Gene Expression Profiles during Embryonic Development in the L. varieagatus sea urchin
This highlight concerns one of the NSF IGERT-funded, Boston University Bioinformatics Program, Challenge Projects for 2010-2011 year. It was mentored by Cynthia Bradham an Associate Professor of Biology at Boston University and involved a four-student, first-year team consisting of Chris Montalbano, an IGERT trainee, Adrian Heilbut, Elham Azizi, and Shile Zhang. The project concerns the analysis of RNAseq data (gene expression data) for several developmental time points in the sea urchin L. varieagatus, a model organism. The goals have been to 1) develop gene models for L. varieagatus (difficult because a complete genome sequence is not yet available) and 2) determine differential expression of those genes to reveal which are turned on and off at the measured developmental time points and under different experimental conditions. The RNAseq data is very high volume, consisting of millions of short sequences derived from messenger RNA in the cells. The messenger RNA is present when a gene is active. The analysis for the first goal has involved two complementary approaches, 1) building gene models de novo, which means assembling the short sequences into longer “transcripts” which represent spliced messenger RNA sequences, and 2) using gene models from a related species, S. purpuratus, as the “core” models and building L. varieagatus models by matching the short sequences to the core models. The analysis for the second goal has involved a quantification to determine how many of the short sequences match each of the gene models.
This is a complex problem and the students have utilized sophisticated tools and developed some of their own elegant approaches to build and quantify the gene models. The work has proceeded over two semesters and also provided a project for our first year Biological Databases course, where the same students have developed a database to access and display the data they are generating.
The importance of this highlight, though, is what it represents for our research and educational program. Dr. Bradham is a young assistant professor biologist with no training in computational methods. She has previously hosted Bioinformatics rotation students and has grasped the need to include computational approaches in her research. But, now that she has worked with a strong student team capable of carrying out the required computational analysis, she has shifted her research strongly in the computational direction. She has become an interdisciplinary researcher and this is, in fact, one of the major goals of our IGERT training and research program: to create new interdisciplinary scientists. We expect that Dr. Bradham will continue as a very active participant in our program and will extensively employ computational analysis in her future research. The Challenge Project students, who have worked very closely with Dr. Bradham, cannot help but be influenced by her and will see this as an important example for their own growth as scientists.
This activity primarily addresses the goal of cultivating an outstanding scientific workforce. It emphasizes the goals of developing strong interdisciplinary research collaborations among our faculty and students and encourages creativity, independence, and quality in student research. With respect to the secondary goal of advancing the frontier of knowledge, the work started by the students in this Challenge Project will be carried forward and ultimately advance our knowledge of gene expression during development in these model organisms.