipment Design Humans Microelectrodes Microfluidics/instrumentation/*methods
	Micromanipulation/*instrumentation/methods Miniaturization Physical
	Stimulation/instrumentation/*methods},
  shorttitle = {Biology on a chip: microfabrication for studying the behavior of cultured
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15139302}
}

@ARTICLE{Lim2001,
  author = {Lim, W. L. and Chew, Y. T. and Chew, T. C. and Low, H. T.},
  title = {Pulsatile flow studies of a porcine bioprosthetic aortic valve in
	vitro: PIV measurements and shear-induced blood damage},
  journal = {J Biomech},
  year = {2001},
  volume = {34},
  pages = {1417-27},
  number = {11},
  month = {Nov},
  note = {21528865 0021-9290 Journal Article},
  abstract = {A two-dimensional particle image tracking velocimetry (PIV) system
	has been used to map the velocity vector fields and Reynolds stresses
	in the immediate downstream vicinity of a porcine bioprosthetic heart
	valve at the aortic root region in vitro under pulsatile flow conditions.
	Measurements were performed at five different time steps of the systolic
	phase of the cardiac cycle. The velocity vector fields and Reynolds
	stress mappings at different time steps allowed us to chart a time
	history of the stress levels experienced by fluid particles as they
	move across the aortic root. This Lagrangian description of the stresses
	experienced by individual blood cells enabled us to estimate the
	propensity of shear-induced damage to platelets and red blood cells.
	Coupled with flow visualization techniques, the hydrodynamic consequences
	of introducing a porcine bioprosthetic heart valve into the aortic
	root was examined. Although the PIV measurements may lack the accuracy
	of single point measuring systems, the overall view of the flow in
	the aortic root region compensates for the shortcoming.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11672716},
  endnotereftype = {Journal Article},
  keywords = {Animal Aortic Valve Biomechanics Blood Flow Velocity/physiology Blood
	Platelets/pathology Erythrocytes/pathology Heart Valve Prosthesis/*standards
	Hemorheology In Vitro Models, Cardiovascular Pulsatile Flow/*physiology
	Stress, Mechanical Swine Video Recording},
  shorttitle = {Pulsatile flow studies of a porcine bioprosthetic aortic valve in
	vitro: PIV measurements and shear-induced blood damage},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11672716}
}

@ARTICLE{Lindmo1977,
  author = {Lindmo, T. and Steen, H. B.},
  title = {Flow cytometric measurement of the polarization of fluorescence from
	intracellular fluorescein in mammalian cells},
  journal = {Biophys J},
  year = {1977},
  volume = {18},
  pages = {173-87},
  number = {2},
  month = {May},
  note = {0006-3495 Journal Article},
  abstract = {Based on the description of a laboratory-built flow cytometer, the
	necessary modifications of this instrument for the measurement of
	fluorescence polarization are described. At a maximum rate exceeding
	1,000 cells/s, the instrument is capable of measuring simultaneously
	the horizontally and vertically polarized component of the fluorescence
	emitted from stained cells excited with vertically polarized light.
	By mathematical analysis of the accumulated data, the distribution
	of polarization values in the population is obtained. Various sources
	of instrumental error have been investigated. The large aperture
	of the detector optics leads to systematic underestimation of the
	polarization values. Other errors are negligible, and the instrument
	is shown to give results consistent with the theory of fluorescence
	polarization. Application of the instrument is illustrated by experiments
	with mammalian cells exposed to the fluorogenic substrate fluorescein
	diacetate (FDA). The polarization of the fluorescence from intracellular
	fluorescein produced by hydrolysis of FDA is measured, giving information
	on the cytoplasmic microviscosity. It appears that this microviscosity
	is constant over the cell cycle. On the other hand, it is significantly
	affected by the osmolarity of the medium.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=140713},
  endnotereftype = {Journal Article},
  keywords = {*Cell Division Cell Line *Cell Physiology Computers Cytological Techniques
	Cytoplasm/physiology Fluoresceins Optical Rotation Osmolar Concentration
	Rheology Scattering, Radiation Spectrometry, Fluorescence/instrumentation/*methods
	Viscosity},
  shorttitle = {Flow cytometric measurement of the polarization of fluorescence from
	intracellular fluorescein in mammalian cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=140713}
}

@ARTICLE{Lindqvist2002,
  author = {Lindqvist, A. and Dreja, K. and Sward, K. and Hellstrand, P.},
  title = {Effects of oxygen tension on energetics of cultured vascular smooth
	muscle},
  journal = {Am J Physiol Heart Circ Physiol},
  year = {2002},
  volume = {283},
  pages = {H110-7},
  number = {1},
  month = {Jul},
  note = {0363-6135 (Print) Journal Article},
  abstract = {Chronic hypoxia is a clinically important condition known to cause
	vascular abnormalities. To investigate the cellular mechanisms involved,
	we kept rings of a rat tail artery for 4 days in hypoxic culture
	(HC) or normoxic culture (NC) (PO(2) = 14 vs. 110 mmHg) and then
	measured contractility, oxygen consumption (JO(2)), and lactate production
	(J(lac)) in oxygenated medium. Compared with fresh rings, basal ATP
	turnover (J(ATP)) was decreased in HC, but not in NC, with a shift
	from oxidative toward glycolytic metabolism. JO(2) during mitochondrial
	uncoupling was reduced by HC but not by NC. Glycogen stores were
	increased 40-fold by HC and fourfold by NC. Maximum tension in response
	to norepinephrine and the JO(2) versus tension relationship (JO(2)
	vs. high K(+) elicited force) were unaffected by either HC or NC.
	Force transients in response to caffeine were increased in HC, whereas
	intracellular Ca(2+) wave activity during adrenergic stimulation
	was decreased. Protein synthesis rate was reduced by HC. The results
	show that long-term hypoxia depresses basal energy turnover, impairs
	mitochondrial capacity, and alters Ca(2+) homeostasis, but does not
	affect contractile energetics. These alterations may form a basis
	for vascular damage by chronic hypoxia.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12063281},
  endnotereftype = {Journal Article},
  keywords = {Animals Arteries/drug effects/*metabolism Calcium Signaling/physiology
	Cell Hypoxia/*physiology Energy Metabolism/drug effects/*physiology
	Female Glucose/deficiency/metabolism Glycogen/metabolism In Vitro
	Intracellular Fluid/metabolism Lactic Acid/metabolism Muscle, Smooth,
	Vascular/drug effects/*metabolism Norepinephrine/pharmacology Oxygen/*metabolism/pharmacology
	Oxygen Consumption Protein Biosynthesis Rats Research Support, Non-U.S.
	Gov't Tail/blood supply Uncoupling Agents/pharmacology Vasoconstriction/drug
	effects/physiology Vasoconstrictor Agents/pharmacology},
  shorttitle = {Effects of oxygen tension on energetics of cultured vascular smooth
	muscle},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12063281}
}

@ARTICLE{Lindqvist2001,
  author = {Lindqvist, A. and Nilsson, B. O. and Ekblad, E. and Hellstrand, P.},
  title = {Platelet-derived growth factor receptors expressed in response to
	injury of differentiated vascular smooth muscle in vitro: effects
	on Ca2+ and growth signals},
  journal = {Acta Physiol Scand},
  year = {2001},
  volume = {173},
  pages = {175-84},
  number = {2},
  month = {Oct},
  note = {0001-6772 (Print) Journal Article},
  abstract = {Vascular smooth muscle cells (VSMCs) in the intact vascular wall are
	differentiated for contraction, whereas the response to vascular
	injury involves transition towards a synthetic phenotype, with increased
	tendency for proliferation. Platelet-derived growth factor (PDGF)
	is thought to be important for this process. We investigated expression
	and functional coupling of PDGF receptors (PDGFRs) alpha and beta
	in rat tail arterial rings kept in organ culture, in order to capture
	early events in the phenotypic transition. In freshly dissected rings
	no PDGFR immunoreactivity was found in medial VSMCs, whereas PDGFR
	alpha was detected in nerve fibres. After organ culture for 1-4 days
	PDGFR alpha and beta as well as phospholipase Cgamma2 (PLCgamma2),
	known to couple to PDGFR, were expressed in VSMCs within 100 microm
	of the cut ends. Calponin, a marker for the contractile phenotype,
	was decreased near the injured area, suggesting that cells were in
	transition towards synthetic phenotype. In these cells, which showed
	functional Ca2+-release from the sarcoplasmic reticulum, PDGF-AB
	(100 ng x mL(-1)) had no effect on [Ca2+]i, whereas cultured VSMCs
	obtained from explants of rat tail arterial rings responded to PDGF-AB
	with an increase in [Ca2+]i. However, PDGFR within the cultured rings
	coupled to growth signalling pathways, as PDGF-AB caused a tyrphostin
	AG1295-sensitive activation of extracellular signal-regulated kinases
	1 and 2 and of [3H]-thymidine incorporation. Thus, early expression
	of PDGFR in VSMC adjacent to sites of vascular injury coincides with
	signs of dedifferentiation. These receptors couple to growth signalling,
	but do not activate intracellular Ca2+ release.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11683675},
  endnotereftype = {Journal Article},
  keywords = {Animals Calcium/*metabolism Calcium-Binding Proteins/analysis Cell
	Differentiation DNA/biosynthesis Female In Vitro Isoenzymes/metabolism
	MAP Kinase Signaling System/drug effects/physiology Mitogen-Activated
	Protein Kinase 1/metabolism Mitogen-Activated Protein Kinase 3 Mitogen-Activated
	Protein Kinases/metabolism Muscle, Smooth, Vascular/chemistry/*injuries/*metabolism
	Norepinephrine/pharmacology Organ Culture Techniques Phospholipase
	C/metabolism Phospholipase C gamma Platelet-Derived Growth Factor/pharmacology
	Rats Rats, Sprague-Dawley Receptors, Platelet-Derived Growth Factor/analysis/*biosynthesis
	Research Support, Non-U.S. Gov't Vasoconstrictor Agents/pharmacology},
  shorttitle = {Platelet-derived growth factor receptors expressed in response to
	injury of differentiated vascular smooth muscle in vitro: effects
	on Ca2+ and growth signals},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11683675}
}

@ARTICLE{Lindqvist1997,
  author = {Lindqvist, A. and Nilsson, B. O. and Hellstrand, P.},
  title = {Inhibition of calcium entry preserves contractility of arterial smooth
	muscle in culture},
  journal = {J Vasc Res},
  year = {1997},
  volume = {34},
  pages = {103-8},
  number = {2},
  month = {Mar-Apr},
  note = {1018-1172 (Print) Journal Article},
  abstract = {The addition of the growth stimulator fetal calf serum (FCS, 10%)
	to rings of rat tail artery causes an increase in [Ca2+]i, accompanied
	by contraction. This response was inhibited by the calcium entry
	blocker verapamil (1 microM). To investigate the effect of Ca2+ entry
	blockade on growth and contractility, rings of rat tail artery were
	cultured for 4 days in medium with or without FCS and then mounted
	for tension registration and stimulated with noradrenaline (NA) or
	high-K+ solution. In cultured rings growth was quantitated by [3H]-thymidine
	incorporation and increase in protein contents. FCS in the medium
	stimulated DNA synthesis by about 2-fold and increased protein contents
	by about 70%. The growth-stimulated cultured rings developed less
	force than freshly prepared rings (2.2 +/- 0.3 vs. 8.3 +/- 1.0 mN/mm).
	The addition of 1 microM verapamil to the medium during culture increased
	maximal NA-evoked force to 5.0 +/- 0.4 mN/mm but had no effect on
	the increases in DNA synthesis and protein contents. Force developed
	by growth-arrested rings, cultured in the absence of FCS, was not
	different from that of freshly prepared rings (7.2 +/- 0.6 mM/mm).
	Verapamil did not affect maximal force in these rings. Similar responses
	were seen when contraction was elicited by high-K+ solution. We conclude
	that verapamil, present during culture, preserves contractility of
	arterial smooth muscle, and that this effect is not parallel to inhibition
	of growth.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9167642},
  endnotereftype = {Journal Article},
  keywords = {Animals Calcium/*physiology Calcium Channel Blockers/pharmacology
	Cell Division/drug effects Culture Media Female Growth Substances/pharmacology
	In Vitro *Muscle Contraction/drug effects Muscle Proteins/metabolism
	Muscle, Smooth, Vascular/*physiology Norepinephrine/pharmacology
	Potassium/pharmacology Rats Rats, Sprague-Dawley Research Support,
	Non-U.S. Gov't Verapamil/pharmacology},
  shorttitle = {Inhibition of calcium entry preserves contractility of arterial smooth
	muscle in culture},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9167642}
}

@ARTICLE{Lindqvist1999,
  author = {Lindqvist, A. and Nordstrom, I. and Malmqvist, U. and Nordenfelt,
	P. and Hellstrand, P.},
  title = {Long-term effects of Ca(2+) on structure and contractility of vascular
	smooth muscle},
  journal = {Am J Physiol},
  year = {1999},
  volume = {277},
  pages = {C64-73},
  number = {1 Pt 1},
  month = {Jul},
  note = {0002-9513 (Print) Journal Article},
  abstract = {Culture of dispersed smooth muscle cells is known to cause rapid modulation
	from the contractile to the synthetic cellular phenotype. However,
	organ culture of smooth muscle tissue, with maintained extracellular
	matrix and cell-cell contacts, may facilitate maintenance of the
	contractile phenotype. To test the influence of culture conditions,
	structural, functional, and biochemical properties of rat tail arterial
	rings were investigated after culture. Rings were cultured for 4
	days in the absence and presence of 10% FCS and then mounted for
	physiological experiments. Intracellular Ca(2+) concentration ([Ca(2+)](i))
	after stimulation with norepinephrine was similar in rings cultured
	with and without FCS, whereas force development after FCS was decreased
	by >50%. The difference persisted after permeabilization with beta-escin.
	These effects were associated with the presence of vasoconstrictors
	in FCS and were dissociated from its growth-stimulatory action. FCS
	treatment increased lactate production but did not affect ATP, ADP,
	or AMP contents. The contents of actin and myosin were decreased
	by culture but similar for all culture conditions. There was no effect
	of FCS on calponin contents or myosin SM1/SM2 isoform composition,
	nor was there any appearance of nonmuscle myosin. FCS-stimulated
	rings showed evidence of cell degeneration not found after culture
	without FCS or with FCS + verapamil (1 microM) to lower [Ca(2+)](i).
	The decreased force-generating ability after culture with FCS is
	thus associated with increased [Ca(2+)](i) during culture and not
	primarily caused by growth-associated modulation of cells from the
	contractile to the synthetic phenotype.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10409109},
  endnotereftype = {Journal Article},
  keywords = {Animals Arteries/metabolism/physiology/ultrastructure Calcium/metabolism/*physiology
	Calcium Channel Blockers/pharmacology Calcium-Binding Proteins/metabolism
	Capillary Permeability/drug effects Cattle/blood/embryology Escin/pharmacology
	Female Fetal Blood/physiology Intracellular Membranes/metabolism
	Muscle, Smooth, Vascular/metabolism/*physiology/*ultrastructure Myosins/metabolism
	Organ Culture Techniques Rats Rats, Sprague-Dawley Research Support,
	Non-U.S. Gov't Tail/blood supply Time Factors Vasoconstriction/*physiology
	Verapamil/pharmacology},
  shorttitle = {Long-term effects of Ca(2+) on structure and contractility of vascular
	smooth muscle},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10409109}
}

@ARTICLE{Lochner1998,
  author = {Lochner, J. E. and Kingma, M. and Kuhn, S. and Meliza, C. D. and
	Cutler, B. and Scalettar, B. A.},
  title = {Real-time imaging of the axonal transport of granules containing
	a tissue plasminogen activator/green fluorescent protein hybrid},
  journal = {Mol Biol Cell},
  year = {1998},
  volume = {9},
  pages = {2463-76},
  number = {9},
  month = {Sep},
  note = {1059-1524 (Print) Journal Article},
  abstract = {A hybrid protein, tPA/GFP, consisting of rat tissue plasminogen activator
	(tPA) and green fluorescent protein (GFP) was expressed in PC12 cells
	and used to study the distribution, secretory behavior, and dynamics
	of secretory granules containing tPA in living cells with a neuronal
	phenotype. High-resolution images demonstrate that tPA/GFP has a
	growth cone-biased distribution in differentiated cells and that
	tPA/GFP is transported in granules of the regulated secretory pathway
	that colocalize with granules containing secretogranin II. Time-lapse
	images of secretion reveal that secretagogues induce substantial
	loss of cellular tPA/GFP fluorescence, most importantly from growth
	cones. Time-lapse images of the axonal transport of granules containing
	tPA/GFP reveal a surprising complexity to granule dynamics. Some
	granules undergo canonical fast axonal transport; others move somewhat
	more slowly, especially in highly fluorescent neurites. Most strikingly,
	granules traffic bidirectionally along neurites to an extent that
	depends on granule accumulation, and individual granules can reverse
	their direction of motion. The retrograde component of this bidirectional
	transport may help to maintain cellular homeostasis by transporting
	excess tPA/GFP back toward the cell body. The results presented here
	provide a novel view of the axonal transport of secretory granules.
	In addition, the results suggest that tPA is targeted for regulated
	secretion from growth cones of differentiated cells, strategically
	positioning tPA to degrade extracellular barriers or to activate
	other barrier-degrading proteases during axonal elongation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9725906},
  endnotereftype = {Journal Article},
  keywords = {Animals Axonal Transport/*physiology Green Fluorescent Proteins *Image
	Processing, Computer-Assisted/methods Luminescent Proteins/genetics/metabolism
	Mutagenesis PC12 Cells Rats Recombinant Fusion Proteins/genetics/metabolism/secretion
	Research Support, U.S. Gov't, Non-P.H.S. Tissue Plasminogen Activator/genetics/*metabolism/secretion},
  shorttitle = {Real-time imaging of the axonal transport of granules containing a
	tissue plasminogen activator/green fluorescent protein hybrid},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9725906}
}

@ARTICLE{Luby-Phelps2000,
  author = {Luby-Phelps, K.},
  title = {Cytoarchitecture and physical properties of cytoplasm: volume, viscosity,
	diffusion, intracellular surface area},
  journal = {Int Rev Cytol},
  year = {2000},
  volume = {192},
  pages = {189-221},
  note = {0074-7696 Journal Article Review},
  abstract = {Classical biochemistry is founded on several assumptions valid in
	dilute aqueous solutions that are often extended without question
	to the interior milieu of intact cells. In the first section of this
	chapter, we present these assumptions and briefly examine the ways
	in which the cell interior may depart from the conditions of an ideal
	solution. In the second section, we summarize experimental evidence
	regarding the physical properties of the cell cytoplasm and their
	effect on the diffusion and binding of macromolecules and vesicles.
	While many details remain to be worked out, it is clear that the
	aqueous phase of the cytoplasm is crowded rather than dilute, and
	that the diffusion and partitioning of macromolecules and vesicles
	in cytoplasm is highly restricted by steric hindrance as well as
	by unexpected binding interactions. Furthermore, the enzymes of several
	metabolic pathways are now known to be organized into structural
	and functional units with specific localizations in the solid phase,
	and as much as half the cellular protein content may also be in the
	solid phase.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10553280},
  endnotereftype = {Journal Article},
  keywords = {Animals Cytoplasm/*chemistry/*ultrastructure Diffusion Humans Macromolecular
	Substances Models, Biological Proteins/chemistry Research Support,
	U.S. Gov't, Non-P.H.S. Solutions Surface Properties Viscosity Water},
  shorttitle = {Cytoarchitecture and physical properties of cytoplasm: volume, viscosity,
	diffusion, intracellular surface area},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10553280}
}

@ARTICLE{Luby-Phelps1994,
  author = {Luby-Phelps, K.},
  title = {Physical properties of cytoplasm},
  journal = {Curr Opin Cell Biol},
  year = {1994},
  volume = {6},
  pages = {3-9},
  number = {1},
  month = {Feb},
  note = {0955-0674 Journal Article Review},
  abstract = {The physical properties of cytoplasm differ considerably from dilute
	aqueous solutions. Recent research has improved our understanding
	of the properties of the fluid phase and provided a more detailed
	picture of cytoarchitecture and its relation to cytomechanics. Several
	recent holistic models indicate novel directions for future research.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8167023},
  endnotereftype = {Journal Article},
  keywords = {Animals *Cell Physiology Cells/ultrastructure Cytoplasm/*chemistry/physiology/*ultrastructure
	Humans Research Support, Non-U.S. Gov't Research Support, U.S. Gov't,
	Non-P.H.S.},
  shorttitle = {Physical properties of cytoplasm},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8167023}
}

@ARTICLE{Luby-Phelps1993,
  author = {Luby-Phelps, K. and Mujumdar, S. and Mujumdar, R. B. and Ernst, L.
	A. and Galbraith, W. and Waggoner, A. S.},
  title = {A novel fluorescence ratiometric method confirms the low solvent
	viscosity of the cytoplasm},
  journal = {Biophys J},
  year = {1993},
  volume = {65},
  pages = {236-42},
  number = {1},
  month = {Jul},
  note = {0006-3495 Journal Article},
  abstract = {Two homologous indocyanine dyes, Cy3.18 and Cy5.18, can be used as
	a ratio pair for fluorometric determination of solvent viscosity.
	Succinimidyl ester derivatives of these dyes can be attached to inert
	carrier macromolecules, such as Ficoll 70, for measurement of intracellular
	or intravesicular solvent viscosity. When the viscosity of the solvent
	was varied by various methods, the fluorescence intensity ratio (Cy3/Cy5)
	in a mixture of Cy3.18-Ficoll 70 (Cy3F70) and Cy5.18-Ficoll 70 (Cy5F70)
	in solution was found to be solely a function of solvent viscosity
	and was insensitive to other solvent parameters such as dielectric
	constant, temperature, and the ability of the solvent to form hydrogen
	bonds. Most important, it was insensitive to the presence of large
	macromolecules, such as proteins, which increase the shear viscosity
	but have little effect on solvent viscosity. Following microinjection
	into the cytoplasm of living tissue culture cells, no binding of
	Cy3F70 or Cy5F70 to intracellular components was detected by fluorescence
	recovery after photobleaching. Fluorescence intensity ratio imaging
	of Cy3F70 and Cy5F70 in non-motile interphase CV1 and PtK1 cells
	showed that the solvent viscosity of cytoplasm was not significantly
	different from water and showed no spatial variation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8369435},
  endnotereftype = {Journal Article},
  keywords = {Biophysics Cell Line Cytoplasm/*chemistry Fluorescent Dyes Fluorometry/*methods
	Microinjections Microscopy, Fluorescence Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Solvents Viscosity},
  shorttitle = {A novel fluorescence ratiometric method confirms the low solvent viscosity
	of the cytoplasm},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8369435}
}

@ARTICLE{Lucas1981,
  author = {Lucas, B.D. and Kanade, T.},
  title = {An Iterative Image Registration Technique with an Application to
	Stereo Vision},
  journal = {DARPA Proceedings of Imaging Understanding Workshop},
  year = {1981},
  pages = {121-130},
  endnotereftype = {Journal Article},
  shorttitle = {An Iterative Image Registration Technique with an Application to Stereo
	Vision}
}

@ARTICLE{Lussi2006,
  author = {Lussi, J. W. and Falconnet, D. and Hubbell, J. A. and Textor, M.
	and Csucs, G.},
  title = {Pattern stability under cell culture conditions--a comparative study
	of patterning methods based on PLL-g-PEG background passivation},
  journal = {Biomaterials},
  year = {2006},
  volume = {27},
  pages = {2534-41},
  number = {12},
  month = {Apr},
  note = {0142-9612 (Print) Journal Article},
  abstract = {Despite the rapidly increasing number of publications on the fabrication
	and use of micro-patterns for cell studies, comparatively little
	is know about the long-term stability of such patterns under cell
	culture conditions. Here, we report on the long-term stability of
	cellular patterns created by three different patterning techniques:
	selective molecular assembly patterning, micro-contact printing and
	molecular assembly patterning by lift-off. We demonstrate that although
	all three techniques were combined with the same background passivation
	chemistry based on assembly of a PEG-graft copolymer, there are considerable
	differences in the long-term stability between the three different
	pattern types under cell culture conditions. Our results suggest
	that these differences are not cell-dependent but are due to different
	(substrate-dependent) interactions between the patterned substrate,
	the passivating molecule and the serum containing cellular medium.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16364431},
  endnotereftype = {Journal Article},
  shorttitle = {Pattern stability under cell culture conditions--a comparative study
	of patterning methods based on PLL-g-PEG background passivation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16364431}
}

@ARTICLE{Ma2001,
  author = {Ma, L. and Yamada, S. and Wirtz, D. and Coulombe, P. A.},
  title = {A 'hot-spot' mutation alters the mechanical properties of keratin
	filament networks},
  journal = {Nat Cell Biol},
  year = {2001},
  volume = {3},
  pages = {503-6},
  number = {5},
  month = {May},
  note = {21231377 1465-7392 Journal Article},
  abstract = {Keratins 5 and 14 polymerize to form the intermediate filament network
	in the progenitor basal cells of many stratified epithelia including
	epidermis, where it provides crucial mechanical support. Inherited
	mutations in K5 or K14 result in epidermolysis bullosa simplex (EBS),
	a skin-fragility disorder. The impact that such mutations exert on
	the intrinsic mechanical properties of K5/K14 filaments is unknown.
	Here we show, by using differential interference contrast microscopy,
	that a 'hot-spot' mutation in K14 greatly reduces the ability of
	reconstituted mutant filaments to bundle under crosslinking conditions.
	Rheological assays measure similar small-deformation mechanical responses
	for crosslinked solutions of wild-type and mutant keratins. The mutation,
	however, markedly reduces the resilience of crosslinked networks
	against large deformations. Single-particle tracking, which probes
	the local organization of filament networks, shows that the mutant
	polymer exhibits highly heterogeneous structures compared to those
	of wild-type filaments. Our results indicate that the fragility of
	epithelial cells expressing mutant keratin may result from an impaired
	ability of keratin polymers to be crosslinked into a functional network.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11331879},
  endnotereftype = {Journal Article},
  keywords = {Biophysics Cytoskeleton/*chemistry Epidermis/*chemistry Human Hydrogen-Ion
	Concentration Keratin/*chemistry/*genetics/ultrastructure Microscopy,
	Electron *Mutation Mutation, Missense Plasmids/metabolism Polymers/chemistry
	Recombinant Proteins/chemistry Support, U.S. Gov't, Non-P.H.S. Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {A 'hot-spot' mutation alters the mechanical properties of keratin
	filament networks},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11331879}
}

@ARTICLE{Maaser1999,
  author = {Maaser, K. and Wolf, K. and Klein, C. E. and Niggemann, B. and Zanker,
	K. S. and Brocker, E. B. and Friedl, P.},
  title = {Functional hierarchy of simultaneously expressed adhesion receptors:
	integrin alpha2beta1 but not CD44 mediates MV3 melanoma cell migration
	and matrix reorganization within three-dimensional hyaluronan-containing
	collagen matrices},
  journal = {Mol Biol Cell},
  year = {1999},
  volume = {10},
  pages = {3067-79},
  number = {10},
  month = {Oct},
  note = {1059-1524 (Print) Journal Article},
  abstract = {Haptokinetic cell migration across surfaces is mediated by adhesion
	receptors including beta1 integrins and CD44 providing adhesion to
	extracellular matrix (ECM) ligands such as collagen and hyaluronan
	(HA), respectively. Little is known, however, about how such different
	receptor systems synergize for cell migration through three-dimensionally
	(3-D) interconnected ECM ligands. In highly motile human MV3 melanoma
	cells, both beta1 integrins and CD44 are abundantly expressed, support
	migration across collagen and HA, respectively, and are deposited
	upon migration, whereas only beta1 integrins but not CD44 redistribute
	to focal adhesions. In 3-D collagen lattices in the presence or absence
	of HA and cross-linking chondroitin sulfate, MV3 cell migration and
	associated functions such as polarization and matrix reorganization
	were blocked by anti-beta1 and anti-alpha2 integrin mAbs, whereas
	mAbs blocking CD44, alpha3, alpha5, alpha6, or alphav integrins showed
	no effect. With use of highly sensitive time-lapse videomicroscopy
	and computer-assisted cell tracking techniques, promigratory functions
	of CD44 were excluded. 1) Addition of HA did not increase the migratory
	cell population or its migration velocity, 2) blocking of the HA-binding
	Hermes-1 epitope did not affect migration, and 3) impaired migration
	after blocking or activation of beta1 integrins was not restored
	via CD44. Because alpha2beta1-mediated migration was neither synergized
	nor replaced by CD44-HA interactions, we conclude that the biophysical
	properties of 3-D multicomponent ECM impose more restricted molecular
	functions of adhesion receptors, thereby differing from haptokinetic
	migration across surfaces.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10512851},
  endnotereftype = {Journal Article},
  keywords = {Antibodies, Monoclonal/pharmacology Antigens, CD44/*metabolism *Cell
	Movement Chondroitin Sulfates/metabolism Collagen/metabolism Extracellular
	Matrix/*metabolism Fluorescent Antibody Technique Humans Hyaluronic
	Acid/metabolism Image Processing, Computer-Assisted Integrins/*metabolism
	Melanoma/*metabolism Membrane Proteins/*metabolism Microscopy, Video
	Receptors, Collagen Research Support, Non-U.S. Gov't Tumor Cells,
	Cultured},
  shorttitle = {Functional hierarchy of simultaneously expressed adhesion receptors:
	integrin alpha2beta1 but not CD44 mediates MV3 melanoma cell migration
	and matrix reorganization within three-dimensional hyaluronan-containing
	collagen matrices},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10512851}
}

@ARTICLE{MacBeath2000,
  author = {MacBeath, G. and Schreiber, S. L.},
  title = {Printing proteins as microarrays for high-throughput function determination},
  journal = {Science},
  year = {2000},
  volume = {289},
  pages = {1760-3},
  number = {5485},
  month = {Sep 8},
  note = {0036-8075 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Systematic efforts are currently under way to construct defined sets
	of cloned genes for high-throughput expression and purification of
	recombinant proteins. To facilitate subsequent studies of protein
	function, we have developed miniaturized assays that accommodate
	extremely low sample volumes and enable the rapid, simultaneous processing
	of thousands of proteins. A high-precision robot designed to manufacture
	complementary DNA microarrays was used to spot proteins onto chemically
	derivatized glass slides at extremely high spatial densities. The
	proteins attached covalently to the slide surface yet retained their
	ability to interact specifically with other proteins, or with small
	molecules, in solution. Three applications for protein microarrays
	were demonstrated: screening for protein-protein interactions, identifying
	the substrates of protein kinases, and identifying the protein targets
	of small molecules.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10976071},
  endnotereftype = {Journal Article},
  keywords = {Biochemistry/*methods Biotin/metabolism Digoxigenin/metabolism Fluorescence
	Fluorescent Dyes Ligands *Molecular Probe Techniques Phosphorylation
	Piperazines/pharmacology *Protein Binding Protein Folding Protein
	Kinases/*metabolism Proteins/*chemistry/*metabolism Robotics Serum
	Albumin, Bovine},
  shorttitle = {Printing proteins as microarrays for high-throughput function determination},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10976071}
}

@ARTICLE{Mallik2004,
  author = {Mallik, R. and Gross, S. P.},
  title = {Molecular motors: strategies to get along},
  journal = {Curr Biol},
  year = {2004},
  volume = {14},
  pages = {R971-82},
  number = {22},
  month = {Nov 23},
  note = {0960-9822 (Print) Journal Article Review},
  abstract = {The majority of active transport in the cell is driven by three classes
	of molecular motors: the kinesin and dynein families that move toward
	the plus-end and minus-end of microtubules, respectively, and the
	unconventional myosin motors that move along actin filaments. Each
	class of motor has different properties, but in the cell they often
	function together. In this review we summarize what is known about
	their single-molecule properties and the possibilities for regulation
	of such properties. In view of new results on cytoplasmic dynein,
	we attempt to rationalize how these different classes of motors might
	work together as part of the intracellular transport machinery. We
	propose that kinesin and myosin are robust and highly efficient transporters,
	but with somewhat limited room for regulation of function. Because
	cytoplasmic dynein is less efficient and robust, to achieve function
	comparable to the other motors it requires a number of accessory
	proteins as well as multiple dyneins functioning together. This necessity
	for additional factors, as well as dynein's inherent complexity,
	in principle allows for greatly increased control of function by
	taking the factors away either singly or in combination. Thus, dynein's
	contribution relative to the other motors can be dynamically tuned,
	allowing the motors to function together differently in a variety
	of situations.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15556858},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport/physiology Dynein ATPase/*metabolism Kinesin/*metabolism
	Microtubule-Associated Proteins/metabolism Microtubules/metabolism/physiology
	*Models, Biological Molecular Motors/metabolism/*physiology Myosins/*metabolism
	Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Molecular motors: strategies to get along},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15556858}
}

@ARTICLE{Marshall1997,
  author = {Marshall, W. F. and Straight, A. and Marko, J. F. and Swedlow, J.
	and Dernburg, A. and Belmont, A. and Murray, A. W. and Agard, D.
	A. and Sedat, J. W.},
  title = {Interphase chromosomes undergo constrained diffusional motion in
	living cells},
  journal = {Curr Biol},
  year = {1997},
  volume = {7},
  pages = {930-9},
  number = {12},
  month = {Dec 1},
  note = {98044280 0960-9822 Journal Article},
  abstract = {BACKGROUND: Structural studies of fixed cells have revealed that interphase
	chromosomes are highly organized into specific arrangements in the
	nucleus, and have led to a picture of the nucleus as a static structure
	with immobile chromosomes held in fixed positions, an impression
	apparently confirmed by recent photobleaching studies. Functional
	studies of chromosome behavior, however, suggest that many essential
	processes, such as recombination, require interphase chromosomes
	to move around within the nucleus. RESULTS: To reconcile these contradictory
	views, we exploited methods for tagging specific chromosome sites
	in living cells of Saccharomyces cerevisiae with green fluorescent
	protein and in Drosophila melanogaster with fluorescently labeled
	topoisomerase ll. Combining these techniques with submicrometer single-particle
	tracking, we directly measured the motion of interphase chromatin,
	at high resolution and in three dimensions. We found that chromatin
	does indeed undergo significant diffusive motion within the nucleus,
	but this motion is constrained such that a given chromatin segment
	is free to move within only a limited subregion of the nucleus. Chromatin
	diffusion was found to be insensitive to metabolic inhibitors, suggesting
	that it results from classical Brownian motion rather than from active
	motility. Nocodazole greatly reduced chromatin confinement, suggesting
	a role for the cytoskeleton in the maintenance of nuclear architecture.
	CONCLUSIONS: We conclude that chromatin is free to undergo substantial
	Brownian motion, but that a given chromatin segment is confined to
	a subregion of the nucleus. This constrained diffusion is consistent
	with a highly defined nuclear architecture, but also allows enough
	motion for processes requiring chromosome motility to take place.
	These results lead to a model for the regulation of chromosome interactions
	by nuclear architecture.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9382846},
  endnotereftype = {Journal Article},
  keywords = {Animal Chromatin/metabolism Chromosomes/*physiology Drosophila melanogaster/*genetics
	Interphase Microtubules/metabolism Models, Biological Reproducibility
	of Results Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Interphase chromosomes undergo constrained diffusional motion in living
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9382846}
}

@ARTICLE{martinBJ2002,
  author = {Martin, D. S. and Forstner, M. B. and Kas, J. A.},
  title = {Apparent subdiffusion inherent to single particle tracking},
  journal = {Biophys J},
  year = {2002},
  volume = {83},
  pages = {2109-17},
  number = {4},
  month = {Oct},
  note = {22235482 0006-3495 Journal Article},
  abstract = {Subdiffusion and its causes in both in vivo and in vitro lipid membranes
	have become the focus of recent research. We report apparent subdiffusion,
	observed via single particle tracking (SPT), in a homogeneous system
	that only allows normal diffusion (a DMPC monolayer in the fluid
	state). The apparent subdiffusion arises from slight errors in finding
	the actual particle position due to noise inherent in all experimental
	SPT systems. A model is presented that corrects this artifact, and
	predicts the time scales after which the effect becomes negligible.
	The techniques and results presented in this paper should be of use
	in all SPT experiments studying normal and anomalous diffusion.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12324428},
  endnotereftype = {Journal Article},
  keywords = {*Biophysics Diffusion Dimyristoylphosphatidylcholine/chemistry Lipids/*chemistry
	Membranes, Artificial Microscopy/*methods Models, Statistical Models,
	Theoretical Movement Reproducibility of Results Support, Non-U.S.
	Gov't},
  shorttitle = {Apparent subdiffusion inherent to single particle tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12324428}
}

@ARTICLE{Martins2006,
  author = {Martins, G. G. and Kolega, J.},
  title = {Endothelial cell protrusion and migration in three-dimensional collagen
	matrices},
  journal = {Cell Motil Cytoskeleton},
  year = {2006},
  volume = {63},
  pages = {101-15},
  number = {2},
  month = {Feb},
  note = {0886-1544 (Print) Journal Article},
  abstract = {Many cells display dramatically different morphologies when migrating
	in 3D matrices vs. on planar substrata. How these differences arise
	and the implications they have on cell migration are not well understood.
	To address these issues, we examined the locomotive structure and
	behavior of bovine aortic endothelial cells (ECs) either inside 3D
	collagen gels or on 2D surfaces. Using time-lapse imaging, immunofluorescence,
	and confocal microscopy, we identified key morphological differences
	between ECs in 3D collagen gels vs. on 2D substrata, and also demonstrated
	important functional similarities. In 3D matrices, ECs formed cylindrical
	branching pseudopodia, while on 2D substrata they formed wide flat
	lamellae. Three distinct cytoplasmic zones were identified in both
	conditions: (i) a small, F-actin-rich, rapidly moving peripheral
	zone, (ii) a larger, more stable, intermediate zone characterized
	by abundant microtubules and small organelles, and (iii) a locomotively
	inert central zone rich in microtubules, and containing the larger
	organelles. There were few differences between 2D and 3D cells in
	the content and behavior of their peripheral and central zones, whereas
	major differences were seen in the shape and types of movements displayed
	by the intermediate zone, which appeared critical in distributing
	cell-matrix adhesions and directing cytoplasmic flow. This morphological
	and functional delineation of cytoplasmic zones provides a conceptual
	framework for understanding differences in the behavior of cells
	in 3D and 2D environments, and indicates that cytoskeletal structure
	and dynamics in the relatively uncharacterized intermediate zone
	may be particularly important in cell motility in general.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16395720},
  endnotereftype = {Journal Article},
  keywords = {Animals Cattle *Cell Culture Techniques Cell Movement/*physiology
	*Collagen Comparative Study Endothelial Cells/*metabolism/*ultrastructure
	Fluorescent Antibody Technique *Gels Microscopy, Confocal Pseudopodia/ultrastructure
	Research Support, Non-U.S. Gov't},
  shorttitle = {Endothelial cell protrusion and migration in three-dimensional collagen
	matrices},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16395720}
}

@ARTICLE{Mastro1984,
  author = {Mastro, A. M. and Babich, M. A. and Taylor, W. D. and Keith, A. D.},
  title = {Diffusion of a small molecule in the cytoplasm of mammalian cells},
  journal = {Proc Natl Acad Sci U S A},
  year = {1984},
  volume = {81},
  pages = {3414-8},
  number = {11},
  month = {Jun},
  note = {0027-8424 Journal Article},
  abstract = {Electron spin resonance was used to measure the diffusion of a small
	(Mr 170) spin label in the aqueous cytoplasm of mammalian cells.
	Translational and rotational motion were determined from the same
	spectra. Based on measurements made in model systems, it was hypothesized
	that calculations of the apparent viscosity from either rotational
	or translational motion would distinguish between the effects of
	cytoplasmic viscosity or cytoplasmic structure on diffusion. The
	diffusion coefficient calculated from spin label collision frequency,
	averaged 3.3 X 10(-6) cm2/sec in several cell lines. It was greater
	in growing cells and in cells treated with cytochalasin B than in
	quiescent cells. The viscosity of the cytoplasm calculated from the
	translational diffusion coefficient or the rotational correlation
	time was 2.0-3.0 centipoise (1 P = 0.1 Pa X sec), about 2-3 times
	that of the spin label in water. Therefore, over the dimensions measured
	by the technique, 50-100 A, solvent viscosity appears to be the major
	determinant of particle movement in cells under physiological conditions.
	However, when cells were subjected to hypertonic conditions, the
	translational motion decreased by 67%, while the rotational motion
	changed less than 20%. These data suggested that the decrease in
	cell volume under hypertonic conditions was accompanied by an increase
	in cytoplasmic barriers and a decrease in the spacing between existing
	components. In addition, a comparison of reported values for diffusion
	of a variety of molecules in water and in cells indicates that cytoplasmic
	structure plays an important role in the diffusion of proteins such
	as bovine serum albumin.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6328515},
  endnotereftype = {Journal Article},
  keywords = {Animals Cells, Cultured Cytochalasin B/pharmacology Cytoplasm/*physiology
	Cytoskeleton/physiology Diffusion Electron Spin Resonance Spectroscopy
	Mice Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S.
	Gov't, P.H.S. Spin Labels Structure-Activity Relationship Viscosity
	Water},
  shorttitle = {Diffusion of a small molecule in the cytoplasm of mammalian cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6328515}
}

@ARTICLE{Mayer2004,
  author = {Mayer, C. and Maaser, K. and Daryab, N. and Zanker, K. S. and Brocker,
	E. B. and Friedl, P.},
  title = {Release of cell fragments by invading melanoma cells},
  journal = {Eur J Cell Biol},
  year = {2004},
  volume = {83},
  pages = {709-15},
  number = {11-12},
  month = {Dec},
  note = {0171-9335 (Print) Journal Article},
  abstract = {Tumor cell invasion requires coordinated cell adhesion to an extracellular
	matrix (ECM) substrate at the leading edge and concomitant detachment
	at the cell rear. Known detachment mechanisms include the slow sliding
	of focal contacts, the detachment of adhesion receptors by affinity
	and avidity regulation, as well as the shedding of adhesion receptors,
	most notably integrins. In highly invasive melanoma cells migrating
	within 3D collagen matrices, beta1 integrins and CD44 are released
	upon retraction of the trailing edge, together with ripping-off complete
	cell fragments to become deposited along the migration trail of remodeled
	matrix. Cell fragments reach a size up to 12 microm in diameter,
	contain cytoplasm and occasionally polymerized actin enclosed by
	intact cell membrane including surface beta1 integrins, but do not
	include nuclear material. The release of cell fragments was migration
	dependent, as impairment of motility by a blocking anti-beta1 integrin
	antibody also blocked cell particle release. Invasion-associated
	deposition of cell fragments combines the secretory-type release
	of vesicles with a physical mechanism of rear retraction and migration
	efficiency. The deposition of cell fragments may further represent
	a disregulated detachment strategy with implications for neoplastic
	cell behavior, such as the paracrine effects on neighbor cells or
	a negative impact on immune effector cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15679115},
  endnotereftype = {Journal Article},
  keywords = {Antigens, CD29/analysis/*metabolism Antigens, CD44/analysis/*metabolism
	Cell Adhesion/physiology Cell Culture Techniques Cell Line, Tumor
	Cell Movement/*physiology Cytoplasm/ultrastructure Extracellular
	Matrix/physiology Humans Melanoma/immunology/metabolism/*ultrastructure
	Neoplasm Invasiveness/*pathology Protein Transport/physiology Research
	Support, Non-U.S. Gov't},
  shorttitle = {Release of cell fragments by invading melanoma cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15679115}
}

@ARTICLE{McDonald2002,
  author = {McDonald, D. and Vodicka, M. A. and Lucero, G. and Svitkina, T. M.
	and Borisy, G. G. and Emerman, M. and Hope, T. J.},
  title = {Visualization of the intracellular behavior of HIV in living cells},
  journal = {J Cell Biol},
  year = {2002},
  volume = {159},
  pages = {441-52},
  number = {3},
  month = {Nov 11},
  note = {0021-9525 (Print) Journal Article},
  abstract = {To track the behavior of human immunodeficiency virus (HIV)-1 in the
	cytoplasm of infected cells, we have tagged virions by incorporation
	of HIV Vpr fused to the GFP. Observation of the GFP-labeled particles
	in living cells revealed that they moved in curvilinear paths in
	the cytoplasm and accumulated in the perinuclear region, often near
	the microtubule-organizing center. Further studies show that HIV
	uses cytoplasmic dynein and the microtubule network to migrate toward
	the nucleus. By combining GFP fused to the NH2 terminus of HIV-1
	Vpr tagging with other labeling techniques, it was possible to determine
	the state of progression of individual particles through the viral
	life cycle. Correlation of immunofluorescent and electron micrographs
	allowed high resolution imaging of microtubule-associated structures
	that are proposed to be reverse transcription complexes. Based on
	these observations, we propose that HIV uses dynein and the microtubule
	network to facilitate the delivery of the viral genome to the nucleus
	of the cell during early postentry steps of the HIV life cycle.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12417576},
  endnotereftype = {Journal Article},
  keywords = {Antigens, CD4/metabolism Biological Transport/*physiology Cell Line
	Cell Membrane/metabolism Cell Nucleus/metabolism/*virology Cytoplasm/metabolism/*virology
	Cytoskeleton/metabolism/virology Dynein ATPase/metabolism Fluorescent
	Dyes/metabolism Gene Products, gag/metabolism Gene Products, vpr/genetics/*metabolism
	Green Fluorescent Proteins HIV Core Protein p24/metabolism HIV-1/*physiology
	Humans Indicators and Reagents/metabolism Luminescent Proteins/genetics/metabolism
	Macromolecular Substances Microscopy, Fluorescence Microscopy, Video
	Microtubules/metabolism Molecular Motors/metabolism Recombinant Fusion
	Proteins/genetics/*metabolism Research Support, Non-U.S. Gov't Research
	Support, U.S. Gov't, P.H.S. Time Factors Transcription, Genetic Virion/genetics/*physiology},
  shorttitle = {Visualization of the intracellular behavior of HIV in living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12417576}
}

@ARTICLE{Meier2001,
  author = {Meier, J. and Vannier, C. and Serge, A. and Triller, A. and Choquet,
	D.},
  title = {Fast and reversible trapping of surface glycine receptors by gephyrin},
  journal = {Nat Neurosci},
  year = {2001},
  volume = {4},
  pages = {253-60},
  number = {3},
  month = {Mar},
  note = {21127806 1097-6256 Journal Article},
  abstract = {Variations in receptor number at a given synapse are known to contribute
	to synaptic plasticity, but methods used to establish this idea usually
	do not allow for the determination of the dynamics of these phenomena.
	We used single-particle tracking to follow in real time, on the cell
	surface, movements of the glycine receptor (GlyR) with or without
	the GlyR stabilizing protein gephyrin. GlyR alternated within seconds
	between diffusive and confined states. In the absence of gephyrin,
	GlyR were mostly freely diffusing. Gephyrin induced long confinement
	periods spatially associated with submembranous clusters of gephyrin.
	However, even when most receptors were stabilized, they still frequently
	made transitions through the diffusive state. These data show that
	receptor number in a cluster results from a dynamic equilibrium between
	the pools of stabilized and freely mobile receptors. Modification
	of this equilibrium could be involved in regulation of the number
	of receptors at synapses.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11224541},
  endnotereftype = {Journal Article},
  keywords = {Animal Binding Sites COS Cells Carrier Proteins/*metabolism Membrane
	Proteins/*metabolism Microspheres Rats Rats, Sprague-Dawley Receptors,
	Glycine/*metabolism Support, Non-U.S. Gov't Synaptic Membranes/*metabolism
	Time Factors},
  shorttitle = {Fast and reversible trapping of surface glycine receptors by gephyrin},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11224541}
}

