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NSF Microarray Grants Awarded May 1 — Aug. 1, 2008

Transfected cell microarray technology based on microfluidic electroporation. Start date: May 1, 2008. Expires: April 30, 2008. Awarded amount to date: $84,092. Principal investigator: Chang Lu. Sponsor: Purdue University
The goal of this project is to develop “microfluidics-based, transfected cell arrays using electroporation as the transfection method for large-scale gene screening based on both cell lines and primary cells. Electroporation occurs when a critical electrical field strength has been achieved and the cell membrane becomes effectively permeable to large biomolecules. This project will study the transfection of cell lines and primary cells based on a “novel microfluidic electroporation technique developed in the PI's laboratory and also demonstrate proof-of-concept transfected cell arrays for gene screening.”

Investigating Mechanisms of Histone Variant Function and Regulation that Affect Transcriptional Control and fertility in C. Elegans. Start date: May 1, 2008. Expires: April 30, 2009. Awarded amount to date: $110,047. Principal investigator: Diana Chu. Sponsor: San Francisco State University.
The project aims to investigate the mechanisms of a sperm-specific histone variant in transcriptional regulation for fertility in C. elegans sperm. In preliminary studies, the first known C. elegans sperm nuclear basic protein, a histone H2A variant called HTAS-1, was identified and found to be required for optimal fertility. According to the project abstract, preliminary data from DNA microarray analyses identified both activated and repressed genes in HTAS-1 mutants compared with wild-type animals. The central hypothesis of this project is that HTAS-1 incorporation modulates the expression of genes that work in concert for optimal fertility in sperm. To test this, “germ cell progression, oocyte development, and sperm behavior will be assessed using array analysis and chromatin immunoprecipitation to determine how each contributes to reduced fertility in HTAS-1 mutants.

Microarray Analysis of Caste Ontogeny in a Social Insect. Start date: May 1, 2008. Expires: April 30, 2009. Awarded amount to date: $28,717. Principal investigator: James Hunt. Sponsor: North Carolina State University.
The project will use a “microarray of genes to identify specific genes in a paper wasp species that are affected by the environment as they regulate the development of workers and reproductives in the wasp colony.” It claims that a “broader impact of the research is that the results should be widely applicable to ants, bees, and termites, including economically important species such as pest ants and endangered pollinators such as bumble bees.”

The Evolutionary Genomics of Facultative Social Behavior in a Tropical Sweat Bee. Start Date: July 1, 2008. Expires: June 30, 2009. Awarded Amount to Date: $11,702. Principal investigator: Peter Nonacs. Sponsor: University of California-Los Angeles
The project seeks to study social evolution based on the similarities between social insect worker behavior and maternal reproductive traits. “The worker caste may have originated in a solitary ancestor when a mutant female exhibited maternal behavior prior to dispersal. This would have resulted in sibling-directed, instead of offspring-directed care. If this theory is correct, genes active throughout the reproductive cycle of solitary ancestors should be differentially regulated in workers and queens of social descendants.”
The project will test this hypothesis by surveying gene-expression patterns in Megalopta genalis bees, using a custom microarray containing probes corresponding to approximately 5,000 genes expressed in the M. genalis brain. The results are expected to “highlight evolutionary pressures consistently important to the origin of eusociality, and have a transformative role in understanding how the social environment affects reproductive behavior.”

