Diss. (sammanfattning) Stockholm : Karolinska institutet, 2002. / Härtill 5 uppsatser.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves [78]-86).

Dissertation (Ph.D.)--University of South Florida, 2008. / Includes vita. Includes bibliographical references. Also available online.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2004. / Bibliography: leaves 85-110.

Helicobacter pylori is one of the most potential and successful human pathogen which colonizes atleast 50% of world population. One of the important characteristics of this pathogen is the degree of allelic diversity and genetic variability which helps it to adapt and colonize. Phase variation is one of the mechanisms used by Helicobacter pylori to generate variation, where presence of homopolymeric nucleotide or dinucleotide repeats in an ORF make it prone to frequent length changes as a consequence of slipped strand mispairing mediated mutagenesis. An important feature of H. pylori biology is the presence of a large number of Restriction-Modification (R-M) systems in its genome. Till date, seven strains have been completely sequenced and each have more than 20 R-M systems. The presence of homopolymeric nucleotide or dinucleotide repeats in many of R-M systems make them an interesting subject for investigation. Here, we show that hp0051 which codes for a C5 cytosine methyltransferase from H. pylori is a hypermutable gene, which undergoes random mutations. In addition it exhibits phase variation due to presence of a dinucleotide (AG) repeat which results in a truncated protein. hp0051 homologs were amplified and sequenced from different clinical isolates of H. pylori. Sequence analysis showed that hp0051 homologs from 23 clinical isolates are different from each other suggesting a hypervariable nature of the sequence. It was observed that when over expressed in E. coli hp0051 undergoes random mutations. These mutations give rise to different variants of HP0051 with different biochemical properties. Different variants of HP0051 were biochemically characterized. All variants recognize 5´-CCTC-3´ and methylate the first cytosine. A few of the isoforms exhibit degeneracy in the recognition site as they recognize 5´- CNCC-3´ (N being any nucleotide) and methylates third cytosine. Molecular modelling studies suggest that HP0051 has two domains, one large domain having catalytic and AdoMet binding motifs and small domain having target recognition domain. DNA sequencing, peptide finger mapping, MALDI MS-MS and CD have been used to establish the differences between the different isoforms of HP0051. Interestingly when a mutant protein which lacks methylation activity was expressed in E.coli random mutations were not observed. To understand the role of methylation in the occurrence of random mutations, microarray analysis was done. Microarray analysis have shown that the overexpression of HP0051 results in the down regulation of deoxyadenine methyltransferase (dam) in E.coli. Microarray data were further authenticated by RT PCR analysis. dam plays a vital role in mismatch repair pathway and down regulation of dam results in enhanced mutation rates. A large number of clinical isolates were analysed for the presence of hp0051 and hp0051 was found to be present in 83% of strains obtained from patients compared to 25 % of strains from healthy volunteers. Single colonies obtained from the same patient were analysed and it was found that variation in hp0051 exists within a patient also. Deletion of an orphan C5 cytosine methyltransferase, hp0051 in H. pylori strains 26695, SS1 and 98.4 has a significant effect on the expression of number of genes belonging to motility, adhesion and virulence. 98.4∆hp0051 mutant strain has a different LPS profile and is able to induce high IL-8 production compared to wild-type. H. pylori strain 26695∆hp0051 is more motile than the wild- type. hp0051 from strain 26695 is able to complement mutant SS1 and 98.4 strains. This study highlights the possible significance of cytosine methylation in the physiology of H. pylori. hp0050 is a N6 DNA adenine methyltransferase which overlaps with the hp0051 ORF .hp0050 was cloned, over expressed and purified to near homogeneity. It recognizes the sequence 5´GRRG 3´ (where R is A or G) and most intriguingly methylates both adenines when R is A (5´GAAG 3´). Kinetic analysis suggest a non processive (repeated hit) mechanism of methylation in which HP0050 methyltransferase methylates one adenine at a time in sequence 5´GAAG 3´. Interestingly, HP0050 homologs from two clinical strains PG227 and 128 methylate only 5´GAGG 3´ compared to 5´GRRG 3´ in strain 26695. HP0050 MTase is highly conserved as it is present in more than 90% of strains. Inactivation of hp0050 in strain PG227 resulted in poor growth suggesting its important role in the physiology of Helicobacter pylori. Collectively, these findings provide impetus for exploring the role(s) of this conserved DNA methyltransferase in the cellular processes of Helicobacter pylori. In one of the clinical isolate it was found that hp0051 and hp0050 can code for a single polypeptide due to an insertion mutation. This mutant ( hp0050 and hp0051 fusion ) was cloned, overexpressed and purified. It was found that fusion protein is able to methylate both adenine and cytosine in the cognate sequence. Similarly, hp1369 - hp1370 is a phase variable type III MTase and it belongs to ɛ group of MTases based on the arrangement of motifs. It has a poly G repeat in its ORF and any change in the number of repeats can result in a functional (full length) or non functional (truncated) protein. Within strain 26695, it has 10 G repeat which results in a truncated protein. Addition of a single nucleotide by site directed mutagenesis in the repeat results in a full length functional protein. HP1369_HP1370 fusion protein recognizes and methylates 5´ TCAGC 3´. DNA methyltransferases are known to play a critical role in gene regulation, cell cycle regulation and pathogenesity in a number of pathogens. H. pylori genome is rich in DNA methyltransferases and this study shows that these methyltransferases exhibit unique features like phase - variation and polymorphism .We propose that high degree of variation that exists in these methyltransferases could play a vital role in enhancing the ability of H. pylori to adapt its host.

