|
Size: 3205
Comment: removed abstract submission; added NSF travel grants.
|
Size: 8140
Comment: Updating news with Interfaces Focus, and adding citation info to papers.
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| === Meeting news === '''Metabolic Pathway Analysis 2013''' will be held in Oxford, 16-20 September. See its [[http://www.accliphot.eu/mpa-2013/|website]] for details. |
== News == == 50 years of Metabolic Control Analysis - an update == . Next year will be the 50th anniversary of the publication in 1973 of the papers by Kacser & Burns and Heinrich & Rapoport that led to the emergence of Metabolic Control Analysis as a distinct field. Following discussions between a section of the community (see [[MCAat50]]), approaches were made to some journals about the possibility of a Special Issue in 2023 devoted to MCA. |
| Line 7: | Line 8: |
| '''News:''' NSF has funded some travel grants for US attendees. ----- '''New paper online ahead of print:''' Maurice Cheung et al, A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions. The Plant Journal .[[http://onlinelibrary.wiley.com/doi/10.1111/tpj.12252/abstract|accepted manuscript]] |
. '''!BioSytems''' accepted our proposal and its Special Issue is now announced at https://www.sciencedirect.com/journal/biosystems/about/forthcoming-special-issues . . Submissions are open from November 2022 until January 2023 through the Editorial Manager portal at https://www.editorialmanager.com/biosys/default1.aspx citing the article type: '''VSI: MCA at 50: an update'''. Potential authors are invited to contact the Guest Editors with an outline of their intended contribution before submission; see [[MCAat50]] or the !BioSystems site for more detail. . . [[https://royalsocietypublishing.org/journal/rsfs|Interfaces Focus]] accepted a proposal from Herbert Sauro and Frank Bruggeman to edit a Themed Issue of the journal on MCA. Research articles and reviews will be commissioned by the editors, but they can be emailed with suggestions for content. See also [[MCAat50]]. |
| Line 11: | Line 13: |
| '''Previous paper: '''Mark G. Poolman, Sudip Kundu, Rahul Shaw and David A Fell. Responses to Light Intensity in a Genome–Scale Model of Rice Metabolism. ''Plant Physiology'', 162, 1060-1072, 2013, [[./Publications/articles|PDF]] available. [ [[http://dx.doi.org/10.1104/pp.113.216762|DOI: 10.1104/pp.113.216762]] ] ----- = Background = Our '''group''' began nearly thirty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results. Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team. Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals. |
== International Study Group for Systems Biology 2022 == . This will be held in September; information is available on the [[https://site.uit.no/isgsb/|current ISGSB site]]. |
| Line 21: | Line 17: |
| == Latest papers: == 1. Emily Stoakes, George Savva, Ruby Coates, Noemi Tejera, Mark Poolman, Andrew J Grant, John Wain, Dipali Singh (2022) ''Substrate utilisation and energy metabolism in non-growing ''Campylobacter jejuni'' M1cam.'' Microorganisms'', '''''10''' (7), 1355, 2022. https://doi.org/10.3390/microorganisms10071355 1. Pearcy N, Garavaglia M, Millat T, Gilbert JP, Song Y, Hartman H, Woods C, Tomi-Andrino C, Bommareddy RR, Cho BK, Fell DA, Poolman M, King JR, Winzer K, Twycross J, Minton NP (2022) ''A genome-scale metabolic model of ''Cupriavidus necator'' H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications''. PLoS Comput Biol 18(5): e1010106. https://doi.org/10.1371/journal.pcbi.1010106 1. Stepan Fenyk, Helen K. Woodfield, Trevor B. Romsdahl, Emma J. Wallington, Ruth E. Bates, David A. Fell, Kent D. Chapman, Tony Fawcett and John L. Harwood. ''Overexpression of phospholipid: diacylglycerol acyltransferase in ''Brassica napus'' results in changes in lipid metabolism and oil accumulation.'' Biochemical Journal '''479''' (6), 805-823 (2022): https://doi.org/10.1042/BCJ20220003 1. Díaz Calvo T, Tejera N, !McNamara I, Langridge GC, Wain J, Poolman M, Singh D. ''Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen ''Staphylococcus epidermidis'' RP62A''. Metabolites. (2022); 12(2):136. https://doi.org/10.3390/metabo12020136 1. Valeria Villanova, Dipali Singh, Julien Pagliardini, David Fell, Adeline Le Monnier, Giovanni Finazzi and Mark Poolman. ''Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom ''Phaeodactylum tricornutum. Frontiers in Plant Science, '''12''', 411 (2021). https://doi.org/10.3389/fpls.2021.642199 1. Noemi Tejera, Lisa Crossman, Bruce Pearson, Emily Stoakes, Fauzy Nasher, Bilal Djeghout, Mark Poolman, John Wain, Dipali Singh. ''Genome-scale metabolic model driven design of a defined medium for ''Campylobacter jejuni'' M1cam. ''Frontiers in Microbiology, '''11, '''1072 (2020). https://doi.org/10.3389/fmicb.2020.01072 1. Thea SB Møller, Gang Liu, Hassan B Hartman, Martin H Rau, Sisse Mortensen, Kristian Thamsborg, Andreas E Johansen, Morten OA Sommer, Luca Guardabassi, Mark G Poolman, John E Olsen. ''Global responses to oxytetracycline treatment in tetracycline-resistant ''Escherichia coli. Sci Rep '''10, '''8438 (2020). https://doi.org/10.1038/s41598-020-64995-1 1. Lieven, C., Beber, M.E., Olivier, B.G., Poolman M.G ''et al.'' ''MEMOTE for standardized genome-scale metabolic model testing.'' Nat Biotechnol '''38, '''272–276 (2020). https://doi.org/10.1038/s41587-020-0446-y == Previous papers: == * Woodfield, Helen; Fenyk, Stepan; Wallington, Emma; Bates, Ruth; Brown, Alexander; Guschina, Irina; Marillia, Elizabeth; Taylor, David; Fell, David; Harwood, John; Fawcett, Tony. ''Increase in lysophosphatidate acyltransferase activity in oilseed rape (Brassica napus L.) increases seed triacylglycerol content despite its low intrinsic flux control coefficient. '' New Phytologist, 224, 700-711 (2019). https://doi.org/10.1111/nph.16100 * Rupert O. J. Norman, Thomas Millat, Sarah Schatschneider, Anne M. Henstra, Ronja Breitkopf, Bart Pander, Florence J. Annan, Pawel Piatek, Hassan B. Hartman, Mark G. Poolman, David A.Fell, Klaus Winzer, Nigel P. Minton and Charlie Hodgman. ''A genome-scale model of ''Clostridium autoethanogenum'' reveals optimal bioprocess conditions for .high-value chemical production from carbon monoxide. ''Engineering Biology, 3:32 (2019). [[http://ietdl.org/t/gbNTm|Open Access]] https://doi.org/10.1049/enb.2018.5003 * Pfau, Christian, Masakapalli, Poolman, Sweetlove & Ebenhoe. ''The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. ''Nature Scientific Reports, 8:12504(2018) https://www.nature.com/articles/s41598-018-30884-x [[https://doi.org/10.1038/s41598-018-30884-x|DOI]] * Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams Yazdani. ''Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production'', Metabolic Engineering, 45, 134-141 (2018). [[https://doi.org/10.1016/j.ymben.2018.01.002|DOI]] = Background = . Our '''group''' began nearly forty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results. . Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team. . Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals. ----- |
|
| Line 22: | Line 44: |
| We also host the following web sites related to our research: | We also used to host the following web sites related to our research, but these are currently off-line.: |
| Line 24: | Line 46: |
| * [[http://sysbio.brookes.ac.uk|The website of the International Study Group for Systems Biology]] |
* The former website of the International Study Group for Systems Biology (at ://sysbio.brookes.ac.uk) |
| Line 27: | Line 48: |
* [[http://mpa.brookes.ac.uk|The website for the Metabolic Pathways Analysis series of meetings]] * [[http://mitoscop.brookes.ac.uk|The website for the BBSRC-ANR project MitoScoP]] * [[http://frim.brookes.ac.uk|The website for the EraSysBio+ project Fruit Integrative Modelling]] |
* The website for the Metabolic Pathways Analysis series of meetings (at ://mpa.brookes.ac.uk) |
News
50 years of Metabolic Control Analysis - an update
Next year will be the 50th anniversary of the publication in 1973 of the papers by Kacser & Burns and Heinrich & Rapoport that led to the emergence of Metabolic Control Analysis as a distinct field. Following discussions between a section of the community (see MCAat50), approaches were made to some journals about the possibility of a Special Issue in 2023 devoted to MCA.
BioSytems accepted our proposal and its Special Issue is now announced at https://www.sciencedirect.com/journal/biosystems/about/forthcoming-special-issues .
Submissions are open from November 2022 until January 2023 through the Editorial Manager portal at https://www.editorialmanager.com/biosys/default1.aspx citing the article type: VSI: MCA at 50: an update. Potential authors are invited to contact the Guest Editors with an outline of their intended contribution before submission; see MCAat50 or the BioSystems site for more detail.
