Biotechnology advances最新文献_第2页

From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis.

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-06 DOI: 10.1016/j.biotechadv.2024.108496

Jie Gu, Wanmeng Mu, Yan Xu, Yao Nie

{"title":"From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis.","authors":"Jie Gu, Wanmeng Mu, Yan Xu, Yao Nie","doi":"10.1016/j.biotechadv.2024.108496","DOIUrl":"10.1016/j.biotechadv.2024.108496","url":null,"abstract":"<p><p>The catalytic conversion of chiral alcohols and corresponding carbonyl compounds by carbonyl reductases (alcohol dehydrogenases), which are NAD(P) or NAD(P)H-dependent oxidoreductases, has attracted considerable attention. However, existing carbonyl reductases are insufficient to meet the demands of diverse industrial applications; hence, new enzymes with functions that can expand the toolbox of biocatalysts are urgently required. Developing precisely controlled chiral biocatalysts is of great significance for the efficient development of a broad spectrum of active pharmaceutical ingredients via biosynthesis. In this review, we summarized methods for discovering novel natural carbonyl reductases from various perspectives. Furthermore, advances in protein engineering, utilizing known sequence and structural information as well as catalytic dynamics mechanisms to improve potential functions, are also addressed. The exponential growth in data-driven tools over the past decade has made it possible to de novo design carbonyl reductases. Additionally, various applications of these high-performance carbonyl reductases and different strategies for coenzyme regeneration involving photocatalysis during the reaction process were reviewed. These advancements will bring new opportunities and challenges to the fields of green chemistry and biosynthesis in the future.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108496"},"PeriodicalIF":12.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794343","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

Direct cloning strategies for large genomic fragments: A review.

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-06 DOI: 10.1016/j.biotechadv.2024.108494

Ya-Nan Chen, You-Zhi Cui, Xiang-Rong Chen, Jun-Yi Wang, Bing-Zhi Li, Ying-Jin Yuan

{"title":"Direct cloning strategies for large genomic fragments: A review.","authors":"Ya-Nan Chen, You-Zhi Cui, Xiang-Rong Chen, Jun-Yi Wang, Bing-Zhi Li, Ying-Jin Yuan","doi":"10.1016/j.biotechadv.2024.108494","DOIUrl":"10.1016/j.biotechadv.2024.108494","url":null,"abstract":"<p><p>Mining large-scale functional regions of the genome helps to understand the essence of cellular life. The rapid accumulation of genomic information provides a wealth of material for genomic functional, evolutionary, and structural research. DNA cloning technology is an important tool for understanding, analyzing, and manipulating the genetic code of organisms. As synthetic biologists engineer greater and broader genetic pathways and expand their research into new organisms, efficient tools capable of manipulating large-scale DNA will offer momentum to the ability to design, modify, and construct engineering life. In this review, we discuss the recent advances in the field of direct cloning of large genomic fragments, particularly of 50-150 kb genomic fragments. We specifically introduce the technological advances in the targeted release and capture steps of these cloning strategies. Additionally, the applications of large fragment cloning in functional genomics and natural product mining are also summarized. Finally, we further discuss the challenges and prospects for these technologies in the future.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108494"},"PeriodicalIF":12.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784052","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

Is it possible to shape the microalgal biomass composition with operational parameters for target compound accumulation?

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-05 DOI: 10.1016/j.biotechadv.2024.108493

