BIOL 319(F) Integrative Bioinformatics, Genomics, and Proteomic Lab (Same as Chemistry 319, Computer Science 319, Mathematics 319 and Physics 319) (Q)
What can computational biology teach us about cancer? In this capstone experience for the Genomics, Proteomics, and Bioinformatics program, computational
analysis and wet-lab investigations will inform each other, as students majoring
in biology, chemistry, computer science, mathematics/statistics, and physics
contribute their own expertise to explore how ever-growing gene and protein
data-sets can provide key insights into human disease. In this course, we will
take advantage of one well-studied system, the highly conserved Ras-related
family of proteins, which play a central role in numerous fundamental processes
within the cell. The course will integrate bioinformatics and molecular biology,
using database searching, alignments and pattern matching, and recombinant
DNA techniques to reconstruct the evolution of the RAS gene family by focusing on the gene duplication events and gene rearrangements that have occurred
over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in various signal transduction pathways,
students will identify pathways that are aberrantly activated in mammalian cell
lines carrying a mutant, constantly active Ras protein. This functional genomic
strategy will be coupled with microscopic examination of tissue sections from a
variety of human colon tumors, using phosphorylation-state specific antisera, to
test our hypotheses. Proteomic analysis will introduce the students to de novo
structural prediction and threading algorithms, as well as data-mining approaches to identify specific amino acids involved in protein-protein contacts.
Phage display and mass spectrometry will be used to study networks of interacting proteins in normal colon and colon tumor tissue. Format: lab, with one-hour
of lecture per week. Evaluation will be based on lab participation and several
short papers/lab reports.
Prerequisite: Biology 202, or Biology 101/AP biology and Computer Science
315 or Physics 315 or Computer Science 106, or permission of instructor. Enrollment: 12 (expected 12). Preference given to seniors, then juniors/sophomores.