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Sequencing-Related NSF Grants Awarded Oct. 25 – Dec. 16, 2008

SBIR Phase I: Surveyor Endonuclease Adaptor-Ligated Libraries for Genomic Mutation Analysis
Start Date: Jan. 1, 2009
Expires: June 30, 2009
Awarded Amount to Date: $99,353
Principal Investigator: Gary Gerard
Sponsor: Transgenomic
This Small Business Innovation Research Phase I project aims to develop a novel process for the rapid and cost-effective analysis of genetic variation between a test genome and a control genome. The method, known as SEAL, will allow researchers to construct DNA libraries containing only these variations. It would improve approaches that use whole-genome sequencing, which produces large amounts of redundant data representing the test genome’s regions that are identical to the control genome. This project will demonstrate the method’s feasibility by developing bacterial genome analysis applications. Each step of the multi-staged method will be tested to find optimal conditions. Phase II aims will be developing more complex human genomic applications.

Elucidating Gene Networks Regulating Development in Tomato
Start Date: Dec. 1, 2008
Expires: Nov. 30, 2009
Awarded Amount to Date: $888,188
Principal Investigator: Neelima Sinha
Sponsor: University of California-Davis
This project uses a genomics approach to understand natural variation in leaf morphology and light response, and to investigate the mechanism by which these two genetic networks are integrated to ensure optimal plant form. These goals will be accomplished by characterizing the differences between tomato species varying in both light response and leaf complexity. The project will characterize these differences using genomic technologies to find differences in DNA sequence and gene expression. Statistical analyses will be used to reconstruct the genetic networks that regulate leaf morphology and light responses. All data, including gene chip data, BIN maps, QTL analysis and networks generated by this project, will be made available to the public as soon as the data has passed quality control. All Solexa sequence data will be deposited in Genbank, and all microarray data will be deposited in the Gene Expression Omnibus database.

SGER: Proof of Concept on Using Spliced Leader to Study Dinoflagellate Gene Expression in the Ocean
Start Date: Nov. 15, 2008
Expires: Oct. 31, 2010
Awarded Amount to Date: $138,000
Principal Investigator: Senjie Lin
Sponsor: University of Connecticut

The ability to measure in situ gene expression for a natural dinoflagellate assemblage amidst other co-existing organisms would increase understanding of dinoflagellate-associated oceanographic processes without experimental manipulation, according to the grant abstract. Recently, the investigator has identified a dinoflagellate-specific trans-spliced leader sequence (DinoSL). These findings strongly suggest that DinoSL can be used to isolate dinoflagellate mRNA from a mixed RNA sample contributed by many organisms, which would facilitate studies of dinoflagellate-associated oceanographic and ecological processes. Proof of the suitability of the DinoSL-based technique will provide a new tool for dinoflagellate oceanographic research. In this project, the investigator will construct and sequence cDNA libraries using DinoSL as the selective primer for dinoflagellate cultures, pure and mixed with other phytoplankton, and verify that only and all dinoflagellate genes will be isolated.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.