@MANUAL{Meijering2004,
  title = {NeuronJ},
  author = {Meijering, Erik},
  year = {2004},
  bdsk-url-1 = {http://www.imagescience.org/meijering/software/neuronj/},
  endnotereftype = {Computer Program},
  shorttitle = {NeuronJ},
  url = {http://www.imagescience.org/meijering/software/neuronj/}
}

@INCOLLECTION{Meijering2008,
  author = {Meijering, Erik and Smal, Ihor and Dzyubachyk, Oleh and Olivo, J.
	C.},
  title = {Time-Lapse Imaging},
  booktitle = {Microscope Image Processing},
  publisher = {Elsevier Academic Press},
  year = {2008},
  pages = {401-440},
  address = {Burlington, MA},
  endnotereftype = {Book Section},
  shorttitle = {Time-Lapse Imaging}
}

@ARTICLE{Mirchev2001,
  author = {Mirchev, R. and Golan, D. E.},
  title = {Single-particle tracking and laser optical tweezers studies of the
	dynamics of individual protein molecules in membranes of intact human
	and mouse red cells},
  journal = {Blood Cells Mol Dis},
  year = {2001},
  volume = {27},
  pages = {143-7},
  number = {1},
  month = {Jan-Feb},
  note = {21257639 1079-9796 Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11358375},
  endnotereftype = {Journal Article},
  keywords = {Animal Erythrocyte Membrane/*chemistry Human Lasers/diagnostic use
	Membrane Proteins/*chemistry Mice Microscopy, Video/instrumentation/methods
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Single-particle tracking and laser optical tweezers studies of the
	dynamics of individual protein molecules in membranes of intact human
	and mouse red cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11358375}
}

@INCOLLECTION{miuraABEB2005,
  author = {Miura, K.},
  title = {Tracking Movement in Cell Biology},
  booktitle = {Advances in Biochemical Engineering/Biotechnology},
  publisher = {Springer Verlag},
  year = {2005},
  editor = {Rietdorf, J.},
  volume = {95},
  pages = {267},
  address = {Heidelberg},
  endnotereftype = {Book Section},
  shorttitle = {Tracking Movement in Cell Biology16080272}
}

@UNPUBLISHED{MiuraVectorFieldPrep,
  author = {Miura, K. and Pepperkok, R.},
  endnotereftype = {Journal Article},
  journal = {in Preparation}
}

@INBOOK{MiuraME2005,
  chapter = {3. Image quantification and analysis},
  pages = {49-72},
  title = {Cell Imaging},
  publisher = {Scion Publishing Ltd.},
  year = {2006},
  editor = {David Stephens},
  author = {Kota Miura and Jens Rietdorf},
  owner = {Kota},
  timestamp = {2011.03.12}
}

@ARTICLE{d6348,
  author = {Miura, K and Siegert, F},
  title = {Light affects cAMP signaling and cell movement activity in Dictyostelium
	discoideum.},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2000},
  volume = {97},
  pages = {2111-2116},
  endnotereftype = {Journal Article},
  keywords = {phototaxis cell-cell signaling 3-DIMENSIONAL SCROLL WAVES PRESTALK
	CELLS CYCLIC-AMP PHOTOTAXIS SLUGS PSEUDOPLASMODIA PROPAGATION MIGRATION},
  shorttitle = {Light affects cAMP signaling and cell movement activity in Dictyostelium
	discoideum.}
}

@INCOLLECTION{Miyawaki2005,
  author = {Miyawaki, A., Nagai, T., Mizuno, H.},
  title = {Engeneering Fluorescent Proteins},
  booktitle = {Microscopy Techniques},
  publisher = {Springer Verlag},
  year = {2005},
  editor = {Rietdorf, J.},
  volume = {95},
  series = {Advances in Biochemical Engineering/Biotechnology},
  pages = {267},
  address = {Heidelberg},
  endnotereftype = {Book Section},
  shorttitle = {Engeneering Fluorescent Proteins}
}

@ARTICLE{Mordant2001,
  author = {Mordant, N. and Metz, P. and Michel, O. and Pinton, J. F.},
  title = {Measurement of Lagrangian velocity in fully developed turbulence},
  journal = {Phys Rev Lett},
  year = {2001},
  volume = {87},
  pages = {214501},
  number = {21},
  month = {Nov 19},
  note = {21604959 0031-9007 Journal Article},
  abstract = {We have developed a new experimental technique to measure the Lagrangian
	velocity of tracer particles in a turbulent flow, based on ultrasonic
	Doppler tracking. This method yields a direct access to the velocity
	of a single particle at a turbulent Reynolds number R(lambda) = 740,
	with two decades of time resolution, below the Lagrangian correlation
	time. We observe that the Lagrangian velocity spectrum has a Lorentzian
	form E(L)(omega) = u(2)(rms)T(L)/[1+(T(L)omega)(2)], in agreement
	with a Kolmogorov-like scaling in the inertial range. The probability
	density functions of the velocity time increments display an intermittency
	which is more pronounced than that of the corresponding Eulerian
	spatial increments.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11736341},
  endnotereftype = {Journal Article},
  shorttitle = {Measurement of Lagrangian velocity in fully developed turbulence},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11736341}
}

@ARTICLE{Morris1993,
  author = {Morris, R. L. and Hollenbeck, P. J.},
  title = {The regulation of bidirectional mitochondrial transport is coordinated
	with axonal outgrowth},
  journal = {J Cell Sci},
  year = {1993},
  volume = {104 ( Pt 3)},
  pages = {917-27},
  month = {Mar},
  note = {0021-9533 (Print) Journal Article},
  abstract = {Although small molecules such as ATP diffuse freely in the cytosol,
	many types of cells nonetheless position their mitochondria in regions
	of intense ATP consumption. We reasoned that in the highly elongated
	axonal processes of growing neurons in culture, the active growth
	cone would form a focus of ATP consumption so distant from the cell
	body as to require the positioning of mitochondria nearby via regulated
	axonal transport. To test this hypothesis, we quantified the distribution
	and transport behavior of mitochondria in live, aerobically respiring
	chick sympathetic neurons. We found that in the distal region of
	actively growing axons, the distribution of mitochondria was highly
	skewed toward the growth cone, with a sevenfold higher density in
	the region immediately adjacent to the growth cone than in the region
	100 microns away. When axonal outgrowth was blocked by substratum-associated
	barriers or mild cytochalasin E treatment, the gradient of mitochondrial
	distribution collapsed as mitochondria exited retrogradely from the
	distal region, becoming uniformly distributed along the axon within
	one hour. Analysis of individual mitochondrial behaviors revealed
	that mitochondrial movement everywhere was bidirectional but balanced
	so that net transport was anterograde in growing axons and retrograde
	in blocked axons. This reversal in net transport derived from two
	separate modulations of mitochondrial movement. First, moving mitochondria
	underwent a transition to a persistently stationary state in the
	region of active growth cones that was reversed when growth cone
	activity was halted. Second, the fraction of time that mitochondria
	spent moving anterogradely was sharply reduced in non-growing axons.
	Together, these could account for the formation of gradients of mitochondria
	in growing axons and their dissipation when outgrowth was blocked.
	This regulated transport behavior was not dependent upon the ability
	of mitochondria to produce ATP. Our data indicate that mitochondria
	possess distinct motor activities for both directions of movement
	and that mitochondrial transport in axons is regulated by both recruitment
	between stationary and moving states, and direct regulation of the
	anterograde motor.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8314882},
  endnotereftype = {Journal Article},
  keywords = {Anaerobiosis Animals Axons/physiology/*ultrastructure Biological Transport/physiology
	Cell Movement/physiology Cells, Cultured Chick Embryo Comparative
	Study Mitochondria/*metabolism Neurons/physiology/ultrastructure
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {The regulation of bidirectional mitochondrial transport is coordinated
	with axonal outgrowth},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8314882}
}

@ARTICLE{Moses2001,
  author = {Moses, S. and Dreja, K. and Lindqvist, A. and Lovdahl, C. and Hellstrand,
	P. and Hultgardh-Nilsson, A.},
  title = {Smooth muscle cell response to mechanical injury involves intracellular
	calcium release and ERK1/ERK2 phosphorylation},
  journal = {Exp Cell Res},
  year = {2001},
  volume = {269},
  pages = {88-96},
  number = {1},
  month = {Sep 10},
  note = {0014-4827 (Print) Journal Article},
  abstract = {We have investigated possible signaling pathways coupled to injury-induced
	ERK1/2 activation and the subsequent initiation of vascular rat smooth
	muscle cell migration and proliferation. Aortic smooth muscle cells
	were cultured to confluency and subjected to in vitro injury under
	serum-free conditions. In fluo-4-loaded cells, injury induced a rapid
	wave of intracellular Ca(2+) release that propagated about 200 microm
	in radius from the injured zone, reached a peak in about 20 s, and
	subsided to the baseline within 2 min. The wave was abolished by
	prior treatment with the sarcoplasmic reticulum ATPase inhibitor
	thapsigargin, but not by omission of extracellular Ca(2+). ERK1/2
	activation reached a peak at 10 min after injury and was inhibited
	by the MEK1 inhibitor PD98059, as well as by thapsigargin, fluphenazine,
	genistein, and the Src inhibitor PP2. These inhibitors also reduced
	[(3)H]thymidine incorporation and migration of cells into the injured
	area determined at 48 h after injury. These results show that mechanical
	injury to vascular smooth muscle cells induces a Ca(2+) wave which
	is dependent on intracellular Ca(2+) release. Furthermore, the injury
	activates ERK1/2 phosphorylation as well as cell migration and replication.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11525642},
  endnotereftype = {Journal Article},
  keywords = {Animals Arteries/*injuries/metabolism/physiopathology Calcimycin/pharmacology
	Calcium/*metabolism Calcium Channel Blockers/pharmacology Calmodulin/antagonists
	& inhibitors/metabolism Cell Division/drug effects/*physiology Cell
	Movement/drug effects/*physiology Cells, Cultured/drug effects/metabolism/secretion
	DNA/biosynthesis/drug effects Egtazic Acid/pharmacology Enzyme Inhibitors/pharmacology
	Flavonoids/pharmacology Fluphenazine/pharmacology Genistein/pharmacology
	Intracellular Fluid/drug effects/metabolism/*secretion Ionomycin/pharmacology
	Ionophores/pharmacology Male Mitogen-Activated Protein Kinases/drug
	effects/*metabolism Muscle, Smooth, Vascular/cytology/drug effects/*metabolism
	Octanols/pharmacology Phosphorylation/drug effects Protein-Tyrosine
	Kinase/antagonists & inhibitors/metabolism Rats Rats, Sprague-Dawley
	Research Support, Non-U.S. Gov't Stress, Mechanical Thapsigargin/pharmacology
	Verapamil/pharmacology},
  shorttitle = {Smooth muscle cell response to mechanical injury involves intracellular
	calcium release and ERK1/ERK2 phosphorylation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11525642}
}

@ARTICLE{Moss2002,
  author = {Moss, W. C. and Irvine, D. J. and Davis, M. M. and Krummel, M. F.},
  title = {Quantifying signaling-induced reorientation of T cell receptors during
	immunological synapse formation},
  journal = {Proc Natl Acad Sci U S A},
  year = {2002},
  volume = {99},
  pages = {15024-9},
  number = {23},
  month = {Nov 12},
  note = {22317449 0027-8424 Journal Article},
  abstract = {Productive T cell recognition of antigen-presenting cells (APCs) is
	normally accompanied by the formation of a cell-cell contact called
	the "immunological synapse." Our understanding of the steps leading
	up to this formation has been limited by the absence of tools for
	analyzing 3D surfaces and surface distributions as they change over
	time. Here we use a 3D fluorescence quantitation method to show that
	T cell receptors are recruited in bulk within the first minute after
	the onset of activation and with velocities ranging from 0.04 to
	0.1 microm/s; a speed significantly greater than unrestricted diffusion.
	Our method reveals a second feature of this reorientation: a conformational
	change as the T cell pushes more total membrane into the interface
	creating a larger contact area for additional receptors. Analysis
	of individual T cell receptor velocities using a single-particle
	tracking method confirms our velocity measurement. This method should
	permit the quantitation of other dynamic membrane events and the
	associated movement of cell-surface molecules.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12415110},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, CD3/immunology Cell Membrane/immunology Cell Movement
	Cell Polarity Clone Cells Genes, Reporter Luminescent Proteins/genetics
	Lymphocyte Activation Mice Mice, Inbred AKR Receptors, Antigen, T-Cell/*immunology
	Signal Transduction/*immunology Support, Non-U.S. Gov't Support,
	U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Synapses/immunology/*physiology
	T-Lymphocytes/*immunology/physiology Transfection},
  shorttitle = {Quantifying signaling-induced reorientation of T cell receptors during
	immunological synapse formation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12415110}
}

@ARTICLE{Mrksich1997,
  author = {Mrksich, M. and Dike, L. E. and Tien, J. and Ingber, D. E. and Whitesides,
	G. M.},
  title = {Using microcontact printing to pattern the attachment of mammalian
	cells to self-assembled monolayers of alkanethiolates on transparent
	films of gold and silver},
  journal = {Exp Cell Res},
  year = {1997},
  volume = {235},
  pages = {305-13},
  number = {2},
  month = {Sep 15},
  note = {0014-4827 (Print) Journal Article Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't,
	P.H.S.},
  abstract = {This paper describes a convenient methodology for patterning substrates
	for cell culture that allows the positions and dimensions of attached
	cells to be controlled. The method uses self-assembled monolayers
	(SAMs) of terminally substituted alkanethiolates (R(CH2)11-15S-)
	adsorbed on optically transparent films of gold or silver to control
	the properties of the substrates. SAMs terminated in methyl groups
	adsorb protein and SAMs terminated in oligo(ethylene glycol) groups
	resist entirely the adsorption of protein. This methodology uses
	microcontact printing (microCP)-an experimentally simple, nonphotolithographic
	process-to pattern the formation of SAMs at the micrometer scale;
	microCP uses an elastomeric stamp having at its surface a pattern
	in relief to transfer an alkanethiol to a surface of gold or silver
	in the same pattern. Patterned SAMs having hydrophobic, methyl-terminated
	lines 10, 30, 60, and 90 microm in width and separated by protein-resistant
	regions 120 microm in width were prepared and coated with fibronectin;
	the protein adsorbed only to the methyl-terminated regions. Bovine
	capillary endothelial cells attached only to the fibronectin-coated,
	methyl-terminated regions of the patterned SAMs. The cells remained
	attached to the SAMs and confined to the pattern of underlying SAMs
	for at least 5-7 days. Because the substrates are optically transparent,
	cells could be visualized by inverted microscopy and by fluorescence
	microscopy after fixing and staining with fluorescein-labeled phalloidin.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9299154},
  endnotereftype = {Journal Article},
  keywords = {Alkanes Animals Capillaries/cytology Cattle *Cell Adhesion Cell Division
	Cells, Cultured Chemistry, Physical/*methods Dimethylpolysiloxanes
	Endothelium, Vascular/cytology Fibronectins *Gold Light Microfilaments
	*Silver *Sulfhydryl Compounds Titanium},
  shorttitle = {Using microcontact printing to pattern the attachment of mammalian
	cells to self-assembled monolayers of alkanethiolates on transparent
	films of gold and silver},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9299154}
}

@ARTICLE{Mueller2008,
  author = {Mueller, F. and Wach, P. and McNally, J. G.},
  title = {Evidence for a common mode of transcription factor interaction with
	chromatin as revealed by improved quantitative fluorescence recovery
	after photobleaching},
  journal = {Biophys J},
  year = {2008},
  volume = {94},
  pages = {3323-39},
  number = {8},
  month = {Apr 15},
  note = {1542-0086 (Electronic) Journal Article Research Support, N.I.H.,
	Intramural},
  abstract = {How site-specific transcription factors scan the genome to locate
	their target sites is a fundamental question in gene regulation.
	The in vivo binding interactions of several different transcription
	factors with chromatin have been investigated recently using quantitative
	fluorescence recovery after photobleaching (FRAP). These analyses
	have yielded significantly different estimates of both the binding
	rates and the number of predicted binding states of the respective
	transcription factors. We show here that these discrepancies are
	not due to fundamental differences among the site-specific transcription
	factors, but rather arise from errors in FRAP modeling. The two principal
	errors are a neglect of diffusion's role and an oversimplified approximation
	of the photobleach profile. Accounting for these errors by developing
	a revised FRAP protocol eliminates most of the previous discrepancies
	in the binding estimates for the three different transcription factors
	analyzed here. The new estimates predict that for each of the three
	transcription factors, approximately 75% of the molecules are freely
	diffusing within the nucleus, whereas the remainder is bound with
	an average residence time of approximately 2.5 s to a single type
	of chromatin binding site. Such consistent predictions for three
	different molecules suggest that many site-specific transcription
	factors may exhibit similar in vivo interactions with native chromatin.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18199661},
  endnotereftype = {Journal Article},
  keywords = {Adenocarcinoma/*metabolism *Algorithms Animals Cell Line, Tumor Chromatin/*metabolism
	Fluorescence Recovery After Photobleaching/*methods Mice Protein
	Binding Protein Interaction Mapping/*methods Transcription Factors/*metabolism},
  shorttitle = {Evidence for a common mode of transcription factor interaction with
	chromatin as revealed by improved quantitative fluorescence recovery
	after photobleaching},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18199661}
}

@ARTICLE{Muller2003,
  author = {Muller, M. and Voros, J. and Csucs, G. and Walter, E. and Danuser,
	G. and Merkle, H. P. and Spencer, N. D. and Textor, M.},
  title = {Surface modification of PLGA microspheres},
  journal = {J Biomed Mater Res A},
  year = {2003},
  volume = {66},
  pages = {55-61},
  number = {1},
  month = {Jul 1},
  note = {1549-3296 (Print) Evaluation Studies Journal Article},
  abstract = {Microspheres made of poly(lactic-co-glycolic acid) (PLGA) are biocompatible
	and biodegradable, rendering them a promising tool in the context
	of drug delivery. However, nonspecific adsorption of plasma proteins
	on PLGA micro- and nanospheres is a main limitation of drug targeting.
	Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG), physisorbed on
	flat metal oxide surfaces, has previously been shown to suppress
	protein adsorption drastically. The goal of our work was to characterize
	the efficiency of the protein repellent character of PLL-g-PEG on
	PLGA microspheres and to show the feasibility of introducing functional
	groups on the PLGA microspheres via functionalized PLL-g-PEG. To
	quantify the adsorbed amount of protein, a semiquantitative method
	that uses confocal laser scanning microscopy (CLSM) was applied.
	The first part of the experiment confirms the feasibility of introducing
	specific functional groups on PLL-g-PEG-coated PLGA microspheres.
	In the second part of the experiment, PLL-g-PEG-coated PLGA microspheres
	show a drastic decrease of adsorbed proteins by two orders of magnitude
	in comparison to uncoated PLGA microspheres. Low protein-binding,
	functionalizable microspheres provide a fundamental basis for the
	design of drug delivery and biosensor systems.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12833431},
  endnotereftype = {Journal Article},
  keywords = {Biosensing Techniques Biotinylation Blood Proteins/*chemistry Coated
	Materials, Biocompatible/*chemistry Comparative Study Drug Carriers
	Feasibility Studies Fibrinogen/chemistry Fibronectins/chemistry Humans
	Immunoglobulin G/chemistry Lactic Acid/*chemistry Materials Testing
	Microspheres Molecular Structure Nephelometry and Turbidimetry Polyethylene
	Glycols/*chemistry Polyglycolic Acid/*chemistry Polylysine/*analogs
	& derivatives/*chemistry Polymers/*chemistry Research Support, Non-U.S.
	Gov't Streptavidin/chemistry Surface Properties},
  shorttitle = {Surface modification of PLGA microspheres},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12833431}
}

@ARTICLE{Murai2004,
  author = {Murai, T. and Miyazaki, Y. and Nishinakamura, H. and Sugahara, K.
	N. and Miyauchi, T. and Sako, Y. and Yanagida, T. and Miyasaka, M.},
  title = {Engagement of CD44 promotes Rac activation and CD44 cleavage during
	tumor cell migration},
  journal = {J Biol Chem},
  year = {2004},
  volume = {279},
  pages = {4541-50},
  number = {6},
  month = {Feb 6},
  note = {0021-9258 Journal Article},
  abstract = {CD44 is a major cell surface adhesion molecule for hyaluronan, a component
	of the extracellular matrix, and is implicated in tumor metastasis
	and invasion. We reported previously that hyaluronan oligosaccharides
	induce CD44 cleavage from tumor cells. Here we show that engagement
	of CD44 promotes CD44 cleavage and tumor cell migration, both of
	which were suppressed by a metalloproteinase inhibitor KB-R7785 and
	tissue inhibitor of metalloproteinases-1 (TIMP-1) but not by TIMP-2.
	We also present evidence that blockade of metalloproteinase-disintegrin
	ADAM10 (a disintegrin and metalloproteinase 10) by RNA interference
	suppresses CD44 cleavage induced by its ligation. Engagement of CD44
	concurrently induced activation of the small GTPase Rac1 and led
	to drastic changes in cell morphology and actin cytoskeleton with
	redistribution of CD44 to newly generated membrane ruffling areas.
	A fluorescence resonance energy transfer approach to visualize GTP-bound
	Rac1 in living cells revealed the localization of the active Rac1
	in the leading edge of the membrane ruffling areas upon ligation
	of CD44. Taken together, our results indicate that the cleavage of
	CD44 catalyzed by ADAM10 is augmented by the intracellular signaling
	elicited by engagement of CD44, through Rac-mediated cytoskeletal
	rearrangement, and suggest that CD44 cleavage contributes to the
	migration and invasion of tumor cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14623895},
  endnotereftype = {Journal Article},
  keywords = {Antibodies, Monoclonal/pharmacology Antigens, CD44/*metabolism Base
	Sequence Cell Line, Tumor Cell Movement/immunology/*physiology DNA,
	Complementary/genetics Enzyme Activation Glioblastoma/*immunology/pathology/*physiopathology
	Human Membrane Proteins/antagonists & inhibitors/genetics/metabolism
	Metalloendopeptidases/antagonists & inhibitors/genetics/metabolism
	Neoplasm Invasiveness/immunology/physiopathology RNA Interference
	RNA, Small Interfering/genetics Recombinant Fusion Proteins/genetics/metabolism
	Signal Transduction Support, Non-U.S. Gov't Tissue Inhibitor-of Metalloproteinase-2/pharmacology
	Tissue-Inhibitor of Metalloproteinase-1/pharmacology rac1 GTP-Binding
	Protein/genetics/*metabolism},
  shorttitle = {Engagement of CD44 promotes Rac activation and CD44 cleavage during
	tumor cell migration},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14623895}
}

@ARTICLE{muraseBJ2004,
  author = {Murase, K. and Fujiwara, T. and Umemura, Y. and Suzuki, K. and Iino,
	R. and Yamashita, H. and Saito, M. and Murakoshi, H. and Ritchie,
	K. and Kusumi, A.},
  title = {Ultrafine membrane compartments for molecular diffusion as revealed
	by single molecule techniques},
  journal = {Biophys J},
  year = {2004},
  volume = {86},
  pages = {4075-93},
  number = {6},
  month = {Jun},
  note = {0006-3495 Journal Article},
  abstract = {Plasma membrane compartments, delimited by transmembrane proteins
	anchored to the membrane skeleton (anchored-protein picket model),
	would provide the membrane with fundamental mosaicism because they
	would affect the movement of practically all molecules incorporated
	in the cell membrane. Understanding such basic compartmentalized
	structures of the cell membrane is critical for further studies of
	a variety of membrane functions. Here, using both high temporal-resolution
	single particle tracking and single fluorescent molecule video imaging
	of an unsaturated phospholipid, DOPE, we found that plasma membrane
	compartments generally exist in various cell types, including CHO,
	HEPA-OVA, PtK2, FRSK, HEK293, HeLa, T24 (ECV304), and NRK cells.
	The compartment size varies from 30 to 230 nm, whereas the average
	hop rate of DOPE crossing the boundaries between two adjacent compartments
	ranges between 1 and 17 ms. The probability of passing a compartment
	barrier when DOPE is already at the boundary is also cell-type dependent,
	with an overall variation by a factor of approximately 7. These results
	strongly indicate the necessity for the paradigm shift of the concept
	on the plasma membrane: from the two-dimensional fluid continuum
	model to the compartmentalized membrane model in which its constituent
	molecules undergo hop diffusion over the compartments.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15189902},
  endnotereftype = {Journal Article},
  keywords = {Animals CHO Cells Cell Compartmentation/*physiology Cell Membrane/*metabolism
	Cells, Cultured Cholesterol/chemistry Cricetulus Cytoskeleton/*metabolism
	Extracellular Matrix/metabolism Fluorescent Dyes/chemistry Hamsters
	Hela Cells Humans *Models, Theoretical Phosphatidylethanolamines/*chemistry
	Rats},
  shorttitle = {Ultrafine membrane compartments for molecular diffusion as revealed
	by single molecule techniques},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15189902}
}

@ARTICLE{Murray2000,
  author = {Murray, J. W. and Bananis, E. and Wolkoff, A. W.},
  title = {Reconstitution of ATP-dependent movement of endocytic vesicles along
	microtubules in vitro: an oscillatory bidirectional process},
  journal = {Mol Biol Cell},
  year = {2000},
  volume = {11},
  pages = {419-33},
  number = {2},
  month = {Feb},
  note = {1059-1524 (Print) Journal Article},
  abstract = {We have previously used the asialoglycoprotein receptor system to
	elucidate the pathway of hepatocytic processing of ligands such as
	asialoorosomucoid (ASOR). These studies suggested that endocytic
	vesicles bind to and travel along microtubules under the control
	of molecular motors such as cytoplasmic dynein. We now report reconstitution
	of this process in vitro with the use of a microscope assay to observe
	the interaction of early endocytic vesicles containing fluorescent
	ASOR with fluorescent microtubules. We find that ASOR-containing
	endosomes bind to microtubules and translocate along them in the
	presence of ATP. This represents the first time that mammalian endosomes
	containing a well-characterized ligand have been directly observed
	to translocate on microtubules in vitro. The endosome movement does
	not require cytosol or exogenous motor protein, is oscillatory, and
	is directed toward the plus and minus ends at equal frequencies.
	We also observe endosomes being stretched in opposite directions
	along microtubules, suggesting that microtubules could provide a
	mechanical basis for endocytic sorting events. The movement of endosomes
	in vitro is consistent with the hypothesis that microtubules actively
	participate in the sorting and distribution of endocytic contents.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10679004},
  endnotereftype = {Journal Article},
  keywords = {Adenosine Triphosphate/*metabolism Adenosinetriphosphatase/antagonists
	& inhibitors/metabolism Adenylyl Imidodiphosphate/pharmacology Animals
	Asialoglycoprotein Receptor Biological Transport, Active/drug effects
	Centrifugation, Density Gradient Endosomes/drug effects/*metabolism
	Fluorescence Kinetics Liver/cytology/enzymology Magnetic Resonance
	Spectroscopy Male Microtubules/chemistry/drug effects/*metabolism
	Molecular Motors/metabolism Movement/drug effects Peripheral Nervous
	System/cytology/enzymology Rats Rats, Sprague-Dawley Receptors, Cell
	Surface/metabolism Research Support, U.S. Gov't, P.H.S. Vanadates/pharmacology},
  shorttitle = {Reconstitution of ATP-dependent movement of endocytic vesicles along
	microtubules in vitro: an oscillatory bidirectional process},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10679004}
}

@ARTICLE{Nagel1983,
  author = {Nagel, H. H.},
  title = {Displacement Vectors Derived from Second-Order Intensity Variations
	in Image Sequences},
  journal = {Computer Vision, Graphics, and Image Processing},
  year = {1983},
  volume = {21},
  pages = {85-117},
  endnotereftype = {Journal Article},
  shorttitle = {Displacement Vectors Derived from Second-Order Intensity Variations
	in Image Sequences}
}

@ARTICLE{Nakata1998,
  author = {Nakata, T. and Terada, S. and Hirokawa, N.},
  title = {Visualization of the dynamics of synaptic vesicle and plasma membrane
	proteins in living axons},
  journal = {J Cell Biol},
  year = {1998},
  volume = {140},
  pages = {659-74},
  number = {3},
  month = {Feb 9},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Newly synthesized membrane proteins are transported by fast axonal
	flow to their targets such as the plasma membrane and synaptic vesicles.
	However, their transporting vesicles have not yet been identified.
	We have successfully visualized the transporting vesicles of plasma
	membrane proteins, synaptic vesicle proteins, and the trans-Golgi
	network residual proteins in living axons at high resolution using
	laser scan microscopy of green fluorescent protein-tagged proteins
	after photobleaching. We found that all of these proteins are transported
	by tubulovesicular organelles of various sizes and shapes that circulate
	within axons from branch to branch and switch the direction of movement.
	These organelles are distinct from the endosomal compartments and
	constitute a new entity of membrane organelles that mediate the transport
	of newly synthesized proteins from the trans-Golgi network to the
	plasma membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9456325},
  endnotereftype = {Journal Article},
  keywords = {Animals *Axonal Transport Axons/*metabolism/ultrastructure Cells,
	Cultured Endosomes/metabolism/ultrastructure GAP-43 Protein/metabolism
	Ganglia, Spinal Golgi Apparatus/metabolism/ultrastructure Green Fluorescent
	Proteins Luminescent Proteins Membrane Proteins/*metabolism Mice
	Mice, Inbred C57BL Microscopy, Confocal Microscopy, Immunoelectron
	Nerve Tissue Proteins/metabolism Organelles/*metabolism/ultrastructure
	Proto-Oncogene Proteins/metabolism Receptor Protein-Tyrosine Kinases/metabolism
	Receptor, trkA Receptors, Nerve Growth Factor/metabolism Recombinant
	Fusion Proteins/metabolism Research Support, Non-U.S. Gov't Synaptic
	Vesicles/*metabolism/ultrastructure Synaptophysin/*metabolism Synaptosomal-Associated
	Protein 25},
  shorttitle = {Visualization of the dynamics of synaptic vesicle and plasma membrane
	proteins in living axons},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9456325}
}

@ARTICLE{Nelissen2000,
  author = {Nelissen, J. M. and Peters, I. M. and de Grooth, B. G. and van Kooyk,
	Y. and Figdor, C. G.},
  title = {Dynamic regulation of activated leukocyte cell adhesion molecule-mediated
	homotypic cell adhesion through the actin cytoskeleton},
  journal = {Mol Biol Cell},
  year = {2000},
  volume = {11},
  pages = {2057-68},
  number = {6},
  month = {Jun},
  note = {20307396 1059-1524 Journal Article},
  abstract = {Restricted expression of activated leukocyte cell adhesion molecule
	(ALCAM) by hematopoietic cells suggests an important role in the
	immune system and hematopoiesis. To get insight into the mechanisms
	that control ALCAM-mediated adhesion we have investigated homotypic
	ALCAM-ALCAM interactions. Here, we demonstrate that the cytoskeleton
	regulates ALCAM-mediated cell adhesion because inhibition of actin
	polymerization by cytochalasin D (CytD) strongly induces homotypic
	ALCAM-ALCAM interactions. This induction of cell adhesion is likely
	due to clustering of ALCAM at the cell surface, which is observed
	after CytD treatment. Single-particle tracking demonstrated that
	the lateral mobility of ALCAM in the cell membrane is increased 30-fold
	after CytD treatment. In contrast, both surface distribution and
	adhesion of a glycosylphosphatidylinositol (GPI)-anchored ALCAM mutant
	are insensitive to CytD, despite the increase in lateral mobility
	of GPI-ALCAM upon CytD treatment. This demonstrates that clustering
	of ALCAM is essential for cell adhesion, whereas enhanced diffusion
	of ALCAM alone is not sufficient for cluster formation. In addition,
	upon ligand binding, both free diffusion and the freely dragged distance
	of wild-type ALCAM, but not of GPI-ALCAM, are reduced over time,
	suggesting strengthening of the cytoskeleton linkage. From these
	findings we conclude that activation of ALCAM-mediated adhesion is
	dynamically regulated through actin cytoskeleton-dependent clustering.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10848629},
  endnotereftype = {Journal Article},
  keywords = {Actins/*metabolism Activated-Leukocyte Cell Adhesion Molecule/*metabolism
	Animal Cell Adhesion/*physiology Cell Membrane/metabolism Cytochalasin
	D/pharmacology Cytoskeleton/metabolism Energy Metabolism Glycosylphosphatidylinositols/metabolism
	Human K562 Cells Mice Mice, Inbred BALB C Temperature Time Factors},
  shorttitle = {Dynamic regulation of activated leukocyte cell adhesion molecule-mediated
	homotypic cell adhesion through the actin cytoskeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10848629}
}

@ARTICLE{AmerSocCellBiology,
  author = {Nelson, C. M. and Pirone, D. M. and Tan, J. L. and Chen, C. S.},
  title = {Vascular endothelial-cadherin regulates cytoskeletal tension, cell
	spreading, and focal adhesions stimulating RhoA},
  journal = {Molecular Biology of the Cell},
  year = {2004},
  volume = {15},
  pages = {2943-2953},
  number = {6},
  month = {JUN},
  note = {Times Cited: 7 Article English Cited References Count: 65 825sj},
  abstract = {Changes in vascular endothelial (VE)-cadherin-mediated cell-cell adhesion
	and integrin-mediated cell-matrix adhesion coordinate to affect the
	physical and mechanical rearrangements of the endothelium, although
	the mechanisms for such cross talk remain undefined. Herein, we describe
	the regulation of focal adhesion formation and cytoskeletal tension
	by intercellular VE-cadherin engagement, and the molecular mechanism
	by which this occurs. Increasing the density of endothelial cells
	to increase cell-cell contact decreased focal adhesions by decreasing
	cell spreading. This contact inhibition of cell spreading was blocked
	by disrupting VE-cadherin engagement with an adenovirus encoding
	dominant negative VE-cadherin. When changes in cell spreading were
	prevented by culturing cells on a micropatterned substrate, VE-cadherin-mediated
	cell-cell contact paradoxically increased focal adhesion formation.
	We show that VE-cadherin engagement mediates each of these effects
	by inducing both a transient and sustained activation of RhoA. Both
	the increase and decrease in cell-matrix adhesion were blocked by
	disrupting intracellular tension and signaling through the Rho-ROCK
	pathway. In all, these findings demonstrate that VE-cadherin signals
	through RhoA and the actin cytoskeleton to cross talk with cell-matrix
	adhesion and thereby define a novel pathway by which cell-cell contact
	alters the global mechanical and functional state of cells.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000221778300038},
  endnotereftype = {Journal Article},
  keywords = {binding protein-rho contact formation family gtpases terminal differentiation
	molecular-mechanisms adherens junction tyrosine kinase stress fibers
	n-cadherin membrane},
  shorttitle = {Vascular endothelial-cadherin regulates cytoskeletal tension, cell
	spreading, and focal adhesions stimulating RhoA},
  url = {<Go to ISI>://000221778300038}
}

@ARTICLE{AmerChemicalSoc,
  author = {Nelson, C. M. and Raghavan, S. and Tan, J. L. and Chen, C. S.},
  title = {Degradation of micropatterned surfaces by cell-dependent and -independent
	processes},
  journal = {Langmuir},
  year = {2003},
  volume = {19},
  pages = {1493-1499},
  number = {5},
  month = {MAR 4},
  note = {Times Cited: 18 Article English Cited References Count: 34 651fj},
  abstract = {This paper describes a study to determine the role of active cellular
	processes in the initial patterning and eventual degradation of different
	micropatterned substrates. We compared the effects of serum and cell
	type on the ability of cells to crawl onto the nonadhesive regions
	of a variety of patterned substrates. Cells initially patterned in
	the presence of serum onto substrates manufactured using agarose,
	pluronics, hexa(ethylene glycol), or polyacrylamide as the nonadhesive.
	While polyacrylamide remained inert and patterned cells for at least
	28 days, agarose and pluronics degraded by gradual desorption of
	the nonadhesive from the surface independently of the presence of
	cells. Hexa(ethylene glycol) degraded by a time-dependent mechanism
	that could be accelerated by cell-dependent oxidative processes.
	In contrast to the other substrates studied, bovine serum albumin
	(BSA) patterned cells only under serum-free conditions. The serum
	did not displace BSA from the surface but instead activated cell-secreted
	proteases that led to degradation of the substrate. These findings
	illustrate the importance of specific cellular and noncellular processes
	in the failure of different nonadhesive chemistries commonly used
	to pattern cells.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000181309600008},
  endnotereftype = {Journal Article},
  keywords = {self-assembled monolayers mammalian-cells matrix metalloproteinases
	alcohol-dehydrogenase geometric control in-vitro protein shape attachment
	gold},
  shorttitle = {Degradation of micropatterned surfaces by cell-dependent and -independent
	processes},
  url = {<Go to ISI>://000181309600008}
}

@ARTICLE{Ng2003,
  author = {Ng, Y. K. and Lu, X. and Gulacsi, A. and Han, W. and Saxton, M. J.
	and Levitan, E. S.},
  title = {Unexpected Mobility Variation among Individual Secretory Vesicles
	Produces an Apparent Refractory Neuropeptide Pool},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {4127-34},
  number = {6},
  month = {Jun},
  note = {22654370 0006-3495 Journal Article},
  abstract = {Most stored neuropeptide cannot be released from nerve terminals suggesting
	the existence of a refractory pool of dense core vesicles (DCVs).
	Past fluorescence photobleaching recovery, single particle tracking
	and release experiments suggested that the refractory neuropeptide
	pool corresponds to a distinct immobile fraction of cytoplasmic DCVs.
	However, tracking of hundreds of individual green fluorescent protein-labeled
	neuropeptidergic vesicles by wide-field or evanescent-wave microscopy
	shows that a separate immobile fraction is not evident. Instead,
	the DCV diffusion coefficient (D) distribution is unusually broad
	and asymmetric. Furthermore, the distribution shifts with a release
	facilitator. This unexpected variation, which could reflect heterogeneity
	among vesicles or in their medium, is shown to generate the appearance
	of a regulated refractory neuropeptide pool.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12770915},
  endnotereftype = {Journal Article},
  shorttitle = {Unexpected Mobility Variation among Individual Secretory Vesicles
	Produces an Apparent Refractory Neuropeptide Pool},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12770915}
}

@ARTICLE{Niessen1997,
  author = {Niessen, W. J. and Duncan, J. S. and Nielsen, M. and Florack, L.
	M. J. and ter Haar Romeny, B. M. and Vierger, M. A.},
  title = {A multiscale approach to image sequence analysis},
  journal = {Comput Vis Imag Understand},
  year = {1997},
  volume = {65},
  pages = {259-268},
  number = {2},
  endnotereftype = {Journal Article},
  shorttitle = {A multiscale approach to image sequence analysis}
}

@ARTICLE{Nomura1991,
  author = {Nomura, A. and Miike, H. and Koga, K.},
  title = {Field theory approach for determining optical flow},
  journal = {Pattern Recog. Lett.},
  year = {1991},
  volume = {12},
  pages = {183-190},
  endnotereftype = {Journal Article},
  shorttitle = {Field theory approach for determining optical flow}
}

@ARTICLE{oberBJ2004,
  author = {Ober, R. J. and Ram, S. and Ward, E. S.},
  title = {Localization accuracy in single-molecule microscopy},
  journal = {Biophys J},
  year = {2004},
  volume = {86},
  pages = {1185-200},
  number = {2},
  month = {Feb},
  note = {0006-3495 Evaluation Studies Journal Article},
  abstract = {One of the most basic questions in single-molecule microscopy concerns
	the accuracy with which the location of a single molecule can be
	determined. Using the Fisher information matrix it is shown that
	the limit of the localization accuracy for a single molecule is given
	by, lambda(em)/2pi n(a) square root of gammaAt, where lambda(em),
	n(a), gamma, A, and t denote the emission wavelength of the single
	molecule, the numerical aperture of the objective, the efficiency
	of the optical system, the emission rate of the single molecule and
	the acquisition time, respectively. Using Monte Carlo simulations
	it is shown that estimation algorithms can come close to attaining
	the limit given in the expression. Explicit quantitative results
	are also provided to show how the limit of the localization accuracy
	is reduced by factors such as pixelation of the detector and noise
	sources in the detection system. The results demonstrate what is
	achievable by single-molecule microscopy and provide guidelines for
	experimental design.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14747353},
  endnotereftype = {Journal Article},
  keywords = {Biopolymers/analysis/*chemistry/*metabolism Computer Simulation Image
	Enhancement/*methods Image Interpretation, Computer-Assisted/*methods
	Microscopy, Fluorescence/*methods *Models, Biological *Models, Chemical
	Models, Statistical Reproducibility of Results Research Support,
	U.S. Gov't, P.H.S. Sensitivity and Specificity Stochastic Processes
	Tissue Distribution},
  shorttitle = {Localization accuracy in single-molecule microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14747353}
}

@ARTICLE{Oddershede2002,
  author = {Oddershede, L. and Dreyer, J. K. and Grego, S. and Brown, S. and
	Berg-Sorensen, K.},
  title = {The motion of a single molecule, the lambda-receptor, in the bacterial
	outer membrane},
  journal = {Biophys J},
  year = {2002},
  volume = {83},
  pages = {3152-61},
  number = {6},
  month = {Dec},
  note = {22383495 0006-3495 Evaluation Studies Journal Article Validation
	Studies},
  abstract = {Using optical tweezers and single particle tracking, we have revealed
	the motion of a single protein, the lambda-receptor, in the outer
	membrane of living Escherichia coli bacteria. We genetically modified
	the lambda-receptor placing a biotin on an extracellular site of
	the receptor in vivo. The efficiency of this in vivo biotinylation
	is very low, thus enabling the attachment of a streptavidin-coated
	bead binding specifically to a single biotinylated lambda-receptor.
	The bead was used as a handle for the optical tweezers and as a marker
	for the single particle tracking routine. We propose a model that
	allows extraction of the motion of the protein from measurements
	of the mobility of the bead-molecule complex; these results are equally
	applicable to analyze bead-protein complexes in other membrane systems.
	Within a domain of radius approximately 25 nm, the receptor diffuses
	with a diffusion constant of (1.5 +/- 1.0) x 10(-9) cm(2)/s and sits
	in a harmonic potential as if it were tethered by an elastic spring
	of spring constant of ~1.0 x 10(-2) pN/nm to the bacterial membrane.
	The purpose of the protein motion might be to facilitate transport
	of maltodextrins through the outer bacterial membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12496085},
  endnotereftype = {Journal Article},
  keywords = {Bacterial Outer Membrane Proteins/chemistry/*physiology Biotin/chemistry/genetics
	Biotinylation/methods Comparative Study Computer Simulation Elasticity
	Escherichia coli/chemistry/*physiology/ultrastructure Lasers Micromanipulation/instrumentation/methods
	Microspheres *Models, Biological Models, Chemical *Motion Nanotechnology/instrumentation/methods
	Optics/instrumentation Particle Size Protein Conformation Receptors,
	Virus/chemistry/genetics/*physiology Recombinant Proteins/chemistry/metabolism
	Streptavidin/chemistry Stress, Mechanical Support, Non-U.S. Gov't},
  shorttitle = {The motion of a single molecule, the lambda-receptor, in the bacterial
	outer membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12496085}
}

@ARTICLE{Oida1993,
  author = {Oida, T. and Sako, Y. and Kusumi, A.},
  title = {Fluorescence lifetime imaging microscopy (flimscopy). Methodology
	development and application to studies of endosome fusion in single
	cells},
  journal = {Biophys J},
  year = {1993},
  volume = {64},
  pages = {676-85},
  number = {3},
  month = {Mar},
  note = {0006-3495 Journal Article},
  abstract = {A new method of fluorescence microscopy for cell imaging has been
	developed that takes advantage of the spatial variations of fluorescence
	lifetimes in single cells as a source of image contrast, and thus
	it is named "fluorescence lifetime imaging microscopy (flimscopy)".
	Since time-resolved fluorescence measurements are sensitive to molecular
	dynamics and interactions, flimscopy allows the molecular information
	to be visualized in single cells. In flimscopy measurements, several
	(nanosecond) time-resolved fluorescence images of a sample are obtained
	at various delay times after pulsed laser excitation of the microscope's
	entire field of view. Lifetimes are calculated pixel-by-pixel from
	these time-resolved images, and the spatial variations of the lifetimes
	are then displayed in a pseudocolor format (flimscopy image). The
	total data acquisition time needed to obtain a flimscopy image with
	the diffraction-limited spatial resolution (approximately 250 nm)
	is decreased to just approximately 30 s for approximately 300 fluorescent
	molecules/micron2. This was achieved by developing a high-frequency
	(400 kHz) nanosecond-gating (9 ns full width at half height)-signal
	accumulation system. This technique allows the extent of resonance
	energy transfer to be visualized in single living cells, and is free
	from the errors due to variations in path length, light scattering,
	and the number of fluorophores that necessitate complex corrections
	in steady-state microfluorometry and fluorescence ratio imaging microscopy.
	Flimscopy was applied here to observe the extent of fusion of individual
	endosomes in single cells. Results revealed the occurrence of extensive
	fusion between primary endocytic vesicles and/or sorting endosomes,
	thereby raising the possibility that the biogenesis of sorting endosomes
	involves multiple fusions of primary endocytic vesicles.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8471720},
  endnotereftype = {Journal Article},
  keywords = {Animals Biophysics Cell Line Comparative Study Endocytosis/*physiology
	Lasers Liposomes Membrane Fusion/physiology Microscopy, Fluorescence/*methods/statistics
	& numerical data Rats Sensitivity and Specificity Time Factors},
  shorttitle = {Fluorescence lifetime imaging microscopy (flimscopy). Methodology
	development and application to studies of endosome fusion in single
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8471720}
}

@ARTICLE{Oosawa1996,
  author = {Oosawa, F.},
  title = {Biophysics: fifty years after Schrodinger},
  journal = {Adv Biophys},
  year = {1996},
  volume = {32},
  pages = {1-15},
  note = {0065-227x Journal Article Review},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8781282},
  endnotereftype = {Journal Article},
  keywords = {Animals Biology *Biophysics Chromosomes Genes Muscle Contraction Publishing
	Textbooks},
  shorttitle = {Biophysics: fifty years after Schrodinger},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8781282}
}

