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Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway

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Title: Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway
Authors: Exley, K
Reynolds, C
Suckling, L
Chee, SM
Tsipa, A
Freemont, P
McClymont, D
Kitney, R
Item Type: Journal Article
Abstract: Background The automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. To manage the design of genetic pathways, researchers have turned to modelling-based computer aided design software tools. Result An automated workflow has been developed for the design and build of heterologous metabolic pathways. In addition, to demonstrate the powers of electronic datasheets we have developed software which can transfer part information from a datasheet to the Design of Experiment software JMP. To this end we were able to use Design of Experiment software to rationally design and test randomised samples from the design space of a lycopene pathway in E. coli. This pathway was optimised by individually modulating the promoter strength, RBS strength, and gene order targets. Conclusion The use of standardised and characterised biological parts will empower a design-oriented synthetic biology for the forward engineering of heterologous expression systems. A Design of Experiment approach streamlines the design-build-test cycle to achieve optimised solutions in biodesign. Developed automated workflows provide effective transfer of information between characterised information (in the form of datasheets) and DoE software.
Issue Date: 18-Jan-2019
Date of Acceptance: 7-Jan-2019
URI: http://hdl.handle.net/10044/1/66973
DOI: https://dx.doi.org/10.1186/s13036-019-0141-z
ISSN: 1754-1611
Publisher: BioMed Central
Journal / Book Title: Journal of Biological Engineering
Volume: 13
Copyright Statement: © The Author(s). 2019Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link tothe Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Sponsor/Funder: Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Funder's Grant Number: EP/K038648/1
EP/L011573/1
EP/M006700/1
EP/N023854/1
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biotechnology & Applied Microbiology
Biochemistry & Molecular Biology
Synthetic biology
Datasheets
Design of Experiment (DoE)
Automation workflow
ESCHERICHIA-COLI
STANDARD
BIOLOGY
Biotechnology
Publication Status: Published
Article Number: ARTN 8
Appears in Collections:Faculty of Engineering
Bioengineering
Department of Medicine
Faculty of Medicine



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