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Sequencing-Related NSF Grants Awarded Nov. 18 – Dec. 17, 2007

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Collaborative Research: Using Comparative Genomics to Study the Evolution of Social Behavior
 
Start Date: Oct. 16, 2007
Expires: May 31, 2008
Awarded Amount to Date: $9,750
Principal Investigator: Michael Henshaw
Sponsor: Grand Valley State University
 
This comparative genomic analysis will focus on two species of social insects that are distantly related to each other, honey bees (Apis mellifera) and paper wasps (Polistes metricus). The hypothesis to be tested is that foraging involves the same genes in different species, even species that regulate foraging socially in different ways. To test this hypothesis, brain gene expression patterns will be compared. A large and diverse team of researchers will be assembled to perform this project with expertise in social behavior, honey bee biology, wasp biology, evolutionary biology, molecular biology, genomics, and bioinformatics. The genome of the honey bee already has been sequenced, so genomic information is readily available for this species. For the wasp, a new approach to obtain the requisite sequences has been developed and tested, and will be used. Results from this project will illuminate our understanding of the evolution of social behavior. Genomic information for the wasp will form a new public resource available freely to the scientific community.
 

 
Comparative Genomics and Biological Signal Discovery in the Human Genome
 
Start Date: Dec. 1, 2007
Expires: Nov. 30, 2008
Awarded Amount to Date: $200,637
Principal Investigator: Manolis Kellis
Sponsor: Massachusetts Institute of Technology
 
The principal investigator has received this Faculty Early Career Development award to develop comparative genomics methods that can maximally use mammalian sequences for biological signal discovery, and to systematically interpret the human genome. Comparative methods for ortholog identification will be developed that can scale to dozens of complete mammals, can account for the complex phylogenies relating them, gene duplication and loss, and varying rates of divergence across gene families, and across species. In addition, a classification framework for gene identification will be constructed. Beyond the use of comparative genomics to recognize conserved regions, evolutionary signatures will be defined specific to protein-coding regions, based on patterns of insertion and deletion, codon mutational biases, and motif abundance in proximity of exons, according to the grant abstract. Finally, “phylogenetically informed tools” for motif discovery and enhancer identification will be developed. Two key model organisms will be the yeast Saccharomyces cerevisiae, and the fruit fly Drosophila melanogaster, which provide unique models for the computational and experimental efforts. Both benefit from large phylogenetic trees with many completely sequenced relatives, compact genomes, and extensive experimental information.
 

 
Maximizing the Utility of Orthologs and Phylogenetic Profiles for Systems-Scale Comparative Genomics
 
Start Date: Dec. 1, 2007
Expires: Nov. 30, 2008
Awarded Amount to Date: $230,604
Principal Investigator: Dennis Wall
Sponsor: Harvard University
 
Researchers plan to develop a freely available, web-accessible system that makes comparative genomics data available and accurately decoded into forms that facilitate further biological investigation at the scale of entire genomes. Specifically, the project will build the largest ortholog repository to date using an improved algorithm for identifying orthologs, based on appropriate evolutionary metrics of similarity. Whole-genome orthology data will be aggregated into matrices of phylogenetic profiles, enabling a series of meta-analyses including the reconstruction of genome phylogenies, and analysis of protein function and network organization. The final product will be a tool to enable any research biologist, regardless of computational expertise, to conduct large-scale comparative genomics investigations that probe functional relationships among genes or phylogenetic relationships among genomes.
 

 
Integrating Genomics Throughout the Undergraduate Microbiology Curriculum
 
Start Date: Jan. 1, 2008
Expires: Dec. 31, 2009
Awarded Amount to Date: $155,365
Principal Investigator: Eric Triplett
Sponsor: University of Florida, Gainesville
 
The goal of this project is to introduce genomics at all levels of undergraduate studies. The recipients plan to create an upper division capstone course, "Bacterial Genome Sequencing and Analysis," at the University of Florida. In collaboration with faculty at Seminole Community College, they also plan to create an introductory level course in genomics, offered at both institutions. Students in the capstone course collaboratively sequence and analyze the genome of a previously unpublished bacterial organism and, to gain experience in scientific communication, write up their research for publication in a journal.
 

 
The Vegetative Transcriptome of Arabidopsis Thaliana
 
Start Date: Jan. 15, 2008
Expires: Dec. 31, 2008
Awarded Amount to Date: $423,584
Principal Investigator: Scott Poethig
Sponsor: University of Pennsylvania
 
The researchers plan to perform a genome-wide analysis of gene expression in leaves at different positions on the shoot of flowering and non-flowering plants of Arabidopsis thaliana. Genes whose expression changes in accordance with the transition between juvenile and adult stages of shoot development are of particular interest, and will be identified by comparing gene expression patterns in normal plants with plants that have been "juvenilized" by the constitutive expression of miR156. mRNA abundance will be determined using the Affymetrix ATH1 microarray, whereas small RNA abundance will be determined by high-throughput sequencing-by-synthesis technology. These data will be accessible via a project-specific page at http://mpss.udel.edu/at/ and will be deposited in the Gene Expression Omnibus at NCBI for long-term storage and dissemination.

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