@ARTICLE{Oudenaarden1999,
  author = {van Oudenaarden, A. and Theriot, J. A.},
  title = {Cooperative symmetry-breaking by actin polymerization in a model
	for cell motility},
  journal = {Nat Cell Biol},
  year = {1999},
  volume = {1},
  pages = {493-9},
  number = {8},
  month = {Dec},
  note = {1465-7392 Journal Article},
  abstract = {Polymerizing networks of actin filaments are capable of exerting significant
	mechanical forces, used by eukaryotic cells and their prokaryotic
	pathogens to change shape or to move. Here we show that small beads
	coated uniformly with a protein that catalyses actin polymerization
	are initially surrounded by symmetrical clouds of actin filaments.
	This symmetry is broken spontaneously, after which the beads undergo
	directional motion. We have developed a stochastic theory, in which
	each actin filament is modelled as an elastic brownian ratchet, that
	quantitatively accounts for the observed emergent symmetry-breaking
	behaviour. Symmetry-breaking can only occur for polymers that have
	a significant subunit off-rate, such as the biopolymers actin and
	tubulin.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10587645},
  endnotereftype = {Journal Article},
  keywords = {Actins/*metabolism Animals Biopolymers/metabolism Cell Extracts *Cell
	Movement *Computer Simulation Diffusion Elasticity Kinetics Listeria
	monocytogenes Microspheres *Models, Biological Motion Polystyrenes
	Protein Binding Research Support, Non-U.S. Gov't Research Support,
	U.S. Gov't, P.H.S. Stochastic Processes Tubulin/metabolism Xenopus
	laevis},
  shorttitle = {Cooperative symmetry-breaking by actin polymerization in a model for
	cell motility},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10587645}
}

@ARTICLE{Parker2002,
  author = {Parker, K. K. and Brock, A. L. and Brangwynne, C. and Mannix, R.
	J. and Wang, N. and Ostuni, E. and Geisse, N. A. and Adams, J. C.
	and Whitesides, G. M. and Ingber, D. E.},
  title = {Directional control of lamellipodia extension by constraining cell
	shape and orienting cell tractional forces},
  journal = {Faseb J},
  year = {2002},
  volume = {16},
  pages = {1195-204},
  number = {10},
  month = {Aug},
  note = {1530-6860 (Electronic) Journal Article},
  abstract = {Directed cell migration is critical for tissue morphogenesis and wound
	healing, but the mechanism of directional control is poorly understood.
	Here we show that the direction in which cells extend their leading
	edge can be controlled by constraining cell shape using micrometer-sized
	extracellular matrix (ECM) islands. When cultured on square ECM islands
	in the presence of motility factors, cells preferentially extended
	lamellipodia, filopodia, and microspikes from their corners. Square
	cells reoriented their stress fibers and focal adhesions so that
	tractional forces were concentrated in these corner regions. When
	cell tension was dissipated, lamellipodia extension ceased. Mechanical
	interactions between cells and ECM that modulate cytoskeletal tension
	may therefore play a key role in the control of directional cell
	motility.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12153987},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animals Cattle Cell Adhesion *Cell Movement Cell Size Cells,
	Cultured Cytoskeleton/ultrastructure Endothelium, Vascular/physiology/ultrastructure
	Extracellular Matrix/ultrastructure Fibroblasts/physiology/ultrastructure
	Focal Adhesions/ultrastructure Mice Pseudopodia/*ultrastructure Research
	Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.
	Research Support, U.S. Gov't, P.H.S. Stress Fibers/ultrastructure
	Stress, Mechanical},
  shorttitle = {Directional control of lamellipodia extension by constraining cell
	shape and orienting cell tractional forces},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12153987}
}

@INCOLLECTION{Pawley1994,
  author = {Pawley, J.},
  title = {Sources of noise in three-dimensional microscopical data sets},
  booktitle = {Three-Dimensional Confocal Microscopy: Volume Investigation of Biological
	Specimens},
  publisher = {Academic Press},
  year = {1994},
  editor = {Stevens, J. and Mills, L. and Trogadis, J.},
  pages = {47-94},
  address = {San Diego, California},
  endnotereftype = {Book Section},
  shorttitle = {Sources of noise in three-dimensional microscopical data sets}
}

@ARTICLE{Pawley2000,
  author = {Pawley, J.},
  title = {The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence
	Microscopy},
  journal = {BioTechniques},
  year = {2000},
  volume = {28},
  pages = {884-888},
  number = {5},
  endnotereftype = {Journal Article},
  shorttitle = {The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy}
}

@ARTICLE{Pelham2000,
  author = {Pelham, H. R. and Rothman, J. E.},
  title = {The debate about transport in the Golgi--two sides of the same coin?},
  journal = {Cell},
  year = {2000},
  volume = {102},
  pages = {713-9},
  number = {6},
  month = {Sep 15},
  note = {0092-8674 Journal Article Review Review Literature},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11030615},
  endnotereftype = {Journal Article},
  keywords = {COP-Coated Vesicles/*metabolism Eukaryotic Cells/*metabolism Golgi
	Apparatus/*metabolism Secretory Vesicles/*metabolism},
  shorttitle = {The debate about transport in the Golgi--two sides of the same coin?},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11030615}
}

@ARTICLE{Peran2001,
  author = {Peran, M. and Hicks, B. W. and Peterson, N. L. and Hooper, H. and
	Salas, R.},
  title = {Lateral mobility and anchoring of recombinant GABA(A) receptors depend
	on subunit composition},
  journal = {Cell Motil Cytoskeleton},
  year = {2001},
  volume = {50},
  pages = {89-100},
  number = {2},
  month = {Oct},
  note = {21610353 0886-1544 Journal Article},
  abstract = {The clustering of type A gamma-aminobutyric acid receptors (GABA(A)R)
	at discrete and functionally significant domains on the nerve cell
	surface is an important determinant in the integration of synaptic
	inputs. To discern the role that the subunits of the GABA(A)R play
	in determining the receptor's cell surface topography and mobility,
	the alpha1, beta1, beta3, and gamma2s subunits were transfected into
	COS7, HEK293, and PC12 cells and the distribution and cell surface
	mobility of these recombinant receptors were examined. Our results
	show that alpha1 subunits are retained in the endoplasmic reticulum
	while beta1 and beta3 subunits are sorted to the plasma membrane
	where they form clusters. Co-expression and co-assembly of alpha1
	and beta3 subunits result in the rescue of intracellular alpha1 subunits,
	which are transported as alphabeta subunit complexes to the cell
	surface where they formed clusters. Fluorescence photobleach recovery
	and single particle tracking of recombinant receptors show that,
	despite clustering, beta3 subunit homooligomers are mobile within
	a cell surface domain. Inclusion of alpha1 in beta3 or beta3gamma2s
	complexes, however, dramatically reduces the receptor's lateral mobility
	in COS 7 and PC12 cells and anchors GABA(A)Rs on the cell surface,
	suggesting the formation of a direct link to a component of the cytoskeleton.
	The mobility of recombinant receptors that include the alpha1 subunit
	mirrors the mobility of GABA(A)Rs on cell bodies and dendrites of
	cortical and spinal cord neurons. The results suggest that incorporation
	of alpha1 subunits give rise to a population of GABA(A)Rs that are
	immobilized on the cell surface.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11746674},
  endnotereftype = {Journal Article},
  shorttitle = {Lateral mobility and anchoring of recombinant GABA(A) receptors depend
	on subunit composition},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11746674}
}

@ARTICLE{AmerChemicalSoc,
  author = {Perez, T. D. and Nelson, W. J. and Boxer, S. G. and Kam, L.},
  title = {E-cadherin tethered to micropatterned supported lipid bilayers as
	a model for cell adhesion},
  journal = {Langmuir},
  year = {2005},
  volume = {21},
  pages = {11963-11968},
  number = {25},
  month = {DEC 6},
  note = {Times Cited: 0 Article English Cited References Count: 37 990gc},
  abstract = {Cell-cell adhesion is a dynamic process requiring recruitment, binding,
	and reorganization of signaling proteins in the plane of the plasma
	membrane. Here, we describe a new system for investigating how this
	lateral mobility influences cadherin-based cell signaling. This model
	is based on tethering of a GPI-modified E-cadherin protein (hEFG)
	to a supported lipid bilayer. In this report, membrane microfluidics
	and micropatterning techniques are used to adopt this tethered protein
	system for studies with the anchorage-dependent c ells. As directly
	formed from proteoliposomes, hEFG exhibits a diffusion coefficient
	of 0.6 +/- 0.3 mu m(2)/s and mobile fraction of 30-60%. Lateral structuring
	of the supported lipid bilayer is used to isolate mobile proteins
	from this mixed mobile/immobile population, and should be widely
	applicable to other proteins. MCF-7 cells seeded onto hEFG-containing
	bilayers recognize and cluster this protein, but do not exhibit cell
	spreading required for survival. By micropatterning small anchors
	into the supported lipid bilayer, we have achieved cell spreading
	across the bilayer surface and concurrent interaction with mobile
	hEFG protein. Together, these techniques will allow more detailed
	analysis of the cellular dynamics involved in cadherin-dependent
	adhesion events.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000233730200063},
  endnotereftype = {Journal Article},
  keywords = {lateral mobility membranes binding proteins surfaces manipulation
	flow},
  shorttitle = {E-cadherin tethered to micropatterned supported lipid bilayers as
	a model for cell adhesion},
  url = {<Go to ISI>://000233730200063}
}

@ARTICLE{Periasamy1991,
  author = {Periasamy, N. and Armijo, M. and Verkman, A. S.},
  title = {Picosecond rotation of small polar fluorophores in the cytosol of
	sea urchin eggs},
  journal = {Biochemistry},
  year = {1991},
  volume = {30},
  pages = {11836-41},
  number = {51},
  month = {Dec 24},
  note = {0006-2960 Journal Article},
  abstract = {A new fluorescence method to measure viscosity in cell cytosol [Fushimi,
	K., & Verkman, A. S. (1991) J. Cell Biol. 112, 719-725] has been
	applied to determine fluid-phase viscosity in sea urchin eggs. Freshly
	harvested eggs from Lytechinus pictus were loaded with the dyes 2,7-bis(2-carboxyethyl)-5-(and-6-)carboxyfluorescein
	(BCECF), 6-carboxyfluorescein (6CF), fluorescein, or calcein. Fluorescence
	lifetimes and anisotropy decay were measured in single eggs by multiharmonic,
	frequency-domain microfluorometry using a 1-2-micron focused laser
	spot and 25x air objective. In calibration solutions consisting of
	glycerol in pH 8 buffered sea water, probe lifetime was single exponential
	and probe rotation was isotropic with a single correlation time which
	increased linearly with viscosity in the range 1-3.6 cP. In eggs
	at 22 degrees C, there were single lifetimes (in nanoseconds) of
	3.6 (BCECF), 3.4 (6CF), 3.2 (fluorescein), and 3.3 (calcein). Probe
	rotation in eggs had two components, a fast component (in picoseconds,
	mean +/- SE, 10-18 eggs) of 568 +/- 39 (BCECF), 311 +/- 21 (6CF),
	313 +/- 15 (fluorescein), and 516 +/- 44 (calcein) and a slow component
	of 10-40 ns. The fractional amplitude of the fast component, corresponding
	to unbound dye, was 0.72-0.81. Apparent viscosities of fluid-phase
	cytoplasm (centipoises) given by the four different probes were in
	good agreement: 2.3 +/- 0.2 (BCECF), 2.1 +/- 0.1 (6CF), 2.5 +/- 0.1
	(fluorescein), and 2.3 +/- 0.2 (calcein). The viscosity in cytosol
	of sea urchin eggs (2.1-2.5 cP) is thus relatively low, yet significantly
	greater than that of water (1 cP) or cytosol in cultured fibroblasts
	(1.2-1.4 cP).(ABSTRACT TRUNCATED AT 250 WORDS)},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1751500},
  endnotereftype = {Journal Article},
  keywords = {Animals Cytosol/physiology/ultrastructure Fluoresceins Fluorescent
	Dyes Kinetics Microscopy, Fluorescence/methods Ovum/cytology/*physiology
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
	Sea Urchins Time Factors Viscosity},
  shorttitle = {Picosecond rotation of small polar fluorophores in the cytosol of
	sea urchin eggs},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1751500}
}

@ARTICLE{Periasamy1992,
  author = {Periasamy, N. and Kao, H. P. and Fushimi, K. and Verkman, A. S.},
  title = {Organic osmolytes increase cytoplasmic viscosity in kidney cells},
  journal = {Am J Physiol},
  year = {1992},
  volume = {263},
  pages = {C901-7},
  number = {4 Pt 1},
  month = {Oct},
  note = {0002-9513 Journal Article},
  abstract = {The hypothesis was tested that accumulation of osmolytes by kidney
	cells grown in hyperosmolar media decreases the rotational and translational
	mobilities of small polar solutes in the cytosolic compartment. Rotational
	mobility was measured by the picosecond rotational correlation times
	(tau c) of 2',7'-bis(2-carboxyethyl)-5(6)carboxylfluorescein (BCECF)
	by multiharmonic microfluorimetry. In isolated segments of rabbit
	proximal tubule, thick ascending limb, and cortical collecting duct
	that were perfused and bathed in 300 mosM media, tau c were in the
	range 180-250 ps, corresponding to apparent rotational viscosities
	(eta r) of 1.1-1.5 cP. In cortical collecting tubule, eta r was not
	influenced by serosal vasopressin. In Madin-Darby canine kidney (MDCK)
	cells grown in 300-1,200 mosM media, eta r increased progressively
	by up to a factor of 1.38 +/- 0.03; measurements of tau c and macroscopic
	viscosity in artificial solutions containing osmolytes supported
	the hypothesis that the increased eta r was due to accumulation of
	organic osmolytes. BCECF translational mobility was measured by fluorescence
	photobleaching recovery using a focused 1.2-microns diameter Ar laser
	beam at 488 nm. Recovery half-times were 36 +/- 3 (SE) ms (n = 10)
	in MDCK cells grown in 300 mosM media and 62 +/- 3 ms (n = 10) when
	grown in 1,200 mosM media. The results suggest that accumulation
	of osmolytes by renal cells is associated with significantly increased
	cytosolic viscosity. The increased viscosity would slow enzymatic
	and transport processes in the cytosolic compartment.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1415675},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cytoplasm/metabolism/*physiology Dogs Fluoresceins
	Kidney Tubules/cytology/metabolism/*physiology Osmolar Concentration
	Rabbits Research Support, Non-U.S. Gov't Research Support, U.S. Gov't,
	P.H.S. Viscosity},
  shorttitle = {Organic osmolytes increase cytoplasmic viscosity in kidney cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1415675}
}

@ARTICLE{Peris2006,
  author = {Peris, L. and Thery, M. and Faure, J. and Saoudi, Y. and Lafanechere,
	L. and Chilton, J. K. and Gordon-Weeks, P. and Galjart, N. and Bornens,
	M. and Wordeman, L. and Wehland, J. and Andrieux, A. and Job, D.},
  title = {Tubulin tyrosination is a major factor affecting the recruitment
	of CAP-Gly proteins at microtubule plus ends},
  journal = {J Cell Biol},
  year = {2006},
  volume = {174},
  pages = {839-49},
  number = {6},
  month = {Sep 11},
  note = {0021-9525 (Print) Journal Article Research Support, N.I.H., Extramural
	Research Support, Non-U.S. Gov't},
  abstract = {Tubulin-tyrosine ligase (TTL), the enzyme that catalyzes the addition
	of a C-terminal tyrosine residue to alpha-tubulin in the tubulin
	tyrosination cycle, is involved in tumor progression and has a vital
	role in neuronal organization. We show that in mammalian fibroblasts,
	cytoplasmic linker protein (CLIP) 170 and other microtubule plus-end
	tracking proteins comprising a cytoskeleton-associated protein glycine-rich
	(CAP-Gly) microtubule binding domain such as CLIP-115 and p150 Glued,
	localize to the ends of tyrosinated microtubules but not to the ends
	of detyrosinated microtubules. In vitro, the head domains of CLIP-170
	and of p150 Glued bind more efficiently to tyrosinated microtubules
	than to detyrosinated polymers. In TTL-null fibroblasts, tubulin
	detyrosination and CAP-Gly protein mislocalization correlate with
	defects in both spindle positioning during mitosis and cell morphology
	during interphase. These results indicate that tubulin tyrosination
	regulates microtubule interactions with CAP-Gly microtubule plus-end
	tracking proteins and provide explanations for the involvement of
	TTL in tumor progression and in neuronal organization.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16954346},
  endnotereftype = {Journal Article},
  keywords = {Animals Cells, Cultured Fibroblasts/*metabolism/ultrastructure Interphase/physiology
	Mice Microtubule-Associated Proteins/*metabolism Microtubules/*metabolism/ultrastructure
	Mitotic Spindle Apparatus/metabolism/ultrastructure Neoplasm Proteins/*metabolism
	Nerve Tissue Proteins/metabolism Peptide Synthases/genetics/metabolism
	Polymers/metabolism Protein Structure, Tertiary/physiology Tubulin/*metabolism
	Tyrosine/*metabolism},
  shorttitle = {Tubulin tyrosination is a major factor affecting the recruitment of
	CAP-Gly proteins at microtubule plus ends},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16954346}
}

@ARTICLE{Peters1999,
  author = {Peters, I. M. and van Kooyk, Y. and van Vliet, S. J. and de Grooth,
	B. G. and Figdor, C. G. and Greve, J.},
  title = {3D single-particle tracking and optical trap measurements on adhesion
	proteins},
  journal = {Cytometry},
  year = {1999},
  volume = {36},
  pages = {189-94},
  number = {3},
  month = {Jul 1},
  note = {99331853 0196-4763 Journal Article},
  abstract = {A three-dimensional single-particle tracking system was combined with
	an optical trap to investigate the behavior of transmembrane adhesion
	proteins. We exploited this setup to investigate which part of the
	cell adhesion protein LFA-1 forms a connection to the cytoskeleton
	after binding to its ligand ICAM-1. LFA-1 is an integrin consisting
	of an alpha and a beta chain. Thus far, only the cytoplasmic tail
	of the beta chain is known to form a connection to the cytoskeleton.
	We investigated cells that express a mutant form of LFA-1 that lacks
	the complete beta cytoplasmic tail and therefore is not thought to
	bind to the cytoskeleton. Interestingly, single-particle tracking
	measurements using beads coated with the ligand ICAM-1 indicate that
	this mutant form of LFA-1 does not move freely within the cell membrane,
	suggesting that LFA-1 is still connected to the cytoskeleton network.
	This finding is strongly supported by the observation that LFA-1
	exhibits a more diffusive motion when the cytoskeleton network is
	disrupted and confirmed by the optical trap measurements used to
	force the proteins to move through the membrane. Collectively, our
	findings suggest that the interaction of LFA-1 with the cytoskeleton
	cannot solely be attributed to the cytoplasmic part of the beta chain.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10404967},
  endnotereftype = {Journal Article},
  keywords = {Cytochalasin D/pharmacology Cytoskeleton/*metabolism Human Intercellular
	Adhesion Molecule-1/metabolism K562 Cells Lymphocyte Function-Associated
	Antigen-1/genetics/*metabolism Mutagenesis},
  shorttitle = {3D single-particle tracking and optical trap measurements on adhesion
	proteins},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10404967}
}

@ARTICLE{Phair2004,
  author = {Phair, R. D. and Gorski, S. A. and Misteli, T.},
  title = {Measurement of dynamic protein binding to chromatin in vivo, using
	photobleaching microscopy},
  journal = {Methods Enzymol},
  year = {2004},
  volume = {375},
  pages = {393-414},
  note = {0076-6879 Journal Article},
  abstract = {We have described procedures for collecting, processing, and analyzing
	kinetic data obtained by photobleaching microscopy of GFP-tagged
	chromatin proteins in nuclei of cultured living cells. These procedures
	are useful for characterizing the in vivo binding of chromatin proteins
	to their natural template--unperturbed, native chromatin in an intact
	cell nucleus. These techniques have revealed several generalizations
	that significantly change our view of the nucleus. At the qualitative
	level, it has become clear that almost all chromatin proteins bind
	only transiently to their targets. More importantly, the combined
	use of in vivo microscopy and kinetic, computational analysis allows
	analysis of the kinetics of protein binding in vivo. These methods
	should prove useful in the further in vivo investigation of the molecular
	mechanisms involved in genome organization and expression.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14870680},
  endnotereftype = {Journal Article},
  keywords = {Binding Sites Biochemistry/*methods Cell Nucleus/metabolism Chromatin/*chemistry/metabolism
	Cytoplasm/metabolism Fluorescence Recovery After Photobleaching/methods
	Image Processing, Computer-Assisted Kinetics Luminescent Proteins/metabolism
	Microscopy, Fluorescence/*methods Models, Biological Protein Binding
	Time Factors},
  shorttitle = {Measurement of dynamic protein binding to chromatin in vivo, using
	photobleaching microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14870680}
}

@ARTICLE{Phair2001,
  author = {Phair, R. D. and Misteli, T.},
  title = {Kinetic modelling approaches to in vivo imaging},
  journal = {Nat Rev Mol Cell Biol},
  year = {2001},
  volume = {2},
  pages = {898-907},
  number = {12},
  month = {Dec},
  note = {1471-0072 Journal Article Review Review, Tutorial},
  abstract = {The ability to visualize protein dynamics and biological processes
	by in vivo microscopy is revolutionizing many areas of biology. These
	methods generate large, kinetically complex data sets, which often
	cannot be intuitively interpreted. The combination of dynamic imaging
	and computational modelling is emerging as a powerful tool for the
	quantitation of biophysical properties of molecules and processes.
	The new discipline of computational cell biology will be essential
	in uncovering the pathways, mechanisms and controls of biological
	processes and systems as they occur in vivo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11733769},
  endnotereftype = {Journal Article},
  keywords = {Animals Biophysics Computational Biology Cyclic AMP/metabolism DNA-Binding
	Protein, Cyclic AMP-Responsive/metabolism Human Kinetics Microscopy,
	Fluorescence/*methods *Models, Biological Photochemistry Protein
	Binding Proteins/chemistry/*metabolism},
  shorttitle = {Kinetic modelling approaches to in vivo imaging},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11733769}
}

@ARTICLE{Polishchuk2000,
  author = {Polishchuk, R. S. and Polishchuk, E. V. and Marra, P. and Alberti,
	S. and Buccione, R. and Luini, A. and Mironov, A. A.},
  title = {Correlative light-electron microscopy reveals the tubular-saccular
	ultrastructure of carriers operating between Golgi apparatus and
	plasma membrane},
  journal = {J Cell Biol},
  year = {2000},
  volume = {148},
  pages = {45-58},
  number = {1},
  month = {Jan 10},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Transport intermediates (TIs) have a central role in intracellular
	traffic, and much effort has been directed towards defining their
	molecular organization. Unfortunately, major uncertainties remain
	regarding their true structure in living cells. To address this question,
	we have developed an approach based on the combination of the green
	fluorescent protein technology and correlative light-electron microscopy,
	by which it is possible to monitor an individual carrier in vivo
	and then take a picture of its ultrastructure at any moment of its
	life-cycle. We have applied this technique to define the structure
	of TIs operating from the Golgi apparatus to the plasma membrane,
	whose in vivo dynamics have been characterized recently by light
	microscopy. We find that these carriers are large (ranging from 0.3-1.7
	microm in maximum diameter, nearly half the size of a Golgi cisterna),
	comprise almost exclusively tubular-saccular structures, and fuse
	directly with the plasma membrane, sometimes minutes after docking
	to the fusion site.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10629217},
  endnotereftype = {Journal Article},
  keywords = {Animals COS Cells Cell Membrane/*metabolism/ultrastructure Golgi Apparatus/*metabolism/ultrastructure
	Humans *Membrane Glycoproteins Microscopy, Electron/methods Microtomy
	Recombinant Fusion Proteins/genetics/metabolism Research Support,
	Non-U.S. Gov't Viral Envelope Proteins/genetics/metabolism},
  shorttitle = {Correlative light-electron microscopy reveals the tubular-saccular
	ultrastructure of carriers operating between Golgi apparatus and
	plasma membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10629217}
}

@ARTICLE{Pollard2003,
  author = {Pollard, T. D. and Borisy, G. G.},
  title = {Cellular motility driven by assembly and disassembly of actin filaments},
  journal = {Cell},
  year = {2003},
  volume = {112},
  pages = {453-65},
  number = {4},
  month = {Feb 21},
  note = {0092-8674 (Print) Journal Article Review},
  abstract = {Motile cells extend a leading edge by assembling a branched network
	of actin filaments that produces physical force as the polymers grow
	beneath the plasma membrane. A core set of proteins including actin,
	Arp2/3 complex, profilin, capping protein, and ADF/cofilin can reconstitute
	the process in vitro, and mathematical models of the constituent
	reactions predict the rate of motion. Signaling pathways converging
	on WASp/Scar proteins regulate the activity of Arp2/3 complex, which
	mediates the initiation of new filaments as branches on preexisting
	filaments. After a brief spurt of growth, capping protein terminates
	the elongation of the filaments. After filaments have aged by hydrolysis
	of their bound ATP and dissociation of the gamma phosphate, ADF/cofilin
	proteins promote debranching and depolymerization. Profilin catalyzes
	the exchange of ADP for ATP, refilling the pool of ATP-actin monomers
	bound to profilin, ready for elongation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12600310},
  endnotereftype = {Journal Article},
  keywords = {Actin Depolymerizing Factors Actins/chemistry/metabolism/*physiology
	Adenosine Diphosphate/metabolism Adenosine Triphosphate/metabolism
	Animals Cattle Cell Division Cell Membrane/metabolism *Cell Movement
	Cell Nucleus/metabolism Crystallography, X-Ray Dendrites/metabolism
	Keratinocytes/ultrastructure Microfilament Proteins/metabolism Models,
	Biological Models, Molecular Phosphates/metabolism Protein Structure,
	Secondary Protein Structure, Tertiary Research Support, U.S. Gov't,
	P.H.S. *Signal Transduction},
  shorttitle = {Cellular motility driven by assembly and disassembly of actin filaments},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12600310}
}

@ARTICLE{PDFavailable,
  author = {Ponti, A. and Vallotton, P. and Salmon, W. C. and Waterman-Storer,
	C. M. and Danuser, G.},
  title = {Computational analysis of f-actin turnover in cortical actin meshworks
	using fluorescent speckle microscopy},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {3336-52},
  number = {5},
  month = {May},
  note = {22604724 0006-3495 Journal Article},
  abstract = {Fluorescent speckle microscopy (FSM) is a new imaging technique with
	the potential for simultaneous visualization of translocation and
	dynamic turnover of polymer structures. However, the use of FSM has
	been limited by the lack of specialized software for analysis of
	the positional and photometric fluctuations of hundreds of thousand
	speckles in an FSM time-lapse series, and for translating this data
	into biologically relevant information. In this paper we present
	a first version of a software for automated analysis of FSM movies.
	We focus on mapping the assembly and disassembly kinetics of a polymer
	meshwork. As a model system we have employed cortical F-actin meshworks
	in live newt lung epithelial cells. We lay out the algorithm in detail
	and present results of our analysis. The high spatial and temporal
	resolution of our maps reveals a kinetic cycling of F-actin, where
	phases of polymerization alternate with depolymerization in a spatially
	coordinated fashion. The cycle rates change when treating cells with
	a low dose of the drug latrunculin A. This shows the potential of
	this technique for future quantitative screening of drugs affecting
	the actin cytoskeleton. Various control experiments demonstrate that
	the algorithm is robust with respect to intensity variations due
	to noise and photobleaching and that effects of focus plane drifts
	can be eliminated by manual refocusing during image acquisition.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12719263},
  endnotereftype = {Journal Article},
  shorttitle = {Computational analysis of f-actin turnover in cortical actin meshworks
	using fluorescent speckle microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12719263}
}

@ARTICLE{Pralle2000,
  author = {Pralle, A. and Keller, P. and Florin, E. L. and Simons, K. and Horber,
	J. K.},
  title = {Sphingolipid-cholesterol rafts diffuse as small entities in the plasma
	membrane of mammalian cells},
  journal = {J Cell Biol},
  year = {2000},
  volume = {148},
  pages = {997-1008},
  number = {5},
  month = {Mar 6},
  note = {20171434 0021-9525 Journal Article},
  abstract = {To probe the dynamics and size of lipid rafts in the membrane of living
	cells, the local diffusion of single membrane proteins was measured.
	A laser trap was used to confine the motion of a bead bound to a
	raft protein to a small area (diam < or = 100 nm) and to measure
	its local diffusion by high resolution single particle tracking.
	Using protein constructs with identical ectodomains and different
	membrane regions and vice versa, we demonstrate that this method
	provides the viscous damping of the membrane domain in the lipid
	bilayer. When glycosylphosphatidylinositol (GPI) -anchored and transmembrane
	proteins are raft-associated, their diffusion becomes independent
	of the type of membrane anchor and is significantly reduced compared
	with that of nonraft transmembrane proteins. Cholesterol depletion
	accelerates the diffusion of raft-associated proteins for transmembrane
	raft proteins to the level of transmembrane nonraft proteins and
	for GPI-anchored proteins even further. Raft-associated GPI-anchored
	proteins were never observed to dissociate from the raft within the
	measurement intervals of up to 10 min. The measurements agree with
	lipid rafts being cholesterol-stabilized complexes of 26 +/- 13 nm
	in size diffusing as one entity for minutes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10704449},
  endnotereftype = {Journal Article},
  keywords = {Animal Bacterial Proteins/biosynthesis/genetics Cell Line Cell Membrane/*metabolism
	Cholesterol/chemistry/*metabolism Diffusion Fluorescent Antibody
	Technique Fluorescent Dyes Glycosylphosphatidylinositols/metabolism
	Hamsters Hemagglutinins, Viral/biosynthesis/genetics Isoenzymes/biosynthesis
	Lasers Lipid Bilayers/metabolism Luminescent Proteins/biosynthesis/genetics
	Membrane Proteins/metabolism Microspheres Particle Size Sphingolipids/chemistry/*metabolism
	Support, Non-U.S. Gov't Transfection Viscosity},
  shorttitle = {Sphingolipid-cholesterol rafts diffuse as small entities in the plasma
	membrane of mammalian cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10704449}
}

@ARTICLE{Pralle1999,
  author = {Pralle, A. and Prummer, M. and Florin, E. L. and Stelzer, E. H. and
	Horber, J. K.},
  title = {Three-dimensional high-resolution particle tracking for optical tweezers
	by forward scattered light},
  journal = {Microsc Res Tech},
  year = {1999},
  volume = {44},
  pages = {378-86},
  number = {5},
  month = {Mar 1},
  note = {99188600 1059-910x Journal Article},
  abstract = {A quadrant photodiode placed in the back-focal plane of the microscope
	of a laser trap provides a high-resolution position sensor. We show
	that in addition to the lateral displacement of a trapped sphere,
	its axial position can be measured by the ratio of the intensity
	of scattered laser light to the total amount of the light reaching
	the detector. The addition of the axial information offers true three-dimensional
	position detection in solution, creating, together with a position
	control, a photonic force microscope with nanometer spatial and microsecond
	temporal resolution. The measured position signals are explained
	as interference of the unscattered trapping laser beam with the laser
	light scattered by the trapped bead. Our model explains experimental
	data for trapped particles in the Rayleigh regime (radius a <0.2lambda)
	for displacements up to the focal dimensions. The cross-talk between
	the signals in the three directions is explained and it is shown
	that this cross-talk can be neglected for lateral displacements smaller
	than 75 nm and axial displacements below 150 nm. The advantages of
	three-dimensional single-particle tracking over conventional video-tracking
	are shown through the example of the diffusion of the GPI-anchored
	membrane protein Thy1.1 on a neurite.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10090214},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, Thy-1/*metabolism Biological Transport Diffusion
	Hippocampus/embryology Lasers Membrane Proteins/*metabolism Micromanipulation
	Microscopy/*instrumentation/*methods Neurites/*metabolism Optics
	Particle Size Photons Rats Scattering, Radiation Support, Non-U.S.
	Gov't},
  shorttitle = {Three-dimensional high-resolution particle tracking for optical tweezers
	by forward scattered light},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10090214}
}

@ARTICLE{Presley1997,
  author = {Presley, J. F. and Cole, N. B. and Schroer, T. A. and Hirschberg,
	K. and Zaal, K. J. and Lippincott-Schwartz, J.},
  title = {ER-to-Golgi transport visualized in living cells},
  journal = {Nature},
  year = {1997},
  volume = {389},
  pages = {81-5},
  number = {6646},
  month = {Sep 4},
  note = {0028-0836 (Print) Journal Article},
  abstract = {Newly synthesized proteins that leave the endoplasmic reticulum (ER)
	are funnelled through the Golgi complex before being sorted for transport
	to their different final destinations. Traditional approaches have
	elucidated the biochemical requirements for such transport and have
	established a role for transport intermediates. New techniques for
	tagging proteins fluorescently have made it possible to follow the
	complete life history of single transport intermediates in living
	cells, including their formation, path and velocity en route to the
	Golgi complex. We have now visualized ER-to-Golgi transport using
	the viral glycoprotein ts045 VSVG tagged with green fluorescent protein
	(VSVG-GFP). Upon export from the ER, VSVG-GFP became concentrated
	in many differently shaped, rapidly forming pre-Golgi structures,
	which translocated inwards towards the Golgi complex along microtubules
	by using the microtubule minus-end-directed motor complex of dynein/dynactin.
	No loss of fluorescent material from pre-Golgi structures occurred
	during their translocation to the Golgi complex and they frequently
	stretched into tubular shapes. Together, our results indicate that
	these pre-Golgi carrier structures moving unidirectionally along
	microtubule tracks are responsible for transporting VSVG-GFP through
	the cytoplasm to the Golgi complex. This contrasts with the traditional
	focus on small vesicles as the primary vehicles for ER-to-Golgi transport.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9288971},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport/drug effects COS Cells Dynein ATPase/metabolism
	Endoplasmic Reticulum/*metabolism Fluorescence Golgi Apparatus/*metabolism
	Green Fluorescent Proteins Image Processing, Computer-Assisted Intracellular
	Membranes/metabolism Luminescent Proteins/genetics/metabolism *Membrane
	Glycoproteins Microscopy, Fluorescence Microtubule-Associated Proteins/metabolism
	Microtubules/drug effects/metabolism Nocodazole/pharmacology Recombinant
	Fusion Proteins/genetics/metabolism Temperature Viral Envelope Proteins/genetics/metabolism},
  shorttitle = {ER-to-Golgi transport visualized in living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9288971}
}

@ARTICLE{Qian2000,
  author = {Qian, H.},
  title = {Single-particle tracking: Brownian dynamics of viscoelastic materials},
  journal = {Biophys J},
  year = {2000},
  volume = {79},
  pages = {137-43},
  number = {1},
  month = {Jul},
  note = {20327271 0006-3495 Journal Article},
  abstract = {A unifying theoretical framework for analyzing stochastic data from
	single-particle tracking (SPT) in viscoelastic materials is presented.
	A generalization of the bead-spring model for linear polymers is
	developed from a molecular point of view and from the standpoint
	of phenomenological linear viscoelasticity. The hydrodynamic interaction
	in the former is identified as the dashpots in the latter. In elementary
	terms, the intimate correspondence between time-correlation of the
	fluctuation measurements and transient relaxation kinetics after
	perturbation is discussed, and the central role of the fluctuation-dissipation
	relation is emphasized. The work presented here provides a bridge
	between the microscopic and the macroscopic views of linear viscoelastic
	biological materials, and is applicable to membrane protein diffusion,
	linear DNA chain dynamics, and mechanics of intracellular cytoskeletal
	networks.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10866942},
  endnotereftype = {Journal Article},
  keywords = {Biopolymers/*chemistry Diffusion Elasticity Fourier Analysis Materials
	Testing Mathematics Membranes/chemistry *Models, Chemical *Nonlinear
	Dynamics *Stochastic Processes Viscosity},
  shorttitle = {Single-particle tracking: Brownian dynamics of viscoelastic materials},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10866942}
}

@ARTICLE{Qian2000a,
  author = {Qian, H.},
  title = {A mathematical analysis for the Brownian dynamics of a DNA tether},
  journal = {J Math Biol},
  year = {2000},
  volume = {41},
  pages = {331-40},
  number = {4},
  month = {Oct},
  note = {20552233 0303-6812 Journal Article},
  abstract = {In the single-particle tracking experiment, the internal motion of
	a single DNA or polymer molecule whose one end is attached to a microsphere
	(optical marker) and the other end is anchored to a substratum is
	studied (Finzi and Gelles, 1995). The stochastic Brownian dynamics
	of the sphere reflect the spontaneous fluctuations, thus the physical
	characteristics, of the DNA or polymer molecule (Qian and Elson,
	1999, Qian, 2000). In this paper, two continuous models of polymer
	molecules, a flexible elastic string and a weakly bendable elastic
	rod, are analyzed. Both models are cast mathematically in terms of
	linear stochastic differential equations. Based on Fourier analyses,
	we calculate the mean square displacement (MSD) of the particle motion,
	the key observable in the experiment. We obtain for both models the
	short-time asymptomatics for the MSD, as well as the long-time behavior
	in terms of the smallest non-zero eigenvalues. It is shown that:
	(i) the long-time dynamics of continuous elastic string model quantitatively
	agree with that of the discrete bead-spring model. (ii) The short-time
	MSD of both models are controlled by the tethered particle, with
	linear dependence on t. (iii) The two models show characteristic
	difference for long-time behavior: The longest relaxation time is
	proportional to L2 for long elastic string and to L for short elastic
	string, but is proportional to L4 for both long and short weakly
	bendable rod.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11103870},
  endnotereftype = {Journal Article},
  keywords = {Comparative Study DNA/*chemistry Elasticity Macromolecular Systems
	Mathematics *Models, Chemical Motion Nucleic Acid Conformation Thermodynamics},
  shorttitle = {A mathematical analysis for the Brownian dynamics of a DNA tether},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11103870}
}

@ARTICLE{Qian1999,
  author = {Qian, H. and Elson, E. L.},
  title = {Quantitative study of polymer conformation and dynamics by single-particle
	tracking},
  journal = {Biophys J},
  year = {1999},
  volume = {76},
  pages = {1598-605},
  number = {3},
  month = {Mar},
  note = {99158633 0006-3495 Journal Article},
  abstract = {We present a new method for analyzing the dynamics of conformational
	fluctuations of individual flexible polymer molecules. In single-particle
	tracking (SPT), one end of the polymer molecule is tethered to an
	immobile substratum. A microsphere attached to the other end serves
	as an optical marker. The conformational fluctuations of the polymer
	molecule can be measured by optical microscopy via the motion of
	the microsphere. The bead-and-spring theory for polymer dynamics
	is further developed to account for the microsphere, and together
	the measurement and the theory yield quantitative information about
	molecular conformations and dynamics under nonperturbing conditions.
	Applying the method to measurements carried out on DNA molecules
	provides information complementary to recent studies of single DNA
	molecules under extensional force. Combining high precision measurements
	with the theoretical analysis presented here creates a powerful tool
	for studying conformational dynamics of biological and synthetic
	macromolecules at the single-molecule level.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10049340},
  endnotereftype = {Journal Article},
  keywords = {Biophysics DNA/chemistry Macromolecular Systems Microspheres Models,
	Chemical Molecular Conformation Polymers/*chemistry Support, U.S.
	Gov't, P.H.S. Thermodynamics},
  shorttitle = {Quantitative study of polymer conformation and dynamics by single-particle
	tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10049340}
}

@ARTICLE{qianBJ1991,
  author = {Qian, H. and Sheetz, M. P. and Elson, E. L.},
  title = {Single particle tracking. Analysis of diffusion and flow in two-dimensional
	systems},
  journal = {Biophys J},
  year = {1991},
  volume = {60},
  pages = {910-21},
  number = {4},
  month = {Oct},
  note = {92075891 0006-3495 Journal Article},
  abstract = {Analysis of the trajectories of small particles at high spatial and
	temporal resolution using video enhanced contrast microscopy provides
	a powerful approach to characterizing the mechanisms of particle
	motion in living cells and in other systems. We present here the
	theoretical basis for the analysis of these trajectories for particles
	undergoing random diffusion and/or systematic transport at uniform
	velocity in two-dimensional systems. The single particle tracking
	method, based on observations of the trajectories of individual particles,
	is compared with methods that characterize the motions of a large
	collection of particles such as fluorescence photobleaching recovery.
	Determination of diffusion coefficients or transport velocities either
	from correlation of positions or of velocities of the particles is
	discussed. A result of practical importance is an analysis of the
	dependence of the expected statistical uncertainty of these determinations
	on the number of position measurements. This provides a way of judging
	the accuracy of the diffusion coefficients and transport velocities
	obtained using this approach.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1742458},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Kinetics Mathematics Membrane Proteins/*physiology *Models,
	Biological Probability Support, Non-U.S. Gov't Support, U.S. Gov't,
	P.H.S.},
  shorttitle = {Single particle tracking. Analysis of diffusion and flow in two-dimensional
	systems},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1742458}
}

@MANUAL{Rasband1997-2011,
  title = {ImageJ},
  author = {Rasband, W.S},
  year = {1997-2011},
  bdsk-url-1 = {http://rsb.info.nih.gov/ij/docs/index.html},
  endnotereftype = {Computer Program},
  shorttitle = {ImageJ documentation},
  url = {http://rsb.info.nih.gov/ij/docs/index.html}
}

@MANUAL{Rasband1997-2005,
  title = {ImageJ},
  author = {Rasband, W.S},
  year = {1997-2005},
  bdsk-url-1 = {http://rsb.info.nih.gov/ij/},
  endnotereftype = {Computer Program},
  shorttitle = {ImageJ},
  url = {http://rsb.info.nih.gov/ij/}
}

@MANUAL{Rasband2000,
  title = {Object Tracker},
  author = {Rasband, W.S},
  year = {2000},
  bdsk-url-1 = {http://rsb.info.nih.gov/ij/plugins/tracker.html},
  endnotereftype = {Computer Program},
  shorttitle = {Object Tracker},
  url = {http://rsb.info.nih.gov/ij/plugins/tracker.html}
}

@ARTICLE{Ray2002,
  author = {Ray, N. and Acton, S. T. and Ley, K.},
  title = {Tracking leukocytes in vivo with shape and size constrained active
	contours},
  journal = {IEEE Trans Med Imaging},
  year = {2002},
  volume = {21},
  pages = {1222-35},
  number = {10},
  month = {Oct},
  note = {22473129 0278-0062 Evaluation Studies Journal Article Validation
	Studies},
  abstract = {Inflammatory disease is initiated by leukocytes (white blood cells)
	rolling along the inner surface lining of small blood vessels called
	postcapillary venules. Studying the number and velocity of rolling
	leukocytes is essential to understanding and successfully treating
	inflammatory diseases. Potential inhibitors of leukocyte recruitment
	can be screened by leukocyte rolling assays and successful inhibitors
	validated by intravital microscopy. In this paper, we present an
	active contour or snake-based technique to automatically track the
	movement of the leukocytes. The novelty of the proposed method lies
	in the energy functional that constrains the shape and size of the
	active contour. This paper introduces a significant enhancement over
	existing gradient-based snakes in the form of a modified gradient
	vector flow. Using the gradient vector flow, we can track leukocytes
	rolling at high speeds that are not amenable to tracking with the
	existing edge-based techniques. We also propose a new energy-based
	implicit sampling method of the points on the active contour that
	replaces the computationally expensive explicit method. To enhance
	the performance of this shape and size constrained snake model, we
	have coupled it with Kalman filter so that during coasting (when
	the leukocytes are completely occluded or obscured), the tracker
	may infer the location of the center of the leukocyte. Finally, we
	have compared the performance of the proposed snake tracker with
	that of the correlation and centroid-based trackers. The proposed
	snake tracker results in superior performance measures, such as reduced
	error in locating the leukocyte under tracking and improvements in
	the percentage of frames successfully tracked. For screening and
	drug validation, the tracker shows promise as an automated data collection
	tool.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12585704},
  endnotereftype = {Journal Article},
  keywords = {*Algorithms Animal Cell Adhesion/physiology Cell Movement/*physiology
	Comparative Study Image Enhancement/*methods Image Interpretation,
	Computer-Assisted/*methods Leukocytes/classification/*cytology/*physiology
	Mice Mice, Knockout Microscopy, Video/*methods Models, Biological
	Pattern Recognition Quality Control Reproducibility of Results Sensitivity
	and Specificity Statistics Stochastic Processes Support, Non-U.S.
	Gov't},
  shorttitle = {Tracking leukocytes in vivo with shape and size constrained active
	contours},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12585704}
}

@ARTICLE{Reits2001,
  author = {Reits, E. A. and Neefjes, J. J.},
  title = {From fixed to FRAP: measuring protein mobility and activity in living
	cells},
  journal = {Nat Cell Biol},
  year = {2001},
  volume = {3},
  pages = {E145-7},
  number = {6},
  month = {Jun},
  note = {1465-7392 Journal Article Review Review, Tutorial},
  abstract = {Experiments with fluorescence recovery after photobleaching (FRAP)
	started 30 years ago to visualize the lateral mobility and dynamics
	of fluorescent proteins in living cells. Its popularity increased
	when non-invasive fluorescent tagging became possible with the green
	fluorescent protein (GFP). Many researchers use GFP to study the
	localization of fusion proteins in fixed or living cells, but the
	same fluorescent proteins can also be used to study protein mobility
	in living cells. Here we review the potential of FRAP to study protein
	dynamics and activity within a single living cell. These measurements
	can be made with most standard confocal laser-scanning microscopes
	equipped with photobleaching protocols.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11389456},
  endnotereftype = {Journal Article},
  keywords = {Animals Cells, Cultured Fluorescence Green Fluorescent Proteins Humans
	Luminescent Proteins/*metabolism Microscopy, Confocal/*methods Recombinant
	Fusion Proteins/metabolism Research Support, Non-U.S. Gov't Subcellular
	Fractions},
  shorttitle = {From fixed to FRAP: measuring protein mobility and activity in living
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11389456}
}

@MANUAL{Rietdorf2005,
  title = {Bleaching Correction},
  author = {Rietdorf, Jens},
  year = {2005},
  bdsk-url-1 = {http://www.embl.de/eamnet/html/bleach_correction.html},
  endnotereftype = {Computer Program},
  shorttitle = {Bleaching Correction},
  url = {http://www.embl.de/eamnet/html/bleach_correction.html}
}

@ARTICLE{ritchieME2003,
  author = {Ritchie, K. and Kusumi, A.},
  title = {Single-particle tracking image microscopy},
  journal = {Methods Enzymol},
  year = {2003},
  volume = {360},
  pages = {618-34},
  note = {22509097 0076-6879 Journal Article},
  abstract = {The techniques of single particle tracking (SPT) and optical force
	microscopy (OFM) as described above allow direct imaging of the motion
	of molecules in the membrane of live cells, and provide a means of
	controlling the movement by an almost noninvasive method. Combination
	of these techniques with other single-molecule methods, such as single-fluorophore
	imaging, allows direct comparison of motion at video rate (because
	faster than video rate imaging of fluorophore is still not generally
	feasible) to determine any effect due to the attached colloidal gold
	particle. Also, simultaneous use of the two techniques allows for
	monitoring two molecules, one at high time resolution. As such, the
	system can then be used in conjunction with green fluorescent protein
	(GFP) transfection to watch simultaneously the motion of an internal
	component of, say, a signaling pathway while seeing the motion of
	the transmembrane signaling receptor.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12622171},
  endnotereftype = {Journal Article},
  keywords = {Microscopy/*methods Proteins/*chemistry},
  shorttitle = {Single-particle tracking image microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12622171}
}

