B Cell Signaling and Bioinformatics: Revealing Components of the MHC Class II Antigen Processing and Presentation Pathway

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dc.contributor.advisor Scheuermann , Richard H . en
dc.creator Lee , Jamie Anne en
dc.date.accessioned 2010 -07 -12T18 :57 :21Z en
dc.date.accessioned 2014 -02 -19T21 :59 :54Z
dc.date.available 2010 -07 -12T18 :57 :21Z en
dc.date.available 2014 -02 -19T21 :59 :54Z
dc.date.issued 2005 -05 -11 en
dc.identifier.other en
dc.identifier.uri http : / /hdl .handle .net /2152 .5 /739 en
dc.description.abstract Stimulation of mature B lymphocytes by extracellular ligands induces phenotypic changes through complex signal transduction pathways . Gene expression is altered as a result of these changes and re -programs the cell to undergo differentiation , activation , effecter function , anergy , and /or apoptosis . Gene expression microarrays are used to determine expression levels of a large number (tens of thousands ) of genes simultaneously , resulting in a gene expression profile of the experimental sample . Microarray data must be appended with biological information in order to be interesting , and this field of microarray bioinformatics is rapidly expanding . These studies prompted the development of a bioinformatics tool termed CLASSIFI (Cluster Assignment for Biological Inference ) , which identifies statistically significant co -clustering of genes with similar Gene Ontology annotation within microarray gene clusters . CLASSIFI was used to analyze microarray results from two B cell projects from the Alliance for Cellular Signaling (AfCS ) : 1 ) the BAFF /CD40L project , which evaluates the effects of BAFF and CD40L on primary mouse B cells in long -term cultures , and 2 ) the B cell single ligand screen project , which evaluates the effects of 32 single ligands on primary mouse B cells in short -term cultures . CLASSIFI was able to identify significant overrepresentation of related genes within gene clusters for both of these data sets and facilitates hypothesis generation as to the biological process affected by a specific ligand . As CLASSIFI is strictly a statistical tool that aids in hypothesis generation , experimental validation of hypotheses was performed . The B cell single ligand screen microarray and CLASSIFI analysis followed by experimental validation revealed a biological process specific to B cell antigen receptor stimulation but not LPS or CD40L stimulation - antigen processing and presentation - and provides the groundwork for new discoveries in this field . As a result , several putative components were identified that are not currently known to play a role in antigen processing and presentation in B cells . en
dc.format.medium Electronic en
dc.format.mimetype application /pdf en
dc.language.iso en en
dc.subject B -Lymphocytes en
dc.subject Signal Transduction en
dc.subject Gene Expression en
dc.title B Cell Signaling and Bioinformatics : Revealing Components of the MHC Class II Antigen Processing and Presentation Pathway en
dc.type.genre dissertation en
dc.type.material Text en
thesis.degree.name Doctor of Philosophy en
thesis.degree.level Ph .D . en
thesis.degree.discipline Immunology en
thesis.degree.grantor Graduate School of Biomedical Sciences en
thesis.degree.department en
dc.format.digitalOrigin born digital en
thesis.date.available 2005 -05 -11 en


B Cell Signaling and Bioinformatics: Revealing Components of the MHC Class II Antigen Processing and Presentation Pathway. Graduate School of Biomedical Sciences. Available electronically from http : / /hdl .handle .net /2152 .5 /739 .

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