Week 8:

Hey guys!

This week was basically the same as all my other weeks. Tons of PCRs and gels. Lately, I've been re-doing PCRs and gels of primers that we have done in the past but haven't gotten nice results. I also re-tested the awns where we extracted DNA from a few weeks ago. Unfortunately, we haven't gotten good results because the awns aren't concentrated enough. One solution we have in mind for now is to re-suspend the DNA pellet, centrifuge, and test their concentrations again.

On Wednesday, I went into a lab meeting. This meeting was basically an introduction to the new PacBio machine that came in couple weeks ago. An employee from the PacBio company came in and talked about how to use the machine, the prep, what to do if anything went wrong (mostly it's to contact the PacBio tech support or the guy that came in), and how to analyze the results. After the meeting, I began scoring and starting to organize the genotypes of the species.

On Friday, it was something different. I didn't go into the lab at all which was kind of strange for me since I've been in the lab basically since day 1 of my internship. I actually got to do some bioinformatics stuff. It's related to rice but I don't think it's quite related to what I'm doing. I've been looking at medium-sized chunks of repeats gathered and organized by Dario and his ____ in Australia. These chunks contain one or both of two different type of viruses that have been present in other plants close to rice such as wheat. So for now, I have been looking at the chunks that are recorded to be present in one rice genome and comparing them to other rice genomes to see if they are present. Basically, I'm looking for polymorphisms even though I haven't seen the different phenotypes. The tools I have been using are these sites called Genome Browser. There are two sites where one helps to track the location of the repeat chunk and nearby genes while the other site helps to compare a certain site (normally the repeat along with at least 2 nearby genes) and compare it to other rice genomes. I found out that it was important to have at least one nearby gene in the window of the chromosome that I was looking at when I was comparing the region with other genomes because if you just have the repeat, it could be present all over another rice genome but in different chromosomes (since it's a repeated sequence). With a gene in the region, it helps to anchor the repeat in the other genomes, if present. Also, most likely when they are present, they should be present in an area on the same chromosome and same area as the first, or what the site calls the reference, genome.

And that was my week. It's getting so close to the end. So this next week, I'll be continuing my lab work and start organizing the information I've gathered and the data I've collected to start working on my final product which is going to be a research paper. Sadly, I haven't done much bioinformatics stuff or analyzed the data so it won't have as many numbers as I had hoped, so no p-value or chi-squared or anything like that sadly. I'll also be looking for more sources.

So that's it for now. Bye!