@ARTICLE{Rossner2004,
  author = {Rossner, M. and Yamada, K. M.},
  title = {What's in a picture? The temptation of image manipulation},
  journal = {J Cell Biol},
  year = {2004},
  volume = {166},
  pages = {11-5},
  number = {1},
  month = {Jul 5},
  note = {0021-9525 (Print) News},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15240566},
  endnotereftype = {Journal Article},
  keywords = {Ethics Image Processing, Computer-Assisted/*methods Publishing Research/methods
	Software},
  shorttitle = {What's in a picture? The temptation of image manipulation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15240566}
}

@ARTICLE{Roy2002,
  author = {Roy, S. and Larachi, F. and Al-Dahhan, M. H. and Dudukovic, M. P.},
  title = {Optimal design of radioactive particle tracking experiments for flow
	mapping in opaque multiphase reactors},
  journal = {Appl Radiat Isot},
  year = {2002},
  volume = {56},
  pages = {485-503},
  number = {3},
  month = {Mar},
  note = {21919406 0969-8043 Journal Article},
  abstract = {In the past decade, radioactive particle tracking techniques have
	emerged in the field of chemical engineering and have become increasingly
	popular for non-invasive flow mapping of the hydrodynamics in multiphase
	reactors. Based on gamma-ray sensitization of an array of scintillation
	detectors, the Computer Automated Radioactive Particle Tracking (CARPT)
	technique measures flow fields by monitoring the actual motion path
	of a single discrete radioactive flow follower which has the physical
	properties of the phase whose motion is being followed. A limitation
	to the accuracy of CARPT lies in the error associated with the reconstruction
	of the tracer particle position which affects the space-resolution
	capability of the technique. It is of interest, therefore, to minimize
	this error by choosing wisely the best hardware and an optimal configuration
	of CARPT detectors' array. Such choices are currently based on experience,
	without firm scientific basis. In this paper, through theoretical
	modeling and simulation, we describe how the accuracy of a radioactive
	particle tracking setup may be assessed a priori. Through an example
	of a proposed implementation of CARPT on a gas-solids riser, we demonstrate
	how this knowledge can be used for choosing the hardware required
	for the experiment. Finally, we show how the optimal arrangement
	of detectors can be effected for maximum accuracy for a given amount
	of monetary investment for the experiment.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11922416},
  endnotereftype = {Journal Article},
  shorttitle = {Optimal design of radioactive particle tracking experiments for flow
	mapping in opaque multiphase reactors},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11922416}
}

@ARTICLE{Rozkiewicz2006,
  author = {Rozkiewicz, D. I. and Kraan, Y. and Werten, M. W. and de Wolf, F.
	A. and Subramaniam, V. and Ravoo, B. J. and Reinhoudt, D. N.},
  title = {Covalent microcontact printing of proteins for cell patterning},
  journal = {Chemistry},
  year = {2006},
  volume = {12},
  pages = {6290-7},
  number = {24},
  month = {Aug 16},
  note = {0947-6539 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {We describe a straightforward approach to the covalent immobilization
	of cytophilic proteins by microcontact printing, which can be used
	to pattern cells on substrates. Cytophilic proteins are printed in
	micropatterns on reactive self-assembled monolayers by using imine
	chemistry. An aldehyde-terminated monolayer on glass or on gold was
	obtained by the reaction between an amino-terminated monolayer and
	terephthaldialdehyde. The aldehyde monolayer was employed as a substrate
	for the direct microcontact printing of bioengineered, collagen-like
	proteins by using an oxidized poly(dimethylsiloxane) (PDMS) stamp.
	After immobilization of the proteins into adhesive "islands", the
	remaining areas were blocked with amino-poly(ethylene glycol), which
	forms a layer that is resistant to cell adhesion. Human malignant
	carcinoma (HeLa) cells were seeded and incubated onto the patterned
	substrate. It was found that these cells adhere to and spread selectively
	on the protein islands, and avoid the poly(ethylene glycol) (PEG)
	zones. These findings illustrate the importance of microcontact printing
	as a method for positioning proteins at surfaces and demonstrate
	the scope of controlled surface chemistry to direct cell adhesion.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16741908},
  endnotereftype = {Journal Article},
  keywords = {Aldehydes/chemistry *Cell Adhesion Collagen Type III/*chemistry/metabolism
	Cytological Techniques/*methods Dimethylpolysiloxanes/chemistry Gold/chemistry
	Hela Cells Humans Imines/chemistry Microscopy, Confocal Polyethylene
	Glycols/chemistry Silicon Dioxide/chemistry Silicones/chemistry Spectroscopy,
	Fourier Transform Infrared},
  shorttitle = {Covalent microcontact printing of proteins for cell patterning},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16741908}
}

@ARTICLE{Ruiz2007,
  author = {Ruiz, S. A. and Chen, C. S.},
  title = {Microcontact printing: A tool to pattern},
  journal = {Soft Matter},
  year = {2007},
  volume = {3},
  pages = {168 - 177},
  abstract = {Microcontact printing has proven to be a useful technique in the patterned
	functionalization of certain chemicals onto surfaces. It has been
	particularly valuable in the patterning of biological materials.
	In this review, we describe the basic principles of the technology
	as well as its use in several applications, with an emphasis on biological
	ones. We also discuss the limitations and future directions of this
	method.},
  endnotereftype = {Journal Article},
  shorttitle = {Microcontact printing: A tool to pattern}
}

@ARTICLE{Ruiz-Taylor2001,
  author = {Ruiz-Taylor, L. A. and Martin, T. L. and Zaugg, F. G. and Witte,
	K. and Indermuhle, P. and Nock, S. and Wagner, P.},
  title = {Monolayers of derivatized poly(L-lysine)-grafted poly(ethylene glycol)
	on metal oxides as a class of biomolecular interfaces},
  journal = {Proc Natl Acad Sci U S A},
  year = {2001},
  volume = {98},
  pages = {852-7},
  number = {3},
  month = {Jan 30},
  note = {0027-8424 Journal Article},
  abstract = {We report on the design and characterization of a class of biomolecular
	interfaces based on derivatized poly(l-lysine)-grafted poly(ethylene
	glycol) copolymers adsorbed on negatively charged surfaces. As a
	model system, we synthesized biotin-derivatized poly(l-lysine)-grafted
	poly(ethylene glycol) copolymers, PLL-g-[(PEGm)((1-x)) (PEG-biotin)(x)],
	where x varies from 0 to 1. Monolayers were produced on titanium
	dioxide substrates and characterized by x-ray photoelectron spectroscopy.
	The specific biorecognition properties of these biotinylated surfaces
	were investigated with the use of radiolabeled streptavidin alone
	and within complex protein mixtures. The PLL-g-PEG-biotin monolayers
	specifically capture streptavidin, even from a complex protein mixture,
	while still preventing nonspecific adsorption of other proteins.
	This streptavidin layer can subsequently capture biotinylated proteins.
	Finally, with the use of microfluidic networks and protein arraying,
	we demonstrate the potential of this class of biomolecular interfaces
	for applications based on protein patterning.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11158560},
  endnotereftype = {Journal Article},
  keywords = {Binding Sites Biotin Escherichia coli Lysine/analogs & derivatives/*chemistry
	*Metals *Oxides Polyethylene Glycols/*chemistry Proteins/*chemistry
	Recombinant Proteins/chemistry Spectrometry, X-Ray Emission Streptavidin/*chemistry
	Streptomyces Surface Properties},
  shorttitle = {Monolayers of derivatized poly(L-lysine)-grafted poly(ethylene glycol)
	on metal oxides as a class of biomolecular interfaces},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11158560}
}

@ARTICLE{Runz2006,
  author = {Runz, H. and Miura, K. and Weiss, M. and Pepperkok, R.},
  title = {Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G},
  journal = {Embo J},
  year = {2006},
  volume = {25},
  pages = {2953-65},
  number = {13},
  month = {Jul 12},
  note = {0261-4189 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Alterations in endoplasmic reticulum (ER) cholesterol are fundamental
	for a variety of cellular processes such as the regulation of lipid
	homeostasis or efficient protein degradation. We show that reduced
	levels of cellular sterols cause a delayed ER-to-Golgi transport
	of the secretory cargo membrane protein ts-O45-G and a relocation
	to the ER of an endogenous protein cycling between the ER and the
	Golgi complex. Transport inhibition is characterized by a delay in
	the accumulation of ts-O45-G in ER-exit sites (ERES) and correlates
	with a reduced mobility of ts-O45-G within ER membranes. A simple
	mathematical model describing the kinetics of ER-exit predicts that
	reduced cargo loading to ERES and not the reduced mobility of ts-O45-G
	accounts for the delayed ER-exit and arrival at the Golgi. Consistent
	with this, membrane turnover of the COPII component Sec23p is delayed
	in sterol-depleted cells. Altogether, our results demonstrate the
	importance of sterol levels in COPII mediated ER-export.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16794576},
  endnotereftype = {Journal Article},
  keywords = {COP-Coated Vesicles/metabolism Cholesterol/*physiology Endoplasmic
	Reticulum/metabolism/*physiology Golgi Apparatus/metabolism Hela
	Cells Humans Intracellular Membranes/metabolism Kinetics Mannose-Binding
	Lectins/metabolism Membrane Glycoproteins/genetics/*metabolism Membrane
	Proteins/metabolism Models, Biological Monomeric GTP-Binding Proteins/metabolism
	Protein Transport Recombinant Fusion Proteins/genetics/metabolism
	Vesicular Transport Proteins/*metabolism Viral Envelope Proteins/genetics/*metabolism},
  shorttitle = {Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16794576}
}

@BOOK{Russ1998,
  title = {The Image Processing Handbook},
  publisher = {CRC Press},
  year = {1998},
  author = {Russ, JC},
  edition = {3rd edition},
  endnotereftype = {Book},
  isbn = {ISBN 0-8493-2532-1},
  shorttitle = {The Image Processing Handbook}
}

@ARTICLE{Sako1995,
  author = {Sako, Y. and Kusumi, A.},
  title = {Barriers for lateral diffusion of transferrin receptor in the plasma
	membrane as characterized by receptor dragging by laser tweezers:
	fence versus tether},
  journal = {J Cell Biol},
  year = {1995},
  volume = {129},
  pages = {1559-74},
  number = {6},
  month = {Jun},
  note = {0021-9525 Journal Article},
  abstract = {Our previous results indicated that the plasma membrane of cultured
	normal rat kidney fibroblastic cell is compartmentalized for diffusion
	of receptor molecules, and that long-range diffusion is the result
	of successive intercompartmental jumps (Sako, Y. and Kusumi, A. 1994.
	J. Cell Biol. 125:1251-1264). In the present study, we characterized
	the properties of intercompartmental boundaries by tagging transferrin
	receptor (TR) with either 210-nm-phi latex or 40-nm-phi colloidal
	gold particles, and by dragging the particle-TR complexes laterally
	along the plasma membrane using laser tweezers. Approximately 90%
	of the TR-particle complexes showed confined-type diffusion with
	a microscopic diffusion coefficient (Dmicro) of approximately 10(-9)
	cm2/s and could be dragged past the intercompartmental boundaries
	in their path by laser tweezers at a trapping force of 0.25 pN for
	gold-tagged TR and 0.8 pN for latex-tagged TR. At lower dragging
	forces between 0.05 and 0.1 pN, particle-TR complexes tended to escape
	from the laser trap at the boundaries, and such escape occurred in
	both the forward and backward directions of dragging. The average
	distance dragged was half of the confined distance of TR, which further
	indicates that particle-TR complexes escape at the compartment boundaries.
	Since variation in the particle size (40 and 210 nm, the particles
	are on the extracellular surface of the plasma membrane) hardly affects
	the diffusion rate and behavior of the particle-TR complexes at the
	compartment boundaries, and since treatment with cytochalasin D or
	vinblastin affects the movements of TR (Sako and Kusumi as cited
	above), argument has been advanced that the boundaries are present
	in the cytoplasmic domain. Rebound of the particle-TR complexes when
	they escape from the laser tweezers at the compartment boundaries
	suggests that the boundaries are elastic structures. These results
	are consistent with the proposal that the compartment boundaries
	consist of membrane skeleton or a membrane-associated part of the
	cytoskeleton (membrane skeleton fence model). Approximately 10% of
	TR exhibited slower diffusion (Dmicro approximately 10(-10)-10(-11)
	cm2/s) and binding to elastic structures.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7790354},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cell Membrane/*metabolism/ultrastructure Comparative
	Study Diffusion Fibroblasts Kidney Kinetics Lasers *Models, Structural
	Rats Receptors, Transferrin/*chemistry/*metabolism Time Factors},
  shorttitle = {Barriers for lateral diffusion of transferrin receptor in the plasma
	membrane as characterized by receptor dragging by laser tweezers:
	fence versus tether},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7790354}
}

@ARTICLE{Sako1994,
  author = {Sako, Y. and Kusumi, A.},
  title = {Compartmentalized structure of the plasma membrane for receptor movements
	as revealed by a nanometer-level motion analysis},
  journal = {J Cell Biol},
  year = {1994},
  volume = {125},
  pages = {1251-64},
  number = {6},
  month = {Jun},
  note = {0021-9525 Journal Article},
  abstract = {Movements of transferrin and alpha 2-macroglobulin receptor molecules
	in the plasma membrane of cultured normal rat kidney (NRK) fibroblastic
	cells were investigated by video-enhanced contrast optical microscopy
	with 1.8 nm spatial precision and 33 ms temporal resolution by labeling
	the receptors with the ligand-coated nanometer-sized colloidal gold
	particles. For both receptor species, most of the movement trajectories
	are of the confined diffusion type, within domains of approximately
	0.25 microns2 (500-700 nm in diagonal length). Movement within the
	domains is random with a diffusion coefficient approximately 10(-9)
	cm2/s, which is consistent with that expected for free Brownian diffusion
	of proteins in the plasma membrane. The receptor molecules move from
	one domain to one of the adjacent domains at an average frequency
	of 0.034 s-1 (the residence time within a domain approximately 29
	s), indicating that the plasma membrane is compartmentalized for
	diffusion of membrane receptors and that long-range diffusion is
	the result of successive intercompartmental jumps. The macroscopic
	diffusion coefficients for these two receptor molecules calculated
	on the basis of the compartment size and the intercompartmental jump
	rate are approximately 2.4 x 10(-11) cm2/s, which is consistent with
	those determined by averaging the long-term movements of many particles.
	Partial destruction of the cytoskeleton decreased the confined diffusion
	mode, increased the simple diffusion mode, and induced the directed
	diffusion (transport) mode. These results suggest that the boundaries
	between compartments are made of dynamically fluctuating membrane
	skeletons (membrane-skeleton fence model).},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8207056},
  endnotereftype = {Journal Article},
  keywords = {Animals *Cell Compartmentation/drug effects Cell Membrane/*metabolism/ultrastructure
	Cells, Cultured Cytochalasin D/pharmacology Cytoskeleton/drug effects
	Diffusion Fibroblasts Gold Colloid Histocytochemistry Kidney/cytology
	LDL-Receptor Related Protein 1 Microscopy, Interference Models, Biological
	Models, Chemical Motion Rats Receptors, Immunologic/*metabolism Receptors,
	Transferrin/*metabolism Video Recording Vinblastine/pharmacology},
  shorttitle = {Compartmentalized structure of the plasma membrane for receptor movements
	as revealed by a nanometer-level motion analysis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8207056}
}

@ARTICLE{Sako2000,
  author = {Sako, Y. and Minoghchi, S. and Yanagida, T.},
  title = {Single-molecule imaging of EGFR signalling on the surface of living
	cells},
  journal = {Nat Cell Biol},
  year = {2000},
  volume = {2},
  pages = {168-72},
  number = {3},
  month = {Mar},
  note = {1465-7392 Journal Article},
  abstract = {The early events in signal transduction from the epidermal growth
	factor (EGF) receptor (EGFR) are dimerization and autophosphorylation
	of the receptor, induced by binding of EGF. Here we observe these
	events in living cells by visualizing single molecules of fluorescent-dye-labelled
	EGF in the plasma membrane of A431 carcinoma cells. Single-molecule
	tracking reveals that the predominant mechanism of dimerization involves
	the formation of a cell-surface complex of one EGF molecule and an
	EGFR dimer, followed by the direct arrest of a second EGF molecule,
	indicating that the EGFR dimers were probably preformed before the
	binding of the second EGF molecule. Single-molecule fluorescence-resonance
	energy transfer shows that EGF-EGFR complexes indeed form dimers
	at the molecular level. Use of a monoclonal antibody specific to
	the phosphorylated (activated) EGFR reveals that the EGFR becomes
	phosphorylated after dimerization.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10707088},
  endnotereftype = {Journal Article},
  keywords = {Antibodies, Monoclonal/pharmacology Calcium/metabolism Carbocyanines
	Carcinoma/metabolism Cell Membrane/*metabolism Dimerization Energy
	Transfer/drug effects Epidermal Growth Factor/*metabolism Fluorescent
	Dyes Human Intracellular Fluid/metabolism Microscopy, Fluorescence/*methods
	Phosphorylation/drug effects Receptor, Epidermal Growth Factor/antagonists
	& inhibitors/*metabolism Rhodamines Signal Transduction/drug effects/*physiology
	Tumor Cells, Cultured},
  shorttitle = {Single-molecule imaging of EGFR signalling on the surface of living
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10707088}
}

@ARTICLE{Sako1998,
  author = {Sako, Y. and Nagafuchi, A. and Tsukita, S. and Takeichi, M. and Kusumi,
	A.},
  title = {Cytoplasmic regulation of the movement of E-cadherin on the free
	cell surface as studied by optical tweezers and single particle tracking:
	corralling and tethering by the membrane skeleton},
  journal = {J Cell Biol},
  year = {1998},
  volume = {140},
  pages = {1227-40},
  number = {5},
  month = {Mar 9},
  note = {0021-9525 Journal Article},
  abstract = {The translational movement of E-cadherin, a calcium-dependent cell-cell
	adhesion molecule in the plasma membrane in epithelial cells, and
	the mechanism of its regulation were studied using single particle
	tracking (SPT) and optical tweezers (OT). The wild type (Wild) and
	three types of artificial cytoplasmic mutants of E-cadherin were
	expressed in L-cells, and their movements were compared. Two mutants
	were E-cadherins that had deletions in the COOH terminus and lost
	the catenin-binding site(s) in the COOH terminus, with remaining
	116 and 21 amino acids in the cytoplasmic domain (versus 152 amino
	acids for Wild); these are called Catenin-minus and Short-tailed
	in this paper, respectively. The third mutant, called Fusion, is
	a fusion protein between E-cadherin without the catenin-binding site
	and alpha-catenin without its NH2-terminal half. These cadherins
	were labeled with 40-nm phi colloidal gold or 210-nm phi latex particles
	via a monoclonal antibody to the extracellular domain of E-cadherin
	for SPT or OT experiments, respectively. E-cadherin on the dorsal
	cell surface (outside the cell-cell contact region) was investigated.
	Catenin-minus and Short-tailed could be dragged an average of 1.1
	and 1.8 micron by OT (trapping force of 0.8 pN), and exhibited average
	microscopic diffusion coefficients (Dmicro) of 1.2 x 10(-10) and
	2.1 x 10(-10) cm2/s, respectively. Approximately 40% of Wild, Catenin-minus,
	and Short-tailed exhibited confined-type diffusion. The confinement
	area was 0.13 micron2 for Wild and Catenin-minus, while that for
	Short-tailed was greater by a factor of four. In contrast, Fusion
	could be dragged an average of only 140 nm by OT. Average Dmicro
	for Fusion measured by SPT was small (0.2 x 10(-10) cm2/s). These
	results suggest that Fusion was bound to the cytoskeleton. Wild consists
	of two populations; about half behaves like Catenin- minus, and the
	other half behaves like Fusion. It is concluded that the movements
	of the wild-type E-cadherin in the plasma membrane are regulated
	via the cytoplasmic domain by (a) tethering to actin filaments through
	catenin(s) (like Fusion) and (b) a corralling effect of the network
	of the membrane skeleton (like Catenin-minus). The effective spring
	constants of the membrane skeleton that contribute to the tethering
	and corralling effects as measured by the dragging experiments were
	30 and 5 pN/micron, respectively, indicating a difference in the
	skeletal structures that produce these two effects.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9490734},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport Cadherins/*metabolism Cell Line Cell
	Membrane/*metabolism Cytochalasins/pharmacology Cytoplasm/metabolism
	Cytoskeleton/metabolism Diffusion Mice Micromanipulation/methods
	Microscopy, Video/methods Optics},
  shorttitle = {Cytoplasmic regulation of the movement of E-cadherin on the free cell
	surface as studied by optical tweezers and single particle tracking:
	corralling and tethering by the membrane skeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9490734}
}

@ARTICLE{Sako1998a,
  author = {Sako, Y. and Nagafuchi, A. and Tsukita, S. and Takeichi, M. and Kusumi,
	A.},
  title = {Cytoplasmic regulation of the movement of E-cadherin on the free
	cell surface as studied by optical tweezers and single particle tracking:
	corralling and tethering by the membrane skeleton},
  journal = {J Cell Biol},
  year = {1998},
  volume = {140},
  pages = {1227-40},
  number = {5},
  month = {Mar 9},
  note = {98158717 0021-9525 Journal Article},
  abstract = {The translational movement of E-cadherin, a calcium-dependent cell-cell
	adhesion molecule in the plasma membrane in epithelial cells, and
	the mechanism of its regulation were studied using single particle
	tracking (SPT) and optical tweezers (OT). The wild type (Wild) and
	three types of artificial cytoplasmic mutants of E-cadherin were
	expressed in L-cells, and their movements were compared. Two mutants
	were E-cadherins that had deletions in the COOH terminus and lost
	the catenin-binding site(s) in the COOH terminus, with remaining
	116 and 21 amino acids in the cytoplasmic domain (versus 152 amino
	acids for Wild); these are called Catenin-minus and Short-tailed
	in this paper, respectively. The third mutant, called Fusion, is
	a fusion protein between E-cadherin without the catenin-binding site
	and alpha-catenin without its NH2-terminal half. These cadherins
	were labeled with 40-nm phi colloidal gold or 210-nm phi latex particles
	via a monoclonal antibody to the extracellular domain of E-cadherin
	for SPT or OT experiments, respectively. E-cadherin on the dorsal
	cell surface (outside the cell-cell contact region) was investigated.
	Catenin-minus and Short-tailed could be dragged an average of 1.1
	and 1.8 micron by OT (trapping force of 0.8 pN), and exhibited average
	microscopic diffusion coefficients (Dmicro) of 1.2 x 10(-10) and
	2.1 x 10(-10) cm2/s, respectively. Approximately 40% of Wild, Catenin-minus,
	and Short-tailed exhibited confined-type diffusion. The confinement
	area was 0.13 micron2 for Wild and Catenin-minus, while that for
	Short-tailed was greater by a factor of four. In contrast, Fusion
	could be dragged an average of only 140 nm by OT. Average Dmicro
	for Fusion measured by SPT was small (0.2 x 10(-10) cm2/s). These
	results suggest that Fusion was bound to the cytoskeleton. Wild consists
	of two populations; about half behaves like Catenin- minus, and the
	other half behaves like Fusion. It is concluded that the movements
	of the wild-type E-cadherin in the plasma membrane are regulated
	via the cytoplasmic domain by (a) tethering to actin filaments through
	catenin(s) (like Fusion) and (b) a corralling effect of the network
	of the membrane skeleton (like Catenin-minus). The effective spring
	constants of the membrane skeleton that contribute to the tethering
	and corralling effects as measured by the dragging experiments were
	30 and 5 pN/micron, respectively, indicating a difference in the
	skeletal structures that produce these two effects.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9490734},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Transport Cadherins/*metabolism Cell Line Cell Membrane/*metabolism
	Cytochalasins/pharmacology Cytoplasm/metabolism Cytoskeleton/metabolism
	Diffusion Mice Micromanipulation/methods Microscopy, Video/methods
	Optics},
  shorttitle = {Cytoplasmic regulation of the movement of E-cadherin on the free cell
	surface as studied by optical tweezers and single particle tracking:
	corralling and tethering by the membrane skeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9490734}
}

@ARTICLE{Sako1997,
  author = {Sako, Y. and Sekihata, A. and Yanagisawa, Y. and Yamamoto, M. and
	Shimada, Y. and Ozaki, K. and Kusumi, A.},
  title = {Comparison of two-photon excitation laser scanning microscopy with
	UV-confocal laser scanning microscopy in three-dimensional calcium
	imaging using the fluorescence indicator Indo-1},
  journal = {J Microsc},
  year = {1997},
  volume = {185 ( Pt 1)},
  pages = {9-20},
  month = {Jan},
  note = {0022-2720 Journal Article},
  abstract = {Two-photon excitation laser scanning fluorescence microscopy (2p-LSM)
	was compared with UV-excitation confocal laser scanning fluorescence
	microscopy (UV-CLSM) in terms of three-dimensional (3-D) calcium
	imaging of living cells in culture. Indo-1 was used as a calcium
	indicator. Since the excitation volume is more limited and excitation
	wavelengths are longer in 2p-LSM than in UV-CLSM, 2p-LSM exhibited
	several advantages over UV-CLSM: (1) a lower level of background
	signal by a factor of 6-17, which enhances the contrast by a factor
	of 6-21: (2) a lower rate of photobleaching by a factor of 2-4; (3)
	slightly lower phototoxicity. When 3-D images were repeatedly acquired,
	the calcium concentration determined by UV-CLSM depended strongly
	on the number of data acquisitions and the nuclear regions falsely
	exhibited low calcium concentrations. probably due to an interplay
	of different levels of photobleaching of Indo-1 and autofluorescence,
	while the calcium concentration evaluated by 2p-LSM was stable and
	homogeneous throughout the cytoplasm. The spatial resolution of 2p-LSM
	was worse by 10% in the focal plane and by 30% along the optical
	axis due to the longer excitation wavelength. This disadvantage can
	be overcome by the addition of a confocal pinhole (two-photon excitation
	confocal laser scanning fluorescence microscopy), which made the
	resolution similar to that in UV-CLSM. These results indicate that
	2p-LSM is preferable for repeated 3-D reconstruction of calcium concentration
	in living cells. In UV-CLSM, 0.18-mW laser power with a 2.6-phi pinhole
	(in normalized optical coordinate) gives better signal-to-noise ratio,
	contrast and resolution than 0.09-mW laser power with a 4.9-phi pinhole.
	However, since the damage to cells and the rate of photobleaching
	is substantially greater under the former condition, it is not suitable
	for repeated acquisition of 3-D images.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9057318},
  endnotereftype = {Journal Article},
  keywords = {Animals Calcium/*analysis Comparative Study *Indoles Mice *Microscopy,
	Confocal Ultraviolet Rays},
  shorttitle = {Comparison of two-photon excitation laser scanning microscopy with
	UV-confocal laser scanning microscopy in three-dimensional calcium
	imaging using the fluorescence indicator Indo-1},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9057318}
}

@ARTICLE{Sako2003,
  author = {Sako, Y. and Yanagida, T.},
  title = {Single-molecule visualization in cell biology},
  journal = {Nat Rev Mol Cell Biol},
  year = {2003},
  volume = {Suppl},
  pages = {SS1-5},
  month = {Sep},
  note = {1471-0072 Journal Article Review Review, Tutorial},
  abstract = {Recent progress in single-molecule detection techniques has allowed
	us to visualize the dynamic behaviour and reaction kinetics of individual
	biological molecules inside living cells. Single-molecule visualization
	provides a direct way to quantify, with a high spatial and temporal
	resolution, biological events inside cells at the single-molecule
	level. In this article, we discuss how single-molecule visualization
	can be used in cell biology.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14587519},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Physiology Eukaryotic Cells/*metabolism Fluorescent Dyes/metabolism
	Human Luminescent Proteins/metabolism Microscopy, Fluorescence Proteins/*metabolism},
  shorttitle = {Single-molecule visualization in cell biology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14587519}
}

@ARTICLE{saxtonBJ1997,
  author = {Saxton, M. J.},
  title = {Single-particle tracking: the distribution of diffusion coefficients},
  journal = {Biophys J},
  year = {1997},
  volume = {72},
  pages = {1744-53},
  number = {4},
  month = {Apr},
  note = {97237200 0006-3495 Journal Article},
  abstract = {In single-particle tracking experiments, the diffusion coefficient
	D may be measured from the trajectory of an individual particle in
	the cell membrane. The statistical distribution of single-trajectory
	diffusion coefficients is examined by Monte Carlo calculations. The
	width of this distribution may be useful as a measure of the heterogeneity
	of the membrane and as a test of models of hindered diffusion in
	the membrane. For some models, the distribution of the short-range
	diffusion coefficient is much narrower than the observed distribution
	for proteins diffusing in cell membranes. To aid in the analysis
	of single-particle tracking measurements, the distribution of D is
	examined for various definitions of D and for various trajectory
	lengths.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9083678},
  endnotereftype = {Journal Article},
  keywords = {Animal Cadherins/*metabolism Cell Membrane/*metabolism Cells, Cultured
	Diffusion Keratinocytes/metabolism Membrane Lipids/metabolism Membrane
	Proteins/metabolism Mice Models, Statistical Monte Carlo Method Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Single-particle tracking: the distribution of diffusion coefficients},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9083678}
}

@ARTICLE{saxtonBJ1995,
  author = {Saxton, M. J.},
  title = {Single-particle tracking: effects of corrals},
  journal = {Biophys J},
  year = {1995},
  volume = {69},
  pages = {389-98},
  number = {2},
  month = {Aug},
  note = {96133313 0006-3495 Journal Article},
  abstract = {Structural proteins of the membrane skeleton are thought to form "corrals"
	at the membrane surface, and these corrals may restrict lateral diffusion
	of membrane proteins. Recent experimental developments in single-particle
	tracking and laser trapping make it possible to examine the corral
	model in detail. Techniques to interpret these experiments are presented.
	First, escape times for a diffusing particle in a corral are obtained
	from Monte Carlo calculations and analytical solutions for various
	corral sizes, shapes, and escape probabilities, and reduced to a
	common curve. Second, the identification of corrals in tracking experiments
	is considered. The simplest way to identify corrals is by sight.
	If the walls are impermeable enough, a trajectory fills the corral
	before the diffusing particle escapes. The fraction of distinct sites
	visited before escape is calculated for corrals of various sizes,
	shapes, and escape probabilities, and reduced to a common curve.
	This fraction is also a measure of the probability that the diffusing
	species will react with another species in the corral before escaping.
	Finally, the effect of the sampling interval on the measurement of
	the short-range diffusion coefficient is examined.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8527652},
  endnotereftype = {Journal Article},
  keywords = {Biophysics Diffusion Human In Vitro Membrane Proteins/*chemistry Models,
	Chemical Motion Probability Support, U.S. Gov't, P.H.S.},
  shorttitle = {Single-particle tracking: effects of corrals},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8527652}
}

@ARTICLE{saxtionBJ1994,
  author = {Saxton, M. J.},
  title = {Single-particle tracking: models of directed transport},
  journal = {Biophys J},
  year = {1994},
  volume = {67},
  pages = {2110-9},
  number = {5},
  month = {Nov},
  note = {95161627 0006-3495 Journal Article},
  abstract = {Single-particle tracking techniques make it possible to measure motion
	of individual particles on the cell surface. In these experiments,
	individual trajectories are observed, so the data analysis must take
	into account the randomness of individual random walks. Methods of
	data analysis are discussed for models combining diffusion and directed
	motion. In the uniform flow model, a tracer simultaneously diffuses
	and undergoes directed motion. In the conveyor belt model, a tracer
	binds and unbinds to a uniform conveyor belt moving with constant
	velocity. If a tracer is bound, it moves at the velocity of the conveyor
	belt; if it is unbound, it diffuses freely. Trajectories are analyzed
	using parameters that measure the extent and asymmetry of the trajectory.
	A method of assessing the usefulness of such parameters is presented,
	and pitfalls in data analysis are discussed. Joint probability distributions
	of pairs of extent and asymmetry parameters are obtained for a pure
	random walk. These distributions can be used to show that a trajectory
	is not likely to have resulted from a pure random walk.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7858148},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport, Active Biophysics Cell Membrane/*metabolism
	Diffusion Human *Models, Biological Monte Carlo Method Movement Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Single-particle tracking: models of directed transport},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7858148}
}

@ARTICLE{SaxtonAnnurevBiophys1997.pdf,
  author = {Saxton, M. J. and Jacobson, K.},
  title = {Single-particle tracking: applications to membrane dynamics},
  journal = {Annu Rev Biophys Biomol Struct},
  year = {1997},
  volume = {26},
  pages = {373-99},
  note = {97385410 1056-8700 Journal Article Review Review, Tutorial},
  abstract = {Measurements of trajectories of individual proteins or lipids in the
	plasma membrane of cells show a variety of types of motion. Brownian
	motion is observed, but many of the particles undergo non-Brownian
	motion, including directed motion, confined motion, and anomalous
	diffusion. The variety of motion leads to significant effects on
	the kinetics of reactions among membrane-bound species and requires
	a revision of existing views of membrane structure and dynamics.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9241424},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Human Membrane Fluidity/*physiology Membrane Lipids/*metabolism
	Membrane Proteins/*metabolism Microscopy, Video/*methods Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Single-particle tracking: applications to membrane dynamics},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9241424}
}

@ARTICLE{sbalzariniBJ2006,
  author = {Sbalzarini, I. F. and Hayer, A. and Helenius, A. and Koumoutsakos,
	P.},
  title = {Simulations of (an)isotropic diffusion on curved biological surfaces},
  journal = {Biophys J},
  year = {2006},
  volume = {90},
  pages = {878-85},
  number = {3},
  month = {Feb 1},
  note = {0006-3495 (Print) Journal Article},
  abstract = {We present a computational particle method for the simulation of isotropic
	and anisotropic diffusion on curved biological surfaces that have
	been reconstructed from image data. The method is capable of handling
	surfaces of high curvature and complex shape, which are often encountered
	in biology. The method is validated on simple benchmark problems
	and is shown to be second-order accurate in space and time and of
	high parallel efficiency. It is applied to simulations of diffusion
	on the membrane of endoplasmic reticula (ER) in live cells. Diffusion
	simulations are conducted on geometries reconstructed from real ER
	samples and are compared to fluorescence recovery after photobleaching
	experiments in the same ER samples using the transmembrane protein
	tsO45-VSV-G, C-terminally tagged with green fluorescent protein.
	Such comparisons allow derivation of geometry-corrected molecular
	diffusion constants for membrane components from fluorescence recovery
	after photobleaching data. The results of the simulations indicate
	that the diffusion behavior of molecules in the ER membrane differs
	significantly from the volumetric diffusion of soluble molecules
	in the lumen of the same ER. The apparent speed of recovery differs
	by a factor of approximately 4, even when the molecular diffusion
	constants of the two molecules are identical. In addition, the specific
	shape of the membrane affects the recovery half-time, which is found
	to vary by a factor of approximately 2 in different ER samples.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16284262},
  endnotereftype = {Journal Article},
  shorttitle = {Simulations of (an)isotropic diffusion on curved biological surfaces},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16284262}
}

@ARTICLE{Sbalzarini2005,
  author = {I. F. Sbalzarini and P. Koumoutsakos},
  title = {Feature point tracking and trajectory analysis for video imaging
	in cell biology.},
  journal = {J Struct Biol},
  year = {2005},
  volume = {151},
  pages = {182--195},
  number = {2},
  month = {Aug},
  __markedentry = {[Kota]},
  abstract = {This paper presents a computationally efficient, two-dimensional,
	feature point tracking algorithm for the automated detection and
	quantitative analysis of particle trajectories as recorded by video
	imaging in cell biology. The tracking process requires no a priori
	mathematical modeling of the motion, it is self-initializing, it
	discriminates spurious detections, and it can handle temporary occlusion
	as well as particle appearance and disappearance from the image region.
	The efficiency of the algorithm is validated on synthetic video data
	where it is compared to existing methods and its accuracy and precision
	are assessed for a wide range of signal-to-noise ratios. The algorithm
	is well suited for video imaging in cell biology relying on low-intensity
	fluorescence microscopy. Its applicability is demonstrated in three
	case studies involving transport of low-density lipoproteins in endosomes,
	motion of fluorescently labeled Adenovirus-2 particles along microtubules,
	and tracking of quantum dots on the plasma membrane of live cells.
	The present automated tracking process enables the quantification
	of dispersive processes in cell biology using techniques such as
	moment scaling spectra.},
  bdsk-url-1 = {http://dx.doi.org/10.1016/j.jsb.2005.06.002},
  doi = {10.1016/j.jsb.2005.06.002},
  institution = {Institute of Computational Science, ETH Z{\"u}rich, 8092 Z{\"u}rich,
	Switzerland. sbalzarini@inf.ethz.ch},
  keywords = {Adenoviridae; Algorithms; Animals; Biology, methods; Cell Line; Cell
	Membrane; Computer Simulation; Endosomes, chemistry; Fluorescent
	Dyes; Humans; Image Processing, Computer-Assisted; Lipoproteins,
	LDL, metabolism; Microscopy, Fluorescence; Microscopy, Video; Microtubules,
	virology; Particle Size; Polyomavirus},
  language = {eng},
  medline-pst = {ppublish},
  owner = {Kota},
  pii = {S1047-8477(05)00126-7},
  pmid = {16043363},
  timestamp = {2011.03.12},
  url = {http://dx.doi.org/10.1016/j.jsb.2005.06.002}
}

@ARTICLE{sbalzarini2005BJ,
  author = {Sbalzarini, I. F. and Mezzacasa, A. and Helenius, A. and Koumoutsakos,
	P.},
  title = {Effects of organelle shape on fluorescence recovery after photobleaching},
  journal = {Biophys J},
  year = {2005},
  volume = {89},
  pages = {1482-92},
  number = {3},
  month = {Sep},
  note = {0006-3495 (Print) Journal Article},
  abstract = {The determination of diffusion coefficients from fluorescence recovery
	data is often complicated by geometric constraints imposed by the
	complex shapes of intracellular compartments. To address this issue,
	diffusion of proteins in the lumen of the endoplasmic reticulum (ER)
	is studied using cell biological and computational methods. Fluorescence
	recovery after photobleaching (FRAP) experiments are performed in
	tissue culture cells expressing GFP-KDEL, a soluble, fluorescent
	protein, in the ER lumen. The three-dimensional (3D) shape of the
	ER is determined by confocal microscopy and computationally reconstructed.
	Within these ER geometries diffusion of solutes is simulated using
	the method of particle strength exchange. The simulations are compared
	to experimental FRAP curves of GFP-KDEL in the same ER region. Comparisons
	of simulations in the 3D ER shapes to simulations in open 3D space
	show that the constraints imposed by the spatial confinement result
	in two- to fourfold underestimation of the molecular diffusion constant
	in the ER if the geometry is not taken into account. Using the same
	molecular diffusion constant in different simulations, the observed
	speed of fluorescence recovery varies by a factor of 2.5, depending
	on the particular ER geometry and the location of the bleached area.
	Organelle shape considerably influences diffusive transport and must
	be taken into account when relating experimental photobleaching data
	to molecular diffusion coefficients. This novel methodology combines
	experimental FRAP curves with high accuracy computer simulations
	of diffusion in the same ER geometry to determine the molecular diffusion
	constant of the solute in the particular ER lumen.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15951382},
  endnotereftype = {Journal Article},
  keywords = {Animals Biophysics/*methods Cell Membrane/metabolism Cercopithecus
	aethiops Computer Simulation Culture Techniques Cytoplasm/metabolism
	DNA/chemistry Diffusion Endoplasmic Reticulum/metabolism Fluorescence
	Green Fluorescent Proteins/chemistry Macromolecular Substances/chemistry
	Microscopy, Confocal Models, Statistical Nucleic Acid Conformation
	Photobleaching Protein Conformation Proteins/chemistry Research Support,
	Non-U.S. Gov't Spectrometry, Fluorescence/*methods Time Factors Vero
	Cells},
  shorttitle = {Effects of organelle shape on fluorescence recovery after photobleaching},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15951382}
}

@INCOLLECTION{Sbarita2004,
  author = {Sbarita, J.-B.},
  title = {Deconvolution Microscopy},
  booktitle = {Microscopy Techniques},
  publisher = {Springer},
  year = {2004},
  editor = {Rietdorf, J.},
  series = {Advances in Biochemical Engineering/Biotechnology},
  address = {Heidelberg},
  endnotereftype = {Book Section},
  shorttitle = {Deconvolution Microscopy}
}

@ARTICLE{Scales1997,
  author = {Scales, S. J. and Pepperkok, R. and Kreis, T. E.},
  title = {Visualization of ER-to-Golgi transport in living cells reveals a
	sequential mode of action for COPII and COPI},
  journal = {Cell},
  year = {1997},
  volume = {90},
  pages = {1137-48},
  number = {6},
  month = {Sep 19},
  note = {0092-8674 (Print) Journal Article},
  abstract = {Exocytic transport from the endoplasmic reticulum (ER) to the Golgi
	complex has been visualized in living cells using a chimera of the
	temperature-sensitive glycoprotein of vesicular stomatitis virus
	and green fluorescent protein (ts-G-GFP[ct]). Upon shifting to permissive
	temperature, ts-G-GFP(ct) concentrates into COPII-positive structures
	close to the ER, which then build up to form an intermediate compartment
	or transport complex, containing ERGIC-53 and the KDEL receptor,
	where COPII is replaced by COPI. These structures appear heterogenous
	and move in a microtubule-dependent manner toward the Golgi complex.
	Our results suggest a sequential mode of COPII and COPI action and
	indicate that the transport complexes are ER-to-Golgi transport intermediates
	from which COPI may be involved in recycling material to the ER.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9323141},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport/physiology Carrier Proteins/*metabolism
	Cell Compartmentation/physiology Cell Membrane/metabolism Cercopithecus
	aethiops Coatomer Protein Endoplasmic Reticulum/*metabolism Exocytosis/physiology
	Golgi Apparatus/*metabolism Green Fluorescent Proteins Luminescent
	Proteins *Membrane Glycoproteins Membrane Proteins/*metabolism Microtubules/metabolism
	Phosphoproteins/*metabolism Recombinant Fusion Proteins/metabolism
	Research Support, Non-U.S. Gov't *Saccharomyces cerevisiae Proteins
	Temperature Vero Cells Viral Envelope Proteins},
  shorttitle = {Visualization of ER-to-Golgi transport in living cells reveals a sequential
	mode of action for COPII and COPI},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9323141}
}

@ARTICLE{schuetzBJ1997,
  author = {Sch\"{u}tz, G. J. and Schindler, H. and Schmidt, T.},
  title = {Single-molecule microscopy on model membranes reveals anomalous diffusion},
  journal = {Biophys J},
  year = {1997},
  volume = {73},
  pages = {1073-80},
  number = {2},
  month = {Aug},
  note = {97395719 0006-3495 Journal Article},
  abstract = {The lateral mobility of lipids in phospholipid membranes has attracted
	numerous experimental and theoretical studies, inspired by the model
	of Singer and Nicholson (1972. Science, 175:720-731) and the theoretical
	description by Saffman and Delbruck (1975. Proc. Natl. Acad. Sci.
	USA. 72:3111-3113). Fluorescence recovery after photobleaching (FRAP)
	is used as the standard experimental technique for the study of lateral
	mobility, yielding an ensemble-averaged diffusion constant. Single-particle
	tracking (SPT) and the recently developed single-molecule imaging
	techniques now give access to data on individual displacements of
	molecules, which can be used for characterization of the mobility
	in a membrane. Here we present a new type of analysis for tracking
	data by making use of the probability distribution of square displacements.
	The potential of this new type of analysis is shown for single-molecule
	imaging, which was employed to follow the motion of individual fluorescence-labeled
	lipids in two systems: a fluid-supported phospholipid membrane and
	a solid polymerstabilized phospholipid monolayer. In the fluid membrane,
	a high-mobility component characterized by a diffusion constant of
	4.4 microns2/s and a low-mobility component characterized by a diffusion
	constant of 0.07 micron2/s were identified. It is proposed that the
	latter characterizes the so-called immobile fraction often found
	in FRAP experiments. In the polymer-stabilized system, diffusion
	restricted to corrals of 140 nm was directly visualized. Both examples
	show the potentials of such detailed analysis in combination with
	single-molecule techniques: with minimal interference with the native
	structure, inhomogeneities of membrane mobility can be resolved with
	a spatial resolution of 100 nm, well below the diffraction limit.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9251823},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Dimyristoylphosphatidylcholine/*chemistry Fluorescent Dyes
	Kinetics Lipid Bilayers/*chemistry Liposomes/*chemistry Microscopy,
	Fluorescence/methods Models, Chemical Molecular Conformation Phosphatidylcholines/*chemistry
	Phosphatidylethanolamines/*chemistry Rhodamines/*chemistry Sensitivity
	and Specificity Support, Non-U.S. Gov't},
  shorttitle = {Single-molecule microscopy on model membranes reveals anomalous diffusion},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9251823}
}

@ARTICLE{Schernewski2001,
  author = {Schernewski, G. and Julich, W. D.},
  title = {Risk assessment of virus infections in the Oder estuary (southern
	Baltic) on the basis of spatial transport and virus decay simulations},
  journal = {Int J Hyg Environ Health},
  year = {2001},
  volume = {203},
  pages = {317-25},
  number = {4},
  month = {May},
  note = {21328255 1438-4639 Journal Article},
  abstract = {The large Oder (Szczecin) Lagoon (687 km2) at the German-Polish border,
	close to the Baltic Sea, suffers from severe eutrophication and water
	quality problems due to high discharge of water, nutrients and pollutants
	by the river Oder. Sewage treatment around the lagoon has been very
	much improved during the last years, but large amounts of sewage
	still enter the Oder river. Human pathogenic viruses generally can
	be expected in all surface waters that are affected by municipal
	sewage. There is an increasing awareness that predisposed persons
	can be infected by a few infective units or even a single active
	virus. Another new aspect is, that at least polioviruses attached
	to suspended particles can be infective for weeks and therefore be
	transported over long distances. Therefore, the highest risk of virus
	inputs arise from the large amounts of untreated sewage of the city
	of Szczecin (Poland), which are released into the river Oder and
	transported to the lagoon and the Baltic Sea. Summer tourism is the
	most important economical factor in this coastal region and further
	growth is expected. Human pathogenic viruses might be a serious problem
	for bathing water quality and sustainable summer tourism. The potential
	hazard of virus infections along beaches and shores of the Oder lagoon
	and adjacent parts of the Baltic Sea is evaluated on the basis of
	model simulations and laboratory results. We used two scenarios for
	the Older Lagoon considering free viruses and viruses attached to
	suspended particle matter. The spatial impact of the average virus
	release in the city of Szczecin during summer (bathing period) was
	simulated with a hydrodynamic and particle tracking model. Simulations
	suggest that due to fast inactivation, free viruses in the water
	represent a risk only in the river and near the river mouth. On the
	other hand, viruses attached to suspended matter can affect large
	areas of the eastern, Polish part of the lagoon (Grosses Haff). At
	the same time the accumulation of viruses on suspended particulate
	matter increases the likelihood of an infection after incorporation
	of such a particle. There is no evidence, that there is a risk of
	virus infections in the western part of the lagoon (Kleines Haff)
	or along the outer Baltic Sea coast.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11434212},
  endnotereftype = {Journal Article},
  keywords = {Bathing Beaches/standards Eutrophication Germany Poland Risk Assessment/*methods
	Seawater/*adverse effects/analysis Sewage/virology Virus Diseases/*transmission
	*Water Microbiology},
  shorttitle = {Risk assessment of virus infections in the Oder estuary (southern
	Baltic) on the basis of spatial transport and virus decay simulations},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11434212}
}

