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Funding Update: Aug 6, 2009

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Title: EAGER: Tool Development for Proteomics and Environmental Metaproteomics
Principal Investigators: Brian Palenik
Sponsor: University of California, San Diego Scripps Institute of Oceanography
Start/End Date: Aug 1, 2009 – July 31, 2010
Award Amounted to Date: $87,596

Funds development of tools to identify previously unknown, putative genes in metagenomic sequence data. According to the abstract, Brian Palenik, the principal investigator, is developing tools for the analysis of metaproteomes using metagenomics data obtained from the same site. Recently a form of "reverse proteomics" is being tested where "mass spectrometry data are used to improve whole genome annotation by demonstrating the presence of proteins not predicted in the initial genome annotation," according to the abstract. "This technology is now beginning to show promise in the analysis of complex environmental samples, such as metaproteomic samples … and can lead to new information about not only the biodiversity but the functioning of ecosystems. However, the coupling of mass spectrometry and genome and metagenome data to analyze environmental samples still requires tool development." The award funds development of tools including include computational procedures to discover new open reading frames and genes, methods to identify what species are present without DNA sequencing, and an approach for the post-translational analysis of Synechococcus metagenomes.


Title: A Mechanics Framework for the Analysis and Design of Protein Based Nano Machines
Principal Investigators: Kazem Kazerounian
Sponsor: University of Connecticut
Start/End Date: Aug. 1, 2009 – July 31, 2012
Award Amounted to Date: $325,108

The award is funded under the American Recovery and Reinvestment Act of 2009. The project is aimed at new mechanical design, analysis, and simulation framework for protein molecules. "The fact that proteins are nano devices developed through evolution by nature suggests that the development of biomimetic artificial nano machines based on polypeptide chain building blocks is not only promising, but may also be the most practical approach to meet these challenges," according to the abstract. The project continues work funded under an NSF Small Grant for Exploratory Research and "builds on a numerical modeling platform called PROTOFOLD developed by the researchers. "The project will make use of mechanical analysis and design tools to accurately model protein molecules as mechanical devices, hence facilitating understanding of their function or ability to design and manipulate protein based molecular devices for specific functional purposes," the researchers said.


Title: Acquisition of Mass Spectrometry Instrumentation for Chemistry and Biology Research
Principal Investigators: Elaine Marzluff; Clark Lindgren; T. Andrew Mobley; Mark Levandoski; Benjamin DeRidder
Sponsor: Grinnell College
Start/End Date: Aug. 1, 2009 – July 31, 2012
Award Amounted to Date: $428,295

Awarded under the American Recovery and Reinvestment Act of 2009, the funds will be used for the purchase of a time-of-flight mass spectrometer and ion trap gas chromatography mass spectrometer for use in multi-departmental research projects, spanning chemistry, biology, and neuroscience. Research activities include investigations probing solution structure, ligand binding, and protein dynamics by hydrogen/deuterium exchange mass spectrometry; investigations into differential Rubisco activase proteins implicated in heat-stress response in plants; and "characterization of organoheterobimetallic complexes to investigate their chemical ionization pathways," according to the abstract.


Title: Acquistion of a Matrix-Assisted Laser Desorption/Ionization Tandem Time-of-Flight Mass Spectrometer
Principal Investigators: Wendell Griffith; Constance Schall; Timothy Mueser; Amanda Bryant-Friedrich; Dragan Isailovic
Sponsor: University of Toledo
Start/End Date: Aug. 1, 2009 – July 31, 2012
Award Amounted to Date: $447,799

The award is funded under the American Recovery and Reinvestment Act of 2009 and will go toward the acquisition of a MALDI-TOF/TOF mass spectrometer equipped with an LC-MALDI spotting system. "The instrument supports multiple disciplines and will be applied to a wide range of materials, including biomolecules (proteins, peptides, carbohydrates, oligonucleotides, lipids), large organic molecules (synthetic polymers), and inorganic materials (nanoparticles)," the researchers said in the abstract.


Title: Acquisition of a Liquid Chromatography-Tandem Mass Spectrometry Instrument for Research and Teaching in the Sciences at Union College
Principal Investigators: Laura MacManus-Spencer; Steven Rice; J. Stephen Horton; Joanne Kehlbeck
Sponsor: Union College
Start/End Date: Aug. 1, 2009 – July 31, 2012
Award Amounted to Date: $259,992

The award is funded under the American Recovery and Reinvestment Act of 2009.
The chemistry department of Union College will acquire an LC-MS/Ms platform to facilitate "sophisticated analysis of a variety of nonvolatile organic chemicals and biomolecules, which will advance multiple areas of current research," according to the abstract. Projects that will be pursued include molecular recognition investigations of biological macromolecules; the identification of potentially novel antifungal compounds produced by bacteria; and research into the environmental fate, transport, and bioaccumulation of ultraviolet filter chemicals.


Title: Ethylene Signal Transduction: Proteomics and Molecular Mechanisms
Principal Investigators: Caren Chang
Sponsor: University of Maryland
Start/End Date: July 15, 2009 – June 30, 2010
Award Amounted to Date:$200,000

Ethylene is a gaseous plant hormone with "profound" effects on numerous aspects of plant growth and development, according to the abstract. What is known about the ethylene signaling pathway is based on genetic dissection in the reference plant Arabidopsis thaliana, but the molecular mechanisms by which these pathway proteins signal is still unknown. The project has two objectives: One is "to attain new levels of understanding of ethylene signal transduction using proteomic methods to identify previously unknown ethylene signaling components and their molecular mechanisms," according to the abstract. The second objective is to analyze mutants and genes currently in hand, with a focus on a gene called RTE1, which regulates signaling by the ETR1 ethylene receptor.


Title: Biochemistry and Genetics of Anaerobic Alkane Metabolism: Interrogation of Sulfate-Reducing Isolates and Enrichments Using Genome-Enabled and Proteomic Approaches
Principal Investigators: Amy Callaghan
Sponsor: University of Oklahoma
Start/End Date: July 15, 2009 – June 30, 2012
Award Amounted to Date: $725,195

The award is funded under the American Recovery and Reinvestment Act of 2009 and will fund genome-enabled proteomic analysis for the identification of proteins whose expression correlates with growth on alkanes in order to elucidate this pathway; the investigation of the genetics and regulation of the putative gene assA1 opron in strain Desulfatibacillum alkenivorans AK-01; and the investigation of the biochemistry and genetics of anaerobic paraffin degradation via metabolite profiling and metagenomic characterization of an anaerobic, paraffin-degrading enrichment culture.


Title: Global Proteome and Signal Pathway Phosphoproteome Dynamics during Appressorium Formation in the Rice Blast Fungus Magnaporthe oryzae
Principal Investigators: Ralph Dean
Sponsor: North Carolina State University
Start/End Date: July 15, 2009 - June 30, 2010
Award Amounted to Date: $168,874

In the abstract, the researchers said that plant pathogenic fungi are responsible for major crop losses. Many fungi "have evolved to form a specialized infection cell, an appressorium," whose formation is regulated by signal transduction pathways, notably cAMP and MAP kinase pathways, "which results in activation of phosphorylation cascades leading to changes in gene expression, including genes involved in protein turnover," according to the abstract. However, information about post-translation modifications and dynamic changes in proteins during appressorium formation is "limited." The researchers aim to perform a comprehensive quantitative analysis of relative changes in protein abundance and phosphorylation patterns during appressorium formation in order to further define and characterize the processes regulating appressorium formation. "The integration of gene expression and proteomics data will contribute substantially to constructing a more comprehensive view of the cellular processes underlying this fundamental biological process," the researchers said.

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