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From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems 从单细胞到空间多组学：揭示动态异构系统中的分子机制。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-08-09 DOI: 10.1016/j.copbio.2024.103174
Ruonan Wu, Marija Veličković, Kristin E Burnum-Johnson
{"title":"From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems","authors":"Ruonan Wu,&nbsp;Marija Veličković,&nbsp;Kristin E Burnum-Johnson","doi":"10.1016/j.copbio.2024.103174","DOIUrl":"10.1016/j.copbio.2024.103174","url":null,"abstract":"<div><p>Single-cell multi-omics and spatial technology have been widely applied to biomedical studies and recently to environmental studies. The cell size detected by single-cell omics ranges from ∼2 µm (e.g., <em>Bacillus subtilis</em>) to ∼120 µm (e.g., human oocytes). Simultaneous detection of single-cell multi-omics is available to human and plant tissues while limited to microbial samples. Spatial technology enables mapping the detected biomolecules <em>in situ</em>. The recent advances in Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging and Micro/Nanodroplet Processing in One Pot for Trace Samples for the first time allow the application of spatial multi-omics in highly heterogeneous environmental samples composed of plants, fungi, and bacteria. We envision that these technologies will continue to advance our understanding of unique cell types, their developmental trajectory, and the intercellular signaling and interaction within biological samples.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Generative artificial intelligence for small molecule drug design 用于小分子药物设计的生成人工智能。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-08-05 DOI: 10.1016/j.copbio.2024.103175
Ganesh Chandan Kanakala , Sriram Devata , Prathit Chatterjee, Udaykumar Deva Priyakumar
{"title":"Generative artificial intelligence for small molecule drug design","authors":"Ganesh Chandan Kanakala ,&nbsp;Sriram Devata ,&nbsp;Prathit Chatterjee,&nbsp;Udaykumar Deva Priyakumar","doi":"10.1016/j.copbio.2024.103175","DOIUrl":"10.1016/j.copbio.2024.103175","url":null,"abstract":"<div><p>In recent years, the rapid advancement of generative artificial intelligence (GenAI) has revolutionized the landscape of drug design, offering innovative solutions to potentially expedite the discovery of novel therapeutics. GenAI encompasses algorithms and models that autonomously create new data, including text, images, and molecules, often mirroring characteristics of existing datasets. This comprehensive review delves into the realm of GenAI for drug design, emphasizing recent advancements and methodologies that have propelled the field forward. Specifically, we focus on three prominent paradigms: transformers, diffusion models, and reinforcement learning algorithms, which have been exceptionally impactful in the last few years. By synthesizing insights from a myriad of studies and developments, we elucidate the potential of these approaches in accelerating the drug discovery process. Through a detailed analysis, we explore the current state and future directions of GenAI in the context of drug design, highlighting its transformative impact on pharmaceutical research and development.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
De novo domestication in the Solanaceae: advances and challenges 茄科植物的新驯化：进展与挑战。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-08-05 DOI: 10.1016/j.copbio.2024.103177
Karla Gasparini , Yuri G Figueiredo , Wagner L Araújo , Lázaro EP Peres , Agustin Zsögön
{"title":"De novo domestication in the Solanaceae: advances and challenges","authors":"Karla Gasparini ,&nbsp;Yuri G Figueiredo ,&nbsp;Wagner L Araújo ,&nbsp;Lázaro EP Peres ,&nbsp;Agustin Zsögön","doi":"10.1016/j.copbio.2024.103177","DOIUrl":"10.1016/j.copbio.2024.103177","url":null,"abstract":"<div><p>The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. <em>De novo</em> domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biomanufacturing of value-added chemicals from lignin 利用木质素生物制造增值化学品。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-08-03 DOI: 10.1016/j.copbio.2024.103178
Arren Liu , Dylan Ellis , Apurv Mhatre , Sumant Brahmankar , Jong Seto , David R Nielsen , Arul M. Varman
