Biotechnology advances最新文献_第3页

Design and application of microfluidics in aptamer SELEX and Aptasensors 微流控技术在适配体 SELEX 和适配体传感器中的设计与应用。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-10-05 DOI: 10.1016/j.biotechadv.2024.108461

Shikun Zhang , Yingming Zhang , Zhiyuan Ning , Mengxia Duan , Xianfeng Lin , Nuo Duan , Zhouping Wang , Shijia Wu

{"title":"Design and application of microfluidics in aptamer SELEX and Aptasensors","authors":"Shikun Zhang , Yingming Zhang , Zhiyuan Ning , Mengxia Duan , Xianfeng Lin , Nuo Duan , Zhouping Wang , Shijia Wu","doi":"10.1016/j.biotechadv.2024.108461","DOIUrl":"10.1016/j.biotechadv.2024.108461","url":null,"abstract":"<div><div>Aptamers are excellent recognition molecules obtained from systematic evolution of ligands by exponential enrichment (SELEX) that have been extensively researched for constructing aptasensors. However, in the process from SELEX to the construction of aptasensors, there are many disadvantages, such as tedious and repetitive operations, interference from external factors, and low efficiency, which seriously limits their application scope and development. Introducing the microfluidic technology can realize the integration and intelligence of SELEX and aptasensing, improve the efficiency of SELEX, and enhance the detection performance and convenience of aptasensing. Hence, in this review, the characteristics of various chips based on different driving forces are described firstly. And then summarizing the design of microfluidic devices based on different SELEX methods and showing the strategies of microfluidic aptasensors based on different detection modes. Finally, discussing the difficulties and challenges encountered when microfluidic is integrated with the SELEX and the aptasensors.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108461"},"PeriodicalIF":12.1,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387647","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

Engineered transcription factor-binding diversed functional nucleic acid-based synthetic biosensor 工程化转录因子结合多样化功能核酸合成生物传感器。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-10-05 DOI: 10.1016/j.biotechadv.2024.108463

Yanger Liu , Ziying Zhou , Yifan Wu , Lei Wang , Jiageng Cheng , Longjiao Zhu , Yulan Dong , Jie Zheng , Wentao Xu

{"title":"Engineered transcription factor-binding diversed functional nucleic acid-based synthetic biosensor","authors":"Yanger Liu , Ziying Zhou , Yifan Wu , Lei Wang , Jiageng Cheng , Longjiao Zhu , Yulan Dong , Jie Zheng , Wentao Xu","doi":"10.1016/j.biotechadv.2024.108463","DOIUrl":"10.1016/j.biotechadv.2024.108463","url":null,"abstract":"<div><div>Engineered transcription factors (eTFs) binding diversed functional nucleic acids (dFNAs), as innovative biorecognition systems, have gradually become indispensable core elements for building synthetic biosensors. They not only circumvent the limitations of the original TF-based biosensing technologies, but also inject new vitality into the field of synthetic biosensing. This review aims to provide the first comprehensive and systematic dissection of the eTF-dFNA synthetic biosensor concept. Firstly, the core principles and interaction mechanisms of eTF-dFNA biosensors are clarified. Next, we elaborate on the construction strategies of eTF-dFNA synthetic biosensors, detailing methods for the personalized customization of eTFs (irrational design, rational design, and semi-rational design) and dFNAs (SELEX, modifying and predicting), along with the exploration of strategies for the flexible selection of signal amplification and output modes. Furthermore, we discuss the exceptional performance and substantial advantages of eTF-dFNA synthetic biosensors, analyzing them from four perspectives: recognition domain, detection speed, sensitivity, and construction methodology. Building upon this analysis, we present their outstanding applications in point-of-care diagnostics, food-safety detection, environmental monitoring, and production control. Finally, we address the current limitations of eTF-dFNA synthetic biosensors candidly and envision the future direction of this technology, aiming to provide valuable insights for further research and applications in this burgeoning field.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108463"},"PeriodicalIF":12.1,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387649","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

Protein representations: Encoding biological information for machine learning in biocatalysis 蛋白质表征：为生物催化中的机器学习编码生物信息。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-10-02 DOI: 10.1016/j.biotechadv.2024.108459

David Harding-Larsen , Jonathan Funk , Niklas Gesmar Madsen , Hani Gharabli , Carlos G. Acevedo-Rocha , Stanislav Mazurenko , Ditte Hededam Welner