Ana F Esteves, Ana L Gonçalves, Vítor J P Vilar, José C M Pires

{"title":"Is it possible to shape the microalgal biomass composition with operational parameters for target compound accumulation?","authors":"Ana F Esteves, Ana L Gonçalves, Vítor J P Vilar, José C M Pires","doi":"10.1016/j.biotechadv.2024.108493","DOIUrl":"10.1016/j.biotechadv.2024.108493","url":null,"abstract":"<p><p>Microalgae, as photosynthetic microorganisms, offer a sustainable source of proteins, lipids, carbohydrates, pigments, vitamins, and antioxidants. Leveraging their advantages, such as fast growth, CO<sub>2</sub> fixation, cultivation without arable land, and wastewater utilisation, microalgae can produce a diverse range of compounds. The extracted products find applications in bioenergy, animal feed, pharmaceuticals, nutraceuticals, cosmetics, and food industries. The selection of microalgal species is crucial, and their biochemical composition varies during growth phases influenced by environmental factors like light, salinity, temperature, and nutrients. Manipulating growth conditions shapes biomass composition, optimising the production of target compounds. This review synthesises research from 2019 onwards, focusing on stress induction and two-stage cultivation in microalgal strategies. This review takes a broader approach, addressing the effects of various operating conditions on a range of biochemical compounds. It explores the impact of operational parameters (light, nutrient availability, salinity, temperature) on biomass composition, elucidating microalgal mechanisms. Challenges include species-specific responses, maintaining stable conditions, and scale-up complexities. A two-stage approach balances biomass productivity and compound yield. Overcoming challenges involves improving upstream and downstream processes, developing sophisticated monitoring systems, and conducting further modelling work. Future efforts should concentrate on strain engineering and refined monitoring, facilitating real-time adjustments for optimal compound accumulation. Moreover, conducting large-scale experiments is essential to evaluate the feasibility and sustainability of the process through techno-economic analysis and life cycle assessments.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108493"},"PeriodicalIF":12.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791164","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

Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives.

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-05 DOI: 10.1016/j.biotechadv.2024.108497

Wenwen Yu, Ke Jin, Xianhao Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Jian Chen, Xueqin Lv, Long Liu

引用次数: 0

Interpretable and explainable predictive machine learning models for data-driven protein engineering.

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-05 DOI: 10.1016/j.biotechadv.2024.108495

David Medina-Ortiz, Ashkan Khalifeh, Hoda Anvari-Kazemabad, Mehdi D Davari

{"title":"Interpretable and explainable predictive machine learning models for data-driven protein engineering.","authors":"David Medina-Ortiz, Ashkan Khalifeh, Hoda Anvari-Kazemabad, Mehdi D Davari","doi":"10.1016/j.biotechadv.2024.108495","DOIUrl":"10.1016/j.biotechadv.2024.108495","url":null,"abstract":"<p><p>Protein engineering through directed evolution and (semi)rational design has become a powerful approach for optimizing and enhancing proteins with desired properties. The integration of artificial intelligence methods has further accelerated protein engineering process by enabling the development of predictive models based on data-driven strategies. However, the lack of interpretability and transparency in these models limits their trustworthiness and applicability in real-world scenarios. Explainable Artificial Intelligence addresses these challenges by providing insights into the decision-making processes of machine learning models, enhancing their reliability and interpretability. Explainable strategies has been successfully applied in various biotechnology fields, including drug discovery, genomics, and medicine, yet its application in protein engineering remains underexplored. The incorporation of explainable strategies in protein engineering holds significant potential, as it can guide protein design by revealing how predictive models function, benefiting approaches such as machine learning-assisted directed evolution. This perspective work explores the principles and methodologies of explainable artificial intelligence, highlighting its relevance in biotechnology and its potential to enhance protein design. Additionally, three theoretical pipelines integrating predictive models with explainable strategies are proposed, focusing on their advantages, disadvantages, and technical requirements. Finally, the remaining challenges of explainable artificial intelligence in protein engineering and future directions for its development as a support tool for traditional protein engineering methodologies are discussed.</p>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":" ","pages":"108495"},"PeriodicalIF":12.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791163","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

Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens.

