The virtual seed (vSEED): Combined mathematical, engineering and post-genomics comparative biology to model the systems biology of seed dormancy, after-ripening and germination.
Final Report Abstract
Major outputs of the vseed project were: 1. Development of on-line computational model of seed germination and associated resources (vseed.nottingham.ac.uk); publically available high-resolution transcriptome datasets: GEO reference GSE41212. 2. The first systems biology approach to the analysis of seed germination, including mathematical modelling of endosperm rupture, cross-species transcriptome and qRT-PCR analyses of major seed compartments, and computational modelling of gene interactions. 3. State-of-the-science analysis of cell walls in Arabidopsis, Lepidium and tobacco seeds indicating the novel aspects of endosperm cell wall molecular architectures including that there is no heteromannan in Arabidopsis/Lepidium cell walls and no detectable tissue-level asymmetry. Tobacco became an important comparative species and this was not envisaged in the original application. Cell wall analysis linked to seed biomechanics on different length scales to analyse dynamic seed material properties.
Publications
- (2011) A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study. The Plant Cell
Graeber K, Linkies A, Wood ATA; Leubner-Metzger G
(See online at https://dx.doi.org/10.1105%2Ftpc.111.084103) - (2011) Axisymmetric indentation of curved elastic membranes by a convex rigid indenter. International Journal of Non-Linear Mechanics, 46 (9) 1128-1138
Pearce, S.P., King, J.R., Holdsworth, M.J.
- (2011) First off the mark: early seed germination. Journal of Experimental Botany
Weitbrecht K, Müller K, Leubner-Metzger G
(See online at https://doi.org/10.1093/jxb/err030) - (2011) Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Datasets. The Plant Cell
Bassel, G.W., Glaab, E., Marquez, J., Holdsworth, M.J., Bacardit, J.
(See online at https://doi.org/10.1105/tpc.111.088153) - (2011) Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. PNAS (USA), 108 (23) 9709-9714
Bassel, G.W., Lan, H., Glaab, E., Gibbs, D.J., Gerjets, T., Krasnogor, N., Bonner, A.J., Holdsworth, M.J., Provart, N.J.
- (2011) Visualization of molecular processes associated with seed dormancy and germination using MapMan. Seed Science Research
Joosen, R.V.L., Ligterink, W., Dekkers, B.J.W., Hilhorst, H.W.M.
(See online at https://doi.org/10.1017/S0960258510000449) - Identification Of Reference Genes For RT-qPCR Expression Analysis In Arabidopsis And Tomato Seeds (2011). Plant Cell Physiol. pcr113; August 18, 2011
Dekkers, B., Willems, L., Bassel, G.W., van Bolderen-Veldkamp, R.P., Ligterink, W., Hilhorst, H.W.M., Bentsink L.
(See online at https://doi.org/10.1093/pcp/pcr113) - Distinct cell wall architectures in seed endosperms in representatives of the Brassicaceae and Solanaceae (2012) Plant Physiol. pp.112.203661; September 6, 2012
Kieran J.D. Lee, Bas J.W. Dekkers, Tina Steinbrecher, Cherie T. Walsh, Tony Bacic, Leonie Bentsink, Gerhard Leubner-Metzger, and J. Paul Knox
(See online at https://doi.org/10.1104/pp.112.203661) - (2013) Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination. Plant Physiology 163 (1) 205-215
Dekkers, B.J.W., Pearce, S., van Bolderen-Veldkamp, R.P.M., Marshall, A., Widera, P., James Gilbert, J., Drost, H-G., George W. BasseL, G.W., Müller, K., King, J.R., Wood, A.T.A., Grosse, I., Quint, M., Krasnogor, N., Leubner-Metzger, G., Holdsworth, M.J., Bentsink, L.
(See online at https://doi.org/10.1104/pp.113.223511) - (2013), Multi-scale spatial heterogeneity of pectic rhamnogalacturonan I (RG–I) structural features in tobacco seed endosperm cell walls. The Plant Journal
Lee, K. J.D., Cornuault, V., Manfield, I. W., Ralet, M.-C. and Paul Knox, J.
(See online at https://doi.org/10.1111/tpj.12263)
