Three New Bioinformatics Tools Available
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.
Microarray Suggestion Criteria
The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.
Proteomics
The PFGRC Proteomics Facility couples sophisticated protein separation technologies with electrospray and MALDI mass spectrometry to conduct research studies and develop publicly available data sets focused on microbial agents of infectious disease and biodefense. Studies conducted thus far have included a comparative protein abundance analysis of three isogenic Staphylococcus aureus strains derived from a clinical vancomcyin-intermediate S. aureus (VISA) isolate (in collaboration with Emmanuel Mongodin, the J. Craig Venter Institute and Steve Gill, SUNY, Buffalo), the characterization of the periplasmic subcellular proteome of the Yersinia pestis strain KIM6+ in defined medium in vitro and in response to temperature shifts (26°C and 37°C) (in collaboration with Robert Perry, University of Kentucky), and a comparison of in vitro and in vivo proteome profiles, including membrane associated proteins of the enteropathogenic bacterium Shigella dysenteriae (in collaboration with Saul Tzipori, Tufts Cummings School of Veterinary Medicine).
In addition to proteome profiling, the PFGRC Proteomics Group is developing high throughput platforms for in vitro and in vivo protein expression and purification utilizing the Gateway® Destination Vector System. Proteins expressed and purified in this manner will be targeted for specific applications utilizing protein microarrays.
The table below provides links to proteome data sets relevant to each of the studies described above.
Project Description / Publications |
Reagents and Resources |
Collaborators |
Proteomic Profiling of Cell Envelope-Associated Proteins from Staphylococcus aureus |
Emmanuel Mongodin (the J. Craig Venter Institute) and Steve Gill (SUNY, Buffalo) |
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Emmanuel Mongodin (the J. Craig Venter Institute) and Steve Gill (SUNY, Buffalo) |
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Proteomic Analysis of the Periplasm of the Yersinia pestis Strain KIM6+ |
Robert Perry, University of Kentucky |
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Proteomic Profiling of the enterophathogenic bacterium Shigella dysenteriae |
Data Presentation Resource |
Saul Tzipori, Tufts University Cummings School of Veterinary Medicine |