Current Opinion in Systems Biology最新文献_第5页

Biodegradation of polystyrene and systems biology-based approaches to the development of new biocatalysts for plastic degradation 聚苯乙烯的生物降解和基于系统生物学的塑料降解新生物催化剂开发方法

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-01-12 DOI: 10.1016/j.coisb.2024.100505

Ye-Bin Kim , Seongmin Kim , Chungoo Park , Soo-Jin Yeom

{"title":"Biodegradation of polystyrene and systems biology-based approaches to the development of new biocatalysts for plastic degradation","authors":"Ye-Bin Kim , Seongmin Kim , Chungoo Park , Soo-Jin Yeom","doi":"10.1016/j.coisb.2024.100505","DOIUrl":"10.1016/j.coisb.2024.100505","url":null,"abstract":"<div><p>Plastic waste has become one of the most pressing environmental issues with rapidly increased their production that also has a severe impact on individual species and ecosystem functioning.</p><p>With recycling technologies in place, the waste plastic will become a valuable resource and hence less material will be lost to the environment. In the pursuit of a sustainable approach to the treatment of plastic waste, biological processes<span> have emerged as an eco-friendly method with significant potential. In this review, we summarize previous research on the biodegradation of polystyrene (PS) as major plastics, including a review of the analytical methods used to investigate the plastic biodegradation, the isolation of PS-degrading microbes from various environment, and the identification of potential enzymes<span> for PS biodegradation. Based on this, we propose a potential PS biodegradation pathway, even though the specific biochemical mechanisms<span> associated with certain enzymes have not yet been fully identified. Finally, we discuss how PS-biodegrading enzymes can be identified using a systems biology-based screening approach that combines culture-based genomic and culture-independent metagenomic methods. This strategy can be applied to searching biodegrading enzymes for other plastics.</span></span></span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100505"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139538705","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 : 2024-03-01 Epub 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 , Jinju Lee , Haseong Kim , Dae-Hee Lee , 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":"2024-03-01","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

Dynamics of T-helper cell differentiation and plasticity: How have computational models improved our understanding? T 辅助细胞分化和可塑性的动力学：计算模型如何增进我们的理解？

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-02-16 DOI: 10.1016/j.coisb.2024.100508

Pradyumna Harlapur, Atchuta Srinivas Duddu, Mohit Kumar Jolly

引用次数: 0

Neural signaling in neuropathic pain: A computational modeling perspective 神经病理性疼痛中的神经信号传导：计算建模视角

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-02-08 DOI: 10.1016/j.coisb.2024.100509

Xinyue Ma , Anmar Khadra

{"title":"Neural signaling in neuropathic pain: A computational modeling perspective","authors":"Xinyue Ma , Anmar Khadra","doi":"10.1016/j.coisb.2024.100509","DOIUrl":"10.1016/j.coisb.2024.100509","url":null,"abstract":"<div><p>Neuropathic pain is a complex condition with a huge unmet medical need. Owing to our incomplete understanding of its perplexing pathology, current therapeutic strategies for treating neuropathic pain remain limited in their efficacy. Computational modeling has emerged as a promising methodology in unraveling the intricate neural mechanisms contributing to neuropathic pain. This review serves as a bridge that links traditional experimental research in neuropathic pain to computational neuroscience. We aim to fill in the gap of knowledge between these two fields by introducing the methodology of computational modeling as well as the neurophysiological background for neuropathic pain. We provide examples of recent advances in using computational modeling at the molecular, cellular, and neural network levels to harness the understanding of pain-associated neural signaling. This integration of computational modeling has yielded crucial insights into neuropathic pain pathophysiology, with great potential to inform novel pharmacological and neurostimulation-based treatments for the disease.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100509"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000052/pdfft?md5=d4c0bbd6bb1f98e6ca3144aab1540c86&pid=1-s2.0-S2452310024000052-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139887002","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

Microbial cell factories for bio-based isoprenoid production to replace fossil resources 用于生产生物基异戊二烯以替代化石资源的微生物细胞工厂

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-01-03 DOI: 10.1016/j.coisb.2023.100502

