It’s time for another guest post today – Katherine Denby writes about the SEB 2012 conference.
Warwick Systems Biology Centre was well represented at the recent SEB conference in Salzburg, with 4 presentations in sessions on Biotic Stress, Environmental Control of Development and Generating New Biological Insights from Complex Data.
First up was Katherine Denby who presented analysis of a gene expression time series from Arabidopsis leaves infected with the fungal pathogen Botrytis cinerea generated in the PRESTA project. Using a variety of network inference algorithms, the group has generated models of the gene regulatory networks underlying the Arabidopsis response to this pathogen. These network models have highlighted specific regulatory interactions, and led to identification of transcription factors with a novel role in defence. Modelling using gene expression time series from other biotic and abiotic stresses has predicted a core regulatory network underlying multiple stress responses with differential flux through the network under different environmental conditions. Katherine also described a novel tool, Wigwams, to identify groups of genes significantly co-expressed across multiple stresses. Integrating this with the network models enables prediction of the upstream regulators of these groups.
Anthony Carter, a PhD student from the Systems Biology Doctoral Training Centre, gave a talk on his work to understand the cell type specificity of developmental pathways. The amazing diversity of plant root architecture derives from variations in development from single, but highly specialised, cell types in the root. For example, root branching in Arabidopsis involves new cell division only in pericycle cells, while a similar sequence of cell division in the cortex occurs in the initial stages of nodule formation (to enable nitrogen fixation) in legumes. He is using a systems biology approach to investigate whether he can identify shared genes and genetic pathways that control these two processes.
Anthony explained that reducing the expression of Arabidopsis orthologues of genes involved in legume (Medicago truncatula) nodulation affects lateral root formation, supporting his hypothesis of shared genetic pathway links. Utilising the technique of Fluorescence-Activated Cell Sorting, he has been able to identify changes in gene expression in single cell-types of the root that are associated with loss of expression of two of these genes. One gene appears to regulate lateral root formation by modulating the gibberellic acid signalling pathway, while the other directly affects initial stages of lateral root development by regulating components of the cell cytoskeleton, and lipid localisation.
David Rand and Till Bretschneider presented their work in the diverse session “Generating New Biological Insight from Complex Data: Methodology, Data Gathering, Inference, Modelling, Validation, Integration and Solutions.” David Rand highlighted tools that have been developed at Warwick Systems Biology Centre to link data to models and contrasted the modelling process in relatively well-defined systems, such as the circadian clock, with modelling data on plant stress responses generated in PRESTA. Although not plant-related, Till Bretschneider discussed his work on analysing the cytoskeleton during mechanotaxis in Dictyostelium. This has required the development of software to track cell shape changes and the pattern of fluorescence within moving cells over time. Till is also tackling new challenges for image reconstruction and cell tracking raised by the latest advances in digital light sheet microscopy that enable imaging of cells during multicellular development.
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