Molecular-biological annotation data is continuously being collected, curated and made accessible in numerous public data sources. Integration of this data is a major challenge in bioinformatics. We present the GenMapper system that physically integrates heterogeneous annotation data in a flexible way and supports large-scale analysis on the integrated data. It uses a generic data model to uniformly represent different kinds of annotations originating from different data sources. Existing associations between objects, which represent valuable biological knowledge, are explicitly utilized to drive data integration and combine annotation knowledge from different sources. To serve specific analysis needs, powerful operators are provided to derive tailored annotation views from the generic data representation. GenMapper is operational and has been successfully used for large-scale functional profiling of genes.

Der Hirninfarkt ist einer der drei häufigsten Todesursachen in Deutschland. Er wird durch eine Unterversorgung des Gewebes mit Sauerstoff und Nährstoffen, häufig infolge von Gefäßverschlüssen, ausgelöst. Die bisher einzige Therapiemöglichkeit ist die Thrombolyse. Deshalb sind neue Therapieansätze nötig. Voraussetzung dafür sind geeignete Modelle. In dieser Arbeit wurden zellbasierte Hypoxiemodelle etabliert und charakterisiert. Es wurde der Einfluss von Sauerstoff- und/oder Glucoseentzug an humanen primären Makrophagen untersucht. Für Screeninguntersuchungen wurden neuronale und periphere (Makrophagen) Zelllinien von Ratte und Mensch verwendet. Im zweiten Teil der Arbeit wurden die Modelle genutzt, um die Wirkung von Adenin, eine rezeptorvermittelte Therapieoption, und des Phytopharmakons STW5 auf mögliche protektive Wirkungen zu untersuchen. Es wurden zellbiologische (MTT-Test, LDH-Test, DAPI-Färbung), immunologische (TNF α- ELISA, immunhistochemische Färbung), elektrophysiologische (Patch Clamp-Technik) und molekularbiologische (RT-PCR, Real-Time-PCR) Methoden angewendet. Es wurde erstmals der Adeninrezeptor an den untersuchten Zelllinien nachgewiesen und der pharmakologische Hinweis für eine bisher unbekannte humane Variante des Rezeptors erbracht. An neuronalen Zellen kam es zu einer Rezeptorinteraktion zwischen Adenin- und Adenosin-A1-Rezeptor. Antagonisten am Adeninrezeptor scheinen zur Behandlung hypoxiebedingter Zellschäden geeignet zu sein. STW5 hemmte unter hypoxischen Bedingungen die TNF α-Freisetzung humaner primärer Makrophagen. Der antiinflammatorischen Wirkung liegt die Blockierung erhöhter Kaliumströme zugrunde. An den untersuchten Zelllinien wirkte STW5 der hypoxieinduzierten Zellschädigung entgegen.

