生物设计研究(英文)最新文献_第5页

Single component CRISPR-mediated base-editors for Agrobacterium and their use to develop an improved suite of strains. 单组分crispr介导的农杆菌碱基编辑器及其在开发一套改良菌株中的应用。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-27 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100001

Vincent J Pennetti, Peter R LaFayette, Wayne Allen Parrott

{"title":"Single component CRISPR-mediated base-editors for Agrobacterium and their use to develop an improved suite of strains.","authors":"Vincent J Pennetti, Peter R LaFayette, Wayne Allen Parrott","doi":"10.1016/j.bidere.2025.100001","DOIUrl":"10.1016/j.bidere.2025.100001","url":null,"abstract":"Agrobacterium mediated plant transformation largely depends on two distinct strain lineages - C58 and Ach5. To better serve the plant transformation community, we have created a suite of auxotrophic and auxotrophic recombinant deficient mutants of C58 derivatives EHA105, GV3101::pMP90, and Ach5 derivative LBA4404. While these derivatives are useful, having additional strain backgrounds available would help expand the repertoire for plant transformation even further. Toward that end, two underutilized hypervirulent strains are K599 (NCPPB 2659), and Chry5-but disarmed variants are not easily accessible. To improve availability, we produced disarmed versions of A. rhizogenes strain K599 and A. tumefaciens strain Chry5 and introduced the same desirable mutations as with the other lineages. Each thymidine auxotrophy and recombination deficiency were introduced to existing and newly disarmed Agrobacterium strains via loss of function mutations conferred to thyA and recA, respectively, through CRISPR-mediated base-editing of codons amenable to nonsense mutation. To streamline the editing process, we created a series of visually marked single component base-editor vectors and a corresponding guide-filtering Geneious Prime wrapper plugin for expedited guide filtering. These new strains, the simplified CRISPR-mediated base-editor plasmids, and streamlined workflow will improve the ease with which future Agrobacterium strain derivatives are created while also supporting plant transformation at large.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100001"},"PeriodicalIF":4.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12709902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards sustainable freshwater systems through plant synthetic biology engineering plants for sustainability. 通过植物合成生物工程实现可持续的淡水系统。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-27 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100009

June I Medford

{"title":"Towards sustainable freshwater systems through plant synthetic biology engineering plants for sustainability.","authors":"June I Medford","doi":"10.1016/j.bidere.2025.100009","DOIUrl":"10.1016/j.bidere.2025.100009","url":null,"abstract":"Approaches are needed to reduce the impact of climate change and provide freshwater. Synthetic biology, and plant synthetic biology specifically, is in an exceptional position to address these needs. Plants are powerful synthetic biology platforms as they derive their energy from the sun (photosynthesis) while capturing the potent greenhouse gas, carbon dioxide. Historically, plants were used in specialized circumstances to provide and store freshwater. Even today many mangrove species can filter seawater while some plants can store massive amounts of water. I propose that starting from nature's own design principles we could engineer plants to filter seawater and/or store freshwater. Moreover, synthetic biologists could derive components found in diverse life forms, modified by water's evolutionarily adaptive properties, to provide source material for engineering plants to filter and transport water. By combining components and inspiration from nature, with advanced synthetic biology tools such as computational protein design and directed evolution, we have the knowledge and technology to make an impact on climate change. Synthetic biologists could engineer plant platforms with the ability to filter saltwater while producing freshwater thus providing a powerful and sustainable means to address freshwater needs while reducing the impact of climate change. With creativity and time, plant synthetic biology could thus help provide sustainable solutions.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100009"},"PeriodicalIF":4.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12709952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Innovative tools for customized yeast cell factory. 创新工具定制酵母细胞工厂。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-06-01 DOI: 10.1016/j.bidere.2025.100010

Shuobo Shi, Congna Li

引用次数: 0

Recent advances on protein engineering for improved stability. 蛋白质工程提高稳定性的最新进展。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100005

Jinghao Shi, Bo Yuan, Hengquan Yang, Zhoutong Sun

引用次数: 0

Protein-based materials: Applications, modification and molecular design. 蛋白质基材料：应用、修饰和分子设计。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100004

Alitenai Tunuhe, Ze Zheng, Xinran Rao, Hongbo Yu, Fuying Ma, Yaxian Zhou, Shangxian Xie