A Lipobead-Based Microarray Platform for the Label-Free Detection of Bacterial Exotoxins. Start Date: July 1, 2008. Expires: June 30, 2009. Awarded Amount to Date: $85,755. Principal investigator: Charles Maldarelli. Sponsor: CUNY City College
The project aims to develop an “ultra-miniaturized microarray platform for the detection of bacterial exotoxins, the primary virulence factors for many human diseases. The microarray includes an assembly of capture molecules, each of which selectively binds to a different toxin. The capture molecules used by the array are the “natural membrane receptors which the exotoxins use to target and attach to cells before infecting them. As such, these receptors bind the toxins with high selectivity and affinity.” This research will also develop a fluorescence detection system for identifying the binding of a toxin to a particular capture molecule in the array without having to label the toxin or perform subsequent assays on the bound toxin. The label-free system is “based on measuring the changes in the resonance energy transfer between donor and acceptor fluorescence pairs pre-labeled in the bilayer.” The miniaturized design also allows for the “display of receptors at different concentrations in the bilayers, which will allow the binding affinity to be measured. This additional information allows toxins to be identified with greater accuracy, particularly in the case where two bind to the same receptor.”

Metabolic Activities and Gene Expression of Marine Psychrophiles in Cold Ice. Start Date: July 15, 2008. Expires: June 30, 2011. Awarded amount to date: $525,000. Principal investigator: Karen Junge. Sponsor: University of Washington
This funded research program has two stated objectives. The first is to “investigate metabolic activities and gene expression of polar marine psychrophilic bacteria, when confronted with freezing conditions at temperatures above the eutectic of seawater, to unveil cold adaptation mechanisms with relevance to wintertime sea-ice ecology.” The second objective is to “discern, if psychrophilic processes of leucine incorporation into proteins, shown to occur to -196 degrees Celsius, amount to metabolic activity providing for the survival of cells, or are merely biochemical reactions still possible in flash-frozen samples without any effect on survival.” 
The research will be accomplished by examining extracellular and intracellular processes of psychrophilic activity above and below the eutectic by: 1) determining the temperature range of metabolic activities such as DNA synthesis, carbon utilization, respiration and ATP generation using radioactive tracer technology, including a control at liquid helium temperature; 2) analyzing gene expression in ice using whole-genome and microarray analyses, and 3) examining the role of exopolymeric substances and ice microphysics for the observed activity using an in situ microscopy technique. “Results of the proposed research can be expected to aid in the determination of cellular and genetic strategies that allow cells to maintain activity at extremely low temperatures within an icy matrix and/or to resume activity again when more growth-permissive conditions are encountered.”

How Does RNase III Regulate Antibiotic Production in Streptomyces Coelicolor?. Start Date: August 1, 2008. Expires: July 31, 2009. Awarded amount to date: $159,503. Principal investigator: George Jones. Sponsor: Emory University
The project will use RNA immunoprecipitation followed by microarray analysis to examine the mechanism of RNase III regulation of antibiotic production. An antibody to a mutant form of RNase III will be used to precipitate complexes formed between the enzyme and its target RNAs. RNAs will be extracted from the immunoprecipitates and used to synthesize complementary DNAs. The cDNAs will then be used in microarray studies to identify RNAs that are enriched in the immunoprecipitates. RNAs that may be involved in the regulation of gene expression, such as mRNAs for RNA polymerase sigma factors, repressors, activators, et cetera, will be studied further and cleavage assays will verify that these mRNAs are substrates for RNase III. Finally, the corresponding genes will be disrupted and the effects of disruption on antibiotic production assessed. “In this way, genes whose products are substrates for RNase III and which regulate antibiotic production in S. coelicolor will be identified.”

Parallel Algorithms and Software for Large Scale Microarray Data Analysis and Gene Network Inference. Start date: August 1, 2008. Expires: July 31, 2009. Awarded amount to date: $120,997. Principal investigator: Srinivas Aluru. Sponsor: Iowa State University
Investigators plan to develop “high-performance, parallel computational methods for large-scale gene expression analysis and gene network inference utilizing tens of thousands of microarray experiments available in public repositories.” Specifically, investigators will develop: 1) parallel algorithms for biclustering large gene expression matrices; 2) parallel algorithms for inferring gene networks using Mutual Information and Bayesian approaches; and 3) methods for querying and analyzing large-scale biological networks. The ultimate goal of the project is to develop “advanced computational methods and open source software programs” that can be used in systems biology.

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.