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Funding Update: Jan 22, 2010

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NIH Grants in Proteomics, Oct. 1, 2009, to Jan. 15, 2010

Principal Investigator: Adams, Joseph A.
Organization : University of California, San Diego
Title: Coordination of SR protein phosphorylation and RNA splicing
Start Date: Feb. 1, 2004
End Date: Nov. 30, 2012
Amount in FY 2010: $269,031

According to the abstract, the goal is to "identify how splicing kinases recognize and phosphorylate specific regions of [domains rich in alternating arginine and serine residues] and determine how these chemical modifications impact splicing componentry."


Principal Investigator: Boyle, John
Organization: Institute for Systems Biology
Title: Providing peptide atlas-based services through the caGRID infrastructure
Start Date: Jan. 1, 2009
End Date: June 30, 2011
Amount in FY 2010: $269,816

Supports the use of a "state-of-the art software integration platform to deliver cutting edge proteomics research to the scientific community," according to the abstract. The caGRID infrastructure developed under the National Cancer Institute's Cancer Biomedical Informatics Grid project "offers such a distributed and interoperable framework, and so a natural progression for the Peptide Atlas is to exploit this technology to ensure its usage by the wider research and clinical community."


Principal Investigator: Casella, James F.
Organization: Johns Hopkins University
Title: Longitudinal SIT trial plasma proteomic biomarker discovery and validation in SCI
Start Date: Jan. 15, 2008
End Date: Dec. 31, 2011
Amount in FY 2010: $361,831

According to the abstract, the researchers seek to identify diagnostic/prognostic plasma biomarkers of silent cerebral infarctions in children ages five to 14 who have sickle cell disease.


Principal Investigator: Cremer, Paul S.
Organization: Texas A&M University System
Title: Creating platforms for the proteomics and membrane proteins
Start Date: April 1, 2004
End Date: Nov. 30, 2012
Amount in FY 2010: $258,001

The long-term goal is to design chromatographic methods to isolate and identify membrane proteins that can be used for proteomics analyses. An additional goal is to develop "supports that allow virtually all transmembrane proteins to remain laterally mobile within the planar bilayer environment," according to the abstract.


Principal Investigator: Feldmesser, Marta L.
Organization: Albert Einstein College of Medicine of Yeshiva University
Title: Protein biomarkers for invasive aspergillosis diagnostics
Start Date: Jan. 1, 2010
End Date: Dec. 31, 2011
Amount in FY 2010: $212,984

As more individuals have become more susceptible to Aspergillus fumigatus, "the burden on disease" due to microbe has increased "substantially," according to the abstract. In addition, the number of reported cases is likely to be "severely underestimated." The award is for a collaboration to identify specific protein biomarkers "associated with invasive disease in animal models of "neutropenic and corticosteroid-treated mice, but that are not found in a model of allergic bronchopulmonary aspergillosis," according to the abstract.


Principal Investigator: Geahlen, Robert L.
Organization: Purdue University
Title: Syk and associated proteins in breast cancer
Start Date: Dec. 6, 2006
End Date: Nov. 30, 2011
Amount in FY 2010: $226,766 and $48,679, through two separate grants

The research will be directed at characterizing the physical and functional interactions between Syk and components of the tumor necrosis factor signaling pathway "with an emphasis on the characterization of a novel Syk-interacting protein thought to participate in this pathway," according to the abstract. The critical structural features and mechanisms by which Syk regulates cell adhesion and motility will also be characterized, as will, through phosphoproteomic studies, the substrates and binding partners that are important for Syk's regulatory functions in breast epithelial cells


Principal Investigator: Giddings, Morgan Corinne
Organization: University of North Carolina, Chapel Hill
Title: Software to identify post-translational modifications from proteomic datasets
Start Date: Sept. 24, 2004
End Date: Nov. 30, 2011
Amount in FY 2010: $294,746

The researchers aim to integrate multiple mass spec resources for determining the type and location of modifications on proteins. They will do this by adding a Markov chain Monte Carlo-based engine to the Proclame program for analyzing top-down data. Enhancement of the GFS program for bottom-up data will also be carried out so that it will be able to perform automatic determination of post-translational modifications. A database system will be developed to manage and integrate results from multiple mass spec measurements and search engines. The investigators will carry out alpha testing in house and beta testing at external sites to assure program reliability and suitability.


