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Current Opinion in Systems Biology最新文献

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Lessons from metabolic perturbations in lysosomal storage disorders for neurodegeneration 神经退行性疾病溶酶体贮积障碍的代谢扰动的教训
IF 3.7
Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100408
Uche N. Medoh , Julie Y. Chen , Monther Abu-Remaileh
{"title":"Lessons from metabolic perturbations in lysosomal storage disorders for neurodegeneration","authors":"Uche N. Medoh ,&nbsp;Julie Y. Chen ,&nbsp;Monther Abu-Remaileh","doi":"10.1016/j.coisb.2021.100408","DOIUrl":"10.1016/j.coisb.2021.100408","url":null,"abstract":"<div><p><span>Age-related neurodegenerative diseases are a clinically unmet need with unabated prevalence around the world. Several genetic studies link these diseases with lysosomal dysfunction; however, a mechanistic understanding of how lysosomal perturbations result in neurodegeneration is unclear. Neuronopathic lysosomal storage disorders represent an attractive model for elucidating such mechanisms as they share several metabolic pathological hallmarks with common neurodegenerative diseases. This review explores how altered lipid metabolism, calcium dyshomeostasis, mitochondrial dysfunction, </span>oxidative stress, and impaired autophagic flux contribute to cellular pathobiology in age-related neurodegeneration and neuronopathic lysosomal storage disorders. It further debates whether general lysosomal dysfunction owing to toxic substrate accumulation or extralysosomal nutrient deprivation drives these downstream processes. With increasing evidence for the latter, future studies should investigate additional lysosomal nutrients that protect against neurodegeneration using emerging subcellular ‘omics’-based technologies with the promise of identifying therapeutic targets for the treatment of neurodegenerative diseases.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"29 ","pages":"Article 100408"},"PeriodicalIF":3.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41515878","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: 4
Editorial overview: ‘Mathematical modelling of high-throughput and high-content data’ 编辑概述:“高通量和高含量数据的数学建模”
IF 3.7
Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100405
Jan Hasenauer, Julio R. Banga
{"title":"Editorial overview: ‘Mathematical modelling of high-throughput and high-content data’","authors":"Jan Hasenauer,&nbsp;Julio R. Banga","doi":"10.1016/j.coisb.2021.100405","DOIUrl":"10.1016/j.coisb.2021.100405","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"29 ","pages":"Article 100405"},"PeriodicalIF":3.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43550177","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
Using resource constraints derived from genomic and proteomic data in metabolic network models 利用代谢网络模型中基因组和蛋白质组学数据得出的资源约束
IF 3.7
Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100400
Kobe De Becker , Niccolò Totis , Kristel Bernaerts , Steffen Waldherr
{"title":"Using resource constraints derived from genomic and proteomic data in metabolic network models","authors":"Kobe De Becker ,&nbsp;Niccolò Totis ,&nbsp;Kristel Bernaerts ,&nbsp;Steffen Waldherr","doi":"10.1016/j.coisb.2021.100400","DOIUrl":"10.1016/j.coisb.2021.100400","url":null,"abstract":"<div><p>The increasing amount of available high-content data in genomics, proteomics, and metabolomics has significantly improved the predictive power and model accuracy of genome-scale metabolic network models in recent years. We review recent constraint-based modeling approaches that incorporate genomics and proteomics data to form resource allocation models. Different modeling approaches to build resource allocation models and the related enzyme-constrained genome-scale metabolic models are discussed and evaluated with respect to differences regarding model features. In addition, an overview of the data required to construct, simulate and validate models for the different approaches is given, together with a list of relevant databases.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"29 ","pages":"Article 100400"},"PeriodicalIF":3.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000950/pdfft?md5=2f27b64fda369764a9aea6b24274176c&pid=1-s2.0-S2452310021000950-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43678873","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: 3
The evolution of the metabolic network over long timelines 长时间内代谢网络的进化
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100402
Markus Ralser , Sreejith J. Varma , Richard A. Notebaart