Interfaces Focus accepted a proposal from Herbert Sauro and Frank Bruggeman to edit a Themed Issue of the journal on MCA. Research articles and reviews will be commissioned by the editors, but they can be emailed with suggestions for content. See also MCAat50.
International Study Group for Systems Biology 2022
This will be held in September; information is available on the current ISGSB site.
Latest papers:
Emily Stoakes, George Savva, Ruby Coates, Noemi Tejera, Mark Poolman, Andrew J Grant, John Wain, Dipali Singh (2022) Substrate utilisation and energy metabolism in non-growing Campylobacter jejuni M1cam. Microorganisms, 10 (7), 1355, 2022. https://doi.org/10.3390/microorganisms10071355
Pearcy N, Garavaglia M, Millat T, Gilbert JP, Song Y, Hartman H, Woods C, Tomi-Andrino C, Bommareddy RR, Cho BK, Fell DA, Poolman M, King JR, Winzer K, Twycross J, Minton NP (2022) A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. PLoS Comput Biol 18(5): e1010106. https://doi.org/10.1371/journal.pcbi.1010106
Stepan Fenyk, Helen K. Woodfield, Trevor B. Romsdahl, Emma J. Wallington, Ruth E. Bates, David A. Fell, Kent D. Chapman, Tony Fawcett and John L. Harwood. Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation. Biochemical Journal 479 (6), 805-823 (2022): https://doi.org/10.1042/BCJ20220003
Díaz Calvo T, Tejera N, McNamara I, Langridge GC, Wain J, Poolman M, Singh D. Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A. Metabolites. (2022); 12(2):136. https://doi.org/10.3390/metabo12020136
Valeria Villanova, Dipali Singh, Julien Pagliardini, David Fell, Adeline Le Monnier, Giovanni Finazzi and Mark Poolman. Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum. Frontiers in Plant Science, 12, 411 (2021). https://doi.org/10.3389/fpls.2021.642199
Noemi Tejera, Lisa Crossman, Bruce Pearson, Emily Stoakes, Fauzy Nasher, Bilal Djeghout, Mark Poolman, John Wain, Dipali Singh. Genome-scale metabolic model driven design of a defined medium for Campylobacter jejuni M1cam. Frontiers in Microbiology, 11, 1072 (2020). https://doi.org/10.3389/fmicb.2020.01072
Thea SB Møller, Gang Liu, Hassan B Hartman, Martin H Rau, Sisse Mortensen, Kristian Thamsborg, Andreas E Johansen, Morten OA Sommer, Luca Guardabassi, Mark G Poolman, John E Olsen. Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli. Sci Rep 10, 8438 (2020). https://doi.org/10.1038/s41598-020-64995-1
Lieven, C., Beber, M.E., Olivier, B.G., Poolman M.G et al. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol 38, 272–276 (2020). https://doi.org/10.1038/s41587-020-0446-y
Previous papers:
Woodfield, Helen; Fenyk, Stepan; Wallington, Emma; Bates, Ruth; Brown, Alexander; Guschina, Irina; Marillia, Elizabeth; Taylor, David; Fell, David; Harwood, John; Fawcett, Tony. Increase in lysophosphatidate acyltransferase activity in oilseed rape (Brassica napus L.) increases seed triacylglycerol content despite its low intrinsic flux control coefficient. New Phytologist, 224, 700-711 (2019). https://doi.org/10.1111/nph.16100
Rupert O. J. Norman, Thomas Millat, Sarah Schatschneider, Anne M. Henstra, Ronja Breitkopf, Bart Pander, Florence J. Annan, Pawel Piatek, Hassan B. Hartman, Mark G. Poolman, David A.Fell, Klaus Winzer, Nigel P. Minton and Charlie Hodgman. A genome-scale model of Clostridium autoethanogenum reveals optimal bioprocess conditions for .high-value chemical production from carbon monoxide. Engineering Biology, 3:32 (2019). Open Access https://doi.org/10.1049/enb.2018.5003
Pfau, Christian, Masakapalli, Poolman, Sweetlove & Ebenhoe. The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Nature Scientific Reports, 8:12504(2018) https://www.nature.com/articles/s41598-018-30884-x DOI
Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams Yazdani. Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production, Metabolic Engineering, 45, 134-141 (2018). DOI
Background
Our group began nearly forty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results.
- Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team.
- Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals.
Related Sites
We also used to host the following web sites related to our research, but these are currently off-line.:
- The former website of the International Study Group for Systems Biology (at ://sysbio.brookes.ac.uk)
- The website for the Metabolic Pathways Analysis series of meetings (at ://mpa.brookes.ac.uk)