DNA methylation in Dictyostelium discoideum

DNA methyltransferases of type Dnmt2 are a highly conserved protein family with enigmatic function. The aim of this work was to characterize DnmA, the Dnmt2 methyltransferase in Dictyostelium discoideum, and further to investigate its implication in DNA methylation and transcriptional gene silencing. The genome of the social amoeba Dictyostelium encodes DnmA as the sole DNA methyltransferase. The enzyme bears all ten characteristic DNA methyltransferase motifs in its catalytic domain. The DnmA mRNA was found by RT-PCR to be expressed during vegetative growth and down regulated during development. Investigations using fluorescence microscopy showed that both DnmA-myc and DnmA-GFP fusions predominantly localised to the nucleus. The function of DnmA remained initially unclear, but later experiment revealed that the enzyme is an active DNA methyltransferase responsible for all DNA (cytosine) methylation in Dictyostelium. Neither in gel retardation assays, nor by the yeast two hybrid system, clues on the functionality of DnmA could be obtained. However, immunological detection of the methylation mark with an α - 5mC antibody gave initial evidence that the DNA of Dictyostelium was methylated. Furthermore, addition of 5-aza-cytidine as demethylating agent to the Dictyostelium medium and subsequent in vitro incubation of the DNA isolated from these cells with recombinant DnmA showed that the enzyme binds slightly better to this target DNA. In order to investigate further the function of the protein, a gene knock-out for dnmA was generated. The gene was successfully disrupted by homologous recombination, the knock-out strain, however, did not show any obvious phenotype under normal laboratory conditions. To identify specific target sequences for DNA methylation, a microarray analysis was carried out. Setting a threshold of at least 1.5 fold for differences in the strength of gene expression, several such genes in the knock-out strain were chosen for further investigation. Among the up-regulated genes were the ESTs representing the gag and the RT genes respectively of the retrotransposon skipper. In addition Northern blot analysis confirmed the up-regulation of skipper in the DnmA knock-out strain. Bisufite treatment and sequencing of specific DNA stretches from skipper revealed that DnmA is responsible for methylation of mostly asymmetric cytosines. Together with skipper, DIRS-1 retrotransposon was found later also to be methylated but was not present on the microarray. Furthermore, skipper transcription was also up-regulated in strains that had genes disrupted encoding components of the RNA interference pathway. In contrast, DIRS 1 expression was not affected by a loss of DnmA but was strongly increased in the strain that had the RNA directed RNA polymerase gene rrpC disrupted. Strains generated by propagating the usual wild type Ax2 and the DnmA knock-out cells over 16 rounds in development were analyzed for transposon activity. Northern blot analysis revealed activation for skipper expression, but not for DIRS-1. A large number of siRNAs were found to be correspondent to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA methylation. In contrast, no siRNAs corresponding to the standard skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene regulation in Dictyostelium and that different, partially overlapping mechanisms control transposon silencing for skipper and DIRS-1. To elucidate the mechanism of targeting the protein to particular genes in the Dictyostelium genome, some more genes which were up-regulated in the DnmA knock-out strain were analyzed by bisulfite sequencing. The chosen genes are involved in the multidrug response in other species, but their function in Dictyostelium is uncertain. Bisulfite data showed that two of these genes were methylated at asymmetrical C-residues in the wild type, but not in DnmA knock-out cells. This suggested that DNA methylation in Dictyostelium is involved not only in transposon regulation but also in transcriptional silencing of specific genes.

Synthesis of N-amino compounds and C2 symmetric N-amino compounds and transformation into aziridines using olefins

Aziridine, Stickstoffanaloga der Epoxide, können regio- und stereoselektive Ringöffnungsreaktionen eingehen, wodurch ihnen als „building blocks“ in der Organischen Synthese eine große Bedeutung zukommt. In dieser Arbeit wurden unterschiedliche N-Aminoverbindungen synthetisiert sowie die Anwendungsmöglichkeit dieser Hydrazinderivate als Stickstoffquellen in Aziridinierungen von Olefinen untersucht. In der vorliegenden Dissertation wurde eine neue Methode zur Darstellung von N-Aminosuccinimid entwickelt und die Einsatzmöglichkeit als Stickstoffquelle in Aziridinierungsreaktionen in einer Reihe von Umsetzungen mit funktionalisierten ebenso wie mit nicht-funktionalisierten Olefinen demonstriert. Die ableitbaren Aziridine wurden hierbei in Ausbeuten von bis zu 80 % erhalten. In der Aziridinierungsreaktion von N-Aminosuccinimid mit 4,7-Dihydro-2-isopropyl-1,3-dioxepin resultieren bicyclische Aziridinierungsprodukte, die als endo/exo-Isomere in einem 1:1-Verhältnis anfallen. Es ist in dieser Arbeit gelungen, die Isomere in guten Ausbeuten zu erhalten, sie säulenchromatographisch zu trennen und ihre Konfiguration im festen Zustand mittels Kristallstrukturanalyse eindeutig zu bestimmen. Enantiomerenangereicherte Olefine, wie z. B. in 2-Position alkylsubstituierte 5-Methyl-4H-1,3-dioxine mit Enantiomerenüberschüssen von 92% ee liefern in der Aziridinierung mit N-Aminosuccinimid und Iodosylbenzol ein 4-Methyl-1,3-oxazolidin-4-carbaldehydderivat in einer zweistufigen Reaktion- der Aziridinierung und einer Umlagerung- ein 4-Methyl-1,3-oxazolidin-4-carbaldehydderivat. Für die Diastereoselektivität des Aziridinierungsschrittes wurde 65 % de bestimmt. In einer neuen Synthese über zwei Stufen ausgehend von (+)-3,4-Dimethoxysuccinanhydrid konnte ein chiraler Stickstoffüberträger - (+)-N-Amino-3,4-dimethoxysuccinimid - in Ausbeuten bis zu 86 % synthetisiert. Die Umsetzung dieser optisch aktiven Stickstoffquelle mit einer Vielzahl prochiraler Alkene führt zu diastereomeren Aziridinen in Ausbeuten bis zu 65% und Diastereoselektivitäten von bis zu 66% de. Anhand ausgewählter Verbindungen konnten die Absolutkonfigurationen der Reaktionsprodukte mittels Kristallstrukturanalyse eindeutig geklärt werden.

Offline Emergence Engineering For Agent Societies

Many examples for emergent behaviors may be observed in self-organizing physical and biological systems which prove to be robust, stable, and adaptable. Such behaviors are often based on very simple mechanisms and rules, but artificially creating them is a challenging task which does not comply with traditional software engineering. In this article, we propose a hybrid approach by combining strategies from Genetic Programming and agent software engineering, and demonstrate that this approach effectively yields an emergent design for given problems.

Applicability of Emergence Engineering to Distributed Systems Scenarios

Genetic Programming can be effectively used to create emergent behavior for a group of autonomous agents. In the process we call Offline Emergence Engineering, the behavior is at first bred in a Genetic Programming environment and then deployed to the agents in the real environment. In this article we shortly describe our approach, introduce an extended behavioral rule syntax, and discuss the impact of the expressiveness of the behavioral description to the generation success, using two scenarios in comparison: the election problem and the distributed critical section problem. We evaluate the results, formulating criteria for the applicability of our approach.