生物设计研究(英文)最新文献_第2页

Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology. 单细胞转录组学在植物系统和合成生物学中的应用进展。

生物设计研究(英文) Pub Date : 2024-02-29 eCollection Date: 2024-01-01 DOI: 10.34133/bdr.0029

Md Torikul Islam, Yang Liu, Md Mahmudul Hassan, Paul E Abraham, Jean Merlet, Alice Townsend, Daniel Jacobson, C Robin Buell, Gerald A Tuskan, Xiaohan Yang

{"title":"Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology.","authors":"Md Torikul Islam, Yang Liu, Md Mahmudul Hassan, Paul E Abraham, Jean Merlet, Alice Townsend, Daniel Jacobson, C Robin Buell, Gerald A Tuskan, Xiaohan Yang","doi":"10.34133/bdr.0029","DOIUrl":"10.34133/bdr.0029","url":null,"abstract":"Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140023395","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

Ice Cores as a Source for Antimicrobials: From Bioprospecting to Biodesign. 冰芯作为抗菌药物的来源：从生物勘探到生物设计。

生物设计研究(英文) Pub Date : 2023-11-02 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0024

Ying-Chiang Jeffrey Lee, Bahar Javdan

{"title":"Ice Cores as a Source for Antimicrobials: From Bioprospecting to Biodesign.","authors":"Ying-Chiang Jeffrey Lee, Bahar Javdan","doi":"10.34133/bdr.0024","DOIUrl":"https://doi.org/10.34133/bdr.0024","url":null,"abstract":"The golden age has passed for antibiotic discovery, and while some antibiotics are currently in various phases of clinical trials in the United States, many pharmaceutical companies have abandoned antibiotic research. With the need for antibiotics, we should expand our horizon for therapeutic mining and can look toward understudied sources such as ice cores. Ice cores contain microorganisms and genetic material that have been frozen in time for thousands of years. The antibiotics used by these organisms are encoded in their genomes, which can be unlocked, identified, and characterized with modern advances in molecular biology, genetic sequencing, various computational approaches, and established natural product discovery pipelines. While synthetic biology can be used in natural product discovery approaches, synthetic biology and bioengineering efforts can also be leveraged in the selection and biodesign of increased compound yields, potency, and stability. Here, we provide the perspective that ice cores can be a source of novel antibiotic compounds and that the tools of synthetic biology can be used to design better antimicrobials.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10623340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489482","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

Design and Construction of Artificial Biological Systems for One-Carbon Utilization. 一碳利用人工生物系统的设计与构建。

生物设计研究(英文) Pub Date : 2023-10-31 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0021

Wei Zhong, Hailong Li, Yajie Wang

{"title":"Design and Construction of Artificial Biological Systems for One-Carbon Utilization.","authors":"Wei Zhong, Hailong Li, Yajie Wang","doi":"10.34133/bdr.0021","DOIUrl":"https://doi.org/10.34133/bdr.0021","url":null,"abstract":"The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10616972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429606","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 Plant Synthetic Genomics. 走向植物合成基因组学。

生物设计研究(英文) Pub Date : 2023-10-16 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0020

Yuling Jiao, Ying Wang

引用次数: 0

CRISPR-Cas-Based Engineering of Probiotics. 基于CRISPR-Cas的益生菌工程。

生物设计研究(英文) Pub Date : 2023-09-29 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0017

Ling Liu, Shimaa Elsayed Helal, Nan Peng

引用次数: 1

Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology. 揭示与生理学相一致的工程遗传逆变器的宿主依赖性。

生物设计研究(英文) Pub Date : 2023-08-16 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0016

Dennis Tin Chat Chan, Geoff S Baldwin, Hans C Bernstein

{"title":"Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology.","authors":"Dennis Tin Chat Chan, Geoff S Baldwin, Hans C Bernstein","doi":"10.34133/bdr.0016","DOIUrl":"https://doi.org/10.34133/bdr.0016","url":null,"abstract":"Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to \"model status,\" synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the \"chassis effect.\" It remains a major challenge to uncover which genome-encoded and biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of genetic circuit performance. This was accomplished using a comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis effect and characterize the performance dynamics of a genetic inverter circuit operating within 6 Gammaproteobacteria. Our results solidify the notion that genetic devices are strongly impacted by the host context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar performance of the genetic inverter, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10432152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241393","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: 1