{"title":"Biomanufacturing of value-added chemicals from lignin","authors":"Arren Liu ,&nbsp;Dylan Ellis ,&nbsp;Apurv Mhatre ,&nbsp;Sumant Brahmankar ,&nbsp;Jong Seto ,&nbsp;David R Nielsen ,&nbsp;Arul M. Varman","doi":"10.1016/j.copbio.2024.103178","DOIUrl":"10.1016/j.copbio.2024.103178","url":null,"abstract":"<div><p>Lignin valorization faces persistent biomanufacturing challenges due to the heterogeneous and toxic carbon substrates derived from lignin depolymerization. To address the heterogeneous nature of aromatic feedstocks, plant cell wall engineering and ‘lignin first’ pretreatment methods have recently emerged. Next, to convert the resulting aromatic substrates into value-added chemicals, diverse microbial host systems also continue to be developed. This includes microbes that (1) lack aromatic metabolism, (2) metabolize aromatics but not sugars, and (3) co-metabolize both aromatics and sugars, each system presenting unique pros and cons. Considering the intrinsic complexity of lignin-derived substrate mixtures, emerging and non-model microbes with native metabolism for aromatics appear poised to provide the greatest impacts on lignin valorization via biomanufacturing.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","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 yeast synthetic biology for human G protein–coupled receptor biology and pharmacology 酵母合成生物学在人类 G 蛋白偶联受体生物学和药理学方面的进展。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-08-01 DOI: 10.1016/j.copbio.2024.103176
Nicholas J Kapolka , Geoffrey J Taghon , Daniel G Isom
{"title":"Advances in yeast synthetic biology for human G protein–coupled receptor biology and pharmacology","authors":"Nicholas J Kapolka ,&nbsp;Geoffrey J Taghon ,&nbsp;Daniel G Isom","doi":"10.1016/j.copbio.2024.103176","DOIUrl":"10.1016/j.copbio.2024.103176","url":null,"abstract":"<div><p>G protein–coupled receptors (GPCRs) are the largest family of transmembrane receptors in humans. Over 800 GPCRs regulate the (patho)biology of every organ, tissue, and cell type. Consequently, GPCRs are the most prominent therapeutic targets in medicine. Although over 30% of current U.S. Food and Drug Administration-approved drugs target GPCR signaling, most receptors remain understudied and therapeutically underutilized. Challenges include an incomplete understanding of GPCR signaling, pharmacology, structural biology, and the multiplicity of endogenous GPCR ligands, in addition to a scarcity of biological and pharmacological tools for elucidating GPCR-mediated cellular processes beyond initial signaling events. Various mammalian, insect, and yeast cell models currently address some of these needs. Here, we review recent advances in yeast synthetic biology that are helping to catalyze new and unexpected conceptual and technical breakthroughs in GPCR-based medicine and biotechnology.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advancing environmental biotechnology with microbial community modeling rooted in functional ‘omics 利用植根于功能 "omics "的微生物群落建模推动环境生物技术的发展
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-07-20 DOI: 10.1016/j.copbio.2024.103165
Pranav Sampara , Christopher E Lawson , Matthew J Scarborough , Ryan M Ziels
{"title":"Advancing environmental biotechnology with microbial community modeling rooted in functional ‘omics","authors":"Pranav Sampara ,&nbsp;Christopher E Lawson ,&nbsp;Matthew J Scarborough ,&nbsp;Ryan M Ziels","doi":"10.1016/j.copbio.2024.103165","DOIUrl":"10.1016/j.copbio.2024.103165","url":null,"abstract":"<div><p>Emerging biotechnologies that solve pressing environmental and climate emergencies will require harnessing the vast functional diversity of the underlying microbiomes driving such engineered processes. Modeling is a critical aspect of process engineering that informs system design as well as aids diagnostic optimization of performance. ‘Conventional’ bioprocess models assume homogenous biomass within functional guilds and thus fail to predict emergent properties of diverse microbial physiologies, such as product specificity and community interactions. Yet, recent advances in functional ‘omics-based approaches can provide a ‘lens’ through which we can probe and measure <em>in situ</em> ecophysiologies of environmental microbiomes. Here, we overview microbial community modeling approaches that incorporate functional ‘omics data, which we posit can advance our ability to design and control new environmental biotechnologies going forward.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanistic and data-driven modeling of carbon respiration with bio-electrochemical sensors 利用生物电化学传感器建立碳呼吸的机理和数据驱动模型
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-07-20 DOI: 10.1016/j.copbio.2024.103173
Rishabh Puri , Seyed A Emaminejad , Roland D Cusick
