HMC Summary of NIH ARRA Opportunities/RFAs

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2009 SIG RFA PAR 09-028

Sundstrom JM, Tash BR, Murakami T, Flanagan JM, Bewley MC, Stanley BA, Gonsar KB, Antonetti DA Identification and Analysis of Occludin Phosphosites: A Combined Mass Spectrometry and Bioinformatics Approach. J Proteome Res. 2009 Jan 6. [Epub ahead of print] PMID: 19125584

Culnan DM, Cooney RN, Stanley B, Lynch CJ.Apolipoprotein A-IV, a Putative Satiety/Antiatherogenic Factor, Rises After Gastric Bypass. Obesity (Silver Spring). 2009 Jan;17(1):46-52. Epub 2008 Oct 23.

Zhao Z, Zhang W, Stanley BA, Assmann SM.Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways. Plant Cell. 2008 Dec 29. [Epub ahead of print] PMID: 19114538

Yerlikaya A, Kimball SR, Stanley BA.Phosphorylation of eIF2alpha in response to 26S proteasome inhibition is mediated by the haem-regulated inhibitor (HRI) kinase. Biochem J. 2008 Jun 15;412(3):579-88.

Chen KM, Spratt TE, Stanley BA, De Cotiis DA, Bewley MC, Flanagan JM, Desai D, Das A, Fiala ES, Amin S, El-Bayoumy K. Inhibition of nuclear factor-kappaB DNA binding by organoselenocyanates through covalent modification of the p50 subunit. Cancer Res. 67(21):10475-83, 2007

Chang SI, El-Bayoumy K, Sinha I, Trushin N, Stanley BA, Pittman B, Prokopczyk B.4-(Methylnitrosamino)-I-(3-Pyridyl)-1-Butanone Enhances the Expression of Apolipoprotein A-I and Clara Cell 17-kDa Protein in the Lung Proteomes of Rats Fed a Corn Oil Diet but not a Fish Oil Diet. Cancer Epidemiol Biomarkers Prev 16(2): 228-35, 2007

Yerlikaya A, Stanley BA. Structural basis for the inactivation of AdoMetDC K12R mutant. Protein Pept Lett.13(3):313-7, 2006

Yerlikaya, A. and Stanley, B.A. S-adenosylmethionine decarboxylase degradation by the 26S proteasome is accelerated by substrate-mediated transamination. J Biol Chem. 279(13):12469-78, 2004

Coleman C.S., Stanley B.A., Jones A.D., Pegg A.E. Spermidine/spermine N 1-acetyltransferase-2 (SSAT2) acetylates thialysine and is not involved in polyamine metabolism. Biochem J. 2004 Nov 15;384(Pt 1):139-48, 2004

Shah, R., Coleman, C.S., Mir, K., Baldwin,  J., Van Etten,  J.L., Grishin, N.V., Pegg, A.E., Stanley, B.A., and Phillips, M.A. Paramecium bursaria Chlorella Virus-1 Encodes an Unusual Arginine Decarboxylase That Is a Close Homolog of Eukaryotic Ornithine Decarboxylases.  J. Biol. Chem 279(34): 35760-35767, 2004

Han X, Kazarinoff MN, Seiler N, Stanley BA Rat colon ornithine and arginine metabolism: coordinated effects after proliferative stimuli. Am J Physiol Gastrointest Liver Physiol. 2001 Mar;280(3):G389-99

Additional publications...

Stanley Lab Fall '99: Bruce Stanley, Kim Stambaugh, Azmi Yerlikaya, & Wil Martin

Stanley Lab Research:

Mass Spectrometric Methods for Proteomic Analysis; Structure-Function Determinants of Rapid Protein Degradation; Arginine/Nitric Oxide/Ornithine Metabolism and Growth Control

      Goals of the lab research program have been to understand the mechanisms of control of intracellular levels of rapidly degraded proteins and how this subclass of proteins is involved in control of cell growth and differentiation, particularly how enzyme half-life changes contribute to rapid cell proliferation. The enzymes of the polyamine biosynthetic pathway, particularly S-adenosylmethionine decarboxylase, are being studied both as general model proteins to define proteolytic signals which target proteins for rapid proteolysis, and for their specific contributions to control of cell growth. Experimental approaches include cell culture and transfection studies, in vitro expression of wildtype versus mutant proteins, and the development of new in vitro systems to study protein degradation. Structure-function studies are done by specific replacement of amino acid residues in the model proteins, and assessment of the effect of these mutations on either degradative rate or other enzymologic characteristics of the proteins.

      A second research focus is development of Mass Spectrometric methods for quantitative proteomic analysis and biomarker discovery. These methods include 1D and 2D liquid chromatographic separations of both whole proteins and proteolytically digested peptide fragments; the use of iTRAQ isotope-coded affinity tags; the development of improved mass spec analysis software (with commercial and other academic centers);  the development of improved MALDI plate surfaces and MALDI matrix deposition methods (in conjunction with the Penn State Nanofabrications Facility), and improved biostatistical methods for calculating the False Discovery Rates required in large scale proteomic studies..

Finally, the lab maintains an interest in Arginine/Nitric Oxide/Ornithine Metabolism and Growth Control, particularly how changes in substrate levels may act as control points in metabolic flux independently of changes in enzyme activity

Polyamine biosynthesis and arginine/nitric oxide/ornithine metabolism.