COBRE: OUHSC: PROTEOMICS/BIOINFORMATICS CORE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In the current funding period the Proteomics/Bioinformatics Module provided the participating vision researchers advices and training, execution, and analyses of proteomic projects as summarized below: COBRE Projects: 1) ~ 5) 1) Dr. John D. Ash Project: The primary project was to characterize the proteome of mouse retinas in development and in transgenic mice expressing leukemia inhibitory factor. This has resulted in one publication, and contributed to funding of an NIH grant. A secondary project was to characterize the retina proteome in a mouse model of oxygen-induced retinopathy. In the next year Dr. Ash plans to use this facility to identify proteins modified by oxidation including 4-HNE, and nitro-tyrosine. The goal of the study is to determine whether LIF protects photoreceptors by reducing global or specific protein oxidation or promoting protection despite protein oxidation. 2) Dr. Raju V. Rajala Project: This project aims to investigate proteins which interact with the retinal insulin receptor. As a result of our effort we have successfully identified actin as one of the retinal insulin receptor interacting proteins. This finding opens a new area of research to study the actin-insulin receptor interactions in diseased states such as diabetic retinopathy and stress-induced retinal degeneration. Another project within this context is to identify novel proteins which bind to p85 subunit of PI3K. We also aim to identify substrates to PTP1B protein tyrosine phosphatase. The results will significantly contribute to the understanding of the retinal insulin receptor signaling. 3) Dr. Xi-Qing Ding Project: Photoreceptor cyclic nucleotide-gated (CNG) channel complex assembly and interaction with adjacent proteins are crucial for the channel function. They plan to identify the modulatory molecules of cone CNG channel using mass spectrometry and MS/MS analysis. Affinity purified channel complexes are analyzed by the proteomics/analytical biochemical approaches. This includes one- and two- dimensional gel electrophoresis, in gel trypsin digestion, mass spectrometry and MS/MS analysis, and database searching. The COBRE Proteomics/Bioinformatics Facility has been heavily used and will be continuously used in performing these studies. The results of this project will significantly contribute to the understanding of the molecular mechanisms of cone CNG function. 4) Dr. Michael H. Elliott Project: Dr. Elliot has made moderate/heavy use of the Proteomics/Analytical Biochemistry Module in the past funding period and they expect their usage to be similar in the upcoming funding period. They have applied a mass spectrometric analysis to examine the protein composition of detergent-resistant membranes from photoreceptor rod outer segments using the Proteomics Module and this work resulted in a 2008 publication in the Journal of Neurochemistry. In addition, the Li-Cor Odyssey IR Imaging system was essential for quantitative immunoblot analysis in this paper and in another study. In the upcoming grant period, they plan to use the Proteomics/Analytical Biochemistry Module to identify protein targets that are present in caveolae isolated from retinal pigment epithelium. The results will significantly contribute to a better understanding of the role of pigment epithelium for keeping the functional integrity of retinal photoreceptor cells. 5) Dr. Anne Kasus-Jacobi Project: Although the usage of this core by Anne Kasus-Jacobi, Ph.D., was minimal in the past 12 months, she plans to use this core to pursue a proteomic approach to: 1-Identify oxidative modification of the retinol dehydrogenase RDH12 in mouse retina, during light-induced oxidative stress. 2-Identify the proteins forming Michael's adducts with 4-Hydroxynonenal in wild-type and Rdh12 knockout mouse retinas, during light-induced oxidative stress. The results to be obtained from these specific aims will reveal the pathological process during the light-induced oxidative stress, which will shed light to the understanding of photoreceptor degeneration. Other Projects: 6) ~ 12) 6) Dr. Muayyad Al-Ubaidi Project: 6a. Proteomics analysis of cultured cone cells. A paper has been published in Recent Advances in Retinal Degeneration in 2007. 6b. Protein sulfation in retina. 7) Dr. Robert E. Anderson Project: Proteomics analysis of detergent-resistant membrane and light-induced 4-HNE protein modification. After Dr. Masaki Tanito went back to Japan the Module has been contacting with Dr. Tanito for the continuation of the project. 8) Dr. Hiro Matsumoto Project: Ocular proteomics of developmental mouse retina. An effort to characterize the protein expression during the postnatal development of mouse retina and its disruption by oxygen-induced retinopathy as a model system for retinopathy of prematurity has been pursued in collaboration with Dr. John Ash. 9) Dr. James McGinnis Project: Proteomic analysis of recoverin-protein complex. In the current period the Module supported this project to prepare the figures and the experimental for a manuscript. A paper has been published in Journal of Neurochemistry in 2007. 10) Dr. Muna Naash Project: 10a. Proteomics analysis of detergent-resistant membrane. A paper has been published in Journal of Neurochemistry in 2007. 10b. Identification of the protein components in the peripherin/rds protein complex. 11) The late Wei Cao Project: Coneal Proteome in Transgenic Mice. 12) This Module also supported the projects of PIs in the non-vision research fields. The PIs in the fields other than vision research supported by this Module are: Dr. Ming-hui Zou (Department of Medicine, Endocrinology) Dr. Aravindan Natarajan (Department of Medicine, Radiation Oncology) Dr. Jim Jarvis (Department of Pediatrics)