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Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses

M. Dobrzy ski, L. K. Nguyen, M. R. Birtwistle, A. von Kriegsheim, A. Blanco Fernandez, A. Cheong, W. Kolch, B. N. Kholodenko
<span title="2014-06-25">2014</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
We show theoretically and experimentally a mechanism behind the emergence of wide or bimodal protein distributions in biochemical networks with nonlinear input-output characteristics (the dose-response  ...  Under the circumstances that we quantify mathematically, the two distinct responses can coexist within cellular population, leading to the emergence of a bimodal protein distribution.  ...  Cell-to-cell variability in protein abundances a↵ects period and (or) phase of cells' oscillations which in turn generates a bimodal protein distribution (Fig. 1C) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2014.0383">doi:10.1098/rsif.2014.0383</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24966234">pmid:24966234</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4233687/">pmcid:PMC4233687</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dysdihgzibdslkiqtn6ndouryq">fatcat:dysdihgzibdslkiqtn6ndouryq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719092106/https://researchrepository.ucd.ie/bitstream/10197/7762/1/Nonlinear%20signalling%20networks%20and%20cell-to-cell%20variability.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/59/e6/59e6e648fd44beed3b69450b91205386eef0c8e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2014.0383"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233687" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamic phenotypic heterogeneity generated by delayed genetic oscillations [article]

Rafael Pena-Miller, Markus Arnoldini, Martin Ackermann, Robert E Beardmore
<span title="2020-05-13">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
protein (GFP).  ...  We conclude that a stochastic dynamical system tailored to the genetic network of fliC is better suited to our data than prior theories where dynamical features, like oscillations and pulsing, are driven  ...  Genes are denoted with rectangles and proteins with circles. heterogeneity in flagellar gene expression.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.05.13.093831">doi:10.1101/2020.05.13.093831</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bkmpmuxd3zagbjzffue5wclvji">fatcat:bkmpmuxd3zagbjzffue5wclvji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711044510/https://www.biorxiv.org/content/biorxiv/early/2020/05/13/2020.05.13.093831.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/5b/25/5b25afd611bb0262db24c6b63ea11ae19d823083.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.05.13.093831"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics

Maria Herberg, Ingmar Glauche, Thomas Zerjatke, Maria Winzi, Frank Buchholz, Ingo Roeder
<span title="">2016</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
In the oscillation model, Nanog and Fgf4/Erk are assumed to be part of an activator-repressor system as illustrated in figure 1d .  ...  Alternatively, in the oscillation model, a cyclic Nanog attractor is generated through an activator -repressor system [27] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2016.0167">doi:10.1098/rsif.2016.0167</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27097654">pmid:27097654</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4874438/">pmcid:PMC4874438</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7sk5aw7kjra5pd2y4zbyvtpcf4">fatcat:7sk5aw7kjra5pd2y4zbyvtpcf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219020337/http://pdfs.semanticscholar.org/138b/4f1711a7a389149f003dc08db2d0f2152f79.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/13/8b/138b4f1711a7a389149f003dc08db2d0f2152f79.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2016.0167"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874438" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Inferring the physical connectivity of complex networks from their functional dynamics

Hung Ta, Chang Yoon, Liisa Holm, Seung Han
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Biological networks, such as protein-protein interactions, metabolic, signalling, transcription-regulatory networks and neural synapses, are representations of large-scale dynamic systems.  ...  Results: We modelled the network system by employing a scale-free network of coupled phase oscillators.  ...  At K = 0.010 a bimodal distribution of PPCs for all pairs of nodes is observed in all the network topologies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-70">doi:10.1186/1752-0509-4-70</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20500902">pmid:20500902</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2887793/">pmcid:PMC2887793</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r5kzn6qk6rgotonnvzimlqpulu">fatcat:r5kzn6qk6rgotonnvzimlqpulu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830053654/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-4-70?site=http://bmcsystbiol.biomedcentral.com" 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/10/67/10679a57befd71e765748bcf9329b27221dc5c56.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-70"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887793" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Delays Induce Novel Stochastic Effects in Negative Feedback Gene Circuits

