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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 Q1 Agricultural and Biological Sciences Pub Date : 2024-07-16 DOI: 10.1093/synbio/ysae011
Anna B. Matuszyńska, O. Ebenhöh, Matias D Zurbriggen, Daniel C Ducat, Ilka M. Axmann
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.
合成生物学将生物复杂性概念化为具有预定功能的生物部件、装置和系统网络,对基础研究和应用研究产生了革命性的影响。由于合成和跨生物体转移任何 DNA 和 RNA 的能力前所未有,合成生物学的范围不断扩大,并以以前无法想象的方式进行再创造。该领域已经发展到可以构建高度复杂网络的水平,例如合成生物的人工群落。与此同时,计算生物学也成为生物学研究不可或缺的一部分,计算模型有助于揭示生物现象不断升级的复杂性和新特性。然而,将建模完全融入合成设计过程仍有巨大的潜力尚未开发,这为科学进步带来了令人兴奋的机遇。在此,我们首先重点介绍微生物群落计算机辅助设计的最新进展。接下来,我们提出,这种设计可以受益于无生物模块建模方法,这种方法将重点放在生物功能模块上,从而设计出多物种群落。我们主张转变视角,从以单一生物为中心的方法转向强调群落内生物的功能贡献。通过使用具有部件和电路数学描述的模块化计算模型组装合成生物系统,我们可以定制生物体,使其在群落中发挥特定的功能作用。这种方法符合合成生物学战略,为设计人工群落提供了令人兴奋的可能性。
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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 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-15 DOI: 10.1093/synbio/ysae009
Alexis Casas, Matthieu Bultelle, Richard Kitney
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. 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). 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.
本文探讨了工程生物学战略和技术在实验室工作流程自动化中的应用--主要是在基于设计、构建、测试和学习范式的生物铸造和生物设计应用中。提高自动化程度的趋势伴随着一系列挑战。一方面,自动化与更高的吞吐量和更高的可复制性相关。另一方面,实施自动化工作流程所需的指令集远比手动工作流程要广泛得多。自动化任务还必须按照工作流程中指定的顺序,以正确的逻辑,利用适当的生物资源,大规模地进行,同时收集测量结果和相关数据。本文介绍了一种自动化工作流程方法,该方法正在伦敦生物实验室 SynbiCITE 试用。该解决方案用有向图表示工作流,使用协调器执行工作流,并依赖于现有标准。该方法非常灵活,不仅适用于单一地点的工作流自动化,也适用于分布式工作流(如生物制造)。最后一节概述了该方法的实施--以基于稀释、测量和数据分析工作流程的化验为例。
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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 Q1 Agricultural and Biological Sciences 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
Giant unilamellar vesicles (GUVs) provide a powerful model compartment for synthetic cells. However, a key challenge is the incorporation of membrane proteins that allow for transport, energy transduction, compartment growth and division. Here, we have successfully incorporated the membrane protein complex SecYEG – the key bacterial translocase that is essential for the incorporation of newly synthesized membrane proteins – in GUVs. Our method consists of fusion of small unilamellar vesicles (SUVs) containing reconstituted SecYEG into GUVs, thereby forming SecGUVs. These are suitable for large scale experiments while maintaining a high protein:lipid ratio. We demonstrate that incorporation of SecYEG into GUVs does not inhibit its translocation efficiency. Robust membrane protein functionalized proteo-GUVs are promising and flexible compartments for use in the formation and growth of synthetic cells.
巨型单拉米尔囊泡 (GUV) 为合成细胞提供了一个强大的模型区室。然而,一个关键的挑战是如何将用于运输、能量转移、细胞生长和分裂的膜蛋白结合到细胞中。在这里,我们成功地在 GUV 中加入了膜蛋白复合物 SecYEG--这是一种关键的细菌转运酶,对于加入新合成的膜蛋白至关重要。我们的方法是将含有重组 SecYEG 的小型单淀粉囊泡 (SUV) 融合到 GUVs 中,从而形成 SecGUVs。这种方法适用于大规模实验,同时还能保持较高的蛋白质:脂质比率。我们证明,将 SecYEG 加入 GUVs 不会抑制其转运效率。强大的膜蛋白功能化蛋白-GUVs 是用于合成细胞形成和生长的前景广阔的灵活隔室。
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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 Q1 Agricultural and Biological Sciences Pub Date : 2024-04-16 DOI: 10.1093/synbio/ysae006
Sonja Billerbeck
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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 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-16 DOI: 10.1093/synbio/ysae003
David M. Truong
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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 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-13 DOI: 10.1093/synbio/ysae002
C. Cialek
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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 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-22 DOI: 10.1093/synbio/ysad017
Alexander Ditzel, Fanglong Zhao, Xue Gao, George N Phillips
Natural products are a valuable source of pharmaceuticals, providing a majority of the small molecule drugs in use today. However, their production through organic synthesis or in heterologous hosts can be difficult and time-consuming. Therefore, to allow for easier screening and production of natural products, we demonstrated the use of a cell-free protein synthesis (CFPS) system to partially assemble natural products in vitro using SAM-dependent methyltransferase enzyme reactions. The tea caffeine synthase TCS1 was utilized to synthesize caffeine within a CFPS system. Cell-free systems also provide the benefit of allowing the use of substrates that would normally be toxic in a cellular environment to synthesize novel products. However, TCS1 is unable to utilize a compound like AdoEt as a cofactor to create ethylated caffeine analogs. The automation and reduced metabolic engineering requirements of CFPS systems, in combination with other synthesis methods, may enable the more efficient generation of new compounds.
