Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, has been a global health problem for years. The emergence of drug resistance in this organism generates the necessity of exploring novel targets and developing new drugs. Topoisomerases are enzymes found in all kingdoms of life responsible for overcoming the topological barriers encountered during essential cellular processes. The genomes of mycobacteria encode only one type IA topoisomerase (MtopI), which has been validated as a novel TB drug target. The goal of this study is to obtain new information on the mechanism and resistance of endogenous and synthetic inhibitors of MtopI. Rv1495 is a M. tuberculosis toxin that belongs to the MazEF family (MazE is the antitoxin and MazF is the toxin), with endoribonuclease activity. Rv1495 (MazF homolog in M. tuberculosis) toxin has been shown to interact directly with the C-terminal domain of MtopI for mutual inhibition. In this study the interaction of Rv1495 with the positively charged C-terminal tail in Mtop I is reported. This new information is useful for rational design and discovery of antibiotics for mycobacteria. Ethacridine, an FDA approved drug has shown activity against MtopI. In this project we studied the mechanisms of resistance associated with this drug as well the use of Ethacridine in combination with Moxifloxacin, to potentiate the bactericidal effect of this current second line drug for TB treatment. Results from sequencing of the genomic DNA isolated from the resistant mutants suggested the involvement of the Holliday-junction Ruv resolvase. Further studies showed that co-treatment with Ethacridine can enhance the moxifloxacin-mediated killing of M. smegmatis. FP-11g, a novel fluoroquinophenoxazine inhibitor of bacterial topoisomerase I, has shown promising activity against M, tuberculosis. We explored the bactericidal activity and resistance mechanisms associated to FP-11g using M. smegmatis as model organism. Additionally, the inhibitory effect of FP-11g was also evaluated on M. abscessus. FP-11g at concentration 4X MIC showed complete bactericidal activity against M. smegmatis after 24 hours. Inhibitory activity against M. abscessus was also observed. Results from sequencing of the genomic DNA isolated from the M. smegmatis resistant mutants revealed mutations in genes associated with general drug resistance.

<p>Heterosis, or hybrid vigor, is a phenomenon observed in both plant and animal systems where hybrid offspring perform better when compared to their parents. For hybrid plants, this can result in increased biomass, crop yields, and vigor when compared to the inbred parents. Even though heterosis has been used in agriculture for over a century, the molecular mechanisms that result in hybrid vigor remain elusive even after years of investigation. A molecular understanding of heterosis is desirable because it will speed up the process of breeding compatible inbred lines for developing hybrid seeds, and it will provide us with the knowledge to potentially engineer inbred lines that can mimic the beneficial phenotypic effects of heterosis, eliminating the need for farmers to buy new hybrid seeds every year. The goal of this research project is to identify genes that are required for heterotic phenotypes in maize. Our working hypothesis is that a mutation in genes that are essential for heterosis will cause an altered heterotic phenotype in hybrid maize plants. To test this hypothesis, we applied combined approaches of EMS mutagenesis, trait phenotyping in field and controlled conditions, bulk segregant analysis, whole genome sequencing, and bioinformatics analysis. First, we applied a forward genetics approach to identify mutant hybrids with altered heterosis and detected potential causal genes <em>via</em> whole genome sequencing. We identified one mutation occurring in a protein coding gene (gene ID <em>Zm00001eb305590</em>) located in a region of interest on chromosome 7, whose genotypes across various samples assayed fit the observed segregation pattern of hybrid traits. This mutation leads to a moderate or high-level codon change, indicating that this gene may play a role in mediating heterosis in maize. By investigating this gene with further studies, the learned knowledge could speed up the process of hybrid maize breeding by selecting compatible inbred lines through sequencing or by engineering hybrids that have favorable alleles for this gene.</p>

