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NSF Microarray Grants Awarded Sept. 1 — Oct. 15, 2008

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Genetic, Genomic, and Biochemical Approaches to Elucidate Control of Sulfur Deprivation Responses. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2010. Awarded Amount to Date: $181,660. Principal investigator: Kristen Whalen. Sponsor: University of California, Santa Barbara.
 
The objective of this project is to develop a sea urchin microarray as a tool for understanding marine herbivore physiology and resistance to dietary chemical stressors. The awardees plan to design an oligonucleotide array targeting over 2,000 genes important in xenobiotic detoxification/efflux, signal transduction, nutrient metabolism and chemoreception. The array will be used to profile gene expression in the Australian urchin Heliocidaris erythrogramma, in response to chemically diverse macroalgal diets. Transcriptome profiling will identify target genes whose temporal expression will be further assessed by real-time quantitative PCR. Additionally, genes identified by transcriptome profiling can be targeted for additional biochemical characterization of algal compound-protein interactions.
 

 
Gene Expression Networks and their Regulators in a Model Perennial Plant. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2009. Awarded Amount to Date: $250,000. Principal investigator: Matias Kirst. Sponsor: University of Florida
 
In this project, a “comprehensive description of the genetic regulation of gene expression” will be generated for the model perennial plant Populus trichocarpa, according to the grant abstract. Transcription networks will be identified and genetic models for their control will be generated for different plant tissues, creating the first description of their ontogeny, diversity, and conservation both within the species and in comparison to other species. Candidates for the regulation of these transcription networks and the mechanisms of regulation will also be pursued. To achieve these objectives, “whole-genome microarrays will be analyzed in combination with the P. trichocarpa genome sequence. Genetic loci that regulate gene transcript abundance variation will be identified and gene-expression networks will be defined based on coordinated regulation of functionally related genes and shared eQTLs.”
 

 
Rhizomics — Comparative Functional Genomic and Proteomic Analysis of Rhizome Specificity Across the Plant Kingdom. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2009. Awarded Amount to Date: $1,555,700. Principal investigator: David Gang. Sponsor: University of Arizona
 
The aim of this project is to “identify genes and proteins that are expressed exclusively in the rhizome and to characterize the function of specific genes that play important roles in rhizome function from plants across the plant kingdom,” the grant abstract states. Genes that are expressed exclusively or predominantly in rhizomes will be identified by constructing cDNA libraries from developing rhizomes from selected rhizomatous species and sequencing random clones from these libraries to provide a large set of expressed sequence tags. Rhizome-specific expression of gene transcripts will be determined using DNA microarrays. Protein levels in the rhizomes versus other tissues will be determined using complementary proteomics technologies. These datasets will be integrated into one database, and will then be comparatively analyzed to identify rhizome-specific genes common to all species and specific to individual species. The roles of specific genes in rhizome differentiation, growth, and development will then be validated using a number of approaches, including more detailed expression profiling and functional analysis by gene knockout or heterologous expression in other species.
 

 
Combinatorial Multiscale Modeling and Simulation of DNA/Surface Interactions for Improved Microarray Design. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded Amount to Date: $401,234. Principal investigator: Thomas Knotts. Sponsor: Brigham Young University
 
The primary goal of this project is to “develop an improved fundamental understanding of the transport mechanisms in porous ceramic-based proton exchange membranes,” according to the grant abstract. The project will “systematically investigate the dependence of transport behavior in [proton exchange membranes] fabricated from modified porous alumina on such key variables.” Physical and chemical characterization of the membranes will inform input files for molecular dynamics based simulations. Results of these simulations will be “coupled with experimental measurements of transport behavior, primarily from impedance spectroscopy, to develop continuum and equivalent circuit models and determine relevant transport parameters such as diffusivities.”
 

 
Physically modeling cross-hybridization error in gene expression microarrays by a novel Boltzmann partition function algorithm for probe-specific position-dependent free energy. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded Amount to Date: $199,902. Principal investigator: Peter Clote. Sponsor: Boston College
 
In this method, fluorescently tagged cRNA or cDNA derived from messenger RNA is washed over a glass slide to which hundreds of thousands up to millions of short cDNA probes are attached. Hybridization between fluorescently tagged molecules and probes occurs, non-hybridized molecules are removed, and fluorescence intensities are measured by an optical scanning device. Despite technical improvements in various commercial platforms, it is still not possible to infer messenger RNA concentrations from microarray fluorescence intensity values, due to noise from cross-hybridization also called non-specific binding. A computer algorithm to compute the cross-hybridization free energy will therefore be developed and implemented, directly allowing one to estimate cross-hybridization effects.
 

 
Acquisition of a Microarray Scanner and Real-Time PCR System for Interdisciplinary Research and Teaching in an Undergraduate College Setting. Start Date: Sept. 1, 2008. Expires: Aug. 31, 2011. Awarded Amount to Date: $87,250. Principal investigator: Margaret Kovach. Sponsor: University of Tennessee Chattanooga
 
A grant has been awarded to the University of Tennessee at Chattanooga to acquire a microarray scanner and real-time PCR system to enhance undergraduate research and education in molecular biology. The instrumentation will be used by faculty and students in the departments of Biological and Environmental Sciences and Chemistry to elucidate changes in gene expression associated with biological processes.
 

 
Genetic, Genomic, and Biochemical Approaches to Elucidate Control of Sulfur Deprivation Responses. Start Date: Oct. 1, 2008. Expires: Sept. 30, 2009. Awarded Amount to Date: $149,141. Principal investigator: Arthur Grossman. Sponsor: Carnegie Institution of Washington
 
This grant continues an “exploration of the regulatory aspects of sulfur deprivation responses in the alga Chlamydomonas.” Regulatory mutants aberrant for sulfur-deprivation responses and suppressor strains will be characterized to help identify interactions among signaling factors. Wild-type and various mutant strains will be queried with genome-wide methods for examining the transcriptome under nutrient-replete and sulfur-starvation conditions, using both microarray and Illumina sequencing technologies. Focused intellectual and technical efforts will be directed toward establishing more biochemical links between identified regulators. A diversity of protein-protein interaction assays, including the yeast two-hybrid system, the split ubiquitin and split GFP systems and the classical co-immunoprecipitation assays will facilitate these studies, providing strong insights into the regulatory circuits that control nutrient limitation responses in photosynthetic organisms. Finally, analyses will be performed to help understand the two tiers of the sulfur-deprivation response that have recently been discovered; one is protein synthesis-independent while the other is protein synthesis-dependent.

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