This is a two-part project. Proton pump inhibitors (PPIs) have been associated with increased risk of C. difficile infections and increased toxin production when combined with antimicrobial therapy. The first part of this project involved characterization of a hypervirulent NAP1 C. difficile strain, including genome sequencing and assembly, and the development of methods to study its transcriptomics using RNA-Seq, which will enable future researchers to study different expression patterns when toxigenic C. difficile is challenged with PPIs and/or antimicrobials in vitro. The second part of this project involved characterizing a clinical isolate of a NAP1 C. difficile displaying a markedly elevated MIC to metronidazole (MIC = 16 mg/mL), which initially exhibited MIC of 32 mg/mL. A method of obtaining a metronidazole-susceptible revertant from this isolate was developed and a revertant was obtained. The genomes of both isolates were sequenced, assembled, and aligned, then compared to each other for polymorphisms.

Using computational methods to identify protein-protein interactions (PPIs) supports experimental techniques by using less time and less resources. Identifying PPIs can be made through a template-based approach that describes how unstudied proteins interact by aligning a common structural template that exists in both interacting proteins. A pipeline that uses this is InterPred, that combines homology modelling and massive template comparison to construct coarse interaction models. These models are reviewed by a machine learning classifier that classifies models that shows traits of being true, which can be further refined with a docking technique. However, InterPred is dependent on using complex structural information, that might not be available from unstudied proteins, while it is suggested that PPIs are dependent of the shape and interface of proteins. A method that aligns structures based on the interface attributes is InterComp, which uses topological and sequence-order independent structural comparison. Implementing this method into InterPred will lead to restricting structural information to the interface of proteins, which could lead to discovery of undetected PPI models. The result showed that the modified pipeline was not comparable based on the receiver operating characteristic (ROC) performance. However, the modified pipeline could identify new potential PPIs that were undetected by InterPred.

As wind energy plants continue to grow in size and complexity, advanced measurement technologies such as scanning Doppler LiDAR are essential for assessing site conditions and prospecting new development areas.   The RUNE project was initiated to determine best practices for the use of scanning LiDARs in resource assessments for near shore wind farms. The purpose of this thesis is to determine the optimum configuration for the plan position indicator (PPI) scan type of a scanning LiDAR. A task specific Automated Analysis Software (AAS) is created, and the sensitivity of the integrated velocity azimuth process (iVAP) reconstruction algorithm is examined using sector sizes ranging from 4 to 60 degrees. Further, a comparison to simultaneous dual Doppler measurement is presented in order to determine the necessity of deploying two LiDARs rather than one.    DTU has developed a coordinated long range coherent scanning multi-LiDAR array (the WindScanner system) based on modified Leosphere WindCube 200S devices and an application specific software framework and communication protocol. The long range WindScanner system was deployed at DTU’s test station in Høvsøre, Denmark and measurement data was collected over a period of 7 days. One WindScanner was performing 60 degree sector scans, while two others were placed in staring dual Doppler mode. All three beams were configured to converge atop a 116.5m instrumented meteorological mast.   A significant result was discovered which indicates that the accuracy of the reconstructed measurements do not differ significantly between sector sizes of 30 and 60 degrees. Using the smallest sector size which does not introduce systematic error has numerous benefits including: increasing the scan speed, measurement distance and angular resolution.   When comparing collocated dual Doppler, sector scan and in-situ met-mast instrumentation, we find very good agreement between all techniques. Dual Doppler is able to measure wind speeds within 0.1%, and 60 degree sector scan within 0.2% on average of the reference values. For retrieval of wind direction, the sector scan approach performs particularly well. This is likely attributable to lower errors introduced by the assumption of flow field homogeneity over the scanned area, in contract to wind direction which tends to be more non-uniform. For applications such as site resource assessments, where generally accurate 10 minute wind speed and direction values are required, a scanning LiDAR performing PPI scans with a sector size of between 30 and 38 degrees is recommended. The laser’s line of sight path should be directed parallel to the predominant wind direction and at the lowest elevation angle possible. / RUNE

The composition and diversity of the gastrointestinal microbiota and its interaction with human cells have been frequently associated with immune system functions and disease development, including autoimmunity and allergy. This is believed to be mediated in part through epigenetic modifications, mainly as DNA methylation. Several studies have collectively supported the beneficial effects of probiotics for the prevention of allergic disease. However, there have been few studies addressing the possibility for probiotic supplementation to induce epigenetic changes and its importance for allergy development. This study aims to investigate whether probiotic treatment with Lactobacillus reuteri, distributed during and after the pregnancy period, leads to epigenetic changes in the offspring and if this have any effect on the development of allergic disease. DNA methylation data received from a clinical allergy prevention study was analysed through a set of bioinformatics methods and basic network analysis. The obtained results suggests that supplementation with L. reuteri indeed induces some significant changes in DNA methylation. These changes did not exhibit any significant correlation with allergy outcome of the children. Furthermore, the methylation changes were found at positions located in genes not enriched for any allergy-related biological pathways. However, when taking the genes interactions with other genes into account an interconnected gene interaction module could be identified that showed enrichment for biological processes involved in the T cell receptor signaling pathway, central for immune response transduction. Further analyses did not fit into the time-frame of this thesis, but the obtained results gives a first informative view of the effects of L. reuteri on methylation patterns, and points out directions for the continuing project work.

