The transcriptome is defined as the set of all RNA molecules transcribed in a cell. These include protein-coding messenger RNAs (mRNAs) as well as non-coding RNAs, such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and small non-coding RNAs (sRNAs). sRNAs are known to play an important role in regulating gene expression and virulence in pathogens. In this thesis, the transcriptome of the food-borne pathogen Campylobacter jejuni was characterized at single nucleotide resolution by use of next-generation sequencing approaches. The first genome of a C. jejuni strain was published in the year 2000. However, its transcriptome remained uncharacterized at large. C. jejuni can survive in a variety of ecological niches and hosts. However, how strain-specific transcriptional changes contribute to such adaptation is not known. In this study, the global transcriptome maps of four closely related C. jejuni strains were defined using a differential RNA-seq (dRNA-seq) approach. This analysis also included a novel automated method to annotate the transcriptional start sites (TSS) at a genome-wide scale. Next, the transcriptomes of four strains were simultaneously mapped and compared by the use of a common coordinate system derived from whole-genome alignment, termed as SuperGenome. This approach helped to refine the promoter maps by comparison of TSS within strains. Most of the TSS were found to be conserved among all four strains, but some single-nucleotide-polymorphisms (SNPs) around promoter regions led to strain-specific transcriptional output. Most of these SNPs altered transcription only slightly, but some others led to a complete abrogation of transcription leading to differential molecular phenotypes. These in turn might help the strains to adapt to their specific host or microniche. The transcriptome also unveiled a plethora of sRNAs, some of which were conserved among the four strains while others were strain specific. Furthermore, a Cas9-dependent minimal type-II CRISPR-Cas system with only three Cas genes and multiple promoters to drive the transcription of the CRISPR locus was also characterized in C. jejuni using the dRNA-seq dataset. Apart from sRNAs, the role of global RNA binding proteins (RBPs) is also unclear in C. jejuni. Aided by the global transcriptome data, the role of RBPs in post-transcriptional regulation of C. jejuni was studied at a global scale. Two of the most widely studied RNA binding proteins in bacteria are Hfq and CsrA. The RNA interactome of the translational regulator CsrA was defined using another global deep-sequencing technique that combines co-immunoprecipitation (coIP) with RNA sequencing (RIP-seq). Using this interactome dataset, the direct targets of this widespread global post-transcriptional regulator were defined, revealing a significant enrichment for mRNAs encoding genes involved in flagella biosynthesis. Unlike Gammaproteobacteria, where sRNAs such as CsrB/C, antagonize CsrA activity, no sRNAs were enriched in the CsrA-coIP in C. jejuni, indicating absence of any sRNA antagonists and novel modes of CsrA activity regulation. Instead, the CsrA regulatory pathway revealed flaA mRNA, encoding the major flagellin, as a dual-function mRNA. flaA mRNA was the main target of CsrA but it also served to antagonize CsrA activity along with the protein antagonist FliW previously identified in the Gram-positive bacterium Bacillus subtilis. Furthermore, this regulatory mRNA was also shown in this thesis to localize to the poles of elongating C. jejuni cells in a translation-dependent manner. It was also shown that this localization is dependent on the CsrA-FliW regulon, which controls the translation of flaA mRNA. The role and mechanism of flaA mRNA localization or mRNA localization in general is not yet clear in bacteria when compared to their eukaryotic counterparts. Overall, this study provides first insights into riboregulation of the bacterial pathogen C. jejuni. The work presented in this thesis unveils several novel modes of riboregulation in C. jejuni, which could be applicable more generally. Moreover, this study also lays out several unsolved intriguing questions, which may pave the way for interesting studies to come. / Das Transkriptom ist definiert als die Summe aller RNA-Moleküle, die in einer Zelle transkribiert werden. Hierzu gehören sowohl protein-kodierende Boten-RNAs (mRNAs für „messenger RNAs“), als auch nicht-kodierende RNAs, wie ribosomale RNAs (rRNAs), transfer RNAs (tRNAs) und kleine nicht-kodierende RNAs (sRNAs für „small RNAs“). Diese sRNAs spielen eine wichtige Rolle in der Regulierung von Genexpression und Virulenz von Pathogenen. In der vorliegenden Arbeit wurde das Transkriptom des Lebensmittelkeims Campylobacter jejuni mit Hilfe von Next-Generation-Sequencing-Methoden charakterisiert, welche eine Auflösung des Transkriptoms auf Einzelnukleotid-Ebene ermöglichen. Obwohl eine erste Genomsequenz für C. jejuni bereits im Jahr 2000 veröffentlicht wurde, war das Transkriptom bisher größtenteils uncharakterisiert. C. jejuni besitzt die Fähigkeit in vielen ökologischen Nischen und Wirten überleben zu können. Es ist jedoch bislang unbekannt, wie stammspezifische Veränderungen des Transkriptoms zu dieser Adaption beitragen. Mittels eines differenziellen RNA-Sequenzierungsansatzes wurden in dieser Arbeit globale Transkriptomkarten von vier