{"title":"Protein representations: Encoding biological information for machine learning in biocatalysis","authors":"David Harding-Larsen , Jonathan Funk , Niklas Gesmar Madsen , Hani Gharabli , Carlos G. Acevedo-Rocha , Stanislav Mazurenko , Ditte Hededam Welner","doi":"10.1016/j.biotechadv.2024.108459","DOIUrl":"10.1016/j.biotechadv.2024.108459","url":null,"abstract":"<div><div>Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that enable the <em>in silico</em> study and engineering of improved enzymatic properties. Such machine learning models, however, require the conversion of the complex biological information to a numerical input, also called protein representations. These inputs demand special attention to ensure the training of accurate and precise models, and, in this review, we therefore examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations — primary sequence, 3D structure, and dynamics — to explore their requirements for employment and inductive biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors to consider. The first one is the model setup, which is influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives such as consideration about the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108459"},"PeriodicalIF":12.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Engineering conditional protein-protein interactions for dynamic cellular control 设计条件性蛋白质-蛋白质相互作用，实现动态细胞控制。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-27 DOI: 10.1016/j.biotechadv.2024.108457

Anthony M. Stohr, Derron Ma, Wilfred Chen, Mark Blenner

引用次数: 0

Microbiome regulation for sustainable wastewater treatment 可持续废水处理的微生物组调控。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-27 DOI: 10.1016/j.biotechadv.2024.108458

Ke Shi , Jia-Min Xu , Han-Lin Cui, Hao-Yi Cheng, Bin Liang, Ai-Jie Wang

{"title":"Microbiome regulation for sustainable wastewater treatment","authors":"Ke Shi , Jia-Min Xu , Han-Lin Cui, Hao-Yi Cheng, Bin Liang, Ai-Jie Wang","doi":"10.1016/j.biotechadv.2024.108458","DOIUrl":"10.1016/j.biotechadv.2024.108458","url":null,"abstract":"<div><div>Sustainable wastewater treatment is essential for attaining clean water and sanitation, aligning with UN Sustainable Development Goals. Wastewater treatment plants (WWTPs) have utilized environmental microbiomes in biological treatment processes in this effort for over a century. However, the inherent complexity and redundancy of microbial communities, and emerging chemical and biological contaminants, challenge the biotechnology applications. Over the past decades, understanding and utilization of microbial energy metabolism and interaction relationships have revolutionized the biological system. In this review, we discuss how microbiome regulation strategies are being used to generate actionable performance for low-carbon pollutant removal and resource recovery in WWTPs. The engineering application cases also highlight the real feasibility and promising prospects of the microbiome regulation approaches. In conclusion, we recommend identifying environmental risks associated with chemical and biological contaminants transformation as a prerequisite. We propose the integration of gene editing and enzyme design to precisely regulate microbiomes for the synergistic control of both chemical and biological risks. Additionally, the development of integrated technologies and engineering equipment is crucial in addressing the ongoing water crisis. This review advocates for the innovation of conventional wastewater treatment biotechnology to ensure sustainable wastewater treatment.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108458"},"PeriodicalIF":12.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340990","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

Bioengineered heparin: Advances in production technology 生物工程肝素：生产技术的进步。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-24 DOI: 10.1016/j.biotechadv.2024.108456

Razia Sultana , Masamichi Kamihira

{"title":"Bioengineered heparin: Advances in production technology","authors":"Razia Sultana , Masamichi Kamihira","doi":"10.1016/j.biotechadv.2024.108456","DOIUrl":"10.1016/j.biotechadv.2024.108456","url":null,"abstract":"<div><div>Heparin, a highly sulfated glycosaminoglycan, is considered an indispensable anticoagulant with diverse therapeutic applications and has been a mainstay in medical practice for nearly a century. Its potential extends beyond anticoagulation, showing promise in treating inflammation, cancer, and infectious diseases such as COVID-19. However, its current sourcing from animal tissues poses challenges due to variable structures and adulterations, impacting treatment efficacy and safety. Recent advancements in metabolic engineering and synthetic biology offer alternatives through bioengineered heparin production, albeit with challenges such as controlling molecular weight and sulfonation patterns. This review offers comprehensive insight into recent advancements, encompassing: (i) the metabolic engineering strategies in prokaryotic systems for heparin production; (ii) strides made in the development of bioengineered heparin; and (iii) groundbreaking approaches driving production enhancements in eukaryotic systems. Additionally, it explores the potential of recombinant Chinese hamster ovary cells in heparin synthesis, discussing recent progress, challenges, and future prospects, thereby opening up new avenues in biomedical research.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108456"},"PeriodicalIF":12.1,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Advances in biosynthesis and downstream processing of diols 二元醇的生物合成和下游加工取得进展。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-19 DOI: 10.1016/j.biotechadv.2024.108455

Yongfei Liu , Chijian Zhang , An-Ping Zeng

引用次数: 0

Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory 构建微生物细胞工厂的多酶共定位策略的进展

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-13 DOI: 10.1016/j.biotechadv.2024.108453