天然产物是宝贵的药物来源,提供了当今使用的大部分小分子药物。然而,通过有机合成或在异源宿主中生产天然产物既困难又耗时。因此,为了更容易地筛选和生产天然产物,我们展示了使用无细胞蛋白质合成(CFPS)系统,利用依赖于SAM的甲基转移酶酶促反应,在体外部分组装天然产物。我们利用茶叶咖啡因合成酶 TCS1 在 CFPS 系统中合成咖啡因。无细胞系统的好处还在于可以使用在细胞环境中通常有毒的底物来合成新产品。但是,TCS1 无法利用像 AdoEt 这样的化合物作为辅助因子来制造乙基化的咖啡因类似物。CFPS 系统与其他合成方法相结合,可实现自动化并降低代谢工程要求,从而更有效地生成新化合物。
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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 Q1 Agricultural and Biological Sciences Pub Date : 2023-01-01 DOI: 10.1093/synbio/ysad014
Matthew W Lux, Elizabeth A Strychalski, Gary J Vora
Abstract Reproducibility has been identified as an outstanding challenge in science, and the field of synthetic biology is no exception. Meeting this challenge is critical to allow the transformative technological capabilities emerging from this field to reach their full potential to benefit the society. We discuss the current state of reproducibility in synthetic biology and how improvements can address some of the central shortcomings in the field. We argue that the successful adoption of reproducibility as a routine aspect of research and development requires commitment spanning researchers and relevant institutions via education, incentivization and investment in related infrastructure. The urgency of this topic pervades synthetic biology as it strives to advance fundamental insights and unlock new capabilities for safe, secure and scalable applications of biotechnology. Graphical Abstract
摘要:可重复性一直被认为是科学领域的一个突出挑战,合成生物学领域也不例外。迎接这一挑战对于让这一领域出现的变革性技术能力充分发挥其造福社会的潜力至关重要。我们讨论了合成生物学中可重复性的现状,以及如何改进可以解决该领域的一些主要缺点。我们认为,要成功地将可重复性作为研究和开发的常规方面,需要研究人员和相关机构通过教育、激励和相关基础设施投资做出承诺。这个主题的紧迫性遍及合成生物学,因为它努力推进基本见解,并为安全、可靠和可扩展的生物技术应用解锁新的能力。图形抽象
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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 Q1 Agricultural and Biological Sciences 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

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.

我们的实验活动采用了美国国防部高级研究计划局协同发现与设计计划开发的新型高通量实验框架:Strateos 的远程机器人实验室执行参数化的实验方案。利用该实验方案和机器人执行,我们生成的流式细胞仪数据比原始实验多出两个数量级。我们讨论了我们的结果,这些结果与原始报告基本一致,但不完全一致,我们还总结了一些经验教训。图表摘要。
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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 Q1 Agricultural and Biological Sciences Pub Date : 2022-05-03 DOI: 10.1093/synbio/ysac007
A. Ellington, Christopher R. Reisch
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
重组是基因编辑的重要工具,能够实现微生物基因组的快速、精确和高度特异性的体内修饰。通过在体内产生单链DNA的寡核苷酸介导的重组可以克服传统重组方法依赖外源传递编辑模板的局限性。通过修改先前报道的基于质粒的全体内单链DNA重组系统,我们展示了独立位点的迭代编辑,利用温度敏感的复制起源,使编辑质粒易于从重组细胞中固化。优化驱动系统功能组件表达的启动子,结合针对Cas9核酸酶未编辑细胞的靶向反选择,使编辑效率达到90-100%。在系统中添加一个显性负互l等位基因允许单核苷酸编辑,否则由于错配修复而无法实现。最后,我们测试了替代重组酶,发现某些目标的效率显著提高。只需要一个克隆步骤重定位,我们的系统提供了一种易于使用的方法,快速,有效地构建所需的突变体。图形抽象
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引用次数: 2
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Synthetic Biology
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