@ARTICLE{Schmundt1998,
  author = {Schmundt, D and Stitt, M and Jﾃ､hne, B and Schurr, U},
  title = {Quantitative analysis of the local rates of growth of dicot leaves
	at a high temporal and spatial resolution, using image sequence analysis},
  journal = {The Plant Journal},
  year = {1998},
  volume = {16},
  pages = {505-514},
  number = {4},
  note = {pdf},
  endnotereftype = {Journal Article},
  shorttitle = {Quantitative analysis of the local rates of growth of dicot leaves
	at a high temporal and spatial resolution, using image sequence analysis}
}

@ARTICLE{schnappCMOT1988,
  author = {Schnapp, B. J. and Gelles, J. and Sheetz, M. P.},
  title = {Nanometer-scale measurements using video light microscopy},
  journal = {Cell Motil Cytoskeleton},
  year = {1988},
  volume = {10},
  pages = {47-53},
  number = {1-2},
  note = {89028766 0886-1544 Journal Article},
  abstract = {Video and digital image processing have been used to amplify the contrast
	of light microscopic images, making it possible to observe in real
	time the diffraction images of cell structures 10 times smaller than
	the Raleigh resolution limit of 0.2 micron. In this paper we discuss
	how quantitative analysis of diffraction images can be used to extract
	information about motion or structure at the nanometer level. This
	issue is considered in the context of a method for tracking the motion
	of kinesin-coated beads on microtubules with 1-2 nm precision (Gelles
	et al.:Nature 331:450-453, 1988).},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3141071},
  endnotereftype = {Journal Article},
  keywords = {Cell Movement Kinesin Microscopy/*methods Microtubule Proteins/analysis
	Nerve Tissue Proteins/analysis Support, Non-U.S. Gov't Support, U.S.
	Gov't, P.H.S. *Video Recording},
  shorttitle = {Nanometer-scale measurements using video light microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3141071}
}

@ARTICLE{Scholl2000,
  author = {Scholl, M. and Sprossler, C. and Denyer, M. and Krause, M. and Nakajima,
	K. and Maelicke, A. and Knoll, W. and Offenhausser, A.},
  title = {Ordered networks of rat hippocampal neurons attached to silicon oxide
	surfaces},
  journal = {J Neurosci Methods},
  year = {2000},
  volume = {104},
  pages = {65-75},
  number = {1},
  month = {Dec 15},
  note = {0165-0270 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {The control of neuronal cell position and outgrowth is of fundamental
	interest in the development of applications ranging from cellular
	biosensors to tissue engineering. We have produced rectangular networks
	of functional rat hippocampal neurons on silicon oxide surfaces.
	Attachment and network formation of neurons was guided by a geometrical
	grid pattern of the adhesion peptide PA22-2 which matches in sequence
	a part of the A-chain of laminin. PA22-2 was applied by contact printing
	onto the functionalised silicon oxide surface and was immobilised
	by hetero-bifunctional cross-linking with sulfo-GMBS. Geometric pattern
	matching was achieved by microcontact printing using a polydimethylsiloxane
	(PDMS) stamp. In this way the produced grid pattern ranged from 3
	to 20 microm in line width and from 50 to 100 microm in line distances.
	As shown by atomic force microscopy (AFM), line widths and line distances
	of the peptide pattern differ less than 0.5 microm from the used
	PDMS stamp. The height of the layer of immobilised PA22-2 was approximately
	3.5 nm implying the layer to be monomolecular. Immobilised PA22-2
	was capable of binding anti-PA22-2 antibodies indicating that the
	function of the peptide was not compromised by immobilisation. Rat
	hippocampal neurons, cultured at low density in serum-free medium,
	were applied to the growth matrix of PA22-2-coated substrates and,
	within 1-3 h of culture, formed a network-like pattern that more
	or less matched the printed grid. Reliability and reproducibility
	of neuronal network formation depended on the geometry, line width
	and node diameter of the grid pattern. The immobilised neurons showed
	resting membrane potentials comparable with controls and, already
	after 1 day of culture, were capable of eliciting action potentials.
	The suitability of the immobilised neurons for the study of man-made
	neural networks and for multi-site recordings from a functional neuronal
	network is discussed.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11163412},
  endnotereftype = {Journal Article},
  keywords = {Animals Biosensing Techniques/instrumentation/methods Cell Adhesion/*drug
	effects/physiology Cell Culture Techniques/instrumentation/*methods
	Cell Size/drug effects/physiology Cells, Cultured/drug effects/physiology
	Electrophysiology/instrumentation/*methods Fetus Hippocampus/cytology/*physiology
	Membrane Potentials/drug effects/physiology Nerve Net/cytology/drug
	effects/*physiology Neurons/cytology/drug effects/*physiology Oxides/*pharmacology
	Peptides/pharmacology Rats Silicon Compounds/*pharmacology},
  shorttitle = {Ordered networks of rat hippocampal neurons attached to silicon oxide
	surfaces},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11163412}
}

@INPROCEEDINGS{Schwarzfischer2011,
  author = {Schwarzfischer, Michael and Marr, Carsten and Krumsiek, Jan and Hoppe,
	PS},
  title = {Efficient fluorescence image normalization for time lapse movies},
  booktitle = {Microscopic Image Analysis with Applications in Biology, Heidelberg,
	Germany, September 2, 2011},
  year = {2011},
  number = {x},
  pages = {3--7},
  file = {:D$\backslash$:/\_Kota/Research\_Ref/bleaching/miaab-2011-h-schwarzfischer.pdf:pdf},
  keywords = {backgroundSubtraction},
  mendeley-tags = {backgroundSubtraction},
  owner = {Kota Miura},
  timestamp = {2011.11.04},
  url = {http://www.helmholtz-muenchen.de/fileadmin/CMB/PDF/jkrumsiek/Schwarzfischer2011\_imageprocessing.pdf}
}

@ARTICLE{Scotchford2003,
  author = {Scotchford, C. A. and Ball, M. and Winkelmann, M. and Voros, J. and
	Csucs, C. and Brunette, D. M. and Danuser, G. and Textor, M.},
  title = {Chemically patterned, metal-oxide-based surfaces produced by photolithographic
	techniques for studying protein- and cell-interactions. II: Protein
	adsorption and early cell interactions},
  journal = {Biomaterials},
  year = {2003},
  volume = {24},
  pages = {1147-58},
  number = {7},
  month = {Mar},
  note = {0142-9612 (Print) Journal Article},
  abstract = {Protein adsorption and adhesion of primary human osteoblasts on chemically
	patterned, metal-oxide-based surfaces comprising combinations of
	titanium, aluminium, vanadium and niobium were investigated. Single
	metal samples with a homogeneous surface and bimetal samples with
	a surface pattern produced by photolithographic techniques were used.
	The physical and chemical properties of the samples have been extensively
	characterised and are presented in a companion paper. Here, we describe
	their properties in terms of cell responses during the initial 24h
	of cell culture. Regarding the cell number and activity there was
	no significant difference between any of the single metal surfaces.
	However the morphology of cells on vanadium surfaces became spindle-like.
	In contrast to the behaviour on single metal samples, cells exhibited
	a pronounced reaction on bimetallic surfaces that contained aluminium.
	Cells tended to stay away from aluminium, which was the least favoured
	metal in all two-metal combinations. An initial cell alignment relative
	to the pattern geometry was detectable after 2h and was fully developed
	after 18h of incubation. The organisation of f-actin and microtubules
	as well as the localisation of vinculin were all more pronounced
	on non-aluminium regions. We hypothesised that the differences in
	cell response could be associated with differences in the adsorption
	of serum proteins onto the various metal oxides. Protein adsorption
	experiments were performed using microscopy in conjunction with immunofluorescent
	stains. They indicated that both fibronectin and albumin adsorption
	were significantly greater on the non-aluminium regions, suggesting
	that differences in cellular response correlate with a modulation
	of the concentration of serum proteins on the surface.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12527255},
  endnotereftype = {Journal Article},
  keywords = {Adsorption Albumins/*metabolism Aluminum/chemistry Biocompatible Materials
	Cell Adhesion Molecules/metabolism *Cell Communication Cell Culture
	Techniques Humans Osteoblasts/*cytology/metabolism Protein Binding
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.
	*Surface Properties Titanium Vanadium},
  shorttitle = {Chemically patterned, metal-oxide-based surfaces produced by photolithographic
	techniques for studying protein- and cell-interactions. II: Protein
	adsorption and early cell interactions},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12527255}
}

@ARTICLE{Seksek1997,
  author = {Seksek, O. and Biwersi, J. and Verkman, A. S.},
  title = {Translational diffusion of macromolecule-sized solutes in cytoplasm
	and nucleus},
  journal = {J Cell Biol},
  year = {1997},
  volume = {138},
  pages = {131-42},
  number = {1},
  month = {Jul 14},
  note = {0021-9525 Journal Article},
  abstract = {Fluorescence recovery after photobleaching (FRAP) was used to quantify
	the translational diffusion of microinjected FITC-dextrans and Ficolls
	in the cytoplasm and nucleus of MDCK epithelial cells and Swiss 3T3
	fibroblasts. Absolute diffusion coefficients (D) were measured using
	a microsecond-resolution FRAP apparatus and solution standards. In
	aqueous media (viscosity 1 cP), D for the FITC-dextrans decreased
	from 75 to 8.4 x 10(-7) cm2/s with increasing dextran size (4-2,000
	kD). D in cytoplasm relative to that in water (D/Do) was 0.26 +/-
	0.01 (MDCK) and 0.27 +/- 0.01 (fibroblasts), and independent of FITC-dextran
	and Ficoll size (gyration radii [RG] 40-300 A). The fraction of mobile
	FITC-dextran molecules (fmob), determined by the extent of fluorescence
	recovery after spot photobleaching, was >>0.75 for RG << 200 A, but
	decreased to <<0.5 for RG >> 300 A. The independence of D/Do on FITC-dextran
	and Ficoll size does not support the concept of solute "sieving"
	(size-dependent diffusion) in cytoplasm. Photobleaching measurements
	using different spot diameters (1.5-4 micron) gave similar D/Do,
	indicating that microcompartments, if present, are of submicron size.
	Measurements of D/Do and fmob in concentrated dextran solutions,
	as well as in swollen and shrunken cells, suggested that the low
	fmob for very large macromolecules might be related to restrictions
	imposed by immobile obstacles (such as microcompartments) or to anomalous
	diffusion (such as percolation). In nucleus, D/Do was 0.25 +/- 0.02
	(MDCK) and 0.27 +/- 0.03 (fibroblasts), and independent of solute
	size (RG 40-300 A). Our results indicate relatively free and rapid
	diffusion of macromolecule-sized solutes up to approximately 500
	kD in cytoplasm and nucleus.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9214387},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animals Cell Line Cell Nucleus/metabolism Cytoplasm/*metabolism
	Dextrans/metabolism/pharmacology Diffusion Dogs Ficoll/analogs &
	derivatives/metabolism/pharmacology Fluorescein-5-isothiocyanate/analogs
	& derivatives/metabolism/pharmacology Fluorescence Macromolecular
	Substances Mice Research Support, Non-U.S. Gov't Research Support,
	U.S. Gov't, P.H.S. Solutions Temperature},
  shorttitle = {Translational diffusion of macromolecule-sized solutes in cytoplasm
	and nucleus},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9214387}
}

@ARTICLE{Serge2002,
  author = {Serge, A. and Fourgeaud, L. and Hemar, A. and Choquet, D.},
  title = {Receptor activation and homer differentially control the lateral
	mobility of metabotropic glutamate receptor 5 in the neuronal membrane},
  journal = {J Neurosci},
  year = {2002},
  volume = {22},
  pages = {3910-20},
  number = {10},
  month = {May 15},
  note = {22014117 1529-2401 Journal Article},
  abstract = {Glutamate receptors are clustered at the membrane through interactions
	with intracellular scaffolding proteins and cytoskeletal elements
	but can also be found in intracellular compartments or dispersed
	in the membrane. This distribution results from an equilibrium between
	the different pools of receptors whose dynamic is poorly known. The
	group I metabotropic glutamate receptor 5 (mGluR5) is concentrated
	in an annulus around the postsynaptic density but also found in large
	amounts in the extrasynaptic membrane. To analyze the dynamic of
	stabilization of mGluR5, we used single-particle tracking, force
	measurements, and fluorescence recovery to measure the mobility of
	mGluR5. We found that receptor activation increases receptor diffusion,
	whereas the scaffolding protein Homer favors confinement of receptor
	movements within clusters of Homer-mGluR5. However, this stabilization
	is reversible, because even in the presence of Homer, receptors still
	enter and exit from clusters at fast rates. Furthermore, clusters
	themselves are highly dynamic both in their movements and in their
	composition, which can vary within tens of seconds. Thus, exchange
	of receptors between dispersed and clustered states is fast and regulated
	during physiological processes. These properties may explain certain
	fast changes in receptor composition observed at postsynaptic densities.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12019310},
  endnotereftype = {Journal Article},
  keywords = {Animal Carrier Proteins/genetics/*metabolism Cell Line Cell Membrane/drug
	effects/*metabolism Cells, Cultured Diffusion/drug effects Epithelial
	Cells/cytology/drug effects/metabolism Excitatory Amino Acid Agonists/pharmacology
	Immunohistochemistry Luminescent Proteins/genetics Microscopy, Video
	Microspheres Neurons/cytology/drug effects/*metabolism Neuropeptides/genetics/*metabolism
	Protein Binding/physiology Protein Isoforms/genetics/metabolism Protein
	Transport/drug effects/*physiology Proto-Oncogene Proteins c-myc/genetics
	Rats Receptor Aggregation/drug effects/physiology Receptors, Metabotropic
	Glutamate/genetics/*metabolism Recombinant Fusion Proteins/genetics/metabolism
	Support, Non-U.S. Gov't Transfection},
  shorttitle = {Receptor activation and homer differentially control the lateral mobility
	of metabotropic glutamate receptor 5 in the neuronal membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12019310}
}

@ARTICLE{Sezgin2004,
  author = {Sezgin, Sankur},
  title = {Survey over image thresholding techniques and quantitative performance
	evaluation},
  journal = {Journal of Electronic Imaging},
  year = {2004},
  volume = {13},
  pages = {146-165},
  endnotereftype = {Journal Article},
  shorttitle = {Survey over image thresholding techniques and quantitative performance
	evaluation}
}

@ARTICLE{Sheets1997,
  author = {Sheets, E. D. and Lee, G. M. and Simson, R. and Jacobson, K.},
  title = {Transient confinement of a glycosylphosphatidylinositol-anchored
	protein in the plasma membrane},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {12449-58},
  number = {41},
  month = {Oct 14},
  note = {98026066 0006-2960 Journal Article},
  abstract = {Glycosylphosphatidylinositol (GPI)-anchored proteins participate in
	many cell surface functions; however, the molecular associations
	of these lipid-linked proteins within the plasma membrane are not
	well understood. Recent biochemical analyses of detergent insoluble
	membrane fractions have suggested that GPI-anchored proteins may
	be associated with glycosphingolipid (GSL)-enriched domains that
	also contain cholesterol and signaling molecules such as Src family
	kinases and, in some cases, caveolae. The movements of two components
	of the putative GSL-enriched domains, Thy-1, a GPI-anchored protein,
	and GM1, a GSL, were followed with single particle tracking on C3H
	10T1/2 cell surfaces and categorized into four modes of lateral transport,
	fast diffusion, slow anomalous diffusion, diffusion confined to 325-370
	nm diameter regions, and a fraction of molecules that was essentially
	stationary on the 6.6 s time scale. Longer observations (60 s) showed
	that Thy-1 and GM1 are transiently confined for 7-9 s to regions
	averaging 260-330 nm in diameter. Approximately 35-37% of both Thy-1
	and GM1 undergo confined diffusion, whereas only 16% of fluorescein
	phosphatidylethanolamine, a phospholipid analog which is not expected
	to be found in the GSL domains, experience confined diffusion to
	regions averaging approximately 230 nm in diameter. Further, when
	glycosphingolipid expression was reduced approximately 40% with the
	glucosylceramide synthase inhibitor, d-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol,
	the percentage of trajectories exhibiting confinement and the size
	of the confining domain for Thy-1 were reduced approximately 1.5-fold.
	In contrast, extraction of cells with Triton X-100 leaves the fraction
	of molecules confined and the domain sizes of Thy-1 and GM1 unchanged.
	Our results are consistent with the preferential association of GPI-anchored
	proteins with glycosphingolipid-enriched domains and suggest that
	the confining domains may be the in vivo equivalent of the detergent
	insoluble membrane fractions.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9376349},
  endnotereftype = {Journal Article},
  keywords = {Animal Biological Transport Cell Line Cell Membrane/*chemistry/metabolism
	Glycosphingolipids/chemistry Glycosylphosphatidylinositols/*chemistry/metabolism
	Membrane Proteins/*chemistry/metabolism Mice Models, Molecular Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Transient confinement of a glycosylphosphatidylinositol-anchored protein
	in the plasma membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9376349}
}

@ARTICLE{Sheetz1990,
  author = {Sheetz, M. and Elson, E. and Kucik, D.},
  title = {To flow or not to flow?},
  journal = {Nature},
  year = {1990},
  volume = {345},
  pages = {28},
  number = {6270},
  month = {May 3},
  note = {90231452 0028-0836 Comment Letter},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2330048},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport Cell Movement Diffusion Membrane Lipids/*metabolism
	Membrane Proteins/metabolism *Models, Biological},
  shorttitle = {To flow or not to flow?},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2330048}
}

@ARTICLE{Sheetz1995,
  author = {Sheetz, M. P.},
  title = {Cellular plasma membrane domains},
  journal = {Mol Membr Biol},
  year = {1995},
  volume = {12},
  pages = {89-91},
  number = {1},
  month = {Jan-Mar},
  note = {95284894 0968-7688 Journal Article Review Review, Tutorial},
  abstract = {The plasma membranes of migrating cells differentiate into at least
	three distinct domains as defined by the laser tweezers and the motile
	behaviour of particles bound to specific membrane glycoproteins.
	These domains are important for steps in the cell migration process.
	First, there is a domain at the leading edge of the lamellipodium
	where preferential attachment of cross-linked glycoproteins to the
	cytoskeleton occurs. The second domain at the rear of the cell is
	differentiated for releasing from substrata and shows decreased support
	of the membrane by the cytoskeleton. The third domain is the highly
	curved region(s) of the plasma membrane wherein certain membrane
	glycoproteins concentrate and is a site for controlling extension
	and attachment. Using single particle tracking and video analysis
	we find that the quantitative differences between plasma membrane
	domains are in the 4-20-fold range at any given time. These values
	are consistent with the rapid fluctuations seen in cell migration
	rates and directions. Over a longer time-scale, cells can possibly
	integrate these selective advantages to give a much higher overall
	fidelity for cell chemotaxis and neuronal path finding.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7767389},
  endnotereftype = {Journal Article},
  keywords = {Cell Membrane/chemistry/*metabolism Fibroblasts/metabolism/ultrastructure
	Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S.},
  shorttitle = {Cellular plasma membrane domains},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7767389}
}

@ARTICLE{sheetzNAT1989,
  author = {Sheetz, M. P. and Turney, S. and Qian, H. and Elson, E. L.},
  title = {Nanometre-level analysis demonstrates that lipid flow does not drive
	membrane glycoprotein movements},
  journal = {Nature},
  year = {1989},
  volume = {340},
  pages = {284-8},
  number = {6231},
  month = {Jul 27},
  note = {89314153 0028-0836 Journal Article},
  abstract = {Nanometre-level analyses of the movements of membrane glycoproteins
	tagged with gold particles demonstrate that diffusing particles are
	not under the influence of a lipid flow, although a subset of particles
	which appear attached to the cytoskeleton are moving rearward.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2747796},
  endnotereftype = {Journal Article},
  keywords = {Animal Benzimidazoles/pharmacology Biological Transport Concanavalin
	A Cytochalasin D Cytochalasins/pharmacology Cytoskeleton/drug effects
	Diffusion Gold Macrophages/metabolism Membrane Glycoproteins/analysis/*metabolism
	Membrane Lipids/*physiology Mice Microchemistry Models, Biological
	Nocodazole Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S.
	Support, U.S. Gov't, P.H.S.},
  shorttitle = {Nanometre-level analysis demonstrates that lipid flow does not drive
	membrane glycoprotein movements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2747796}
}

@ARTICLE{Shima1999,
  author = {Shima, D. T. and Scales, S. J. and Kreis, T. E. and Pepperkok, R.},
  title = {Segregation of COPI-rich and anterograde-cargo-rich domains in endoplasmic-reticulum-to-Golgi
	transport complexes},
  journal = {Curr Biol},
  year = {1999},
  volume = {9},
  pages = {821-4},
  number = {15},
  month = {Jul 29-Aug 12},
  note = {0960-9822 (Print) Journal Article},
  abstract = {Membrane traffic between the endoplasmic reticulum (ER) and the Golgi
	complex is regulated by two vesicular coat complexes, COPII and COPI.
	COPII has been implicated in the selective packaging of anterograde
	cargo into coated transport vesicles budding from the ER [1]. In
	mammalian cells, these vesicles coalesce to form tubulo-vesicular
	transport complexes (TCs), which shuttle anterograde cargo from the
	ER to the Golgi complex [2] [3] [4]. In contrast, COPI-coated vesicles
	are proposed to mediate recycling of proteins from the Golgi complex
	to the ER [1] [5] [6] [7]. The binding of COPI to COPII-coated TCs
	[3] [8] [9], however, has led to the proposal that COPI binds to
	TCs and specifically packages recycling proteins into retrograde
	vesicles for return to the ER [3] [9]. To test this hypothesis, we
	tracked fluorescently tagged COPI and anterograde-transport markers
	simultaneously in living cells. COPI predominated on TCs shuttling
	anterograde cargo to the Golgi complex and was rarely observed on
	structures moving in directions consistent with retrograde transport.
	Furthermore, a progressive segregation of COPI-rich domains and anterograde-cargo-rich
	domains was observed in the TCs. This segregation and the directed
	motility of COPI-containing TCs were inhibited by antibodies that
	blocked COPI function. These observations, which are consistent with
	previous biochemical data [2] [9], suggest a role for COPI within
	TCs en route to the Golgi complex. By sequestering retrograde cargo
	in the anterograde-directed TCs, COPI couples the sorting of ER recycling
	proteins [10] to the transport of anterograde cargo.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10469566},
  endnotereftype = {Journal Article},
  keywords = {Animals Antibodies, Monoclonal/pharmacology Biological Transport,
	Active Carbocyanines Cercopithecus aethiops Coat Protein Complex
	I/antagonists & inhibitors/immunology/*metabolism Endoplasmic Reticulum/*metabolism
	Fluorescent Dyes Golgi Apparatus/*metabolism Green Fluorescent Proteins
	Luminescent Proteins/metabolism Microscopy, Confocal Models, Biological
	Research Support, Non-U.S. Gov't Vero Cells},
  shorttitle = {Segregation of COPI-rich and anterograde-cargo-rich domains in endoplasmic-reticulum-to-Golgi
	transport complexes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10469566}
}

@ARTICLE{d4847rohtuA,
  author = {Siegert, F and Weijer, C J and Nomura, A and Miike, H},
  title = {A gradient method for the quantitative analysis of cell movement
	and tissue flow and its application to the analysis of multicellular
	Dictyostelium development.},
  journal = {J. Cell Sci.},
  year = {1994},
  volume = {107},
  pages = {97-104},
  endnotereftype = {Journal Article},
  keywords = {locomotion motility locomotion motility development pattern formation
	morphogenesis},
  shorttitle = {A gradient method for the quantitative analysis of cell movement and
	tissue flow and its application to the analysis of multicellular
	Dictyostelium development.}
}

@ARTICLE{Simson1995,
  author = {Simson, R. and Sheets, E. D. and Jacobson, K.},
  title = {Detection of temporary lateral confinement of membrane proteins using
	single-particle tracking analysis},
  journal = {Biophys J},
  year = {1995},
  volume = {69},
  pages = {989-93},
  number = {3},
  month = {Sep},
  note = {96050424 0006-3495 Journal Article},
  abstract = {Techniques such as single-particle tracking allow the characterization
	of the movements of single or very few molecules. Features of the
	molecular trajectories, such as confined diffusion or directed transport,
	can reveal interesting biological interactions, but they can also
	arise from simple Brownian motion. Careful analysis of the data,
	therefore, is necessary to identify interesting effects from pure
	random movements. A method was developed to detect temporary confinement
	in the trajectories of membrane proteins that cannot be accounted
	for by Brownian motion. This analysis was applied to trajectories
	of two lipid-linked members of the immunoglobulin superfamily, Thy-1
	and a neural cell adhesion molecule (NCAM 125), and the results were
	compared with those for simulated random walks. Approximately 28%
	of the trajectories for both proteins exhibited periods of transient
	confinement, which were < 0.07% likely to arise from random movements.
	In contrast to these results, only 1.5% of the simulated trajectories
	showed confined periods. Transient confinement for both proteins
	lasted on average 8 s in regions that were approximately 280 nm in
	diameter.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8519998},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, Thy-1/analysis/*chemistry Cell Line Diffusion Fibroblasts
	Membrane Proteins/analysis/*chemistry Mice Mice, Inbred C3H Muscle,
	Skeletal Neural Cell Adhesion Molecules/analysis/*chemistry Probability
	Protein Structure, Secondary Support, U.S. Gov't, P.H.S.},
  shorttitle = {Detection of temporary lateral confinement of membrane proteins using
	single-particle tracking analysis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8519998}
}

@ARTICLE{Simson1998,
  author = {Simson, R. and Yang, B. and Moore, S. E. and Doherty, P. and Walsh,
	F. S. and Jacobson, K. A.},
  title = {Structural mosaicism on the submicron scale in the plasma membrane},
  journal = {Biophys J},
  year = {1998},
  volume = {74},
  pages = {297-308},
  number = {1},
  month = {Jan},
  note = {98109384 0006-3495 Journal Article},
  abstract = {The lateral mobility of the neural cell adhesion molecule (NCAM) was
	examined using single particle tracking (SPT). Various isoforms of
	human NCAM, differing in their ectodomain, their membrane anchorage
	mode, or the size of their cytoplasmic domain, were expressed in
	National Institutes of Health 3T3 cells and C2C12 muscle cells. On
	a 6.6-s time scale, SPT measurements on both transmembrane and glycosylphosphatidylinositol
	(GPI) anchored isoforms of NCAM expressed in 3T3 cells could be classified
	into mobile (Brownian diffusion), slow diffusion, corralled diffusion,
	and immobile subpopulations. On a 90-s time scale, SPT studies in
	C2C12 cells revealed that 40-60% of transfected NCAM was mobile,
	whereas a smaller fraction (approximately 10-30%) experienced much
	slower diffusion. In addition, a fraction of approximately 30% of
	both transfected GPI and transmembrane isoforms and endogenous NCAM
	isoforms in C2C12 cells experienced transient confinement for approximately
	8 s within regions of approximately 300-nm diameter. Diffusion within
	both these and the slow diffusion regions was anomalous, consistent
	with movements through a dense field of obstacles, whereas diffusion
	outside these regions was normal. Thus the membrane appears as a
	mosaic containing regions that permit free diffusion as well as regions
	in which NCAM is transiently confined to small or more extended domains.
	These results, including a large, freely diffusing fraction, similar
	confinement of transmembrane and GPI isoforms, a significant slowly
	diffusing fraction, and relatively large interdomain distances, are
	at some variance with the membrane skeleton fence model (Kusumi and
	Sako, 1996). Possible revisions to the model that incorporate these
	data are discussed.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9449330},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animal Cadherins/physiology Cell Line Cell Membrane/*physiology/*ultrastructure
	Cytoplasm/physiology Cytoskeleton/physiology Diffusion Human Membrane
	Lipids/physiology Mice Models, Biological Muscle, Skeletal Neural
	Cell Adhesion Molecules/biosynthesis/*physiology Recombinant Proteins/biosynthesis
	Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S. Transfection},
  shorttitle = {Structural mosaicism on the submicron scale in the plasma membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9449330}
}

@ARTICLE{Singhvi1994,
  author = {Singhvi, R. and Kumar, A. and Lopez, G. P. and Stephanopoulos, G.
	N. and Wang, D. I. and Whitesides, G. M. and Ingber, D. E.},
  title = {Engineering cell shape and function},
  journal = {Science},
  year = {1994},
  volume = {264},
  pages = {696-8},
  number = {5159},
  month = {Apr 29},
  note = {0036-8075 (Print) Journal Article},
  abstract = {An elastomeric stamp, containing defined features on the micrometer
	scale, was used to imprint gold surfaces with specific patterns of
	self-assembled monolayers of alkanethiols and, thereby, to create
	islands of defined shape and size that support extracellular matrix
	protein adsorption and cell attachment. Through this technique, it
	was possible to place cells in predetermined locations and arrays,
	separated by defined distances, and to dictate their shape. Limiting
	the degree of cell extension provided control over cell growth and
	protein secretion. This method is experimentally simple and highly
	adaptable. It should be useful for applications in biotechnology
	that require analysis of individual cells cultured at high density
	or repeated access to cells placed in specified locations.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8171320},
  endnotereftype = {Journal Article},
  keywords = {Albumins/secretion Amino Acid Sequence Animals Cell Adhesion Cell
	Differentiation Cell Division *Cell Size Cells, Cultured/*cytology/metabolism
	Culture Media *Cytological Techniques Dimethylpolysiloxanes Gold
	Liver/*cytology Molecular Sequence Data Rats Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Silicones Sulfhydryl
	Compounds},
  shorttitle = {Engineering cell shape and function},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8171320}
}

@ARTICLE{Smith2001,
  author = {Smith, D. A. and Simmons, R. M.},
  title = {Models of motor-assisted transport of intracellular particles},
  journal = {Biophys J},
  year = {2001},
  volume = {80},
  pages = {45-68},
  number = {1},
  month = {Jan},
  note = {0006-3495 (Print) Journal Article},
  abstract = {One-dimensional models are presented for the macroscopic intracellular
	transport of vesicles and organelles by molecular motors on a network
	of aligned intracellular filaments. A motor-coated vesicle or organelle
	is described as a diffusing particle binding intermittently to filaments,
	when it is transported at the motor velocity. Two models are treated
	in detail: 1) a unidirectional model, where only one kind of motor
	is operative and all filaments have the same polarity; and 2) a bidirectional
	model, in which filaments of both polarities exist (for example,
	a randomly polarized actin network for myosin motors) and/or particles
	have plus-end and minus-end motors operating on unipolar filaments
	(kinesin and dynein on microtubules). The unidirectional model provides
	net particle transport in the absence of a concentration gradient.
	A symmetric bidirectional model, with equal mixtures of filament
	polarities or plus-end and minus-end motors of the same characteristics,
	provides rapid transport down a concentration gradient and enhanced
	dispersion of particles from a point source by motor-assisted diffusion.
	Both models are studied in detail as a function of the diffusion
	constant and motor velocity of bound particles, and their rates of
	binding to and detachment from filaments. These models can form the
	basis of more realistic models for particle transport in axons, melanophores,
	and the dendritic arms of melanocytes, in which networks of actin
	filaments and microtubules coexist and motors for both types of filament
	are implicated.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11159382},
  endnotereftype = {Journal Article},
  keywords = {Actins/physiology Animals Axonal Transport/physiology Biological Transport,
	Active Biophysics Comparative Study Cytoskeleton/physiology Dendrites/physiology
	Melanocytes/physiology Melanosomes/physiology Microtubules/physiology
	*Models, Molecular Molecular Motors/*physiology Movement Myosins/physiology
	Organelles/*physiology Research Support, Non-U.S. Gov't},
  shorttitle = {Models of motor-assisted transport of intracellular particles},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11159382}
}

@ARTICLE{Smith2001a,
  author = {Smith, G. A. and Gross, S. P. and Enquist, L. W.},
  title = {Herpesviruses use bidirectional fast-axonal transport to spread in
	sensory neurons},
  journal = {Proc Natl Acad Sci U S A},
  year = {2001},
  volume = {98},
  pages = {3466-70},
  number = {6},
  month = {Mar 13},
  note = {0027-8424 (Print) Journal Article},
  abstract = {Alpha herpesviruses infect the vertebrate nervous system resulting
	in either mild recurrent lesions in mucosal epithelia or fatal encephalitis.
	Movement of virions within the nervous system is a critical factor
	in the outcome of infection; however, the dynamics of individual
	virion transport have never been assessed. Here we visualized and
	tracked individual viral capsids as they moved in axons away from
	infected neuronal cell bodies in culture. The observed movement was
	compatible with fast axonal flow mediated by multiple microtubule
	motors. Capsids accumulated at axon terminals, suggesting that spread
	from infected neurons required cell contact.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11248101},
  endnotereftype = {Journal Article},
  keywords = {Animals Axonal Transport/*physiology Axons/*metabolism Capsid/genetics/*metabolism
	*Capsid Proteins Cells, Cultured Chick Embryo Ganglia, Spinal/cytology
	Genes, Reporter Green Fluorescent Proteins Herpesvirus 1, Suid/genetics/*metabolism
	Humans Luminescent Proteins/genetics/metabolism Neurons, Afferent/cytology/*metabolism
	Recombinant Fusion Proteins/genetics/metabolism Research Support,
	Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Swine},
  shorttitle = {Herpesviruses use bidirectional fast-axonal transport to spread in
	sensory neurons},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11248101}
}

@ARTICLE{Smith1999,
  author = {Smith, P. R. and Morrison, I. E. and Wilson, K. M. and Fernandez,
	N. and Cherry, R. J.},
  title = {Anomalous diffusion of major histocompatibility complex class I molecules
	on HeLa cells determined by single particle tracking},
  journal = {Biophys J},
  year = {1999},
  volume = {76},
  pages = {3331-44},
  number = {6},
  month = {Jun},
  note = {99284858 0006-3495 Journal Article},
  abstract = {Single-particle tracking (SPT) was used to determine the mobility
	characteristics of MHC (major histocompatibility complex) class I
	molecules at the surface of HeLa cells at 22 degrees C and on different
	time scales. MHC class I was labeled using the Fab fragment of a
	monoclonal antibody (W6/32), covalently bound to either R-phycoerythrin
	or fluorescent microspheres, and the particles were tracked using
	high-sensitivity fluorescence imaging. Analysis of the data for a
	fixed time interval suggests a reasonable fit to a random diffusion
	model. The best fit values of the diffusion coefficient D decreased
	markedly, however, with increasing time interval, demonstrating the
	existence of anomalous diffusion. Further analysis of the data shows
	that the diffusion is anomalous over the complete time range investigated,
	4-300 s. Fitting the results obtained with the R-phycoerythrin probe
	to D = D0talpha-1, where Do is a constant and t is the time, gave
	D0 = (6.7 +/- 4.5) x 10(-11) cm2 s-1 and alpha = 0.49 +/- 0.16. Experiments
	with fluorescent microspheres were less reproducible and gave slower
	anomalous diffusion. The R-phycoerythrin probe is considered more
	reliable for fluorescent SPT because it is small (11 x 8 nm) and
	monovalent. The type of motion exhibited by the class I molecules
	will greatly affect their ability to migrate in the plane of the
	membrane. Anomalous diffusion, in particular, greatly reduces the
	distance a class I molecule can travel on the time scale of minutes.
	The present data are discussed in relation to the possible role of
	diffusion and clustering in T-cell activation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10354459},
  endnotereftype = {Journal Article},
  keywords = {Adenosine Triphosphate/metabolism Antibodies, Monoclonal Biophysics
	Cell Membrane/immunology Diffusion Fluorescent Dyes Hela Cells Histocompatibility
	Antigens Class I/*metabolism Human Microscopy, Fluorescence Models,
	Biological Support, Non-U.S. Gov't},
  shorttitle = {Anomalous diffusion of major histocompatibility complex class I molecules
	on HeLa cells determined by single particle tracking},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10354459}
}

@ARTICLE{So1998,
  author = {So, P. T. and Konig, K. and Berland, K. and Dong, C. Y. and French,
	T. and Buhler, C. and Ragan, T. and Gratton, E.},
  title = {New time-resolved techniques in two-photon microscopy},
  journal = {Cell Mol Biol (Noisy-le-grand)},
  year = {1998},
  volume = {44},
  pages = {771-93},
  number = {5},
  month = {Jul},
  note = {98435776 0145-5680 Journal Article Review Review, Tutorial},
  abstract = {Microscopy is traditionally a tool for determining biological structures.
	Many recent advances in optical microscopy involves the incorporation
	of spectroscopy techniques to monitor biochemical states of microscopic
	structures in living cells and tissues. By minimizing tissue photodamage,
	two-photon excitation microscopy provides a new opportunity to study
	the dynamics of biological systems on time scales from nanoseconds
	to hours. This review will focus on a number of these new methods:
	two-photon time-lapse microscopy, two-photon photoactivation, two-photon
	correlated spectroscopy, two-photon single particle tracking and
	two-photon lifetime microscopy.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9764747},
  endnotereftype = {Journal Article},
  keywords = {Animal Human Image Processing, Computer-Assisted Microscopy/*methods
	Microscopy, Fluorescence/methods Models, Theoretical Molecular Biology/*methods
	*Photons Spectrometry, Fluorescence/*methods Time Factors},
  shorttitle = {New time-resolved techniques in two-photon microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9764747}
}

@ARTICLE{Sobel,
  author = {Sobel, I.},
  title = {"An isotropic 3x3x3 volume gradient operator"},
  endnotereftype = {Journal Article},
  shorttitle = {"An isotropic 3x3x3 volume gradient operator"}
}

@MANUAL{Soll_Technologies,
  title = {DIAS},
  author = {Soll_Technologies},
  bdsk-url-1 = {http://www.geocities.com/solltech/dias/},
  endnotereftype = {Computer Program},
  shorttitle = {DIAS},
  url = {http://www.geocities.com/solltech/dias/}
}

@ARTICLE{Soni2003,
  author = {Soni, G. V. and Ali, B. M. and Hatwalne, Y. and Shivashankar, G.
	V.},
  title = {Single particle tracking of correlated bacterial dynamics},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {2634-7},
  number = {4},
  month = {Apr},
  note = {22554118 0006-3495 Journal Article},
  abstract = {Pattern formation in 3D random media has been a topic of interest
	in soft matter and biological systems. However, the onset of long-range
	microscopic ordering has not been explored in randomly moving self-propelled
	particles due to a lack of model systems as well as local probe techniques.
	In this article, we report on a novel experiment, using motile Escherichia
	coli bacteria as a model system, to study the onset of dynamic correlation
	and collective movement in three-dimension. We use fluctuation of
	an optically trapped micron-size bead as a detector of correlated
	bacterial motion, and further study this behavior by analyzing the
	motility of fluorescent bacteria in a confocal volume. We find evidence
	of dynamic correlation at very low volume fractions (0.01). We show
	that the magnitude of this correlation strongly depends on the interbacterial
	distances and their coupling modes. This opens up possibilities to
	probe long-range pattern formation in actively propelled cells or
	organisms coupled through hydrodynamics and/or chemical signaling.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12668471},
  endnotereftype = {Journal Article},
  shorttitle = {Single particle tracking of correlated bacterial dynamics},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12668471}
}

@ARTICLE{Soumpasis1983,
  author = {Soumpasis, D. M.},
  title = {Theoretical analysis of fluorescence photobleaching recovery experiments},
  journal = {Biophys J},
  year = {1983},
  volume = {41},
  pages = {95-7},
  number = {1},
  month = {Jan},
  note = {0006-3495 Journal Article},
  abstract = {We derive an exact closed formula for the fluorescence recovery curve
	measured in fluorescence photobleaching recovery experiments employing
	uniform circular laser beams. In contrast to the expression used
	currently, this result is very simple and free of mathematical drawbacks,
	thus facilitating the quantitative analysis of experimental data.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6824758},
  endnotereftype = {Journal Article},
  keywords = {Mathematics Membranes/*analysis Models, Biological *Photochemistry
	Research Support, Non-U.S. Gov't Spectrometry, Fluorescence/*methods},
  shorttitle = {Theoretical analysis of fluorescence photobleaching recovery experiments},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6824758}
}

@ARTICLE{Sprague2005,
  author = {Sprague, B. L. and McNally, J. G.},
  title = {FRAP analysis of binding: proper and fitting},
  journal = {Trends Cell Biol},
  year = {2005},
  volume = {15},
  pages = {84-91},
  number = {2},
  month = {Feb},
  note = {0962-8924 Journal Article},
  abstract = {Dynamic molecular interactions are fundamental to all cellular processes.
	In vivo analyses of these interactions are frequently done using
	fluorescence recovery after photobleaching (FRAP). Proper interpretation
	of FRAP data yields information about the binding interactions of
	fluorescently tagged molecules, including the number of binding states
	and the binding strength of each state. This binding information
	can be gleaned from appropriate models of the process underlying
	a FRAP recovery. Continued application and development of these approaches
	promise to provide crucial information for a quantitative description
	of the molecular networks that regulate cellular function.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15695095},
  endnotereftype = {Journal Article},
  shorttitle = {FRAP analysis of binding: proper and fitting},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15695095}
}

@ARTICLE{Sprague2004,
  author = {Sprague, B. L. and Pego, R. L. and Stavreva, D. A. and McNally, J.
	G.},
  title = {Analysis of binding reactions by fluorescence recovery after photobleaching},
  journal = {Biophys J},
  year = {2004},
  volume = {86},
  pages = {3473-95},
  number = {6},
  month = {Jun},
  note = {0006-3495 Journal Article},
  abstract = {Fluorescence recovery after photobleaching (FRAP) is now widely used
	to investigate binding interactions in live cells. Although various
	idealized solutions have been identified for the reaction-diffusion
	equations that govern FRAP, there has been no comprehensive analysis
	or systematic approach to serve as a guide for extracting binding
	information from an arbitrary FRAP curve. Here we present a complete
	solution to the FRAP reaction-diffusion equations for either single
	or multiple independent binding interactions, and then relate our
	solution to the various idealized cases. This yields a coherent approach
	to extract binding information from FRAP data which we have applied
	to the question of transcription factor mobility in the nucleus.
	We show that within the nucleus, the glucocorticoid receptor is transiently
	bound to a single state, with each molecule binding on average 65
	sites per second. This rapid sampling is likely to be important in
	finding a specific promoter target sequence. Further we show that
	this predominant binding state is not the nuclear matrix, as some
	studies have suggested. We illustrate how our analysis provides several
	self-consistency checks on a FRAP fit. We also define constraints
	on what can be estimated from FRAP data, show that diffusion should
	play a key role in many FRAP recoveries, and provide tools to test
	its contribution. Overall our approach establishes a more general
	framework to assess the role of diffusion, the number of binding
	states, and the binding constants underlying a FRAP recovery.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15189848},
  endnotereftype = {Journal Article},
  keywords = {*Algorithms Animals Cell Nucleus/*metabolism Cloning, Molecular Fluorescence
	Recovery After Photobleaching Green Fluorescent Proteins/metabolism
	*Image Processing, Computer-Assisted Mice Receptors, Glucocorticoid/*metabolism
	Tumor Cells, Cultured},
  shorttitle = {Analysis of binding reactions by fluorescence recovery after photobleaching},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15189848}
}

@ARTICLE{Srivastava1997,
  author = {Srivastava, A. and Krishnamoorthy, G.},
  title = {Cell type and spatial location dependence of cytoplasmic viscosity
	measured by time-resolved fluorescence microscopy},
  journal = {Arch Biochem Biophys},
  year = {1997},
  volume = {340},
  pages = {159-67},
  number = {2},
  month = {Apr 15},
  note = {0003-9861 Journal Article},
  abstract = {Information on the cell type and spatial location dependence of cytoplasmic
	viscosity would be very useful in understanding some of the processes
	occurring in the cell. For this purpose, fluorescent dye kiton red
	(sulforhodamine B) was loaded into a variety of cells such as Swiss
	3T3 fibroblasts, human mononuclear cells, Sarcoma-180 tumor cells,
	Chinese hamster ovary cells, plant cells from Digitalis lanata, stamen
	hair cells of Tradescantia, and guard mother cells of Allium cepa.
	Space-resolved measurements of cytoplasmic viscosity were carried
	out by using an experimental set-up wherein a picosecond laser system
	was coupled with an epifluorescence microscope. The spatial resolution
	of this set-up was approximately 1.0 micron, and reliable dynamic
	fluorescence measurements could be obtained from 10(2) to 10(3) fluorescent
	molecules. Fluorescence lifetime measurements showed that a large
	fraction (approximately 70%) of kiton red was in the free form. Fluorescence
	anisotropy decay of kiton red in cells was analyzed by a two population
	(free and bound) model. The microviscosity of cytoplasm was estimated
	from the anisotropy decay kinetics of the free probe. It was found
	that the cytoplasmic viscosity is dependent on both the cell type
	and spatial location within a cell. Furthermore, both the average
	value of viscosity and spatial variation within a cell were larger
	in the plant cells when compared to the animal cells. Model studies
	in various simpler systems have shown that the higher viscosity observed
	in some part of the cell could be due to either physical restriction
	and/or the presence of high concentrations of small solutes and macromolecules.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9143317},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animals CHO Cells Cytoplasm/*physiology Diffusion Fluorescent
	Dyes Hamsters Humans Mice Microscopy, Fluorescence Plants Research
	Support, Non-U.S. Gov't Time Factors Viscosity},
  shorttitle = {Cell type and spatial location dependence of cytoplasmic viscosity
	measured by time-resolved fluorescence microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9143317}
}

@ARTICLE{Stamhuis1995,
  author = {Stamhuis, E. and Videler, J.},
  title = {Quantitative flow analysis around aquatic animals using laser sheet
	particle image velocimetry},
  journal = {J Exp Biol},
  year = {1995},
  volume = {198},
  pages = {283-94},
  number = {Pt 2},
  note = {0 0022-0949 Journal article},
  abstract = {Two alternative particle image velocimetry (PIV) methods have been
	developed, applying laser light sheet illumination of particle-seeded
	flows around marine organisms. Successive video images, recorded
	perpendicular to a light sheet parallel to the main stream, were
	digitized and processed to map the flow velocity in two-dimensional
	planes. In particle tracking velocimetry (PTV), displacements of
	single particles in two subsequent images were determined semi-automatically,
	resulting in flow diagrams consisting of non-uniformly distributed
	velocity vectors. Application of grid-cell averaging resulted in
	flow field diagrams with uniform vector distribution. In sub-image
	correlation PIV (SCPIV), repetitive convolution filtering of small
	sub-areas of two subsequent images resulted in automatic determination
	of cross-correlation peaks, yielding flow field diagrams with regularly
	spaced velocity vectors. In both PTV and SCPIV, missing values, caused
	by incomplete particle displacement information in some areas of
	the images or due to rejection of some erroneous vectors by the vector
	validation procedure, were interpolated using a two-dimensional spline
	interpolation technique. The resultant vector flow fields were used
	to study the spatial distribution of velocity, spatial acceleration,
	vorticity, strain and shear. These flow fields could also be used
	to test for flow in the third dimension by studying the divergence,
	and to detect the presence and location of vortices. The results
	offer detailed quantitative descriptions of the flow morphology and
	can be used to assess dissipated energy. The versatile character
	of the technique makes it applicable to a wide range of fluid mechanical
	subjects within biological research. So far it has been successfully
	applied to map the flow around swimming copepods, fish larvae and
	juvenile fish and the ventilation current of a tube-living shrimp.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9317812},
  endnotereftype = {Journal Article},
  shorttitle = {Quantitative flow analysis around aquatic animals using laser sheet
	particle image velocimetry},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9317812}
}

