Transcript ASU
ASU TVDC Progress Report 2/23/10 Kathryn F. Sykes and Stephen A. Johnston Completed Milestones: 25, 26, 28 and 32, 33, 34, 35, 36 Active Milestones: UNM 29 Activating Milestones: 28, 37 Slide 1 Multi-type Data Analyses All data from FTU experiments can be examined in two preferred ways: 1) Each datatype can be analyzed with results integrated at a high level (a normative analysis vs. positive analysis) 2) Each datatype can be converted to a common format and re-analyzed without bias (positive analysis) For this method we need to convert data to ratios (gene a > gene b at time c, etc.) Each result is a +, -, 0, or no-call Each set of results (gene family, operon, peptide, vaccine group, etc.) is then checked for some revealing consensus * Consensus denotes common effect per datatype; * Common effect denotes biological activity; * Common biological activity assumes a natural synergy or antagonism * Lack of common biological activity assumes independence Continued: consistency of multitype data analyses • Each analysis method described above can have an associated confidence level or a chi-square but not true significance since data is no longer continuous (converted to binary) Slide 3 Re-opening MS28 • Objective: – Remake the FTU SCHUS4 proteome as individual ~400 amino acid polypeptides (mostly full length proteins) in order to repeat the T cell assay (ELISpot) screen in NHPs. – Fresh cells from spleen and lymph tissues will be used. • Status: – – – – – Tien is completing her post-doc Feb 28th. Andrey Luskutov has agreed to take over her role in the project and has been working with Tien for the past 2 weeks to ensure a smooth, accurate, timely transition of the samples, protocols and database. Stored templates have been QC’ed and quantitated. PCR primers have been QC’ed Quotes for lysate, antibody, and E-gel reagents are being generated. Opening MS 37 • Objective: Make and purify a set of FTU proteins recombinantly in ~mg quantities for testing in challenge-protection assays. Status: • IglC is on the list. • Standard recombinant bacterial expression will be explored initially. • Any difficulties with expression will be addressed with molecular manipulations Additional Points • Description of deliverables completed for each active milestone: – MS 35: Microarray results with qPCR verification – MS 36: Set of 9 proteins for testing as vaccine candidates • List of relevant publications from the past month • ASU reports no TVDC publications in January 2010 • MSCR status – – – – MS33: Barbara will review edits received from Mitch on 2/3/10 MS34: Mitch, ver 0.1 is pending at ASU; overdue to UNM approximately 2/1/10 MS35: Mitch- completed work; ASU will write MSCR MS36: Mitch- completed work; ASU will write MSCR Slide 6 Action Items • • • • • • Phil needs a list of all experiments that will contribute to the final integrated data and questions. Then assign people to integrated approach. Phil/ASU may start with the T cell epitope data to simplify for consolidating the data analysis ASU will run a minor pilot to assure that the smaller beads work at least as well as the prior larger beads in the FT polypeptide synthesis Kathy will coordinate the synthesis of the new Ft polypeptide library with Terry so Terry can have the vaccinated NHP at the coordinated time. Terry, determine when UNM can do the ELIspot assay after the micro beads pilot is completed at ASU. ASU will write the MS 34,35, and 36 MSCRs. Slide 7