nahverwandten C. jejuni Stämmen erstellt. Diese Analyse beinhaltet auch eine neue automatisierte Methode zur genomweiten Identifizierung von Transkriptionsstartstellen (TSS). Anschließend wurde aus den Genomsequenzen der vier Campylobacter Stämme ein SuperGenom erstellt. Dieses wiederum diente als Referenz, anhand dessen die Transkriptome kartiert und miteinander verglichen werden konnten. Dieser Ansatz ermöglichte eine verfeinerte Kartierung der Promotoren mittels des Vergleichs verschiedener Stämme. Die meisten TSS waren innerhalb der vier Stämme konserviert. Allerdings kam es durch SNPs („single-nucleotide polymorphisms“) in den Promoterregionen zu stammspezifischem Transkriptoutput. Die meisten dieser SNPs hatten nur geringe Veränderungen der Transkription zur Folge. Manche jedoch führten zu einem kompletten Verlust der Transkription und damit zu verschiedenen molekularen Phänotypen. Diese wiederum könnten es den verschiedenen Stämmen ermöglichen, sich an ihre spezifische Wirts- oder Mikronische anzupassen. Das Transkriptom wies auch eine Fülle von sRNAs auf, von denen manche in allen vier Stämmen konserviert, andere jedoch stammspezifisch waren. Zudem wurde mittels des C. jejuni-dRNA-seq-Datensatzes ein minimales Cas9-abhängiges CRISPR-Cas-System des Typs II entdeckt. Dieses beinhaltet lediglich drei Cas-Gene, jedoch mehrere Promotoren, die die Expression des CRISPR-Lokus antreiben. Neben der Funktion von sRNAs ist auch die Rolle globaler RNA-Bindeproteine (RBPs) in C. jejuni weitestgehend unklar. Mithilfe der Transkriptomdaten wurde die Rolle von RBPs in der posttranskriptionellen Regulierung in C. jejuni untersucht. Zwei der am besten untersuchten RNA-Bindeproteine in Bakterien sind Hfq und CsrA. Das RNA-Interaktom des Translationsregulators CsrA wurde mittels eines weiteren globalen Deep-Squencing-Ansatzes definiert. Bei dieser Methode werden Coimmunopräzipitation (coIP) und RNA-Sequenzierung zum so genannten RIP-seq kombiniert. Mithilfe dieses Interaktionsdatensatzes wurden die Zielgene dieses weitverbreiteten, globalen posttranskriptionellen Regulators definiert. Hierbei wurde eine signifikante Anreicherung von mRNAs, die in die Biosynthese von Flagellen involviert sind, erkennbar. Anders als in Gammaproteobakterien, in denen sRNAs wie CsrB und CsrC die CsrA-Aktivität antagonisieren, wurden in C. jejuni keine sRNAs in der CsrA-CoIP angereichert. Dies deutet auf das Fehlen jeglicher sRNA-Antagonisten, und damit auf eine neue Art der CsrA-Aktivitätskontrolle hin. Anstelle der sRNAs wurde die flaA mRNA, welche für das Hauptflagellin kodiert, als mRNA mit dualer Funktion identifiziert. Sie ist zum einen das Hauptzielgen von CsrA, fungiert aber gleichzeitig, zusammen mit dem Protein FliW, als Antagonist von CsrA. FliW wurde bereits zuvor in dem Grampositiven Bakterium Bacillus subtilis identifiziert. In dieser Arbeit konnte zudem gezeigt werden, dass die regulatorische flaA mRNA translationsabhängig an den Polen der wachsenden C. jejuni-Zellen lokalisiert ist. Außerdem war zu erkennen, dass diese Lokalisierung abhängig von dem CsrA-FliW-Regulon stattfindet, welches die Translation der flaA-mRNA kontrolliert. Im Gegensatz zu Eukaryoten ist die Rolle, die die Lokalisation der flaA-mRNA, oder bakterieller mRNA im Allgemeinen, spielt, sowie der Mechanismus, der zu dieser Lokalisierung führt, bisher noch unklar. Zusammenfassend ermöglicht diese Arbeit einen ersten Einblick in die Riboregulierung des bakteriellen Pathogens C. jejuni. Es konnten einige neue Mechanismen dieser Art der Regulierung aufgedeckt werden, welche auch allgemeine Gültigkeit finden könnten. Zudem werden in dieser Arbeit neue, faszinierende Fragen aufgeworfen, die den Weg für weitere interessante Studien bereiten.

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The hierarchical taxonomy of psychopathology (HiTOP) is a novel classification system that adopts both a dimensional and hierarchical approach to psychopathology to address shortcomings. However, the HiTOP framework is descriptive in nature and requires additional research to consider potential mechanisms for the onset and maintenance of psychopathology, such as cognitive-behavioral emotion regulation strategies. To redress this gap, a sample of 341 adults who endorsed ongoing mental health concerns completed self-report measures of emotion regulation strategies and psychopathology. The data revealed a three-spectra HiTOP model consisting of internalizing, thought disorder, and antagonistic externalizing. Results found that psychopathology was most strongly associated with avoidance, catastrophizing, expressive suppression, and self-blame. In contrast, adaptive strategies were generally unrelated to the HiTOP spectra. This pattern was strongest for internalizing, distress, and detachment. Fewer, yet noteworthy unique relationships between the strategies and specific spectra/subfactors were also found. These findings suggest that psychopathology may be best conceptualized as an overutilization of maladaptive emotion regulation strategies. Furthermore, the results indicate there is added benefit to considering these strategies within a hierarchical approach to psychopathology. These associations alert clinicians to potential treatment targets and contribute to an ongoing literature that seeks to identify underlying mechanisms of the structure of psychopathology.