Principal Investigator: Green William N.
Organization: University of Chicago
Title: Proteomic assays of neuronal protein palmitoylation
Start Date: Dec. 4, 2009
End Date: Nov. 30, 2011
Amount in FY 2010: $221,859

"Evidence is mounting that the post-translational process palmitoylation has a major role in neuronal development and function, in particular, the formation and functioning of synapses," according to the abstract. The researchers recently developed assays of protein palmitoylation based on hydroxylamine cleavage of the thioester bond between the fatty acid and cysteine side chain followed by "by reaction of the newly generated free sulfhydryl with sulfhydryl-specific reagents, such as 3H-N-ethyl maleimide (NEM) and biotinylated reagents." With the grant, they will adapt the assays for palmitoylation to a proteomic scale in order to do two things: to modify techniques to identify the specific sites on palmitoylation on the "different ionotropic glutamate receptors we are currently studying in our laboratory and all of which we have found to be palmitoylated." Also, the researchers are developing protocols that allow a set of palmitoylated proteins to be purified from highly complex protein extracts so that palmitoylation differences in neuronal preparations can be quantified.

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Principal Investigator: Hachey, David L.
Organization: Vanderbilt University
Title: Proteomics Core
Start Date: Dec. 1, 2008
End Date: Nov. 30, 2013
Amount in FY 2010: $219,983

No abstract available


Principal Investigator: Iavarone, Antonio
Organization: Columbia University Health and Sciences
Title: Mechanisms and regulation of post-translational modifications of Id proteins
Start Date: Dec. 3, 2007
End Date: Nov. 30, 2012
Amount in FY 2010: $300,668

The researchers plan to build on an earlier discovery that colon cancer cells acquire "a missense mutation in the Id2 gene that converts threonine-27 into the unphosphorylateable amino acid, alanine. They also found that threonine-27 is phosphorylated by the Dyrk 1 kinases in vitro and in vivo. In continuing work, they will investigate the regulation and function of this phosphorylation event and the destruction signals they've identified in Id proteins.


Principal Investigator: Janigro, Damir
Organization: Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
Title: Serum markers of brain barriers
Start Date: Jan. 1, 2006
End Date: Dec. 31, 2010
Amount in FY 2010: $303,790

Using molecular and protein-detection technologies, the researchers aim to discover new markers of blood-brain barrier intactness or leakage and "test the hypothesis that an increased plasma-to CSF ratio of S100P or other BBB markers correlates temporally and qualitatively with radiological measures of BBB impairment," according to the abstract. They also will validate such markers.


Principal Investigator: Kashina, Anna S.
Organization: University of Pennsylvania
Title: Role of protein arginylation in cardiovascular development
Start Date: Jan. 1, 2007
End Date: Dec. 31, 2011
Amount in FY 2010: $393,750

Supports the investigation of a newly rediscovered post-translational modification, N-terminal protein arginylation, in cardiovascular development. The research is directed at better understanding the role of protein arginylation in cardiovascular development and understanding the mechanisms and ways of treating congenital heart disease.


Principal Investigator: Kasumov, Takhar
Organization: Case Western Reserve University
Title: Enabling studies of proteome dynamics
Start Date: April 1, 2009
End Date: Dec. 31, 2011
Amount in FY 2010: $176,625

According to the abstract, proteomic studies are limited because they "typically yield information regarding static gene expression profiles." The grant supports research into how to obtain a "functional image of gene action by measuring protein dynamics in response to stimuli in vivo," and to enable the routine application of the technology for studying the development of proteome expression profiles.


