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Christopher Jay van Belle (Molecular and Cell Biology major)
“Mapping the World's Genome: Global Protein Demographics"
Sponsor: Professor Steven Brenner, Plant and Microbial Biology
Project Description
As a part of Steven Brenner's lab, Chris will be analyzing a large set of novel sequences extracted from oceanic and other environmental microbes. Using computational methods such as Hidden Markov Model searches, he will compare novel environmental peptides to currently known peptides that are available in public databases like Ensembl, TIGR, and nr. Chris will help identify protein domains that are over- or under-represented in the ocean relative to the public datasets, as well as identify domains that may have crossed kingdom barriers. He will also investigate how these new data change our perception of protein space by, for example, illuminating biases that exist in currently available sequence datasets.
Scholar's Photo
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After long hours of research on the computer, Chris takes a quick break and smiles for the camera.
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Scholar's Journal
I've hardly realized that summer is over. It went by too quickly yet again. But over this last summer, I've been able to focus on and participate in an informative and very enjoyable research project. In Steven Brenner's lab, I've been working on analyzing and describing a large set of novel sequences sampled from environments across the globe. Our team has found intriguing information in the new proteins, like new protein families, but we've also had our fair share of difficult, and sometimes tedious, times.
When the project began, we faced a few frustrating glitches, such as incompatible data-output formats, technical issues, and I had to spend much more time fixing and cleaning and preparing information than I had originally expected. Thank goodness Perl can handle these sorts of issues relatively quickly and easily, but my perceptions of how easily something can be accomplished have definitely relaxed. Doing research is very rewarding, and the intellectual journey may be rigorous, but experimentation is sometimes slow.
The researchers in the lab were, for me, an excellent resource and working with them provided a great opportunity to see how researchers dealt with creating knowledge in uncharted waters. Published literature provides a solid framework for research, but analyses may be unique and some analyses may have never been done before. In these cases, I've found that the best solutions are those that have drawn from many different classes and many different fields of research. For us, we've applied techniques from demographic studies to analyze the biological information in the environment at large. And even though navigating in uncharted waters may be error-prone or may require much more time than one would think, it also allows research to be creative and outgoing.
I look forward to continuing this research and working in the lab. As school begins again and classes and midterms consume the day, it becomes much harder to spend enough time on any one endeavor. As an undergraduate, it's challenging to juggle classes, future plans, research, and an extracurricular life. If you'd like to research a topic in-depth, however, you should pursue that interest; you won't be bored, and if you're doing what you love, you definitely won't regret doing it.
Chris is in Mozambique , working with the Peace Corps since the summer of 2006. Click here to read his blog about the experience!
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