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在一个分区空间世界中自催化集的种群动态

Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World.

作者信息

Hordijk Wim, Naylor Jonathan, Krasnogor Natalio, Fellermann Harold

机构信息

Institute for Advanced Study, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.

Interdisciplinary Computing and Complex BioSystems Research Group (ICOS), School of Computing, Newcastle University, Newcastle upon Tyne NE98, UK.

出版信息

Life (Basel). 2018 Aug 18;8(3):33. doi: 10.3390/life8030033.

DOI:10.3390/life8030033
PMID:30126201
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6161236/
Abstract

Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called . However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in of compartments in a spatial environment. Here, we use a recently developed software tool to simulate exactly this scenario, as an important first step towards more realistic simulations and experiments on autocatalytic sets in protocells.

摘要

自催化集是自我维持且具有集体催化作用的化学反应网络,被认为在生命起源中发挥了重要作用。模拟研究表明,原则上,如果多个自催化子集能够以不同组合存在于隔室内,即所谓的……,那么自催化集是可进化的。然而,迄今为止,这些先前的研究尚未明确模拟空间环境中隔室形成过程中自催化集的出现和动态。在此,我们使用一种最近开发的软件工具来精确模拟这一情景,这是朝着对原细胞中自催化集进行更现实的模拟和实验迈出的重要第一步。

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引用本文的文献

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Multistable Protocells Can Aid the Evolution of Prebiotic Autocatalytic Sets.多稳态原细胞有助于益生元自催化集的进化。
Life (Basel). 2023 Dec 12;13(12):2327. doi: 10.3390/life13122327.
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Biological Catalysis and Information Storage Have Relied on -Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life.自生命起源以来,生物催化和信息存储一直依赖于β-D-核糖呋喃糖的糖苷衍生物。
Biomolecules. 2023 Apr 30;13(5):782. doi: 10.3390/biom13050782.
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The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life.

本文引用的文献

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Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations.共生生物:用于细菌群体三维建模的多尺度整合平台。
ACS Synth Biol. 2017 Jul 21;6(7):1194-1210. doi: 10.1021/acssynbio.6b00315. Epub 2017 May 22.
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Chasing the tail: The emergence of autocatalytic networks.追逐尾巴:自催化网络的出现。
Biosystems. 2017 Feb;152:1-10. doi: 10.1016/j.biosystems.2016.12.002. Epub 2016 Dec 25.
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Necessary and sufficient conditions for protocell growth.原始细胞生长的充分必要条件。
自催化反应网络的层次组织及其与生命起源的关系。
PLoS Comput Biol. 2022 Sep 9;18(9):e1010498. doi: 10.1371/journal.pcbi.1010498. eCollection 2022 Sep.
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Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets.自催化集的 RNA 随机连接的基因组进化。
Int J Mol Sci. 2021 Dec 16;22(24):13526. doi: 10.3390/ijms222413526.
5
Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems.自催化化学反应系统中的自我复制与达尔文式进化
Life (Basel). 2021 Apr 1;11(4):308. doi: 10.3390/life11040308.
6
Thresholds in Origin of Life Scenarios.生命起源情景中的阈值。
iScience. 2020 Nov 1;23(11):101756. doi: 10.1016/j.isci.2020.101756. eCollection 2020 Nov 20.
7
Formation of Polarized, Functional Artificial Cells from Compartmentalized Droplet Networks and Nanomaterials, Using One-Step, Dual-Material 3D-Printed Microfluidics.利用一步法双材料3D打印微流控技术,从分隔的液滴网络和纳米材料中形成极化的功能性人工细胞。
Adv Sci (Weinh). 2019 Oct 24;7(1):1901719. doi: 10.1002/advs.201901719. eCollection 2020 Jan.
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Molecular Diversity Required for the Formation of Autocatalytic Sets.自催化集形成所需的分子多样性。
Life (Basel). 2019 Mar 1;9(1):23. doi: 10.3390/life9010023.
9
Autocatalytic Networks at the Basis of Life's Origin and Organization.生命起源与组织基础的自催化网络
Life (Basel). 2018 Dec 8;8(4):62. doi: 10.3390/life8040062.
J Math Biol. 2016 Dec;73(6-7):1627-1664. doi: 10.1007/s00285-016-0998-0. Epub 2016 Apr 18.
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Prebiotic network evolution: six key parameters.益生元网络进化:六个关键参数。
Mol Biosyst. 2015 Dec;11(12):3206-17. doi: 10.1039/c5mb00593k.
5
Autocatalytic sets in metabolism.新陈代谢中的自催化集。
J Syst Chem. 2015;6(1):4. doi: 10.1186/s13322-015-0009-7. Epub 2015 Apr 1.
6
Algorithms for detecting and analysing autocatalytic sets.用于检测和分析自催化集的算法。
Algorithms Mol Biol. 2015 Apr 28;10:15. doi: 10.1186/s13015-015-0042-8. eCollection 2015.
7
Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life.在波动的热液池中发生的偶联相和组合选择:指导细胞生命起源实验方法的一个方案。
Life (Basel). 2015 Mar 13;5(1):872-87. doi: 10.3390/life5010872.
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Quasispecies in population of compositional assemblies.群体中组成性组装的准种。
BMC Evol Biol. 2014 Dec 30;14:265. doi: 10.1186/s12862-014-0265-1.
9
Growth and division in a dynamic protocell model.动态原细胞模型中的生长和分裂。
Life (Basel). 2014 Dec 3;4(4):837-64. doi: 10.3390/life4040837.
10
Conditions for evolvability of autocatalytic sets: a formal example and analysis.自催化集的进化条件:一个形式化示例与分析
Orig Life Evol Biosph. 2014 Apr;44(2):111-24. doi: 10.1007/s11084-014-9374-5. Epub 2014 Dec 5.