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Current Opinion in Systems Biology最新文献

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Advances in engineering genetic circuits for microbial biocontainment 微生物控制工程基因电路的研究进展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-11-04 DOI: 10.1016/j.coisb.2023.100483
Yuefeng Ma , Abhijit Manna , Tae Seok Moon
{"title":"Advances in engineering genetic circuits for microbial biocontainment","authors":"Yuefeng Ma ,&nbsp;Abhijit Manna ,&nbsp;Tae Seok Moon","doi":"10.1016/j.coisb.2023.100483","DOIUrl":"10.1016/j.coisb.2023.100483","url":null,"abstract":"<div><p><span>The development of synthetic biology has resulted in the use of genetically engineered microbes<span> (GEMs), becoming increasingly critical for addressing global issues such as health, food shortage, climate crisis, and environmental pollution. However, GEMs also pose a potential threat to the ecosystem, necessitating the implementation of biocontainment strategies. Synthetic genetic circuits have the potential to provide an additional level of safety and control beyond traditional physical containment measures. The development of biocontainment strategies is ongoing, including the use of kill switches, </span></span>auxotrophy, and stringent response circuits, to control the viability of GEMs. This review discusses the application and future directions of genetic circuits for microbial biocontainment strategies.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100483"},"PeriodicalIF":3.7,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135454736","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
Microbial production of fuels, commodity chemicals, and materials from sustainable sources of carbon and energy 微生物生产的燃料，商品化学品和材料从可持续的碳和能源来源
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-10-31 DOI: 10.1016/j.coisb.2023.100482
Aidan E. Cowan , Sarah H. Klass , Peter H. Winegar , Jay D. Keasling
{"title":"Microbial production of fuels, commodity chemicals, and materials from sustainable sources of carbon and energy","authors":"Aidan E. Cowan ,&nbsp;Sarah H. Klass ,&nbsp;Peter H. Winegar ,&nbsp;Jay D. Keasling","doi":"10.1016/j.coisb.2023.100482","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100482","url":null,"abstract":"<div><p>Anthropogenic carbon emissions are driving rapid changes to the earth's climate, disrupting whole ecosystems and endangering the stability of human society. Innovations in engineered microbial fermentation enable the fossil resource-free production of fuels, commodity chemicals, and materials, thereby reducing the carbon emissions associated with these products. Microorganisms have been engineered to catabolize sustainable sources of carbon and energy (<em>i.e.</em>, plant biomass, plastic waste, and one-carbon feedstocks) and biosynthesize carbon-neutral or carbon-negative products. These engineering efforts exploit and optimize natural biological pathways or generate unnatural pathways which can biosynthesize chemicals that have not yet been accessed using synthetic chemistry. Recent advances in microbial fermentation seek not only to maximize the titer, rate, and yield of desired products, but also to tailor microbial catabolism to utilize inexpensive feedstocks. Ultimately, these advances aim to lower the cost of bioproduction so that microorganism-derived chemicals can be economically competitive with fossil-derived chemicals.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100482"},"PeriodicalIF":3.7,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136571775","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
Shedding light on spatial structure and dynamics in phototrophic biofilms 揭示光养生物膜的空间结构和动态
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-10-06 DOI: 10.1016/j.coisb.2023.100480
Freddy Bunbury, Amanda N. Shelton, Devaki Bhaya
{"title":"Shedding light on spatial structure and dynamics in phototrophic biofilms","authors":"Freddy Bunbury,&nbsp;Amanda N. Shelton,&nbsp;Devaki Bhaya","doi":"10.1016/j.coisb.2023.100480","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100480","url":null,"abstract":"<div><p><span>Microbial phototrophic communities dominated early Earth and thrive to this day, particularly in extreme environments. We focus on the impact of diel oscillations on phototrophic biofilms, especially in hot springs, where oxygenic phototrophs are keystone species that use light energy to fix carbon and often nitrogen. They exhibit photo-motility and stratification, and alter the physicochemical environment by driving O</span><sub>2</sub>, CO<sub>2,</sub><span> and pH oscillations. Omics analyses reveal extensive genomic and functional diversity in biofilms, but linking this to a predictive understanding of their structure and dynamics remains challenging. This can be addressed by better spatiotemporal resolution of microbial interactions, improved tools for building and manipulating synthetic communities, and integration of empirical and theoretical approaches.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100480"},"PeriodicalIF":3.7,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90029760","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