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-03 DOI: 10.1016/j.biotechadv.2024.108492

Saber Imani, Shuojie Lv, Hongbo Qian, Yulan Cui, XiaoYan Li, Ali Babaeizad, Qingjing Wang

引用次数: 0

Selection of aptamers targeting small molecules by capillary electrophoresis: Advances, challenges, and prospects 通过毛细管电泳选择以小分子为靶标的适配体：进展、挑战与前景。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-26 DOI: 10.1016/j.biotechadv.2024.108491

Yangyang Hu , Guangyu Jiang , Yalun Wen , Yuchen Shao , Ge Yang , Feng Qu

{"title":"Selection of aptamers targeting small molecules by capillary electrophoresis: Advances, challenges, and prospects","authors":"Yangyang Hu , Guangyu Jiang , Yalun Wen , Yuchen Shao , Ge Yang , Feng Qu","doi":"10.1016/j.biotechadv.2024.108491","DOIUrl":"10.1016/j.biotechadv.2024.108491","url":null,"abstract":"<div><div>Aptamers, as novel recognition molecules, hold immense potential across various domains such as biosensing, nucleic acid drugs, medical diagnostics, as well as environmental and food analysis. The majority of aptamer selection processes targeting small molecules and protein commonly employ magnetic bead-based methodologies, wherein the target is initially immobilized on magnetic beads, followed by magnetic separation. The Evolutionary Systematic Evolution of Ligands by Exponential Enrichment technique based on capillary electrophoresis (CE-SELEX) is acknowledged as one of the most efficient screening methods. Our research group has achieved breakthroughs in employing CE-SELEX for the selection of aptamers targeting small molecules. This paper outlines specific methodologies utilized from 2005 to 2023 for CE-SELEX screening for small-molecule targets. It summarizes the methods for the separation of small molecules and oligonucleotide complexes, as well as the identification of candidate aptamers. Drawing upon our research group's extensive experience in CE-SELEX for selecting aptamers targeting multi-scale targets, we offer strategic guidance specifically tailored to the screening of aptamers for small-molecule targets using CE-SELEX. This includes systematic insights into each technical aspect of the screening process: analysis of the structure of small-molecule targets and characteristics of ssDNA libraries, patterns of CE separation and collection of complexes, screening strategies, and CE-based methods for the affinity and specificity characterization of aptamers. This comprehensive review aims to contribute to the widespread adoption of CE-SELEX technology, enhancing the efficiency and success rate of selecting aptamers for small-molecule targets.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108491"},"PeriodicalIF":12.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738184","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

Expanding the frontiers of genome engineering: A comprehensive review of CRISPR-associated transposons 拓展基因组工程的前沿：CRISPR相关转座子的全面回顾。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-22 DOI: 10.1016/j.biotechadv.2024.108481

Cheng Chen , Ya-Wen Li , Yuan-Yuan Zheng , Xiu-Juan Li , Na Wu , Qi Guo , Tian-Qiong Shi , He Huang

{"title":"Expanding the frontiers of genome engineering: A comprehensive review of CRISPR-associated transposons","authors":"Cheng Chen , Ya-Wen Li , Yuan-Yuan Zheng , Xiu-Juan Li , Na Wu , Qi Guo , Tian-Qiong Shi , He Huang","doi":"10.1016/j.biotechadv.2024.108481","DOIUrl":"10.1016/j.biotechadv.2024.108481","url":null,"abstract":"<div><div>Genome engineering is extensively utilized in diverse scientific disciplines, advancing human welfare and addressing various challenges. Numerous genome engineering tools have been developed to modify genomic sequences. Among these, the CRISPR-Cas system has transformed the field and remains the most commonly employed genome-editing tool. However, the CRISPR-Cas system relies on induced double-strand breaks, with editing efficiency often limited by factors such as cell type and homologous recombination, impeding further progress. CRISPR-associated transposons (CASTs) represent programmable mobile genetic elements. CASTs identified as active were developed as CAST systems, which can perform RNA-guided DNA integration and are featured by high precision, programmability, and kilobase-level payload capacity. Moreover, CAST system allows for precise genome modifications independent of host DNA repair mechanisms, addressing the constraints of conventional CRISPR-Cas systems. It expands the genome engineering toolkit and is poised to become a representative of next-generation genome editing tools. This review thoroughly examines the research progress on CASTs, highlighting the current challenges faced in genome engineering based on CASTs, and offering insights into the ongoing development of this transformative technology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108481"},"PeriodicalIF":12.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695054","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

