Techniques used: Genetics, biochemistry, molecular biology, bioinformatics
Background:
I study Cryptococcus neoformans, a common fungus found in the soil that is normally harmless to humans. If someone with a compromised immune system inhales it, however, the fungus causes an infection in the lungs. This infection is fatal if not treated, and treatment options are currently limited.
In order to establish an infection, C. neoformans needs to import copper and iron from its surroundings. Using computer databases to search the entire genome sequence of C. neoformans and related fungi, I hope to discover unique molecular pathways related to metal import.
Projects:
- Copper starvation and excess in C. neoformans: C. neoformans needs a way to bring copper (and other metals) into the cell whenever the surroundings are low in copper concentration. The cells also need a way to sequester it if it is too high (too high a concentration is toxic). Before we find out more about the mechanism, we need to set the limits the bug can withstand.
- Copper regulation in C. neoformans: The main protein that brings in copper is called Ctr4p. It is expressed in all subspecies of C. neoformans. However, the upstream DNA regions of Ctr4p in these different subspecies are not the same. We would like to figure out if the different subspecies use similar or different mechanisms to regulate the expression of this protein
- Bioinformatic searching of the C. neoformans genome: The regulating DNA binding site for the expression of Ctr4p is fairly well conserved. Using it as a template, and the entire genome sequence of C. neoformans, can we find other genes that might be regulated by copper levels?
- Characterizing wild yeast populations from soil: C. neoformans is found in the soil and especially concentrated in bird feces. In collaberation with Dr. Barr, we would like to isolate DNA from local soil samples and catalogue their fungal populations.
- Identification of
wild yeast: Dr. Barr and I brew hard cider using
commercial and natural yeast. Using samples of the
flora found in naturally fermented products and
PCR/DNA sequencing methods, can we identify the
microbial communities?