哺乳动物生物钟的多尺度复杂性。
Multiscale complexity in the mammalian circadian clock.
机构信息
Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, United States.
出版信息
Curr Opin Genet Dev. 2010 Dec;20(6):626-33. doi: 10.1016/j.gde.2010.09.006.
Abstract
The field of systems biology studies how the interactions among individual components (e.g. genes and proteins) yield interesting and complex behavior. The circadian (daily) timekeeping system in mammals is an ideal system to study complexity because of its many biological scales (from genes to animal behavior). A wealth of data at each of these scales has recently been discovered. Within each scale, modeling can advance our understanding of challenging problems that arise in studying mammalian timekeeping. However, future work must focus on bridging the multiple spatial and temporal scales in the modeling of SCN network. Here we review recent advances, and then delve into a few areas that are promising research directions. We also discuss the flavor of modeling needed (simple or detailed) as well as new techniques that are needed to meet the challenges in modeling data across scales.
摘要
系统生物学领域研究的是个体组成部分（例如基因和蛋白质）之间的相互作用如何产生有趣而复杂的行为。哺乳动物的昼夜（日常）计时系统是研究复杂性的理想系统，因为它具有许多生物学尺度（从基因到动物行为）。最近在每个尺度上都发现了大量数据。在每个尺度内，建模可以增进我们对研究哺乳动物计时过程中出现的具有挑战性问题的理解。但是，未来的工作必须集中在 SCN 网络建模的多个时空尺度上。在这里，我们回顾了最近的进展，然后深入探讨了一些有前途的研究方向。我们还讨论了建模所需的模型风格（简单或详细）以及在跨尺度建模数据方面所需的新技术。
相似文献
1
Multiscale complexity in the mammalian circadian clock.哺乳动物生物钟的多尺度复杂性。
Curr Opin Genet Dev. 2010 Dec;20(6):626-33. doi: 10.1016/j.gde.2010.09.006.
2
Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping.γ-氨基丁酸（GABA）在哺乳动物昼夜节律计时的多个时间尺度上具有不同作用。
Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):E3911-9. doi: 10.1073/pnas.1420753112. Epub 2015 Jun 30.
3
Circuit development in the master clock network of mammals.哺乳动物主时钟网络中的电路发育。
Eur J Neurosci. 2020 Jan;51(1):82-108. doi: 10.1111/ejn.14259. Epub 2018 Dec 5.
4
[Clock genes and clock-controlled genes in mammals].[哺乳动物中的生物钟基因和生物钟调控基因]
Nihon Rinsho. 2012 Jul;70(7):1109-14.
5
Computational modeling of the cell-autonomous mammalian circadian oscillator.细胞自主哺乳动物昼夜节律振荡器的计算建模
BMC Syst Biol. 2017 Feb 24;11(Suppl 1):379. doi: 10.1186/s12918-016-0379-8.
6
Mammalian circadian biology: elucidating genome-wide levels of temporal organization.哺乳动物的昼夜节律生物学：阐明全基因组水平的时间组织。
Annu Rev Genomics Hum Genet. 2004;5:407-41. doi: 10.1146/annurev.genom.5.061903.175925.
7
New insights into the mammalian circadian clock.对哺乳动物生物钟的新见解。
Sleep. 1996 Oct;19(8):641-67. doi: 10.1093/sleep/19.8.641.
8
Neuron-Astrocyte Interactions and Circadian Timekeeping in Mammals.哺乳动物中的神经元 - 星形胶质细胞相互作用与昼夜节律计时
Neuroscientist. 2025 Feb;31(1):65-79. doi: 10.1177/10738584241245307. Epub 2024 Apr 11.
9
Synchronization of the mammalian circadian timing system: Light can control peripheral clocks independently of the SCN clock: alternate routes of entrainment optimize the alignment of the body's circadian clock network with external time.哺乳动物昼夜节律计时系统的同步：光可以独立于视交叉上核（SCN）时钟控制外周时钟：交替的昼夜节律调节途径优化了身体昼夜节律时钟网络与外部时间的同步。
Bioessays. 2015 Oct;37(10):1119-28. doi: 10.1002/bies.201500026. Epub 2015 Aug 7.
10
Mammalian circadian signaling networks and therapeutic targets.哺乳动物昼夜节律信号网络与治疗靶点。
Nat Chem Biol. 2007 Oct;3(10):630-9. doi: 10.1038/nchembio.2007.37.
引用本文的文献
1
Plasticity manifolds and degeneracy govern circadian oscillations of neuronal intrinsic properties in the suprachiasmatic nucleus.可塑性流形和简并性支配视交叉上核中神经元内在特性的昼夜节律振荡。
iScience. 2023 Mar 27;26(4):106503. doi: 10.1016/j.isci.2023.106503. eCollection 2023 Apr 21.
