India-UK Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research
Lead Research Organisation:
Oxford Brookes University
Department Name: Faculty of Health and Life Sciences
Abstract
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Publications
Adlakha N
(2015)
Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008.
in Biotechnology for biofuels
Ahmad A
(2017)
A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate.
in Journal of biotechnology
Fatma Z
(2018)
Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production.
in Metabolic engineering
Description | Metabolic modelling can be used to design metabolic engineering strategies for biotechnological production. We designed genetic modifications to increase the production of alkanes suitable for biofuel in the organism E. coli. (This work has been published in Metabolic Engineering and the model made available for others to use.) We have devised strategies to produce platform chemicals from carbohydrates in Geobacillus thermoglucosidasius using our genome scale metabolic model. This work was continued as part of the RiceFuel follow-on award, These results have also been published and the model made available. |
Exploitation Route | The metabolic engineering strategy can equally be applied to other potential products from G. thermoglucosidasius and E. coli. |
Sectors | Chemicals Energy Manufacturing including Industrial Biotechology |
URL | https://wwwdev.ebi.ac.uk/biomodels/MODEL1703060000 |
Description | BBSRC - India DBT Sustainable Bioenergy and Biofuels |
Amount | £1,393,966 (GBP) |
Funding ID | BB/K020358/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2013 |
End | 11/2017 |
Title | E coli central carbon metabolism model for alkane synthesis |
Description | Currently available from our web server at http://mudshark.brookes.ac.uk/Models/EcoliCCM. Submitted to https://wwwdev.ebi.ac.uk/biomodels/ as MODEL1802080001; awaiting validation. |
Type Of Material | Computer model/algorithm |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Currently the highest yield of alkane from fermentation by E coli, after genetic manipulations designed by analysis of the model. |
URL | http://mudshark.brookes.ac.uk/Models/EcoliCCM |
Title | GSM of Geobacillus |
Description | Genome scale metabolic model of Geobacillus thermoglucosidasius - thermophile of interest for development as a biotechnological chassis. |
Type Of Material | Computer model/algorithm |
Provided To Others? | No |
Impact | None to date. |
Description | Indian partners |
Organisation | International Centre for Genetic Engineering and Biotechnology |
Country | Italy |
Sector | Academic/University |
PI Contribution | Training of visiting students from the partners in metabolic modelling techniques to assist in their metabolic engineering projects. Running two one week modelling workshops in ICGEB, New Delhi, to train staff and students from the collaborators in techniques of metabolic modelling and their application to biotechnology. |
Collaborator Contribution | Provision of visiting PhD students to work in our group (4 visits by 3 PhD students), and one to work at University of Aberdeen with partner Oliver Ebenhoeh. |
Impact | Three articles in biotechnology journals. Two metabolic models submitted to BioModels database. Follow-on funding through BBSRC/India RiceFuel award to Nigel Minton. (PI, University of Nottingham). |
Start Year | 2012 |
Description | Indian partners |
Organisation | Jawaharlal Nehru University, India |
Country | India |
Sector | Academic/University |
PI Contribution | Training of visiting students from the partners in metabolic modelling techniques to assist in their metabolic engineering projects. Running two one week modelling workshops in ICGEB, New Delhi, to train staff and students from the collaborators in techniques of metabolic modelling and their application to biotechnology. |
Collaborator Contribution | Provision of visiting PhD students to work in our group (4 visits by 3 PhD students), and one to work at University of Aberdeen with partner Oliver Ebenhoeh. |
Impact | Three articles in biotechnology journals. Two metabolic models submitted to BioModels database. Follow-on funding through BBSRC/India RiceFuel award to Nigel Minton. (PI, University of Nottingham). |
Start Year | 2012 |
Title | ScrumPy |
Description | Integrated set of Python modules for metabolic modelling, encompassing kinetic models, metabolic control analysis, elementary modes analysis and flux balance analysis. It has been continually updated and extended since its initial public release in 2009. |
Type Of Technology | Software |
Open Source License? | Yes |
Impact | It has been the major modelling tool used to generate all outputs from my research group since 2003. It has been adopted as a modelling tool in a number of other research groups, including the Ebenhoeh group (Aberdeen and Dortmund), the University of Nottingham Synthetic Biology Centre (Minton et al), Yazdani group (International Centre for genetic Engineering and Biotechnology, Delhi) and Kundu group (University of Calcutta). It has been used as a teaching tool in metabolic modelling workshops run as part of a UK-India Partnering award and for the NIBB C1 net. |
URL | http://mudshark.brookes.ac.uk/ScrumPy |