Qi Guo , Yu-Xin Yang , Dong-Xun Li , Xiao-Jun Ji , Na Wu , Yue-Tong Wang , Chao Ye , Tian-Qiong Shi

{"title":"Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory","authors":"Qi Guo , Yu-Xin Yang , Dong-Xun Li , Xiao-Jun Ji , Na Wu , Yue-Tong Wang , Chao Ye , Tian-Qiong Shi","doi":"10.1016/j.biotechadv.2024.108453","DOIUrl":"10.1016/j.biotechadv.2024.108453","url":null,"abstract":"<div><p>Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108453"},"PeriodicalIF":12.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142243033","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

The biosynthesis of L-phenylalanine-derived compounds by engineered microbes 工程微生物对 L-苯丙氨酸衍生化合物的生物合成

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-11 DOI: 10.1016/j.biotechadv.2024.108448

Min Qiu , Jie Jiang , Wankui Jiang , Wenming Zhang , Yujia Jiang , Fengxue Xin , Min Jiang

{"title":"The biosynthesis of L-phenylalanine-derived compounds by engineered microbes","authors":"Min Qiu , Jie Jiang , Wankui Jiang , Wenming Zhang , Yujia Jiang , Fengxue Xin , Min Jiang","doi":"10.1016/j.biotechadv.2024.108448","DOIUrl":"10.1016/j.biotechadv.2024.108448","url":null,"abstract":"<div><p>L-Phenylalanine (L-Phe) is an important aromatic amino acid, which has been widely used in food, health care products, medicine and other fields. Based on the relatively mature microbial biosynthesis process, a variety of <em>L</em>-phenylalanine-derived compounds have attracted more and more attentions owing to their extensively potential applications in the fields of food, medicine, spices, cosmetics, and pesticides. However, the challenge of biosynthesis of <em>L</em>-phenylalanine-derived compounds remains the issue of low production and productivity. With the development of metabolic engineering and synthetic biology, the biosynthesis of <em>L</em>-phenylalanine has reached a high level. Therefore, the synthesis of <em>L</em>-phenylalanine-derived compounds based on high production strains of <em>L</em>-phenylalanine has broad prospects. In addition, some <em>L</em>-phenylalanine-derived compounds are more suitable for efficient synthesis by exogenous addition of precursors due to their longer metabolic pathways and the inhibitory effects of many intermediate products. This review systematically summarized the research progress of <em>L</em>-phenylalanine-derived compounds, including phenylpyruvate derivatives, <em>trans</em>-cinnamic derivatives, <em>p</em>-coumaric acid derivatives and other <em>L</em>-phenylalanine-derived compounds (such as flavonoids). Finally, the main strategies to improve the production of <em>L</em>-phenylalanine-derived compounds were summarized, and the development trends of the synthesis of <em>L</em>-phenylalanine-derived compounds by microbial method were also prospected.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108448"},"PeriodicalIF":12.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142167376","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

Droplet-based single-cell sequencing: Strategies and applications 基于液滴的单细胞测序：策略与应用

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-09-11 DOI: 10.1016/j.biotechadv.2024.108454

Yuting Shang , Zhengzheng Wang , Liqing Xi , Yantao Wang , Meijing Liu , Ying Feng , Juan Wang , Qingping Wu , Xinran Xiang , Moutong Chen , Yu Ding

{"title":"Droplet-based single-cell sequencing: Strategies and applications","authors":"Yuting Shang , Zhengzheng Wang , Liqing Xi , Yantao Wang , Meijing Liu , Ying Feng , Juan Wang , Qingping Wu , Xinran Xiang , Moutong Chen , Yu Ding","doi":"10.1016/j.biotechadv.2024.108454","DOIUrl":"10.1016/j.biotechadv.2024.108454","url":null,"abstract":"<div><p>Notable advancements in single-cell omics technologies have not only addressed longstanding challenges but also enabled unprecedented studies of cellular heterogeneity with unprecedented resolution and scale. These strides have led to groundbreaking insights into complex biological systems, paving the way for a more profound comprehension of human biology and diseases. The droplet microfluidic technology has become a crucial component in many single-cell sequencing workflows in terms of throughput, cost-effectiveness, and automation. Utilizing a microfluidic chip to encapsulate and profile individual cells within droplets has significantly improved single-cell research. Therefore, this review aims to comprehensively elaborate the droplet microfluidics-assisted omics methods from a single-cell perspective. The strategies for using droplet microfluidics in the realms of genomics, epigenomics, transcriptomics, and proteomics analyses are first introduced. On this basis, the focus then turns to the latest applications of this technology in different sequencing patterns, including mono- and multi-omics. Finally, the challenges and further perspectives of droplet-based single-cell sequencing in both foundational research and commercial applications are discussed.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108454"},"PeriodicalIF":12.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242996","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