2
Sleep Modelling across Physiological Levels.跨生理水平的睡眠建模
Clocks Sleep. 2019 Mar 4;1(1):166-184. doi: 10.3390/clockssleep1010015. eCollection 2019 Mar.
3
Systems Level Understanding of Circadian Integration with Cell Physiology.系统水平理解生物钟与细胞生理学的整合。
J Mol Biol. 2020 May 29;432(12):3547-3564. doi: 10.1016/j.jmb.2020.02.002. Epub 2020 Feb 13.
4
Interventions to Minimize Jet Lag After Westward and Eastward Flight.减少向西和向东飞行后时差反应的干预措施。
Front Physiol. 2019 Jul 31;10:927. doi: 10.3389/fphys.2019.00927. eCollection 2019.
5
Understanding Quantitative Circadian Regulations Are Crucial Towards Advancing Chronotherapy.理解定量的生物钟规律对于推进时间治疗至关重要。
Cells. 2019 Aug 13;8(8):883. doi: 10.3390/cells8080883.
6
Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks.真核生物钟中磷酸化依赖的计时设计原理。
Cold Spring Harb Perspect Biol. 2018 Aug 1;10(8):a028357. doi: 10.1101/cshperspect.a028357.
7
Protein sequestration versus Hill-type repression in circadian clock models.生物钟模型中的蛋白质隔离与希尔型抑制
IET Syst Biol. 2016 Aug;10(4):125-35. doi: 10.1049/iet-syb.2015.0090.
8
Melatonin signaling and its modulation of PfNF-YB transcription factor expression in Plasmodium falciparum.褪黑素信号传导及其对恶性疟原虫中PfNF-YB转录因子表达的调节
Int J Mol Sci. 2013 Jul 1;14(7):13704-18. doi: 10.3390/ijms140713704.
9
Chronobiology of Melatonin beyond the Feedback to the Suprachiasmatic Nucleus-Consequences to Melatonin Dysfunction.褪黑素的非超交叉核反馈的生物钟作用-褪黑素功能障碍的后果。
Int J Mol Sci. 2013 Mar 12;14(3):5817-41. doi: 10.3390/ijms14035817.
10
A mechanism for robust circadian timekeeping via stoichiometric balance.通过化学计量平衡实现稳健的生物钟计时机制。
Mol Syst Biol. 2012;8:630. doi: 10.1038/msb.2012.62.
本文引用的文献
1
Deterministic versus stochastic models for circadian rhythms.昼夜节律的确定性模型与随机模型
J Biol Phys. 2002 Dec;28(4):637-53. doi: 10.1023/A:1021286607354.
2
The Influence of Look-Ahead on the Error Rate of Transcription.前瞻对转录错误率的影响。
Math Model Nat Phenom. 2010 Jan 27;5(3):206-227. doi: 10.1051/mmnp/20105313.
3
Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA.果蝇生物钟中 PER 的动态 PER 抑制机制：从 DNA 上到 DNA 外。
Genes Dev. 2010 Feb 15;24(4):358-67. doi: 10.1101/gad.1883910.
4
A synchronized quorum of genetic clocks.一个同步的遗传时钟多数派。
Nature. 2010 Jan 21;463(7279):326-30. doi: 10.1038/nature08753.
5
Building biological memory by linking positive feedback loops.通过链接正反馈回路构建生物记忆。
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):175-80. doi: 10.1073/pnas.0908314107. Epub 2009 Dec 14.
6
Quantification of circadian rhythms in single cells.单细胞中生物钟节律的量化。
PLoS Comput Biol. 2009 Nov;5(11):e1000580. doi: 10.1371/journal.pcbi.1000580. Epub 2009 Nov 26.
7
Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock.CKIdelta 和 CKIepsilon 在哺乳动物生物钟中的基本作用。
Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21359-64. doi: 10.1073/pnas.0906651106. Epub 2009 Nov 30.
8
Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism.节律性 PER 丰度定义了生物钟机制内负反馈的关键节点。
Mol Cell. 2009 Nov 13;36(3):417-30. doi: 10.1016/j.molcel.2009.10.012.
9
Model aggregation: a building-block approach to creating large macromolecular regulatory networks.模型聚合：构建大型大分子调控网络的积木方法。
Bioinformatics. 2009 Dec 15;25(24):3289-95. doi: 10.1093/bioinformatics/btp581. Epub 2009 Oct 29.
10
AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation.腺苷酸活化蛋白激酶通过隐花色素的磷酸化和降解来调节生物钟。
Science. 2009 Oct 16;326(5951):437-40. doi: 10.1126/science.1172156.
Zotero 插件