Joint Research Laboratory in Genomics and Nutriomics

University of Western Australia - Zhejiang University

PhD Projects

A variety of Ph. D. projects are available that can be carried out in association with the joint laboratory.

Applicants are requested to contact the person listed for each project. Note due to Scholarship application deadlines it is advisable to contact approximately 6 months in advance of the time that studies may commence.

Project 1: Characterisation of oxygen responsive elements in the promoter regions of rice genes

Contact Person – Professor Jim Whelan (seamus@cyllene.uwa.edu.au)

Background Reading
Holt KE, Millar AH and Whelan J (2006) ModuleFinder and CoReg: linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. Plant Methods 2:8

Clifton R, Millar AH, Whelan J. (2006) Alternative oxidases in Arabidopsis: a comparative analysis of differential expression in the gene family provides new insights into function of non-phosphorylating bypasses. Biochim Biophys Acta. 1757(7): 730-41.

Clifton, R. Lister, R. Parker, K.L., Sappl, P.G., Elhafez, D., Millar, A.H., Day, D.A. and Whelan, J. (2005). Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Molecular Biology 58: 193-212.

Thirkettle-Watts, D. McCabe, T.C., Clifton, R., Moore, C., Finnegan, P.M., Day, D.A., Whelan, J. (2003). Analysis of alternative oxidase promoters from soybean. Plant Physiology 133: 1158-1169.

Ho LH, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J. (2007).Characterisation of the Regulatory and Expression Context of an Alternative Oxidase Gene Provides Insights into Cyanide Insensitive Respiration during Growth and Development. Plant Physiol. 2007 Feb 23; [Epub ahead of print] PMID: 17322330

Aim: To define oxygen responsive elements in the promoter regions of rice genes

Background: Previous studies in our laboratory have defined that the transcript abundance of genes in rice increase or decrease dramatically in response to oxygen or anoxia (5 to 10 fold changes in 1 to 6 hours). To obtain a comprehensive list of genes that respond in this manner, microarray analysis has been carried out and thus by the end of 2006 we will have sets of genes in rice that A) are responsive to oxygen, B) increase or decrease in transcript abundance and C) show differences in timing or kinetics of these changes. These analyses will provide groups of genes that are co-expressed – defined as genes whose transcript abundances change in a similar manner in response to a defined number of treatments. In this case the treatment is oxygen.
The next stage of this project is to define the cis-acting regulatory elements (CAREs) in the promoter regions of these genes that are responsible for these changes in transcript abundance and to define the transcription factors that regulate changes in gene expression in response to changes in oxygen concentration.

Research Plan:
1) Define groups of genes whose transcript abundance changes in a similar manner in response to oxygen.
2) Predict CAREs in the promoter regions in genes from these different groups.
3) Determine if the promoter regions of these genes contain oxygen responsive regions.
4) Determine if the predicted CAREs are functional and are responsive to oxygen.
5) Identify transcription factors that bind functional CAREs