Synthetic Biology最新文献

A new era of Synthetic Biology - microbial community design 合成生物学的新时代--微生物群落设计

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-07-16 DOI: 10.1093/synbio/ysae011

Anna B. Matuszyńska, O. Ebenhöh, Matias D Zurbriggen, Daniel C Ducat, Ilka M. Axmann

{"title":"A new era of Synthetic Biology - microbial community design","authors":"Anna B. Matuszyńska, O. Ebenhöh, Matias D Zurbriggen, Daniel C Ducat, Ilka M. Axmann","doi":"10.1093/synbio/ysae011","DOIUrl":"https://doi.org/10.1093/synbio/ysae011","url":null,"abstract":"\u0000 Synthetic biology conceptualises biological complexity as a network of biological parts, devices and systems with predetermined functionalities, and has had a revolutionary impact on fundamental and applied research. With the unprecedented ability to synthesise and transfer any DNA and RNA across organisms, the scope of synthetic biology is expanding and being recreated in previously unimaginable ways. The field has matured to a level where highly complex networks, such as artificial communities of synthetic organisms can be constructed. In parallel, computational biology became an integral part of biological studies, with computational models aiding the unravelling of the escalating complexity and emerging properties of biological phenomena. However, there is still a vast untapped potential for the complete integration of modelling into the synthetic design process, presenting exciting opportunities for scientific advancements. Here, we first highlight the most recent advances in computer-aided design of microbial communities. Next, we propose that such a design can benefit from an organism-free modular modelling approach that places its emphasis on modules of organismal function towards the design of multi-species communities. We argue for a shift in perspective from single organism-centred approaches to emphasising the functional contributions of organisms within the community. By assembling synthetic biological systems using modular computational models with mathematical descriptions of parts and circuits, we can tailor organisms to fulfil specific functional roles within the community. This approach aligns with synthetic biology strategies and presents exciting possibilities for the design of artificial communities.","PeriodicalId":22158,"journal":{"name":"Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Engineering Biology Approach to Automated Workflow and BioDesign 自动化工作流程和生物设计的工程生物学方法

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-06-15 DOI: 10.1093/synbio/ysae009

Alexis Casas, Matthieu Bultelle, Richard Kitney

{"title":"An Engineering Biology Approach to Automated Workflow and BioDesign","authors":"Alexis Casas, Matthieu Bultelle, Richard Kitney","doi":"10.1093/synbio/ysae009","DOIUrl":"https://doi.org/10.1093/synbio/ysae009","url":null,"abstract":"\u0000 The paper addresses the application of engineering biology strategy and techniques to the automation of laboratory workflow - primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend towards greater automation comes with its own set of challenges. On the one hand, automation is associated with higher throughput and with higher replicability. On the other hand, implementation of an automated workflow requires an instruction set that is far more extensive than for a manual workflow. Automated tasks must also be conducted in the order specified in the workflow, with the right logic, utilising suitable biofoundry resources, and at scale - whilst simultaneously collecting measurements and associated data.\u0000 The paper describes an approach to automated workflow that is being trialled at the London Biofoundry at SynbiCITE. The solution represents workflows with directed graphs, uses orchestrators for their execution and relies on existing standards. The approach is highly flexible and applies to not only workflow automation in single locations but also distributed workflows (e.g for biomanufacturing).\u0000 The final section presents an overview of the implementation - using the simple example of an assay based on a dilution, measurement and data analysis workflow.","PeriodicalId":22158,"journal":{"name":"Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141337572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SecYEG-mediated Translocation in a Model Synthetic Cell 合成细胞模型中 SecYEG 介导的转运

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-05-10 DOI: 10.1093/synbio/ysae007

Ludo L J Schoenmakers, Max J den Uijl, Jelle Postma, Tim A P van den Akker, Wilhelm T S Huck, Arnold J. M. Driessen

引用次数: 0

A new Editor-in-chief for Synthetic Biology 合成生物学》新任主编

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-04-16 DOI: 10.1093/synbio/ysae006

Sonja Billerbeck

引用次数: 0

Writing the Dark Matter of the Human Genome into Mice to better replicate human disease. 将人类基因组的暗物质写入小鼠体内，以更好地复制人类疾病。

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-01-16 DOI: 10.1093/synbio/ysae003

David M. Truong

引用次数: 0

On the path to generate electricity from wastewater through genetic engineering of Escherichia coli 通过大肠杆菌基因工程利用废水发电之路

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2024-01-13 DOI: 10.1093/synbio/ysae002

C. Cialek

引用次数: 0

Utilizing a Cell-free Protein Synthesis Platform for the Biosynthesis of a Natural Product, Caffeine 利用无细胞蛋白质合成平台生物合成天然产品咖啡因

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2023-12-22 DOI: 10.1093/synbio/ysad017