Min-Kyoung Kang , Sang-Hwal Yoon , Moonhyuk Kwon , Seon-Won Kim

{"title":"Microbial cell factories for bio-based isoprenoid production to replace fossil resources","authors":"Min-Kyoung Kang , Sang-Hwal Yoon , Moonhyuk Kwon , Seon-Won Kim","doi":"10.1016/j.coisb.2023.100502","DOIUrl":"10.1016/j.coisb.2023.100502","url":null,"abstract":"<div><p>Concerns about environmental issues and limited fossil resources have increased interest and efforts in developing sustainable production of bio-based chemicals and fuels using microorganisms. Advanced metabolic engineering has developed microbial cell factories (MCFs) with the support of synthetic biology and systems biology. Isoprenoids are one of the largest classes of natural products and possess many practical industrial applications. However, it is challenging to meet the market demand for isoprenoids because of the current inefficient and unsustainable strategies for isoprenoid production such as chemical synthesis and plant extraction. Therefore, many efforts have been made to build isoprenoid-producing MCFs by applying metabolic engineering strategies, biological devices, and machinery from synthetic biology and systems biology. This review introduces recent studies of strain engineering and applications of biological tools and systems for developing isoprenoid MCFs. In addition, we also reviewed the isoprenoid fermentation strategies that lead to the best performance of isoprenoid-producing MCFs.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100502"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139392603","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

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 : 2024-03-01 Epub Date: 2023-11-21 DOI: 10.1016/j.coisb.2023.100488

So Jeong Lee, Dong-Myung Kim

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 : 2024-03-01 Epub Date: 2023-11-13 DOI: 10.1016/j.coisb.2023.100484

Raja Selvakumar, Ishita Kumar, Glory J. Onajobi, Yongjoon Yu, Corey J. Wilson

引用次数: 0

Accelerate acetogenic bioproduction: Acetogens as sustainable producers of biocommodities 加速醋酸生物生产：作为可持续生物商品生产者的产酸菌

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2023-12-12 DOI: 10.1016/j.coisb.2023.100500

Maximilian Flaiz , Diana Z. Sousa

{"title":"Accelerate acetogenic bioproduction: Acetogens as sustainable producers of biocommodities","authors":"Maximilian Flaiz , Diana Z. Sousa","doi":"10.1016/j.coisb.2023.100500","DOIUrl":"10.1016/j.coisb.2023.100500","url":null,"abstract":"<div><p>Gas fermentation using autotrophic acetogenic bacteria has been industrialized, however, its full potential remains untapped, with only native products like ethanol being produced thus far. Advancements in synthetic biology have enabled the recombinant production of diverse biocommodities to broaden their limited natural product spectrum from C1-gases. Additionally, co-culturing acetogens with other microorganisms holds the potential for expanding the product spectrum further. However, commercialization remains challenging due to complex pathway and (co)culturing optimizations. To address this, novel synthetic biology tools, including the use of high throughput biopart screenings using reporter proteins, the deployment of cell-free systems to combine best-performing enzymes, and the identification and elimination of competing pathways, can be employed. Incorporating genetically engineered strains in co-cultures improves dependencies, directs product formation, and increases resilience, enhancing bioproduction efficiency. This review emphasizes using these tools to enhance the recombinant production of biocommodities, offering promising solutions to overcome existing challenges.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100500"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310023000574/pdfft?md5=b34324e70ac5822168b823c24989c3e6&pid=1-s2.0-S2452310023000574-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139024556","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

Capped or uncapped? Techniques to assess the quality of mRNA molecules 有封顶还是无封顶？评估 mRNA 分子质量的技术

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-01-04 DOI: 10.1016/j.coisb.2023.100503

Ying Tu, Akashaditya Das, Chileab Redwood-Sawyerr, Karen M. Polizzi

引用次数: 0

The critical role of co-translational folding: An evolutionary and biophysical perspective 共翻译折叠的关键作用：进化与生物物理视角

IF 3.7

Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2023-11-23 DOI: 10.1016/j.coisb.2023.100485

Amir Bitran , William M. Jacobs , Eugene Shakhnovich

引用次数: 0