@ARTICLE{Stelzer1998,
  author = {Stelzer, E.H.K.},
  title = {Contrast, resolution, pixelation, dynamic range and signal-to-noise
	ratio: fundamental limits to resolution in fluorescence light microscopy},
  journal = {Journal of Microscopy},
  year = {1998},
  volume = {189},
  pages = {15-24},
  number = {1},
  endnotereftype = {Journal Article},
  shorttitle = {Contrast, resolution, pixelation, dynamic range and signal-to-noise
	ratio: fundamental limits to resolution in fluorescence light microscopy}
}

@ARTICLE{Stelzer2000,
  author = {Stelzer, EHK and Grill, S},
  title = {The uncertainty principle applied to estimate focal spot dimensions},
  journal = {Opt Commun},
  year = {2000},
  volume = {173},
  pages = {51-56},
  endnotereftype = {Journal Article},
  shorttitle = {The uncertainty principle applied to estimate focal spot dimensions}
}

@ARTICLE{Stephens2003,
  author = {Stephens, D. J. and Allan, V. J.},
  title = {Light microscopy techniques for live cell imaging},
  journal = {Science},
  year = {2003},
  volume = {300},
  pages = {82-6},
  number = {5616},
  month = {Apr 4},
  note = {1095-9203 (Electronic) Journal Article Review},
  abstract = {Since the earliest examination of cellular structures, biologists
	have been fascinated by observing cells using light microscopy. The
	advent of fluorescent labeling technologies plus the plethora of
	sophisticated light microscope techniques now available make studying
	dynamic processes in living cells almost commonplace. For anyone
	new to this area, however, it can be daunting to decide which techniques
	or equipment to try. Here, we aim to give a brief overview of the
	main approaches to live cell imaging, with some mention of their
	pros and cons.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12677057},
  endnotereftype = {Journal Article},
  keywords = {*Cell Physiology Fluorescence Fluorescence Resonance Energy Transfer
	Fluorescent Dyes Imaging, Three-Dimensional Light Microscopy/instrumentation/*methods
	Microscopy, Confocal/instrumentation/methods Microscopy, Fluorescence/instrumentation/*methods
	Optics Research Support, Non-U.S. Gov't Spectrometry, Fluorescence},
  shorttitle = {Light microscopy techniques for live cell imaging},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12677057}
}

@ARTICLE{Stephens2000,
  author = {Stephens, D. J. and Lin-Marq, N. and Pagano, A. and Pepperkok, R.
	and Paccaud, J. P.},
  title = {COPI-coated ER-to-Golgi transport complexes segregate from COPII
	in close proximity to ER exit sites},
  journal = {J Cell Sci},
  year = {2000},
  volume = {113 ( Pt 12)},
  pages = {2177-85},
  month = {Jun},
  note = {0021-9533 (Print) Journal Article},
  abstract = {Transport of proteins between the endoplasmic reticulum and Golgi
	apparatus is mediated by two distinct membrane coat complexes, COPI
	and COPII. Genetic, biochemical and morphological data have accumulated
	into a model which suggests a sequential mode of action with COPII
	mediating the selection of cargo and formation of transport vesicles
	at the ER membrane for ER-to-Golgi transport and COPI mediating recycling
	of the transport machinery from post-ER membranes. To test this transport
	model directly in vivo, and to study the precise temporal sequence
	of COPI and COPII action in ER-to-Golgi transport, we have used time
	lapse microscopy of living cells to visualise simultaneously the
	dynamics of COPII and COPI, as well as COPII and GFP tagged secretory
	markers in living cells. The majority of COPII labelling appears
	tightly associated with ER membranes that move only within a limited
	area (less than 2 microm). Secretory cargo segregates from these
	sites and is then transported to the Golgi apparatus without any
	apparent association with COPII. COPI-coated transport complexes
	are seen to form adjacent to the COPII sites on the ER before segregating
	and moving directionally towards the Golgi apparatus. COPII is not
	present on these transport complexes and remains associated with
	the ER. These data demonstrate for the first time directly in vivo
	that ER-to-Golgi transport is organised in two steps characterised
	by a sequential mode of action of COPII and COPI.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10825291},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport Carrier Proteins/*metabolism Cercopithecus
	aethiops Coat Protein Complex I/*metabolism Endoplasmic Reticulum/*metabolism
	Golgi Apparatus/*metabolism Membrane Proteins/metabolism Phosphoproteins/*metabolism
	Research Support, Non-U.S. Gov't *Saccharomyces cerevisiae Proteins
	Vero Cells},
  shorttitle = {COPI-coated ER-to-Golgi transport complexes segregate from COPII in
	close proximity to ER exit sites},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10825291}
}

@ARTICLE{Stephens2004,
  author = {Stephens, D. J. and Pepperkok, R.},
  title = {Differential effects of a GTP-restricted mutant of Sar1p on segregation
	of cargo during export from the endoplasmic reticulum},
  journal = {J Cell Sci},
  year = {2004},
  volume = {117},
  pages = {3635-44},
  number = {Pt 16},
  month = {Jul 15},
  note = {0021-9533 (Print) Journal Article},
  abstract = {Export of cargo from the endoplasmic reticulum (ER) is the first membrane
	trafficking step in the secretory pathway. To date, all cargo proteins
	appear to use a common set of machinery for the initial stages of
	export, namely the COPII coat complex. Recent data from both yeast
	and mammalian systems have emerged suggesting that specific cargoes
	could be sorted from one another at the point of exit from the endoplasmic
	reticulum or immediately afterwards. Here, we have examined the mechanisms
	used for export of different types of cargo molecule from the endoplasmic
	reticulum. All cargoes examined utilise the COPII machinery, but
	specific differences are seen in the accumulation of cargo into ER-derived
	pre-budding complexes following expression of a GTP-restricted mutant
	of the Sar1p GTPase. Glycosylphosphatidylinositol (GPI)-anchored
	GFP is seen to be restricted to the ER under these conditions whereas
	other cargoes, including ts045-G and lumFP accumulate in pre-budding
	complexes. Following exit, GPI-FP, lumFP and ts045-G-FP all travel
	to the Golgi in the same vesicular tubular clusters (VTCs). These
	data show a differential requirement for efficient GTP hydrolysis
	by the Sar1p GTPase in export of cargo from the ER.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15252131},
  endnotereftype = {Journal Article},
  keywords = {Endoplasmic Reticulum/*metabolism Guanosine Triphosphate/*metabolism
	Hela Cells Humans Microscopy, Confocal Monomeric GTP-Binding Proteins/genetics/metabolism/*physiology
	Mutation Protein Transport Research Support, Non-U.S. Gov't},
  shorttitle = {Differential effects of a GTP-restricted mutant of Sar1p on segregation
	of cargo during export from the endoplasmic reticulum},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15252131}
}

@ARTICLE{Stephens2002,
  author = {Stephens, D. J. and Pepperkok, R.},
  title = {Imaging of procollagen transport reveals COPI-dependent cargo sorting
	during ER-to-Golgi transport in mammalian cells},
  journal = {J Cell Sci},
  year = {2002},
  volume = {115},
  pages = {1149-60},
  number = {Pt 6},
  month = {Mar 15},
  note = {0021-9533 (Print) Journal Article},
  abstract = {We have examined the ER-to-Golgi transport of procollagen, which,
	when assembled in the lumen of the ER, is thought to be physically
	too large to fit in classically described 60-80 nm COPI- and COPII-coated
	transport vesicles. We found that procollagen exits the ER via COPII-
	coated ER exit sites and is transported to the Golgi along microtubules
	in defined transport complexes. These procollagen-containing transport
	complexes are, however, distinct from those containing other cargo
	proteins like ERGIC-53 and ts-045-G. Furthermore, they do not label
	for the COPI coat complex in contrast to those containing ts-045-G.
	Inhibition of COPII or COPI function before addition of ascorbate,
	which is required for the folding of procollagen, inhibits export
	of procollagen from the ER. Inactivation of COPI coat function after
	addition of ascorbate results in the localisation of procollagen
	to transport complexes that now also contain ERGIC-53 and are inhibited
	in their transport to the Golgi complex. These data reveal the existence
	of an early COPI-dependent, pre-Golgi cargo sorting step in mammalian
	cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11884515},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport, Active Cells, Cultured Cercopithecus
	aethiops Coat Protein Complex I/*physiology Endoplasmic Reticulum/*metabolism
	Golgi Apparatus/*metabolism Green Fluorescent Proteins Hela Cells
	Humans Luminescent Proteins/chemistry Mammals Microscopy, Confocal
	Microscopy, Fluorescence Procollagen/chemistry/genetics/*metabolism
	Protein Conformation Protein Transport Research Support, Non-U.S.
	Gov't Transport Vesicles/physiology Vero Cells},
  shorttitle = {Imaging of procollagen transport reveals COPI-dependent cargo sorting
	during ER-to-Golgi transport in mammalian cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11884515}
}

@ARTICLE{Stephens2001,
  author = {Stephens, D. J. and Pepperkok, R.},
  title = {The many ways to cross the plasma membrane},
  journal = {Proc Natl Acad Sci U S A},
  year = {2001},
  volume = {98},
  pages = {4295-8},
  number = {8},
  month = {Apr 10},
  note = {0027-8424 (Print) Journal Article},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11274366},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport Cell Membrane/*metabolism Cell Membrane Permeability
	Research Support, Non-U.S. Gov't},
  shorttitle = {The many ways to cross the plasma membrane},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11274366}
}

@ARTICLE{Stephens2001a,
  author = {Stephens, D. J. and Pepperkok, R.},
  title = {Illuminating the secretory pathway: when do we need vesicles?},
  journal = {J Cell Sci},
  year = {2001},
  volume = {114},
  pages = {1053-9},
  number = {Pt 6},
  month = {Mar},
  note = {0021-9533 (Print) Journal Article Review},
  abstract = {Recent studies using GFP-tagged markers and time-lapse microscopy
	have allowed direct visualisation of membrane traffic in the secretory
	pathway in living mammalian cells. This work shows that larger membrane
	structures, 300-500 nm in size, are the vehicles responsible for
	long distance, microtubule-dependent ER-to-Golgi and trans-Golgi
	to plasma membrane transport of secretory markers. At least two retrograde
	transport pathways from the Golgi to the ER exist, both of which
	are proposed to involve a further class of long, tubular membrane
	carrier that forms from the Golgi and fuses with the ER. Together,
	this has challenged established transport models, raising the question
	of whether larger pleiomorphic structures, rather than small 60-80
	nm transport vesicles, mediate long-range transport between the ER
	and Golgi and between the Golgi and plasma membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11228150},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport, Active/*physiology Endoplasmic Reticulum/*metabolism
	Golgi Apparatus/*metabolism Secretory Vesicles trans-Golgi Network/metabolism},
  shorttitle = {Illuminating the secretory pathway: when do we need vesicles?},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11228150}
}

@ARTICLE{Struder1998,
  author = {Struder, L. and Meidinger, N. and Stotter, D. and Kemmer, J. and
	Lechner, P. and Leutenegger, P. and Soltau, H. and Eggert, F. and
	Rohde, M. and Schulein, T.},
  title = {High-Resolution X-ray Spectroscopy Close to Room Temperature},
  journal = {Microscopy and Microanalysis},
  year = {1998},
  volume = {4},
  pages = {622-631},
  number = {6},
  month = {Nov},
  note = {0 1431-9276 Journal article},
  abstract = {: Originally designed as position-sensitive detectors for particle
	tracking, silicon drift detectors (SDDs) are now used for high-count
	rate X-ray spectroscopy, operating close to room temperature. Their
	low-capacitance read-node concept places them among the fastest high-resolution
	detector systems. They have been used in a new spectrum of experiments
	in the wide field of X-ray spectroscopy: fluorescent analysis, diffractometry,
	materials analysis, and synchrotron experiments such as X-ray holography
	and element imaging in scanning electron microscopes. The fact that
	the detector system can be used at room temperature with good spectroscopic
	performance and at -10 degrees C with excellent energy resolution,
	avoiding liquid nitrogen for cooling and high-quality vacuum, guarantees
	a large variety of new applications, independent of the laboratory
	environment. A brief description of the device principles is followed
	by basics on low noise amplification. The performance results of
	a complete detector system are presented as well as some dedicated
	applications already realized, including use in a surface mapping
	instrument and use of a "mini-spectrometer" for the analysis of works
	of art. Fully depleted pn-charge-coupled devices (pn-CCDs) have been
	fabricated for the European X-ray Multi-Mirror mission (XMM) and
	the German X-ray satellite ABRIXAS, enabling high-speed, low-noise,
	position-resolving X-ray spectroscopy. The detector was designed
	and fabricated with a homogeneously sensitive area of 36 cm2. At
	-70 degrees C it has a noise of 4 e- rms, with a readout time of
	the total focal plane array of 4 msec. The maximum count rate for
	single photon counting was 10(5) cps under flat field conditions.
	In the integration mode, more than 10(9) cps can be detected at 6
	keV. Its position resolution is on the order of 100 microm. The quantum
	efficiency is higher than 90%, ranging from carbon K X-rays (277
	eV) up to 10 keV.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10087285},
  endnotereftype = {Journal Article},
  shorttitle = {High-Resolution X-ray Spectroscopy Close to Room Temperature},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10087285}
}

@ARTICLE{suhADDR2005,
  author = {Suh, J. and Dawson, M. and Hanes, J.},
  title = {Real-time multiple-particle tracking: applications to drug and gene
	delivery},
  journal = {Adv Drug Deliv Rev},
  year = {2005},
  volume = {57},
  pages = {63-78},
  number = {1},
  month = {Jan 2},
  note = {0169-409x Journal Article Review},
  abstract = {Complex biological environments, such as the cell cytoplasm or the
	mucus lining the airways of the lungs, can pose significant barriers
	to efficient therapeutic drug and gene delivery. Biological barriers
	are particularly important in controlled drug delivery applications
	that utilize a large carrier particle, such as a liposome or a polymer
	micro- or nanosphere. The dynamic transport of particulate drug and
	gene delivery vehicles through these barriers is poorly understood,
	having been primarily studied with static methods in the past. Recently,
	the transport of synthetic drug and gene carriers has been investigated
	quantitatively with real-time particle tracking technology, providing
	new insight into particle behavior in complex biological environments
	that is guiding rational improvements in particle design. This review
	briefly highlights basic principles of particle tracking and its
	application to elucidate important phenomena that limit effective
	particulate drug and gene delivery.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15518921},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport, Active/physiology Cystic Fibrosis/*drug therapy
	Cytoplasm/physiology Drug Delivery Systems/*methods Expectorants/*administration
	& dosage/therapeutic use Genetic Vectors/*metabolism Humans Intracellular
	Membranes/*physiology Rheology Technology, Pharmaceutical/*methods},
  shorttitle = {Real-time multiple-particle tracking: applications to drug and gene
	delivery},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15518921}
}

@ARTICLE{Suomalainen1999,
  author = {Suomalainen, M. and Nakano, M. Y. and Keller, S. and Boucke, K. and
	Stidwill, R. P. and Greber, U. F.},
  title = {Microtubule-dependent plus- and minus end-directed motilities are
	competing processes for nuclear targeting of adenovirus},
  journal = {J Cell Biol},
  year = {1999},
  volume = {144},
  pages = {657-72},
  number = {4},
  month = {Feb 22},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Adenovirus (Ad) enters target cells by receptor-mediated endocytosis,
	escapes to the cytosol, and then delivers its DNA genome into the
	nucleus. Here we analyzed the trafficking of fluorophore-tagged viruses
	in HeLa and TC7 cells by time-lapse microscopy. Our results show
	that native or taxol-stabilized microtubules (MTs) support alternating
	minus- and plus end-directed movements of cytosolic virus with elementary
	speeds up to 2.6 micrometer/s. No directed movement was observed
	in nocodazole-treated cells. Switching between plus- and minus end-directed
	elementary speeds at frequencies up to 1 Hz was observed in the periphery
	and near the MT organizing center (MTOC) after recovery from nocodazole
	treatment. MT-dependent motilities allowed virus accumulation near
	the MTOC at population speeds of 1-10 micrometer/min, depending on
	the cell type. Overexpression of p50/dynamitin, which is known to
	affect dynein-dependent minus end-directed vesicular transport, significantly
	reduced the extent and the frequency of minus end-directed migration
	of cytosolic virus, and increased the frequency, but not the extent
	of plus end-directed motility. The data imply that a single cytosolic
	Ad particle engages with two types of MT-dependent motor activities,
	the minus end- directed cytoplasmic dynein and an unknown plus end-
	directed activity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10037788},
  endnotereftype = {Journal Article},
  keywords = {Adenoviruses, Human/pathogenicity/*physiology Animals Base Sequence
	Cell Line Cell Nucleus/*virology Cercopithecus aethiops Cytosol/virology
	DNA Primers/genetics Dynein ATPase/physiology Fluorescent Dyes Green
	Fluorescent Proteins Hela Cells Humans Luminescent Proteins/genetics
	Microscopy, Fluorescence Microtubule-Associated Proteins/physiology
	Microtubules/drug effects/*physiology/virology Molecular Motors/physiology
	Movement Nocodazole/pharmacology Paclitaxel/pharmacology Research
	Support, Non-U.S. Gov't Virus Replication},
  shorttitle = {Microtubule-dependent plus- and minus end-directed motilities are
	competing processes for nuclear targeting of adenovirus},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10037788}
}

@ARTICLE{Suzuki2000,
  author = {Suzuki, K. and Sterba, R. E. and Sheetz, M. P.},
  title = {Outer membrane monolayer domains from two-dimensional surface scanning
	resistance measurements},
  journal = {Biophys J},
  year = {2000},
  volume = {79},
  pages = {448-59},
  number = {1},
  month = {Jul},
  note = {20327299 0006-3495 Journal Article},
  abstract = {Cellular plasma membranes have domains that are defined, in most cases,
	by cytoskeletal elements. The outer half of the bilayer may also
	contain domains that organize glycosylphosphatidylinositol (GPI)-linked
	proteins. To define outer membrane barriers, we measured the resistive
	force on membrane bound beads as they were scanned across the plasma
	membrane of HEPA-OVA cells with optical laser tweezers. Beads were
	bound by antibodies to fluorescein-phosphatidylethanolamine (Fl-PE)
	or to the class I major histocompatibility complex (MHC class I)
	Qa-2 (a GPI-anchored protein). Two-dimensional scans of resistive
	force showed both occasional, resistive barriers and a velocity-dependent,
	continuous resistance. At the lowest antibody concentration, which
	gave specific binding, the continuous friction coefficient of Qa-2
	was consistent with that observed by single-particle tracking (SPT)
	of small gold particles. At high antibody concentrations, the friction
	coefficient was significantly higher but decreased with increasing
	temperature, addition of deoxycholic acid, or treatment with heparinase
	I. Barriers to lateral movement (>3 times the continuous resistance)
	were consistently observed. Elastic barriers (with elastic constants
	from 1 to 20 pN/microm and sensitive to cytochalasin D) and small
	nonelastic barriers (<100 nm) were specifically observed with beads
	bound to the GPI-linked Qa-2. We suggest that GPI-linked proteins
	interact with transmembrane proteins when aggregated by antibody-coated
	beads and the transmembrane proteins encounter cytoplasmic barriers
	to lateral movement. The barriers to lateral movement are dynamic,
	discontinuous, and low in density.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10866970},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport/physiology Cell Line Cell Membrane/*chemistry/*metabolism
	Fluorescein/chemistry Friction Glycosylphosphatidylinositols/*metabolism
	Histocompatibility Antigens Class I/chemistry/genetics/metabolism
	Lasers Lipid Bilayers/metabolism Membrane Proteins/*metabolism Microspheres
	Phosphatidylethanolamines/chemistry Sensitivity and Specificity Stress,
	Mechanical Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S. Surface
	Properties Temperature Torque Transfection Viscosity},
  shorttitle = {Outer membrane monolayer domains from two-dimensional surface scanning
	resistance measurements},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10866970}
}

@ARTICLE{Sydor2003,
  author = {Sydor, J. R. and Nock, S.},
  title = {Protein expression profiling arrays: tools for the multiplexed high-throughput
	analysis of proteins},
  journal = {Proteome Sci},
  year = {2003},
  volume = {1},
  pages = {3},
  number = {1},
  month = {Jun 10},
  note = {1477-5956 (Electronic) Journal article},
  abstract = {The completion of the human genome sequence has led to a rapid increase
	in genetic information. The invention of DNA microarrays, which allow
	for the parallel measurement of thousands of genes on the level of
	mRNA, has enabled scientists to take a more global view of biological
	systems. Protein microarrays have a big potential to increase the
	throughput of proteomic research. Microarrays of antibodies can simultaneously
	measure the concentration of a multitude of target proteins in a
	very short period of time. The ability of protein microarrays to
	increase the quantity of data points in small biological samples
	on the protein level will have a major impact on basic biological
	research as well as on the discovery of new drug targets and diagnostic
	markers. This review highlights the current status of protein expression
	profiling arrays, their development, applications and limitations.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12831399},
  endnotereftype = {Journal Article},
  shorttitle = {Protein expression profiling arrays: tools for the multiplexed high-throughput
	analysis of proteins},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12831399}
}

@ARTICLE{Szabo2004,
  author = {Szabo, B. and Kornyei, Z. and Zach, J. and Selmeczi, D. and Csucs,
	G. and Czirok, A. and Vicsek, T.},
  title = {Auto-reverse nuclear migration in bipolar mammalian cells on micropatterned
	surfaces},
  journal = {Cell Motil Cytoskeleton},
  year = {2004},
  volume = {59},
  pages = {38-49},
  number = {1},
  month = {Sep},
  note = {0886-1544 (Print) Journal Article},
  abstract = {A novel assay based on micropatterning and time-lapse microscopy has
	been developed for the study of nuclear migration dynamics in cultured
	mammalian cells. When cultured on 10-20-microm wide adhesive stripes,
	the motility of C6 glioma and primary mouse fibroblast cells is diminished.
	Nevertheless, nuclei perform an unexpected auto-reverse motion: when
	a migrating nucleus approaches the leading edge, it decelerates,
	changes the direction of motion, and accelerates to move toward the
	other end of the elongated cell. During this process, cells show
	signs of polarization closely following the direction of nuclear
	movement. The observed nuclear movement requires a functioning microtubular
	system, as revealed by experiments disrupting the main cytoskeletal
	components with specific drugs. On the basis of our results, we argue
	that auto-reverse nuclear migration is due to forces determined by
	the interplay of microtubule dynamics and the changing position of
	the microtubule organizing center as the nucleus reaches the leading
	edge. Our assay recapitulates specific features of nuclear migration
	(cell polarization, oscillatory nuclear movement), while it allows
	the systematic study of a large number of individual cells. In particular,
	our experiments yielded the first direct evidence of reversive nuclear
	motion in mammalian cells, induced by attachment constraints.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15259054},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells Animals Cell Nucleus/*physiology Cytoskeletal Proteins/*physiology
	Mice Microscopy, Phase-Contrast Microtubules/physiology Research
	Support, Non-U.S. Gov't Time Factors},
  shorttitle = {Auto-reverse nuclear migration in bipolar mammalian cells on micropatterned
	surfaces},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15259054}
}

@ARTICLE{Takeuchi1998,
  author = {Takeuchi, M. and Miyamoto, H. and Sako, Y. and Komizu, H. and Kusumi,
	A.},
  title = {Structure of the erythrocyte membrane skeleton as observed by atomic
	force microscopy},
  journal = {Biophys J},
  year = {1998},
  volume = {74},
  pages = {2171-83},
  number = {5},
  month = {May},
  note = {0006-3495 Journal Article},
  abstract = {The structure of the membrane skeleton on the cytoplasmic surface
	of the erythrocyte plasma membrane was observed in dried human erythrocyte
	ghosts by atomic force microscopy (AFM), taking advantage of its
	high sensitivity to small height variations in surfaces. The majority
	of the membrane skeleton can be imaged, even on the extracellular
	surface of the membrane. Various fixation and drying methods were
	examined for preparation of ghost membrane samples for AFM observation,
	and it was found that freeze-drying (freezing by rapid immersion
	in a cryogen) of unfixed specimens was a fast and simple way to obtain
	consistently good results for observation without removing the membrane
	or extending the membrane skeleton. Observation of the membrane skeleton
	at the external surface of the cell was possible mainly because the
	bilayer portion of the membrane sank into the cell during the drying
	process. The average mesh size of the spectrin network observed at
	the extracellular and cytoplasmic surfaces of the plasma membrane
	was 4800 and 3000 nm2, respectively, which indicates that spectrin
	forms a three-dimensionally folded meshwork, and that 80% of spectrin
	can be observed at the extracellular surface of the plasma membrane.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9591644},
  endnotereftype = {Journal Article},
  keywords = {Cell Fractionation/methods Erythrocyte Membrane/*ultrastructure Freezing
	Hemolysis Human Microscopy, Atomic Force/methods Spectrin/*analysis},
  shorttitle = {Structure of the erythrocyte membrane skeleton as observed by atomic
	force microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9591644}
}

@ARTICLE{Tang2003,
  author = {Tang, Q. and Edidin, M.},
  title = {Lowering the barriers to random walks on the cell surface},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {400-7},
  number = {1},
  month = {Jan},
  note = {22411889 0006-3495 Journal Article},
  abstract = {We used fluorescence recovery after photobleaching (FRAP) and single
	particle tracking (SPT) techniques to compare diffusion of class
	I major histocompatibility complex molecules (MHC) on normal and
	alpha-spectrin-deficient murine erythroleukemia (MEL) cells. Because
	the cytoskeleton mesh acts as a barrier to lateral mobility of membrane
	proteins, we expected that diffusion of membrane proteins in alpha-spectrin-deficient
	MEL cells would differ greatly from that in normal MEL cells. In
	the event, diffusion coefficients derived from either FRAP or SPT
	analysis were similar for alpha-spectrin-deficient and normal MEL
	cells, differing by a factor of approximately 2, on three different
	timescales: tens of seconds, 1-10 s, and 100 ms. SPT analysis showed
	that the diffusion of most class I MHC molecules was confined on
	both cell types. On the normal MEL cells, the mean diagonal length
	of the confined area was 330 nm with a mean residency time of 40s.
	On the alpha-spectrin-deficient MEL cells, the mean diagonal length
	was 650 nm with a mean residency time of 45s. Thus there are fewer
	barriers to lateral diffusion on cytoskeleton mutant MEL cells than
	on normal MEL cells, but this difference does not strongly affect
	lateral diffusion on the scales measured here.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12524293},
  endnotereftype = {Journal Article},
  keywords = {Animal Cell Membrane/chemistry/metabolism Comparative Study Diffusion
	Fluorescence Recovery After Photobleaching/*methods Histocompatibility
	Antigens Class I/*chemistry/*metabolism Leukemia, Erythroblastic,
	Acute/*metabolism Mice Microscopy, Fluorescence/*methods Microscopy,
	Video/*methods Motion Receptors, Cell Surface/chemistry/metabolism
	Reference Values Spectrin/deficiency Support, U.S. Gov't, P.H.S.
	Tumor Cells, Cultured/chemistry/metabolism},
  shorttitle = {Lowering the barriers to random walks on the cell surface},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12524293}
}

@ARTICLE{TardinEJ_2003.pdf,
  author = {Tardin, C. and Cognet, L. and Bats, C. and Lounis, B. and Choquet,
	D.},
  title = {Direct imaging of lateral movements of AMPA receptors inside synapses},
  journal = {Embo J},
  year = {2003},
  volume = {22},
  pages = {4656-65},
  number = {18},
  month = {Sep 15},
  note = {22850113 0261-4189 Journal Article},
  abstract = {Trafficking of AMPA receptors in and out of synapses is crucial for
	synaptic plasticity. Previous studies have focused on the role of
	endo/exocytosis processes or that of lateral diffusion of extra-synaptic
	receptors. We have now directly imaged AMPAR movements inside and
	outside synapses of live neurons using single-molecule fluorescence
	microscopy. Inside individual synapses, we found immobile and mobile
	receptors, which display restricted diffusion. Extra-synaptic receptors
	display free diffusion. Receptors could also exchange between these
	membrane compartments through lateral diffusion. Glutamate application
	increased both receptor mobility inside synapses and the fraction
	of mobile receptors present in a juxtasynaptic region. Block of inhibitory
	transmission to favor excitatory synaptic activity induced a transient
	increase in the fraction of mobile receptors and a decrease in the
	proportion of juxtasynaptic receptors. Altogether, our data show
	that rapid exchange of receptors between a synaptic and extra-synaptic
	localization occurs through regulation of receptor diffusion inside
	synapses.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12970178},
  endnotereftype = {Journal Article},
  shorttitle = {Direct imaging of lateral movements of AMPA receptors inside synapses},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12970178}
}

@BOOK{Teklap1995,
  title = {Digital Video Processing},
  publisher = {Prentice Hall},
  year = {1995},
  author = {Teklap, M.},
  address = {Englewood Cliffs, N.J.},
  endnotereftype = {Book},
  shorttitle = {Digital Video Processing}
}

@ARTICLE{Thery2007,
  author = {Thery, M. and Bornens, M.},
  title = {[Cell adhesion guides cell polarity]},
  journal = {Med Sci (Paris)},
  year = {2007},
  volume = {23},
  pages = {230-2},
  number = {3},
  month = {Mar},
  note = {0767-0974 (Print) News},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17349273},
  endnotereftype = {Journal Article},
  keywords = {Actins/analysis Animals Cell Adhesion/*physiology Cell Adhesion Molecules/physiology
	Cell Culture Techniques/instrumentation Cell Nucleus/ultrastructure
	Cell Polarity/*physiology Cells, Cultured/physiology/ultrastructure
	Centrosome/ultrastructure Cortactin Cytoskeleton/ultrastructure Fibronectins
	Golgi Apparatus/ultrastructure Microchip Analytical Procedures Organelles/*ultrastructure},
  shorttitle = {[Cell adhesion guides cell polarity]},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17349273}
}

@ARTICLE{Thery2006,
  author = {Thery, M. and Bornens, M.},
  title = {Cell shape and cell division},
  journal = {Curr Opin Cell Biol},
  year = {2006},
  volume = {18},
  pages = {648-57},
  number = {6},
  month = {Dec},
  note = {0955-0674 (Print) Journal Article Research Support, Non-U.S. Gov't
	Review},
  abstract = {The correlation between cell shape elongation and the orientation
	of the division axis described by early cell biologists is still
	used as a paradigm in developmental studies. However, analysis of
	early embryo development and tissue morphogenesis has highlighted
	the role of the spatial distribution of cortical cues able to guide
	spindle orientation. In vitro studies of cell division have revealed
	similar mechanisms. Recent data support the possibility that the
	orientation of cell division in mammalian cells is dominated by cell
	adhesion and the associated traction forces developed in interphase.
	Cell shape is a manifestation of these adhesive and tensional patterns.
	These patterns control the spatial distribution of cortical signals
	and thereby guide spindle orientation and daughter cell positioning.
	From these data, cell division appears to be a continuous transformation
	ensuring the maintenance of tissue mechanical integrity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17046223},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion/physiology Cell Division/*physiology Cell Polarity/*physiology
	Cell Shape/*physiology Cytokinesis/physiology Humans Interphase/physiology
	Microfilament Proteins/metabolism Mitotic Spindle Apparatus/physiology
	Tensile Strength/physiology},
  shorttitle = {Cell shape and cell division},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17046223}
}

@ARTICLE{Thery2007a,
  author = {Thery, M. and Jimenez-Dalmaroni, A. and Racine, V. and Bornens, M.
	and Julicher, F.},
  title = {Experimental and theoretical study of mitotic spindle orientation},
  journal = {Nature},
  year = {2007},
  volume = {447},
  pages = {493-6},
  number = {7143},
  month = {May 24},
  note = {1476-4687 (Electronic) Journal Article},
  abstract = {The architecture and adhesiveness of a cell microenvironment is a
	critical factor for the regulation of spindle orientation in vivo.
	Using a combination of theory and experiments, we have investigated
	spindle orientation in HeLa (human) cells. Here we show that spindle
	orientation can be understood as the result of the action of cortical
	force generators, which interact with spindle microtubules and are
	activated by cortical cues. We develop a simple physical description
	of this spindle mechanics, which allows us to calculate angular profiles
	of the torque acting on the spindle, as well as the angular distribution
	of spindle orientations. Our model accounts for the preferred spindle
	orientation and the shape of the full angular distribution of spindle
	orientations observed in a large variety of different cellular microenvironment
	geometries. It also correctly describes asymmetric spindle orientations,
	which are observed for certain distributions of cortical cues. We
	conclude that, on the basis of a few simple assumptions, we can provide
	a quantitative description of the spindle orientation of adherent
	cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17495931},
  endnotereftype = {Journal Article},
  keywords = {Cell Adhesion *Cell Polarity Cues Fibronectins/metabolism Hela Cells
	Humans Microtubules/metabolism Mitotic Spindle Apparatus/*chemistry/*metabolism},
  shorttitle = {Experimental and theoretical study of mitotic spindle orientation},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17495931}
}

@ARTICLE{Thery2006a,
  author = {Thery, M. and Pepin, A. and Dressaire, E. and Chen, Y. and Bornens,
	M.},
  title = {Cell distribution of stress fibres in response to the geometry of
	the adhesive environment},
  journal = {Cell Motil Cytoskeleton},
  year = {2006},
  volume = {63},
  pages = {341-55},
  number = {6},
  month = {Jun},
  note = {0886-1544 (Print) Journal Article},
  abstract = {Cells display a large variety of shapes when plated in classical culture
	conditions despite their belonging to a common cell type. These shapes
	are transitory, since cells permanently disassemble and reassemble
	their cytoskeleton while moving. Adhesive micropatterns are commonly
	used to confine cell shape within a given geometry. In addition the
	micropattern can be designed so as to impose cells to spread upon
	adhesive and nonadhesive areas. Modulation of the pattern geometry
	allows the analysis of the mechanisms governing the determination
	of cell shape in response to external adhesive conditions. In this
	study, we show that the acquisition of cell shape follows two stages
	where initially the cell forms contact with the micropattern. Here,
	the most distal contacts made by the cell with the micropattern define
	the apices of the cell shape. Then secondly, the cell borders that
	link two apices move so as to minimise the distance between the two
	apices. In these cell borders, the absence of an underlying adhesive
	substrate is overcome by stress fibres forming between the apices,
	which in turn are marked by an accumulation of focal adhesions. By
	inhibiting myosin function, cell borders on nonadhesive zones become
	more concave, suggesting that the stress fibres work against the
	membrane tension in the cell border. Moreover, this suggested that
	traction forces are unevenly distributed in stationary, nonmigrating,
	cells. By comparing the stress fibres in cells with one, two, or
	three nonadherent cell borders it was reasoned that stress fibre
	strength is inversely proportional to number. We conclude that cells
	of a given area can generate the same total sum of tractional forces
	but that these tractional forces are differently spaced depending
	on the spatial distribution of its adherence contacts.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16550544},
  endnotereftype = {Journal Article},
  keywords = {Actins/*physiology Cell Adhesion/*physiology Cell Line Cell Polarity/physiology
	Cell Shape/*physiology Cell Surface Extensions/physiology/ultrastructure
	Cytoskeleton/*physiology/ultrastructure Fibronectins/physiology Focal
	Adhesions/physiology Hela Cells Humans Stress Fibers/*physiology
	Vinculin/physiology},
  shorttitle = {Cell distribution of stress fibres in response to the geometry of
	the adhesive environment},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16550544}
}

@ARTICLE{Thery2005,
  author = {Thery, M. and Racine, V. and Pepin, A. and Piel, M. and Chen, Y.
	and Sibarita, J. B. and Bornens, M.},
  title = {The extracellular matrix guides the orientation of the cell division
	axis},
  journal = {Nat Cell Biol},
  year = {2005},
  volume = {7},
  pages = {947-53},
  number = {10},
  month = {Oct},
  note = {1465-7392 (Print) Letter},
  abstract = {The cell division axis determines the future positions of daughter
	cells and is therefore critical for cell fate. The positioning of
	the division axis has been mostly studied in systems such as embryos
	or yeasts, in which cell shape is well defined. In these cases, cell
	shape anisotropy and cell polarity affect spindle orientation. It
	remains unclear whether cell geometry or cortical cues are determinants
	for spindle orientation in mammalian cultured cells. The cell environment
	is composed of an extracellular matrix (ECM), which is connected
	to the intracellular actin cytoskeleton via transmembrane proteins.
	We used micro-contact printing to control the spatial distribution
	of the ECM on the substrate and demonstrated that it has a role in
	determining the orientation of the division axis of HeLa cells. On
	the basis of our analysis of the average distributions of actin-binding
	proteins in interphase and mitosis, we propose that the ECM controls
	the location of actin dynamics at the membrane, and thus the segregation
	of cortical components in interphase. This segregation is further
	maintained on the cortex of mitotic cells and used for spindle orientation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16179950},
  endnotereftype = {Journal Article},
  keywords = {Actins/physiology Cell Division/physiology Cell Membrane/physiology
	Cell Polarity/*physiology Cell Shape/physiology Extracellular Matrix/*physiology
	Hela Cells Humans Research Support, Non-U.S. Gov't Time Factors},
  shorttitle = {The extracellular matrix guides the orientation of the cell division
	axis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16179950}
}

@ARTICLE{Thery2006b,
  author = {Thery, M. and Racine, V. and Piel, M. and Pepin, A. and Dimitrov,
	A. and Chen, Y. and Sibarita, J. B. and Bornens, M.},
  title = {Anisotropy of cell adhesive microenvironment governs cell internal
	organization and orientation of polarity},
  journal = {Proc Natl Acad Sci U S A},
  year = {2006},
  volume = {103},
  pages = {19771-6},
  number = {52},
  month = {Dec 26},
  note = {0027-8424 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Control of the establishment of cell polarity is an essential function
	in tissue morphogenesis and renewal that depends on spatial cues
	provided by the extracellular environment. The molecular role of
	cell-cell or cell-extracellular matrix (ECM) contacts on the establishment
	of cell polarity has been well characterized. It has been hypothesized
	that the geometry of the cell adhesive microenvironment was directing
	cell surface polarization and internal organization. To define how
	the extracellular environment affects cell polarity, we analyzed
	the organization of individual cells plated on defined micropatterned
	substrates imposing cells to spread on various combinations of adhesive
	and nonadhesive areas. The reproducible normalization effect on overall
	cell compartmentalization enabled quantification of the spatial organization
	of the actin network and associated proteins, the spatial distribution
	of microtubules, and the positioning of nucleus, centrosome, and
	Golgi apparatus. By using specific micropatterns and statistical
	analysis of cell compartment positions, we demonstrated that ECM
	geometry determines the orientation of cell polarity axes. The nucleus-centrosome
	orientations were reproducibly directed toward cell adhesive edges.
	The anisotropy of the cell cortex in response to the adhesive conditions
	did not affect the centrosome positioning at the cell centroid. Based
	on the quantification of microtubule plus end distribution we propose
	a working model that accounts for that observation. We conclude that,
	in addition to molecular composition and mechanical properties, ECM
	geometry plays a key role in developmental processes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17179050},
  endnotereftype = {Journal Article},
  keywords = {Anisotropy Cell Adhesion Cell Nucleus/metabolism *Cell Polarity Cells,
	Cultured Centrosome/metabolism Extracellular Matrix/metabolism Golgi
	Apparatus/metabolism Humans Microtubules/metabolism Retina/chemistry/cytology/metabolism},
  shorttitle = {Anisotropy of cell adhesive microenvironment governs cell internal
	organization and orientation of polarity},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17179050}
}

@ARTICLE{ThompsonBJ2002.pdf,
  author = {Thompson, R. E. and Larson, D. R. and Webb, W. W.},
  title = {Precise nanometer localization analysis for individual fluorescent
	probes},
  journal = {Biophys J},
  year = {2002},
  volume = {82},
  pages = {2775-83},
  number = {5},
  month = {May},
  note = {21961515 0006-3495 Journal Article},
  abstract = {Calculation of the centroid of the images of individual fluorescent
	particles and molecules allows localization and tracking in light
	microscopes to a precision about an order of magnitude greater than
	the microscope resolution. The factors that limit the precision of
	these techniques are examined and a simple equation derived that
	describes the precision of localization over a wide range of conditions.
	In addition, a localization algorithm motivated from least-squares
	fitting theory is constructed and tested both on image stacks of
	30-nm fluorescent beads and on computer-generated images (Monte Carlo
	simulations). Results from the algorithm show good agreement with
	the derived precision equation for both the simulations and actual
	images. The availability of a simple equation to describe localization
	precision helps investigators both in assessing the quality of an
	experimental apparatus and in directing attention to the factors
	that limit further improvement. The precision of localization scales
	as the inverse square root of the number of photons in the spot for
	the shot noise limited case and as the inverse of the number of photons
	for the background noise limited case. The optimal image magnification
	depends on the expected number of photons and background noise, but,
	for most cases of interest, the pixel size should be about equal
	to the standard deviation of the point spread function.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11964263},
  endnotereftype = {Journal Article},
  keywords = {Fluorescent Dyes/*analysis Least-Squares Analysis Microscopy, Confocal/methods
	Normal Distribution Photons Sensitivity and Specificity Support,
	U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.},
  shorttitle = {Precise nanometer localization analysis for individual fluorescent
	probes},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11964263}
}

@ARTICLE{Tomishige1997,
  author = {Tomishige, M. and Kusumi, A.},
  title = {[Analysis of membrane protein movement by single particle tracking
	and laser-beam gradient force optical trap]},
  journal = {Nippon Seirigaku Zasshi},
  year = {1997},
  volume = {59},
  pages = {11-21},
  number = {1},
  note = {97279642 0031-9341 Journal Article Review Review, Tutorial},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9213590},
  endnotereftype = {Journal Article},
  keywords = {Animal Cell Membrane/metabolism/ultrastructure Gold Colloid Image
	Processing, Computer-Assisted Latex Membrane Proteins/*metabolism/ultrastructure
	*Microscopy, Confocal/methods *Microscopy, Video/methods Molecular
	Probes},
  shorttitle = {[Analysis of membrane protein movement by single particle tracking
	and laser-beam gradient force optical trap]},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9213590}
}

@ARTICLE{Tomishige1998,
  author = {Tomishige, M. and Sako, Y. and Kusumi, A.},
  title = {Regulation mechanism of the lateral diffusion of band 3 in erythrocyte
	membranes by the membrane skeleton},
  journal = {J Cell Biol},
  year = {1998},
  volume = {142},
  pages = {989-1000},
  number = {4},
  month = {Aug 24},
  note = {0021-9525 Journal Article},
  abstract = {Mechanisms that regulate the movement of a membrane spanning protein
	band 3 in erythrocyte ghosts were investigated at the level of a
	single or small groups of molecules using single particle tracking
	with an enhanced time resolution (0.22 ms). Two-thirds of band 3
	undergo macroscopic diffusion: a band 3 molecule is temporarily corralled
	in a mesh of 110 nm in diameter, and hops to an adjacent mesh an
	average of every 350 ms. The rest (one-third) of band 3 exhibited
	oscillatory motion similar to that of spectrin, suggesting that these
	band 3 molecules are bound to spectrin. When the membrane skeletal
	network was dragged and deformed/translated using optical tweezers,
	band 3 molecules that were undergoing hop diffusion were displaced
	toward the same direction as the skeleton. Mild trypsin treatment
	of ghosts, which cleaves off the cytoplasmic portion of band 3 without
	affecting spectrin, actin, and protein 4.1, increased the intercompartmental
	hop rate of band 3 by a factor of 6, whereas it did not change the
	corral size and the microscopic diffusion rate within a corral. These
	results indicate that the cytoplasmic portion of band 3 collides
	with the membrane skeleton, which causes temporal confinement of
	band 3 inside a mesh of the membrane skeleton.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9722611},
  endnotereftype = {Journal Article},
  keywords = {Anion Exchange Protein 1, Erythrocyte/metabolism Cell Membrane/*metabolism
	Cytoskeleton/physiology Diffusion Erythrocyte Membrane/chemistry
	Erythrocytes/*physiology Gold Colloid/metabolism Human Membrane Proteins/metabolism
	Microscopy, Video Spectrin/metabolism Trypsin/pharmacology},
  shorttitle = {Regulation mechanism of the lateral diffusion of band 3 in erythrocyte
	membranes by the membrane skeleton},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9722611}
}

@ARTICLE{Toomre1999,
  author = {Toomre, D. and Keller, P. and White, J. and Olivo, J. C. and Simons,
	K.},
  title = {Dual-color visualization of trans-Golgi network to plasma membrane
	traffic along microtubules in living cells},
  journal = {J Cell Sci},
  year = {1999},
  volume = {112 ( Pt 1)},
  pages = {21-33},
  month = {Jan},
  note = {0021-9533 (Print) Journal Article},
  abstract = {The mechanisms and carriers responsible for exocytic protein trafficking
	between the trans-Golgi network (TGN) and the plasma membrane remain
	unclear. To investigate the dynamics of TGN-to-plasma membrane traffic
	and role of the cytoskeleton in these processes we transfected cells
	with a GFP-fusion protein, vesicular stomatitis virus G protein tagged
	with GFP (VSVG3-GFP). After using temperature shifts to block VSVG3-GFP
	in the endoplasmic reticulum and subsequently accumulate it in the
	TGN, dynamics of TGN-to-plasma membrane transport were visualized
	in real time by confocal and video microscopy. Both small vesicles
	(<250 nm) and larger vesicular-tubular structures (>1.5 microm long)
	are used as transport containers (TCs). These TCs rapidly moved out
	of the Golgi along curvilinear paths with average speeds of approximately
	0.7 micrometer/second. Automatic computer tracking objectively determined
	the dynamics of different carriers. Fission and fusion of TCs were
	observed, suggesting that these late exocytic processes are highly
	interactive. To directly determine the role of microtubules in post-Golgi
	traffic, rhodamine-tubulin was microinjected and both labeled cargo
	and microtubules were simultaneously visualized in living cells.
	These studies demonstrated that exocytic cargo moves along microtubule
	tracks and reveals that carriers are capable of switching between
	tracks.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9841901},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport/physiology Cell Line Cell Membrane/*metabolism
	Cytoskeleton/physiology Exocytosis/physiology Fluorescent Antibody
	Technique Golgi Apparatus/*metabolism Green Fluorescent Proteins
	Luminescent Proteins/genetics/metabolism Macropodidae *Membrane Glycoproteins
	Microinjections Microscopy, Video Microtubules/*metabolism/physiology
	Organelles/metabolism Recombinant Fusion Proteins/genetics/metabolism
	Research Support, Non-U.S. Gov't Viral Envelope Proteins/genetics/metabolism},
  shorttitle = {Dual-color visualization of trans-Golgi network to plasma membrane
	traffic along microtubules in living cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9841901}
}