Plant Promoters and Terminators for High-Precision Bioengineering. 高精度生物工程的植物启动子和终止子。

生物设计研究(英文) Pub Date : 2023-07-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0013

Emily G Brooks, Estefania Elorriaga, Yang Liu, James R Duduit, Guoliang Yuan, Chung-Jui Tsai, Gerald A Tuskan, Thomas G Ranney, Xiaohan Yang, Wusheng Liu

引用次数: 0

Atligator Web: A Graphical User Interface for Analysis and Design of Protein-Peptide Interactions. Atligator Web：用于分析和设计蛋白质-肽相互作用的图形用户界面。

生物设计研究(英文) Pub Date : 2023-05-04 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0011

Josef Paul Kynast, Birte Höcker

{"title":"Atligator Web: A Graphical User Interface for Analysis and Design of Protein-Peptide Interactions.","authors":"Josef Paul Kynast, Birte Höcker","doi":"10.34133/bdr.0011","DOIUrl":"https://doi.org/10.34133/bdr.0011","url":null,"abstract":"A key functionality of proteins is based on their ability to form interactions with other proteins or peptides. These interactions are neither easily described nor fully understood, which is why the design of specific protein-protein interaction interfaces remains a challenge for protein engineering. We recently developed the software ATLIGATOR to extract common interaction patterns between different types of amino acids and store them in a database. The tool enables the user to better understand frequent interaction patterns and find groups of interactions. Furthermore, frequent motifs can be directly transferred from the database to a user-defined scaffold as a starting point for the engineering of new binding capabilities. Since three-dimensional visualization is a crucial part of ATLIGATOR, we created ATLIGATOR web-a web server offering an intuitive graphical user interface (GUI) available at https://atligator.uni-bayreuth.de. This new interface empowers users to apply ATLIGATOR by providing easy access with having all parts directly connected. Moreover, we extended the web by a design functionality so that, overall, ATLIGATOR web facilitates the use of ATLIGATOR with a more intuitive UI and advanced design options.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241384","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

Exploring the Trans-Cleavage Activity with Rolling Circle Amplification for Fast Detection of miRNA. 用滚环扩增技术探索miRNA的反式切割活性。

生物设计研究(英文) Pub Date : 2023-03-27 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0010

Chenqi Niu, Juewen Liu, Xinhui Xing, Chong Zhang

引用次数: 0

SLICER: A Seamless Gene Deletion Method for Deinococcus radiodurans. SLICER:一种针对耐辐射球菌的无缝基因缺失方法。

生物设计研究(英文) Pub Date : 2023-03-15 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0009

Stephanie L Brumwell, Katherine D Van Belois, Daniel P Nucifora, Bogumil J Karas

{"title":"SLICER: A Seamless Gene Deletion Method for Deinococcus radiodurans.","authors":"Stephanie L Brumwell, Katherine D Van Belois, Daniel P Nucifora, Bogumil J Karas","doi":"10.34133/bdr.0009","DOIUrl":"10.34133/bdr.0009","url":null,"abstract":"Deinococcus radiodurans' high resistance to various stressors combined with its ability to utilize sustainable carbon sources makes it an attractive bacterial chassis for synthetic biology and industrial bioproduction. However, to fully harness the capabilities of this microbe, further strain engineering and tool development are required. Methods for creating seamless genome modifications are an essential part of the microbial genetic toolkit to enable strain engineering. Here, we report the development of the SLICER method, which can be used to create seamless gene deletions in D. radiodurans. This process involves (a) integration of a seamless deletion cassette replacing a target gene, (b) introduction of the pSLICER plasmid to mediate cassette excision by I-SceI endonuclease cleavage and homologous recombination, and (c) curing of the helper plasmid. We demonstrate the utility of SLICER for creating multiple gene deletions in D. radiodurans by sequentially targeting 5 putative restriction-modification system genes, recycling the same selective and screening markers for each subsequent deletion. While we observed no significant increase in transformation efficiency for most of the knockout strains, we demonstrated SLICER as a promising method to create a fully restriction-minus strain to expand the synthetic biology applications of D. radiodurans, including its potential as an in vivo DNA assembly platform.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241394","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