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Current Opinion in Systems Biology最新文献

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Recent development on DNA & genome synthesis DNA 和基因组合成的最新发展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-11-23 DOI: 10.1016/j.coisb.2023.100490
Wenfei Yu , Junbiao Dai , Yingxin Ma
{"title":"Recent development on DNA & genome synthesis","authors":"Wenfei Yu ,&nbsp;Junbiao Dai ,&nbsp;Yingxin Ma","doi":"10.1016/j.coisb.2023.100490","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100490","url":null,"abstract":"<div><p><span>After decades of development, DNA synthesis, assembly, and sequencing technologies have reached a high level, allowing faster and cheaper acquirements of synthetic genes or even </span><em>de novo</em><span> synthesis of an entire genome. Meanwhile, the value of synthetic genomes keeps increasing, and the target organisms have covered viruses, bacteria, and yeast and moved toward higher eukaryotes. However, as the length of genomes moves from kilobase to gigabase, the cost of synthetic genome projects increases sharply and requires years of effort to complete. Therefore, new DNA synthesis technology and a next-generation DNA synthesizer are urgently needed. In this review, we focus mainly on the advances in DNA and genome synthesis and discuss difficulties that need to be addressed in both areas.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100490"},"PeriodicalIF":3.7,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138570495","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
Advancing high-throughput screening systems for synthetic biology and biofoundry 推进合成生物学和生物铸造的高通量筛选系统
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-11-21 DOI: 10.1016/j.coisb.2023.100487
Kil Koang Kwon , Jinju Lee , Haseong Kim , Dae-Hee Lee , Seung-Goo Lee
{"title":"Advancing high-throughput screening systems for synthetic biology and biofoundry","authors":"Kil Koang Kwon ,&nbsp;Jinju Lee ,&nbsp;Haseong Kim ,&nbsp;Dae-Hee Lee ,&nbsp;Seung-Goo Lee","doi":"10.1016/j.coisb.2023.100487","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100487","url":null,"abstract":"<div><p>High-throughput (HT) methodologies are extensively applied in synthetic biology for the rapid enrichment and selection of desired properties from a wide range of genetic diversity. In order to effectively analyze these vast variants, HT tools must offer parallel experiments and compact reaction capabilities to enhance overall throughput. Here, we discuss about various aspects of three representative high-throughput screening (HTS) systems: microwell-, droplet-, and single-cell-based screening. These systems can be categorized based on their reaction volume, which in turn determines the associated technology, machinery, and supporting applications. Furthermore, HT techniques that rapidly connect numerous genotypes and phenotypes have evolved to enhance the precision of predictions through the integration of digital technologies like machine learning and artificial intelligence. The use of advanced HT techniques within biofoundry will enable rapid selection and analysis from extensive genetic diversity, making it a driving force for the advancement of synthetic biology.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100487"},"PeriodicalIF":3.7,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310023000446/pdfft?md5=c79f76a94a5c0e68e948902ca3894d28&pid=1-s2.0-S2452310023000446-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138549932","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
Cell-free synthetic biology: Navigating the new frontiers of biomanufacturing and biological engineering 无细胞合成生物学：开拓生物制造和生物工程的新领域
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-11-21 DOI: 10.1016/j.coisb.2023.100488
So Jeong Lee, Dong-Myung Kim
{"title":"Cell-free synthetic biology: Navigating the new frontiers of biomanufacturing and biological engineering","authors":"So Jeong Lee,&nbsp;Dong-Myung Kim","doi":"10.1016/j.coisb.2023.100488","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100488","url":null,"abstract":"<div><p>Cell-free synthetic biology is swiftly progressing and is poised to revolutionize multiple domains within synthetic biology. By departing from the constraints of living cells, it dramatically expands potential applications, surmounting the intrinsic limitations associated with cellular systems<span>, especially where access to cytosolic conditions poses challenges. The open nature of cell-free systems means their potential applications are vast, limited only by creative imagination. A burgeoning number of studies underline its versatility across a broad spectrum of fields. This review article offers an insight into the recent advancements in this vibrant area, pinpointing key achievements and challenges in arenas such as biomanufacturing, pathway prototyping, and material sciences.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100488"},"PeriodicalIF":3.7,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138570597","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
Engineering living therapeutics and diagnostics: A new frontier in human health 活体治疗和诊断工程：人类健康的新领域
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-11-13 DOI: 10.1016/j.coisb.2023.100484
Raja Selvakumar, Ishita Kumar, Glory J. Onajobi, Yongjoon Yu, Corey J. Wilson
{"title":"Engineering living therapeutics and diagnostics: A new frontier in human health","authors":"Raja Selvakumar,&nbsp;Ishita Kumar,&nbsp;Glory J. Onajobi,&nbsp;Yongjoon Yu,&nbsp;Corey J. Wilson","doi":"10.1016/j.coisb.2023.100484","DOIUrl":"10.1016/j.coisb.2023.100484","url":null,"abstract":"<div><p>Traditional therapeutics aim to diagnose, treat, and cure diseases through various synthetic and natural approaches. The emerging field of engineered living therapeutics (ELTs) genetically functionalizes living cells to alter the paradigm of designed solutions. In this review, we focus on ELTs derived from microbial cell scaffolds. We propose three synergistic modalities for the rational design of ELTs: first, use of regulatory operations to regulate genetic expression; second, integration of alternative biosensing inputs for directed application; third, choice of microbial chassis to deliver solutions. We highlight the challenges and future opportunities within each group and conclude by providing a prospective outlook for ELTs.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100484"},"PeriodicalIF":3.7,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135715588","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
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
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