Biotechnology advances最新文献_第9页

HEK-omics: The promise of omics to optimize HEK293 for recombinant adeno-associated virus (rAAV) gene therapy manufacturing hek组学：利用组学优化重组腺相关病毒（rAAV）基因治疗生产的HEK293的前景。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-19 DOI: 10.1016/j.biotechadv.2024.108506

Sai Guna Ranjan Gurazada , Hannah M. Kennedy , Richard D. Braatz , Steven J. Mehrman , Shawn W. Polson , Irene T. Rombel

{"title":"HEK-omics: The promise of omics to optimize HEK293 for recombinant adeno-associated virus (rAAV) gene therapy manufacturing","authors":"Sai Guna Ranjan Gurazada , Hannah M. Kennedy , Richard D. Braatz , Steven J. Mehrman , Shawn W. Polson , Irene T. Rombel","doi":"10.1016/j.biotechadv.2024.108506","DOIUrl":"10.1016/j.biotechadv.2024.108506","url":null,"abstract":"<div><div>Gene therapy is poised to transition from niche to mainstream medicine, with recombinant adeno-associated virus (rAAV) as the vector of choice. However, robust, scalable, industrialized production is required to meet demand and provide affordable patient access, which has not yet materialized. Closing the chasm between demand and supply requires innovation in biomanufacturing to achieve the essential step change in rAAV product yield and quality. Omics provides a rich source of mechanistic knowledge that can be applied to HEK293, the most commonly used cell line for rAAV production. In this review, the findings from a growing number of diverse studies that apply genomics, epigenomics, transcriptomics, proteomics, and metabolomics to HEK293 bioproduction are explored. Learnings from CHO-omics, application of omics approaches to improve CHO bioproduction, provide a framework to explore the potential of “HEK-omics” as a multi-omics-informed approach providing actionable mechanistic insights for improved transient and stable production of rAAV and other recombinant products in HEK293.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108506"},"PeriodicalIF":12.1,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870709","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

Terahertz scanning near-field optical microscopy for biomedical detection: Recent advances, challenges, and future perspectives 太赫兹扫描近场光学显微镜用于生物医学检测：最新进展、挑战和未来展望。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-19 DOI: 10.1016/j.biotechadv.2024.108507

Shihan Yan , Guanyin Cheng , Zhongbo Yang , Yuansen Guo , Ligang Chen , Ying Fu , Fucheng Qiu , Jonathan J. Wilksch , Tianwu Wang , Yiwen Sun , Junchao Fan , Xunbin Wei , Jiaguang Han , Fei Sun , Shixiang Xu , Huabin Wang

{"title":"Terahertz scanning near-field optical microscopy for biomedical detection: Recent advances, challenges, and future perspectives","authors":"Shihan Yan , Guanyin Cheng , Zhongbo Yang , Yuansen Guo , Ligang Chen , Ying Fu , Fucheng Qiu , Jonathan J. Wilksch , Tianwu Wang , Yiwen Sun , Junchao Fan , Xunbin Wei , Jiaguang Han , Fei Sun , Shixiang Xu , Huabin Wang","doi":"10.1016/j.biotechadv.2024.108507","DOIUrl":"10.1016/j.biotechadv.2024.108507","url":null,"abstract":"<div><div>Terahertz (THz) radiation is widely recognized as a non-destructive, label-free, and highly- sensitive tool for biomedical detections. Nevertheless, its application in precision biomedical fields faces challenges due to poor spatial resolution caused by intrinsically long wavelength characteristics. THz scanning near-field optical microscopy (THz-SNOM), which surpasses the Rayleigh criterion, offers micrometer and nanometer-scale spatial resolution, making it possible to perform precise bioinspection with THz imaging. THz-SNOM is attracting considerable attention for its potential in advanced biomedical research and diagnosis. Currently, its family typically includes four members based on distinct principles, which are suitable for different biological applications. This review provides an overview of the principles of these THz-SNOM modalities, outlines their various applications, identifies the obstacles hindering their performance, and envisions their future development.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108507"},"PeriodicalIF":12.1,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870820","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 role of the proteosurfaceome and exoproteome in bacterial coaggregation 蛋白质表面组和外蛋白质组在细菌共聚集中的作用。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-12-16 DOI: 10.1016/j.biotechadv.2024.108505

