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Towards multiscale modeling of the CD8+ T cell response to viral infections. CD8+ T细胞对病毒感染反应的多尺度建模。
IF 7.9 Q1 Medicine Pub Date : 2019-07-01 Epub Date: 2019-02-27 DOI: 10.1002/wsbm.1446
Subhasish Baral, Rubesh Raja, Pramita Sen, Narendra M Dixit

The CD8+ T cell response is critical to the control of viral infections. Yet, defining the CD8+ T cell response to viral infections quantitatively has been a challenge. Following antigen recognition, which triggers an intracellular signaling cascade, CD8+ T cells can differentiate into effector cells, which proliferate rapidly and destroy infected cells. When the infection is cleared, they leave behind memory cells for quick recall following a second challenge. If the infection persists, the cells may become exhausted, retaining minimal control of the infection while preventing severe immunopathology. These activation, proliferation and differentiation processes as well as the mounting of the effector response are intrinsically multiscale and collective phenomena. Remarkable experimental advances in the recent years, especially at the single cell level, have enabled a quantitative characterization of several underlying processes. Simultaneously, sophisticated mathematical models have begun to be constructed that describe these multiscale phenomena, bringing us closer to a comprehensive description of the CD8+ T cell response to viral infections. Here, we review the advances made and summarize the challenges and opportunities ahead. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Cell Fates Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models.

CD8+ T细胞反应对病毒感染的控制至关重要。然而,定量定义CD8+ T细胞对病毒感染的反应一直是一个挑战。抗原识别触发细胞内信号级联反应后,CD8+ T细胞可以分化为效应细胞,效应细胞迅速增殖并破坏感染细胞。当感染被清除后,它们会留下记忆细胞,以便在第二次挑战后快速回忆起来。如果感染持续存在,细胞可能会耗尽,在防止严重免疫病理的同时保持对感染的最小控制。这些激活、增殖和分化过程以及效应反应的增加本质上是多尺度和集体现象。近年来,特别是在单细胞水平上,显著的实验进展使几个潜在过程的定量表征成为可能。同时,描述这些多尺度现象的复杂数学模型已经开始构建,使我们更接近于全面描述CD8+ T细胞对病毒感染的反应。在这里,我们回顾了取得的进展,并总结了未来的挑战和机遇。本文分类为:分析与计算方法>计算方法生物学机制>细胞命运生物学机制>系统特性和过程的细胞信号传导模型>机制模型。
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引用次数: 14
Systems biology of robustness and homeostatic mechanisms. 鲁棒性和稳态机制的系统生物学。
IF 7.9 Q1 Medicine Pub Date : 2019-05-01 Epub Date: 2018-10-29 DOI: 10.1002/wsbm.1440
H Frederik Nijhout, Janet A Best, Michael C Reed

All organisms are subject to large amounts of genetic and environmental variation and have evolved mechanisms that allow them to function well in spite of these challenges. This property is generally referred to as robustness. We start with the premise that phenotypes arise from dynamical systems and are therefore system properties. Phenotypes occur at all levels of the biological organizational hierarchy, from gene products, to biochemical pathways, to cells, tissues, organs, appendages, and whole bodies. Phenotypes at all these levels are subject to environmental and genetic challenges against which their form and function need to be protected. The mechanisms that can produce robustness are diverse and several different kinds often operate simultaneously. We focus, in particular, on homeostatic mechanisms that dynamically maintain form and function against varying environmental and genetic factors. Understanding how homeostatic mechanisms operate, how they reach their set point, and the nature of the set point pose difficult challenges. In developmental systems, homeostatic mechanisms make the progression of morphogenesis relatively insensitive to genetic and environmental variation so that the outcomes vary little, even in the presence of severe mutational and environmental stress. Accordingly, developmental systems give the appearance of being goal-oriented, but how the target phenotype is encoded is not known. We discuss why and how individual variation poses challenges for mathematical modeling of biological systems, and conclude with an explanation of how system population models are a useful method for incorporating individual variation into deterministic ordinary differential equation (ODE) models. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Physiology > Mammalian Physiology in Health and Disease Physiology > Organismal Responses to Environment Biological Mechanisms > Regulatory Biology.

