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Funding Update: Mar 15, 2011

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NSF Microarray Grants Awarded Jan. 1, 2011 — March 15, 2011

The Role of Protein Arginine Methylation in the Co-transcriptional Recruitment of pre-mRNA Splicing Factors
Start date: March 1, 2011
Expires: Feb. 29, 2012
Awarded amount to date: $180,000
Principal investigator: Michael Yu
Sponsor: The State University of New York at Buffalo

As a way to expand or to regulate the function of a protein, many RNA-binding proteins are modified chemically by specific enzymes, the investigators note. Arginine methylation is one such type of chemical modification that is found on many RNA binding proteins, and this modification is catalyzed by protein arginine methyltransferases, or PRMT. This enzyme family has been identified in species ranging from the budding yeast to humans, with the most conserved member of this family being PRMT1. In the budding yeast Saccharomyces cerevisiae, it was established that yeast PRMT1 plays a functional role in promoting the recruitment of splicing factors during transcription, which is vital to mRNP formation. The goals of this project are to examine the mechanisms by which protein arginine methylation modulates the co-transcriptional recruitment of splicing factors in S. cerevisiae. A combination of molecular biology, biochemistry, proteomic, and genomic methodologies will be used in the project. Because of the high conservation between yeast Hmt1 and its homologs in higher eukaryotes, the investigators believe information obtained from this project will provide insights that will likely be applicable to those organisms. The microarray data generated from this project will be made available to the public.


Development of a Teretoxin Neuropeptide Array for Investigating Neuronal Circuits
Start date: March 1, 2011
Expires: Feb. 28, 2013 (Estimated)
Awarded amount to date: $330,000
Principal investigator: Mande Holford
Sponsor: The City University of New York — York College

This research project is designed to identify, synthesize, and characterize novel neurotoxins from the venom of terebrid marine snails, or teretoxins, in a high-throughput manner. A biodiversity-centered toxin discovery strategy, coupled with mass spectrometric techniques, will be used to expedite the discovery of novel teretoxin peptide sequences. Identified teretoxins will then be immobilized via an oligosaccharide glycosylphosphatidylinositol linker on a solid support to form a teretoxin-GPI microarray. The ability to access teretoxins in a microarray format should enable the discovery of ligands for probing the mechanics and functional activity of ion channels in neuronal circuits, according to the investigators. They believe that the successful completion of their research objectives will produce a systematic approach with broad appeal for identifying cysteine-rich neurotoxins from the enormous peptide toxin libraries of scorpions, snakes, and spiders, in addition to marine snails, and will provide a neurotoxin microarray for high-throughput screening of ion channel ligands, an advance in the characterization of the neuronal circuit.


Microfluidic 3D Apoptosis Cell Arrays
Start date: March 1, 2011
Expires: Feb. 29, 2016
Awarded amount to date: $400,000
Principal investigator: Sihong Wang
Sponsor: The City University of New York — City College

The investigators aim to produce a high-throughput functional microfluidic platform and cellular constructs to measure signals associated with cell-death pathways, such as apoptosis. The platform will be used to examine the mechanism of action of anticancer drugs, and ultimately be used in rapid drug screening. Investigators believe the research will lead to a reduction in time to development of new drugs, not just for cancer, but for a variety of diseases.


Modeling and Prediction of Protein and Protein/Ligand Behavior on Surfaces
Start date: March 1, 2011
Expires: Feb. 29, 2012
Awarded amount to date: $81,884
Principal investigator: Thomas Knotts
Sponsor: Brigham Young University

The investigators propose that better protein arrays can be designed from an improved understanding of the factors affecting protein-surface interactions. The goals are to create interfacial models that can predict how to tether proteins of interest to various surfaces to achieve maximum ligand-binding ability, and to outline a set of heuristics to use when designing technologies involving protein-surface interactions. The experimental plan uses advanced sampling methods to probe the stability of proteins and protein-ligand complexes on different types of surfaces. Goals include examining the effects of surface crowding on the function of tethered proteins, stability when tethering in non-loop regions, and changes in folding mechanisms of surface tethered, multistate folders. The project will culminate in modeling complete protein A/antibody/antigen complexes. The investigators ultimately aim to produce a detailed, molecular-level picture of how surfaces change the structure, stability, and ligand-binding ability of tethered proteins.


Inhibition of Nitrosomonas europaea by Ag+ and Ag-NP : Determining the influence of aqueous chemistry, capping agents, growth stage and gene expression on inhibition
Start date: April 1, 2011
Expires: March 31, 2014
Awarded amount to date: $331,179
Principal investigator: Lewis Semprini
Sponsor: Oregon State University

This proposal integrates the application of genomic and physiological assays with physical and chemical characterization techniques to determine the fate of silver nanoparticles, or Ag-NP, in various water matrices, to identify the inhibition mechanisms of Ag-NP, and to characterize the defense and recovery mechanisms employed by Nitrosomonas europaea, the model ammonia oxidizing bacteria, upon exposure to Ag-NP. The inhibition of N. europaea by silver ions (Ag+) and Ag-NP will be evaluated in batch systems with tests focusing on the combinations of Ag-NP and aqueous chemistries. The investigators will conduct microarray experiments to determine if Ag+ and Ag-NP cause differential gene expression and will identify new sentinel genes for Ag+ and Ag-NP. Sequencing batch reactors and biofilm experiments will be performed to determine the effects of both long- and short-term Ag+ and Ag-NP exposure on N. europaea. They will determine how well sentinel genes are correlated with Ag-NP concentrations. They will also investigate vertical profiles of nitrification within natural and artificial biofilms using microsensor techniques and will evaluate the spatial distribution of Ag-NP using a laser capture microdissection microscope.

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