@ARTICLE{Tourovskaia2005,
  author = {Tourovskaia, A. and Figueroa-Masot, X. and Folch, A.},
  title = {Differentiation-on-a-chip: a microfluidic platform for long-term
	cell culture studies},
  journal = {Lab Chip},
  year = {2005},
  volume = {5},
  pages = {14-9},
  number = {1},
  month = {Jan},
  note = {1473-0197 (Print) Journal Article},
  abstract = {Here we demonstrate a microfluidic perfusion system suitable for a
	long-term (>2 week) culture of muscle cells spanning the whole process
	of differentiation from myoblasts to myotubes. Cell-adhesive surface
	microdomains alternating with a robust cell-repellent coating mimic
	in vivo spatial cues for muscle cell assembly and allow for confining
	the fusion of myoblasts into aligned, isolated multinucleated myotubes.
	The microfluidic system provides accurate control of the perfusion
	rates and biochemical composition of the environment surrounding
	the cells. Comparing muscle cell-specific differentiation markers
	and the timing of fusion, we observed no differences in differentiation
	between microfluidic and traditional cultures. All differentiation
	assays were fully microfluidic, i.e. they were performed by sequentially
	changing the fluids in the micro-channels. By delivering fluorescent
	markers using heterogeneous laminar flows, it was possible to confine
	a membrane receptor labeling assay to a region smaller than a myotube.
	Our method can serve as an improved in vitro model for studying muscle
	cell differentiation and for characterizing extracellular molecules
	and mechanisms involved in neuromuscular differentiation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15616734},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Adhesion Cell Culture Techniques/instrumentation/methods
	*Cell Differentiation Cell Fusion Cell Line Culture Media Mice *Microfluidic
	Analytical Techniques/instrumentation/methods Muscle Fibers/cytology/metabolism
	Muscle, Skeletal/*cytology/metabolism Myoblasts, Skeletal/cytology/metabolism
	Receptors, Nicotinic/biosynthesis Research Support, Non-U.S. Gov't
	Research Support, U.S. Gov't, P.H.S.},
  shorttitle = {Differentiation-on-a-chip: a microfluidic platform for long-term cell
	culture studies},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15616734}
}

@ARTICLE{Tourovskaia2006,
  author = {Tourovskaia, A. and Kosar, T. F. and Folch, A.},
  title = {Local induction of acetylcholine receptor clustering in myotube cultures
	using microfluidic application of agrin},
  journal = {Biophys J},
  year = {2006},
  volume = {90},
  pages = {2192-8},
  number = {6},
  month = {Mar 15},
  note = {0006-3495 (Print) Journal Article},
  abstract = {During neuromuscular synaptogenesis, the exchange of spatially localized
	signals between nerve and muscle initiates the coordinated focal
	accumulation of the acetylcholine (ACh) release machinery and the
	ACh receptors (AChRs). One of the key first steps is the release
	of the proteoglycan agrin focalized at the axon tip, which induces
	the clustering of AChRs on the postsynaptic membrane at the neuromuscular
	junction. The lack of a suitable method for focal application of
	agrin in myotube cultures has limited the majority of in vitro studies
	to the application of agrin baths. We used a microfluidic device
	and surface microengineering to focally stimulate muscle cells with
	agrin at a small portion of their membrane and at a time and position
	chosen by the user. The device is used to verify the hypothesis that
	focal application of agrin to the muscle cell membrane induces local
	aggregation of AChRs in differentiated C2C12 myotubes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16387765},
  endnotereftype = {Journal Article},
  shorttitle = {Local induction of acetylcholine receptor clustering in myotube cultures
	using microfluidic application of agrin},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16387765}
}

@ARTICLE{Wirtz2001.pdf,
  author = {Tseng, Y. and Kole, T. P. and Wirtz, D.},
  title = {Micromechanical mapping of live cells by multiple-particle-tracking
	microrheology},
  journal = {Biophys J},
  year = {2002},
  volume = {83},
  pages = {3162-76},
  number = {6},
  month = {Dec},
  note = {22383496 0006-3495 Evaluation Studies Journal Article},
  abstract = {This paper introduces the method of live-cell multiple-particle-tracking
	microrheology (MPTM), which quantifies the local mechanical properties
	of living cells by monitoring the Brownian motion of individual microinjected
	fluorescent particles. Particle tracking of carboxylated microspheres
	imbedded in the cytoplasm produce spatial distributions of cytoplasmic
	compliances and frequency-dependent viscoelastic moduli. Swiss 3T3
	fibroblasts are found to behave like a stiff elastic material when
	subjected to high rates of deformations and like a soft liquid at
	low rates of deformations. By analyzing the relative contributions
	of the subcellular compliances to the mean compliance, we find that
	the cytoplasm is much more mechanically heterogeneous than reconstituted
	actin filament networks. Carboxylated microspheres embedded in cytoplasm
	through endocytosis and amine-modified polystyrene microspheres,
	which are microinjected or endocytosed, often show directed motion
	and strong nonspecific interactions with cytoplasmic proteins, which
	prevents computation of local moduli from the microsphere displacements.
	Using MPTM, we investigate the mechanical function of alpha-actinin
	in non-muscle cells: alpha-actinin-microinjected cells are stiffer
	and yet mechanically more heterogeneous than control cells, in agreement
	with models of reconstituted cross-linked actin filament networks.
	MPTM is a new type of functional microscopy that can test the local,
	rate-dependent mechanical and ultrastructural properties of living
	cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12496086},
  endnotereftype = {Journal Article},
  keywords = {3T3 Cells/cytology/drug effects/physiology Actinin/administration
	& dosage Actins/physiology/ultrastructure Animal Comparative Study
	Cytoplasm/drug effects/*physiology/*ultrastructure Diffusion Elasticity
	Mice Microinjections Microscopy, Fluorescence/*methods Microspheres
	Motion Nanotechnology/instrumentation/methods Particle Size Reference
	Values Rheology/instrumentation/*methods Sensitivity and Specificity
	Stress, Mechanical Support, U.S. Gov't, Non-P.H.S. Viscosity},
  shorttitle = {Micromechanical mapping of live cells by multiple-particle-tracking
	microrheology},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12496086}
}

@ARTICLE{Ueda2001,
  author = {Ueda, M. and Sako, Y. and Tanaka, T. and Devreotes, P. and Yanagida,
	T.},
  title = {Single-molecule analysis of chemotactic signaling in Dictyostelium
	cells},
  journal = {Science},
  year = {2001},
  volume = {294},
  pages = {864-7},
  number = {5543},
  month = {Oct 26},
  note = {0036-8075 Journal Article},
  abstract = {Single-molecule imaging techniques were used to reveal the binding
	of individual cyclic adenosine 3',5'-monophosphate molecules to heterotrimeric
	guanine nucleotide-binding protein coupled receptors on the surface
	of living Dictyostelium discoideum cells. The binding sites were
	uniformly distributed and diffused rapidly in the plane of the membrane.
	The probabilities of individual association and dissociation events
	were greater for receptors at the anterior end of the cell. Agonist-induced
	receptor phosphorylation had little effect on any of the monitored
	properties, whereas G protein coupling influenced the binding kinetics.
	These observations illustrate the dynamic properties of receptors
	involved in gradient sensing and suggest that these may be polarized
	in chemotactic cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11679673},
  endnotereftype = {Journal Article},
  keywords = {Animals Carbocyanines/metabolism Cell Membrane/metabolism *Chemotaxis
	Cyclic AMP/*metabolism Dictyostelium/cytology/genetics/metabolism/*physiology
	Diffusion Guanosine Diphosphate/pharmacology Guanosine Triphosphate/pharmacology
	Heterotrimeric GTP-Binding Proteins/genetics/*metabolism Kinetics
	Microscopy, Fluorescence Mutation Phosphorylation Pseudopodia/metabolism
	Receptors, Cyclic AMP/*metabolism *Signal Transduction},
  shorttitle = {Single-molecule analysis of chemotactic signaling in Dictyostelium
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11679673}
}

@ARTICLE{Uras1988,
  author = {Uras, S and Girosi, F and Verri, A and Torre, V},
  title = {A computational approach to motion perception},
  journal = {Biol Cybern},
  year = {1988},
  volume = {60},
  pages = {79-87},
  endnotereftype = {Journal Article},
  shorttitle = {A computational approach to motion perception}
}

@ARTICLE{Uttenweiler2000,
  author = {Uttenweiler, D. and Veigel, C. and Steubing, R. and Gotz, C. and
	Mann, S. and Haussecker, H. and Jahne, B. and Fink, R. H.},
  title = {Motion determination in actin filament fluorescence images with a
	spatio-temporal orientation analysis method},
  journal = {Biophys J},
  year = {2000},
  volume = {78},
  pages = {2709-15},
  number = {5},
  month = {May},
  note = {20241901 0006-3495 Journal Article},
  abstract = {We present a novel approach of automatically measuring motion in series
	of microscopic fluorescence images. As a differential method, the
	three-dimensional structure tensor technique is used to calculate
	the displacement vector field for every image of the sequence, from
	which the velocities are subsequently derived. We have used this
	method for the analysis of the movement of single actin filaments
	in the in vitro motility assay, where fluorescently labeled actin
	filaments move over a myosin decorated surface. With its fast implementation
	and subpixel accuracy, this approach is, in general, very valuable
	for analyzing dynamic processes by image sequence analysis.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10777767},
  endnotereftype = {Journal Article},
  keywords = {Actins/*chemistry Animal Biophysics Image Processing, Computer-Assisted
	In Vitro Microscopy, Fluorescence Motion Myosins/chemistry Rabbits
	Support, Non-U.S. Gov't},
  shorttitle = {Motion determination in actin filament fluorescence images with a
	spatio-temporal orientation analysis method},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10777767}
}

@ARTICLE{Valberg1985,
  author = {Valberg, P. A. and Albertini, D. F.},
  title = {Cytoplasmic motions, rheology, and structure probed by a novel magnetic
	particle method},
  journal = {J Cell Biol},
  year = {1985},
  volume = {101},
  pages = {130-40},
  number = {1},
  month = {Jul},
  note = {0021-9525 Journal Article},
  abstract = {The motions of magnetic particles contained within organelles of living
	cells were followed by measuring magnetic fields generated by the
	particles. The alignment of particles was sensed magnetometrically
	and was manipulated by external fields, allowing non-invasive detection
	of particle motion as well as examination of cytoplasmic viscoelasticity.
	Motility and rheology data are presented for pulmonary macrophages
	isolated from lungs of hamsters 1 d after the animals had breathed
	airborne gamma-Fe2O3 particles. The magnetic directions of particles
	within phagosomes and secondary lysosomes were aligned, and the weak
	magnetic field produced by the particles was recorded. For dead cells,
	this remanent field was constant, but for viable macrophages, the
	remanent field decreased rapidly so that only 42% of its initial
	magnitude remained 5 min after alignment. A twisting field was applied
	perpendicular to the direction of alignment and the rate at which
	particles reoriented to this new direction was followed. The same
	twisting was repeated for particles suspended in a series of viscosity
	standards. Based on this approach, the low-shear apparent intracellular
	viscosity was estimated to be 1.2-2.7 X 10(3) Pa.s (1.2-2.7 X 10(4)
	poise). Time-lapse video microscopy confirmed the alignment of ingested
	particles upon magnetization and showed persistent cellular motility
	during randomization of alignment. Cytochalasin D and low temperature
	both reduced cytoplasmic activity and remanent-field decay, but affected
	rheology differently. Magnetic particles were observed in association
	with the microtubule organizing center by immunofluorescence microscopy;
	magnetization did not affect microtubule distribution. However, both
	vimentin intermediate filaments and f-actin reorganized after magnetization.
	These data demonstrate that magnetometry of isolated phagocytic cells
	can probe organelle movements, rheology, and physical properties
	of the cytoskeleton in living cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=4040136},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Movement Cells, Cultured Cold Cytochalasin D Cytochalasins/pharmacology
	Cytoplasm/*physiology Cytoskeleton/*physiology/ultrastructure Hamsters
	Lysosomes/physiology Macrophages/*physiology Magnetics Microscopy,
	Electron Microtubules/physiology/ultrastructure Pulmonary Alveoli/cytology
	Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't,
	P.H.S. Rheology Viscosity},
  shorttitle = {Cytoplasmic motions, rheology, and structure probed by a novel magnetic
	particle method},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=4040136}
}

@ARTICLE{Valberg1987,
  author = {Valberg, P. A. and Feldman, H. A.},
  title = {Magnetic particle motions within living cells. Measurement of cytoplasmic
	viscosity and motile activity},
  journal = {Biophys J},
  year = {1987},
  volume = {52},
  pages = {551-61},
  number = {4},
  month = {Oct},
  note = {0006-3495 Journal Article},
  abstract = {Submicrometer magnetic particles, ingested by cells and monitored
	via the magnetic fields they generate, provide an alternative to
	optical microscopy for probing movement and viscosity of living cytoplasm,
	and can be used for cells both in vitro and in vivo. We present methods
	for preparing lung macrophages tagged with magnetic particles for
	magnetometric study. Interpretation of the data involves fitting
	experimental remanent-field decay curves to nonlinear mechanistic
	models of intracellular particle motion. The model parameters are
	sensitive to mobility and apparent cytoplasmic viscosity experienced
	by particle-containing organelles. We present results of parameter
	estimation for intracellular particle behavior both within control
	cells and after (a) variable magnetization duration, (b) incubation
	with cytochalasin D, and (c) particle twisting by external fields.
	Magnetometric analysis showed cytoplasmic elasticity, dose-dependent
	motion inhibition by cytochalasin D, and a shear-thinning apparent
	viscosity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3676436},
  endnotereftype = {Journal Article},
  keywords = {Animals Cytoplasm/drug effects/physiology/ultrastructure Ferric Compounds/*pharmacology
	Hamsters Macrophages/drug effects/*physiology *Magnetics Mathematics
	Microscopy, Electron/methods Models, Biological Research Support,
	U.S. Gov't, P.H.S. Viscosity},
  shorttitle = {Magnetic particle motions within living cells. Measurement of cytoplasmic
	viscosity and motile activity},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3676436}
}

@ARTICLE{Valentine2005,
  author = {Valentine, M. T. and Perlman, Z. E. and Mitchison, T. J. and Weitz,
	D. A.},
  title = {Mechanical properties of Xenopus egg cytoplasmic extracts},
  journal = {Biophys J},
  year = {2005},
  volume = {88},
  pages = {680-9},
  number = {1},
  month = {Jan},
  note = {0006-3495 Journal Article},
  abstract = {Cytoplasmic extracts prepared from Xenopus laevis eggs are used for
	the reconstitution of a wide range of processes in cell biology,
	and offer a unique environment in which to investigate the role of
	cytoplasmic mechanics without the complication of preorganized cellular
	structures. As a step toward understanding the mechanical properties
	of this system, we have characterized the rheology of crude interphase
	extracts. At macroscopic length scales, the extract forms a soft
	viscoelastic solid. Using a conventional mechanical rheometer, we
	measure the elastic modulus to be in the range of 2-10 Pa, and loss
	modulus in the range of 0.5-5 Pa. Using pharmacological and immunological
	disruption methods, we establish that actin filaments and microtubules
	cooperate to give mechanical strength, whereas the intermediate filament
	cytokeratin does not contribute to viscoelasticity. At microscopic
	length scales smaller than the average network mesh size, the response
	is predominantly viscous. We use multiple particle tracking methods
	to measure the thermal fluctuations of 1 mum embedded tracer particles,
	and measure the viscosity to be approximately 20 mPa-s. We explore
	the impact of rheology on actin-dependent cytoplasmic contraction,
	and find that although microtubules modulate contractile forces in
	vitro, their interactions are not purely mechanical.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15501931},
  endnotereftype = {Journal Article},
  shorttitle = {Mechanical properties of Xenopus egg cytoplasmic extracts},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15501931}
}

@ARTICLE{Valetti1999,
  author = {Valetti, C. and Wetzel, D. M. and Schrader, M. and Hasbani, M. J.
	and Gill, S. R. and Kreis, T. E. and Schroer, T. A.},
  title = {Role of dynactin in endocytic traffic: effects of dynamitin overexpression
	and colocalization with CLIP-170},
  journal = {Mol Biol Cell},
  year = {1999},
  volume = {10},
  pages = {4107-20},
  number = {12},
  month = {Dec},
  note = {1059-1524 (Print) Journal Article},
  abstract = {The flow of material from peripheral, early endosomes to late endosomes
	requires microtubules and is thought to be facilitated by the minus
	end-directed motor cytoplasmic dynein and its activator dynactin.
	The microtubule-binding protein CLIP-170 may also play a role by
	providing an early link to endosomes. Here, we show that perturbation
	of dynactin function in vivo affects endosome dynamics and trafficking.
	Endosome movement, which is normally bidirectional, is completely
	inhibited. Receptor-mediated uptake and recycling occur normally,
	but cells are less susceptible to infection by enveloped viruses
	that require delivery to late endosomes, and they show reduced accumulation
	of lysosomally targeted probes. Dynactin colocalizes at microtubule
	plus ends with CLIP-170 in a way that depends on CLIP-170's putative
	cargo-binding domain. Overexpression studies using p150(Glued), the
	microtubule-binding subunit of dynactin, and mutant and wild-type
	forms of CLIP-170 indicate that CLIP-170 recruits dynactin to microtubule
	ends. These data suggest a new model for the formation of motile
	complexes of endosomes and microtubules early in the endocytic pathway.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10588646},
  endnotereftype = {Journal Article},
  keywords = {Animals COS Cells Cell Movement Cercopithecus aethiops Dynein ATPase/*metabolism
	Endocytosis/*physiology Endoplasmic Reticulum/metabolism Endosomes/*metabolism
	Fluorescent Antibody Technique Golgi Apparatus/metabolism Hela Cells
	Humans Mice Microtubule-Associated Proteins/*metabolism Microtubules/*metabolism
	Neoplasm Proteins Rabbits Research Support, Non-U.S. Gov't Research
	Support, U.S. Gov't, P.H.S. Transfection Vero Cells},
  shorttitle = {Role of dynactin in endocytic traffic: effects of dynamitin overexpression
	and colocalization with CLIP-170},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10588646}
}

@ARTICLE{Vallotton2003,
  author = {Vallotton, P. and Ponti, A. and Waterman-Storer, C. M. and Salmon,
	E. D. and Danuser, G.},
  title = {Recovery, visualization, and analysis of actin and tubulin polymer
	flow in live cells: a fluorescent speckle microscopy study},
  journal = {Biophys J},
  year = {2003},
  volume = {85},
  pages = {1289-306},
  number = {2},
  month = {Aug},
  note = {22767689 0006-3495 Journal Article},
  abstract = {Fluorescent speckle microscopy (FSM) is becoming the technique of
	choice for analyzing in vivo the dynamics of polymer assemblies,
	such as the cytoskeleton. The massive amount of data produced by
	this method calls for computational approaches to recover the quantities
	of interest; namely, the polymerization and depolymerization activities
	and the motions undergone by the cytoskeleton over time. Attempts
	toward this goal have been hampered by the limited signal-to-noise
	ratio of typical FSM data, by the constant appearance and disappearance
	of speckles due to polymer turnover, and by the presence of flow
	singularities characteristic of many cytoskeletal polymer assemblies.
	To deal with these problems, we present a particle-based method for
	tracking fluorescent speckles in time-lapse FSM image series, based
	on ideas from operational research and graph theory. Our software
	delivers the displacements of thousands of speckles between consecutive
	frames, taking into account that speckles may appear and disappear.
	In this article we exploit this information to recover the speckle
	flow field. First, the software is tested on synthetic data to validate
	our methods. We then apply it to mapping filamentous actin retrograde
	flow at the front edge of migrating newt lung epithelial cells. Our
	results confirm findings from previously published kymograph analyses
	and manual tracking of such FSM data and illustrate the power of
	automated tracking for generating complete and quantitative flow
	measurements. Third, we analyze microtubule poleward flux in mitotic
	metaphase spindles assembled in Xenopus egg extracts, bringing new
	insight into the dynamics of microtubule assemblies in this system.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12885672},
  endnotereftype = {Journal Article},
  shorttitle = {Recovery, visualization, and analysis of actin and tubulin polymer
	flow in live cells: a fluorescent speckle microscopy study},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12885672}
}

@ARTICLE{JohnWiley&SonsInc,
  author = {VandeVondele, S. and Voros, J. and Hubbell, J. A.},
  title = {RGD-Grafted poly-l-lysine-graft-(polyethylene glycol) copolymers
	block non-specific protein adsorption while promoting cell adhesion},
  journal = {Biotechnology and Bioengineering},
  year = {2003},
  volume = {82},
  pages = {784-790},
  number = {7},
  month = {JUN 30},
  note = {Times Cited: 30 Article English Cited References Count: 23 679gx},
  abstract = {A novel class of surface-active copolymers is described, designed
	to protect surfaces from nonspecific protein adsorption while still
	inducing specific cell attachment and spreading. A graft copolymer
	was synthesized, containing poly-(L-lysine) (PLL) as the backbone
	and substrate binding and poly(ethylene glycol) (PEG) as protein
	adsorption-resistant pendant side chains. A fraction of the grafted
	PEG was pendantly functionalized by covalent conjugation to the peptide
	motif RGD to induce cell binding. The graft copolymer spontaneously
	adsorbs from dilute aqueous solution onto negatively charged surfaces.
	The performance of RGD-modified PLL-g-PEG copolymers was analyzed
	in protein adsorption and cell culture assays. These coatings efficiently
	blocked the adsorption of serum proteins to Nb2O5 and tissue culture
	polystyrene while specifically supporting attachment and spreading
	of human dermal fibroblasts. This surface functionalization technology
	is expected to be valuable in both the biomaterial and biosensor
	fields, because different signals can easily be combined, and sterilization
	and application are straightforward and cost-effective. (C) 2003
	Wiley Periodicals, Inc.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000182913300004},
  endnotereftype = {Journal Article},
  keywords = {biomaterials protein adsorption adhesion peptide cell adhesion surface
	modification spectroscopy plasma fibrinogen attachment polymers},
  shorttitle = {RGD-Grafted poly-l-lysine-graft-(polyethylene glycol) copolymers block
	non-specific protein adsorption while promoting cell adhesion},
  url = {<Go to ISI>://000182913300004}
}

@ARTICLE{Verkhovsky1999,
  author = {Verkhovsky, A. B. and Svitkina, T. M. and Borisy, G. G.},
  title = {Self-polarization and directional motility of cytoplasm},
  journal = {Curr. Bio.},
  year = {1999},
  volume = {9},
  pages = {11-20},
  endnotereftype = {Journal Article},
  shorttitle = {Self-polarization and directional motility of cytoplasm}
}

@ARTICLE{Verkman1991,
  author = {Verkman, A. S. and Armijo, M. and Fushimi, K.},
  title = {Construction and evaluation of a frequency-domain epifluorescence
	microscope for lifetime and anisotropy decay measurements in subcellular
	domains},
  journal = {Biophys Chem},
  year = {1991},
  volume = {40},
  pages = {117-25},
  number = {1},
  month = {Apr},
  note = {0301-4622 Journal Article},
  abstract = {The measurement of time-resolved fluorescence parameters in living
	cells provides a powerful approach to study cell structure and dynamics.
	An epifluorescence microscope was constructed to resolve multi-component
	fluorescence lifetimes and complex anisotropy decay rapidly in labile
	biological samples. The excitation source consisted of focused, polarized
	laser light modulated by an impulse-driven Pockels' cell; parallel
	acquisition of phase angles and modulation amplitudes at more than
	40 frequencies (5-250 MHz) was obtained by multi-harmonic cross-correlation
	detection. Lifetime decay was measured against standard solutions
	introduced into the light path proximal to the microscope objective.
	Anisotropy decay was measured by rotation of a Glan-Thompson polarizer
	in the emission path. Phase reference light was split from the beam
	proximal to the microscope. Optical components were selected to avoid
	depolarization and to optimize fluorescence detection efficiency.
	The dichoric was replaced by a 1 mm square mirror. Fitting routine
	statistics were optimized for model discrimination in realistic biological
	samples. Instrument performance was evaluated using fluorescein in
	H2O/glycerol and H2O/ethylene glycol mixtures and in Swiss 3T3 fibroblasts
	in monolayer culture. Objective depolarization effects were evaluated
	by measurement of anisotropy decay using objectives of different
	numerical aperture. Lifetime and anisotropy decay measured by microscopy
	(0.5 micron laser spot) agreed with data obtained by cuvette fluorimetry.
	New biological applications for time-resolved fluorescence microscopy
	are discussed.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1873470},
  endnotereftype = {Journal Article},
  keywords = {Animals Cells, Cultured Fibroblasts/ultrastructure Fluorescein Fluoresceins/diagnostic
	use Fluorescent Dyes Fourier Analysis Mice Microscopy, Fluorescence/*instrumentation
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
	Spectrometry, Fluorescence Subcellular Fractions/*ultrastructure
	Thermodynamics},
  shorttitle = {Construction and evaluation of a frequency-domain epifluorescence
	microscope for lifetime and anisotropy decay measurements in subcellular
	domains},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1873470}
}

@ARTICLE{Wacker1997,
  author = {Wacker, I. and Kaether, C. and Kromer, A. and Migala, A. and Almers,
	W. and Gerdes, H. H.},
  title = {Microtubule-dependent transport of secretory vesicles visualized
	in real time with a GFP-tagged secretory protein},
  journal = {J Cell Sci},
  year = {1997},
  volume = {110 ( Pt 13)},
  pages = {1453-63},
  month = {Jul},
  note = {0021-9533 (Print) Journal Article},
  abstract = {Biosynthetic transport from the trans-Golgi network (TGN) to the plasma
	membrane (PM) is mediated by secretory vesicles. We analyzed secretory
	vesicle transport in real time using a GFP-tagged secretory protein,
	hCgB-GFP, consisting of human chromogranin B (hCgB) and green fluorescent
	protein (GFP). The fusion protein was expressed transiently in Vero
	cells or in a stable clone after induction with butyrate. After arrest
	of the biosynthetic protein transport at 20 degrees C, fluorescent
	hCgB-GFP colocalized with TGN38, a marker of the TGN. Subsequent
	release of the secretion block at 37 degrees C led to the formation
	of green fluorescent vesicles. Confocal analysis revealed that these
	vesicles were devoid of TGN38 and of Texas Red-coupled transferrin
	and cathepsin D, markers of the endosomal/lysosomal pathway. As determined
	by fluorometry and metabolic labelling hCgB-GFP was secreted from
	the TGN to the PM with a t(1/2) of 20-30 minutes. Video-microscope
	analysis of green fluorescent vesicles showed brief periods of rapid
	directed movement with maximal velocities of 1 microm/second. Vesicle
	movement occurred in all directions, centrifugal, centripetal and
	circumferential, and 50% of the vesicles analyzed reversed their
	direction of movement at least once within an observation period
	of 45 seconds. In the presence of nocodazole the movement of fluorescent
	vesicles ceased. Concomitantly, secretion of hCgB-GFP was slowed
	but not completely blocked. We suggest that microtubules (MT) facilitate
	the delivery of secretory vesicles to the PM by a stochastic transport,
	thereby increasing the probability for a vesicle/target membrane
	encounter.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9224763},
  endnotereftype = {Journal Article},
  keywords = {Animals Biological Transport, Active/drug effects Cell Membrane/physiology
	Cercopithecus aethiops Chromogranins/secretion Cytoplasmic Granules/*physiology
	Endosomes/physiology Golgi Apparatus/physiology Green Fluorescent
	Proteins Humans Luminescent Proteins/secretion Lysosomes/physiology
	Microtubules/drug effects/*physiology Movement Nocodazole/pharmacology
	Recombinant Fusion Proteins/secretion Research Support, Non-U.S.
	Gov't Vero Cells},
  shorttitle = {Microtubule-dependent transport of secretory vesicles visualized in
	real time with a GFP-tagged secretory protein},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9224763}
}

@ARTICLE{Wallace2001,
  author = {Wallace, W and Schaefer, L H and Swedlow, J R},
  title = {A workingperson's guide to deconvolution in light microscopy.},
  journal = {BioTechniques},
  year = {2001},
  volume = {31},
  pages = {1076--8, 1080, 1082 passim},
  number = {5},
  month = nov,
  __markedentry = {[Kota Miura]},
  abstract = {Thefluorescence microscope is routinely used to study cellular structure
	in many biomedical research laboratories and is increasingly used
	as a quantitative assay system for cellular dynamics. One of the
	major causes of image degradation in the fluorescence microscope
	is blurring. Deconvolution algorithms use a model of the microscope
	imaging process to either subtract or reassign out-of-focus blur.
	A variety of algorithms are now commercially available, each with
	its own characteristic advantages and disadvantages. In this article,
	we review the imaging process in the fluorescence microscope and
	then discuss how the various deconvolution methods work. Finally,
	we provide a summary of practical tips for using deconvolution and
	discuss imaging artifacts and how to minimize them.},
  file = {:D$\backslash$:/\_Kota/Research\_Ref/noise/BioTechniquesGuidetoDeconvolution.pdf:pdf},
  issn = {0736-6205},
  keywords = {Algorithms,Animals,Artifacts,Filtration,Fluorescence,Humans,Microscopy,deconvolution,review},
  mendeley-tags = {deconvolution,review},
  owner = {Kota Miura},
  pmid = {11730015},
  timestamp = {2011.11.04},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/11730015}
}

@ARTICLE{Walter2002,
  author = {Walter, A. and Spies, H. and Terjung, S. and Kﾃｼsters, R. and
	Kirchgeﾃ殤er, N. and Schurr, U.},
  title = {Spatio-temporal dynamics of expansion growth in roots: automatic
	quantification of diurnal course and temperature response by digital
	image sequence processing},
  journal = {Journal of Experimental Botany},
  year = {2002},
  volume = {53},
  pages = {689-698},
  number = {369},
  note = {pdf},
  endnotereftype = {Journal Article},
  shorttitle = {Spatio-temporal dynamics of expansion growth in roots: automatic quantification
	of diurnal course and temperature response by digital image sequence
	processing}
}

@ARTICLE{WalterNATM2010,
  author = {Thomas Walter and David W Shattuck and Richard Baldock and Mark E
	Bastin and Anne E Carpenter and Suzanne Duce and Jan Ellenberg and
	Adam Fraser and Nicholas Hamilton and Steve Pieper and Mark A Ragan
	and Jurgen E Schneider and Pavel Tomancak and Jean-Karim H{\'e}rich{\'e}},
  title = {Visualization of image data from cells to organisms.},
  journal = {Nat Methods},
  year = {2010},
  volume = {7},
  pages = {S26--S41},
  number = {3 Suppl},
  month = {Mar},
  abstract = {Advances in imaging techniques and high-throughput technologies are
	providing scientists with unprecedented possibilities to visualize
	internal structures of cells, organs and organisms and to collect
	systematic image data characterizing genes and proteins on a large
	scale. To make the best use of these increasingly complex and large
	image data resources, the scientific community must be provided with
	methods to query, analyze and crosslink these resources to give an
	intuitive visual representation of the data. This review gives an
	overview of existing methods and tools for this purpose and highlights
	some of their limitations and challenges.},
  bdsk-url-1 = {http://dx.doi.org/10.1038/nmeth.1431},
  doi = {10.1038/nmeth.1431},
  institution = {European Molecular Biology Laboratory, Heidelberg, Germany.},
  keywords = {Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Microscopy,
	methods},
  language = {eng},
  medline-pst = {ppublish},
  owner = {Kota},
  pii = {nmeth.1431},
  pmid = {20195255},
  timestamp = {2011.03.10},
  url = {http://dx.doi.org/10.1038/nmeth.1431}
}

@ARTICLE{Wang1994,
  author = {Wang, Y. L. and Silverman, J. D. and Cao, L. G.},
  title = {Single particle tracking of surface receptor movement during cell
	division},
  journal = {J Cell Biol},
  year = {1994},
  volume = {127},
  pages = {963-71},
  number = {4},
  month = {Nov},
  note = {95050976 0021-9525 Journal Article},
  abstract = {We have used fluorescent latex beads to label membrane receptors on
	cultured NRK cells. Movement of individual beads during cell division
	was recorded with digital imaging techniques. Surface-bound beads
	showed no organized movement during metaphase but started to migrate
	toward the equator approximately 1 min after anaphase onset, when
	chromosomes moved out of the equatorial region to create the interzone.
	The movement was most active in the central region of the cell near
	separating chromosomes, while beads located near the poles of the
	cell underwent primarily random motion. Most beads showed a surge
	in speed upon the passage of chromosomes, suggesting a possible link
	between chromosome separation and cortical reorganization. Furthermore,
	treatment of anaphase cells with cytochalasin D induced a rapid,
	simultaneous collapse of beads and cortical actin filaments into
	aggregates, indicating that the movement of beads was closely related
	to the reorganization of the actin cortex. In contrast to normal
	directional movement, cytochalasin-induced movement occurred in random
	directions and caused some beads in the equatorial region to move
	toward poles. Our results indicate that cytokinesis involves contractile
	activities, not only along the equator, but over a wide area of the
	actin-containing cortex. In addition, organized cortical activities
	appear to be temporally activated at anaphase onset, and spatially
	modulated by the spindle interzone or separating chromosomes.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7962078},
  endnotereftype = {Journal Article},
  keywords = {Anaphase Animal *Cell Cycle *Cell Division Cell Line Cell Membrane/drug
	effects/physiology/ultrastructure Cytochalasin D/pharmacology Kidney
	Latex Microscopy, Fluorescence Microspheres Rats Receptors, Cell
	Surface/analysis/drug effects/*physiology Support, Non-U.S. Gov't
	Support, U.S. Gov't, P.H.S. Telophase},
  shorttitle = {Single particle tracking of surface receptor movement during cell
	division},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7962078}
}

@ARTICLE{Ward2001,
  author = {Ward, T. H. and Polishchuk, R. S. and Caplan, S. and Hirschberg,
	K. and Lippincott-Schwartz, J.},
  title = {Maintenance of Golgi structure and function depends on the integrity
	of ER export},
  journal = {J Cell Biol},
  year = {2001},
  volume = {155},
  pages = {557-70},
  number = {4},
  month = {Nov 12},
  note = {0021-9525 Journal Article},
  abstract = {The Golgi apparatus comprises an enormous array of components that
	generate its unique architecture and function within cells. Here,
	we use quantitative fluorescence imaging techniques and ultrastructural
	analysis to address whether the Golgi apparatus is a steady-state
	or a stable organelle. We found that all classes of Golgi components
	are dynamically associated with this organelle, contrary to the prediction
	of the stable organelle model. Enzymes and recycling components are
	continuously exiting and reentering the Golgi apparatus by membrane
	trafficking pathways to and from the ER, whereas Golgi matrix proteins
	and coatomer undergo constant, rapid exchange between membrane and
	cytoplasm. When ER to Golgi transport is inhibited without disrupting
	COPII-dependent ER export machinery (by brefeldin A treatment or
	expression of Arf1[T31N]), the Golgi structure disassembles, leaving
	no residual Golgi membranes. Rather, all Golgi components redistribute
	into the ER, the cytoplasm, or to ER exit sites still active for
	recruitment of selective membrane-bound and peripherally associated
	cargos. A similar phenomenon is induced by the constitutively active
	Sar1[H79G] mutant, which has the additional effect of causing COPII-associated
	membranes to cluster to a juxtanuclear region. In cells expressing
	Sar1[T39N], a constitutively inactive form of Sar1 that completely
	disrupts ER exit sites, Golgi glycosylation enzymes, matrix, and
	itinerant proteins all redistribute to the ER. These results argue
	against the hypothesis that the Golgi apparatus contains stable components
	that can serve as a template for its biogenesis. Instead, they suggest
	that the Golgi complex is a dynamic, steady-state system, whose membranes
	can be nucleated and are maintained by the activities of the Sar1-COPII
	and Arf1-coatomer systems.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11706049},
  endnotereftype = {Journal Article},
  keywords = {ADP-Ribosylation Factor 1/metabolism Brefeldin A/metabolism/pharmacology
	COP-Coated Vesicles/metabolism Endoplasmic Reticulum/*metabolism
	Golgi Apparatus/drug effects/*metabolism/physiology Guanosine Diphosphate/metabolism
	Guanosine Triphosphate/metabolism Intracellular Membranes/metabolism
	Membrane Proteins/metabolism Monomeric GTP-Binding Proteins/metabolism
	Protein Transport *Saccharomyces cerevisiae Proteins},
  shorttitle = {Maintenance of Golgi structure and function depends on the integrity
	of ER export},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11706049}
}

@ARTICLE{Waters2009,
  author = {Jennifer C Waters},
  title = {Accuracy and precision in quantitative fluorescence microscopy.},
  journal = {J Cell Biol},
  year = {2009},
  volume = {185},
  pages = {1135--1148},
  number = {7},
  month = {Jun},
  abstract = {The light microscope has long been used to document the localization
	of fluorescent molecules in cell biology research. With advances
	in digital cameras and the discovery and development of genetically
	encoded fluorophores, there has been a huge increase in the use of
	fluorescence microscopy to quantify spatial and temporal measurements
	of fluorescent molecules in biological specimens. Whether simply
	comparing the relative intensities of two fluorescent specimens,
	or using advanced techniques like F{\"o}rster resonance energy transfer
	(FRET) or fluorescence recovery after photobleaching (FRAP), quantitation
	of fluorescence requires a thorough understanding of the limitations
	of and proper use of the different components of the imaging system.
	Here, I focus on the parameters of digital image acquisition that
	affect the accuracy and precision of quantitative fluorescence microscopy
	measurements.},
  bdsk-url-1 = {http://dx.doi.org/10.1083/jcb.200903097},
  doi = {10.1083/jcb.200903097},
  institution = {Harvard Medical School, Department of Cell Biology, Boston, MA 02115,
	USA. jennifer_waters@hms.harvard.edu},
  keywords = {Fluorescent Dyes, metabolism; Image Interpretation, Computer-Assisted;
	Light; Microscopy, Fluorescence, instrumentation/methods/standards;
	Sensitivity and Specificity},
  language = {eng},
  medline-pst = {ppublish},
  owner = {Kota},
  pii = {jcb.200903097},
  pmid = {19564400},
  timestamp = {2011.03.10},
  url = {http://dx.doi.org/10.1083/jcb.200903097}
}

@ARTICLE{Weele2003,
  author = {van der Weele, C. M. and Jiang, H. S. and Palaniappan, K. K. and
	Ivanov, V. B. and Palaniappan, K. and Baskin, T. I.},
  title = {A new algorithm for computational image analysis of deformable motion
	at high spatial and temporal resolution applied to root growth. Roughly
	uniform elongation in the meristem and also, after an abrupt acceleration,
	in the elongation zone},
  journal = {Plant Physiol},
  year = {2003},
  volume = {132},
  pages = {1138-48},
  number = {3},
  month = {Jul},
  note = {0032-0889 Journal Article},
  abstract = {A requirement for understanding morphogenesis is being able to quantify
	expansion at the cellular scale. Here, we present new software (RootflowRT)
	for measuring the expansion profile of a growing root at high spatial
	and temporal resolution. The software implements an image processing
	algorithm using a novel combination of optical flow methods for deformable
	motion. The algorithm operates on a stack of nine images with a given
	time interval between each (usually 10 s) and quantifies velocity
	confidently at most pixels of the image. The root does not need to
	be marked. The software calculates components of motion parallel
	and perpendicular to the local tangent of the root's midline. A variation
	of the software has been developed that reports the overall root
	growth rate versus time. Using this software, we find that the growth
	zone of the root can be divided into two distinct regions, an apical
	region where the rate of motion, i.e. velocity, rises gradually with
	position and a subapical region where velocity rises steeply with
	position. In both zones, velocity increases almost linearly with
	position, and the transition between zones is abrupt. We observed
	this pattern for roots of Arabidopsis, tomato (Lycopersicon lycopersicum),
	lettuce (Lactuca sativa), alyssum (Aurinia saxatilis), and timothy
	(Phleum pratense). These velocity profiles imply that relative elongation
	rate is regulated in a step-wise fashion, being low but roughly uniform
	within the meristem and then becoming high, but again roughly uniform,
	within the zone of elongation. The executable code for RootflowRT
	is available from the corresponding author on request.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12857796},
  endnotereftype = {Journal Article},
  keywords = {*Algorithms Angiosperms/growth & development Image Processing, Computer-Assisted/*methods
	Meristem/*growth & development *Movement Software Support, U.S. Gov't,
	Non-P.H.S.},
  shorttitle = {A new algorithm for computational image analysis of deformable motion
	at high spatial and temporal resolution applied to root growth. Roughly
	uniform elongation in the meristem and also, after an abrupt acceleration,
	in the elongation zone},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12857796}
}

@ARTICLE{Welte2004,
  author = {Welte, M. A.},
  title = {Bidirectional transport along microtubules},
  journal = {Curr Biol},
  year = {2004},
  volume = {14},
  pages = {R525-37},
  number = {13},
  month = {Jul 13},
  note = {0960-9822 (Print) Journal Article Review},
  abstract = {Active transport by microtubule motors has a plethora of crucial roles
	in eukaryotic cells. Organelles often move bidirectionally, employing
	both plus-end and minus-end directed motors. Bidirectional motion
	is widespread and may allow dynamic regulation, error correction
	and the establishment of polarized organelle distributions. Emerging
	evidence suggests that motors for both directions are simultaneously
	present on cellular 'cargo', but that their activity is coordinated
	so that when plus-end motors are active, minus-end motors are not,
	and vice versa. Both the dynein cofactor dynactin and the Klarsicht
	(Klar) protein appear to be important for such coordination. The
	direction of net transport depends on the balance between plus-end
	directed and minus-end directed motion. In several model systems,
	factors crucial for setting this balance have now been identified,
	setting the stage for a molecular dissection of the underlying regulatory
	mechanisms. These analyses will likely provide insight into motor
	cooperation in general.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15242636},
  endnotereftype = {Journal Article},
  keywords = {Biological Transport, Active Drosophila Proteins/metabolism Lipid
	Metabolism Membrane Transport Proteins/metabolism Microtubule-Associated
	Proteins/metabolism Microtubules/*metabolism/physiology Mitochondria/metabolism
	*Models, Biological Molecular Motors/*metabolism/physiology Pigments,
	Biological/metabolism Research Support, Non-U.S. Gov't Research Support,
	U.S. Gov't, P.H.S. Viruses/metabolism},
  shorttitle = {Bidirectional transport along microtubules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15242636}
}

@ARTICLE{Wheeler1999,
  author = {Wheeler, B. C. and Corey, J. M. and Brewer, G. J. and Branch, D.
	W.},
  title = {Microcontact printing for precise control of nerve cell growth in
	culture},
  journal = {J Biomech Eng},
  year = {1999},
  volume = {121},
  pages = {73-8},
  number = {1},
  month = {Feb},
  note = {0148-0731 (Print) Journal Article Research Support, Non-U.S. Gov't},
  abstract = {Microcontact printing, facilitated by silane linker chemistry and
	high-relief stamps, creates precise patterns of proteins, which in
	turn control growth of hippocampal neurons in culture. This additive,
	multi-mask technique permits several different molecules to be patterned
	on the same substrate. The covalent linker technology permits relatively
	long-term (two-week) compliance of neurons to the stamped pattern
	against a polyethylene glycol background. When polylysine was stamped
	adjacent to a laminin/polylysine mixture, neural somata and dendrites
	preferred the polylysine while axons prefer the mixture or the border
	between the two.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10080092},
  endnotereftype = {Journal Article},
  keywords = {Animals Axons/metabolism *Biocompatible Materials Cell Culture Techniques/*instrumentation/methods
	Cell Division Cells, Cultured Dendrites/metabolism Hippocampus/*cytology/metabolism
	*Laminin *Materials Testing Neurons/cytology/metabolism *Polylysine
	Proteins/metabolism Pyramidal Cells/cytology/metabolism Rats Rats,
	Sprague-Dawley Surface Properties},
  shorttitle = {Microcontact printing for precise control of nerve cell growth in
	culture},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10080092}
}

@ARTICLE{Whitesides2001,
  author = {Whitesides, G. M. and Ostuni, E. and Takayama, S. and Jiang, X. and
	Ingber, D. E.},
  title = {Soft lithography in biology and biochemistry},
  journal = {Annu Rev Biomed Eng},
  year = {2001},
  volume = {3},
  pages = {335-73},
  note = {1523-9829 (Print) Journal Article Review},
  abstract = {Soft lithography, a set of techniques for microfabrication, is based
	on printing and molding using elastomeric stamps with the patterns
	of interest in basrelief. As a technique for fabricating microstructures
	for biological applications, soft lithography overcomes many of the
	shortcomings of photolithography. In particular, soft lithography
	offers the ability to control the molecular structure of surfaces
	and to pattern the complex molecules relevant to biology, to fabricate
	channel structures appropriate for microfluidics, and to pattern
	and manipulate cells. For the relatively large feature sizes used
	in biology (> or = 50 microns), production of prototype patterns
	and structures is convenient, inexpensive, and rapid. Self-assembled
	monolayers of alkanethiolates on gold are particularly easy to pattern
	by soft lithography, and they provide exquisite control over surface
	biochemistry.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11447067},
  endnotereftype = {Journal Article},
  keywords = {Animals Biochemistry/*methods Biocompatible Materials Biology/methods
	Biomedical Engineering/methods Elasticity Research Support, Non-U.S.
	Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Soft lithography in biology and biochemistry},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11447067}
}

@ARTICLE{Wildman2000,
  author = {Wildman, R. D. and Huntley, J. M. and Hansen, J. P. and Parker, D.
	J. and Allen, D. A.},
  title = {Single-particle motion in three-dimensional vibrofluidized granular
	beds},
  journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics},
  year = {2000},
  volume = {62},
  pages = {3826-35},
  number = {3 Pt B},
  month = {Sep},
  note = {0 1063-651x Journal article},
  abstract = {A technique to probe the interior of three-dimensional dynamic granular
	systems is presented. Positron emission particle tracking (PEPT)
	allows a single tracer particle to be followed around a three dimensional
	vibrofluidized granular bed for periods up to six hours. At present
	the technique is able to resolve the position of the grains to +/-4
	mm, with an average temporal resolution of about 7 ms. Packing fraction
	profiles are calculated by making use of the ergodicity of the system,
	and granular temperature profiles are obtained, in the dilute case,
	from the short time behavior of the mean squared displacement. At
	longer times, the mean squared displacement shows a range of behavior
	which can be explained by the presence of strong gradients in the
	packing fraction. Convection currents were observed, but were sufficiently
	small in magnitude to be ignored during the analysis of grain motion.
	The system was modeled using the Smoluchowski equation, which was
	solved numerically, and the results compared with the experimentally
	determined displacement probability density functions. Good agreement
	between experiment and numerical results was achieved using Brownian
	motion relationships modified to accommodate differences between
	granular systems and thermal systems.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=0011088900},
  endnotereftype = {Journal Article},
  shorttitle = {Single-particle motion in three-dimensional vibrofluidized granular
	beds},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=0011088900}
}