所有生物都受到大量遗传和环境变化的影响,并已进化出使它们能够在这些挑战中良好运作的机制。这种特性通常被称为鲁棒性。我们从表型产生于动力系统的前提开始,因此表型是系统属性。表型发生在生物组织层次的各个层面,从基因产物到生化途径,再到细胞、组织、器官、附属物和整个身体。所有这些水平上的表型都受到环境和遗传的挑战,它们的形式和功能需要得到保护。产生鲁棒性的机制是多种多样的,而且常常有几种不同的机制同时起作用。我们特别关注动态维持形式和功能对抗各种环境和遗传因素的稳态机制。了解稳态机制是如何运作的,它们是如何达到设定点的,以及设定点的性质构成了艰巨的挑战。在发育系统中,内稳态机制使得形态发生的进程相对不受遗传和环境变化的影响,因此即使在存在严重的突变和环境压力的情况下,结果变化也很小。因此,发育系统看起来是目标导向的,但目标表型是如何编码的尚不清楚。我们讨论了个体变异为何以及如何对生物系统的数学建模构成挑战,并最后解释了系统种群模型如何成为将个体变异纳入确定性常微分方程(ODE)模型的有用方法。本文分类如下:系统特性和过程模型>机制模型生理学>健康和疾病生理学中的哺乳动物生理学>生物体对环境的反应生物学机制>调节生物学。
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引用次数: 42
Chromatin imaging and new technologies for imaging the nucleome. 染色质成像及核体成像新技术。
IF 7.9 Q1 Medicine Pub Date : 2019-05-01 Epub Date: 2018-11-19 DOI: 10.1002/wsbm.1442
Nicole A Szydlowski, Jane S Go, Ying S Hu

Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.

先进荧光成像和标记技术的协同发展使染色质结构和动态在纳米级和活细胞的直接可视化成为可能。超分辨率成像包含了一类不断发展的技术,突破了荧光显微镜的衍射极限。结构照明显微镜提供了两倍的分辨率改进,可以很容易地实现使用传统的荧光团实时多色成像。单分子定位显微镜以较慢的采集速度为代价,将空间分辨率提高了大约10倍。受激发射损耗显微镜产生大约五倍的分辨率提高与成像速度成正比的扫描面积。同时,先进的标记策略已经发展到“点亮”全球和序列特异性DNA区域。DNA结合染料已被用于在单分子定位显微镜中实现高标记密度,并在相关光学和电子显微镜中增强对比度。新一代Oligopaint利用生物信息学分析来优化荧光原位杂交探针的设计。通过顺序和组合标记,DNA结构域的体积和长度以及不同拓扑相关结构域的空间组织的直接表征已被报道。在活细胞中,基因座特异性标记可以通过在目标基因旁边插入人工基因座来实现,例如阻遏因子-操作符阵列系统,或者利用基因组编辑工具,包括锌精细蛋白、转录激活因子样效应物和聚集规律间隔的短回文重复系统。结合单分子跟踪,这些标记技术可以直接可视化染色质内和染色质间的相互作用。本文分类如下:实验室方法与技术>成像。
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引用次数: 6
Integrating molecular networks with genetic variant interpretation for precision medicine. 整合分子网络与基因变异解释的精准医学。
IF 7.9 Q1 Medicine Pub Date : 2019-05-01 Epub Date: 2018-12-12 DOI: 10.1002/wsbm.1443
Emidio Capriotti, Kivilcim Ozturk, Hannah Carter