Eder Zavala, Tatiana T. Marquez-Lago
<span title="2014-01-21">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;
Finally, we demonstrate that explicitly accounting for delays increases the number of accessible states in the multimodal regime, and also introduces features typical of excitable systems.  ...  feedback is associated with oscillations triggered by bursts.  ...  In the protein PDFs, excursions of the system are reflected by the appearance of tail distributions: the higher the transcription delay, the wider the tail of the PDF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2013.12.010">doi:10.1016/j.bpj.2013.12.010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24461022">pmid:24461022</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3907244/">pmcid:PMC3907244</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/glyw4ejm5zdopdx6zl2o7dpglm">fatcat:glyw4ejm5zdopdx6zl2o7dpglm</a> </span>
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Positive feedback in cellular control systems

Alexander Y. Mitrophanov, Eduardo A. Groisman
<span title="">2008</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4b3nxjjiivaspl2bdv5q6xppru" style="color: black;">Bioessays</a> </i> &nbsp;
Feedback loops have been identified in a variety of regulatory systems and organisms.  ...  While feedback loops of the same type (negative or positive) tend to have properties in common, they can play distinctively diverse roles in different regulatory systems, where they can affect virulence  ...  (32, 49, 64) In rigorous terms, bistability is not equivalent to distributional bimodality.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bies.20769">doi:10.1002/bies.20769</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18478531">pmid:18478531</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2486260/">pmcid:PMC2486260</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lmx4mb7wsnb4plkitfxic2cfre">fatcat:lmx4mb7wsnb4plkitfxic2cfre</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331225241/http://opal.biology.gatech.edu/~amit/Mitrophanov--Groisman%20Bioessays%202008.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/b7/33/b733f889891154084d0abb5df12e0d4c450941be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bies.20769"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2486260" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Nanog Variability and Pluripotency Regulation of Embryonic Stem Cells - Insights from a Mathematical Model Analysis

Ingmar Glauche, Maria Herberg, Ingo Roeder, Diego Di Bernardo
<span title="2010-06-21">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
In particular we show that these variations can occur under different assumptions yielding similar experimental characteristics.  ...  Applying a novel mathematical transcription factor network model we explore mechanisms and feedback regulations to describe the observed variation of the Nanog levels in mouse ES cells.  ...  In contrast, if the Nanog variation is the result of an oscillating activator/repressor system (oscillation scenario), the residence times are expected to show rather symmetric distributions in which the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0011238">doi:10.1371/journal.pone.0011238</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20574542">pmid:20574542</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2888652/">pmcid:PMC2888652</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mm76qyg5irb5hevehb3i5vwb44">fatcat:mm76qyg5irb5hevehb3i5vwb44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925193015/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0011238&amp;type=printable" 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/25/f5/25f54edbd4dcdab0e68b2e5c30c8851d0c3786a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0011238"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888652" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication [article]

JaeAnn M Dwulet, Jennifer K Briggs, Richard KP Benninger
<span title="2020-10-28">2020</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Using a multicellular model of the islet, we generated continuous or bimodal distributions of β-cell heterogeneity and examined how islet [Ca2+] dynamics depended on the presence of cells with increased  ...  The majority of cells in the islet are insulin-producing β-cells, which are excitable cells that are electrically coupled via gap junction channels. β-cells have long been known to display heterogeneous  ...  As in B. for bimodal distribution in GK activity where the populations only have 2.5% variation in GK activity. J). As in D. for bimodal distribution in GK activity. K).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.28.358457">doi:10.1101/2020.10.28.358457</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lcv42qzf6newretkda7w23cqvm">fatcat:lcv42qzf6newretkda7w23cqvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715224716/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1008948/2/pcbi.1008948.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210715%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210715T183250Z&amp;X-Goog-Expires=86400&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" 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/39/be/39bedf6e58cad199aaa156649ac752f186bf9fa5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.28.358457"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency

Steffen Rulands, Heather J. Lee, Stephen J. Clark, Christof Angermueller, Sébastien A. Smallwood, Felix Krueger, Hisham Mohammed, Wendy Dean, Jennifer Nichols, Peter Rugg-Gunn, Gavin Kelsey, Oliver Stegle (+2 others)
<span title="">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqzh5s6rlnf5hginbk2cz4aatm" style="color: black;">Cell Systems</a> </i> &nbsp;
Highlights d Co-expression of DNMT3s and TETs promotes genomescale oscillations in DNA methylation d Oscillation amplitude is greatest at a CpG density characteristic of enhancers d Cell synchronization  ...  reveals oscillation period and link with primary transcripts d Multi-omic single-cell profiling provides evidence for oscillatory dynamics in vivo  ...  window is bimodally distributed between cells.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cels.2018.06.012">doi:10.1016/j.cels.2018.06.012</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30031774">pmid:30031774</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6066359/">pmcid:PMC6066359</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dmhkmfectbec3htvshvdzylaxq">fatcat:dmhkmfectbec3htvshvdzylaxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501041105/https://www.repository.cam.ac.uk/bitstream/handle/1810/284118/1-s2.0-S2405471218302795-main.pdf;jsessionid=D625A9A5C427C48E08CA31C0784E19CB?sequence=3" 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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cels.2018.06.012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6066359" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cell population heterogeneity in expression of a gene-switching network with fluorescent markers of different half-lives

S PORTLE, T CAUSEY, K WOLF, G BENNETT, K SAN, N MANTZARIS
<span title="2007-02-01">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/se63ciaet5axrek43i2fdqnqui" style="color: black;">Journal of Biotechnology</a> </i> &nbsp;
Transient studies revealed that even in cases where the distribution at the reference state is unimodal, the distribution becomes bimodal for a period of time required for the population to pass through  ...  On the contrary, for intermediate IPTG concentrations, two distinct subpopulations were formed below and above a single-cell threshold, resulting in distributions with a bimodal shape.  ...  Collins for donation of the plasmid pTAK117, Michael Elowitz for the plasmid pZE21-GFPAAV, Ronald J Parry for the use of shakers in his lab and Kyriacos Zygourakis for useful suggestions throughout the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbiotec.2006.09.026">doi:10.1016/j.jbiotec.2006.09.026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17092594">pmid:17092594</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nmvz3x374rahhm6orrv4uzc3pe">fatcat:nmvz3x374rahhm6orrv4uzc3pe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808185402/http://2013.igem.org/wiki/images/e/ef/BGU_1-s2.0-S0168165606008613-main_-1-.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/9a/85/9a85886f3c02babcd7c357462b7e23649248d5b8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbiotec.2006.09.026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Cell-to-Cell Variability in PI3K Protein Level Regulates PI3K-AKT Pathway Activity in Cell Populations

Tina L. Yuan, Gerburg Wulf, Laura Burga, Lewis C. Cantley
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/waxwzq3cnbet3cmwccpuk4bel4" style="color: black;">Current Biology</a> </i> &nbsp;
We show that AKT activity is bimodal in response to EGF stimulation and correlates with PI3K protein level, such that only cells with high PI3K protein can activate AKT.  ...  We further show that heterogeneity in PI3K protein levels is invariably maintained in cell populations through a degradation/resynthesis cycle that can be regulated by cell density.  ...  bimodal distribution of activated EGFR or total AKT protein, we next looked for variability in PI3K protein abundance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cub.2010.12.047">doi:10.1016/j.cub.2010.12.047</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21256021">pmid:21256021</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3394538/">pmcid:PMC3394538</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wiqyg33jj5azre3rfcwcdgr3ge">fatcat:wiqyg33jj5azre3rfcwcdgr3ge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190312105932/https://core.ac.uk/download/pdf/82714457.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/41/ba/41ba6b3fecec61f9a8b047cbe2bf0bf11c804341.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cub.2010.12.047"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394538" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Delay-Induced Transient Increase and Heterogeneity in Gene Expression in Negatively Auto-Regulated Gene Circuits

