Wiley Interdisciplinary Reviews-Systems Biology and Medicine最新文献_第6页

Committing the primordial germ cell: An updated molecular perspective. 提交原始生殖细胞:一个更新的分子视角。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-01-01 Epub Date: 2018-09-17 DOI: 10.1002/wsbm.1436

Haihan Tan, Wee-Wei Tee

{"title":"Committing the primordial germ cell: An updated molecular perspective.","authors":"Haihan Tan, Wee-Wei Tee","doi":"10.1002/wsbm.1436","DOIUrl":"https://doi.org/10.1002/wsbm.1436","url":null,"abstract":"The germ line is a crucial cell lineage that is distinct from somatic cells, and solely responsible for the trans-generational transmission of hereditary information in metazoan sexual reproduction. Primordial germ cells (PGCs)-the precursors to functional germ cells-are among the first cell types to be allocated in embryonic development, and this lineage commitment is a critical event in partitioning germ line and somatic tissues. Classically, mammalian PGC development has been largely informed by investigations on mouse embryos and embryonic stem cells. Recent findings from corresponding nonrodent systems, however, have indicated that murine PGC specification may not be fully archetypal. In this review, we outline the current understanding of molecular mechanisms in PGC specification, emphasizing key transcriptional events, and focus on salient differences between early human and mouse PGC commitment. Beyond these latest findings, we also contemplate the future outlook of inquiries in this field, highlighting the importance of comprehensively understanding early fate decisions that underlie the segregation of this unique lineage. This article is categorized under: Developmental Biology > Stem Cell Biology and Regeneration Biological Mechanisms > Cell Fates Physiology > Mammalian Physiology in Health and Disease.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 1","pages":"e1436"},"PeriodicalIF":7.9,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1436","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36500930","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: 17

The mechanistic basis for chromatin regulation by pioneer transcription factors. 先驱转录因子调控染色质的机制基础。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2019-01-01 Epub Date: 2018-06-27 DOI: 10.1002/wsbm.1427

Makiko Iwafuchi-Doi

{"title":"The mechanistic basis for chromatin regulation by pioneer transcription factors.","authors":"Makiko Iwafuchi-Doi","doi":"10.1002/wsbm.1427","DOIUrl":"https://doi.org/10.1002/wsbm.1427","url":null,"abstract":"Pioneer transcription factors play a primary role in establishing competence for gene expression and initiating cellular programming and reprogramming, and their dysregulation causes severe effects on human health, such as promoting tumorigenesis. Although more than 200 transcription factors are expressed in each cell type, only a small number of transcription factors are necessary to elicit dramatic cell-fate changes in embryonic development and cell-fate conversion. Among these key transcription factors, a subset called \"pioneer transcription factors\" have a remarkable ability to target nucleosomal DNA, or closed chromatin, early in development, often leading to the local opening of chromatin, thereby establishing competence for gene expression. Although more key transcription factors have been identified as pioneer transcription factors, the molecular mechanisms behind their special properties are only beginning to be revealed. Understanding the pioneering mechanisms will enhance our ability to precisely control cell fate at will for research and therapeutic purposes. This article is categorized under: Biological Mechanisms > Cell Fates Biological Mechanisms > Regulatory Biology Developmental Biology > Lineages.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"11 1","pages":"e1427"},"PeriodicalIF":7.9,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1427","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36262769","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: 58

Cell cycle regulation of folate-mediated one-carbon metabolism. 叶酸介导的单碳代谢的细胞周期调控。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-11-01 Epub Date: 2018-06-11 DOI: 10.1002/wsbm.1426

Xu Lan, Martha S Field, Patrick J Stover

引用次数: 0

Computational anatomy and diffeomorphometry: A dynamical systems model of neuroanatomy in the soft condensed matter continuum. 计算解剖学和微分形态学:软凝聚态连续体中神经解剖学的动力系统模型。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-11-01 Epub Date: 2018-06-04 DOI: 10.1002/wsbm.1425

Michael I Miller, Sylvain Arguillère, Daniel J Tward, Laurent Younes

{"title":"Computational anatomy and diffeomorphometry: A dynamical systems model of neuroanatomy in the soft condensed matter continuum.","authors":"Michael I Miller, Sylvain Arguillère, Daniel J Tward, Laurent Younes","doi":"10.1002/wsbm.1425","DOIUrl":"https://doi.org/10.1002/wsbm.1425","url":null,"abstract":"The nonlinear systems models of computational anatomy that have emerged over the past several decades are a synthesis of three significant areas of computational science and biological modeling. First is the algebraic model of biological shape as a Riemannian orbit, a set of objects under diffeomorphic action. Second is the embedding of anatomical shapes into the soft condensed matter physics continuum via the extension of the Euler equations to geodesic, smooth flows with inverses, encoding divergence for the compressibility of atrophy and expansion of growth. Third, is making human shape and form a metrizable space via geodesic connections of coordinate systems. These three themes place our formalism into the modern data science world of personalized medicine supporting inference of high-dimensional anatomical phenotypes for studying neurodegeneration and neurodevelopment. The dynamical systems model of growth and atrophy that emerges is one which is organized in terms of forces, accelerations, velocities, and displacements, with the associated Hamiltonian momentum and the diffeomorphic flow acting as the state, and the smooth vector field the control. The forces that enter the model derive from external measurements through which the dynamical system must flow, and the internal potential energies of structures making up the soft condensed matter. We examine numerous examples on growth and atrophy. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Imaging Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 6","pages":"e1425"},"PeriodicalIF":7.9,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1425","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36189906","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: 7

