Trends in biotechnology最新文献_第4页

Driving the future of proteome-based innovations: the π-HuB project. 推动蛋白质组创新的未来：π-HuB项目。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-10-01 Epub Date: 2026-07-27 DOI: 10.1016/j.tibtech.2026.07.009

Wilson Wen Bin Goh, Cheng Chang, Hui Peng, Linhai Xie, Fuchu He

引用次数: 0

Leveraging large language models for metabolic engineering design. 利用大型语言模型进行代谢工程设计。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-10-01 Epub Date: 2026-04-23 DOI: 10.1016/j.tibtech.2026.03.026

Xiongwen Li, Zhetao Guo, Yi Li, Zhu Liang, Ziyi Liu, Ke Wu, Jiahao Luo, Yuesheng Zhang, Lizheng Liu, Manda Sun, Yuanyuan Huang, Yu Chen, Tao Yu, Jens Nielsen, Hongting Tang, Feiran Li

{"title":"Leveraging large language models for metabolic engineering design.","authors":"Xiongwen Li, Zhetao Guo, Yi Li, Zhu Liang, Ziyi Liu, Ke Wu, Jiahao Luo, Yuesheng Zhang, Lizheng Liu, Manda Sun, Yuanyuan Huang, Yu Chen, Tao Yu, Jens Nielsen, Hongting Tang, Feiran Li","doi":"10.1016/j.tibtech.2026.03.026","DOIUrl":"10.1016/j.tibtech.2026.03.026","url":null,"abstract":"Establishing efficient cell factories involves a continuous process of trial and error due to metabolic complexity. This complexity makes predicting effective engineering targets a challenging task. Therefore, successful previous designs are vital for future cell factory development. In this study, we developed a method using large language models to extract metabolic engineering strategies from research articles. We created a database containing over 29 006 metabolic engineering entries, 1210 products, and 751 organisms. Using this database, we trained a deep learning model to predict engineering targets for cell factories. Our model outperformed traditional algorithms, demonstrated strong generalization to unseen products and multigene combinations, and was experimentally validated with geraniol overproduction in yeast, leading to the identification of several novel targets. Our study provides a valuable dataset, a chatbot, and an engineering target prediction model for the metabolic engineering field and exemplifies an efficient method for leveraging existing knowledge for future predictions.","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"3104-3125"},"PeriodicalIF":16.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147782442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Integrated directed evolution and semirational design of Pyrococcus furiosus Argonaute for ultrasensitive tetracycline detection. 用于四环素超灵敏检测的红色焦球菌的定向进化与半种群设计。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-10-01 Epub Date: 2026-05-05 DOI: 10.1016/j.tibtech.2026.04.008

Yanyan Chai, Bosheng Zhou, Wanqi Chen, Yuxuan Hu, Bingjie Zheng, Guozhen Liu, Yonggang Hu

{"title":"Integrated directed evolution and semirational design of Pyrococcus furiosus Argonaute for ultrasensitive tetracycline detection.","authors":"Yanyan Chai, Bosheng Zhou, Wanqi Chen, Yuxuan Hu, Bingjie Zheng, Guozhen Liu, Yonggang Hu","doi":"10.1016/j.tibtech.2026.04.008","DOIUrl":"10.1016/j.tibtech.2026.04.008","url":null,"abstract":"In this study, we report an integrated strategy combining directed evolution and semirational design to engineer a high-performance Pyrococcus furiosus Argonaute (PfAgo) variant. The optimized variant exhibited an 8.85-fold increase in catalytic efficiency, substantially enhanced soluble expression, and improved tolerance to elevated salt and metal ion conditions, enabling sensitive nucleic acid detection with a detection limit in the picomolar range. Mechanistic analyses suggested that these improvements may arise from reinforcement of the dimerization interface to stabilize the enzyme's active state, optimization of the catalytic center, and the introduction of charge-shielding salt bridges. Finally, a biosensing platform based on the engineered PfAgo achieved a detection limit of 10 fmol l-1 for tetracycline, demonstrating its strong potential for sensitive and robust detection. This work provides a generalizable framework for enhancing Argonaute performance and advances their application in field-deployable diagnostics across clinical, environmental, and food safety settings.","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"3054-3079"},"PeriodicalIF":16.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Metabolic engineering of Saccharomyces cerevisiae for the biosynthesis of indole-derived compounds. 酿酒酵母合成吲哚衍生化合物的代谢工程。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-29 DOI: 10.1016/j.tibtech.2026.09.006

Mengchu Sun, Xiaolin Shen, Xinxiao Sun, Jia Wang, Qipeng Yuan

引用次数: 0

Unnatural amino acids program thermoresponsive protein-polymer diblocks into shape-shifting nanostructures. 非天然氨基酸将热响应性蛋白质-聚合物双块编程为可变形的纳米结构。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-29 DOI: 10.1016/j.tibtech.2026.09.008

Daniela S Strugach, Yuval Pasternak, Oren Tiv, Federico Kaufman, Itzhak Levi, Miriam Amiram

