Week 10, 11, and beginning of 12

Hey guys. So everything has been winding down with our SRPs. I've been working on my presentation and still trying to wrap my head around my paper. While everyone seems to be done with their internships, I have still been going to mine. I was given the opportunity to continue working with the AGI team until the end of May (after all the SRP stuff) which is really great since I get more experience in the lab. I may even begin helping with their new PacBio project on sequencing two different rice varieties before I get into my summer vacation.

Lately, I've been catching up on some reading to see if there's anything more relevant I can add into my presentation background-wise. I also have been questioning about my researched lab report as my final product. Although I have been testing out primers on certain shattering genes, we haven't been able to make conclusive results, so I don't think I'll be able to add in a "results" section at all. Also, we have been working on primers on shattering genes that greatly affected the domestication of Oryza sativa called sh4 and qsh1 but they haven't been working. Sh4 is a quantitative trait locus (QTL) on chromosome 4 in rice and qsh1 is a QTL on chromosome 1 in rice. From different experiments, both of these primers explained 69% of the phenotypic variance between shattering and non-shattering. Currently, I am designing new primers on these genes but won't be able to test them until after my SRP presentation, so I won't get any results until then.

I am possibly thinking of continuing my paper as just a research paper and maybe including some of my experiences in it. But, I will be talking to my advisors about it (hopefully today).

Week 9

Week 9! I can't believe it's almost over!

This week was pretty quiet. I haven't been going to the lab as much. I've been mainly doing to EFE repeat characterization with Dario that I mentioned last week. We should be finishing up soon. I also did a PCR with some primer combinations on a qSh1 gene, which is related to shattering. However, when I tested this last time, the bands in the gels were the same length which shouldn't happen since it seems that O. glaberrima has an insertion in this qSh1 gene of about 100 base pairs, so there should be two bands of different lengths, about 100 bp apart. Sadly, we don't see that, so we may have the rest of the PCR products and sequence them.

gel of the qSh1 combos

I also did a PCR and ran a gel on Friday (mostly because I was bored from staring at my computer screen doing EFE characterizations). I tested a primer that was not linked to a shattering gene and was successful in showing two different bands in the parents (barthii and glaberrima). This primer was on chromosome 8 in O. barthii but since the two parents are related, the primers should also attach to the same region in O. glaberrima. I tested this primer on some DNA plates like I did with the up1 primer few weeks back.   

I also started my outline for my final project. It's going to be more of a lab report even though I don't have a lot of conclusive results since this shattering project isn't completely over. I hope to finish up my outline, look for some more sources, and at least start on my introduction by end of next week.