Parsing Based on Programmed Grammars

Tato práce se zabývá syntaktickou analýzou na programovaných gramatikách. Modifikuje postupy prediktivní syntaktické analýzy známé pro bezkontextové gramatiky a aplikuje je na gramatiky programované. Studuje síly této metody a zamuje se především na některé jazyky, které nejsou bezkontextové.This thesis is researching methods of parsing based on programmed grammars. It modifies known algorithm of table driven non-recursive predictive parser for context-free grammars and applies it on programmed grammars. It studies strength of this method, focusing on some languages which are not context-free.

Remnants of an ancient deltaretrovirus in the genomes of horseshoe aats (Rhinolophidae)

Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient , despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses

LIME: A New Membrane Raft-associated Adaptor Protein Involved in CD4 and CD8 Coreceptor Signaling

Lymphocyte membrane rafts contain molecules critical for immunoreceptor signaling. Here, we report identification of a new raft-associated adaptor protein LIME (Lck-interacting molecule) expressed predominantly in T lymphocytes. LIME becomes tyrosine phosphorylated after cross-linking of the CD4 or CD8 coreceptors. Phospho-LIME associates with the Src family kinase Lck and its negative regulator, Csk. Ectopic expression of LIME in Jurkat T cells results in an increase of Csk in lipid rafts, increased phosphorylation of Lck and higher Ca2+ response to CD3 stimulation. Thus, LIME appears to be involved in regulation of T cell activation by coreceptors

Characterization of the distribution and dynamics of the antigen-presenting cells using MHC II-EGFP knock-in mouse model

Results of recent studies indicate that dendritic cells are capable of transporting commensal intestinal bacteria into the mammary glands, which ultimately leads to their occurrence in breast milk. We have therefore decided to evaluate the phenotype of immunologically relevant antigen presenting cells (APCs) present in the mammary glands and the small intestine, respectively and perform a comparison study. We also studied plasticity of these populations during lactation. In situ immunodetection and flow cytometry methods were used to determine phenotype. We succeeded in optimising the methods for preparation of samples for flow cytometry and microscopy. We thoroughly tested protocols for 3D visualisation of APC populations and quantitative image analysis for correlation with flow cytometry, further optimization is nevertheless needed. We found out that during lactation large numbers of MHC II+ cells cluster around the alveoli and milk ducts. These cells are of a distinctly dendritic shape and their phenotype does not correspond to the APCs in the surrounding tissue. A pronounced increase of APC cells in the mammary glands between the fourth and sixth days of lactation was observed, with the majority of these cells expressing the CD103 antigen typical for cell populations of immune cells of the..

Characterization of the distribution and dynamics of the antigen-presenting cells using MHC II-EGFP knock-in mouse model

Výsledky nedávno publikovaných studií naznačují, že dendritické buňky mají schopnost do mléčné žlázy transportovat komenzální střevní bakterie, které se odtud dostávají do mléka. Proto jsme se rozhodli provézt fenotypizaci imunologicky relevantních populací antigen prezentujících buněk (APC) v mléčné žláze a srovnat je s populacemi v tenkém střevě. Dále jsme se zaměřili na jejich změny během kojení. Fenotyp jsme určovali imunodetekcí in situ a průtokovou cytometrií. Podařilo se nám optimalizovat přípravu materiálu pro průtokovou cytometrii a mikroskopické metody. Prověřili jsme možnosti 3D vizualizace populací APC v celé tkáni a kvantitativní analýzy obrazových dat pro jejich korelaci s průtokovou cytometrií, zavedení těchto metod si ještě vyžádá další optimalizaci. Zjistili jsme, že se během kojení velké množství MHC II+ buněk shlukuje okolo alveolů a kanálků mléčné žlázy. Tyto buňky mají výrazně dendritický tvar a fenotypicky se liší od APC v okolní tkáni. Byl prokázán výrazný nárůst zastoupení APC v mléčné žláze mezi 4. a 6. dnem kojení, přičemž většina těchto buněk exprimuje molekulu CD103, která je typická pro populace buněk imunitního systému lokalizované ve střevě. Výrazné je též zastoupení CD64+ buněk. B- lymfocyty se naopak vyskytují prakticky jen v lymfatické uzlině mléčné žlázy a jejím...Results of recent studies indicate that dendritic cells are capable of transporting commensal intestinal bacteria into the mammary glands, which ultimately leads to their occurrence in breast milk. We have therefore decided to evaluate the phenotype of immunologically relevant antigen presenting cells (APCs) present in the mammary glands and the small intestine, respectively and perform a comparison study. We also studied plasticity of these populations during lactation. In situ immunodetection and flow cytometry methods were used to determine phenotype. We succeeded in optimising the methods for preparation of samples for flow cytometry and microscopy. We thoroughly tested protocols for 3D visualisation of APC populations and quantitative image analysis for correlation with flow cytometry, further optimization is nevertheless needed. We found out that during lactation large numbers of MHC II+ cells cluster around the alveoli and milk ducts. These cells are of a distinctly dendritic shape and their phenotype does not correspond to the APCs in the surrounding tissue. A pronounced increase of APC cells in the mammary glands between the fourth and sixth days of lactation was observed, with the majority of these cells expressing the CD103 antigen typical for cell populations of immune cells of the...Department of Cell BiologyKatedra buněčné biologiePřírodovědecká fakultaFaculty of Scienc

Bioinformatics: Tools for analysis of biological sequences

The field of Genomics is aimed at complex analysis of genomes based on our knowledge of the nucleotide sequences in DNA. Bioinformatics is a tool for analysis of the long strings of nucleotide or aminoacid sequences. Here we describe basic methods of bioinformatics

Characterization of the distribution and dynamics of the antigen-presenting cells using MHC II-EGFP knock-in mouse model

Results of recent studies indicate that dendritic cells are capable of transporting commensal intestinal bacteria into the mammary glands, which ultimately leads to their occurrence in breast milk. We have therefore decided to evaluate the phenotype of immunologically relevant antigen presenting cells (APCs) present in the mammary glands and the small intestine, respectively and perform a comparison study. We also studied plasticity of these populations during lactation. In situ immunodetection and flow cytometry methods were used to determine phenotype. We succeeded in optimising the methods for preparation of samples for flow cytometry and microscopy. We thoroughly tested protocols for 3D visualisation of APC populations and quantitative image analysis for correlation with flow cytometry, further optimization is nevertheless needed. We found out that during lactation large numbers of MHC II+ cells cluster around the alveoli and milk ducts. These cells are of a distinctly dendritic shape and their phenotype does not correspond to the APCs in the surrounding tissue. A pronounced increase of APC cells in the mammary glands between the fourth and sixth days of lactation was observed, with the majority of these cells expressing the CD103 antigen typical for cell populations of immune cells of the..