Biotechnology advances最新文献_第9页

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

引用次数: 0

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}

引用次数: 0

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

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

Leveraging independent component analysis to unravel transcriptional regulatory networks: A critical review and future directions 利用独立成分分析揭示转录调控网络：重要综述与未来方向。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-20 DOI: 10.1016/j.biotechadv.2024.108479

Yuhan Zhang , Jianxiao Zhao , Xi Sun , Yangyang Zheng , Tao Chen , Zhiwen Wang

{"title":"Leveraging independent component analysis to unravel transcriptional regulatory networks: A critical review and future directions","authors":"Yuhan Zhang , Jianxiao Zhao , Xi Sun , Yangyang Zheng , Tao Chen , Zhiwen Wang","doi":"10.1016/j.biotechadv.2024.108479","DOIUrl":"10.1016/j.biotechadv.2024.108479","url":null,"abstract":"<div><div>Transcriptional regulatory networks (TRNs) play a crucial role in exploring microbial life activities and complex regulatory mechanisms. The comprehensive reconstruction of TRNs requires the integration of large-scale experimental data, which poses significant challenges due to the complexity of regulatory relationships. The application of machine learning tools, such as clustering analysis, has been employed to investigate TRNs, but these methods have limitations in capturing both global and local co-expression effects. In contrast, Independent Component Analysis (ICA) has emerged as a powerful analysis algorithm for modularizing independently regulated gene sets in TRNs, allowing it to account for both global and local co-expression effects. In this review, we comprehensively summarize the application of ICA in unraveling TRNs and highlight the research progress in three key aspects: (1) extending TRNs with iModulon analysis; (2) elucidating the regulatory mechanisms triggered by environmental perturbation; and (3) exploring the mechanisms of transcriptional regulation triggered by changes in microbial physiological state. At the end of this review, we also address the challenges facing ICA in TRN analysis and outline future research directions to promote the advancement of ICA-based transcriptomics analysis in biotechnology and related fields.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108479"},"PeriodicalIF":12.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692671","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

Recent advances in culture medium design for enhanced production of monoclonal antibodies in CHO cells: A comparative study of machine learning and systems biology approaches 用于提高 CHO 细胞单克隆抗体产量的培养基设计的最新进展：机器学习与系统生物学方法的比较研究。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-19 DOI: 10.1016/j.biotechadv.2024.108480

Hossein Kavoni , Iman Shahidi Pour Savizi , Nathan E. Lewis , Seyed Abbas Shojaosadati

{"title":"Recent advances in culture medium design for enhanced production of monoclonal antibodies in CHO cells: A comparative study of machine learning and systems biology approaches","authors":"Hossein Kavoni , Iman Shahidi Pour Savizi , Nathan E. Lewis , Seyed Abbas Shojaosadati","doi":"10.1016/j.biotechadv.2024.108480","DOIUrl":"10.1016/j.biotechadv.2024.108480","url":null,"abstract":"<div><div>The production of monoclonal antibodies (mAbs) using Chinese Hamster Ovary (CHO) cells has revolutionized the treatment of numerous diseases, solidifying their position as a cornerstone of the biopharmaceutical industry. However, achieving maximum mAb production while upholding strict product quality standards remains a significant hurdle. Optimizing cell culture media emerges as a critical factor in this endeavor, requiring a nuanced understanding of the complex interplay of nutrients, growth factors, and other components that profoundly influence cellular growth, productivity, and product quality. Significant strides have been made in media optimization, including techniques such as media blending, one factor at a time, and statistical design of experiments approaches. The present review provides a comprehensive analysis of the recent advancements in culture media design strategies, focusing on the comparative application of systems biology (SB) and machine learning (ML) approaches. The applications of SB and ML in optimizing CHO cell culture medium and successful examples of their use are summarized. Finally, we highlight the immense potential of integrating SB and ML, emphasizing the development of hybrid models that leverage the strengths of both approaches for robust, efficient, and scalable optimization of mAb production in CHO cells. This review provides a roadmap for researchers and industry professionals to navigate the complex landscape of mAb production optimization, paving the way for developing next-generation CHO cell culture media that drive significant improvements in yield and productivity.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108480"},"PeriodicalIF":12.1,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685908","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

Bacterial 5′ UTR: A treasure-trove for post-transcriptional regulation 细菌 5' UTR：转录后调控的宝库。

IF 12.1 1区工程技术

Biotechnology advances Pub Date : 2024-11-17 DOI: 10.1016/j.biotechadv.2024.108478

Ya-Jun Liu , Xiaoqing Wang , Yuman Sun , Yingang Feng

引用次数: 0