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Current Opinion in Systems Biology最新文献

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Sustainable diversity of phage-bacteria systems 噬菌体系统的可持续多样性
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 DOI: 10.1016/j.coisb.2023.100468
Namiko Mitarai, Anastasios Marantos, Kim Sneppen
{"title":"Sustainable diversity of phage-bacteria systems","authors":"Namiko Mitarai,&nbsp;Anastasios Marantos,&nbsp;Kim Sneppen","doi":"10.1016/j.coisb.2023.100468","DOIUrl":"10.1016/j.coisb.2023.100468","url":null,"abstract":"<div><p>Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here, we review some of the known aspects that modulate phage–bacteria interaction in a way that naturally promotes their coexistence. We focus on the modulations that arise from structural, physical, or physiological constraints. We argue they should play roles in many phage–bacteria systems providing sustainable diversity.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100468"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46699023","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: 0
Control of tissue dimensions in the developing neural tube and somites 发育中的神经管和小体组织尺寸的控制
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 DOI: 10.1016/j.coisb.2023.100459
Thomas Minchington , Stefanie Lehr , Anna Kicheva
{"title":"Control of tissue dimensions in the developing neural tube and somites","authors":"Thomas Minchington ,&nbsp;Stefanie Lehr ,&nbsp;Anna Kicheva","doi":"10.1016/j.coisb.2023.100459","DOIUrl":"10.1016/j.coisb.2023.100459","url":null,"abstract":"<div><p>Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100459"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47108392","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: 0
Corrigendum to: Entropy as a measure of variability and stemness in single-cell transcriptomics 勘误表：熵作为单细胞转录组学变异性和干性的衡量标准
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 DOI: 10.1016/j.coisb.2023.100458
Olivier Gandrillon , Mathilde Gaillard , Thibault Espinasse , Nicolas B. Garnier , Charles Dussiaud , Olivier Kosmider , Pierre Sujobert
{"title":"Corrigendum to: Entropy as a measure of variability and stemness in single-cell transcriptomics","authors":"Olivier Gandrillon ,&nbsp;Mathilde Gaillard ,&nbsp;Thibault Espinasse ,&nbsp;Nicolas B. Garnier ,&nbsp;Charles Dussiaud ,&nbsp;Olivier Kosmider ,&nbsp;Pierre Sujobert","doi":"10.1016/j.coisb.2023.100458","DOIUrl":"10.1016/j.coisb.2023.100458","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100458"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44077606","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: 0
Editorial Board Page 编委会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 DOI: 10.1016/S2452-3100(23)00031-8
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(23)00031-8","DOIUrl":"10.1016/S2452-3100(23)00031-8","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100474"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41253448","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: 0
New faces of prokaryotic mobile genetic elements: Guide RNAs link transposition with host defense mechanisms 原核可移动遗传元件的新面孔：引导RNA与宿主防御机制的连接
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-29 DOI: 10.1016/j.coisb.2023.100473
Eugene V. Koonin , Mart Krupovic
{"title":"New faces of prokaryotic mobile genetic elements: Guide RNAs link transposition with host defense mechanisms","authors":"Eugene V. Koonin ,&nbsp;Mart Krupovic","doi":"10.1016/j.coisb.2023.100473","DOIUrl":"10.1016/j.coisb.2023.100473","url":null,"abstract":"<div><p><span><span><span>Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in </span>prokaryotes revealed a novel mechanism, RNA-guided transposition, where a transposon-encoded guide </span>RNA<span><span><span> directs the transposase to a unique site in the host genome. Tn7-like transposons, on multiple occasions, recruited </span>CRISPR systems that lost the capacity to cleave target </span>DNA<span> and instead mediate RNA-guided transposition via CRISPR RNA. Conversely, the abundant transposon-associated, RNA-guided nucleases IscB and TnpB that appear to promote proliferation of IS</span></span></span><em>200</em>/IS<em>605</em> and IS<em>607</em><span> transposons were the likely evolutionary ancestors of type II and type V CRISPR systems, respectively. Thus, RNA-guided target recognition is a major biological phenomenon that connects MGE with host defense mechanisms. More RNA-guided defensive and MGE-associated functionalities are likely to be discovered.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100473"},"PeriodicalIF":3.7,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41166361","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
Evolution of new metabolic pathways and microbial communities 新代谢途径和微生物群落的进化
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-25 DOI: 10.1016/j.coisb.2023.100472
Dan Kehila, Kimberly Tsz Ching Wong, Nobuhiko Tokuriki
{"title":"Evolution of new metabolic pathways and microbial communities","authors":"Dan Kehila,&nbsp;Kimberly Tsz Ching Wong,&nbsp;Nobuhiko Tokuriki","doi":"10.1016/j.coisb.2023.100472","DOIUrl":"10.1016/j.coisb.2023.100472","url":null,"abstract":"<div><p>The evolution of metabolic pathways in microbes is traditionally envisioned to take place within a single organism. The diverse repertoire of enzymes in the microbial community points to another exciting possibility: namely, that new metabolic pathways may evolve in a community setting, where pathway steps are distributed across several strains. The readiness with which microbes form stable relationships to collectively degrade manmade ‘xenobiotic’ pollutants, as evidenced from natural and laboratory-enriched consortia, provides valuable insights into the evolution of enzymes and pathways. Nonetheless, many open questions remain to be addressed. In this review, we consider the key determinants of pathway evolution in microbial communities, drawing from principles of social evolutionary theory in microbes, and also exploring the role of diffusion and horizontal gene transfer.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100472"},"PeriodicalIF":3.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45099772","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: 0