More reliable and cheaper sequencing technologies have revealed the vast mutational landscapes characteristic of many phenotypes. The analysis of such genetic variants has led to successful identification of altered proteins underlying many Mendelian disorders. Nevertheless the simple one-variant one-phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders. Although experimental and computational approaches have improved detection of functionally deleterious variants and important interactions between gene products, the development of comprehensive models relating genotype and phenotypes remains a challenge in the field of genomic medicine. In this context, a new view of the pathologic state as significant perturbation of the network of interactions between biomolecules is crucial for the identification of biochemical pathways associated with complex phenotypes. Seminal studies in systems biology combined the analysis of genetic variation with protein-protein interaction networks to demonstrate that even as biological systems evolve to be robust to genetic variation, their topologies create disease vulnerabilities. More recent analyses model the impact of genetic variants as changes to the "wiring" of the interactome to better capture heterogeneity in genotype-phenotype relationships. These studies lay the foundation for using networks to predict variant effects at scale using machine-learning or algorithmic approaches. A wealth of databases and resources for the annotation of genotype-phenotype relationships have been developed to support developments in this area. This overview describes how study of the molecular interactome has generated insights linking the organization of biological systems to disease mechanism, and how this information can enable precision medicine. This article is categorized under: Translational, Genomic, and Systems Medicine > Translational Medicine Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models Analytical and Computational Methods > Computational Methods.

更可靠和更便宜的测序技术已经揭示了许多表型特征的巨大突变景观。对这种基因变异的分析已经成功地鉴定了许多孟德尔疾病背后的改变蛋白。然而,对许多单基因疾病有效的简单单变单表型模型并没有捕捉到多基因性状和疾病的复杂性。尽管实验和计算方法已经改进了对功能有害变异和基因产物之间重要相互作用的检测,但开发与基因型和表型相关的综合模型仍然是基因组医学领域的一个挑战。在这种情况下,病理状态作为生物分子之间相互作用网络的显著扰动的新观点对于识别与复杂表型相关的生化途径至关重要。系统生物学的开创性研究将遗传变异与蛋白质-蛋白质相互作用网络的分析结合起来,证明即使生物系统进化到对遗传变异具有鲁棒性,其拓扑结构也会产生疾病脆弱性。最近的分析将遗传变异的影响建模为相互作用组“连线”的变化,以更好地捕捉基因型-表型关系中的异质性。这些研究为使用网络通过机器学习或算法方法大规模预测变量效应奠定了基础。为了支持这一领域的发展,已经开发了丰富的基因型-表型关系注释数据库和资源。本文概述了分子相互作用组的研究如何产生了将生物系统组织与疾病机制联系起来的见解,以及这些信息如何使精准医学成为可能。本文分类如下:转化、基因组和系统医学>转化医学生物学机制>系统特性和过程的细胞信号模型>机制模型分析和计算方法>计算方法。
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引用次数: 31
Context-dependent regulation of receptor tyrosine kinases: Insights from systems biology approaches. 受体酪氨酸激酶的上下文依赖性调控:来自系统生物学方法的见解。
IF 7.9 Q1 Medicine Pub Date : 2019-03-01 Epub Date: 2018-09-26 DOI: 10.1002/wsbm.1437
Inez Lam, Christina M Pickering, Feilim Mac Gabhann

Receptor tyrosine kinases (RTKs) are cell membrane proteins that provide cells with the ability to sense proteins in their environments. Many RTKs are essential to development and organ growth. Derangement of RTKs-by mutation or by overexpression-is central to several developmental and adult disorders including cancer, short stature, and vascular pathologies. The mechanism of action of RTKs is complex and is regulated by contextual components, including the existence of multiple competing ligands and receptors in many families, the intracellular location of the RTK, the dynamic and cell-specific coexpression of other RTKs, and the commonality of downstream signaling pathways. This means that both the state of the cell and the microenvironment outside the cell play a role, which makes sense given the pivotal location of RTKs as the nexus linking the extracellular milieu to intracellular signaling and modification of cell behavior. In this review, we describe these different contextual components through the lens of systems biology, in which both computational modeling and experimental "omics" approaches have been used to better understand RTK networks. The complexity of these networks is such that using these systems biology approaches is necessary to get a handle on the mechanisms of pathology and the design of therapeutics targeting RTKs. In particular, we describe in detail three concrete examples (involving ErbB3, VEGFR2, and AXL) that illustrate how systems approaches can reveal key mechanistic and therapeutic insights. This article is categorized under: Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models Translational, Genomic, and Systems Medicine > Therapeutic Methods.

