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Modern mathematical methods in the research of immune reconstitutions and immunodeficiencies
Stuchlý, Jan ; Kalina, Tomáš (advisor) ; Šinkora, Jiří (referee) ; Štěpánek, Ondřej (referee)
In this thesis we present new analytical and integrative approaches for broad spectrum of applications of flow cytometry. CVID Large (88 individuals) cohort of CVID patients was immunopheno- typed by flow cytometry. The "probability binning" algorithm was used to au- tomatically assess the immunophenotype which presented unprecedented stabi- lity. We were able to define sub-group of CVID patients with highly activated immunophenotype showing hallmarks of immunosenescence and common clinical characteristics (thrombocytopenia, lung fibrosis and bronchiectasis). The severity of clinical complications correlated quantitatively with the immunophenotype. Analysis of cellular proteome We have designed technics which allow for highly multiplexed (>1000 of antibodies) analysis of human proteome using af- finity proteomics. We analyzed the changes of proteome of human cell lines and characterized the proteome of acute leukemias. The yet undescribed stability of proteome with respect the sub-cellular localization is shown and theoretical and practical background for antibody standardization and validation for the use in a nity proteomics is presented. Topological analysis of cytometry data Multiparametric flow cytometry allows for description of complex topological relationships of the cells in di erent stages of...
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Prenatal deverlopment of the intestinal and extraintestinal T cell receptor repertoire: identical, dominant TCRDV3 transcripts are present in different fetal piglets
Holrmeier, W. ; Geisel, W. ; Bernert, K. ; Butler, J. ; Šinkora, Marek ; Šinkora, Jiří ; Caspary, W. F.
Specimens from the small andf large intestine, spleen, thymus, liver, bone marrow and PBMC were obtained from fetal piglets between 38 and 114 days of gestation.
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