{"title":"Unnatural amino acids program thermoresponsive protein-polymer diblocks into shape-shifting nanostructures.","authors":"Daniela S Strugach, Yuval Pasternak, Oren Tiv, Federico Kaufman, Itzhak Levi, Miriam Amiram","doi":"10.1016/j.tibtech.2026.09.008","DOIUrl":"https://doi.org/10.1016/j.tibtech.2026.09.008","url":null,"abstract":"Control over the morphology and function of self-assembling polymers remains a central challenge in engineering adaptive biomaterials and synthetic biological systems. Here, we establish that recombinant elastin-like polypeptide-resilin-like polypeptide diblocks can be programmed through incorporation of unnatural amino acids (uAAs) to undergo multistep, temperature-dependent phase transitions that generate shape-shifting nanostructures, including micelles, vesicles, and higher-order assemblies not typically accessible in conventional protein materials, thereby expanding their structural and functional design space. Incorporation of only six uAAs (<1.5% of residues) is sufficient to program phase behavior and assembly pathways, with uAA hydrophobicity and sequence position governing morphology and structural transitions. Photo-switchable uAAs further enable reversible, light-driven control over nanostructure morphology, modulating substrate encapsulation and enzymatic activity. Together, these findings define a genetically encoded design framework for adaptive protein materials and expand opportunities for their use in biotechnology, including synthetic organelle-like systems, dynamic biomolecular assemblies, responsive biocatalysis, and drug delivery.","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 mRNA therapeutics from design to delivery. 推进mRNA治疗从设计到交付。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-28 DOI: 10.1016/j.tibtech.2026.09.005

Yongdan Wang, Saeyoung Kim, Zhen Qin, Zhao Wang, Seongkyu Yoon

引用次数: 0

Engineering Pseudomonas putida KT2440 for open-loop upcycling of mixed plastics. 工程恶臭假单胞菌KT2440用于混合塑料的开环升级回收。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-24 DOI: 10.1016/j.tibtech.2026.08.017

Hao Meng, Tobias Karmainski, Aziz Ben Ammar, Anka Sieberichs, Yannick Branson, Peer Vossen, Tobias Schwanemann, Hendrik Ballerstedt, Uwe T Bornscheuer, Ren Wei, Lars M Blank

{"title":"Engineering Pseudomonas putida KT2440 for open-loop upcycling of mixed plastics.","authors":"Hao Meng, Tobias Karmainski, Aziz Ben Ammar, Anka Sieberichs, Yannick Branson, Peer Vossen, Tobias Schwanemann, Hendrik Ballerstedt, Uwe T Bornscheuer, Ren Wei, Lars M Blank","doi":"10.1016/j.tibtech.2026.08.017","DOIUrl":"https://doi.org/10.1016/j.tibtech.2026.08.017","url":null,"abstract":"Current recycling technologies address less than 10% of global plastic waste, necessitating alternative valorization routes. Biological upcycling via enzymatic depolymerization combined with microbial conversion of the resulting monomers offers a promising pathway to transform mixed-plastic waste into valuable alternatives. In this research article, we employed a single engineered Pseudomonas putida KT2440 for simultaneous co-utilization of five plastic monomers including ethylene glycol, terephthalate, adipate, 1,4-butanediol, and l-lactic acid, which can be derived from enzymatic hydrolysis of polyethylene terephthalate (PET), poly(butylene adipate-co-terephthalate) (PBAT), polyester polyurethanes (PUs), and polylactic acid. Continuous fermentation over 21 days with alternating mixed-monomer feeds achieved steady-state growth and complete substrate depletion, yielding adaptive mutations that informed iterative strain improvement. Further engineering enabled the biosynthesis of (R)-3-hydroxybutyrate (R-3HB), and 0.70 g l-1 R-3HB was produced directly from enzymatic hydrolysates of blended PET, PBAT, and thermoplastic PU. These results establish a viable bio-based approach for upcycling realistic mixed plastics into value-added bioproducts.","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Nanozymes and the restoration of immune tolerance in autoimmune diseases. 纳米酶与自身免疫性疾病免疫耐受的恢复。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-23 DOI: 10.1016/j.tibtech.2026.09.002

Suyeon Kim, Yu-Jin Kim, Jin Yoo, Jinkee Hong, Youngmee Jung

引用次数: 0

Plasmid copy number control offers a versatile tool in synthetic biology applications. 质粒拷贝数控制在合成生物学应用中提供了一个通用的工具。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-23 DOI: 10.1016/j.tibtech.2026.07.005

Chentao Yong, Andrés Felipe Carrillo Rincón, Shivang Hina-Nilesh Joshi, Rumail Memon, Andras Gyorgy

引用次数: 0

Innovations and applications in synthetic biology: a PhD researcher's perspective. 合成生物学的创新和应用：一个博士研究人员的观点。

IF 16.6 1区工程技术

Trends in biotechnology Pub Date : 2026-09-22 DOI: 10.1016/j.tibtech.2026.09.015

Jeremy Garb, Itamar Menuhin-Gruman, Eliya Milshtein, Keren Roas, Ilana Kolodkin-Gal, Tamir Tuller

引用次数: 0