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乳酸菌的系统生物学:批判性评价。

Systems biology of lactic acid bacteria: a critical review.

机构信息

Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.

出版信息

Microb Cell Fact. 2011 Aug 30;10 Suppl 1(Suppl 1):S11. doi: 10.1186/1475-2859-10-S1-S11.

Abstract

Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute. There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them. We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.

摘要

理解系统的属性是如何从描述良好的部分相互作用中涌现出来的,这是系统生物学最重要的目标。虽然在乳酸菌(LAB)生理学的实践中,我们最常将部分视为蛋白质和代谢物,但对部分的更广泛解释可能会有所帮助。例如,不同的菌株或物种可以是群落的部分,或者我们可以只研究代谢的化学反应作为部分(而忘记催化它们的酶),就像通量平衡分析那样。只要我们对这些部分的性质有一定的了解,我们就可以研究它们的相互作用是否导致它们构成的系统产生新的或意外的行为。在系统生物学社区中,有一种倾向认为数据的收集和整合应该无限期地继续,否则我们将无法详细了解我们研究的系统。然而,有时退后一步考虑一下我们已经掌握的知识是否可以解释我们发现的如此有趣的系统行为,可能会很有用。对系统进行推理可能很困难,并且可能需要应用数学技术。回报有时是意外结论的实现,或者在最坏的情况下,我们仍然不知道部分的足够细节,或者它们之间的相互作用。我们将讨论一些案例,重点是与 LAB 相关的工作,在这些案例中,典型的系统方法带来了新的知识或观点,这些观点往往与直观相悖,与更简单方法的结论相冲突。系统方法还可能产生新类型的可测试假设,我们将对此进行说明。最后,我们将展望系统方法可能为近期指明研究方向的研究领域。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/47f1/3231918/90de94978326/1475-2859-10-S1-S11-1.jpg

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