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: A Statisticans Overview. Surajit Ray sray@samsi.info Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #1
The Chinese are credited with making the observation that deliberately infecting people with mild forms of smallpox could prevent infection with more deadly forms and provide life long protection. Introduction of first generation of vaccines for use in humans 1798 Smallpox 1926 Pertussis 1885 Rabies 1927 Tuberculosis (BCG) 1897 Plague 1923 Diphtheria 1927 Tetanus 1935 Yellow Fever Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #2
Live attenuated vaccines Inactivated or killed vaccines Recombinant sub-unit envelope vaccines Recombinant vectored vaccines DNA vaccines and replicons Involve HIV genetic sequences which, once injected, induce expression of HIV antigens by human cells. In the case of replicons, these sequences are wrapped in the outer coat of an unrelated virus. Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #3
Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #4
Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #5
Sequence Analysis Viral/Microbial Evolution. Being Lower forms of life ( or even unicellular organism) they can mutate much easily. But we cannot. Gene Expression Analysis Which Genes/Molecules/Protiens are expressed at certain time point in the viral life cycle. Classification and Prediction Which of these proteins will bind to the MHC Molecule present in a particular human being. Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #6
Destruction of infected cells and tumor cells by cytotoxic T-lymphocytes or CTLs. CTLs are effector cells derived from T8-lymphocytes during cell-mediated immunity. The TCRs and CD8 on the surface of naive T8-lymphocytes are designed to recognize peptide epitopes bound to MHC-I on antigen-presenting cells (APCs). Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #7
Major Histo Compatibility, also known as human leukocyte antigens or HLA Present on various human cells e.g. dendritic cells. Typically epitopes of length 9. MHC I animation MHC I movie 1 Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #8
Mechanism different from MHC I. More complicated as the binding length may be more than 9. MHC II animation MHC II movie 2 Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #9
Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #10
>A85A_MYCTU 48 GLPVEYLQV MQLVDRVRGAVTGMSRRLVVGAVGAALVSGLVGAVGGTATAGAFSRPGLPVEYLQVPSPS MGRDIKVQFQSGGANSPALYLLDGLRAQDDFSGWDINTPAFEWYDQSGLSVVMPVGGQSS FYSDWYQPACGKAGCQTYKWETFLTSELPGWLQANRHVKPTGSAVVGLSMAASSALTLAI YHPQQFVYAGAMSGLLDPSQAMGPTLIGLAMGDAGGYKASDMWGPKEDPAWQRNDPLLNV GKLIANNTRVWVYCGNGKPSDLGGNNLPAKFLEGFVRTSNIKFQDAYNAGGGHNGVFDFP DSGTHSWEYWGAQLNAMKPDLQRALGATPNTGPAPQGA >A85A_MYCTU 242 KLIANNTRV MQLVDRVRGAVTGMSRRLVVGAVGAALVSGLVGAVGGTATAGAFSRPGLPVEYLQVPSPS MGRDIKVQFQSGGANSPALYLLDGLRAQDDFSGWDINTPAFEWYDQSGLSVVMPVGGQSS FYSDWYQPACGKAGCQTYKWETFLTSELPGWLQANRHVKPTGSAVVGLSMAASSALTLAI YHPQQFVYAGAMSGLLDPSQAMGPTLIGLAMGDAGGYKASDMWGPKEDPAWQRNDPLLNV GKLIANNTRVWVYCGNGKPSDLGGNNLPAKFLEGFVRTSNIKFQDAYNAGGGHNGVFDFP DSGTHSWEYWGAQLNAMKPDLQRALGATPNTGPAPQGA >A85B_MYCTU 239 KLVANNTRL MTDVSRKIRAWGRRLMIGTAAAVVLPGLVGLAGGAATAGAFSRPGLPVEYLQVPSPSMGR DIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYS DWYSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHP QQFIYAGSLSALLDPSQGMGPSLIGLAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKL VANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNG THSWEYWGAQLNAMKGDLQSSLGAG >ACTB_HUMAN 180 ALPHAILRL MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ EYDESGPSIVHRKCF Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #11
MHC class I genes (HLA-A, HLA-B and HLA-C) MHC class II genes (HLA-DP, HLA-DQ and HLA-DR) Database ALPHAILRL Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #12
We want to classify the peptides into Binders and non Binders. Binders of specific HLA-super types. Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #13
A supermotif is a motif which confers the ability to bind to several different HLA A supertype, the corresponding assembly of HLA As of October 2001, nine major HLA class I supertypes have been defined HLA-A1, A2, A3, A24 HLA-B7, B27, B44, B58, B62 e.g the 5 alleles belonging to HLA-A3 supertype: A*0301 A*1101 A*3101 A*3301 A*6801. Sette et al, Immunogenetics (1999) 50:201-212 Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #14
Mostly +ve examples. No good database of -ve examples. Include structural information of peptides in the classifier. In case of we do not know the position of binding. Supertypes are still being defined. Work in Progress... Slides produced with HA-prosper latex package Surajit Ray Samsi PostDoc Seminar: Nov 2: 2004 - slide #15