BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 16 December 2008.
PRESTA stands for Plant Resposes to Environmental STress in Arabidopsis. Even though the environment is changing rapidly, investment in plant research has declined. Abiotic and biotic stresses will function via core response networks embellished with stress-specific pathways. A fundamental component of these responses is transcriptional change. It seems that in many of the components in stress responses, hormones are key: also, everything seems to focus through key pathways. Two approaches are used: top-down modelling via network inference, or bottom-up modelling via already extant knowledge of key genes. This talk focused on the former.
They used high-resolution time-course microarrays which use 31,000 genome sequence tags (you need these to get the information to the modellers). Then, they use a range of different stress response to reveal commonalities (developmental e.g. senesence, pathogens, and abiotic stress). One example: over 48 hours there were 24 time points taken with 4 biololgical and 3 technical replicates. Two-color arrays allow complex loop design. They've been using the MAANOVA program, and even altered it to make it more efficient. You basically end up with an f test that tells you which genes have changed over time. How to select genes for Network Inference Modeling?: GO annotations, genes known to be involved in stress-related processes, trancription factors known to be involved, early response genes and prior knowledge.
There goes the battery again! Grrr…. transcribed paper notes follow, which aren't generally as detailed in my case…
Vairation of network models: 4 out of the 12 prospective genes shown to have altered pathogen growth phenotype. Knockouts in a hub gene showed both up or down-regulation of senesence. They want to add validation to the network model, and have validated various genes via experimental work). Developed APPLE, which is tha tAnalysis of Plant Promoter-Linked Elements. Discovered if overexpress HSF3 the plants are more tolerant to drought and show increased seed yield. HSF3 is part of the stress response but has a wide range of interactions, which is a good thing for building parameterized models. In the future, wants to look at the genetic diversity in the crops, and try to express a more robust response to the environment.
These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. 🙂