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NSF Microarray Grants Awarded Oct. 15 — Dec. 23, 2008

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.

Sensor for Probing Intercellular Communications. Start Date: Dec. 1, 2008. Expires: Nov. 30, 2011. Awarded Amount to Date: $230,000. Principal Investigator: Zonglu Susan Hua. Sponsor: State University of New York at Buffalo
This project aims to develop a microfluidic sensor that is capable of probing intercellular communications via gap junction channels at the single-cell level. The approach will use the multi-stream laminar flow characteristics of a microfluidic chip to confine adjacent cells to different environments, enabling a controlled means to study intercellular communications between a single pair of cells in real time by both fluorescence and impedance methods. The investigators believe the described sensor would provide an ability to study the specificity of reagents and response of gap junctions to extracellular stimuli. Project research goals include the design and control of the multi-stream flow in a microfluidic channel; on-chip cell culture in the functionalized regions of the sensor; detection of intercellular communication pathways using fluorescence and impedance measurements and their response to extracellular stimuli; and develop sensing strategies for studying water permeability of gap junction channels.

Arabidopsis 2010: The Arabidopsis Localizome. Start Date: Dec. 1, 2008. Expires: Nov. 30, 2010. Awarded Amount to Date: $250,000. Principal Investigator: Jose Alonso. Sponsor: North Carolina State University.
The project aims to examine the efficiency and effectiveness of a bacterial recombination system for large-scale gene function analysis in Arabidopsis. The accuracy of the obtained information will be evaluated generating GFP-tagged Arabidopsis lines for genes with well-characterized expression patterns, as well as with well-defined mutant phenotypes. The project will also evaluate the efficiency of each step in the process and the "scalability" to a whole-genome level. Finally, the utility of using additional reporter gene tags such as those based on GAL4 will be investigated, exploring the potential of employing the generated tagged clones to confer specific well-defined expression patterns to any gene of interest and to test the functional relevance of a particular expression pattern. All biological materials generated in the project will be made available, upon testing, to the research community from the Arabidopsis Biological Resource Center. Long-term project goals include the production of tools for generating the Arabidopsis "localizome", including high-resolution expression maps of all Arabidopsis genes.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.