{"title":"Protein-based materials: Applications, modification and molecular design.","authors":"Alitenai Tunuhe, Ze Zheng, Xinran Rao, Hongbo Yu, Fuying Ma, Yaxian Zhou, Shangxian Xie","doi":"10.1016/j.bidere.2025.100004","DOIUrl":"10.1016/j.bidere.2025.100004","url":null,"abstract":"Proteins are the fundamental building blocks of nature, constructing complex molecular machines and dynamic materials. They form the protein complexes that drive life cycles and the cellular skeletal components and muscle fibers responsible for movements. Due to their extensive molecular diversity, many biomedical and industrial challenges associated with natural proteins remain unsolved. This review presents a comprehensive analysis of the structure and function of fibrous proteins, elastin, and mucins, emphasizing their roles as protein materials. It also explores their diverse applications across food, environmental, and biomedical sectors. Additionally, we focus on strategies for optimizing protein structure, including chemical modifications and molecular design, by comparing current design methods and software to summarize recent technological developments. Finally, we explore the challenges and prospects of applying artificial intelligence to complex protein structure design. This application has the potential to advance the development and application of intricate protein materials, address functional defects or instability in biomedicine, and enhance our understanding of natural protein mechanisms. These interdisciplinary collaborations will pave the way for designing new multifunctional proteins.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100004"},"PeriodicalIF":4.7,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12709883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fermentation design and process optimization strategy based on machine learning. 基于机器学习的发酵设计与工艺优化策略。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100002

Zhen-Zhi Wang, Du-Wen Zeng, Yi-Fan Zhu, Ming-Hai Zhou, Akihiko Kondo, Tomohisa Hasunuma, Xin-Qing Zhao

{"title":"Fermentation design and process optimization strategy based on machine learning.","authors":"Zhen-Zhi Wang, Du-Wen Zeng, Yi-Fan Zhu, Ming-Hai Zhou, Akihiko Kondo, Tomohisa Hasunuma, Xin-Qing Zhao","doi":"10.1016/j.bidere.2025.100002","DOIUrl":"10.1016/j.bidere.2025.100002","url":null,"abstract":"Fermentation optimization is important for industrialization of biological manufacturing, and has been widely applied to diverse sectors including medicine, food, cosmetics and bioenergy, which is related to substantial economic benefits. Strain development is considered to be the core part of fermentation technology, as it directly influences the product yield and overall success of the fermentation process. However, fermentation design and process optimization also play a crucial role in fully exploring the genetic potential of engineered strains for efficient bioproduction. Due to the fact that fermentation process is influenced by complex factors, so far, machine learning has been widely used in this area with its strong capabilities of simulation and prediction. This review provides a brief introduction to the process of fermentation design and process optimization based on machine learning. In the workflow, experimental design strategy is fundamental to explore and characterize the performance of fermentation system. Then, machine learning modelling is employed to simulate the operation of fermentation system and the appropriate fermentation conditions, such as medium composition and process parameters, will be determined. Moreover, in recent years, some extension ideas of fermentation design based on machine learning have also been proposed, including automated fermentation process control, data mining for exploring strain characteristics, transfer learning, hybrid model building, and soft sensor construction. These strategies have created more application scenarios for machine learning, enhancing its adaptability in designing and optimizing the complex fermentation system for efficient bioproduction.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100002"},"PeriodicalIF":4.7,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12709886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering Corynebacterium glutamicum cell factory for producing biochemicals. 工程谷氨酸棒状杆菌细胞工厂生产生物化学品。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100008

Kai Li, Meng-Lin Sun, Bing Yuan, Cheng Li, Xin-Qing Zhao, Chen-Guang Liu, Anthony J Sinskey, Feng-Wu Bai

{"title":"Engineering Corynebacterium glutamicum cell factory for producing biochemicals.","authors":"Kai Li, Meng-Lin Sun, Bing Yuan, Cheng Li, Xin-Qing Zhao, Chen-Guang Liu, Anthony J Sinskey, Feng-Wu Bai","doi":"10.1016/j.bidere.2025.100008","DOIUrl":"10.1016/j.bidere.2025.100008","url":null,"abstract":"As an essential industrial microorganism, Corynebacterium glutamicum has been employed in amino acids production with a long history. Recent progress in its metabolic engineering has accelerated the establishment and optimization of this species as cell factories, making it another unique chassis. In this comprehensive review, we first highlight the progress made in the metabolic engineering of C. glutamicum to broaden its substrate spectrum, including sugars in lignocellulosic hydrolysate, cheap glycerol, and one-carbon compounds. Furthermore, we discuss the development of C. glutamicum as cell factories to produce various amino acids, with a focus on bulk, branched-chain and aromatic amino acids, organic acids such as succinic acid, lactic acid, and shikimic acid, and terpenoids. Finally, potential challenges faced by engineering C. glutamicum cell factories when using non-model feedstocks for biochemical production are discussed, focusing on stress tolerance, non-model substrate utilization, and the design of multifunctional cell factories, along with envisioned directions for future research.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100008"},"PeriodicalIF":4.7,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12709890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discussion of the possibility of increasing the efficiency of photosynthesis using genetic and metabolic engineering methods. 讨论利用遗传和代谢工程方法提高光合作用效率的可能性。