{"title":"The evolution of the metabolic network over long timelines","authors":"Markus Ralser ,&nbsp;Sreejith J. Varma ,&nbsp;Richard A. Notebaart","doi":"10.1016/j.coisb.2021.100402","DOIUrl":"10.1016/j.coisb.2021.100402","url":null,"abstract":"<div><p>Metabolism is executed by an efficient, interconnected and ancient biochemical system, the metabolic network. Its evolutionary origins are, however, barely understood. We here discuss that because of niche adaptation, the evolutionary selection acting on the metabolic network structure distinguishes modern species and early life forms. Yet, its basic structure remained conserved over more than three billion years of diverging evolution. We speculate that this situation attributes key roles in metabolic network evolution to (i) the reaction properties of central metabolites, (ii) simple catalysts (e.g. metal ions, amino acids) whose importance remained unchanged during evolution, and (iii) the interconnectivity of the network that limits its expansion. The conservation of network structure hence implies that early life forms already used similar metabolic reaction topologies as modern species.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100402"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000974/pdfft?md5=4bad2063148f98b62f38ae026e235900&pid=1-s2.0-S2452310021000974-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47343395","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: 3
Experimental tools to reduce the burden of bacterial synthetic biology 实验工具减轻细菌合成生物学负担
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100393
Alice Grob , Roberto Di Blasi , Francesca Ceroni
{"title":"Experimental tools to reduce the burden of bacterial synthetic biology","authors":"Alice Grob ,&nbsp;Roberto Di Blasi ,&nbsp;Francesca Ceroni","doi":"10.1016/j.coisb.2021.100393","DOIUrl":"10.1016/j.coisb.2021.100393","url":null,"abstract":"<div><p>Cellular burden limits the applications of bacterial synthetic biology. Experimental approaches for burden minimisation have recently become available. Tools to identify construct design with low footprint on the host include capacity monitors that quantify cellular capacity, high-throughput approaches and cell-free systems for construct prototyping. Orthogonal ribosomes and feedback controllers are instead useful to seek control of resource allocation and lower burden. Other approaches include genome reduction to increase the available resource pool and synthetic addiction to couple cell fitness and product accumulation. However, controlling the cellular response to exogenous expression is still a challenge, and more tools are needed to widen the applications of synthetic biology. Further effort that combines novel evolutionary data with burden-aware tools can set the foundation to increase the stability and robustness of future genetic systems.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100393"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000883/pdfft?md5=a6f739a545d3dbf5f04da061e5f75ff1&pid=1-s2.0-S2452310021000883-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42350391","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
Convergence and divergence in the metabolic network of Mycobacterium tuberculosis 结核分枝杆菌代谢网络的趋同与分化
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100384
Catherine B. Hubert, Luiz Pedro S. de Carvalho
{"title":"Convergence and divergence in the metabolic network of Mycobacterium tuberculosis","authors":"Catherine B. Hubert,&nbsp;Luiz Pedro S. de Carvalho","doi":"10.1016/j.coisb.2021.100384","DOIUrl":"10.1016/j.coisb.2021.100384","url":null,"abstract":"<div><p><span>Metabolism is still often regarded as a set of canonical reactions, identical in all organisms, yet that is far from correct. Metabolism and the metabolic networks required for cellular functions vary dramatically even within species. This diversity is also present in bacterial pathogens. This mini-review explores the role of metabolic convergence and divergence in shaping the metabolic network of </span><span><em>Mycobacterium tuberculosis</em></span> and its ability to survive in the host. With the help of a few selected examples, we aim to illustrate the magnitude of changes observed in <em>M. tuberculosis</em> metabolic network.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100384"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42467734","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: 3
Adaptive circuits in synthetic biology 合成生物学中的自适应电路
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100399
Timothy Frei, Mustafa Khammash
