Assay Development Platforms

检测开发平台

• 批准号: BB/M025659/1
• 负责人: Susan Rosser
• 金额: $ 302.73万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM025659%2F1
• 关键词: Assay; Development; Platforms

Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature and to redesign existing biological systems to perform new functions. The construction de novo of large and complex genetic circuits or metabolic pathways will enable us to for example, program stem cell differentiation, detect multiple changes in cancer cells, or engineer cell factories to produce completely novel drugs or greener chemicals and biofuels. The conventional approach of engineering cells at the bench is inherently slow and expensive. Automation and industrialization reduce development time and the economies of scale of medium to high throughput processes can reduce the cost of organism development democratising the endeavour and allowing an expansion in the number of academic groups and industries that can undertake such complex organism engineering. To realise our ambitions for synthetic biology we need enabling technologies that can not only provide robust, reliable and cost effective methodologies for the design, construction and incorporation of synthetic DNA we need to understand the interaction of the component or pathway with the host and capture holistic datasets that report back on synthetic part and pathway performance, cell growth and health.The initial BBSRC investment (BBM00029X1 andBBM00094X1) has helped found two DNA synthesis centres, the Edinburgh Genome Foundry (EGF, based in the School of Biological Sciences) and Liverpool GeneMill (LGM, based within the Centre for Genomic Research CGR) offering DNA design, synthesis and validation of large gene constructs (up to 1Mbp). However, we need to further expand our capabilities to include high throughput assay development suited to assessing whether the DNA construct delivers the desired output (i.e. phenotype) in the host cell. Here we request support for capital equipment that will enable us to set up multi parallel medium throughput assays for cell health, function and productivity. Alongside these platforms we build the software tools for automation and analysis, together with software to integrate this data with the design and fabrication pipelines. This will provide the data needed to inform the future design of refined DNA constructs, accelerate the design build test cycle, improve efficiency and reduce the cost of application of synthetic biology applications. Ultimately this will help drive growth of the markets than can benefit from synthetic biology and add value to the initial investment in the DNA synthesis centres.

合成生物学寻求建模和构建自然界中不存在的生物成分、功能和生物体，并重新设计现有的生物系统以执行新功能。例如，从头构建大型复杂的遗传回路或代谢途径将使我们能够对干细胞分化进行编程，检测癌细胞的多种变化，或设计细胞工厂以生产全新的药物或更环保的化学品和生物燃料。在工作台上设计细胞的传统方法本质上是缓慢且昂贵的。自动化和工业化减少了开发时间，中高通量过程的规模经济可以降低生物体开发的成本，使工作民主化，并允许扩大能够进行此类复杂生物体工程的学术团体和行业的数量。为了实现我们对合成生物学的雄心，我们需要的技术不仅能够为合成 DNA 的设计、构建和掺入提供稳健、可靠和具有成本效益的方法，我们还需要了解成分或途径与宿主的相互作用，并捕获报告合成部分和途径性能、细胞生长和健康状况的整体数据集。BBSRC 的初始投资（BBM00029X1 和 BBM00094X1） 帮助建立了两个 DNA 合成中心，爱丁堡基因组铸造厂（EGF，位于生物科学学院）和利物浦 GeneMill（LGM，位于基因组研究中心 CGR），提供大型基因构建体（高达 1Mbp）的 DNA 设计、合成和验证。然而，我们需要进一步扩展我们的能力，包括适合评估 DNA 构建体是否在宿主细胞中提供所需输出（即表型）的高通量测定开发。在此，我们请求对固定设备的支持，使我们能够针对细胞健康、功能和生产力建立多个并行介质通量测定。除了这些平台之外，我们还构建了用于自动化和分析的软件工具，以及将这些数据与设计和制造流程集成的软件。这将提供所需的数据，为未来精制 DNA 构建体的设计提供信息、加快设计构建测试周期、提高效率并降低合成生物学应用的应用成本。最终，这将有助于推动市场的增长，从而受益于合成生物学，并为 DNA 合成中心的初始投资增加价值。

项目成果

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

Galaxy-SynBioCAD：Galaxy 工作流程中的合成生物学设计自动化工具

• DOI: 10.1101/2020.06.14.145730
• 发表时间: 2020
• 作者: Du Lac M

SynBiopython: an open-source software library for Synthetic Biology

• DOI: 10.1093/synbio/ysab001
• 发表时间: 2021-02-22
• 期刊: Synthetic Biology
• 影响因子: 3.2
• 作者: Yeoh JW;Swainston N;Vegh P;Zulkower V;Carbonell P;Holowko MB;Peddinti G;Poh CL
• 通讯作者: Poh CL

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

Leaf LIMS：以合成生物学为重点的灵活实验室信息管理系统。

• DOI: 10.1021/acssynbio.7b00212
• 发表时间: 2017
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Craig T

CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax

• DOI: 10.1104/pp.18.01401
• 发表时间: 2019-05-01
• 期刊: PLANT PHYSIOLOGY
• 影响因子: 7.4
• 作者: Vasudevan, Ravendran;Gale, Grant A. R.;McCormick, Alistair J.
• 通讯作者: McCormick, Alistair J.

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.

• DOI: 10.1038/s41467-022-32661-x
• 发表时间: 2022-08-29
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Herisson, Joan;Duigou, Thomas;du Lac, Melchior;Bazi-Kabbaj, Kenza;Azad, Mahnaz Sabeti;Buldum, Gizem;Telle, Olivier;El Moubayed, Yorgo;Carbonell, Pablo;Swainston, Neil;Zulkower, Valentin;Kushwaha, Manish;Baldwin, Geoff S.;Faulon, Jean-Loup
• 通讯作者: Faulon, Jean-Loup