The glycine decarboxylase complex (GDC) of Succharomyces cerevisiae composed of four subunits (P, H, T and L) and plays an important role in the interconversion of serine and glycine and balancing the one-carbon unit requirements of the cell. It also enables the cell to use glycine as sole nitrogen source. This study was concerned with characterising the molecular mechanism of transcriptional regulation of the GCVgenes encoding the subunits of the GDC. The important findings of this work can be summarised as follows: i) Transcription of the GCV genes are regulated by glycine and rich nitrogen sources, which are mediated by different cis-acting elements. The LPDl gene did not show a glycine response since its transcriptional regulation is distinct from that of the other genes encoding the GDC subunits. ii) Glycine analogues or serine did not affect expression of GCV2, and therefore glycine probably needs to be metabolised to effect the glycine response of the GCV genes. iii) The repression of the GCV2 gene expression by rich nitrogen sources is mediated by a sequence between -227 and -205 of GCV2, and NCR-regulatory mutant studies showed that repression is not directly controlled by the known NCR system. iv) The glycine response of GCV2 is mediated by a motif (the glycine regulatory region; GRR; 5'-CATCN7CTTCTT-3') with CTTCTT at its core. Additional sequence immediately 5' of this motif (between -310 to -289) plays a minor role for the gene's full glycine response. v) The GRR of the GCV genes can mediate the glycine response by either activation or repression, indicating that the transcription factor(s) mediating the glycine response is/are dual-functional in nature. vi) Studies of GCV2 gene expression using different regulatory mutants showed that expression of the gene is further modulated by other transcription factors such as and Baslp which are distinct from the glycine response and possibly involved in setting up the basal expression level. vii) I n vitro studies of the GRR-protein interaction revealed THF affects the affinity of the DNA-binding protein(s) for the GRR. The importance of THF in regulation of the GCV2 gene was also shown in vivo using a foll mutant that is unable to synthesise any folates. THF or a C1-bound derivative of it acts as a ligand for the transcription factor, thus influencing transcription of the GCV genes in the appropriate physiological manner. viii) Using heparin-Sepharose chromatography fractions, four complex formations (complex I to IV) were observed with the GRR. The protein responsible for one of these was separable from the others. EMSA profiles using the GRR of the GCVI and GCV2 genes (in the presence or absence of THF) were very similar, indicating that these genes bind the same proteins and are regulated in a similar manner. ix) Mutation of the CTTCTT motif within the GRR caused significant reduction in in vitro DNA-protein complex formation, however, THF addition overcame this reduction. x) Only complex II formation was observed with a DNA fragment spanning -322 to -295, and THF affected this complex formation. xi) Footprinting analyses of complex I revealed that the binding protein protected the GRR of the GCV2 gene from DNaseI activity. This protein is an excellent candidate for the glycine response regulatory protein. Titration experiments using EMSA showed that this protein can dimerise. A preliminary genome-wide analysis of the S. cerevisiae transcriptome was carried out using miniarray membrane hybridisation. This investigated the global transcriptional changes within the cell in response to the addition of glycine into the medium. Identification of genes related to various cellular processes including onecarbon metabolism gave an insight into the regulation of the cellular metabolic flow, especially that of one-carbon metabolism. The results indicated that: xii) Glycine is transported into mitochondria to be used as substrate for the GDC which (with mitochondria1 SHMT) produces serine that is subsequently utilised for the various one-carbon metabolic pathways, such as methionine synthesis and purine synthesis. xiii) A gene of unknown function (YER183C) which showed homology to the gene for human 5,lO-CH-THF synthetase was identified from gene-array analysis to be upregulated on glycine addition, indicating the protein encoded by this gene may be involved in balancing the metabolic flow between methionine and purine synthesis when THF pools are disturbed by glycine addition. xiv) Addition of glycine to the medium also triggers the expression of other metabolic genes related to amino acid biosynthetic pathways and that of many other genes which are not directly related to one-carbon metabolism. This may be due to prolonged culturing with glycine in the medium resulting in altered expression of genes mediated by one or more secondary factors. These may reflect an adaptive response rather than a direct consequence of glycine induction. On the basis of the above data, a model for the mechanisms regulating glycine response is presented.

Copy of author's previously published work inserted. Includes bibliographical references (leaves 160-182). Concentrates mainly on the characterisation of the molecular mechanism of action of the tec protein tyrosine kinase using biochemical and genetic approaches.

Bibliography: leaves 139-165.