IF 4.7

生物设计研究(英文) Pub Date : 2025-02-26 eCollection Date: 2025-03-01 DOI: 10.1016/j.bidere.2025.100006

Viktor Melnik

{"title":"Discussion of the possibility of increasing the efficiency of photosynthesis using genetic and metabolic engineering methods.","authors":"Viktor Melnik","doi":"10.1016/j.bidere.2025.100006","DOIUrl":"10.1016/j.bidere.2025.100006","url":null,"abstract":"Photosynthesis is the main process by which biomass of living matter is created from inorganic carbon. However, the efficiency of photosynthesis is low. The main reason for the low efficiency of photosynthesis is the properties of the enzyme that fixes carbon dioxide - ribulose-1,5-bisphosphate carboxylase/oxidase (RuBisCO). There are reasons to believe that it is impossible to improve the properties of RuBisCO. It is apparently possible to significantly increase the efficiency of photosynthesis only by replacing RuBisCO with another enzyme. Among the known enzymes capable of fixing CO2, there is only one enzyme whose kinetic properties exceed those of RuBisCO, this is phosphoenolpyruvate carboxylase (PEPC). However, plants using PEPC are not able to use it as the only carbon dioxide fixer and to do without RubisCO. The cause for this is the absence of a metabolic cycle reproducing the substrate PEPC from its product. Advances in techniques of genetic, metabolic, protein and enzymes engineering make it possible to accomplish tasks that were previously considered impossible. Arren Bar-Even et al. suggested a hypothetical MOG cycle (from malonyl-CoA-oxaloacetate-glyoxylate) for the reproduction of PEPC substrate from its product, which should make it possible to abandon the use of RuBisCO and replace it with PEPC, which is expected to increase the efficiency of plant photosynthesis. This review analyzes the properties of the MOG cycle, and also suggests options for its modifications by adding other metabolic pathways. The possibility of further increasing the efficiency of photosynthesis through CO2 fixation at night is also being discussed.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"7 1","pages":"100006"},"PeriodicalIF":4.7,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12710033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Erratum to "Multidimensional Optimization of Saccharomyces cerevisiae for Carotenoid Overproduction". “酿酒酵母对类胡萝卜素过量生产的多维优化”的勘误。

生物设计研究(英文) Pub Date : 2024-12-11 eCollection Date: 2024-01-01 DOI: 10.34133/bdr.0061

Jian Fan, Yang Zhang, Wenhao Li, Zhizhen Li, Danli Zhang, Qiwen Mo, Mingfeng Cao, Jifeng Yuan

引用次数: 0

Multiomics Research: Principles and Challenges in Integrated Analysis. 多组学研究：综合分析的原则和挑战。

IF 7.2

生物设计研究(英文) Pub Date : 2024-12-05 eCollection Date: 2024-01-01 DOI: 10.34133/bdr.0059

Yunqing Luo, Chengjun Zhao, Fei Chen

{"title":"Multiomics Research: Principles and Challenges in Integrated Analysis.","authors":"Yunqing Luo, Chengjun Zhao, Fei Chen","doi":"10.34133/bdr.0059","DOIUrl":"10.34133/bdr.0059","url":null,"abstract":"Multiomics research is a transformative approach in the biological sciences that integrates data from genomics, transcriptomics, proteomics, metabolomics, and other omics technologies to provide a comprehensive understanding of biological systems. This review elucidates the fundamental principles of multiomics, emphasizing the necessity of data integration to uncover the complex interactions and regulatory mechanisms underlying various biological processes. We explore the latest advances in computational methodologies, including deep learning, graph neural networks (GNNs), and generative adversarial networks (GANs), which facilitate the effective synthesis and interpretation of multiomics data. Additionally, this review addresses the critical challenges in this field, such as data heterogeneity, scalability, and the need for robust, interpretable models. We highlight the potential of large language models to enhance multiomics analysis through automated feature extraction, natural language generation, and knowledge integration. Despite the important promise of multiomics, the review acknowledges the substantial computational resources required and the complexity of model tuning, underscoring the need for ongoing innovation and collaboration in the field. This comprehensive analysis aims to guide researchers in navigating the principles and challenges of multiomics research to foster advances in integrative biological analysis.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"6 ","pages":"0059"},"PeriodicalIF":7.2,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0