Suppr超能文献

遍历性、隐藏偏差与增长率增益。

Ergodicity, hidden bias and the growth rate gain.

作者信息

Rochman Nash D, Popescu Dan M, Sun Sean X

机构信息

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America.

出版信息

Phys Biol. 2018 Mar 14;15(3):036006. doi: 10.1088/1478-3975/aab0e6.

Abstract

Many single-cell observables are highly heterogeneous. A part of this heterogeneity stems from age-related phenomena: the fact that there is a nonuniform distribution of cells with different ages. This has led to a renewed interest in analytic methodologies including use of the 'von Foerster equation' for predicting population growth and cell age distributions. Here we discuss how some of the most popular implementations of this machinery assume a strong condition on the ergodicity of the cell cycle duration ensemble. We show that one common definition for the term ergodicity, 'a single individual observed over many generations recapitulates the behavior of the entire ensemble' is implied by the other, 'the probability of observing any state is conserved across time and over all individuals' in an ensemble with a fixed number of individuals but that this is not true when the ensemble is growing. We further explore the impact of generational correlations between cell cycle durations on the population growth rate. Finally, we explore the 'growth rate gain'-the phenomenon that variations in the cell cycle duration leads to an improved population-level growth rate-in this context. We highlight that, fundamentally, this effect is due to asymmetric division.

摘要

许多单细胞观测结果具有高度的异质性。这种异质性的一部分源于与年龄相关的现象:即不同年龄的细胞分布不均匀。这使得人们重新对包括使用“冯·福斯特方程”来预测种群增长和细胞年龄分布在内的分析方法产生了兴趣。在这里,我们讨论了这种机制的一些最流行的实现方式是如何对细胞周期持续时间总体的遍历性假设了一个强条件的。我们表明,遍历性这一术语的一个常见定义,即“在多代中观察到的单个个体概括了整个总体的行为”,在另一个定义,即在具有固定个体数量的总体中“观察到任何状态的概率在时间上和所有个体中都是守恒的”中是隐含的,但当总体在增长时情况并非如此。我们进一步探讨了细胞周期持续时间之间的代际相关性对种群增长率的影响。最后,我们在这种背景下探讨了“增长率增益”——即细胞周期持续时间的变化导致种群水平增长率提高的现象。我们强调,从根本上说,这种效应是由于不对称分裂。

相似文献

1
Ergodicity, hidden bias and the growth rate gain.
Phys Biol. 2018 Mar 14;15(3):036006. doi: 10.1088/1478-3975/aab0e6.
2
Reconstructing the single-cell-level behavior of a toggle switch from population-level measurements.
FEBS Lett. 2008 Apr 2;582(7):1067-72. doi: 10.1016/j.febslet.2008.02.057. Epub 2008 Mar 4.
3
Weak ergodicity breaking induced by global memory effects.
Phys Rev E. 2016 Aug;94(2-1):022108. doi: 10.1103/PhysRevE.94.022108. Epub 2016 Aug 8.
4
Noise-driven growth rate gain in clonal cellular populations.
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3251-6. doi: 10.1073/pnas.1519412113. Epub 2016 Mar 7.
5
Dynamic modeling of microbial cell populations.
Curr Opin Biotechnol. 2003 Oct;14(5):460-7. doi: 10.1016/s0958-1669(03)00104-6.
6
Universal protein distributions in a model of cell growth and division.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Oct;92(4):042713. doi: 10.1103/PhysRevE.92.042713. Epub 2015 Oct 23.
7
Individual cell heterogeneity in Predictive Food Microbiology: Challenges in predicting a "noisy" world.
Int J Food Microbiol. 2017 Jan 2;240:3-10. doi: 10.1016/j.ijfoodmicro.2016.06.021. Epub 2016 Jun 21.
9
The Synchronization of Replication and Division Cycles in Individual E. coli Cells.
Cell. 2016 Jul 28;166(3):729-739. doi: 10.1016/j.cell.2016.06.052.
10
Self-averaging and weak ergodicity breaking of diffusion in heterogeneous media.
Phys Rev E. 2017 Aug;96(2-1):022156. doi: 10.1103/PhysRevE.96.022156. Epub 2017 Aug 30.

引用本文的文献

1
Ecological Determinants of Altruism in Prokaryote Antivirus Defense.
bioRxiv. 2024 Nov 5:2024.11.05.622165. doi: 10.1101/2024.11.05.622165.
2
Balance between asymmetric allocation and repair of somatic damage in unicellular life forms as an ancient form of r/K selection.
Proc Natl Acad Sci U S A. 2024 May 28;121(22):e2400008121. doi: 10.1073/pnas.2400008121. Epub 2024 May 24.
3
Prolonged culture in aerobic environments alters H production capacity.
Eng Rep. 2020 May;2(5). doi: 10.1002/eng2.12161. Epub 2020 Apr 30.
6
A unified framework for measuring selection on cellular lineages and traits.
Elife. 2022 Dec 6;11:e72299. doi: 10.7554/eLife.72299.
8
Bacterial cell proliferation: from molecules to cells.
FEMS Microbiol Rev. 2021 Jan 8;45(1). doi: 10.1093/femsre/fuaa046.
9
YAP and TAZ regulate cell volume.
J Cell Biol. 2019 Oct 7;218(10):3472-3488. doi: 10.1083/jcb.201902067. Epub 2019 Sep 3.

本文引用的文献

1
Making sense of snapshot data: ergodic principle for clonal cell populations.
J R Soc Interface. 2017 Nov;14(136). doi: 10.1098/rsif.2017.0467.
2
Asymmetric cell division requires specific mechanisms for adjusting global transcription.
Nucleic Acids Res. 2017 Dec 1;45(21):12401-12412. doi: 10.1093/nar/gkx974.
3
The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth.
Cell Syst. 2017 Oct 25;5(4):358-367.e4. doi: 10.1016/j.cels.2017.08.015. Epub 2017 Oct 4.
4
Phenotypic heterogeneity promotes adaptive evolution.
PLoS Biol. 2017 May 9;15(5):e2000644. doi: 10.1371/journal.pbio.2000644. eCollection 2017 May.
5
To grow is not enough: impact of noise on cell environmental response and fitness.
Integr Biol (Camb). 2016 Oct 10;8(10):1030-1039. doi: 10.1039/c6ib00119j.
6
Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness.
Curr Biol. 2016 May 9;26(9):1138-47. doi: 10.1016/j.cub.2016.03.010. Epub 2016 Apr 7.
7
Noise-driven growth rate gain in clonal cellular populations.
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3251-6. doi: 10.1073/pnas.1519412113. Epub 2016 Mar 7.
8
Lineage correlations of single cell division time as a probe of cell-cycle dynamics.
Nature. 2015 Mar 26;519(7544):468-71. doi: 10.1038/nature14318. Epub 2015 Mar 11.
9
The art of choreographing asymmetric cell division.
Dev Cell. 2013 Jun 10;25(5):439-50. doi: 10.1016/j.devcel.2013.05.003.
10
Age-dependent stochastic models for understanding population fluctuations in continuously cultured cells.
J R Soc Interface. 2013 Jun 12;10(85):20130325. doi: 10.1098/rsif.2013.0325. Print 2013 Aug 6.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验