Biotechnology advances最新文献

{"title":"Machine learning for the advancement of genome-scale metabolic modeling","authors":"Pritam Kundu ,&nbsp;Satyajit Beura ,&nbsp;Suman Mondal ,&nbsp;Amit Kumar Das ,&nbsp;Amit Ghosh","doi":"10.1016/j.biotechadv.2024.108400","DOIUrl":"10.1016/j.biotechadv.2024.108400","url":null,"abstract":"<div><p>Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the interrelations between genotype, phenotype, and external environment. The recent advancement of high-throughput experimental approaches and multi-omics strategies has generated a plethora of new and precise information from wide-ranging biological domains. On the other hand, the continuously growing field of machine learning (ML) and its specialized branch of deep learning (DL) provide essential computational architectures for decoding complex and heterogeneous biological data. In recent years, both multi-omics and ML have assisted in the escalation of CBM. Condition-specific omics data, such as transcriptomics and proteomics, helped contextualize the model prediction while analyzing a particular phenotypic signature. At the same time, the advanced ML tools have eased the model reconstruction and analysis to increase the accuracy and prediction power. However, the development of these multi-disciplinary methodological frameworks mainly occurs independently, which limits the concatenation of biological knowledge from different domains. Hence, we have reviewed the potential of integrating multi-disciplinary tools and strategies from various fields, such as synthetic biology, CBM, omics, and ML, to explore the biochemical phenomenon beyond the conventional biological dogma. How the integrative knowledge of these intersected domains has improved bioengineering and biomedical applications has also been highlighted. We categorically explained the conventional genome-scale metabolic model (GEM) reconstruction tools and their improvement strategies through ML paradigms. Further, the crucial role of ML and DL in omics data restructuring for GEM development has also been briefly discussed. Finally, the case-study-based assessment of the state-of-the-art method for improving biomedical and metabolic engineering strategies has been elaborated. Therefore, this review demonstrates how integrating experimental and in silico strategies can help map the ever-expanding knowledge of biological systems driven by condition-specific cellular information. This multiview approach will elevate the application of ML-based CBM in the biomedical and bioengineering fields for the betterment of society and the environment.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108400"},"PeriodicalIF":12.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466006","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}

{"title":"Advancing microbial production through artificial intelligence-aided biology","authors":"Xinyu Gong ,&nbsp;Jianli Zhang ,&nbsp;Qi Gan ,&nbsp;Yuxi Teng ,&nbsp;Jixin Hou ,&nbsp;Yanjun Lyu ,&nbsp;Zhengliang Liu ,&nbsp;Zihao Wu ,&nbsp;Runpeng Dai ,&nbsp;Yusong Zou ,&nbsp;Xianqiao Wang ,&nbsp;Dajiang Zhu ,&nbsp;Hongtu Zhu ,&nbsp;Tianming Liu ,&nbsp;Yajun Yan","doi":"10.1016/j.biotechadv.2024.108399","DOIUrl":"10.1016/j.biotechadv.2024.108399","url":null,"abstract":"<div><p>Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for value-added compound production. To optimize metabolism and reach optimal productivity, synthetic biology has developed various genetic devices to engineer microbial systems by gene editing, high-throughput protein engineering, and dynamic regulation. However, current synthetic biology methodologies still rely heavily on manual design, laborious testing, and exhaustive analysis. The emerging interdisciplinary field of artificial intelligence (AI) and biology has become pivotal in addressing the remaining challenges. AI-aided microbial production harnesses the power of processing, learning, and predicting vast amounts of biological data within seconds, providing outputs with high probability. With well-trained AI models, the conventional Design-Build-Test (DBT) cycle has been transformed into a multidimensional Design-Build-Test-Learn-Predict (DBTLP) workflow, leading to significantly improved operational efficiency and reduced labor consumption. Here, we comprehensively review the main components and recent advances in AI-aided microbial production, focusing on genome annotation, AI-aided protein engineering, artificial functional protein design, and AI-enabled pathway prediction. Finally, we discuss the challenges of integrating novel AI techniques into biology and propose the potential of large language models (LLMs) in advancing microbial production.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108399"},"PeriodicalIF":12.1,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455189","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}

{"title":"Advances in microbial community, mechanisms and stimulation effects of direct interspecies electron transfer in anaerobic digestion","authors":"","doi":"10.1016/j.biotechadv.2024.108398","DOIUrl":"10.1016/j.biotechadv.2024.108398","url":null,"abstract":"<div><p>Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"76 ","pages":"Article 108398"},"PeriodicalIF":12.1,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445356","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}

