scholarly journals 1PT204 An optimal heterogeneity in a cell population maximizes the effects of growth factors directing stochastic PC12 cell fate decisions(The 50th Annual Meeting of the Biophysical Society of Japan)

2012 ◽  
Vol 52 (supplement) ◽  
pp. S102-S103
Author(s):  
Kazunari Mouri ◽  
Yasushi Sako
Keyword(s):  
Growth Factors ◽  
Annual Meeting ◽  
Cell Fate ◽  
Cell Population ◽  
Pc12 Cell ◽  
Cell Fate Decisions ◽  
Biophysical Society ◽  
A Cell

scholarly journals UPMaBoSS: a novel framework for dynamic cell population modeling

2020 ◽  
Author(s):  
Gautier Stoll ◽  
Aurélien Naldi ◽  
Vincent Noël ◽  
Eric Viara ◽  
Emmanuel Barillot ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Cell Fate ◽  
Cellular Networks ◽  
Cell Population ◽  
Cell Fate Decisions ◽  
Dynamic Cell ◽  
Drug Treatments ◽  
A Cell ◽  
The Impact

AbstractOne of the aims of mathematical modeling is to understand and simulate the effects of biological perturbations and suggest ways to intervene and reestablish proper cell functioning. However, it remains a challenge, especially when considering the dynamics at the level of a cell population, with cells dying, dividing and interacting. Here, we introduce a novel framework for the dynamical modelling of cell populations packaged into a dedicated tool, UPMaBoSS. We rely on the preexisting tool MaBoSS, which enables probabilistic simulations of cellular networks, and add a novel layer to account for cell interactions and population dynamics. We illustrate our methodology by means of a case study dealing with TNF-induced cell death. Interestingly, the simulation of cell population dynamics with UPMaBoSS reveals a mechanism of resistance triggered by TNF treatment. This appoach can be applied to diverse models of cellular networks, for example to study the impact of ligand release or drug treatments on cell fate decisions, such as commitment to proliferation, differentiation, apoptosis, etc. Relatively easy to encode, UPMaBoSS simulations require only moderate computational power and execution time.To ease the reproduction of simulations, we provide several Jupyter notebooks that can be accessed within a new release of the CoLoMoTo Docker image, which contains all required software and the example models.

scholarly journals 3P101 Development of a cell/well-based bioassay for the biological activity of Aβ42-binding peptides(Protein: Engineering,The 48th Annual Meeting of the Biophysical Society of Japan)

2010 ◽  
Vol 50 (supplement2) ◽  
pp. S162
Author(s):  
Ran Gu ◽  
Mizuho Sawada ◽  
Sachika Ueno-Tsuji ◽  
Masayuki Komatsu ◽  
Koichiro Kitamura ◽  
...  
Keyword(s):  
Biological Activity ◽  
Protein Engineering ◽  
Annual Meeting ◽  
Biophysical Society ◽  
A Cell ◽  
Binding Peptides

scholarly journals Genomic insights into chromatin reprogramming to totipotency in embryos

2018 ◽  
Vol 218 (1) ◽  
pp. 70-82 ◽  
Author(s):  
Sabrina Ladstätter ◽  
Kikuë Tachibana
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Chromatin Accessibility ◽  
Early Embryo ◽  
Epigenetic Reprogramming ◽  
Mammalian Embryo ◽  
Cell Fate Decisions ◽  
A Cell ◽  
Early Mouse ◽  
Chromatin Reprogramming

The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.

United colours of chromatin? Developmental genome organisation in flies

2019 ◽  
Vol 47 (2) ◽  
pp. 691-700
Author(s):  
Caroline Delandre ◽  
Owen J. Marshall
Keyword(s):  
Cell Fate ◽  
Fruit Fly ◽  
Genome Organisation ◽  
Chromatin Protein ◽  
Cell Type ◽  
Chromatin States ◽  
Cell Fate Decisions ◽  
A Cell ◽  
Cell Type Specific ◽  
Chromatin Biology

Abstract The organisation of DNA into differing forms of packaging, or chromatin, controls many of the cell fate decisions during development. Although early studies focused on individual forms of chromatin, in the last decade more holistic studies have attempted to determine a complete picture of the different forms of chromatin present within a cell. In the fruit fly, Drosophila melanogaster, the study of chromatin states has been aided by the use of complementary and cell-type-specific techniques that profile the marks that recruit chromatin protein binding or the proteins themselves. Although many questions remain unanswered, a clearer picture of how different chromatin states affect development is now emerging, with more unusual chromatin states such as Black chromatin playing key roles. Here, we discuss recent findings regarding chromatin biology in flies.

3P201 Characterization of chemotaxis-related signaling components of Vibrio cholerae that localize to a cell pole(Cell biology,The 48th Annual Meeting of the Biophysical Society of Japan)

2010 ◽  
Vol 50 (supplement2) ◽  
pp. S180
Author(s):  
Tomoyuki Nakamura ◽  
Geetha Hiremath ◽  
Takehiko Inaba ◽  
Soichiro Nishiyama ◽  
Ikuro Kawagishi
Keyword(s):  
Vibrio Cholerae ◽  
Annual Meeting ◽  
Cell Biology ◽  
Cell Pole ◽  
Pole Cell ◽  
Biophysical Society ◽  
A Cell ◽  
Signaling Components
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