Systems approaches to optimizing deep brain stimulation therapies in Parkinson's disease. 优化帕金森病深部脑刺激疗法的系统方法。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-09-01 DOI: 10.1002/wsbm.1421

Sabato Santaniello, John T Gale, Sridevi V Sarma

{"title":"Systems approaches to optimizing deep brain stimulation therapies in Parkinson's disease.","authors":"Sabato Santaniello, John T Gale, Sridevi V Sarma","doi":"10.1002/wsbm.1421","DOIUrl":"https://doi.org/10.1002/wsbm.1421","url":null,"abstract":"Over the last 30 years, deep brain stimulation (DBS) has been used to treat chronic neurological diseases like dystonia, obsessive-compulsive disorders, essential tremor, Parkinson's disease, and more recently, dementias, depression, cognitive disorders, and epilepsy. Despite its wide use, DBS presents numerous challenges for both clinicians and engineers. One challenge is the design of novel, more efficient DBS therapies, which are hampered by the lack of complete understanding about the cellular mechanisms of therapeutic DBS. Another challenge is the existence of redundancy in clinical outcomes, that is, different DBS programs can result in similar clinical benefits but very little information (e.g., predictive models, longitudinal data, metrics, etc.) is available to select one program over another. Finally, there is high variability in patients' responses to DBS, which forces clinicians to carefully adjust the stimulation settings to each patient via lengthy programming sessions. Researchers in neural engineering and systems biology have been tackling these challenges over the past few years with the specific goal of developing novel DBS therapies, design methodologies, and computational tools that optimize the therapeutic effects of DBS in each patient. Furthermore, efforts are being made to automatically adapt the DBS treatment to the fluctuations of disease symptoms. A review of the quantitative approaches currently available for the treatment of Parkinson's disease is presented here with an emphasis on the contributions that systems theoretical approaches have provided to understand the global dynamics of complex neuronal circuits in the brain under DBS. This article is categorized under: Translational, Genomic, and Systems Medicine > Therapeutic Methods Analytical and Computational Methods > Computational Methods Analytical and Computational Methods > Dynamical Methods Physiology > Mammalian Physiology in Health and Disease.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 5","pages":"e1421"},"PeriodicalIF":7.9,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1421","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9092286","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: 19

Mechanisms of Wnt signaling and control. Wnt信号和控制的机制。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-09-01 DOI: 10.1002/wsbm.1422

Stephanie Grainger, Karl Willert

{"title":"Mechanisms of Wnt signaling and control.","authors":"Stephanie Grainger, Karl Willert","doi":"10.1002/wsbm.1422","DOIUrl":"https://doi.org/10.1002/wsbm.1422","url":null,"abstract":"The Wnt signaling pathway is a highly conserved system that regulates complex biological processes across all metazoan species. At the cellular level, secreted Wnt proteins serve to break symmetry and provide cells with positional information that is critical to the patterning of the entire body plan. At the organismal level, Wnt signals are employed to orchestrate fundamental developmental processes, including the specification of the anterior-posterior body axis, induction of the primitive streak and ensuing gastrulation movements, and the generation of cell and tissue diversity. Wnt functions extend into adulthood where they regulate stem cell behavior, tissue homeostasis, and damage repair. Disruption of Wnt signaling activity during embryonic development or in adults results in a spectrum of abnormalities and diseases, including cancer. The molecular mechanisms that underlie the myriad of Wnt-regulated biological effects have been the subject of intense research for over three decades. This review is intended to summarize our current understanding of how Wnt signals are generated and interpreted. This article is categorized under: Biological Mechanisms > Cell Signaling Developmental Biology > Stem Cell Biology and Regeneration.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 5","pages":"e1422"},"PeriodicalIF":7.9,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1422","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9076452","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: 69

Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. 转录因子-DNA相互作用的多样化和基因调控网络的进化。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-09-01 Epub Date: 2018-04-25 DOI: 10.1002/wsbm.1423

