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Sequencing-Related NSF Grants Awarded Oct. 21 – Nov. 17, 2007

STTR Phase I: Network Offloading for Genome Sequence Searching using the SmartNIC
Start Date: Jan. 1, 2008
Expires: Dec. 31, 2008
Awarded Amount to Date: $149,704
Principal Investigator: Gerald Sabin
Sponsor: RNET Technologies, Palo Alto, Calif.
This Small Business Technology Transfer phase I project aims to develop a Field Programmable Gate Array-based co-processing unit that will enable more rapid searches of protein and nucleic acid databases by allowing, among other functions, one core of a multi-core system to be used as a co-processing unit for data management. This will allow researchers to perform more efficient alignment and identification of molecules such as proteins and nucleic acids.

Microbial Genome Sequencing: Insight into the Evolutionary History of Bacillus Subtilis Through Whole Genome Sequencing
Start Date: Sept. 1, 2007
Expires: Sept. 30, 2008
Awarded Amount to Date: $413,156
Principal Investigator: Jacques Ravel
Sponsor: University of Maryland at Baltimore
This is a comparative genome sequencing project of bacteria in the Bacillus subtilis group. B. subtilis can be divided into two major subgroups: 168 and W23. The only genome sequence available to date is a representative of the 168 group that has been extensively adapted to laboratory conditions. This process has resulted in the loss of a number of ecologically relevant social behaviors exhibited by newly isolated environmental members of this species. To fully appreciate the diversity within this model organism, a whole genome shotgun sequencing approach will be used to sequence the genome of an additional four B. subtilis isolates: B. subtilis TU-B-10 (type strain of the W23 group), Bacillus mojavensis RO-H-1 (close relative associated with wheat blight, hydrocarbon recovery and novel antifungal properties), B. subtilis NCIB3610 (the ancestor to B. subtilis 168) and B. subtilis RO-NN-1 (a recent environmental isolate within the 168 group that has a larger genome than other B. subtilis strains). The comparative analysis of these genome sequences is expected to generate a better insight into the evolution of this model organism.

Microbial Genome Sequencing: Whole Genome Sequencing of Bacillus Megaterium QM B1551
Start Date: Sept. 1, 2007
Expires: Sept. 30, 2008
Awarded Amount to Date: $251,252
Principal Investigator: Jacques Ravel
Sponsor: University of Maryland at Baltimore
This goal of this project is to sequence the complete genome of Bacillus megaterium, a bacterium that has a number of properties that are of economic and scientific interest. Its cells are approximately 100 times larger in volume than most other bacteria, allowing for the localization of certain proteins and protein complexes. Also, B. megaterium's ability to synthesize and secrete products without degradation allows for the large-scale production of compounds, including vitamin B12, antiviral compounds such as oxetanocin, which is active against HIV, and penicillin amidase, used to construct synthetic penicillins. The bacterium also contains a number of plasmids, thought to contain genes responsible for the organism's ability to grow in environmentally contaminated sites. B. megaterium is an ancestral relative to other Bacillus species, including B. anthracis as well as the model bacterial species B. subtilis. The genome sequencing and comparative genomics of this bacterium may provide additional insights into the development of treatments and therapies for pathogens.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.