{"title":"Mechanistic and data-driven modeling of carbon respiration with bio-electrochemical sensors","authors":"Rishabh Puri ,&nbsp;Seyed A Emaminejad ,&nbsp;Roland D Cusick","doi":"10.1016/j.copbio.2024.103173","DOIUrl":"10.1016/j.copbio.2024.103173","url":null,"abstract":"<div><p>Bioelectrochemical sensor (BES) technologies have been developed to measure soluble carbon concentrations in wastewater. However, architectures and analytical methods developed in controlled laboratory environments fail to predict BES behavior during field deployments at water resource recovery facilities (WRRFs). Here, we examine the possibilities and obstacles associated with integrating BESs into environmental sensing networks and machine learning algorithms to monitor the biodegradable carbon dynamics and microbial metabolism at WRRFs. This approach highlights the potential of BESs to provide real-time insights into full-scale biodegradable carbon consumption across WRRFs.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0958166924001095/pdfft?md5=cc786865a004b1011d3266ae775abc7a&pid=1-s2.0-S0958166924001095-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Roots of synthetic ecology: microbes that foster plant resilience in the changing climate 合成生态学的根基：微生物促进植物在不断变化的气候中的恢复能力
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-07-18 DOI: 10.1016/j.copbio.2024.103172
Ekaterina Kozaeva , Abdul Aziz Eida , Ella F Gunady , Jeffery L Dangl , Jonathan M Conway , Jennifer AN Brophy
{"title":"Roots of synthetic ecology: microbes that foster plant resilience in the changing climate","authors":"Ekaterina Kozaeva ,&nbsp;Abdul Aziz Eida ,&nbsp;Ella F Gunady ,&nbsp;Jeffery L Dangl ,&nbsp;Jonathan M Conway ,&nbsp;Jennifer AN Brophy","doi":"10.1016/j.copbio.2024.103172","DOIUrl":"10.1016/j.copbio.2024.103172","url":null,"abstract":"<div><p>Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant–microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Single-cell protein: overcoming technological and biological challenges towards improved industrialization 单细胞蛋白质：克服技术和生物学挑战，提高产业化水平
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-07-17 DOI: 10.1016/j.copbio.2024.103171
Lijuan Ye , Biljana Bogicevic , Christoph J Bolten , Christoph Wittmann
{"title":"Single-cell protein: overcoming technological and biological challenges towards improved industrialization","authors":"Lijuan Ye ,&nbsp;Biljana Bogicevic ,&nbsp;Christoph J Bolten ,&nbsp;Christoph Wittmann","doi":"10.1016/j.copbio.2024.103171","DOIUrl":"10.1016/j.copbio.2024.103171","url":null,"abstract":"<div><p>The commercialization of single-cell protein (SCP) obtained from microbial fermentation in large-scale bioreactors emerged almost 50 years ago, with Pruteen marketed as animal feed in the 1970s and Quorn®, released for human nutrition in 1985. SCP holds great promises to feed the meanwhile doubled world population in a sustainable way, but its application is still limited by price and availability on scale. There is a need to optimize the underlying manufacturing processes with enhanced affordability and productivity. From the industrial perspective, it is crucial to identify key process components and prioritize innovations that best promote cost efficiency and large-scale production. Here, we present the state-of-art in SCP manufacturing and provide a comprehensive insight into recent techno-economic analyses and life-cycle assessments of different production scenarios. Thereby, we identified the most influential technical hotspots and challenges for each of the main production scenarios and evaluated the technological opportunities to overcome them.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0958166924001071/pdfft?md5=9ad613124efdfa74477e248a7aeb6e84&pid=1-s2.0-S0958166924001071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bacterial degradation of perfluoroalkyl acids 细菌降解全氟烷基酸
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2024-07-16 DOI: 10.1016/j.copbio.2024.103170
Chiara M Smorada, Matthew W Sima, Peter R Jaffé
{"title":"Bacterial degradation of perfluoroalkyl acids","authors":"Chiara M Smorada,&nbsp;Matthew W Sima,&nbsp;Peter R Jaffé","doi":"10.1016/j.copbio.2024.103170","DOIUrl":"10.1016/j.copbio.2024.103170","url":null,"abstract":"<div><p>Advances in biological degradation of per- and polyfluoroalkyl substances (PFAS) have shown that bioremediation is a promising method of PFAS mineralization; however, most of these studies focus on remediation of more reactive polyfluorinated compounds. This review focuses on the defluorination of the more recalcitrant perfluorinated alkyl acids (PFAAs) by bacteria. We highlight key studies that report PFAA degradation products, specific bacteria, and relevant genes. Among these studies, we discuss trends in anaerobic versus aerobic conditions with specific bacterial species or consortia. This holistic review seeks to elucidate the state of PFAA biodegradation research and discuss the need for future research for environmental application.</p></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S095816692400106X/pdfft?md5=492d2cd8d8e96c88d48cfdf2c57b25af&pid=1-s2.0-S095816692400106X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141623587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","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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