Manchester Institute for Biotechnology

Overview
No description specified

Programme: Independent Projects

SEEK ID: https://fairdomhub.org/projects/18

Public web page: Not specified

Organisms: Escherichia coli

FAIRDOM PALs: No PALs for this Project

Project created: 27th Aug 2014

Related items

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RobOKoD applied to e.coli for butanol production.
Manchester Institute for Biotechnology

RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).

Submitter: Natalie Stanford

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

OptKnock applied to e.coli for butanol production.
Manchester Institute for Biotechnology

OptKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

Submitter: Natalie Stanford

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

RobustKnock applied to e.coli for butanol production.
Manchester Institute for Biotechnology

RobustKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

Submitter: Natalie Stanford

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

1 hidden item
FBA result of RobOKoD designed e.coli strain.
Manchester Institute for Biotechnology

FBA result of flux distribution in butanol producing e.coli strain, which designed using RobOKoD.

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
2 hidden items
iNS142 RobOKoD Redesigned Butanol Producing.
Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology

Butanol producing iNS142, redesigned using RobOKoD.

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
E.coli Core Model with Beta Oxidation Cycle.
Manchester Institute for Biotechnology

E.coli Core model, with additional reactions added to generate the beta-oxadation cycle. This is the basic model used in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
RobOKoD SOP for Redesigning Butanol Producing Strain of E.coli.
Manchester Institute for Biotechnology

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
OptKnock SOP for Redesigning Butanol Producing Strain of E.coli.
Manchester Institute for Biotechnology

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for OptKnock.

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
RobustKnock SOP for Redesigning Butanol Producing Strain of E.coli.
Manchester Institute for Biotechnology

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for RobustKnock.

Creator: Natalie Stanford

Submitter: Natalie Stanford

Download
RobOKoD: microbial strain design for (over)production of target compounds
Manchester Institute for Biotechnology

Abstract (Expand)

Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical, and chemical industries is becoming an increasing priority given their current … dependency upon diminishing petrochemical resources. Designing these strains is difficult, with current methods focusing primarily on knocking-out genes, dismissing other vital steps of strain design including the overexpression and dampening of genes. The design predictions from current methods also do not translate well-into successful strains in the laboratory. Here, we introduce RobOKoD (Robust, Overexpression, Knockout and Dampening), a method for predicting strain designs for overproduction of targets. The method uses flux variability analysis to profile each reaction within the system under differing production percentages of target-compound and biomass. Using these profiles, reactions are identified as potential knockout, overexpression, or dampening targets. The identified reactions are ranked according to their suitability, providing flexibility in strain design for users. The software was tested by designing a butanol-producing Escherichia coli strain, and was compared against the popular OptKnock and RobustKnock methods. RobOKoD shows favorable design predictions, when predictions from these methods are compared to a successful butanol-producing experimentally-validated strain. Overall RobOKoD provides users with rankings of predicted beneficial genetic interventions with which to support optimized strain design.

Authors: N. J. Stanford, P. Millard, N. Swainston

Date Published: 24th Mar 2015

Publication Type: Not specified

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