Protein-peptide interactions play a major role in several biological processes, such as cellproliferation and cancer cell life-cycles. Accurate computational methods for predictingprotein-protein interactions exist, but few of these method can be extended to predictinginteractions between a protein and a particularly small or intrinsically disordered peptide. In this thesis, PePIP is presented. PePIP is a pipeline for predicting where on a given proteina given peptide will most probably bind. The pipeline utilizes structural aligning to perusethe Protein Data Bank for possible templates for the interaction to be predicted, using thelarger chain as the query. The possible templates are then evaluated as to whether they canrepresent the query protein and peptide using a Random Forest classifier machine learningalgorithm, and the best templates are found by using the evaluation from the Random Forest in combination with hierarchical clustering. These final templates are then combined to givea prediction of binding site. PePIP is proven to be highly accurate when testing on a set of 502 experimentally determinedprotein-peptide structures, suggesting a binding site on the correct part of the protein- surfaceroughly 4 out of 5 times.

Le Lupus Erythémateux Systémique est une pathologie inflammatoire chronique. L’étiologie de cette maladie auto-immune est encore méconnue bien que certains facteurs génétiques et environnementaux aggravants aient été mis en évidence. Les traitements proposés aux patients ont pour but de réduire les symptômes et aucun remède curatif n’a encore été mis au point. Nous avons observé de forts taux de sCD95L dans le sérum de patients atteints de LES comparé à celui de sujets sains. Nos données indiquent que ce facteur soluble agit comme une cytokine pro-inflammatoire et promeut la transmigration des lymphocytes T CD4+ Th17 dans les organes, au détriment des lymphocytes T régulateurs (Treg). L’accumulation de ces cellules Th17 est responsable du maintien d’une réponse inflammatoire chronique chez les patients lupiques. Nous mettons en évidence qu’il existe une interaction directe entre le récepteur CD95 et la Phospholipase Cγ1, par l’identification du Calcium Inducing Domain impliqué dans ce recrutement. L’identification du couple CD95/CD95L comme acteur aggravant le LES et la mise en évidences des mécanismes cellulaires et moléculaires sous-jacents nous ont conduit à l’élaboration de stratégies thérapeutiques innovantes. En collaboration avec les chimistes et modélisateurs de notre Unité, nous avons généré une petite librairie d’inhibiteurs, composée de peptides et peptidomimétiques sélectifs. Parmi ces composés, le TAT-CID est une protéine piège comprenant la zone d’interaction de CD95 (domaine CID des aa 175 à 210) à la PLCγ1. L’injection de ce peptide dans un modèle de souris lupiques restaure la fonction biologique rénale de ces souris et diminue la production d’auto-anticorps (anti-DNA) et de complexes immuns, marqueurs biologiques associés à la progression de la pathologie. En parallèle, le criblage d’une librairie chimique commerciale constituée de médicaments approuvés par la FDA et l’EMA a permis d’identifier un inhibiteur efficace de notre interaction. In vivo, ce composé est capable de réduire drastiquement les signes cliniques de la pathologie lupique. Ces nouvelles données enrichissent notre compréhension du processus mis en place par le système CD95/CD95L dans l’aggravation du LES, et nous permettent de proposer des outils thérapeutiques interessants. Ces molécules pourraient représenter de nouvelles options thérapeutiques originales et attrayantes pour prévenir l’inflammation dans les pathologies inflammatoires chroniques. / Systemic Lupus Erythematosus (SLE) is a chronic inflammatory disease. The etiology of this autoimmune disease is still unknown although some aggravating genetic and environmental factors have been identified. The treatments used for patients are intended to reduce the symptoms and no curative one has been developed yet. We observed high levels of sCD95L in the serum of patients with SLE compared to healthy subjects. Our data indicate that this soluble factor acts as a pro-inflammatory cytokine and promotes the transmigration of CD4 + Th17 T lymphocytes to the detriment of regulatory T lymphocytes (Treg) in the enflammed organs of patients. The accumulation of these Th17 cells is responsible for maintaining a chronic inflammatory response in lupus patients. We show that there is a direct interaction between the CD95 receptor and the phospholipase Cγ1, by the identification of the Calcium Inducing Domain involved in this recruitment. The identification of the CD95/CD95L couple as an aggravating factor in SLE context and the underlying cellular and molecular mechanisms led us to the development of innovative therapeutic strategies. In collaboration with the chemists and modellers of our research Unit, we have generated a small library of inhibitors, composed of selective peptides and peptidomimetics. Among these compounds, TAT-CID is a decoy peptide comprising the interaction zone of CD95 (CID domain 175 to 210 aa) with PLCγ1. Repeated treatments of lupus-prone mice with this peptide restore the biological function of these mice and decrease the production of autoantibodies (anti-DNA) and immune complexes, biological markers associated with the progression of the pathology. In parallel, the screening of a commercial chemical library consisting of FDA and EMA-approved drugs allowed us to identify an effective inhibitor of our targeted interaction. In vivo, this compound is able to drastically reduce the clinical signs of lupus pathology. These new data enrich our understanding of the process implemented by the CD95/CD95L system in the aggravation of SLE, and allow us to propose interesting therapeutic tools. These molecules could represent novel and attractive therapeutic options for preventing inflammation in chronic inflammatory pathologies.