Insertion sequences: Simple mobile elements with rich ecological and evolutionary structures 插入序列：具有丰富生态和进化结构的简单移动元素
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-24 DOI: 10.1016/j.coisb.2023.100481
Yuki Kanai , Saburo Tsuru , Chikara Furusawa
{"title":"Insertion sequences: Simple mobile elements with rich ecological and evolutionary structures","authors":"Yuki Kanai ,&nbsp;Saburo Tsuru ,&nbsp;Chikara Furusawa","doi":"10.1016/j.coisb.2023.100481","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100481","url":null,"abstract":"<div><p><span>Over the past two decades, genome sequencing has uncovered the diversity and distribution of insertion sequences within prokaryotic genomes. However, the complexity of insertion sequence ecology and evolution hinders us from understanding their nature. Recent studies have employed experimental and </span>computational models to study insertion sequences, emphasizing their role in shaping prokaryotic genome structures. Nonetheless, related areas remain with limited understanding, such as the speciation of insertion sequences. We believe that future studies should continue to develop tractable experimental and computational models to advance our understanding of IS ecology and evolution and their influence on the evolution of prokaryotic genomes.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100481"},"PeriodicalIF":3.7,"publicationDate":"2023-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50173552","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
Robustness of microbiome function 微生物组功能的稳健性
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-14 DOI: 10.1016/j.coisb.2023.100479
Kiseok Keith Lee , Yeonwoo Park , Seppe Kuehn
{"title":"Robustness of microbiome function","authors":"Kiseok Keith Lee ,&nbsp;Yeonwoo Park ,&nbsp;Seppe Kuehn","doi":"10.1016/j.coisb.2023.100479","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100479","url":null,"abstract":"<div><p><span>Microbial communities perform metabolic processes that sustain life on Earth and promote human health. Microbial consortia sustain these functions in the face of constant structural and environmental perturbations. How do complex communities robustly sustain their functional properties despite perturbations? Most studies of functional robustness in the </span>microbiome have been limited to biodiversity and functional redundancy, the idea that there are multiple members of the community that can sustain a specific function. Here, we propose that ideas from other complex biological systems may be applied to deepen our understanding of microbiome robustness. By surveying the causes of functional robustness in a variety of biological systems, including proteins and cells, and discussing how they can be applied to the microbiome, we build conceptual and experimental frameworks for understanding the functional robustness of microbial communities. We hope that these insights might help better predict and engineer microbiome function.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100479"},"PeriodicalIF":3.7,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50173551","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
Prophage mediated control of higher order interactions - Insights from multi-level approaches 噬菌体介导的高阶相互作用的控制——来自多层次方法的见解
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 DOI: 10.1016/j.coisb.2023.100469
Carolin C. Wendling
{"title":"Prophage mediated control of higher order interactions - Insights from multi-level approaches","authors":"Carolin C. Wendling","doi":"10.1016/j.coisb.2023.100469","DOIUrl":"10.1016/j.coisb.2023.100469","url":null,"abstract":"<div><p><span>Prophages, latent viral elements residing in </span>bacterial genomes<span> affect bacterial ecology and evolution in diverse ways. Do these prophage-mediated effects extend beyond the prophage-bacterial relationship? Here, I summarize the latest advances exploring how the impacts of prophages are transmitted through multiple levels of biological systems with potential impacts on ecosystem stability and functioning. The diverse effects of prophages on higher-order interactions are context-specific, ranging from contributions to global biogeochemical processes and mutualistic interactions to increased disease severity with negative impacts on ecosystem engineers and potential cascading effects for multiple species. While we have a solid understanding of the mechanisms by which prophages modulate their bacterial hosts at the cellular and population levels, future research may take an integrative approach to quantify their effects in complex ecosystems.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100469"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47770957","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
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
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