Problems from the Fourth Mathematics in the Plant Sciences Study Group, 4-7 January 2011, at the University of Nottingham
1. Modelling anther opening and pollen release
Problem presented by Zoe Wilson (University of Nottingham)
Report: Biomechanical modelling of anther dehiscence and pollen release, compiled by Martin Nelson (Nottingham)
Contributors: Martin Nelson (Nottingham), Leah Band, Rosemary Dyson, Kel Heymer (UNSW), Jonathon Hiorns (Nottingham), Arnd Korn (Nottingham), Thomas Lessines (Oxford), Simon Pearce, Sophy Thomas (Chester), David Toner (Edinburgh), Feng Xu (Nottingham), Cai-yun Yang (Nottingham)
For further details regarding this report, please contact martin.nelson at nottingham.ac.uk
2. Modelling effects of photosynthetic adaptations on source sink relationships and yield patterns of recurrent flowering vegetable crops
Problem presented by Ryan Ramsey & Kim Travis (Syngenta)
Report compiled by Jonathan Wattis (Nottingham)
Contributors: Oliver Bain (Nottingham), John Billingham (Nottingham), John Fozard, Sunny Modhara (Nottingham), Adrian Pratt (Nottingham), John King, Arnd Korn (Nottingham), Jonathan Wattis (Nottingham)
3. Construction of the jasmonates gene regulatory network in Arabidopsis and identification of major players and novel components
Problem presented by Alessandra Devoto (Royal Holloway University of London)
Report: Modelling the interactions for JA signalling and response
Abstract: The current central dogma of jasmonate signalling is based on the evidence that when the jasmonate (JA) signal emerges, the SCFCOI1 complex mediates degradation of repressors so that transcription of down-stream regulators is activated. The main aim of this work is to model the interactions between regulators from receptor activation to the ultimate gene expression in the JA pathway and their cross-talk with other hormone-dependent pathways. In a simplified view, the approaches chosen here were aimed to model two modules separately: (A) the “JA repressor complex”, which includes the JAZ transcription factors and (B) “the downstream interactions occurring during the JA response”. To model (A), Hampstead, Lovrics, Mellor, and Ward decided to use a system of ordinary differential equations (ODEs). Kreim applied to this model stochastic simulation, to take into consideration the elements of discreteness and randomness of the system. Regulatory genes can be identified based on the knowledge gained from whole genome datasets. These regulatory genes may have the capacity to control sets of genes involved in a particular pathway. Jayaraman, Muraro and Oles tested Bayesian networks and dynamical models on gene expression data obtained from Arabidopsis microarray experiments including timecourse studies following JAs treatment (selected from publicly available datasets), to construct a transcriptional network modelling (B) “the downstream interactions occurring during the JA response”. Devoto and Lavenus, provided curated sets of genes known to be induced by JAs and involved in the JAs biosynthesis and response to be used in the modelling procedure.
Authors: Anthony Hampstead, Siddharth Jayaraman (Exeter), Michael Kreim (Karlsruhe Institute of Technology), Julien Lavenus (Nottingham), Anna Lovrics (Nottingham), Nathan Mellor, Daniele Muraro, John Ward (Loughborough) and Alessandra Devoto (Royal Holloway University of London)
Contributors: Anthony Hampstead, Siddharth Jayaraman (Exeter), Michael Kreim (Karlsruhe Institute of Technology), Julien Lavenus (Nottingham), Anna Lovrics (Nottingham), Nathan Mellor, Daniele Muraro, Katarzyna Oles (Stirling), John Ward (Loughborough) and Alessandra Devoto (Royal Holloway University of London)
For further details regarding this report, please contact Alessandra.Devoto at rhul.ac.uk
4. Defining ideotypes in the biomass crop Miscanthus
Problem presented by Kerrie Farrar, Elaine Jensen & Gordon Allison (IBERS, Aberystwyth University)
Report contributors and authors: Kerrie Ferrar (IBERS, University of Aberystwyth), Kim Kenobi, Simon Preston (Nottingham), Theodore Kypraios (Nottingham), Simon Pearce, Simon White (Cambridge), Sophy Thomas (Chester)