Molecular & Computational Biology Summer Research Fellowship 2014

How do phage drive bacterial diversity in Lake Michigan nearshore waters?


Project Description: With the advent of next-generation sequencing (NGS) instrumentation, the throughput and cost-effectiveness
of studying entire complex environmental communities is now feasible. A critical member of many ecological niches, the viral species which infect bacteria (phage) play an important role in maintaining the bacterial diversity within the community as well as nutrient cycling. Despite advances in sequencing technology, identifying and/or classifying the viruses present in a particular habitat is a significant challenge as relatively little genomic data is available for this the most abundant species on earth. This project focuses on the development and application of new tools for the synthesis of next-generation viral metagenomic sequence data. Classifying novel species will be achieved by fusing existing and new tools, integrating our knowledge of viral biosynthetic compatibility with their host. This will be conducted in concert with a long-term study of the viral diversity present within Loyola University Chicago’s own backyard - the nearshore waters of Lake Michigan. Utilizing novel computational methods, this research will ascertain if and how phage are shaping the bacterial diversity and density in this environment. The tools developed and data generated will benefit future studies of environmental viriomes.


Information About the Fellowship:
The Molecular & Computational Biology Summer Research Fellowship, in its 2nd year, will sponsor two Loyola Chicago undergraduate students each summer. This project is interdisciplinary in nature, combining both molecular biology techniques and computer science. Each summer, fellows will conduct surveys of the bacteria and viruses present within the nearshore waters of Lake Michigan.

Molecular techniques will include isolating, characterizing and sequencing of bacteria and viruses. You'll actually be going out into the "field" to collect samples. (So you've got to be okay with sand and water.) Prior molecular experience is not required.

Computational efforts will focus on the development of tools for analysis of the viral sequences generated. Students interested in the computational aspects of this project are expected to have some prior experience with computer programming (eg, Python, Perl, C#, C++, Java, etc.).

Expected Commitment: Fellows are expected to commit a minimum of 15-18 hours a week for 12 weeks, May 19-Aug 8. (Note, schedule is flexible for family vacations, etc.)

Applications are only accepted through the LUROP application site, due March 1, 2014.

This fellowship is supported through a grant to Dr. Catherine Putonti from the National Science Foundation (award # 1149387).