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Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking

Grace A. McLaughlin, Erin M. Langdon, John M. Crutchley, Liam J. Holt, M. Gregory Forest, Jay M. Newby, Amy S. Gladfelter, Sophie Martin
<span title="2020-07-01">2020</span> <i title="American Society for Cell Biology (ASCB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/btmjitlxs5by3dntmzk67gakxi" style="color: black;">Molecular Biology of the Cell</a> </i> &nbsp;
The structure of the cytosol across different length scales is a debated topic in cell biology.  ...  Here we present tools to measure the physical state of the cytosol by analyzing the 3D motion of nanoparticles expressed in cells.  ...  Motion model used to define spatially varying diffusion The notion of a spatially varying diffusivity assumes an underlying particle motion model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1091/mbc.e20-03-0210">doi:10.1091/mbc.e20-03-0210</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rd565i6ku5etzcjpmzi5gee2qe">fatcat:rd565i6ku5etzcjpmzi5gee2qe</a> </span>
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Combined Selective Plane Illumination Microscopy and FRAP maps intranuclear diffusion of NLS-GFP [article]

Chad M Hobson, E. Timothy O'Brien, Michael R. Falvo, Richard Superfine
<span title="2020-05-27">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
With the recent rise of accessibility of SPIM systems, SPIM-FRAP is set to provide a simple and quick means of quantifying the spatial distribution of protein recovery or diffusion in living cells.  ...  Since its initial development in 1976, fluorescence recovery after photobleaching (FRAP) has been one of the most popular tools for studying diffusion and protein dynamics in living cells.  ...  Waldeck, and J. Langowski. 2000. Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy.  ... 
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Brownian Dynamics Simulations of a Self-Avoiding Chain Model of a Chromosome in a Spherical Confinement

Young-Gui Yoon, Changbong Hyeon
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.512">doi:10.1016/j.bpj.2013.11.512</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b4d2mk5wqvalzemiaijoti55qq">fatcat:b4d2mk5wqvalzemiaijoti55qq</a> </span>
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Coarse-Grained Simulations of Nucleoid Structure

Tyler M. Earnest, Zaida Luthey-Schulten
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.513">doi:10.1016/j.bpj.2013.11.513</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x77aspdatbf7dpki7x3kberxfe">fatcat:x77aspdatbf7dpki7x3kberxfe</a> </span>
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Structure and Mechanical Properties of the Bacterial Chromosome in E.Coli

Nastaran Hadizadeh, Calin C. Guet, Reid C. Johnson, John F. Marko
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.510">doi:10.1016/j.bpj.2013.11.510</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ehtpr5ywlbg4bmlyw7crfwv3qq">fatcat:ehtpr5ywlbg4bmlyw7crfwv3qq</a> </span>
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Chromosome Territories Reposition During DNA Damage-Repair Response

Ishita S. Mehta, Mugdha Kulshreshtha, Sandeep Chakraborty, Ullas Kolthur-Seetharam, Basuthkar J. Rao
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.509">doi:10.1016/j.bpj.2013.11.509</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rlqgkq6anffh3e3oisg2i3utae">fatcat:rlqgkq6anffh3e3oisg2i3utae</a> </span>
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Shape Pairing of Cholesterol with Oxidized Phospholipid Species in Lipid Bilayers

Bastien Loubet, Piotr Jurkiewicz, Agnieszka Olzynska, Martin Hof, Himanshu Khandelia
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.515">doi:10.1016/j.bpj.2013.11.515</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s24zthoqyjexvg2jqiebidf5la">fatcat:s24zthoqyjexvg2jqiebidf5la</a> </span>
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Nucleoid Reorganization by the Stress Response Protein Dps

Elio A. Abbondanzieri, Natalia Vtyurina, Anne Meyer
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Our report investigates the effect of DNA damage on spatial organization of chromosome territories (CTs) within interphase nuclei of human cells.  ...  We show that DNA damage, in a dose dependent manner, induces a large-scale spatial (nuclear interior to periphery and vice versa) repositioning of CTs that are relatively gene dense.  ...  The NAPs diffuse freely in the cell and when bound to the nucleoid can diffuse in one dimension and unbind depending on the binding affinity to that locus.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.11.511">doi:10.1016/j.bpj.2013.11.511</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/455vtavduvaexficrhax42e7xa">fatcat:455vtavduvaexficrhax42e7xa</a> </span>
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A Model for Motor Endplate Morphogenesis: Diffusible Morphogens, Transmembrane Signaling, and Compartmentalized Gene Expression

Michel Kerszberg, Jean-Pierre Changeux
<span title="">1993</span> <i title="MIT Press - Journals"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rckx6fqoszfvva5c53bqivu5am" style="color: black;">Neural Computation</a> </i> &nbsp;
We neglect, in this simple model, spatial fluctuations in k: the nuclei are indifferently spaced and the diffusion rates between them (assumed to be controlled mostly by the nuclear membrane barrier rather  ...  Imaging mammalian nerve cells and their connections over time in living animals. Trends Neurosci. 10, 398-404. Salpeter, M., and Loring, R. H. 1985.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1162/neco.1993.5.3.341">doi:10.1162/neco.1993.5.3.341</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7rxznnpgs5flzowzveqfdgcig4">fatcat:7rxznnpgs5flzowzveqfdgcig4</a> </span>
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Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient

Paola Lecca, Adaoha E C Ihekwaba, Lorenzo Dematté, Corrado Priami
<span title="2010-11-23">2010</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
In this paper we propose a stochastic model of reaction-diffusion systems, in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces.  ...  Reaction-diffusion systems are mathematical models that describe how the concentrations of substances distributed in space change under the influence of local chemical reactions, and diffusion which causes  ...  living cells and, more generally in biological tissues.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2010-150">doi:10.2390/biecoll-jib-2010-150</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21098882">pmid:21098882</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yhup77bgyfa6xd256opwtghcgq">fatcat:yhup77bgyfa6xd256opwtghcgq</a> </span>
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Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient

Paola Lecca, Adaoha E. C. Ihekwaba, Lorenzo Dematté, Corrado Priami
<span title="2010-03-01">2010</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
In this paper we propose a stochastic model of reaction-diffusion systems, in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces.  ...  SummaryReaction-diffusion systems are mathematical models that describe how the concentrations of substances distributed in space change under the influence of local chemical reactions, and diffusion which  ...  living cells and, more generally in biological tissues.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2010-150">doi:10.1515/jib-2010-150</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ccya4xkemvgu3o2ohkn2gnmhnm">fatcat:ccya4xkemvgu3o2ohkn2gnmhnm</a> </span>
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3D neural network-based particle tracking reveals spatial heterogeneity of the cytosol [article]

Grace A McLaughlin, Erin M Langdon, John M Crutchley, Liam J Holt, Mark Gregory Forest, Jay M Newby, Amy S Gladfelter
<span title="2019-10-30">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
By analyzing the spatial diffusivity patterns, we saw an enrichment of low diffusivity zones at hyphal tips and near some nuclei.  ...  Using these probes to spatially resolve diffusivity of a cytoplasmic volume within a cell requires accurate and automated 3D tracking methods.  ...  This work was supported by Google Cloud, the National Science Foundation (NSF), the National Institutes of Health (NIH), and the Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/823286">doi:10.1101/823286</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yus7mtkluvcgxkjhqmjf4rfeta">fatcat:yus7mtkluvcgxkjhqmjf4rfeta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325001447/https://www.biorxiv.org/content/biorxiv/early/2019/10/30/823286.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/53/3c538dc95bbb21e5d00199fff5f5eefa1f38f962.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/823286"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

G1/S transcription factors assemble in discrete clusters that increase in number as cells grow [article]

Labe Black, Sylvain Tollis, Jean-Bernard Fiche, Savanna Dorsey, Jing Cheng, Stephen Notley, Benjamin Crevier, Jeremy Bigness, Marcelo Nollmann, Mike Tyers, Catherine A. Royer
<span title="2019-03-11">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
A prediction of the model that SBF/MBF should exhibit both fast and slow dynamics was confirmed in PALM experiments on live cells.  ...  Stochastic simulations with a mathematical model based on co-localization of promoters in clusters recapitulated observed cluster behavior.  ...  Single particle tracking PALM in live cell nuclei reveals two modes of TF mobility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/574772">doi:10.1101/574772</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/umtqnaoxsjbytlvoenxjfmjf6i">fatcat:umtqnaoxsjbytlvoenxjfmjf6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711034233/https://www.biorxiv.org/content/biorxiv/early/2019/03/11/574772.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/46/fe/46fe87990675d66849cdf88e59557849b6a5bbb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/574772"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Hi-D: nanoscale mapping of nuclear dynamics in single living cells

Haitham A. Shaban, Roman Barth, Ludmila Recoules, Kerstin Bystricky
<span title="2020-04-20">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
Hi-D combines reconstruction of chromatin motion and classification of local diffusion processes by Bayesian inference.  ...  We show that DNA dynamics in the nuclear interior are spatially partitioned into 0.3-3-μm domains in a mosaic-like pattern, uncoupled from chromatin compaction.  ...  Acknowledgements We thank Maxime Dahan (Curie Institute) for generously providing the U2OS cell line expressing RPB1, Amy Strom (Gary Karpen Lab, UC Berkeley, USA) for providing images of HP1 in NIH3T3  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-020-02002-6">doi:10.1186/s13059-020-02002-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32312289">pmid:32312289</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lbsrtxoyybe7fojptdpyxvfsn4">fatcat:lbsrtxoyybe7fojptdpyxvfsn4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502085028/https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02002-6" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/54/dc54d099dde4ac69a245c0ae522b40dd60f9814b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-020-02002-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

An image model and segmentation algorithm for reflectance confocal images of in vivo cervical tissue

B.L. Luck, K.D. Carlson, A.C. Bovik, R.R. Richards-Kortum
<span title="">2005</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dhlhr4jqkbcmdbua2ca45o7kru" style="color: black;">IEEE Transactions on Image Processing</a> </i> &nbsp;
Using our model in conjunction with a powerful image enhancement tool (anisotropic median-diffusion), appropriate statistical image modeling of spatial interactions (Gaussian Markov random fields), and  ...  To enable a deeper understanding of confocal reflectance microscopy images of cervical tissue, and to supply a basis for parameter selection in a classification algorithm, we have developed a model that  ...  Our simplistic tissue model simulates nonnuclear area based on the cytoplasm surrounding nuclei; it does not include the small objects attached to the cell membrane.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tip.2005.852460">doi:10.1109/tip.2005.852460</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16190463">pmid:16190463</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bjltm62xu5d7jnfn6qv2wsqsfy">fatcat:bjltm62xu5d7jnfn6qv2wsqsfy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160421184217/http://remicalm.com/publications/2005/pubs_2005_luck_image%20model.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/7d/c87dee547eadfa22bce1ca8c8be2fadfda098fbf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tip.2005.852460"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>
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