Magister Commercii - MCom / This study analyses the extent to which stock returns provide forecasts of changes in interest rates and inflation for the South African market. The period under investigation, January 1966 - February 1989, is characterised by structural changes in the South African economy, especially in the financial markets. The earnings yield on shares is used as a measure of the return on stocks. Stock returns of 10 specific industries are used in addition to the overall market return. Monthly inflation series were constructed by employing both the Consumer Price Index (CPI) and the Producer Price Index (PPI). Before examining that relationship, tests were done to examine the relationship between nominal stock returns and expected inflation. The relation between the stock market and expected inflation is estimated by using three measures of expected inflation. The results appear to suggest that the stock market reacted positively to expected inflation during the 1966 - 1982 period. Two proxies of expected inflation. Best results inflation are used to were obtained with measure future the Fama-Gibbons measure. In addition, the results suggest that stock returns provide additional information of future inflation to that contained in the Fama-Gibbons and interest rate models. Returns for specific industries, used in this study, appear to provide marginally better forecasts of inflation than the overall market return. The results also suggest that stock returns provide forecasts of changes in interest rates and inflation. There is no evidence that the specific industries used, provide consistent better forecasts of interest rate changes than the overall market.

Erosiv esofagit (EE) innebär uppkomst av inflammation och slemhinneskador i matstrupen. Den huvudsakliga orsaken till EE är gastroesofageal reflux (GERD), då det sura maginnehållet stöts upp i matstrupen. Bristande funktion av nedre esofagussfinktern (LES) och diafragmabråck kan också orsaka EE. Obehandlad EE kan leda till komplikationer såsom Barretts esofagus (BE), adenocarcinom, förträngning av matstrupen och gastrointestinala blödningar. Diagnostiken sker med hjälp av endoskopi. Behandlingen av EE går bland annat ut på att påskynda läkning av slemhinneskador i matstrupen. Den består huvudsakligen av läkemedelsterapi och livsstil- och kostförändringar, men även kirurgi kan vara en möjlig behandling. Läkemedelsterapi består av syrahämmande läkemedel som hämmar produktionen av magsyra. Protonpumpshämmare (PPI), till exempel lansoprazol (LPZ), är standardbehandlingen vid syrarelaterade sjukdomar, bland annat EE. PPI har dock begränsningar och upp till 20 % med svårare EE uppnår inte läkning. Vonoprazan (VPZ) tillhör kalium kompetitivasyrablockerare (P-CAB) och är ett nytt syrahämmande läkemedel som är godkänt i bland annat Japan och USA för behandling av EE. Syftet med detta litteraturarbete var att undersöka effekten av 20 mg VPZ jämfört med 30 mg LPZ efter åtta veckors behandling av EE, genom att ta del av publicerade kliniska studier. Fyra olika RCT-studier hämtade från databasen PubMed användes i detta litteraturarbete. Alla fyra studier resulterade i att VPZ inte var sämre än LPZ vid behandling av EE i upp till åtta veckor. Fler patienter i VPZ-gruppen uppnådde läkning av EE i samtliga studier. Dessutom visade VPZ ha bättre effekt hos patienter med svårare EE. Number Needed to Treat (NNT) för de olika studierna varierade mycket, därför kunde inte den användas för att beskriva den kliniska effekten av VPZ vid behandling av EE. Både VPZ och LPZ tolererades väl. Slutsatsen var att VPZ 20 mg en gång dagligen var inte sämre än LPZ 30 mg en gång dagligen vid behandling av EE i 8 veckor. VPZ var effektiv och visade bättre resultat än LPZ när det gäller EE-läkning. Detta gäller speciellt patienter med svårare EE. Båda läkemedlen tolererades väl.