Alexander Ditzel, Fanglong Zhao, Xue Gao, George N Phillips

引用次数: 0

Advancing reproducibility can ease the ‘hard truths’ of synthetic biology 提高可重复性可以缓解合成生物学的“残酷事实”

4区生物学

Synthetic Biology Pub Date : 2023-01-01 DOI: 10.1093/synbio/ysad014

Matthew W Lux, Elizabeth A Strychalski, Gary J Vora

引用次数: 0

Highly-automated, high-throughput replication of yeast-based logic circuit design assessments. 基于酵母的逻辑电路设计评估的高自动化、高通量复制。

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2022-10-06 eCollection Date: 2022-01-01 DOI: 10.1093/synbio/ysac018

Robert P Goldman, Robert Moseley, Nicholas Roehner, Breschine Cummins, Justin D Vrana, Katie J Clowers, Daniel Bryce, Jacob Beal, Matthew DeHaven, Joshua Nowak, Trissha Higa, Vanessa Biggers, Peter Lee, Jeremy P Hunt, Lorraine Mosqueda, Steven B Haase, Mark Weston, George Zheng, Anastasia Deckard, Shweta Gopaulakrishnan, Joseph F Stubbs, Niall I Gaffney, Matthew W Vaughn, Narendra Maheshri, Ekaterina Mikhalev, Bryan Bartley, Richard Markeloff, Tom Mitchell, Tramy Nguyen, Daniel Sumorok, Nicholas Walczak, Chris Myers, Zach Zundel, Benjamin Hatch, James Scholz, John Colonna-Romano

{"title":"Highly-automated, high-throughput replication of yeast-based logic circuit design assessments.","authors":"Robert P Goldman, Robert Moseley, Nicholas Roehner, Breschine Cummins, Justin D Vrana, Katie J Clowers, Daniel Bryce, Jacob Beal, Matthew DeHaven, Joshua Nowak, Trissha Higa, Vanessa Biggers, Peter Lee, Jeremy P Hunt, Lorraine Mosqueda, Steven B Haase, Mark Weston, George Zheng, Anastasia Deckard, Shweta Gopaulakrishnan, Joseph F Stubbs, Niall I Gaffney, Matthew W Vaughn, Narendra Maheshri, Ekaterina Mikhalev, Bryan Bartley, Richard Markeloff, Tom Mitchell, Tramy Nguyen, Daniel Sumorok, Nicholas Walczak, Chris Myers, Zach Zundel, Benjamin Hatch, James Scholz, John Colonna-Romano","doi":"10.1093/synbio/ysac018","DOIUrl":"10.1093/synbio/ysac018","url":null,"abstract":"We describe an experimental campaign that replicated the performance assessment of logic gates engineered into cells of Saccharomyces cerevisiae by Gander et al. Our experimental campaign used a novel high-throughput experimentation framework developed under Defense Advanced Research Projects Agency's Synergistic Discovery and Design program: a remote robotic lab at Strateos executed a parameterized experimental protocol. Using this protocol and robotic execution, we generated two orders of magnitude more flow cytometry data than the original experiments. We discuss our results, which largely, but not completely, agree with the original report and make some remarks about lessons learned. Graphical Abstract.","PeriodicalId":22158,"journal":{"name":"Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9583850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87759237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient and iterative retron-mediated in vivo recombineering in Escherichia coli 高效迭代逆转录介导的大肠杆菌体内重组

IF 3.2 4区生物学

Synthetic Biology Pub Date : 2022-05-03 DOI: 10.1093/synbio/ysac007

A. Ellington, Christopher R. Reisch

{"title":"Efficient and iterative retron-mediated in vivo recombineering in Escherichia coli","authors":"A. Ellington, Christopher R. Reisch","doi":"10.1093/synbio/ysac007","DOIUrl":"https://doi.org/10.1093/synbio/ysac007","url":null,"abstract":"Abstract Recombineering is an important tool in gene editing, enabling fast, precise and highly specific in vivo modification of microbial genomes. Oligonucleotide-mediated recombineering via the in vivo production of single-stranded DNA can overcome the limitations of traditional recombineering methods that rely on the exogenous delivery of editing templates. By modifying a previously reported plasmid-based system for fully in vivo single-stranded DNA recombineering, we demonstrate iterative editing of independent loci by utilizing a temperature-sensitive origin of replication for easy curing of the editing plasmid from recombinant cells. Optimization of the promoters driving the expression of the system’s functional components, combined with targeted counterselection against unedited cells with Cas9 nuclease, enabled editing efficiencies of 90–100%. The addition of a dominant-negative mutL allele to the system allowed single-nucleotide edits that were otherwise unachievable due to mismatch repair. Finally, we tested alternative recombinases and found that efficiency significantly increased for some targets. Requiring only a single cloning step for retargeting, our system provides an easy-to-use method for rapid, efficient construction of desired mutants. Graphical Abstract","PeriodicalId":22158,"journal":{"name":"Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2022-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74123254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2