@MISC{Wilhelm2004,
  author = {Wilhelm, S., Grﾃｶbler, B., Gluch, M., Heinz, H.},
  title = {Confocal Laser Scanning Microscopy},
  howpublished = {Carl Zeiss Jena GmbH},
  year = {2004},
  bdsk-url-1 = {http://www.zeiss.de/C1256D18002CC306/0/F99A7F3E8944EEE3C1256E5C0045F68B/$file/45-0029_e.pdf},
  endnotereftype = {Electronic Source},
  shorttitle = {Confocal Laser Scanning Microscopy},
  url = {http://www.zeiss.de/C1256D18002CC306/0/F99A7F3E8944EEE3C1256E5C0045F68B/$file/45-0029_e.pdf}
}

@ARTICLE{Wilson1996,
  author = {Wilson, K. M. and Morrison, I. E. and Smith, P. R. and Fernandez,
	N. and Cherry, R. J.},
  title = {Single particle tracking of cell-surface HLA-DR molecules using R-phycoerythrin
	labeled monoclonal antibodies and fluorescence digital imaging},
  journal = {J Cell Sci},
  year = {1996},
  volume = {109 ( Pt 8)},
  pages = {2101-9},
  month = {Aug},
  note = {97009401 0021-9533 Journal Article},
  abstract = {The mobility of cell surface MHC molecules and their ability to form
	dynamic associations may be related to the physiological status of
	the cell and to the potential to bind effector T lymphocytes. To
	investigate these properties, we have prepared HLA DR specific monoclonal
	antibodies coupled in a 1:1 mole ratio to the fluorescent phycobiliprotein,
	R-phycoerythrin (PE). We show that these small particles can be sequentially
	imaged using a cooled slow-scan charge coupled device camera and
	hence can be used for single particle tracking experiments. We have
	applied this technique to investigate the movements of HLA DR molecules
	on fibroblasts transfected with human DR alpha and DR beta genes.
	PE-IgG was bound to the transfected fibroblasts and particle tracks
	were obtained by sequential imaging over a period of typically 30
	minutes. Analysis of particle tracks revealed the presence of directed
	motion and domain-limited diffusion in addition to random diffusion.
	The contributions of these three types of motion showed cell to cell
	variability. Velocities of directed motion were of the order of 2
	nm second-1 whilst domain diameters were in the range 200-800 nm.
	Diffusion coefficients for random diffusion were in the range 1 x
	10(-13)-5 x 10(-12) cm2 second-1. The higher mobilities were observed
	for the lower intensity fluorescent spots, which possibly correspond
	to images of single particles. Much lower mobility was observed with
	a cell where the spot intensities were approximately double that
	of the lower intensity spots. These spots could be images of double
	particles implying the association of at least two HLA DR alpha beta
	dimers. These data are relevant to the study of MHC class II cell
	surface redistribution and antigen presentation in specific immunity.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8856506},
  endnotereftype = {Journal Article},
  keywords = {*Antibodies, Monoclonal B-Lymphocytes/chemistry Flow Cytometry HLA-DR
	Antigens/*chemistry Human Image Enhancement/*methods *Phycoerythrin
	Receptors, Antigen, T-Cell/chemistry Support, Non-U.S. Gov't},
  shorttitle = {Single particle tracking of cell-surface HLA-DR molecules using R-phycoerythrin
	labeled monoclonal antibodies and fluorescence digital imaging},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8856506}
}

@ARTICLE{witt2005PLOSB2005,
  author = {Witt, C. M. and Raychaudhuri, S. and Schaefer, B. and Chakraborty,
	A. K. and Robey, E. A.},
  title = {Directed migration of positively selected thymocytes visualized in
	real time},
  journal = {PLoS Biol},
  year = {2005},
  volume = {3},
  pages = {e160},
  number = {6},
  month = {Jun},
  note = {1545-7885 Journal Article},
  abstract = {Development of many vertebrate tissues involves long-range cell migrations.
	In most cases, these migrations have been inferred from analysis
	of single time points and the migration process has not been directly
	observed and quantitated in real time. In the mammalian adult thymus,
	immature CD4+ CD8+ double-positive (DP) thymocytes are found in the
	outer cortex, whereas after T cell antigen receptor (TCR) repertoire
	selection, CD4+ CD8- and CD4- CD8+ single-positive (SP) thymocytes
	are found in the central medulla. Here we have used two-photon laser-scanning
	microscopy and quantitative analysis of four-dimensional cell migration
	data to investigate the movement of thymocytes through the cortex
	in real time within intact thymic lobes. We show that prior to positive
	selection, cortical thymocytes exhibit random walk migration. In
	contrast, positive selection is correlated with the appearance of
	a thymocyte population displaying rapid, directed migration toward
	the medulla. These studies provide our first glimpse into the dynamics
	of developmentally programmed, long-range cell migration in the mammalian
	thymus.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15869324},
  endnotereftype = {Journal Article},
  shorttitle = {Directed migration of positively selected thymocytes visualized in
	real time},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15869324}
}

@ARTICLE{Wohlgemuth2000,
  author = {Wohlgemuth, M. and Machtle, W. and Mayer, C.},
  title = {Improved preparation and physical studies of polybutylcyanoacrylate
	nanocapsules},
  journal = {J Microencapsul},
  year = {2000},
  volume = {17},
  pages = {437-48},
  number = {4},
  month = {Jul-Aug},
  note = {20354449 0265-2048 Journal Article},
  abstract = {An improved method for the preparation of alkylcyanoacrylate nanocapsules
	is proposed that involves the intermediate synthesis of a well defined
	adduct of a single monomer unit to an ethanol molecule. It leads
	to thinner capsule walls and, generally, to a more reproducible capsule
	structure. The chemical composition of the intermediate organic phase
	has been studied by nuclear magnetic resonance spectroscopy. The
	morphology and size of resulting structures is analysed, applying
	analytical ultracentrifugation and light microscopic particle tracking.
	The sizes of capsules prepared in the described manner depend on
	the concentrations of the oil and the monomer components, as is shown
	by the results of a set of experiments following a simple factorial
	design.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10898084},
  endnotereftype = {Journal Article},
  keywords = {Capsules/chemical synthesis/chemistry/*isolation & purification Drug
	Compounding Enbucrilate/chemical synthesis/chemistry/*isolation &
	purification Human Magnetic Resonance Spectroscopy Particle Size
	Ultracentrifugation},
  shorttitle = {Improved preparation and physical studies of polybutylcyanoacrylate
	nanocapsules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10898084}
}

@ARTICLE{Wojcieszyn1981,
  author = {Wojcieszyn, J. W. and Schlegel, R. A. and Wu, E. S. and Jacobson,
	K. A.},
  title = {Diffusion of injected macromolecules within the cytoplasm of living
	cells},
  journal = {Proc Natl Acad Sci U S A},
  year = {1981},
  volume = {78},
  pages = {4407-10},
  number = {7},
  month = {Jul},
  note = {0027-8424 Journal Article},
  abstract = {The diffusion of macromolecules introduced into the cytoplasm of human
	fibroblasts by erythrocyte-mediated microinjection was measured by
	the fluorescence recovery after photobleaching technique. The apparent
	diffusion coefficients for fluorescein-labeled IgG and fluorescein-labeled
	bovine serum albumin were approximately 10(-8) cm2/sec at 22 degrees
	C, consistent with the kinetics of spreading of the fluorescent probe
	following microinjection and approximately 1/70 the values in aqueous
	buffer. The diffusion of labeled bovine serum albumin was shown to
	be strongly dependent on temperature and, in fact, similar to that
	expected in a 61% aqueous sucrose solution. However, the marked reduction
	in diffusion at 5 degrees C could be fully reversed by incubation
	with 0.1 mM colchicine. These findings suggest that cytoplasmic diffusion
	rates are reduced relative to rates in aqueous media as a result
	of increased aqueous phase viscosity or the impedence provided by
	structural elements. Several simple models to account for the data
	are presented.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6945591},
  endnotereftype = {Journal Article},
  keywords = {Cells, Cultured Colchicine/pharmacology Cytoplasm/physiology/*ultrastructure
	Diffusion Fluoresceins Humans Immunoglobulin G Male Photochemistry
	Research Support, U.S. Gov't, P.H.S. Serum Albumin, Bovine/diagnostic
	use Spectrometry, Fluorescence Temperature Viscosity},
  shorttitle = {Diffusion of injected macromolecules within the cytoplasm of living
	cells},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=6945591}
}

@ARTICLE{Wolf2003,
  author = {Wolf, K. and Mazo, I. and Leung, H. and Engelke, K. and von Andrian,
	U. H. and Deryugina, E. I. and Strongin, A. Y. and Brocker, E. B.
	and Friedl, P.},
  title = {Compensation mechanism in tumor cell migration: mesenchymal-amoeboid
	transition after blocking of pericellular proteolysis},
  journal = {J Cell Biol},
  year = {2003},
  volume = {160},
  pages = {267-77},
  number = {2},
  month = {Jan 20},
  note = {0021-9525 (Print) Journal Article},
  abstract = {Invasive tumor dissemination in vitro and in vivo involves the proteolytic
	degradation of ECM barriers. This process, however, is only incompletely
	attenuated by protease inhibitor-based treatment, suggesting the
	existence of migratory compensation strategies. In three-dimensional
	collagen matrices, spindle-shaped proteolytically potent HT-1080
	fibrosarcoma and MDA-MB-231 carcinoma cells exhibited a constitutive
	mesenchymal-type movement including the coclustering of beta 1 integrins
	and MT1-matrix metalloproteinase (MMP) at fiber bindings sites and
	the generation of tube-like proteolytic degradation tracks. Near-total
	inhibition of MMPs, serine proteases, cathepsins, and other proteases,
	however, induced a conversion toward spherical morphology at near
	undiminished migration rates. Sustained protease-independent migration
	resulted from a flexible amoeba-like shape change, i.e., propulsive
	squeezing through preexisting matrix gaps and formation of constriction
	rings in the absence of matrix degradation, concomitant loss of clustered
	beta 1 integrins and MT1-MMP from fiber binding sites, and a diffuse
	cortical distribution of the actin cytoskeleton. Acquisition of protease-independent
	amoeboid dissemination was confirmed for HT-1080 cells injected into
	the mouse dermis monitored by intravital multiphoton microscopy.
	In conclusion, the transition from proteolytic mesenchymal toward
	nonproteolytic amoeboid movement highlights a supramolecular plasticity
	mechanism in cell migration and further represents a putative escape
	mechanism in tumor cell dissemination after abrogation of pericellular
	proteolysis.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12527751},
  endnotereftype = {Journal Article},
  keywords = {Actins/metabolism Amoeba/cytology/metabolism Animals Antigens, CD29/metabolism
	Cell Movement/*physiology Cell Size/physiology Collagen/metabolism
	Dermis/cytology/metabolism Endopeptidases/drug effects/metabolism
	Extracellular Matrix Proteins/*metabolism Female Humans Mesoderm/cytology/*metabolism/transplantation
	Metalloendopeptidases/metabolism Mice Neoplasm Metastasis/*physiopathology
	Neoplasms/*metabolism Peptide Hydrolases/metabolism Protease Inhibitors/pharmacology
	Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
	Tissue Transplantation Tumor Cells, Cultured},
  shorttitle = {Compensation mechanism in tumor cell migration: mesenchymal-amoeboid
	transition after blocking of pericellular proteolysis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12527751}
}

@ARTICLE{Wolf2003a,
  author = {Wolf, K. and Muller, R. and Borgmann, S. and Brocker, E. B. and Friedl,
	P.},
  title = {Amoeboid shape change and contact guidance: T-lymphocyte crawling
	through fibrillar collagen is independent of matrix remodeling by
	MMPs and other proteases},
  journal = {Blood},
  year = {2003},
  volume = {102},
  pages = {3262-9},
  number = {9},
  month = {Nov 1},
  note = {0006-4971 (Print) Journal Article},
  abstract = {The passage of leukocytes through basement membranes involves proteolytic
	degradation of extracellular matrix (ECM) components executed by
	focalized proteolysis. We have investigated whether the migration
	of leukocytes through 3-dimensional collagenous tissue scaffolds
	requires similar ECM breakdown. Human T blasts and SupT1 lymphoma
	cells expressed mRNA of MMP-9, MT1-MMP, MT4-MMP, cathepsin L, uPA,
	and uPAR as well as ADAM-9, -10, -11, -15, and -17. Upon long-term
	migration within 3-dimensional collagen matrices, however, no in
	situ collagenolysis was obtained by sensitive fluorescein isothiocyanate-collagen
	fragmentation analysis and confocal fluorescence/backscatter microscopy.
	Consistent with nonproteolytic migration, T-cell crawling and path
	generation were not impaired by protease inhibitor cocktail targeting
	MMPs, serine proteases, cysteine proteases, and cathepsins. Dynamic
	imaging of cell-ECM interactions showed T-cell migration as an amoeba-like
	process driven by adaptive morphology, crawling along collagen fibrils
	(contact guidance) and squeezing through pre-existing matrix gaps
	by vigorous shape change. The concept of nonproteolytic amoeboid
	migration was confirmed for multicomponent collagen lattices containing
	hyaluronan and chondroitin sulfate and for other migrating leukocytes
	including CD8+ T blasts, monocyte-derived dendritic cells, and U937
	monocytic cells. Together, amoeboid shape change and contact guidance
	provide constitutive protease-independent mechanisms for leukocyte
	trafficking through interstitial tissues that are insensitive toward
	pharmacologic protease inhibitors.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12855577},
  endnotereftype = {Journal Article},
  keywords = {Blood Cells Cathepsins/antagonists & inhibitors/genetics Cell Adhesion
	Cell Line, Tumor Cell Size *Chemotaxis, Leukocyte Collagen/*metabolism
	Cysteine Endopeptidases/genetics Extracellular Matrix/*metabolism
	Humans Matrix Metalloproteinases/antagonists & inhibitors/genetics
	Microscopy, Confocal Protease Inhibitors/pharmacology RNA, Messenger/analysis
	Research Support, Non-U.S. Gov't T-Lymphocytes/*cytology/*physiology},
  shorttitle = {Amoeboid shape change and contact guidance: T-lymphocyte crawling
	through fibrillar collagen is independent of matrix remodeling by
	MMPs and other proteases},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12855577}
}

@ARTICLE{AnnualReviewsInc,
  author = {Xia, Y. N. and Whitesides, G. M.},
  title = {Soft lithography},
  journal = {Annual Review of Materials Science},
  year = {1998},
  volume = {28},
  pages = {153-184},
  note = {Times Cited: 434 Review English Cited References Count: 184 110tc},
  abstract = {Soft lithography represents a non-photolithographic strategy based
	on self-assembly and replica molding for carrying out micro- and
	nanofabrication. It provides a convenient, effective, and low-cost
	method for the formation and manufacturing of micro- and nanostructures.
	In soft lithography, an elastomeric stamp with patterned relief structures
	on its surface is used to generate patterns and structures with feature
	sizes ranging from 30 nm to 100 mu m. Five techniques have been demonstrated:
	microcontact printing (mu CP), replica molding (REM), microtransfer
	molding (mu TM), micromolding in capillaries (MIMIC), and solvent-assisted
	micromolding (SAMIM). In this chapter we discuss the procedures for
	these techniques and their applications in micro- and nanofabrication,
	surface chemistry, materials science, optics, MEMS, and microelectronics.},
  bdsk-url-1 = {%3CGo%20to%20ISI%3E://000075395600009},
  endnotereftype = {Journal Article},
  keywords = {patterning microfabrication nanofabrication elastomers self-assembled
	monolayers self-assembled monolayers scanning electron-microscopy
	pattern transfer organic-surfaces polymer microstructures alkanethiol
	monolayers 2-dimensional arrays silicon dioxide micron-scale gold},
  shorttitle = {Soft lithography},
  url = {<Go to ISI>://000075395600009}
}

@ARTICLE{Xu1998,
  author = {Xu, C. and Prince, J.L.},
  title = {Snakes, Shapes, and Gradient Vector Flow},
  journal = {IEEE Transactions on Image Processing},
  year = {1998},
  volume = {7},
  pages = {359-369},
  number = {3},
  endnotereftype = {Journal Article},
  shorttitle = {Snakes, Shapes, and Gradient Vector Flow}
}

@ARTICLE{Xu1998a,
  author = {Xu, C. and Prince, J.L.},
  title = {Generalized gradient vector flow external forces for active contours},
  journal = {Signal Processing},
  year = {1998},
  volume = {71},
  pages = {131-139},
  endnotereftype = {Journal Article},
  shorttitle = {Generalized gradient vector flow external forces for active contours}
}

@ARTICLE{Xu2003,
  author = {Xu, W. and Jericho, M. H. and Kreuzer, H. J. and Meinertzhagen, I.
	A.},
  title = {Tracking particles in four dimensions with in-line holographic microscopy},
  journal = {Opt Lett},
  year = {2003},
  volume = {28},
  pages = {164-6},
  number = {3},
  month = {Feb 1},
  note = {22542681 0146-9592 Journal Article},
  abstract = {We describe a simple holographic method that has enabled us to capture
	as a single data set the trajectories of micrometer-sized objects
	suspended in water. By subtracting consecutive holograms of a particle
	suspension and then adding these difference holograms, we constructed
	a final data set that contains the time evolution of the particle
	trajectories free from spurious background interference effects.
	The method is illustrated by a recording of the motion of 5-10-microm
	diameter algae in water.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12656319},
  endnotereftype = {Journal Article},
  shorttitle = {Tracking particles in four dimensions with in-line holographic microscopy},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12656319}
}

@ARTICLE{Xu2002,
  author = {Xu, W. and Jericho, M. H. and Meinertzhagen, I. A. and Kreuzer, H.
	J.},
  title = {Digital in-line holography of microspheres},
  journal = {Appl Opt},
  year = {2002},
  volume = {41},
  pages = {5367-75},
  number = {25},
  month = {Sep 1},
  note = {22196358 0003-6935 Journal Article},
  abstract = {We have used digital in-line holography (DIH) with numerical reconstruction
	to image micrometer-sized latex spheres as well as ferrimagnetic
	beads suspended in gelatin. We have examined in detail theoretically
	and experimentally the conditions necessary to achieve submicrometer
	resolution of holographic reconstructions. We found that both transparent
	and opaque particles could be imaged with a resolution that was limited
	only by the wavelength of the light used. Simple inspection of intensity
	profiles through a particle allowed an estimate to be made of the
	particle's three position coordinates within an accuracy of a few
	hundred nanometers. When the derivative of a second-order polynomial
	fitted to the intensity profiles was taken, the X, Y, Z position
	coordinates of particles could be determined within +/-50 nm. More-accurate
	positional resolution should be possible with the help of more-advanced
	computer averaging techniques. Because a single hologram can give
	information about a large collection of distributed particles, DIH
	offers the prospect of a powerful new tool for three-dimensional
	tracking of particles.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12211566},
  endnotereftype = {Journal Article},
  keywords = {*Holography Image Processing, Computer-Assisted *Microspheres *Online
	Systems},
  shorttitle = {Digital in-line holography of microspheres},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12211566}
}

@ARTICLE{Yauch1997,
  author = {Yauch, R. L. and Felsenfeld, D. P. and Kraeft, S. K. and Chen, L.
	B. and Sheetz, M. P. and Hemler, M. E.},
  title = {Mutational evidence for control of cell adhesion through integrin
	diffusion/clustering, independent of ligand binding},
  journal = {J Exp Med},
  year = {1997},
  volume = {186},
  pages = {1347-55},
  number = {8},
  month = {Oct 20},
  note = {97477418 0022-1007 Journal Article},
  abstract = {Previous studies have shown that integrin alpha chain tails make strong
	positive contributions to integrin-mediated cell adhesion. We now
	show here that integrin alpha4 tail deletion markedly impairs static
	cell adhesion by a mechanism that does not involve altered binding
	of soluble vascular cell adhesion molecule 1 ligand. Instead, truncation
	of the alpha4 cytoplasmic domain caused a severe deficiency in integrin
	accumulation into cell surface clusters, as induced by ligand and/
	or antibodies. Furthermore, alpha4 tail deletion also significantly
	decreased the membrane diffusivity of alpha4beta1, as determined
	by a single particle tracking technique. Notably, low doses of cytochalasin
	D partially restored the deficiency in cell adhesion seen upon alpha4
	tail deletion. Together, these results suggest that alpha4 tail deletion
	exposes the beta1 cytoplasmic domain, leading to cytoskeletal associations
	that apparently restrict integrin lateral diffusion and accumulation
	into clusters, thus causing reduced static cell adhesion. Our demonstration
	of integrin adhesive activity regulated through receptor diffusion/clustering
	(rather than through altered ligand binding affinity) may be highly
	relevant towards the understanding of inside-out signaling mechanisms
	for beta1 integrins.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9334374},
  endnotereftype = {Journal Article},
  keywords = {Animal CHO Cells Cell Adhesion/genetics Epitopes/biosynthesis Hamsters
	Human Integrin alpha4beta1 Integrins/chemistry/*genetics/*metabolism
	Leukemia, Erythroblastic, Acute Ligands Manganese *Mutagenesis Protein
	Binding/genetics Protein Conformation Receptors, Lymphocyte Homing/chemistry/*genetics/*metabolism
	Receptors, Very Late Antigen/drug effects Sequence Deletion Sodium
	Azide Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S. Transfection
	Tumor Cells, Cultured Vascular Cell Adhesion Molecule-1/metabolism},
  shorttitle = {Mutational evidence for control of cell adhesion through integrin
	diffusion/clustering, independent of ligand binding},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9334374}
}

@ARTICLE{Yguerabide1982,
  author = {Yguerabide, J. and Schmidt, J. A. and Yguerabide, E. E.},
  title = {Lateral mobility in membranes as detected by fluorescence recovery
	after photobleaching},
  journal = {Biophys J},
  year = {1982},
  volume = {40},
  pages = {69-75},
  number = {1},
  month = {Oct},
  note = {0006-3495 Journal Article},
  abstract = {The evaluation of lateral diffusion coefficients of membrane components
	by the technique of fluorescence recovery after photobleaching (FRAP)
	is often complicated by uncertainties in the values of the intensities
	F(O), immediately after bleaching, and F(infinity), after full recovery.
	These uncertainties arise from instrumental settling time immediately
	after bleaching and from cell, tissue, microscope, or laser beam
	movements at the long times required to measure F(infinity). We have
	developed a method for precise analysis of FRAP data that minimizes
	these problems. The method is based on the observation that a plot
	of the reciprocal function R(tau) = F(infinity)/[F(infinity)-F(tau)]
	is linear over a large time range when (a) the laser beam has a Gaussian
	profile, (b) recovery involves a single diffusion coefficient, and
	(c) there is no membrane flow. Moreover, the ratio of intercept to
	slope of the linear plot is equal to tau 1/2, the time required for
	the bleached fluorescence to rise to 50% of the full recovery value,
	F(infinity). The lateral diffusion coefficient D is related to tau
	1/2 by tau 1/2 = beta w2/4D where beta is a defined parameter and
	w is the effective radius of the focused laser beam. These results
	are shown to indicate that the recovery of fluorescence F(tau) can
	be represented over a large range of percent bleach, and recovery
	time tau by the relatively simple expression F(tau) = [ F(o) + F(infinity)
	(tau/tau 1/2)]/[1 + tau/tau 1/2)]. FRAP data can therefore be easily
	evaluated by a nonlinear regression analysis with this equation or
	by a linear fit to the reciprocal function R(tau). It is shown that
	any error in F(infinity) can be easily detected in a plot of R(tau)
	vs. tau which deviates significantly from a straight line when F(infinity)
	is in error by as little as 5%. A scheme for evaluating D by linear
	analysis is presented. It is also shown that the linear reciprocal
	plot provides a simple method for detecting flow or multiple diffusion
	coefficients and for establishing conditions (data precision, differences
	in multiple diffusion coefficients, magnitude of flow rate compared
	to lateral diffusion) under which flow or multiple diffusion coefficients
	can be detected. These aspects are discussed in some detail.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7139035},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Lasers *Lipid Bilayers Mathematics *Membrane Fluidity Models,
	Biological Photolysis Spectrometry, Fluorescence/methods},
  shorttitle = {Lateral mobility in membranes as detected by fluorescence recovery
	after photobleaching},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7139035}
}

@ARTICLE{Yguerabide1982a,
  author = {Yguerabide, J. and Schmidt, J. A. and Yguerabide, E. E.},
  title = {Lateral mobility in membranes as detected by fluorescence recovery
	after photobleaching},
  journal = {Biophys J},
  year = {1982},
  volume = {40},
  pages = {69-75},
  number = {1},
  month = {Oct},
  note = {0006-3495 Journal Article},
  abstract = {The evaluation of lateral diffusion coefficients of membrane components
	by the technique of fluorescence recovery after photobleaching (FRAP)
	is often complicated by uncertainties in the values of the intensities
	F(O), immediately after bleaching, and F(infinity), after full recovery.
	These uncertainties arise from instrumental settling time immediately
	after bleaching and from cell, tissue, microscope, or laser beam
	movements at the long times required to measure F(infinity). We have
	developed a method for precise analysis of FRAP data that minimizes
	these problems. The method is based on the observation that a plot
	of the reciprocal function R(tau) = F(infinity)/[F(infinity)-F(tau)]
	is linear over a large time range when (a) the laser beam has a Gaussian
	profile, (b) recovery involves a single diffusion coefficient, and
	(c) there is no membrane flow. Moreover, the ratio of intercept to
	slope of the linear plot is equal to tau 1/2, the time required for
	the bleached fluorescence to rise to 50% of the full recovery value,
	F(infinity). The lateral diffusion coefficient D is related to tau
	1/2 by tau 1/2 = beta w2/4D where beta is a defined parameter and
	w is the effective radius of the focused laser beam. These results
	are shown to indicate that the recovery of fluorescence F(tau) can
	be represented over a large range of percent bleach, and recovery
	time tau by the relatively simple expression F(tau) = [ F(o) + F(infinity)
	(tau/tau 1/2)]/[1 + tau/tau 1/2)]. FRAP data can therefore be easily
	evaluated by a nonlinear regression analysis with this equation or
	by a linear fit to the reciprocal function R(tau). It is shown that
	any error in F(infinity) can be easily detected in a plot of R(tau)
	vs. tau which deviates significantly from a straight line when F(infinity)
	is in error by as little as 5%. A scheme for evaluating D by linear
	analysis is presented. It is also shown that the linear reciprocal
	plot provides a simple method for detecting flow or multiple diffusion
	coefficients and for establishing conditions (data precision, differences
	in multiple diffusion coefficients, magnitude of flow rate compared
	to lateral diffusion) under which flow or multiple diffusion coefficients
	can be detected. These aspects are discussed in some detail.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7139035},
  endnotereftype = {Journal Article},
  keywords = {Diffusion Lasers *Lipid Bilayers Mathematics *Membrane Fluidity Models,
	Biological Photolysis Spectrometry, Fluorescence/methods},
  shorttitle = {Lateral mobility in membranes as detected by fluorescence recovery
	after photobleaching},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7139035}
}

@ARTICLE{Yi2002,
  author = {Yi, Y. B. and Sastry, A. M.},
  title = {Analytical approximation of the two-dimensional percolation threshold
	for fields of overlapping ellipses},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  year = {2002},
  volume = {66},
  pages = {066130},
  number = {6 Pt 2},
  month = {Dec},
  note = {22402530 1539-3755 Journal Article},
  abstract = {Percolation of particle arrays is of high interest in microstructural
	design of materials. While there have been numerous contributions
	to theoretical modeling of percolation in particulate systems, no
	analytical approximation for the generalized problem of variable
	aspect-ratio ellipses has been reported. In the present work, we
	(1) derive, and verify through simulation, an analytical percolation
	approach capable of identifying the percolation point in two-phase
	materials containing generalized ellipses of uniform shape and size;
	and (2) explore the dependence of percolation on the particle aspect
	ratio. We validate our technique with simulations tracking both cluster
	sizes and percolation status, in networks of elliptical and circular
	particles. We also outline the steps needed to extend our approach
	to three-dimensional particles (ellipsoids). For biological materials,
	we ultimately aim to provide direct insight into the contribution
	of each single phase in multiphase tissues to mechanical or conductive
	properties. For engineered materials, we aim to provide insight into
	the minimum amount of a particular phase needed to strongly influence
	properties.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12513370},
  endnotereftype = {Journal Article},
  shorttitle = {Analytical approximation of the two-dimensional percolation threshold
	for fields of overlapping ellipses},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12513370}
}

@ARTICLE{Zaal1999,
  author = {Zaal, K. J. and Smith, C. L. and Polishchuk, R. S. and Altan, N.
	and Cole, N. B. and Ellenberg, J. and Hirschberg, K. and Presley,
	J. F. and Roberts, T. H. and Siggia, E. and Phair, R. D. and Lippincott-Schwartz,
	J.},
  title = {Golgi membranes are absorbed into and reemerge from the ER during
	mitosis},
  journal = {Cell},
  year = {1999},
  volume = {99},
  pages = {589-601},
  number = {6},
  month = {Dec 10},
  note = {0092-8674 Journal Article},
  abstract = {Quantitative imaging and photobleaching were used to measure ER/Golgi
	recycling of GFP-tagged Golgi proteins in interphase cells and to
	monitor the dissolution and reformation of the Golgi during mitosis.
	In interphase, recycling occurred every 1.5 hr, and blocking ER egress
	trapped cycling Golgi enzymes in the ER with loss of Golgi structure.
	In mitosis, when ER export stops, Golgi proteins redistributed into
	the ER as shown by quantitative imaging in vivo and immuno-EM. Comparison
	of the mobilities of Golgi proteins and lipids ruled out the persistence
	of a separate mitotic Golgi vesicle population and supported the
	idea that all Golgi components are absorbed into the ER. Moreover,
	reassembly of the Golgi complex after mitosis failed to occur when
	ER export was blocked. These results demonstrate that in mitosis
	the Golgi disperses and reforms through the intermediary of the ER,
	exploiting constitutive recycling pathways. They thus define a novel
	paradigm for Golgi genesis and inheritance.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10612395},
  endnotereftype = {Journal Article},
  keywords = {Animals Cell Line Cytokines/metabolism Endoplasmic Reticulum/*metabolism/ultrastructure
	Fluorescent Antibody Technique Galactosyltransferases/genetics Golgi
	Apparatus/*metabolism/ultrastructure Human Interphase/physiology
	Intracellular Membranes/metabolism Luminescent Proteins/genetics
	Metaphase/physiology Microscopy, Electron Mitosis/*physiology Monomeric
	GTP-Binding Proteins/metabolism Recombinant Fusion Proteins/genetics/metabolism
	*Saccharomyces cerevisiae Proteins Support, U.S. Gov't, P.H.S.},
  shorttitle = {Golgi membranes are absorbed into and reemerge from the ER during
	mitosis},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10612395}
}

@BOOK{Zar1999,
  title = {Biostatistical analysis},
  publisher = {Prentice Hall},
  year = {1999},
  author = {Zar, J.H.},
  address = {Upper Saddle River, NJ},
  endnotereftype = {Book},
  isbn = {0-13-081542-X},
  shorttitle = {Biostatistical analysis}
}

@ARTICLE{Zhang1993,
  author = {Zhang, F. and Lee, G. M. and Jacobson, K.},
  title = {Protein lateral mobility as a reflection of membrane microstructure},
  journal = {Bioessays},
  year = {1993},
  volume = {15},
  pages = {579-88},
  number = {9},
  month = {Sep},
  note = {94059055 0265-9247 Journal Article Review Review, Tutorial},
  abstract = {The lateral mobility of membrane lipids and proteins is presumed to
	play an important functional role in biomembranes. Photobleaching
	studies have shown that many proteins in the plasma membrane have
	diffusion coefficients at least an order of magnitude lower than
	those obtained when the same proteins are reconstituted in artificial
	bilayer membranes. Depending on the protein, it has been shown that
	either the cytoplasmic domain or the ectodomain is the key determinant
	of its lateral mobility. Single particle tracking microscopy, which
	allows the motions of single or small groups of membrane molecules
	to be followed, promises not only to reveal new features of membrane
	dynamics, but also to help explain longstanding puzzles presented
	by the photobleaching studies, particularly the so-called immobile
	fraction. The combination of the two complementary technologies should
	measurably enhance our understanding of membrane microstructure.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8240310},
  endnotereftype = {Journal Article},
  keywords = {Cell Membrane/*ultrastructure Diffusion Genetic Engineering Gold Colloid
	Membrane Fluidity Membrane Proteins/genetics/*metabolism/radiation
	effects Microscopy/methods Photochemistry Protein Conformation Support,
	U.S. Gov't, P.H.S.},
  shorttitle = {Protein lateral mobility as a reflection of membrane microstructure},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8240310}
}

@ARTICLE{Zhou2000,
  author = {Zhou, X. and Li, J.},
  title = {Macrophage-enriched myristoylated alanine-rich C kinase substrate
	and its phosphorylation is required for the phorbol ester-stimulated
	diffusion of beta 2 integrin molecules},
  journal = {J Biol Chem},
  year = {2000},
  volume = {275},
  pages = {20217-22},
  number = {26},
  month = {Jun 30},
  note = {20347941 0021-9258 Journal Article},
  abstract = {An early event of beta(2) integrin activation is the increased diffusion
	rate of this molecule on the cell surface, thereby providing integrin
	molecules with a better chance to meet the ligands. The activation
	of protein kinase C (PKC) stimulates integrin diffusion by releasing
	the cytoskeletal constraint on integrin molecules. We report here
	that macrophage-enriched myristoylated alanine-rich C kinase substrate
	(MacMARCKS), a membrane-associated PKC substrate involved in integrin
	activation, is required for this PKC-stimulated diffusion of integrin
	molecules. Using the single-particle tracking technique, we observed
	that the activation of PKC stimulated an 11-fold increase in the
	diffusion rate of beta(2) integrins in wild type J774 macrophage
	cells but not in those expressing mutant MacMARCKS. Further evidence
	is provided from a MacMARCKS-deficient cell line in which phorbol
	esters failed to stimulate the diffusion of integrin. Transfection
	of wild type MacMARCKS into these cells restored the rapid diffusion
	rate of the beta(2) integrins. The phosphorylation of MacMARCKS is
	important because transfection of a nonphosphorylatable MacMARCKS
	mutant or the addition of staurosporine eliminates the rapid diffusion
	rate of integrin. Furthermore, adding cytochalasin D bypasses the
	MacMARCKS deficiency and stimulates beta(2) integrin diffusion, suggesting
	that MacMARCKS's involvement in integrin activation is prior or at
	the site of cytoskeleton. Therefore, we conclude that MacMARCKS is
	required for releasing the cytoskeletal constraint on integrin molecules
	during PKC-mediated integrin activation.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10779523},
  endnotereftype = {Journal Article},
  keywords = {Animal Antigens, CD18/*metabolism Cell Line Cytoskeleton/metabolism
	Electrophoresis, Gel, Two-Dimensional Enzyme Activation Fluorescent
	Dyes/metabolism Macrophages/*metabolism Membrane Proteins/genetics/*metabolism/*physiology
	Mice Microscopy, Video Microspheres Models, Statistical Movement
	Mutation Phorbol Esters/*pharmacology Phosphorylation Protein Kinase
	C/*metabolism Support, U.S. Gov't, P.H.S. Time Factors},
  shorttitle = {Macrophage-enriched myristoylated alanine-rich C kinase substrate
	and its phosphorylation is required for the phorbol ester-stimulated
	diffusion of beta 2 integrin molecules},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10779523}
}

@ARTICLE{Zimmer2002,
  author = {Zimmer, C. and Labruyere, E. and Meas-Yedid, V. and Guillen, N. and
	Olivo-Marin, J. C.},
  title = {Segmentation and tracking of migrating cells in videomicroscopy with
	parametric active contours: a tool for cell-based drug testing},
  journal = {IEEE Trans Med Imaging},
  year = {2002},
  volume = {21},
  pages = {1212-21},
  number = {10},
  month = {Oct},
  note = {22473128 0278-0062 Evaluation Studies Journal Article Validation
	Studies},
  abstract = {This paper presents a segmentation and tracking method for quantitative
	analysis of cell dynamics from in vitro videomicroscopy data. The
	method is based on parametric active contours and includes several
	adaptations that address important difficulties of cellular imaging,
	particularly the presence of low-contrast boundary deformations known
	as pseudopods, and the occurence of multiple contacts between cells.
	First, we use an edge map based on the average intensity dispersion
	that takes advantage of relative background homogeneity to facilitate
	the detection of both pseudopods and interfaces between adjacent
	cells. Second, we introduce a repulsive interaction between contours
	that allows correct segmentation of objects in contact and overcomes
	the shortcomings of previously reported techniques to enforce contour
	separation. Our tracking technique was validated on a realistic data
	set by comparison with a manually defined ground-truth and was successfully
	applied to study the motility of amoebae in a biological research
	project.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12585703},
  endnotereftype = {Journal Article},
  keywords = {Algorithms Animal Cell Adhesion/physiology Cell Aggregation/physiology
	Cell Division/physiology Cell Movement/*physiology Cell Size/physiology
	Cells, Cultured Comparative Study Drug Evaluation/methods Entamoeba
	histolytica/classification/*cytology/*physiology Image Enhancement/*methods
	Image Interpretation, Computer-Assisted/*methods Microscopy, Video/*methods
	Models, Biological Pattern Recognition Pseudopodia/physiology/ultrastructure
	Reproducibility of Results Sensitivity and Specificity Support, Non-U.S.
	Gov't},
  shorttitle = {Segmentation and tracking of migrating cells in videomicroscopy with
	parametric active contours: a tool for cell-based drug testing},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12585703}
}

@ARTICLE{Zoccolan2001,
  author = {Zoccolan, D. and Giachetti, A. and Torre, V.},
  title = {The use of optical flow to characterize muscle contraction},
  journal = {J Neurosci Methods},
  year = {2001},
  volume = {110},
  pages = {65-80},
  number = {1-2},
  month = {Sep 30},
  note = {21448847 0165-0270 Journal Article},
  abstract = {Muscle contraction is usually measured and characterized with force
	and displacement transducers. The contraction of muscle fibers, however,
	evokes in the tissue a two and even three-dimensional displacement
	field, which is not properly quantified by these transducers because
	they provide just a single scalar quantity. This problem can be circumvented
	by using optical measurements and standard tools of computer vision,
	developed for the analysis of time varying image sequences. By computing
	the so called optical flow, i.e. the apparent motion of points in
	a time varying image sequence, it is possible to recover a two-dimensional
	motion field, describing rather precisely the displacement caused
	by muscle contraction in a flattened piece of skin. The obtained
	two-dimensional optical flow can be further analyzed by computing
	its elementary deformation components, providing a novel and accurate
	characterization of the contraction induced by different motoneurons.
	This technique is demonstrated analyzing the displacement caused
	by muscle contraction in the skin of the leech, Hirudo medicinalis.
	The proposed technique can be applied to monitor and characterize
	all contractions in almost flat tissues with enough visual texture.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11564526},
  endnotereftype = {Journal Article},
  keywords = {Action Potentials/physiology Algorithms Animal Automatic Data Processing/instrumentation/*methods
	Biomechanics Image Processing, Computer-Assisted/instrumentation/*methods
	Leeches/cytology/physiology Mechanoreceptors/cytology/physiology
	*Microscopy, Video/instrumentation/methods Models, Neurological Motor
	Neurons/cytology/physiology Muscle Contraction/*physiology Nervous
	System/cytology/metabolism Neurons, Afferent/cytology/physiology
	Neurophysiology/instrumentation/*methods Support, Non-U.S. Gov't},
  shorttitle = {The use of optical flow to characterize muscle contraction},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11564526}
}

@ARTICLE{Zoccolan2002,
  author = {Zoccolan, D. and Pinato, G. and Torre, V.},
  title = {Highly variable spike trains underlie reproducible sensorimotor responses
	in the medicinal leech},
  journal = {J Neurosci},
  year = {2002},
  volume = {22},
  pages = {10790-800},
  number = {24},
  month = {Dec 15},
  note = {22374005 1529-2401 Journal Article},
  abstract = {The nervous system of the leech is a particularly suitable model to
	investigate neural coding of sensorimotor responses because it allows
	both observation of behavior and the simultaneous measurement of
	a large fraction of its underlying neuronal activity. In this study,
	we used a combination of multielectrode recordings, videomicroscopy,
	and computation of the optical flow to investigate the reproducibility
	of the motor response caused by local mechanical stimulation of the
	leech skin. We analyzed variability at different levels of processing:
	mechanosensory neurons, motoneurons, muscle activation, and behavior.
	Spike trains in mechanosensory neurons were very reproducible, unlike
	those in motoneurons. The motor response, however, was reproducible
	because of two distinct biophysical mechanisms. First, leech muscles
	contract slowly and therefore are poorly sensitive to the jitter
	of motoneuron spikes. Second, the motor response results from the
	coactivation of a population of motoneurons firing in a statistically
	independent way, which reduces the variability of the population
	firing. These data show that reproducible spike trains are not required
	to sustain reproducible behaviors and illustrate how the nervous
	system can cope with unreliable components to produce reliable action.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12486172},
  endnotereftype = {Journal Article},
  keywords = {*Action Potentials Animal Cats Cells, Cultured Decapoda (Crustacea)/physiology
	Gastric Mucosa/innervation/physiology Kinetics Leeches/*physiology
	Mechanoreceptors/physiology Microscopy, Video Models, Neurological
	Motor Neurons/*physiology *Muscle Contraction Muscle Fibers/physiology
	Nerve Net Neurons, Afferent/*physiology Reproducibility of Results
	Stress, Mechanical Support, Non-U.S. Gov't Visual Pathways},
  shorttitle = {Highly variable spike trains underlie reproducible sensorimotor responses
	in the medicinal leech},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12486172}
}

@ARTICLE{Zoccolan2002a,
  author = {Zoccolan, D. and Torre, V.},
  title = {Using optical flow to characterize sensory-motor interactions in
	a segment of the medicinal leech},
  journal = {J Neurosci},
  year = {2002},
  volume = {22},
  pages = {2283-98},
  number = {6},
  month = {Mar 15},
  note = {21893501 1529-2401 Journal Article},
  abstract = {Activation of motoneurons innervating leech muscles causes the appearance
	of a two-dimensional vector field of deformations on the skin surface
	that can be fully characterized using a new technique (Zoccolan et
	al., 2001) based on the computation of the optical flow, the two-dimensional
	vector field describing the point displacements on the skin. These
	vector fields are characterized by their origin (i.e., the singular
	point) and by four elementary components that combine linearly: expansion
	(or compression), rotation, longitudinal shear, and oblique shear.
	All motoneurons can be classified and recognized according to the
	components of the deformations they elicit: longitudinal motoneurons
	give rise almost exclusively to longitudinal negative shear, whereas
	circular motoneurons give rise to both positive longitudinal shear
	and significant negative expansion. Oblique motoneurons induce strong
	oblique shear, in addition to longitudinal shear and negative expansion.
	Vector fields induced by the contraction of longitudinal, circular,
	and oblique fibers superimpose linearly. Skin deformations can therefore
	be attributed rather reliably to the contraction of distinct longitudinal,
	circular, and oblique muscle fibers. We compared the deformation
	patterns produced by touching the skin with those produced by intracellular
	stimulation of P, T, and N cells: vector fields resulting from the
	activation of P cells were almost identical to those produced by
	mechanical stimulation. Therefore, motor responses triggered by light
	or moderate touch are almost entirely mediated by excitation of P
	cells, with minor contributions from T and N cells.},
  bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11896168},
  endnotereftype = {Journal Article},
  keywords = {Action Potentials/physiology Animal In Vitro Leeches Mechanoreceptors/*physiology
	Microscopy, Video Motor Neurons/*physiology Muscle Contraction/physiology
	Neurons, Afferent/*physiology Physical Stimulation Reflex/physiology
	Skin/innervation Support, Non-U.S. Gov't Time Factors Touch/*physiology},
  shorttitle = {Using optical flow to characterize sensory-motor interactions in a
	segment of the medicinal leech},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11896168}
}

@ARTICLE{Zwier2004,
  author = {Zwier, J.M., Van Rooij,G. J. , Hofstraat, J. W., Brakenhoff, G. J.},
  title = {Image calibration in fluorescence microscopy},
  journal = {Journal of Microscopy},
  year = {2004},
  volume = {216},
  pages = {15-24},
  number = {1},
  endnotereftype = {Journal Article},
  shorttitle = {Image calibration in fluorescence microscopy}
}

@BOOK{Darzynkiewicz2004,
  title = {Cytometry, New Developments},
  publisher = {Elsevier Academic Press},
  year = {2004},
  editor = {Darzynkiewicz, Z., Roederer, M.,Tanke, H.J.},
  volume = {75},
  series = {Methods in Cell Biology},
  endnotereftype = {Edited Book},
  shorttitle = {Cytometry, New Developments}
}

@BOOK{Stephens200602,
  title = {Cell Imaging (Methods Express)},
  publisher = {Scion Publishing},
  year = {2006},
  editor = {David Stephens},
  edition = {illustrated edition},
  month = {2},
  bdsk-url-1 = {http://amazon.co.jp/o/ASIN/1904842267/},
  isbn = {9781904842262},
  price = {￥ 9,713},
  timestamp = {2011.03.11},
  totalpages = {300},
  url = {http://amazon.co.jp/o/ASIN/1904842267/}
}

@BOOK{Stephens2006,
  title = {Cell Imaging},
  publisher = {Scion Publishing},
  year = {2006},
  editor = {Stephens, D. J.},
  series = {Methods Express},
  address = {Oxfordshire},
  endnotereftype = {Edited Book},
  shorttitle = {Cell Imaging}
}

@book{Pawley2006,
abstract = {Includes descriptions and comparisons of parts of the microscope, digital aspects of data acquisition and properties of fluorescent dyes, and the techniques of 3D specimen preparation and the fundamental limitations. This third edition of a text in biological microscopy also includes complexities of quantitative confocal fluorescence imaging. This third edition of a classic text in biological microscopy includes detailed descriptions and in-depth comparisons of parts of the microscope itself, digital aspects of data acquisition and properties of fluorescent dyes, the techniques of 3D specimen preparation and the fundamental limitations, and practical complexities of quantitative confocal fluorescence imaging.},
author = {Pawley, J B},
booktitle = {Journal of Biomedical Optics},
chapter = {13},
doi = {10.1117/1.600871},
editor = {Pawley, James B},
isbn = {9780387259215},
issn = {00913286},
keywords = {textbook},
mendeley-tags = {textbook},
number = {9},
pages = {985},
pmid = {13938623},
publisher = {Springer},
series = {Language of science},
title = {{Handbook of biological confocal microscopy}},
url = {http://link.aip.org/link/?JBOPFO/13/029902/1},
volume = {13},
year = {2006}
}
@book{Zar1999,
address = {New Jersey},
author = {Zar, J. H.},
booktitle = {PsycCRITIQUES},
edition = {4},
isbn = {978-0130815422},
issn = {1554-0138},
keywords = {textbook},
mendeley-tags = {textbook},
number = {6},
publisher = {Prentice Hall},
title = {{Statistical Analysis, Fourth Edition.}},
url = {http://www.amazon.com/Biostatistical-Analysis-4th-Edition-Jerrold/dp/013081542X},
volume = {19},
year = {1999}
}

%}