Principal Investigator: Lampe, Paul
Organization: Fred Hutchinson Cancer Research Center
Title: Phosphorylation of gap junction proteins
Start Date: May 1, 1997
End Date: Dec. 31, 2013
Amount in FY 2010: $376,907

Gap junctions are specialized matched membrane domains containing channels that allow the exchange of small molecules between neighboring cells. "The gap junction protein connexin43 (Cx43) is regulated via phosphorylation and its interactions with other proteins," the abstract notes. The grant supports research into the role "that these two regulatory processes play and interplay in vivo to affect tissue development and function."


Principal Investigator: Leary, Julie Ann
Organization: University of California, Davis
Title: Mass spectrometry of metal-coordinated oligosaccharides
Start Date: May 1, 1992
End Date: Nov. 31, 2012
Amount in FY 2010: $226,947

Supports research into carbohydrate:protein and protein:protein non-covalent interactions. Specifically, the researchers seek to investigate the binding and interactions of glycosaminoglycans with chemokine ligands of the N-terminal G-protein coupled receptors CCR2 and CCR5. The also aim to study their ternary structures.


Principal Investigator: Lim, Megan S.
Organization: University of Michigan
Title: Proteomic biomarkers of ALK+ lymphoma
Start Date: Dec. 3, 2009
End Date: Nov. 30, 2013
Amount in FY 2010: $320,588

Supports research to identify proteomic biomarkers of nucleophosmin-anaplastic lymphoma kinase-positive lymphomas. Quantitative mass spectrometry will be coupled with "sophisticated" bioinformatics approaches. A quantitative proteomic analysis done in an unbiased manner will be performed to identify proteomic and phosphoproteomic changes associated with the expression of NPM/ALK in human lymphoid cells. Then the researchers will "establish the functional relevance of selected components of the MS-derived NPM/ALK signaling pathways," according to the abstract.

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Principal Investigator: McLafferty, Fred Warren
Organization: Cornell University
Title: Mass spectrometry in biomedical research
Start Date: Jan. 1977
End Date: Dec. 31, 2010
Amount in FY 2010: $221,335

The researchers have "championed" the top-down approach to proteomics, and in continuing work, plan to build out the methodology. ”A major future research effort will be in expanding the top-down applicability from 74 kDa to far larger proteins using segmented nozzle-skimmer dissociation," according to the abstract. Further, "a wild idea could do [electron-capture dissociation] during electrospray," and the investigators will try to "extend the far higher top down identification reliability to such far larger proteins, defining its capabilities as a possible replacement for bottom up identifications."


Principal Investigator: Myung, Sunnie
Organization: Rockefeller University
Title: Novel mass spectrometer for comprehensive no-loss MS/MS of all stored ions
Start Date: Jan. 1, 2008
End Date: June 30, 2010
Amount in FY 2010: $25,855

The researchers seek to develop an ultra-sensitive ion trap mass spec technique to carry out MS/MS analysis of complex biological mixtures. Specifically, they will optimize a high-capacity ion trap instrument by "isolating the pressure with the ion trap to allow us to use optimal gases in the various regions of the instrument," according to the abstract. In the next phase, they will couple an orthogonal injection reflectron TOP mass analyzer to the high-capacity ion trap. "Finally, future experiments will be geared toward the comprehensive sample analysis using this new high-capacity ion trap TOP-MS instrument."


Principal Investigator: Sabatine, Marc S.
Organization: Brigham and Women's Hospital
Title: Novel biomarkers to identify vulnerable patients with coronary artery disease
Start Date: Jan. 1, 2009
End Date: Dec. 31, 2012
Amount in FY 2010: $312,950

Utilizing proteomic and metabolomic methods, the researchers will "determine the ability of novel biomarkers to predict major adverse cardiovascular outcomes in patients with chronic coronary artery disease." Specifically, they will investigate the prognostic ability of 14 novel protein biomarkers for adverse cardiovascular outcomes. Metabolomic methods will be used to identify and validate the association of metabolites with adverse cardiovascular outcomes, as well.