A non-classical view of antibody properties: Allosteric effect between variable and constant regions 抗体特性的非经典观点：可变区和恒定区之间的异化作用

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-21 DOI: 10.1016/j.biotechadv.2024.108482

Xiaoting Yu , Huiling Zhang , Tao Zhou , Kangliang Pan , Sayed Haidar Abbas Raza , Xing Shen , Hongtao Lei

{"title":"A non-classical view of antibody properties: Allosteric effect between variable and constant regions","authors":"Xiaoting Yu , Huiling Zhang , Tao Zhou , Kangliang Pan , Sayed Haidar Abbas Raza , Xing Shen , Hongtao Lei","doi":"10.1016/j.biotechadv.2024.108482","DOIUrl":"10.1016/j.biotechadv.2024.108482","url":null,"abstract":"<div><div>Historically, antibodies have been divided into two functionally independent domains, the variable (V) region for antigen binding and the constant (C) region for mediating effector functions. However, this classical view of antibody function has been severely challenged by a large and growing number of studies, which reveal long-range conformational interactions and allosteric links between the V and C regions. This review comprehensively summarizes the existing studies on antibody allostery, including allosteric conformational changes induced by covalent modifications or noncovalent ligand binding. In addition, we discuss how intramolecular allosteric signals are transmitted from the V to C regions and <em>vice versa</em>. This review argues that there is sufficient evidence to revisit the structure-function relationship of antibodies. These advances in antibody allostery will provide a blueprint for regulating antibody functions in a simple and highly predictable manner. More focus on antibody allostery will definitely benefit antibody engineering and vaccine design in the field of biotechnology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108482"},"PeriodicalIF":12.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695019","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

Advances and challenges in preparing membrane proteins for native mass spectrometry 为原生质谱法制备膜蛋白的进展与挑战

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-20 DOI: 10.1016/j.biotechadv.2024.108483

Di Cheng , Yi Guo , Jixing Lyu , Yang Liu , Wenhao Xu , Weiyi Zheng , Yuchen Wang , Pei Qiao

{"title":"Advances and challenges in preparing membrane proteins for native mass spectrometry","authors":"Di Cheng , Yi Guo , Jixing Lyu , Yang Liu , Wenhao Xu , Weiyi Zheng , Yuchen Wang , Pei Qiao","doi":"10.1016/j.biotechadv.2024.108483","DOIUrl":"10.1016/j.biotechadv.2024.108483","url":null,"abstract":"<div><div>Native mass spectrometry (nMS) is becoming a crucial tool for analyzing membrane proteins (MPs), yet challenges remain in solubilizing and stabilizing their native conformations while resolving and characterizing the heterogeneity introduced by post-translational modifications and ligand binding. This review highlights recent advancements and persistent challenges in preparing MPs for nMS. Optimizing detergents and additives can significantly reduce sample heterogeneity and surface charge, enhancing MP signal quality and structural preservation in nMS. A strategic workflow incorporating affinity capture, stabilization agents, and size-exclusion chromatography to remove unfolded species demonstrates success in improving nMS characterization. Continued development of customized detergents and reagents tailored for specific MPs may further minimize heterogeneity and boost signals. Instrumental advances are also needed to elucidate more dynamically complex and labile MPs. Effective sample preparation workflows may provide insights into MP structures, dynamics, and interactions underpinning membrane biology. With ongoing methodological innovation, nMS shows promise to complement biophysical studies and facilitate drug discovery targeting this clinically important yet technically demanding protein class.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108483"},"PeriodicalIF":12.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684169","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