{"title":"Functional roles and engineering strategies to improve the industrial functionalities of lactic acid bacteria during food fermentation","authors":"Huan Yang ,&nbsp;Liying Hao ,&nbsp;Yao Jin ,&nbsp;Jun Huang ,&nbsp;Rongqing Zhou ,&nbsp;Chongde Wu","doi":"10.1016/j.biotechadv.2024.108397","DOIUrl":"10.1016/j.biotechadv.2024.108397","url":null,"abstract":"<div><p>In order to improve the flavor profiles, food security, probiotic effects and shorten the fermentation period of traditional fermented foods, lactic acid bacteria (LAB) were often considered as the ideal candidate to participate in the fermentation process. In general, LAB strains possessed the ability to develop flavor compounds via carbohydrate metabolism, protein hydrolysis and amino acid metabolism, lipid hydrolysis and fatty acid metabolism. Based on the functional properties to inhibit spoilage microbes, foodborne pathogens and fungi, those species could improve the safety properties and prolong the shelf life of fermented products. Meanwhile, influence of LAB on texture and functionality of fermented food were also involved in this review. As for the adverse effect carried by environmental challenges during fermentation process, engineering strategies based on exogenous addition, cross protection, and metabolic engineering to improve the robustness and of LAB were also discussed in this review. Besides, this review also summarized the potential strategies including microbial co-culture and metabolic engineering for improvement of fermentation performance in LAB strains. The authors hope this review could contribute to provide an understanding and insight into improving the industrial functionalities of LAB.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108397"},"PeriodicalIF":12.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442102","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}

{"title":"Cordyceps militaris: A novel mushroom platform for metabolic engineering","authors":"Jiapeng Zeng ,&nbsp;Yue Zhou ,&nbsp;Mengdi Lyu ,&nbsp;Xinchang Huang ,&nbsp;Muyun Xie ,&nbsp;Mingtao Huang ,&nbsp;Bai-Xiong Chen ,&nbsp;Tao Wei","doi":"10.1016/j.biotechadv.2024.108396","DOIUrl":"https://doi.org/10.1016/j.biotechadv.2024.108396","url":null,"abstract":"<div><p><em>Cordyceps militaris</em>, widely recognized as a medicinal and edible mushroom in East Asia, contains a variety of bioactive compounds, including cordycepin (COR), pentostatin (PTN) and other high-value compounds. This review explores the potential of developing <em>C. militaris</em> as a cell factory for the production of high-value chemicals and nutrients. This review comprehensively summarizes the fermentation advantages, metabolic networks, expression elements, and genome editing tools specific to <em>C. militaris</em> and discusses the challenges and barriers to further research on <em>C. militaris</em> across various fields, including computational biology, existing DNA elements, and genome editing approaches. This review aims to describe specific and promising opportunities for the in-depth study and development of <em>C. militaris</em> as a new chassis cell. Additionally, to increase the practicability of this review, examples of the construction of cell factories are provided, and promising strategies for synthetic biology development are illustrated.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108396"},"PeriodicalIF":12.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0734975024000909/pdfft?md5=bdc99791c7ea807eb642b82e4f245805&pid=1-s2.0-S0734975024000909-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434589","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}

{"title":"Development and applications of lipid hydrophilic headgroups for nucleic acid therapy","authors":"Wanting Ma ,&nbsp;Xingxing Fu ,&nbsp;Tianyi Zhao ,&nbsp;Yanfei Qi ,&nbsp;Shubiao Zhang ,&nbsp;Yinan Zhao","doi":"10.1016/j.biotechadv.2024.108395","DOIUrl":"10.1016/j.biotechadv.2024.108395","url":null,"abstract":"<div><p>Nucleic acid therapy is currently the most promising method for treating tumors and genetic diseases and for preventing infectious diseases. However, the biggest obstacle to this therapy is delivery of the nucleic acids to the target site, which requires overcoming problems such as capture by the immune system, the need to penetrate biofilms, and degradation of nucleic acid performance. Designing suitable delivery vectors is key to solving these problems. Lipids—which consist of a hydrophilic headgroup, a linker, and a hydrophobic tail—are crucial components for the construction of vectors. The headgroup is particularly important because it affects the drug encapsulation rate, the vector cytotoxicity, and the transfection efficiency. Herein, we focus on various headgroup structures (tertiary amines, quaternary ammonium salts, peptides, piperazines, dendrimers, and several others), and we summarize and classify important lipid-based carriers that have been developed in recent years. We also discuss applications of cationic lipids with various headgroups for delivery of nucleic acid drugs, and we analyze how headgroup structure affects transport efficiency and carrier toxicity. Finally, we briefly describe the challenges of developing novel lipid carriers, as well as their prospects.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108395"},"PeriodicalIF":12.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436625","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}