Intracellular recordings were made from isolated frog sciatic-sartorius nerve-muscle preparations, and the effects of sphingosine 1-phosphate (S1-P) on miniature endplate potentials (MEPPs) were studied. Extracellular application of S1-P (1 and 30 μM) had no significant effects on the frequency and amplitude of MEPPs. Delivery into nerve terminals by liposomes containing 10-5, 10-4 or 10-3 M S1-P was associated with a concentration-dependent increase in MEPP frequency of 37, 63 and 86%. The per cent of median MEPP amplitude was not significantly changed, but there was an increase in the number of 'giant' MEPPs. Pre-exposure of the preparations to S1-P 10-5 but not 10-8 M entrapped in liposomes for 15 min blocked the effects of subsequent superfusion of S1-P (10-4 M)-filled liposomes on MEPP frequency. Thus, intracellular S1-P receptors seem to undergo 'desensitization' to higher concentrations of S1-P. The result provides the first evidence that S1-P acting intracellularly but not extracellularly enhances spontaneous transmitter release at the frog neuromuscular junction.

The F420-dependent NADP reductase of Methanobrevibacter smithii has been partially purified employing a combination of affinity chromatography with Blue Sepharose (Cl-6B) and molecular sieve chromatography with Sephacryl S-200, The enzyme, which requires reduced F420 as an electron donor, has been purified over 145 fold with a recovery of 6%. A molecular weight of 120,00 for the native enzyme was determined by Sephacryl S-200 chromatography. A subunit molecular weight of 28,200 was determined by SDS-PAGE, indicating that the native enzyme is a tetramer. The optimal temperature for enzymatic activity was found to be 45°C, with a pH optimum of 7.5. The NADP reductase had an apparent Km of 42 uM for reduced F420, and an apparent Km of 4l uM for NADP. The enzyme was stable in 0.05 M sodium phosphate buffer (plus 10 mM cysteine) at pH 7.0, when gassed with nitrogen or hydrogen and stored at 4°C.

Isolated adult rat myocytes were subjected to 180 min of metabolic inhibition or incubated in ischaemic pellets, in the presence and absence of 10 μm okadaic acid (OA) or calyculin A (CL-A). Contracture and viability was determined by light microscopic analysis of trypan blue-stained preparations and ATP levels by HPLC. Osmotic fragility was assessed by brief hypotonic swelling of cells in 170 or 85 mOsm media prior to determination of viability. Neither drug significantly affected the relatively rapid rates of contracture of myocytes during metabolic inhibition, and both afforded significant protection from development of trypan blue permeability and osmotic fragility. Both OA and CL-A significantly accelerated the rates of contracture and ATP depletion of myocytes during ischaemic incubations. Despite an enhanced rate of ATP depletion, which would be expected to accelerate development of injury, neither drug accelerated development of loss of viability or development of osmotic fragility as measured by 170 mOsm swelling. Mathematical compensation for different rates of ATP depletion confirmed that a protective effect of the drugs, during ischaemic incubation, was masked by their enhancement of the rate of injury, following swelling at 170 mOsm. When the effects of CL-A on ischaemic cells were examined at 85 mOsm, a more stringent test for osmotic fragility, protection was found without compensation for differing rates of ATP depletion. A dose/response curve for CL-A showed some effect at 100 nm and a nearly full effect during metabolic inhibition at 1 μm concentrations. It is concluded that protein phosphatase inhibitors reduce the rates of development of osmotic fragility of metabolically inhibited cells and reduces the rate of injury relative to the rate of ATP depletion of ischaemic cardiomyocytes. Phosphorylation mechanisms may be important to development of irreversible myocardial cell injury.