R. Maithreye, Ram Rup Sarkar, Veena K. Parnaik, Somdatta Sinha, Mark Isalan
<span title="2008-08-13">2008</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Theoretically time delay is known to be the source of instability, and has been attributed to lead to oscillations or transient dynamics in several biological functions.  ...  We show, both theoretically and experimentally, that delayed repression induces transient increase and heterogeneity in gene expression before the gain of stability effected by the negative feedback.  ...  A gene circuit realisation of this was also shown to produce oscillations in an artificial three-regulator system [28] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0002972">doi:10.1371/journal.pone.0002972</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18698420">pmid:18698420</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2494610/">pmcid:PMC2494610</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3v4adep2bng3dectatzzpvyv5i">fatcat:3v4adep2bng3dectatzzpvyv5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922201135/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0002972&amp;type=printable" 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/0d/38/0d388d9697a8dd072ef51ec1d66088fdf7275bb0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0002972"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2494610" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Self-Organized Criticality in the Brain

Dietmar Plenz, Tiago L. Ribeiro, Stephanie R. Miller, Patrick A. Kells, Ali Vakili, Elliott L. Capek
<span title="2021-07-07">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/im246jdlofanriyhr3bpyw2cwy" style="color: black;">Frontiers in Physics</a> </i> &nbsp;
The precise interactions between up-states, nested oscillations, and avalanches in superficial layers of the cortex provide compelling evidence for SOC in the brain.  ...  that are beneficial for system performance.  ...  Recent models have combined system-wide synchronization and hysteresis, i.e., to support an oscillation cycle, with structural heterogeneity, i.e., to capture the variability observed in avalanches, in  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphy.2021.639389">doi:10.3389/fphy.2021.639389</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wrvcvfvw4vcvxm6rr5usohyptq">fatcat:wrvcvfvw4vcvxm6rr5usohyptq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210710084330/https://fjfsdata01prod.blob.core.windows.net/articles/files/639389/pubmed-zip/.versions/1/.package-entries/fphy-09-639389.pdf?sv=2018-03-28&amp;sr=b&amp;sig=DjdE2BZuPoCcAy0gnkHEsIeRVMhsj8SjsUIUVvfF%2FAw%3D&amp;se=2021-07-10T08%3A43%3A59Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fphy-09-639389.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/9f/db/9fdb3ea2fb1d96af30211165c98ba0d745306322.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphy.2021.639389"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a>

What's all the noise about developmental stochasticity?

A. C. Oates
<span title="2011-01-25">2011</span> <i title="The Company of Biologists"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p74htnr5yvfmxn6hgfmprxrxiq" style="color: black;">Development</a> </i> &nbsp;
In simulating the cavitation of the blastocyst, the model successfully generated the characteristic bimodal distribution of cell sizes observed in the embryo.  ...  Further analysis showed that the bimodal elt-2 distribution appears to derive from a threshold effect: in those cells that accumulate enough END-1 to initiate elt-2 expression, the auto-regulatory action  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1242/dev.059923">doi:10.1242/dev.059923</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21266404">pmid:21266404</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/plzlzvf525dujho45mdryor7ra">fatcat:plzlzvf525dujho45mdryor7ra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430014755/http://dev.biologists.org/content/develop/138/4/601.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/6e/f2/6ef2d0d24e33578b44466e2f54b263533784fe25.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1242/dev.059923"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Are Proteins Dynamically Heterogeneous? Neutron Scattering Analysis of Hydrogen Displacement Distributions

Wolfgang Doster
<span title="2018-04-06">2018</span> <i title="Symbiosis Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/676tvfoqozcptaxhfw5nagredq" style="color: black;">International Journal of Molecular and Theoretical Physics</a> </i> &nbsp;
Exponential, Gamma and also bimodal distributions have been suggested in dynamical heterogeneity work of globular proteins [20].  ...  acids one expects a heterogeneous system of local sites, which gives rise to considerable dynamical heterogeneity.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15226/2576-4934/2/1/00112">doi:10.15226/2576-4934/2/1/00112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h3fwgvsu25fildmvwfdf4haxhm">fatcat:h3fwgvsu25fildmvwfdf4haxhm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429001735/https://symbiosisonlinepublishing.com/molecular-theoretical-physics/molecular-theoretical-physics12.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/95/90/9590d4537d625070d9ab35871d266529976ad87d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15226/2576-4934/2/1/00112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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