{"title":"Adaptive circuits in synthetic biology","authors":"Timothy Frei,&nbsp;Mustafa Khammash","doi":"10.1016/j.coisb.2021.100399","DOIUrl":"10.1016/j.coisb.2021.100399","url":null,"abstract":"<div><p>One of the most remarkable features of biological systems is their ability to adapt to the constantly changing environment. By harnessing principles of control theory, synthetic biologists are starting to mimic this adaptation in regulatory gene circuits. Doing so allows for the construction of systems that perform reliably under non-optimal conditions. Furthermore, making a system adaptive can make up for imperfect knowledge of the underlying biology and, hence, avoid unforeseen complications in the implementation. Here, we review recent developments in the analysis and implementation of adaptive regulatory networks in synthetic biology with a particular focus on genetic circuits that can realize perfect adaptation.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100399"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000949/pdfft?md5=4663c6a4dfdd14bb5c0f9f4d6841b62d&pid=1-s2.0-S2452310021000949-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42758680","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
Antibiotic resistance: Insights from evolution experiments and mathematical modeling 抗生素耐药性:来自进化实验和数学模型的见解
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100365
Gabriela Petrungaro , Yuval Mulla , Tobias Bollenbach
{"title":"Antibiotic resistance: Insights from evolution experiments and mathematical modeling","authors":"Gabriela Petrungaro ,&nbsp;Yuval Mulla ,&nbsp;Tobias Bollenbach","doi":"10.1016/j.coisb.2021.100365","DOIUrl":"10.1016/j.coisb.2021.100365","url":null,"abstract":"<div><p><span>Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with next-generation sequencing techniques, laboratory automation, and </span>mathematical modeling are enabling the investigation of resistance development at an unprecedented level of detail. Recent work has directly tracked the intricate stochastic dynamics of bacterial populations in which resistant mutants emerge and compete. In addition, new approaches have enabled measuring how prone a large number of genetically perturbed strains are to evolve resistance. Based on advances in quantitative cell physiology, predictive theoretical models of resistance are increasingly being developed. Taken together, a new strategy for observing, predicting, and ultimately controlling resistance evolution is emerging.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100365"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.coisb.2021.100365","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46490738","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
Synthetic biology-based optogenetic approaches to control therapeutic designer cells 基于合成生物学的光遗传学方法控制治疗设计细胞
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100396
Maysam Mansouri , Martin Fussenegger
{"title":"Synthetic biology-based optogenetic approaches to control therapeutic designer cells","authors":"Maysam Mansouri ,&nbsp;Martin Fussenegger","doi":"10.1016/j.coisb.2021.100396","DOIUrl":"10.1016/j.coisb.2021.100396","url":null,"abstract":"<div><p>Optogenetics uses light as a traceless inducer to remotely control cellular behavior with high safety and spatiotemporal precision, and its implementation for therapeutic synthetic biology enable customizable user-defined remedial outputs to be generated from suitably engineered cells. Here, we focus on non-neural optogenetics, describing the tools and strategies available to engineer light-responsive, therapeutic mammalian designer cells and highlighting recent advances in design and translational applications, including cell and gene therapies. We also discuss current limitations in engineering genetically encoded light-sensitive systems and suggest some possible solutions.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100396"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000913/pdfft?md5=7904dcf7df39ed3f040ba8e89584ddda&pid=1-s2.0-S2452310021000913-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48042013","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: 5
Erratum to “Regarding missing Editorial Disclosure statements in previously published articles” – Part I “关于以前发表的文章中缺少编辑披露声明”的勘误-第一部分
IF 3.7
Current Opinion in Systems Biology Pub Date : 2021-12-01 DOI: 10.1016/j.coisb.2021.100387
{"title":"Erratum to “Regarding missing Editorial Disclosure statements in previously published articles” – Part I","authors":"","doi":"10.1016/j.coisb.2021.100387","DOIUrl":"10.1016/j.coisb.2021.100387","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"28 ","pages":"Article 100387"},"PeriodicalIF":3.7,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021000822/pdfft?md5=54855021c605f6e9a282ea9963bb0b2d&pid=1-s2.0-S2452310021000822-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48205074","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
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