Julia M Rogers, Martha L Bulyk

{"title":"Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks.","authors":"Julia M Rogers, Martha L Bulyk","doi":"10.1002/wsbm.1423","DOIUrl":"10.1002/wsbm.1423","url":null,"abstract":"Sequence-specific transcription factors (TFs) bind short DNA sequences in the genome to regulate the expression of target genes. In the last decade, numerous technical advances have enabled the determination of the DNA-binding specificities of many of these factors. Large-scale screens of many TFs enabled the creation of databases of TF DNA-binding specificities, typically represented as position weight matrices (PWMs). Although great progress has been made in determining and predicting binding specificities systematically, there are still many surprises to be found when studying a particular TF's interactions with DNA in detail. Paralogous TFs' binding specificities can differ in subtle ways, in a manner that is not immediately apparent from looking at their PWMs. These differences affect gene regulatory outputs and enable TFs to rewire transcriptional networks over evolutionary time. This review discusses recent observations made in the study of TF-DNA interactions that highlight the importance of continued in-depth analysis of TF-DNA interactions and their inherent complexity. This article is categorized under: Biological Mechanisms > Regulatory Biology.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 5","pages":"e1423"},"PeriodicalIF":7.9,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6202284/pdf/nihms954947.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9092282","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

PharmGKB: A worldwide resource for pharmacogenomic information. PharmGKB：全球药物基因组学信息资源。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-07-01 Epub Date: 2018-02-23 DOI: 10.1002/wsbm.1417

Julia M Barbarino, Michelle Whirl-Carrillo, Russ B Altman, Teri E Klein

引用次数: 0

Multiscale systems biology of trauma-induced coagulopathy. 创伤性凝血病的多尺度系统生物学。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-07-01 Epub Date: 2018-02-27 DOI: 10.1002/wsbm.1418

Evan Tsiklidis, Carrie Sims, Talid Sinno, Scott L Diamond

{"title":"Multiscale systems biology of trauma-induced coagulopathy.","authors":"Evan Tsiklidis, Carrie Sims, Talid Sinno, Scott L Diamond","doi":"10.1002/wsbm.1418","DOIUrl":"https://doi.org/10.1002/wsbm.1418","url":null,"abstract":"Trauma with hypovolemic shock is an extreme pathological state that challenges the body to maintain blood pressure and oxygenation in the face of hemorrhagic blood loss. In conjunction with surgical actions and transfusion therapy, survival requires the patient's blood to maintain hemostasis to stop bleeding. The physics of the problem are multiscale: (a) the systemic circulation sets the global blood pressure in response to blood loss and resuscitation therapy, (b) local tissue perfusion is altered by localized vasoregulatory mechanisms and bleeding, and (c) altered blood and vessel biology resulting from the trauma as well as local hemodynamics control the assembly of clotting components at the site of injury. Building upon ongoing modeling efforts to simulate arterial or venous thrombosis in a diseased vasculature, computer simulation of trauma-induced coagulopathy is an emerging approach to understand patient risk and predict response. Despite uncertainties in quantifying the patient's dynamic injury burden, multiscale systems biology may help link blood biochemistry at the molecular level to multiorgan responses in the bleeding patient. As an important goal of systems modeling, establishing early metrics of a patient's high-dimensional trajectory may help guide transfusion therapy or warn of subsequent later stage bleeding or thrombotic risks. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Regulatory Biology Models of Systems Properties and Processes > Mechanistic Models.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 4","pages":"e1418"},"PeriodicalIF":7.9,"publicationDate":"2018-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1418","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35866911","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: 10

Systems analysis of dilated cardiomyopathy in the next generation sequencing era. 下一代测序时代扩张型心肌病的系统分析。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2018-07-01 Epub Date: 2018-02-27 DOI: 10.1002/wsbm.1419

Magdalena Harakalova, Folkert W Asselbergs

{"title":"Systems analysis of dilated cardiomyopathy in the next generation sequencing era.","authors":"Magdalena Harakalova, Folkert W Asselbergs","doi":"10.1002/wsbm.1419","DOIUrl":"https://doi.org/10.1002/wsbm.1419","url":null,"abstract":"Dilated cardiomyopathy (DCM) is a form of severe failure of cardiac muscle caused by a long list of etiologies ranging from myocardial infarction, DNA mutations in cardiac genes, to toxics. Systems analysis integrating next-generation sequencing (NGS)-based omics approaches, such as the sequencing of DNA, RNA, and chromatin, provide valuable insights into DCM mechanisms. The outcome and interpretation of NGS methods can be affected by the localization of cardiac biopsy, level of tissue degradation, and variable ratios of different cell populations, especially in the presence of fibrosis. Heart tissue composition may even differ between sexes, or siblings carrying the same disease causing mutation. Therefore, before planning any experiments, it is important to fully appreciate the complexities of DCM, and the selection of samples suitable for given research question should be an interdisciplinary effort involving clinicians and biologists. The list of NGS omics datasets in DCM to date is short. More studies have to be performed to contribute to public data repositories and facilitate systems analysis. In addition, proper data integration is a difficult task requiring complex computational approaches. Despite these complications, there are multiple promising implications of systems analysis in DCM. By combining various types of datasets, for example, RNA-seq, ChIP-seq, or 4C, deep insights into cardiac biology, and possible biomarkers and treatment targets, can be gained. Systems analysis can also facilitate the annotation of noncoding mutations in cardiac-specific DNA regulatory regions that play a substantial role in maintaining the tissue- and cell-specific transcriptional programs in the heart. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > RNA Methods.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"10 4","pages":"e1419"},"PeriodicalIF":7.9,"publicationDate":"2018-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1419","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35866791","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: 10