Principal Investigator: Stirewalt, Derek L.
Organization: Fred Hutchinson Cancer Research Center
Title: IRF8 as a biomarker of aging, malignant transformation, and AML prognosis
Start Date: Dec. 15, 2009
End Date: Nov. 30, 2011
Amount in FY 2010: $192,989

"A better understanding of how aging promotes malignant transformation may identify novel biomarkers for cancer detection and potential targets for future therapies," according to the abstract. Preliminary studies suggest that IRF8 expression decreases with aging in hematopoietic progenitor/stem cells and in myeloid malignancies. Murine studies also have indicated that silencing IRF8 promotes the development of pre-leukemic clones "that transform into an acute myeloid leukemia with secondary genetic hits. … Therefore, decreased IRF8 expression in aging HPCs/HSCs may be an early pre-transforming event that leads to myeloid malignancies upon the acquisition of secondary 'hits.'" The grant supports research into determining whether silencing IRF8 in human CD34+ cells promotes transformation into AML. Another goal is to investigate the prognostic significance of IRF8 expression in AML.


Principal Investigator: Tezel, Gulgun
Organization: University of Louisville
Title: Proteomic analysis of retinal ganglion cell death in glaucoma
Start Date: Dec. 1, 2007
End Date: Nov. 30, 2010
Amount in FY 2010: $333,000

The researchers hypothesize that "an innovative analytical approach using proteomics technology can identify time-dependent alterations in the [retinal ganglion cell] protein complement on a large scale, which characterize precise mechanisms of the RGC response to injury from initial insult to execution of cell death in glaucoma," according to the abstract. The grant supports research that will test this hypothesis by identifying the alterations of the RGC protein expression and PTMs during glaucomatous neurodegeneration. "Time-dependent alterations of the RGC proteome … will be quantitatively evaluated by comparing the proteomic datasets between ocular hypertensive and control eyes using RGC protein samples obtained at different time points by pooling from rat eyes matched for intraocular pressure exposure and axon loss," the researchers said.


Principal Investigator: Turk, Benjamin E.
Organization: Yale University
Title: Application of peptide arrays and mass spectrometry to proteases
Start Date: Dec. 1, 2007
End Date: Nov. 30, 2010
Amount in FY 2010: $186,188

Supports the development of a platform that combines peptide microarrays with mass spectrometry "to allow for rapid, general, and thorough analysis of protease cleavage selectivity," according to the abstract. The investigators will immobilize dually labled fluorescence resonance energy transfer peptide substrates on modified glass slides at high density "via their amino termini." They then will treat the slides with a protease of interest, resulting in site-specific cleavage of a subset of peptides. Changes in fluorescence are detected on a microarray reader "allowing quantitative assessment of the extent of cleavage of each peptide on the array." Specific sites of cleavage within each substrate peptide will be determined by "subjecting the released amino terminal fragments to liquid chromatography-electrospray mass spectrometry. Consensus cleavage motifs are subsequently derived from sequence alignments of the cleaved peptides."


Principal Investigator: Vestal, Marvin L.
Organization: Virgin Instruments
Title: Merged beam MALDI TOF-TOF using ion-ion reactions to determine the structure of [biological molecules]
Start Date: Jan. 1, 2010
End Date: Dec. 31, 2012
Amount in FY 2010: $156,250

Supports investigation of practical techniques for MALDI-TOF-TOF on "biologically significant molecules using electron-transfer dissociation of position ions and proton transfer dissociation of negative ions to determine molecular structure," according to the abstract. The research will provide techniques for determining the molecular structure of singly and doubly charged molecular ions produced by MALDI, which should be applicable to proteins, peptides, and other molecules.


Principal Investigators: Yates, John Robert; Balch, William Edward
Organization: Scripps Research Institute
Title: Proteomic profiling of CFTR protein interaction
Start Date: Dec. 10, 2004
End Date: Dec. 31, 2014
Amount in FY 2010: $474,750

Previous work by the researchers has led to "substantial progress [developing] a proteomic methodologies platform to study" cystic fibrosis using semi-quantitative MudPIT technology and absolute quantification strategies using single-reaction monitoring, according to the abstract. The grant "will develop and apply quantitative proteomic methods to determine the mechanism of newly discovered chemicals (drugs) and biologics that restore deltaF508-CFTR channel activity at the cell surface."

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