Proteinmethylierung spielt eine immer größere Rolle in der Regulierung zellulärer Prozesse. Die Entwicklung effizienter proteomweiter Methoden zur Detektion von Methylierung auf Proteinen ist limitiert und technisch schwierig. In dieser Arbeit haben wir einen neuen Hefe-Zwei-Hybrid-Ansatz (Y2H) entwickelt, der Proteine, die miteinander wechselwirken, mit Hilfe von Sequenzierungen der zweiten Generation identifiziert (Y2H-Seq). Der neue Y2H-Seq-Ansatz wurde systematisch mit dem Y2H-Seq-Ansatz verglichen. Dafür wurde ein Bait-Set von 8 Protein-Arginin-Methyltransferasen, 17 Protein-Lysin-Methyltransferasen und 10 Demethylasen gegen 14,268 Prey-Proteine getestet. Der Y2H-Seq-Ansatz ist weniger arbeitsintensiv, hat eine höhere Sensitivität als der Standard Y2H-Matrix-Ansatz und ist deshalb besonders geeignet, um schwache Interaktionen zwischen Substraten und Protein-Methyltransferasen zu detektieren. Insgesamt wurden 523 Wechselwirkungen zwischen 22 Bait-Proteinen und 324 Prey-Pr oteinen etabliert, darunter 11 bekannte Methyltransferasen-Substrate. Netzwerkanalysen zeigen, dass Methyltransferasen bevorzugt mit Transkriptionsregulatoren, DNA- und RNA-Bindeproteinen wechselwirken. Diese Daten repräsentieren das erste proteomweite Wechselwirkungsnetzwerk über Protein-Methyltransferasen und dienen als Ressource für neue potentielle Methylierungssubstrate. In einem in vitro Methylierungsassay wurden exemplarisch mit Hilfe massenspektrometrischer Analysen die methylierten Aminosäurereste einiger Kandidatenproteine bestimmt. Von neun getesteten Proteinen waren sieben methyliert, zu denen gehören SPIN2B, DNAJA3, QKI, SAMD3, OFCC1, SYNCRIP und WDR42A. Wahrscheinlich sind viele Methylierungssubstrate im Netzwerk vorhanden. Das vorgestellte Protein-Protein-Wechselwirkungsnetzwerk zeigt, dass Proteinmethylierung sehr unterschiedliche zelluläre Prozesse beeinflusst und ermöglicht die Aufstellung neuer Hypothesen über die Regulierung Molekularer Mechanismen durch Methylierung. / Protein methylation on arginine and lysine residues is a largely unexplored posttranslational modification which regulates diverse cellular processes. The development of efficient proteome-wide approaches for detecting protein methylation is limited and technically challenging. We developed a novel workload reduced yeast-two hybrid (Y2H) approach to detect protein-protein interactions utilizing second generation sequencing. The novel Y2H-seq approach was systematically evaluated against our state of the art Y2H-matrix screening approach and used to screen 8 protein arginine methyltransferases, 17 protein lysine methyltransferases and 10 demethylases against a set of 14,268 proteins. Comparison of the two approaches revealed a higher sensitivity of the new Y2H-seq approach. The increased sampling rate of the Y2H-seq approach is advantageous when assaying transient interactions between substrates and methyltransferases. Overall 523 interactions between 22 bait proteins and 324 prey proteins were identified including 11 proteins known to be methylated. Network analysis revealed enrichment of transcription regulator activity, DNA- and RNA-binding function of proteins interacting with protein methyltransferases. The dataset represents the first proteome-wide interaction network of enzymes involved in methylation and provides a comprehensively annotated resource of potential new methylation substrates. An in vitro methylation assay coupled to mass spectrometry revealed amino acid methylation of candidate proteins. Seven of nine proteins tested were methylated including SPIN2B, DNAJA3, QKI, SAMD3, OFCC1, SYNCRIP and WDR42A indicating that the interaction network is likely to contain many putative methyltransferase substrate pairs. The presented protein-protein interaction network demonstrates that protein methylation is involved in diverse cellular processes and can inform hypothesis driven investigation into molecular mechanisms regulated through methylation.

Proteins in Escherichia coli were compared in terms of essentiality, centrality, and conservation. The hypotheses of this study are: for proteins in Escherichia coli, (1) there is a positive, measureable correlation between protein conservation and essentiality, (2) there is a positive relationship between conservation and degree centrality, and (3) essentiality and centrality also have a positive correlation. The third hypothesis was supported by a moderate correlation, the first with a weak correlation, and the second hypotheis was not supported. When proteins that did not map to orthologous groups and proteins that had no interactions were removed, the relationship between essentality and conservation increased to a strong relationship. This was due to the effect of proteins that did not map to orthologus groups and suggests that protein orthology represented by clusters of orthologus groups does not accurately dipict protein conservation among the species studied.