<p>  </p> <p><em>Fusobacterium necrophorum</em> is a Gram-negative, anaerobic, opportunistic pathogen that causes necrotic infections in cattle leading to liver abscess, foot rot, and calf diphtheria. Particularly, liver abscess in cattle is reported at 20.7% annually, and leads to liver condemnation and an annual economic burden of about 62 million dollars to the feedlot industry. Antibiotic administration is the mainstay of treating these infections, but antibiotic resistance is unavoidable and demand for antibiotic-free, natural, and organic beef has demanded alternative therapies and preventatives. Vaccination is one of the best alternatives to prophylactic antibiotic administration. In this study, we have explored outer membrane proteins (OMPs) and outer membrane vesicles (OMVs) for potential vaccine candidates. OMPs and OMVs are vaccine targets because of their antigenic properties and host specificity. Additionally, we performed comparative genomic analysis of <em>F. necrophorum</em> species to identify additional virulence genes with vaccine potential, unique to the <em>F. necrophorum</em> and its virulent subspecies <em>necrophorum</em>. </p> <p>Protein- protein interaction investigation through binding assay and pulldown assay identified novel OMPs, namely 17kDa, 22kDa, and 66.3 kDa proteins, which were further characterized as OmpH, OmpA and Cell Surface Protein (CSP), respectively. In this study, these novel OMPs including previously characterized 43kDa OMPs were cloned, and recombinant proteins were expressed and purified. These recombinant proteins were used to generate polyclonal antibodies in rabbits, and their efficacy was studied using <em>in vitro</em> adhesion inhibition assays. The combination of two or more antibodies raised against the recombinant OMPs was significantly effective in reducing/neutralizing bacterial binding to bovine endothelial cells compared to individual antibody treatment. This suggests that a multiple subunit vaccine could be effective and provide sufficient evidence to perform <em>in vivo</em> studies. </p> <p>Similarly, we purified OMVs of <em>F. necrophorum</em> subspecies <em>necrophorum</em> 8L1 and analyzed its content using proteomics and lipidomics. Out of 342 proteins identified by tandem liquid chromatography mass spectrometry (LC-MS), OMPs and toxins were the most abundant. These included OMPs and toxins namely, 43 kDa OMP, OmpH, OmpA, CSP, FadA, leukotoxin family filamentous adhesin, N-terminal domain of hemagglutinin and other OMP transport and assembly factor protein. The presence of a subset of these proteins was further confirmed by western blot analysis. Lipidomics analysis showed that OMVs contained phospholipid, sphingolipid, and acetyl carnitine as the main lipid contents. Cytotoxicity assay on BL-3 cell line showed that these OMVs have a toxic effect on host immune cells and could impart immunomodulatory effect. All these findings suggest the vaccine potential of OMVs and demand dose-based <em>in vivo</em> study.</p> <p>In addition, we identified and characterized 5 clinical isolates of <em>F. necrophorum</em> using comparative genomics, UBCG (Up-to-date Bacterial Core Gene) based analysis enabled phylogenetic characterization of 46 <em>F. necrophorum</em> genomes into subspecies specific clades. The pangenome and recombination analysis showed the extensive disparity in accessory genes resulting in species divergence. Strikingly, we detected antimicrobial resistance gene for macrolides and tetracycline in one strain of <em>F. necrophorum</em>, a harbinger of the start of resistance and necessitating search for an alternative prophylactic method. We also noted common virulence genes, including toxins, outer membrane adhesion proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters and transporter proteins in <em>F. necrophorum</em> strains. A focused study on these genes could help identify the main genes of virulence and inform effective vaccination strategies against fusobacterial infections. </p> <p>Overall, the studies suggest adhesins and toxin and/or OMV-based subunit vaccine could be potential targets for vaccine development against fusobacterial infections.  </p>

Cette étude pilote vise à développer une méthode d'analyse intégrative qui permet d'augmenter le taux de réussite du diagnostic clinique des mutations génétiques rares. De plus, l'identification de nouveaux gènes associés à l'ataxie épisodique (EA) et l'évaluation de nouveaux algorithmes de prédiction, pour un examen de variants plus robuste, découleront de l'enquête. Caractérisé par une perte sporadique de la coordination des mouvements volontaires, l'EA se manifeste généralement tardivement, avec une hétérogénéité clinique et génétique élevée, compliquant largement l’obtention d’un diagnostic précis. Alors que quatre gènes ont été liés aux huit sous-types d'EA, de nombreux patients demeurent sans diagnostic moléculaire dû aux limites des méthodes de séquençage d’ADN. Ces lacunes accentuent l’intérêt d’implanter le séquençage de l’ARN en milieu clinique, afin d’obtenir l’information fonctionnelle offerte par l’approche. Des patients atteints d’EA, sans diagnostic moléculaire malgré un examen approfondi, ont été recrutés à Montréal. Le séquençage du génome entier (WGS) et de l'ARN a été effectué sur des échantillons de sang pour identifier les variants nucléotidiques, l'expression différentielle, les événements d'épissage ainsi que les expansions de microsatellites. Plusieurs algorithmes de prédiction de la pathogénicité récents ont été choisis pour être testés parallèlement aux algorithmes standard. Des