Third Rotation

I started my third rotation on Friday. I'm working on two projects in Dr. Phillip's lab. The first one, which has funding, is a metagenomics project. A group on campus has a mouse model for colorectal cancer, and they are interested in how feeding resistant starch might affect the gut. We get samples from them and we're supposed to do next generation sequencing to see if there is a change in the gut microbiota. Right now we've used 454 pyrosequencing, but we might start using Illumina MiSeq. I don't know how to do any of this stuff so it will be exciting to learn. The second project is more of an investment so it's something to do on the side rather than as a main project. It's a proof of concept of a type of sequencing called transposon sequencing. You mutate a bacterium with a Mariner transposon, then subject some of the colonies to selection pressure, and then sequence to determine which genes might be essential for survival and propagation. Transposon sequencing isn't very common so we have to get a publication first and then we can probably get some grant money. So I'm working on transposon sequencing of Yersinia pestis, which is bubonic plague. Right now the selection pressure is simple, it's just growing them in media without leucine, but if this works well then we can put some of the Y. pestis into mice and that will be the selection pressure. So far it's very interesting and I think it's very likely that I'll do my thesis in this lab!