Recent advances in non-model bacterial chassis construction 非模型细菌底盘结构研究进展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-19 DOI: 10.1016/j.coisb.2023.100471
Soonkyu Hwang , Chanyoung Joung , Woori Kim , Bernhard Palsson , Byung-Kwan Cho
{"title":"Recent advances in non-model bacterial chassis construction","authors":"Soonkyu Hwang ,&nbsp;Chanyoung Joung ,&nbsp;Woori Kim ,&nbsp;Bernhard Palsson ,&nbsp;Byung-Kwan Cho","doi":"10.1016/j.coisb.2023.100471","DOIUrl":"10.1016/j.coisb.2023.100471","url":null,"abstract":"<div><p>The development of bacterial chassis to increase productivity and reduce industrial costs in value-added biochemical production has gained significant attention. Current efforts have focused on model bacteria, thus limiting their suitability to produce specialized products. Therefore, there is a growing emphasis on developing specialized non-model bacterial chassis to expand the repertoire of bioproducts. However, the lack of genetic information and tools for non-model bacteria remains challenging. In this review, we categorize and introduce non-model chassis based on their characteristics in relation to the target products. We also provide an overview of the trends in the development of genome-reduced chassis to enhance productivity. Furthermore, we propose synthetic biology technologies that can be applied to a broad range of non-model bacteria.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100471"},"PeriodicalIF":3.7,"publicationDate":"2023-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43537194","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: 1
How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution 微生物在自然界中是如何生长的?种群动态在微生物生态学和进化中的作用
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-09 DOI: 10.1016/j.coisb.2023.100470
Justus Wilhelm Fink , Michael Manhart
{"title":"How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution","authors":"Justus Wilhelm Fink ,&nbsp;Michael Manhart","doi":"10.1016/j.coisb.2023.100470","DOIUrl":"10.1016/j.coisb.2023.100470","url":null,"abstract":"<div><p>The growth of microbial populations in nature is dynamic, as the cellular physiology and environment of these populations change. Population dynamics have wide-ranging consequences for ecology and evolution, determining how species interact and which mutations fix. Understanding these dynamics is also critical for clinical and environmental applications in which we need to promote or inhibit microbial growth<span>. We first address the latest efforts and outstanding challenges in measuring microbial population dynamics in natural environments. We next summarize fundamental concepts and empirical data on how population dynamics both shape and are shaped by evolutionary processes. Finally, we discuss the role of tradeoffs in microbial population dynamics, which may reveal physiological constraints and help to maintain ecological diversity. We find that current evidence for tradeoffs in population dynamics is limited, but that consideration of the evolutionary context of these tradeoffs is necessary for designing future experiments that can better address this problem.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100470"},"PeriodicalIF":3.7,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42046217","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: 1
How prebiotic complexity increases through Darwinian evolution 达尔文进化如何增加益生元的复杂性
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/j.coisb.2023.100456
Kohtoh Yukawa , Ryo Mizuuchi , Norikazu Ichihashi
{"title":"How prebiotic complexity increases through Darwinian evolution","authors":"Kohtoh Yukawa ,&nbsp;Ryo Mizuuchi ,&nbsp;Norikazu Ichihashi","doi":"10.1016/j.coisb.2023.100456","DOIUrl":"10.1016/j.coisb.2023.100456","url":null,"abstract":"<div><p>Present-day life is amazingly diverse and complex owing to Darwinian evolution. Despite the simplicity of the principle of Darwinian evolution, the process and its outcomes are largely unpredictable. Evolutionary simulation and experiments are useful methods for gaining insights into the process and outcomes of Darwinian evolution. In this short review, we discuss recent progress in theoretical and experimental approaches to understanding the possible evolutionary processes of prebiotic self-replicators. We especially focus on research addressing how a prebiotic self-replicator increases complexity through evolution, including our recent experiments, in which a complex replication network consisting of multiple self-replicating molecules spontaneously evolved from a single replicating RNA.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100456"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49417919","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: 0
Editorial Board Page 编辑委员会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/S2452-3100(23)00021-5
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(23)00021-5","DOIUrl":"https://doi.org/10.1016/S2452-3100(23)00021-5","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100464"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50172800","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: 0
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