Ben Alleva ’13: Black Fellow in Bioscience
As this was my final week working in the lab at Baylor College of Medicine, I did my best to get as much done on each project; especially since I had to present my research to the entire lab on Wednesday. Although I thought I would be done with the microsatellite project once I had sifted through the information I had received last week, I was quite mistaken. Once I had sifted through the information and presented it to Claudia through a PowerPoint presentation, I was given 17 more DNA samples from the mothers of patients within the cohort. Microsatellite genotyping of these DNA samples would give us further proof that the mechanism behind the duplication of the MECP2 loci is in fact inter-chromosomal. Unfortunately, I did not finish the analysis of this data before my presentation Wednesday. After the presentation, I was told I would be given co-authorship on the paper Claudia is currently working. I am very excited about this and can’t wait to see the finished manuscript. By the end of the week I had finished my portion of the research on this project.
My second project, the Moebius Project, was a bit disappointing in terms of results, but this project has been going on for over a year so I did not expect too much. Of the five possible de novo mutations I had found, I was only able to test three. This was due to the DNA sequencing of two of the parents (of two different patients) was of poor quality. Of the three that I was able to test, I found only one of the mutations sites to be de novo. More likely than not, this is just a point mutation rather than it being the cause of the syndrome. After I got these results, my part in this project was complete.
For my final project, the fusion gene project, I received the primers I designed for the five patients as well as the twins with Rett Syndrome early in the week. I worked as quickly as I could so that I could present as much of my findings as possible to the lab. Sadly, only one of the primer sets for the five patients actually worked, but we also saw bands on the agarose gel for the twins with Rett Syndrome. We then sent positive results for sequencing. Once we received the results, we found that the one patient that actually had the band (the amplified product) only part of the fusion gene was amplified. We were only able to successfully amplify the exon of one of the genes involved in the fusion, but we only amplified a small portion of the exon from the other gene involved in the fusion. Unfortunately, my time in the lab ran out before I was able to design another set of primers and test them to see if we could amplify both genes involved in the fusion. With the twins with Rett Syndrome, our first PCR amplification gave us bands, showing we had successfully amplified the MECP2 gene. When we repeated these results, the bands appeared in different places, and in some cases the bands didn’t appear at all. After seeing these results, we decided that the bands were artifactual due to the primers not binding correctly. After we received these results, my work on this project was finished.
The end of this week was very bittersweet. I thoroughly enjoyed working in Dr. Lupski’s lab this summer. I learned a great amount about genetics and experimental science. I also discovered where I would like my future to head and I was given the knowledge of how to get there. I am very grateful for all the people who made this fantastic opportunity for me possible.
The pictures below are of my mentor, Dr. Claudia Fonseca, and I and the other is of me working in the lab.