research in development


(a) use of full-genome DNA microarrays to determine gene expression levels throughout development (Jiang et al.,2001).

In this paper, Jiang et al. (2001) constructed DNA microarrays containing 17,871 genes, representing 94% of the total C.elegans genome. They used these microarrays in conjunction with ChIPs to look for relative levels of gene expression amongst all the genes throughout development - from embryo to worm.

In brief, this was done by creating DNA fragments (about 1-2kB in length), using polymerase chain reaction (PCR) . DNA sequences were found on the Stanford Microarray Database. cDNA from each developmental stage was labelled with Cy3-dUTP while Cy5-dUTP was used to label the mixed-stage reference. Cells at a given stage of development are lysed and their contents (essentially mRNA) is hybridized to the array and measured for expression.

In one experiment, the researcher's compared gene expression between males and hermaphrodites. Using the methods stated above, they concluded that there are at least 2,171 sex-related genes. This aspect of the experiment was confirmed by some previously known sex-related differences. Nonetheless, their paper demonstrates the usefulness of using the whole genome. They have also shown that many of these genes show strong homology to humans and our developmental pathways - particularly with respect to some transcription factors, kinases, phosphotases, cell-signalling proteins, genes repsonsible for clearing dead cells and toxins as well as specific development genes. The next step in research is to use the human homologues in the worm using the microinjection technique and to see if and how these highly conserved, specific factors work.

(b) use of hundreds of microarrays to develop a new tool for the mapping of gene expression patterns (Kim et al., 2001).

This paper by Kim et al.(2001) shows how the expanding field of development yields new techniques and tools. They assembled data from hundreds of microarray experiments dealing with development and created a software tool known as an expression map which is used for identifying genes which are coregulated with known gene sets. In this way, the type of gene expression assays demonstrated above can be viewed with clearer resolution.

For instance, in a few previous germline experiments, 758 genes that were enriched in the hermaphrodite over the regular male were found. When these microarrays were looked at through the gene expression tool, the terrain map subdivided these 758 into four distinct groupings, indicating a distinct biological function. This tool is currently being used to identify human homologs and their specific expression patterns which will inevitably lead to further research in various pathways.

(c) examination of protein interaction via traditional two-yeast hybridizations using the C.elegans genome as guidence (Walhout et al.,2000).

This paper by Walhout et al.(2000) uses the C.elegans genome knowledge as more than a simple research tool. In this experiment, they looked at developmental protein interactions using two-yeast hybrid analysis. Besides finding that 27 proteins were involved in vulval development, they were able to use the growing amount of functional data to ensure that their results were correct - essentially using this information as a guidance tool ensuring accurate results. More and more scientists have been turning to these databases as further validation of their results. With respect to research on humans, studies like Walhout's may soon be used to replace human homolgs in the worm (using the microinjection technique) in order to look at such things as cancer or other developmental abnormalities.

references
1. Jiang, M., Jubin, R., Kiraly, M., Duke, K., Reinke, V., and Kim, S.K. 2001. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proceedings of the National Academy of Science of the United States of America 98(1):218-223.

2. Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J.M., Eizinger, A., Wylie, B.N., and Davidson, G. 2001. A gene expression map for Caenorhabditis elegans. Science 293(5537): 2087-2092.

3. Walhout, A.J.M., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N., and Vidal, M. 2000. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287(5450):116-122