Ben Alleva ’13: Black Fellow in Bioscience
This week, I started off by working on the MECP2 gene related project that Claudia had alluded to the previous week. Claudia explained to me that I was to put this project at the very top of my to-do list, as it was of the utmost importance to complete quickly. After coming back from her weeks of conferences, she realized that more support is needed for her paper before it can be sent for publishing. To provide this extra support, I would have to find microsatellites (tandem repeats in DNA) in the Xq28 band on chromosome X. Monday and most of Tuesday I spent my time going through a website with a large list of microsatellites near the MECP2 gene on the X chromosome. Then I went through through multiple literature sites to find previously studied microsatellites in the Xq28 band; I also went through the human reference genome to find other microsatellites that have not previously been mentioned in the literature. This was a long, tiring task, but at Cornell College I have spent countless hours working with literature as well as with microsatellites. That experience made this part of the project infinitely easier. The toughest part of doing this was finding microsatellites that were not contained within LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), containing SNPs (single nucleotide polymorphisms), or having LINEs/SINEs surrounding these microsatellites (this occurs A LOT). The reason we don’t want any of these is because it would make it almost impossible (if not entirely impossible) to create primers that would bind and amplify the specific microsatellite without amplifying other segments in the genome (SINEs and LINEs are long sequence repeats in the human genome and comprise approximately 15% of the entire human genome). Once I found 5 good microsatellites (yes, I was only able to find 5 good microsatellites of the many I looked at, which was easily over 100), I had to design primers to amplify these microsatellite segments. I worked on this Tuesday and finished them late Thursday. I ended up using previously designed primers, for exons, near the locations of the microsatellites. Although, in some cases I had to modify them so that SNPs were not in the segment of DNA that the primers would bind to. The presence of SNPs in these genomic segments would cause the likelihood of the primers to bind to decrease, definitely not what we want to happen. Once I was able to finish designing these primers and we double-checked that, in theory, they would work correctly, we sent the data for them to be created and have a special fluorescence label be put on them. We were told these primers would not be delivered to us for two weeks (cutting it close to the end of my Fellowship). Claudia then decided that next week we will start working on the fusion gene project she had originally planned for us to work on, at least until the specially made primers are delivered.
Friday I went back to the Moebius Syndrome project and ran PCR on 11 different samples to, hopefully, find more possibilities of gene-linkage. At the beginning of next week, I will clean the PCR products and send them off to be sequenced. In the meantime, I have received chromatograms of the previous PCR products we sent for sequencing and will begin analyzing them.
On the fourth of July, a group of us in the SMART Program put together an afternoon long volleyball tournament. We then headed over to Hermann Park to listen to the Houston Symphony Orchestra (they had 18 cannons go off during the 1812 Overture) and watch fireworks.
Below is a picture of one of the BCM buildings in the skyline.