données WGS provenant d’un trio familial atteint de pathologies neurologiques ont également été soumises au pipeline génomique développé pour la cohorte EA. Des variants candidats ont été identifiés pour chaque patient en fonction des scores de pathogénicité, de la rareté des événements génétiques et des informations fonctionnelles et cliniques connues pour un gène altéré donné. Parmi les découvertes figurent des mutations non-sens, des faux-sens, de l'épissage alternatif ainsi que des expansions nucléotidiques dans des gènes associés aux ataxies spinocérébelleuses ou aux paraplégies spastiques. En plus d'être présents dans les ensembles de données de séquençage disponibles pour chaque patient, les événements génomiques ont été vérifiés par séquençage Sanger de l'ADN et de l'ARN lorsque possible. Les effets fonctionnels potentiels, prédits principalement à partir du RNA-seq et suggérant une expression anormale de l'ARNm, ont également été évalués par amplification PCR et qPCR traditionnelle. À ce jour, quatre des dix patients ont reçu ou sont en voie de recevoir un diagnostic clinique, et quatre autres présentent d’excellents candidats moléculaires pour expliquer une pathologie ataxique. Ce projet devrait permettre un diagnostic mieux défini, conduisant à une meilleure qualité de vie, une meilleure évaluation du pronostic et une meilleure prise en charge des patients. L’identification de modulateurs génétiques chez certains d’entre eux devrait également permettre une meilleure caractérisation clinique des conditions rapportées, bénéficiant les évaluations symptomatiques futures. De plus, la méta-analyse des données RNA-seq offre le potentiel de découvrir des régulateurs de pathogenèse communs à l’EA. Il favorisera également l'approche intégrative pour un plus large éventail de troubles et pourrait éventuellement conduire à de nouvelles stratégies thérapeutiques. / This pilot study aims to develop an integrative analysis method that allows for an increased diagnosis success rate of rare genetic mutations. Moreover, identification of novel genes associated with Episodic Ataxia (EA) and evaluation of new AI-generated prediction algorithms, for a more robust variant examination, will ensue from the investigation. Characterized by sporadic loss of voluntary movement coordination, EA typically manifest with a late onset as well as high-clinical and genetic heterogeneity, setting additional hurdles to diagnosis. While four genes have been linked to the eight subtypes of EA, many patients are left without molecular diagnosis due to the limitations of individual DNA-sequencing methods, which can be mitigated by the functional overview that RNA sequencing (RNA-seq) offers. EA patients, lacking molecular diagnosis despite in-depth examination, were recruited in Montreal. Whole-Genome sequencing (WGS) and RNA-seq were performed on blood samples to identify single nucleotide variants, differential expression, splicing events, structural variants and repeat expansions. Multiple recent pathogenicity prediction algorithms were chosen for testing concurrently to standard ones, in order to evaluate their performance and potential for clinical pipelines integration. WGS data of a family trio from France, in which the father and the daughter present neurologic pathologies, were also processed through the genomic pipeline that was developed for the EA cohort in order to identify the cause of their disorder. Candidate variants were identified for each patient according to pathogenicity scores, rarity of genetic events, and known functional as well as clinical information for a given altered gene. Among the findings are truncations, missenses, alternative splicing, and repeat expansions in genes already associated to either spinocerebellar ataxia or spastic paraplegia. In addition to being present in both datasets when available, validation of these interesting genomic events has been performed through Sanger Sequencing of both DNA and RNA when feasible. For strong candidates where the available functional information from RNA-seq suggests abnormal mRNA expression, validation includes PCR amplification as well as a traditional qPCR to support effects on transcripts. To this day, four out of ten patients have received or are on the verge of receiving a diagnosis, and four others are carrying excellent molecular candidates requiring further validation to explain their ataxic pathologies. This project should provide more defined diagnosis, leading to better quality of life, better evaluation of prognosis and better management of care for patients. Identification of genetic modifier in some of them should also allow for a better clinical characterization of the reported conditions, benefiting future patient examinations. A meta-analysis of our patients’ transcriptomic profiles could also uncover commonly affected pathways in EA development. It will also promote the integrative approach for a larger spectrum of disorders and might eventually lead to new therapeutic strategies.