受体酪氨酸激酶(RTKs)是一种细胞膜蛋白,为细胞提供在其环境中感知蛋白质的能力。许多RTK对发育和器官生长至关重要。RTKs突变或过度表达导致的紊乱是多种发育和成人疾病的核心,包括癌症、身材矮小和血管病变。RTK的作用机制是复杂的,受上下文成分的调节,包括许多家族中存在多种竞争性配体和受体,RTK的细胞内位置,其他RTK的动态和细胞特异性共表达,以及下游信号通路的共同性。这意味着细胞的状态和细胞外的微环境都发挥着作用,考虑到RTK的关键位置,这是有意义的,因为RTK是连接细胞外环境与细胞内信号传导和细胞行为修饰的纽带。在这篇综述中,我们通过系统生物学的视角描述了这些不同的上下文组件,其中计算建模和实验“组学”方法都被用来更好地理解RTK网络。这些网络的复杂性使得使用这些系统生物学方法对于掌握病理机制和针对RTK的治疗方法的设计是必要的。特别是,我们详细描述了三个具体的例子(涉及ErbB3、VEGFR2和AXL),这些例子说明了系统方法如何揭示关键的机制和治疗见解。本文分类如下:生物学机制>系统特性和过程的细胞信号模型>机制模型转化、基因组和系统医学>治疗方法。
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引用次数: 3
Mathematical modeling of circadian rhythms. 昼夜节律的数学模型。
IF 7.9 Q1 Medicine Pub Date : 2019-03-01 Epub Date: 2018-10-17 DOI: 10.1002/wsbm.1439
Ameneh Asgari-Targhi, Elizabeth B Klerman

Circadian rhythms are endogenous ~24-hr oscillations usually entrained to daily environmental cycles of light/dark. Many biological processes and physiological functions including mammalian body temperature, the cell cycle, sleep/wake cycles, neurobehavioral performance, and a wide range of diseases including metabolic, cardiovascular, and psychiatric disorders are impacted by these rhythms. Circadian clocks are present within individual cells and at tissue and organismal levels as emergent properties from the interaction of cellular oscillators. Mathematical models of circadian rhythms have been proposed to provide a better understanding of and to predict aspects of this complex physiological system. These models can be used to: (a) manipulate the system in silico with specificity that cannot be easily achieved using in vivo and in vitro experimental methods and at lower cost, (b) resolve apparently contradictory empirical results, (c) generate hypotheses, (d) design new experiments, and (e) to design interventions for altering circadian rhythms. Mathematical models differ in structure, the underlying assumptions, the number of parameters and variables, and constraints on variables. Models representing circadian rhythms at different physiologic scales and in different species are reviewed to promote understanding of these models and facilitate their use. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.

昼夜节律是内源性的~24小时振荡,通常伴随着每天的光/暗环境周期。许多生物过程和生理功能,包括哺乳动物的体温、细胞周期、睡眠/觉醒周期、神经行为表现,以及包括代谢、心血管和精神疾病在内的广泛疾病,都受到这些节律的影响。昼夜节律时钟作为细胞振荡器相互作用的新兴特性存在于单个细胞内、组织和生物体水平。已经提出了昼夜节律的数学模型,以更好地理解和预测这种复杂生理系统的各个方面。这些模型可用于:(a)以较低的成本在计算机上以体内和体外实验方法无法轻易实现的特异性操纵系统,(b)解决明显矛盾的经验结果,(c)产生假设,(d)设计新的实验,以及(e)设计改变昼夜节律的干预措施。数学模型在结构、基本假设、参数和变量的数量以及对变量的约束方面有所不同。综述了在不同生理尺度和不同物种中代表昼夜节律的模型,以促进对这些模型的理解并促进其使用。本文分类在:生理学>健康和疾病中的哺乳动物生理学系统特性和过程模型>器官、组织和生理模型。
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引用次数: 0
Quantitative systems models illuminate arrhythmia mechanisms in heart failure: Role of the Na+ -Ca2+ -Ca2+ /calmodulin-dependent protein kinase II-reactive oxygen species feedback. 定量系统模型阐明心衰心律失常机制:Na+ -Ca2+ -Ca2+ /钙调素依赖性蛋白激酶ii -活性氧反馈的作用。
IF 7.9 Q1 Medicine Pub Date : 2019-03-01 Epub Date: 2018-07-17 DOI: 10.1002/wsbm.1434
Stefano Morotti, Eleonora Grandi

