IBHonors students complete RNAi studies: Still the only course at UIUC to include this modern technique
Professor Whitfield's students complete final preps before presenting the results of their RNAi studies to their class and a group of interested lookers.
RNA interference, or RNAi, is a mechanism to degrade double stranded RNA. Evolutionarily it serves as an antiviral mechanism (against viruses containing dsRNA), but in recent years it has become a powerful tool for the molecular geneticist. It is so new, in fact, that there are still no rock bands named RNAi or siRNA, or even songs about it.It is also so new that biology laboratory courses incorporating it are rare. At Illinois, only one course (IB270), open only to sophomores in the IB Honors Biology program, offers that experience.
Each year, Professor Charles Whitfield finishes the semester by assigning a "Discovery Project". Students, working in groups, are required to develop a hypothesis concerning gene function in C. elegans, transform E. coli with a plasmid for the dsRNA complementary to the gene, and infect their worms with the bacteria to, in effect, knock out the function of the worm gene. The project is made more interesting by the requirement that the gene not have been targeted before.
In the end, each group prepares the results for presentation to the class and to previous classes of IB Honors students, as though they were presenting at a scientific meeting.
This year, there were four projects. Although the number of reps possible in the short time available clouded the statistical significance of some of the results, the overall experience was unique and valuable.
The first group targeted mechanisms for heavy metal tolerance, in particular Cadmium, used the worm genome database to find a candidate gene (cdr-4), and then challenge wild-type and cdr-4 mutants with varying concentrations of Cd. Within a few hours, the number of RNAi worms surviving (e.g. 15 mM Cd) was substantially lower than the number of wild-type survivors.
The second group went after a thermosensor, beginning with a gene (gon-2) analogous to a well characterized gene fromDrosophila. They used RNAi knockdown to study the ability of the worms to "thermotaxize" (I think they made this word up), or move along a thermal gradient to an optimal temperature. One clear outcome of that study was that just making the gear to do the experiment is challenging in itself, even if the mutation went well.
Group 3 also paid attention to the movement of the worms, but in this case, in the importance of the trp-2 gene and its interaction with caffeine. Others (published studies) had looked at the relationship between trp-2 and nicotine, but with Illinois restaurants and bars going smoke free this year, and with coffee shops doing better by the week, the different approach was clearly critical. It turns out that worms with functioning trp-2 decreased their movements, while the knockouts increased their speed on plates containing caffeine. Students and professors alike took this to heart.
Finally, the last group investigated a worm equivalent of squamous cell carcinoma, the second most common type of skin cancer in humans. They compared protein sequences through NCBI BLAST, and found a worm protein very similar to a SCC antigen, coded by the srp-7 gene. The role of srp-7 otherwise is not well understood. They tested the hypothesis that trp-7 is important for the immune response to UV-radiation, and the results may actually have been positive.
IBH students travel the world, publish research papers, and do all sorts of amazing things