Wiley Interdisciplinary Reviews-Systems Biology and Medicine最新文献_第3页

Going low to reach high: Small‐scale ChIP‐seq maps new terrain 从低到高:小尺度ChIP - seq绘制新的地形

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-09-03 DOI: 10.1002/wsbm.1465

Madeleine Fosslie, Adeel Manaf, Mads Lerdrup, K. Hansen, G. Gilfillan, J. Dahl

{"title":"Going low to reach high: Small‐scale ChIP‐seq maps new terrain","authors":"Madeleine Fosslie, Adeel Manaf, Mads Lerdrup, K. Hansen, G. Gilfillan, J. Dahl","doi":"10.1002/wsbm.1465","DOIUrl":"https://doi.org/10.1002/wsbm.1465","url":null,"abstract":"Chromatin immunoprecipitation (ChIP) enables mapping of specific histone modifications or chromatin‐associated factors in the genome and represents a powerful tool in the study of chromatin and genome regulation. Importantly, recent technological advances that couple ChIP with whole‐genome high‐throughput sequencing (ChIP‐seq) now allow the mapping of chromatin factors throughout the genome. However, the requirement for large amounts of ChIP‐seq input material has long made it challenging to assess chromatin profiles of cell types only available in limited numbers. For many cell types, it is not feasible to reach high numbers when collecting them as homogeneous cell populations in vivo. Nonetheless, it is an advantage to work with pure cell populations to reach robust biological conclusions. Here, we review (a) how ChIP protocols have been scaled down for use with as little as a few hundred cells; (b) which considerations to be aware of when preparing small‐scale ChIP‐seq and analyzing data; and (c) the potential of small‐scale ChIP‐seq datasets for elucidating chromatin dynamics in various biological systems, including some examples such as oocyte maturation and preimplantation embryo development.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"1 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2019-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89403934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Circadian rhythms and proteomics: It's all about posttranslational modifications! 昼夜节律和蛋白质组学:都是关于翻译后修饰的!

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-09-01 Epub Date: 2019-04-29 DOI: 10.1002/wsbm.1450

Daniel Mauvoisin

{"title":"Circadian rhythms and proteomics: It's all about posttranslational modifications!","authors":"Daniel Mauvoisin","doi":"10.1002/wsbm.1450","DOIUrl":"https://doi.org/10.1002/wsbm.1450","url":null,"abstract":"The circadian clock is a molecular endogenous timekeeping system and allows organisms to adjust their physiology and behavior to the geophysical time. Organized hierarchically, the master clock in the suprachiasmatic nuclei, coordinates peripheral clocks, via direct, or indirect signals. In peripheral organs, such as the liver, the circadian clock coordinates gene expression, notably metabolic gene expression, from transcriptional to posttranslational level. The metabolism in return feeds back on the molecular circadian clock via posttranslational-based mechanisms. During the last two decades, circadian gene expression studies have mostly been relying primarily on genomics or transcriptomics approaches and transcriptome analyses of multiple organs/tissues have revealed that the majority of protein-coding genes display circadian rhythms in a tissue specific manner. More recently, new advances in mass spectrometry offered circadian proteomics new perspectives, that is, the possibilities of performing large scale proteomic studies at cellular and subcellular levels, but also at the posttranslational modification level. With important implications in metabolic health, cell signaling has been shown to be highly relevant to circadian rhythms. Moreover, comprehensive characterization studies of posttranslational modifications are emerging and as a result, cell signaling processes are expected to be more deeply characterized and understood in the coming years with the use of proteomics. This review summarizes the work studying diurnally rhythmic or circadian gene expression performed at the protein level. Based on the knowledge brought by circadian proteomics studies, this review will also discuss the role of posttranslational modification events as an important link between the molecular circadian clock and metabolic regulation. This article is categorized under: Laboratory Methods and Technologies > Proteomics Methods Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Signaling.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 5","pages":"e1450"},"PeriodicalIF":7.9,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1450","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37192184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 23

MRI in systems medicine 磁共振成像在系统医学中的应用

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-07-31 DOI: 10.1002/wsbm.1463

Thomas T. Liu

引用次数: 6

Models of polymer physics for the architecture of the cell nucleus. 细胞核结构的聚合物物理模型。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-07-01 Epub Date: 2018-12-19 DOI: 10.1002/wsbm.1444

Andrea Esposito, Carlo Annunziatella, Simona Bianco, Andrea M Chiariello, Luca Fiorillo, Mario Nicodemi

引用次数: 13

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

Wiley Interdisciplinary Reviews-Systems Biology and 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

{"title":"Towards multiscale modeling of the CD8+ T cell response to viral infections.","authors":"Subhasish Baral, Rubesh Raja, Pramita Sen, Narendra M Dixit","doi":"10.1002/wsbm.1446","DOIUrl":"10.1002/wsbm.1446","url":null,"abstract":"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.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 4","pages":"e1446"},"PeriodicalIF":7.9,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0d/f0/WSBM-11-na.PMC6614031.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37003738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Systems biology of robustness and homeostatic mechanisms. 鲁棒性和稳态机制的系统生物学。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and 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

{"title":"Systems biology of robustness and homeostatic mechanisms.","authors":"H Frederik Nijhout, Janet A Best, Michael C Reed","doi":"10.1002/wsbm.1440","DOIUrl":"https://doi.org/10.1002/wsbm.1440","url":null,"abstract":"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.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 3","pages":"e1440"},"PeriodicalIF":7.9,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1440","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36670870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Wiley Interdisciplinary Reviews-Systems Biology and 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

{"title":"Chromatin imaging and new technologies for imaging the nucleome.","authors":"Nicole A Szydlowski, Jane S Go, Ying S Hu","doi":"10.1002/wsbm.1442","DOIUrl":"https://doi.org/10.1002/wsbm.1442","url":null,"abstract":"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.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 3","pages":"e1442"},"PeriodicalIF":7.9,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1442","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36701202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

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

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-03-01 Epub Date: 2018-09-26 DOI: 10.1002/wsbm.1437

Inez Lam, Christina M Pickering, Feilim Mac Gabhann

{"title":"Context-dependent regulation of receptor tyrosine kinases: Insights from systems biology approaches.","authors":"Inez Lam, Christina M Pickering, Feilim Mac Gabhann","doi":"10.1002/wsbm.1437","DOIUrl":"10.1002/wsbm.1437","url":null,"abstract":"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.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 2","pages":"e1437"},"PeriodicalIF":7.9,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537588/pdf/nihms-986528.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10379417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical modeling of circadian rhythms. 昼夜节律的数学模型。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-03-01 Epub Date: 2018-10-17 DOI: 10.1002/wsbm.1439

Ameneh Asgari-Targhi, Elizabeth B Klerman

{"title":"Mathematical modeling of circadian rhythms.","authors":"Ameneh Asgari-Targhi, Elizabeth B Klerman","doi":"10.1002/wsbm.1439","DOIUrl":"10.1002/wsbm.1439","url":null,"abstract":"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.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":" ","pages":"e1439"},"PeriodicalIF":7.9,"publicationDate":"2019-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375788/pdf/nihms-991117.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36582140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-01-01 Epub Date: 2018-09-25 DOI: 10.1002/wsbm.1438

Ghee Chuan Lai, Tze Guan Tan, Norman Pavelka

引用次数: 56