Quantitative systems modeling aims to integrate knowledge in different research areas with models describing biological mechanisms and dynamics to gain a better understanding of complex clinical syndromes. Heart failure (HF) is a chronic complex cardiac disease that results from structural or functional disorders impairing the ability of the ventricle to fill with or eject blood. Highly interactive and dynamic changes in mechanical, structural, neurohumoral, metabolic, and electrophysiological properties collectively predispose the failing heart to cardiac arrhythmias, which are responsible for about a half of HF deaths. Multiscale cardiac modeling and simulation integrate structural and functional data from HF experimental models and patients to improve our mechanistic understanding of this complex arrhythmia syndrome. In particular, they allow investigating how disease-induced remodeling alters the coupling of electrophysiology, Ca2+ and Na+ handling, contraction, and energetics that lead to rhythm derangements. The Ca2+ /calmodulin-dependent protein kinase II, which expression and activity are enhanced in HF, emerges as a critical hub that modulates the feedbacks between these various subsystems and promotes arrhythmogenesis. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Mechanistic Models Models of Systems Properties and Processes > Cellular Models Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.

定量系统建模旨在将不同研究领域的知识与描述生物学机制和动力学的模型相结合,以更好地理解复杂的临床综合征。心力衰竭(HF)是一种慢性复杂的心脏疾病,由结构或功能障碍导致心室充血或排出血液的能力受损。机械、结构、神经体液、代谢和电生理特性的高度相互作用和动态变化共同使衰竭的心脏易发生心律失常,而心律失常是HF死亡的一半原因。多尺度心脏建模和模拟整合了心衰实验模型和患者的结构和功能数据,以提高我们对这种复杂心律失常综合征的机制理解。特别是,它们允许研究疾病诱导的重塑如何改变导致节律紊乱的电生理、Ca2+和Na+处理、收缩和能量学的耦合。Ca2+ /钙调素依赖性蛋白激酶II,其表达和活性在心衰中增强,成为调节这些不同子系统之间反馈和促进心律失常的关键枢纽。本文分类如下:生理学>健康和疾病中的哺乳动物生理学系统特性和过程模型>机制模型系统特性和过程模型>细胞模型系统特性和过程模型>器官、组织和生理模型。
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引用次数: 7
The mammalian mycobiome: A complex system in a dynamic relationship with the host. 哺乳动物真菌群系:一个与宿主动态关系的复杂系统。
IF 7.9 Q1 Medicine Pub Date : 2019-01-01 Epub Date: 2018-09-25 DOI: 10.1002/wsbm.1438
Ghee Chuan Lai, Tze Guan Tan, Norman Pavelka

Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise known as the mycobiota, is increasingly recognized as a critical player in the maintenance of health and homeostasis of the host. Here we discuss the impact of the mycobiota on host physiology and disease, the factors influencing mycobiota composition, and the current technologies used for identifying symbiont fungal species. Understanding the tripartite interactions among the host, mycobiota, and other members of the microbiota, will help to guide the development of novel prevention and therapeutic strategies for a variety of human diseases. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Organismal Models.

