Problem descriptions.
Problem 1:
The tetrapyrrole biosynthesis pathway in higher plants as an example of a subcellular network
Tetrapyrroles, such as chlorophyll and haem, are the most abundant pigment molecules on the planet, and chlorophyll is the only biological molecule visible from space. As well as chlorophyll and haem, plants make two other tetrapyrroles, sirohaem and phytochromobilin, in a complex branched pathway. Because the levels of the different endproducts vary considerably in different tissues or under different growth conditions, and because the intermediates are all phototoxic, the pathway must be exquisitely regulated. Moreover, there is a need to coordinate production of the tetrapyrroles with their cognate binding proteins.
We know a great deal about the biosynthetic pathway for tetrapyrroles, including all the steps involved, and a lot about the regulation, but much of the evidence for the feedback/feedforward circuits is circumstantial. We think that the regulation of the pathway is an ideal one for mathematical modelling because we can collect large data sets on the expression of the genes, and the metabolite levels. This leads to several possible questions that might be answered by mathematical modelling:
- Do the data we have on the gene expression and levels of intermediates account for the timecourse of chlorophyll synthesis on illumination of dark-grown seedlings?
- Which intermediates correlate best with inhibition of expression of apoprotein genes?
- Can the endproduct feed-back model account for the levels of intermediates seen in mutants with defects the pathway?
Problem 2:
Network properties underlying seed germination control
Seed germination control requires the assimilation of signalling from multiple input pathways. Environmental signals such as light control the level of the hormones gibberellin (GA) and abscisic acid (ABA) in seeds. Since the 1960s is has been hypothesised that the 'balance' of the germination-promoting hormone GA and the germination inhibiting hormone ABA controls the decision to germinate. However, to date, despite massive advances in the understanding of the molecular basis of germination control, it is still unclear exactly how hormone balance works.
The decision to germinate (or not) is essentially a binary output of a complex molecular network. This germination-controlling network comprises a set of complex interlocking feedback loops involving regulation at the mRNA and protein levels, through which the abundance of GA and ABA is managed. Furthermore, the output of the network is transduced through a transcription factor complex that is also integral to the function of the feedback loops themselves. The same complex also performs a key step in environmental signal transduction.
The primary goal will be to create a platform for modelling the effect of one key input, light, and to ask which, if any, of the current conceptual models of germination control can account for observed behaviour. In the future model solutions will be integrated with traditional hydrothermal time models linking molecular events to seed germination studies under field conditions.
Problem 3:
Measuring genetic diversity?
The relationship between biodiversity and the functioning of essential ecosystem process should be quantified at the intraspecific level, and in terms of the relative abundances of ecologically important significant plant life-history traits. Maximum uptake of this approach for environmental monitoring purposes demands that genetic data must be acquired using an easy and universal method. To this end, Inter Simple Sequence Repeat (ISSR) genotyping has been used to acquire data for ca. 150 individual accessions of the common annual weed Capsella bursa pastoris L. Medic (shepherds purse): that is being developed as a (global) biomonitor species. The data provides specific markers (peaks), the presence of which can ascribe accessions into particular trait-groups. As the accessions were collected from different environments across the UK (that were also characterised), and with several accessions per site, we ask the key question: 'can the success and utility of the data be extended even further to provide information on the biodiversity within communities too?'. This provision of this information is critical: the tools that allow this evaluation would relate diversity estimates directly to heritable phenotypic traits and the environment. Consequently, and most significantly: could this information generate a predictive model that assesses the future resilience of species within changing environments?'.
- What statistic from the ISSR data would provide a measure of genetic diversity?
- How would the statistic be estimated?
- How would the statistic be compared between populations?
- Can the statistic relate phenotypic variation within and between populations?
- Could this be modelled in a way which includes predictions based on knowledge of the selective effects of environmental changes?
- How many loci would have to be considered?
- How many individuals from each population would have to be tested?
Problem 4:
The Mechanics of Seedling Germination
Germination is defined as the protrusion of the embryonic radicle through the seed coat layers (endosperm and testa). As the radicle elongates, the testa ruptures. This is followed by rupture of the endosperm. Arabidopsis seeds exhibit a two-step germination process with sequential testa and endosperm rupture.We are interested in exploring the physical process of germination. Whilst much effort has been placed on the genetic networks involved in this process, a mathematical approach for furthering the understanding of the physical/mechanical properties of germination has not yet been described.
During the study group, we would like to gain insight into the pressure that is required for the seed to germinate. How does the size and shape of the radicle and the thickness of the testa affect the force required for the seed to germinate? We are also interested in the role of the endosperm. What sort of mechanical restraint does the endosperm offer? And by how much does the endosperm have to be weakened (enzymatically) for the radicle to protrude?
Problem 5:
A systems approach for improving tea aroma
Tea researchers aim to understand the genetic and biochemical connections that govern the flavour and aroma of tea, given a specified set of growth conditions. Conventional crop breeding is often used as a tool to improve crop varieties, but, tea plants have a life-cycle of one century, so crop breeding is not an option for improving tea aroma. This proposal focuses only on the aroma aspect of this work, and we are concentrating on terpenoid / isoprenoid pathways, as these show most transcriptional changes.
- Can we produce a simple dynamical model of terpenoid and isoprenoid biosynthesis that can account for the changes in floral notes that correspond to the levels of metabolites, and build on this model to account for observations?
- Can we use a predictive mathematical model to define parts of the pathway that are amenable to change using the manufacturing process in order to produce new types of tea with desirable characteristics (e.g. floral notes)?
- How should the manufacturing process be changed so that the final product is the same irrespective of the differences in picked tea leaves from one year to the next?
- How might growth conditions and manufacturing process be changed to produce new aroma profiles for the preferences of the consumer?
CPIB is a Centre for Integrative Systems Biology supported by BBSRC and EPSRC.