{"title":"Enzyme-mediated green synthesis of glycosaminoglycans and catalytic process intensification","authors":"Jie Zheng ,&nbsp;Xiao-jun Lin ,&nbsp;Han Xu ,&nbsp;Muhammad Sohail ,&nbsp;Liang-an Chen ,&nbsp;Xing Zhang","doi":"10.1016/j.biotechadv.2024.108394","DOIUrl":"10.1016/j.biotechadv.2024.108394","url":null,"abstract":"<div><p>Glycosaminoglycans (GAGs) are a family of structurally complex heteropolysaccharides that play pivotal roles in biological functions, including the regulation of cell proliferation, enzyme inhibition, and activation of growth factor receptors. Therefore, the synthesis of GAGs is a hot research topic in drug development. The enzymatic synthesis of GAGs has received widespread attention due to their eco-friendly nature, high regioselectivity, and stereoselectivity. The enhancement of the enzymatic synthesis process is the key to its industrial applications. In this review, we overviewed the construction of more efficient <em>in vitro</em> biomimetic synthesis systems of glycosaminoglycans and presented the different strategies to improve enzyme catalysis, including the combination of chemical and enzymatic methods, solid-phase synthesis, and protein engineering to solve the problems of enzyme stability, separation and purification of the product, preparation of structurally defined sugar chains, <em>etc.</em>, and discussed the challenges and opportunities in large-scale green synthesis of GAGs.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108394"},"PeriodicalIF":16.0,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141299954","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}

{"title":"Advances and opportunities in process analytical technologies for viral vector manufacturing","authors":"Sobhana A. Sripada ,&nbsp;Mahshid Hosseini ,&nbsp;Srivatsan Ramesh ,&nbsp;Junhyeong Wang ,&nbsp;Kimberly Ritola ,&nbsp;Stefano Menegatti ,&nbsp;Michael A. Daniele","doi":"10.1016/j.biotechadv.2024.108391","DOIUrl":"10.1016/j.biotechadv.2024.108391","url":null,"abstract":"<div><p>Viral vectors are an emerging, exciting class of biologics whose application in vaccines, oncology, and gene therapy has grown exponentially in recent years. Following first regulatory approval, this class of therapeutics has been vigorously pursued to treat monogenic disorders including orphan diseases, entering hundreds of new products into pipelines. Viral vector manufacturing supporting clinical efforts has spurred the introduction of a broad swath of analytical techniques dedicated to assessing the diverse and evolving panel of Critical Quality Attributes (CQAs) of these products. Herein, we provide an overview of the current state of analytics enabling measurement of CQAs such as capsid and vector identities, product titer, transduction efficiency, impurity clearance etc. We highlight orthogonal methods and discuss the advantages and limitations of these techniques while evaluating their adaptation as process analytical technologies. Finally, we identify gaps and propose opportunities in enabling existing technologies for real-time monitoring from hardware, software, and data analysis viewpoints for technology development within viral vector biomanufacturing.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108391"},"PeriodicalIF":16.0,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141287685","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}

{"title":"Nucleic acid-responsive smart systems for controlled cargo delivery","authors":"Akbar Hasanzadeh ,&nbsp;Arefeh Ebadati ,&nbsp;Sara Saeedi ,&nbsp;Babak Kamali ,&nbsp;Hamid Noori ,&nbsp;Behnam Jamei ,&nbsp;Michael R. Hamblin ,&nbsp;Yong Liu ,&nbsp;Mahdi Karimi","doi":"10.1016/j.biotechadv.2024.108393","DOIUrl":"10.1016/j.biotechadv.2024.108393","url":null,"abstract":"<div><p>Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108393"},"PeriodicalIF":16.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199169","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}

{"title":"Toward biomanufacturing of next-generation bacterial nanocellulose (BNC)-based materials with tailored properties: A review on genetic engineering approaches","authors":"Dariela Núñez ,&nbsp;Patricio Oyarzún ,&nbsp;Sebastián González ,&nbsp;Irene Martínez","doi":"10.1016/j.biotechadv.2024.108390","DOIUrl":"10.1016/j.biotechadv.2024.108390","url":null,"abstract":"<div><p>Bacterial nanocellulose (BNC) is a biopolymer that is drawing significant attention for a wide range of applications thanks to its unique structure and excellent properties, such as high purity, mechanical strength, high water holding capacity and biocompatibility. Nevertheless, the biomanufacturing of BNC is hindered due to its low yield, the instability of microbial strains and cost limitations that prevent it from being mass-produced on a large scale. Various approaches have been developed to address these problems by genetically modifying strains and to produce BNC-based biomaterials with added value. These works are summarized and discussed in the present article, which include the overexpression and knockout of genes related and not related with the nanocellulose biosynthetic operon, the application of synthetic biology approaches and CRISPR/Cas techniques to modulate BNC biosynthesis. Further discussion is provided on functionalized BNC-based biomaterials with tailored properties that are incorporated <em>in-vivo</em> during its biosynthesis using genetically modified strains either in single or co-culture systems (<em>in-vivo</em> manufacturing). This novel strategy holds potential to open the road toward cost-effective production processes and to find novel applications in a variety of technology and industrial fields.</p></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"74 ","pages":"Article 108390"},"PeriodicalIF":16.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186173","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}