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Funding Update: Aug 27, 2009

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Title: Acquisition of a high resolution Accela-LTQ FT Ultra mass spectrometer system
Principal Investigators: Basil Nikolau; Young-Jin Lee; Ann Perera
Sponsor: Iowa State University
Start/End Date: Sept. 15, 2009 - Aug. 31, 2012
Award Amounted to Date: $821,504

The Major Research Instrumentation award is for the acquisition of a Bruker Daltonics solariX FTMS mass spectrometer. The purchase, according to the grant abstract, "empowers multidisciplinary research from a wide sweep of departments that integrate disciplines of chemistry and biochemistry, biological sciences and engineering." Projects supported by the instrument "attempt to meet the challenge of deciphering functional understanding of genome expression at the metabolic level, and are a mixture of hypothesis-driven research on the structure and regulation of specific metabolic and gene networks, and high-throughput global profiling projects that seek to generate hypotheses concerning gene functionalities."


Title: Discovery, revision, and validation of maize genes by proteogenomics
Principal Investigators: Steven Briggs; Laurie Smith; Vineet Bafna
Sponsor: University of California, San Diego
Start/End Date: Sept. 15, 2009 – Aug. 31, 2010
Award Amounted to Date: $1,335,644

The project being funded has two goals. One is to create an Atlas of Maize Proteins that would include the identity and relative amount of 40,000 to 50,000 proteins in each of 37 different tissues and stages of maize development. It would also include the protein composition of the plasma membrane, chloroplast, mitochondrion, and peroxisome and information about protein changes caused by abiotic and biotic stress. The second goal is for the proteogenomic discovery, revision, and confirmation of 40,000 to 50,000 maize gene models, including the identification of exons, the definition of translation starts and exon borders, and the determination of the correct exon reading frames.


Title: Development of ion-mobility enhanced electron-transfer dissociation for elucidating biological networks using a systems biology approach
Principal Investigator: Leroy Hood
Sponsor: Institute for Systems Biology
Start/End Date: Sept. 1, 2009 – Aug. 31, 2013
Award Amounted to Date: $1,544,620

According to the abstract, the development of high-field asymmetric waveform ion mobility spectrometry "to exploit the full potential of electron-transfer dissociation of peptides will provide steps toward more extensive measurement of these proteins." The project being funded will enhance the research infrastructure at ISB as well as integrate educational activities and research goals "to enhance the teaching, training, and learning by providing innovative tools to maintain the cutting edge curriculum of courses held by ISB."


Title: Acquisition of LTQ-Orbitrap high resolution mass spectrometer
Principal Investigator: Leslie Hicks
Sponsor: Donald Danforth Plant Science Center
Start/End Date: Sept. 1, 2009 – Aug. 31, 2010
Award Amounted to Date: $869,695

The grant is for the purchase of a Thermo Fisher Scientific LTQ Orbitrap mass spec, Eksigent 2D-nanoLC, and Advion Triversa nanospray robot to support research in proteomics and metabolomics. Projects supported by the grant include analysis of the mechanism and function of lipid post-translational modification of proteins, the direct and collateral consequences of proteome alterations, and the determination of the alkaloid metabolome of transgenic opium poppies.


Title: Automated proteogenomic annotation for prokaryotic genomes
Principal Investigator: Samuel Payne
Sponsor: J Craig Venter Institute
Start/End Date: Sept. 1, 2009 – Aug. 31, 2012
Award Amounted to Date: $707,345

"This project seeks to build a proteogenomics software pipeline that will enable and improve primary genome annotation," according to the abstract. Initially, the pipeline will be used to reannotate 3 prokaryotic genomes from six representative phyla: euryarchaeota, cyanobacteria, actinobacteria, firmicutes, deinococcus-thermus, and proteobacteria. Tens of thousands of validated gene models or verified protein maturation events are anticipated to be established. As target genomes are improved, 300 additional highly homologous genomes can be corrected.


Title: Orientations of proteins in membranes: tools and database
Principal Investigators: Andrei Lomize; Irina Pogozheva
Sponsor: University of Michigan
Start/End Date: Sept. 1, 2009 – Aug. 31, 2011
Award Amounted to Date: $416,510

Grant is for the development of computational tools and a database for structural studies, modeling, and comparative analysis of membrane-associated proteins and peptides. In particular, a fast computational method is needed to shed more information about the spatial organization and function of membranes as supra-molecular assemblies. A fast computational method "determine the optimal rotational and translational positions of proteins in membranes" has been recently developed, according to the abstract. With the grant the method will be extended, improved, and adopted for automated large-scale analysis of membrane-associated proteins from the Protein Data Bank "and for the modeling alpha-helical domains of single-spanning transmembrane proteins."


Title: Separating proteins via dynamic light scattering guidance of drop splitting
Principal Investigators: Antonio Garcia; Rafat Ansari
Sponsor: Arizona State University
Start/End Date: Aug. 15, 2009 – April 30, 2010
Award Amounted to Date: $49,921

ASU and the NASA Glenn Research Center will combine two "relatively new" techniques to "change the existing paradigm on how proteins can be separated from a complex biological fluid," according to the abstract. "The paradigm of light scattering visualization as a means of controlling separation in a single drop would represent a fundamental change from current state of the art bioseparations in many ways: (1) there is no confinement of the liquid samples within a capillary, gel plate, or tube; (2) complex biological samples can be used; (3) simultaneous molecular weight and isoelectric point detection of proteins coincident with the separation process; (4) sequences of fractionations can be programmed and accomplished within minutes using the digital (e.g., drop-wise) nature of the liquid handling; and (5) the ability to modify focusing conditions on-the fly to better identify the proteins being detected during separation," the researchers said in the abstract. The project will result in the generation of data and the enhancement of modeling capabilities so that proteins in fluids such as saliva, urine, and blood can be separated and analyzed.


Title: MALDI acquisition for collaborative species and biomolecule identification
Principal Investigators: John Wertz; David Benson; Chad Tatko; Amy Wilstermann; Randall DeJong
Sponsor: Calvin College
Start/End Date: Aug. 15, 2009 - July 31, 2012
Award Amounted to Date: $279,000

A MALDI-TOF mass spec will be purchased to support five "major research projects" under way at the college. Included is the identification of novel proteins involved in oxygen-consumption or tolerance in termite gut organisms "previously thought to be strict anaerobes," according to the abstract; analysis of eukaryotic proteinase expression following stimulation by prokaryotic collagenases; profiling of proteins involved in immunity to parasites among snails; identification of cross-linked redox-active amino acid sidechains in proteins; and identification of biocatalytic peptide-substrate complexes.

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