Ana C. Afonso , Maria J. Saavedra , Manuel Simões , Lúcia C. Simões

{"title":"The role of the proteosurfaceome and exoproteome in bacterial coaggregation","authors":"Ana C. Afonso , Maria J. Saavedra , Manuel Simões , Lúcia C. Simões","doi":"10.1016/j.biotechadv.2024.108505","DOIUrl":"10.1016/j.biotechadv.2024.108505","url":null,"abstract":"<div><div>Bacterial coaggregation is a critical process in multispecies biofilm formation, driven by specific molecular interactions that facilitate the adhesion and aggregation of bacterial cells. These interactions are essential for the development and persistence of complex microbial communities. This review provides a comprehensive analysis of the roles of the proteosurfaceome and exoproteome in bacterial coaggregation. The proteosurfaceome, comprising surface-bound molecules such as adhesins, drives species-specific interactions crucial for partner recognition and adhesion. In parallel, the exoproteome, particularly extracellular polymeric substances (EPS), enhances aggregate stability by reinforcing structural integrity and facilitating intercellular communication, although its direct role in coaggregation remains to be fully clarified. By integrating these perspectives, this review aims to elucidate how the proteosurfaceome and exoproteome influence bacterial coaggregation, offering insights into their combined impact on microbial community structure and function. Furthermore, we highlight existing knowledge gaps and propose directions for future research.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108505"},"PeriodicalIF":12.1,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852254","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

From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis 从发现到应用：使基于技术的优化羰基还原酶生物催化活性药物成分合成。

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":"<div><div>The catalytic conversion of chiral alcohols and corresponding carbonyl compounds by carbonyl reductases (alcohol dehydrogenases), which are NAD(P) or NAD(<em>P</em>)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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 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 大片段基因组直接克隆策略综述

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":"<div><div>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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 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? 是否有可能用目标化合物积累的操作参数来塑造微藻生物量组成？

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":"<div><div>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.</div><div>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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives 通过多重时空控制细胞代谢的工程微生物细胞工厂：进展、挑战和未来展望。

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

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Interpretable and explainable predictive machine learning models for data-driven protein engineering 用于数据驱动蛋白质工程的可解释和可解释的预测机器学习模型。

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":"<div><div>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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens 针对多药耐药ESKAPE病原体的mRNA疫苗的最新创新。

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

{"title":"Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens","authors":"Saber Imani , Shuojie Lv , Hongbo Qian , Yulan Cui , XiaoYan Li , Ali Babaeizad , Qingjing Wang","doi":"10.1016/j.biotechadv.2024.108492","DOIUrl":"10.1016/j.biotechadv.2024.108492","url":null,"abstract":"<div><div>The prevalence of multidrug-resistant (MDR) ESKAPE pathogens, including <em>Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa</em>, represents a critical global public health challenge. In response, mRNA vaccines offer an adaptable and scalable platform for immunotherapy against ESKAPE pathogens by encoding specific antigens that stimulate B-cell-driven antibody production and CD8<sup>+</sup> T-cell-mediated cytotoxicity, effectively neutralizing these pathogens and combating resistance. This review examines recent advancements and ongoing challenges in the development of mRNA vaccines targeting MDR ESKAPE pathogens. We explore antigen selection, the nuances of mRNA vaccine technology, and the complex interactions between bacterial infections and antibiotic resistance. By assessing the potential efficacy of mRNA vaccines and addressing key barriers to their paraclinical implementation, this review highlights the promising function of mRNA-based immunization in combating MDR ESKAPE pathogens.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"79 ","pages":"Article 108492"},"PeriodicalIF":12.1,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784050","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

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