哺乳动物的屏障表面密集地分布着共生真菌,就像前者被共生细菌定植一样。真菌菌群,也被称为真菌菌群,越来越被认为是维持宿主健康和体内平衡的关键角色。在这里,我们讨论真菌菌群对宿主生理和疾病的影响,影响真菌菌群组成的因素,以及目前用于鉴定共生真菌物种的技术。了解宿主、真菌群和其他微生物群成员之间的三方相互作用,将有助于指导各种人类疾病的新型预防和治疗策略的发展。本文分类如下:生理学>健康和疾病中的哺乳动物生理学实验室方法和技术>遗传/基因组方法系统特性和过程模型>有机体模型。
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引用次数: 56
Computational methods for analyzing and modeling genome structure and organization. 用于分析和建模基因组结构和组织的计算方法。
IF 7.9 Q1 Medicine Pub Date : 2019-01-01 Epub Date: 2018-07-18 DOI: 10.1002/wsbm.1435
Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S Noble

Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.

染色体构象捕获技术的最新进展导致发现了以前未被重视的染色质结构特征。计算分析在检测这些特征方面至关重要,从而有助于揭示基因组结构的构建块。正在开发算法来整合这些结构特征,以构建更好的基因组三维(3D)模型。这些计算方法揭示了三维基因组组织对基本生物过程的重要性。在这篇文章中,我们回顾了分析和建模技术的现状,重点是它们在回答与染色质结构相关的各种生物学问题方面的应用。我们总结了这些计算技术的局限性,并提出了未来的方向,包括在构建更全面的基因组模型时结合多种实验数据来源的重要性。本文分类如下:分析和计算方法>计算方法实验室方法和技术>系统特性和过程的遗传/基因组方法模型>机械模型。
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引用次数: 30
Kinetic models of hematopoietic differentiation. 造血分化动力学模型。
IF 7.9 Q1 Medicine Pub Date : 2019-01-01 Epub Date: 2018-04-16 DOI: 10.1002/wsbm.1424
Victor Olariu, Carsten Peterson

As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. The final goal of these models is to provide experimental predictions, which is now taking on. However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico. Once formulated, kinetic models can be executed in terms of molecular rate equations for concentrations or by stochastic simulations when only a limited number of copies are involved. Developmental processes, in particular those of stem and progenitor cell commitments, are not only topical but also particularly suitable for kinetic modeling due to the finite number of key genes involved in cellular decisions. Stem and progenitor cell commitment processes have been subject to intense experimental studies over the last decade with some emphasis on embryonic and hematopoietic stem cells. Gene and protein interactions governing these processes can be modeled by binary Boolean rules or by continuous-valued models with interactions set by binding strengths. Conceptual insights along with tested predictions have emerged from such kinetic models. Here we review kinetic modeling efforts applied to stem cell developmental systems with focus on hematopoiesis. We highlight the future challenges including multi-scale models integrating cell dynamical and transcriptional models. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Developmental Biology > Stem Cell Biology and Regeneration.

随着细胞和分子生物学变得越来越定量,人们对不同分辨率的机制建模产生了浓厚的兴趣。这些模型主要关注动力学,包括基因和蛋白质的相互作用以及细胞群体动力学。这些模型的最终目标是提供实验性的预测,目前正在进行中。然而,即使没有成熟的预测,动力学模型也可以将多个实验结果压缩成可以解释数据的东西,重要的是,通过在计算机上转动“旋钮”来建议新的实验。一旦形成,动力学模型就可以根据浓度的分子速率方程来执行,或者在只涉及有限数量拷贝的情况下通过随机模拟来执行。发育过程,特别是那些干细胞和祖细胞的承诺,不仅是局部的,而且特别适合于动力学建模,因为参与细胞决策的关键基因数量有限。在过去的十年中,干细胞和祖细胞的承诺过程受到了大量的实验研究,其中一些重点是胚胎和造血干细胞。控制这些过程的基因和蛋白质相互作用可以通过二进制布尔规则或通过结合强度设置相互作用的连续值模型来建模。概念性的见解和经过验证的预测已经从这样的动力学模型中出现。在这里,我们回顾了动力学建模在干细胞发育系统中的应用,重点是造血。我们强调未来的挑战包括整合细胞动力学和转录模型的多尺度模型。本文分类如下:系统特性和过程模型>机制模型发育生物学>干细胞生物学和再生。
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引用次数: 15
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Wiley Interdisciplinary Reviews-Systems Biology and Medicine
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