生物设计研究(英文)最新文献_第2页

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: 2

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

Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease. 活酵母生物传感器通过表位选择性蛋白酶检测肽变体。

生物设计研究(英文) Pub Date : 2023-03-15 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0003

Tea Crnković, Benjamin J Bokor, Mead E Lockwood, Virginia W Cornish

{"title":"Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease.","authors":"Tea Crnković, Benjamin J Bokor, Mead E Lockwood, Virginia W Cornish","doi":"10.34133/bdr.0003","DOIUrl":"https://doi.org/10.34133/bdr.0003","url":null,"abstract":"We previously demonstrated that we could hijack the fungal pheromone signaling pathway to provide a living yeast biosensor where peptide biomarkers were recognized by G-protein-coupled receptors and engineered to transcribe a readout. Here, we demonstrated that the protease could be reintroduced to the biosensor to provide a simple mechanism for distinguishing single-amino-acid changes in peptide ligands that, otherwise, would likely be difficult to detect using binding-based assays. We characterized the dose-response curves for five fungal pheromone G-protein-coupled receptors, peptides, and proteases-Saccharomyces cerevisiae, Candida albicans, Schizosaccharomyces pombe, Schizosaccharomyces octosporus, and Schizosaccharomyces japonicus. Alanine scanning was carried out for the most selective of these-S. cerevisiae and C. albicans-with and without the protease. Two peptide variants were discovered, which showed diminished cleavage by the protease (CaPep2A and CaPep2A13A). Those peptides were then distinguished by utilizing the biosensor strains with and without the protease, which selectively cleaved and altered the apparent concentration of peptide required for half-maximal activation for 2 peptides-CaPep and CaPep13A, respectively-by more than one order of magnitude. These results support the hypothesis that the living yeast biosensor with a sequence-specific protease can translate single-amino-acid changes into more than one order of magnitude apparent shift in the concentration of peptide required for half-maximal activation. With further engineering by computational modeling and directed evolution, the biosensor could likely distinguish a wide variety of peptide sequences beyond the alanine scanning carried out here. In the future, we envision incorporating proteases into our living yeast biosensor for use as a point of care diagnostic, a scalable communication language, and other applications.","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/PMC10084949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241389","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

The Need for Biosecurity Education in Biotechnology Curricula. 生物技术课程中生物安全教育的必要性。

生物设计研究(英文) Pub Date : 2023-03-14 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0008

Ying-Chiang J Lee, Xuanqi Chen, Siddharth Marwaha

引用次数: 0

Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution. 用于合成固氮的工程固氮酶：从路径工程到定向进化。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0005

Emily M Bennett, James W Murray, Mark Isalan

引用次数: 5

De Novo Design and Synthesis of Polypeptide Immunomodulators for Resetting Macrophage Polarization. 用于重置巨噬细胞极化的多肽免疫调节剂的De Novo设计和合成。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0006

Na Kong, Hongru Ma, Zhongji Pu, Fengju Wan, Dongfang Li, Lei Huang, Jiazhang Lian, Xingxu Huang, Shengjie Ling, Haoran Yu, Yuan Yao

{"title":"De Novo Design and Synthesis of Polypeptide Immunomodulators for Resetting Macrophage Polarization.","authors":"Na Kong, Hongru Ma, Zhongji Pu, Fengju Wan, Dongfang Li, Lei Huang, Jiazhang Lian, Xingxu Huang, Shengjie Ling, Haoran Yu, Yuan Yao","doi":"10.34133/bdr.0006","DOIUrl":"https://doi.org/10.34133/bdr.0006","url":null,"abstract":"Modulating the extracellular matrix microenvironment is critical for achieving the desired macrophage phenotype in immune investigations or tumor therapy. Combining de novo protein design and biosynthesis techniques, herein, we designed a biomimetic polypeptide self-assembled nano-immunomodulator to trigger the activation of a specific macrophage phenotype. It was intended to be made up of (GGSGGPGGGPASAAANSASRATSNSP)n, the RGD motif from collagen, and the IKVAV motif from laminin. The combination of these domains allows the biomimetic polypeptide to assemble into extracellular matrix-like nanofibrils, creating an extracellular matrix-like milieu for macrophages. Furthermore, changing the concentration further provides a facile route to fine-tune macrophage polarization, which enhances antitumor immune responses by precisely resetting tumor-associated macrophage immune responses into an M1-like phenotype, which is generally considered to be tumor-killing macrophages, primarily antitumor, and immune-promoting. Unlike metal or synthetic polymer-based nanoparticles, this polypeptide-based nanomaterial exhibits excellent biocompatibility, high efficacy, and precise tunability in immunomodulatory effectiveness. These encouraging findings motivate us to continue our research into cancer immunotherapy applications in the future.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241386","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

qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing. qSanger：通过Sanger测序对细菌培养物中的遗传变异进行量化。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0007

Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo

{"title":"qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing.","authors":"Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo","doi":"10.34133/bdr.0007","DOIUrl":"10.34133/bdr.0007","url":null,"abstract":"Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241392","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