Detta projekt har utförts på uppdrag av Saab Dynamics. Syftet med projektet var att skapa ett system för att ersätta den befintliga utrustning som fanns för att simulera radar vid testning av vissa vapensystem.   Systemet byggdes upp med hjälp av GPRS, GPS och transportprotokollen TCP och UDP. Huvuddelen av arbetet berörde GPS och GPRS.   Denna rapport är en redogörelse för systemets framtagning och de verktyg och metoder som användes, samt en fördjupning i ämnena GPS, GPRS och deras olika protokoll. Rapporten tar även kort upp alternativa lösningar till datasamtal.   Slutsatsen som kan dras utifrån resultatet av detta projekt är att systemet fungerar och kan vara användbart i framtiden efter vidareutveckling. / This project has been carried out on behalf of Saab Dynamics. The purpose of the project was to create a system to replace the existing equipment for simulating radar when testing certain weapon systems.   The system was created using GPRS, GPS and the transport protocols TCP and UDP. GPS and GPRS were used the most.   This report is a description of the system's design and the tools and methods used to create it, as well as an in depth look into the subjects of GPS, GPRS and their various protocols. The report also briefly discusses some alternative solutions that could have been used instead of data calls.   The conclusion that can be drawn from the results of this project is that the system works and can be useful in the future with further development.

Among the various heterogeneous catalytic reactions three way catalysis (TWC), catalytic combustion of hydrogen, water gas shift reaction (WGS) and preferential oxidation of CO (PROX) in the hydrogen rich stream are some of the important reactions receiving the attention presently. Three-way catalysis (TWC) involves simultaneous removal of the three pollutants (i.e., CO, NOx, and HCs) from the automobile exhaust. Catalytic combustion of hydrogen by oxygen or hydrogen-oxygen recombination reaction is an industrially important reaction. It has variety of application such as in sealed lead acid batteries and nuclear reactors. Water gas shift (WGS) reaction is of specific importance to produce hydrogen from carbonaceous material. PROX is an important step to further purify hydrogen produced form WGS. Hydrogen purified using PROX can be directly fed to polymer electrolyte membrane fuel cells. By and large, noble metals Pt, Pd, Rh, Ru and some of their alloys are dispersed on oxide or high surface area carbon are the active catalysts. An alternative approach can be to make Pt2+, Pd2+, Rh3+, Ru4+ ions substituted in reducible support such as CeO2, Ce1-xTixO2-δ and TiO2 to increase the dispersion and bring down the cost. In this thesis we have followed this new approach and show that noble metal ionic catalysts are superior to noble metal nano particles. In the 1st chapter we present an overview of heterogeneous catalysis and important heterogeneous catalytic reactions. Monolithic catalyst and various ways to coat catalysts for application have been reviewed. Metal-support interaction till date is also reviewed. In the 2nd chapter, synthesis of noble metal ionic catalysts by solution combustion method is described. Coating of washcoat and active catalyst phase over ceramic honeycomb by a new combustion method is described. Solution combustion reaction and characterization of the catalyst by x-ray diffraction, x-ray photoelectron spectroscopy, temperature programmed reduction and reaction is given. We have fabricated experimental systems to carryout catalytic reaction and in this chapter they have been presented. In the 3rd chapter, we report a new process of coating of active exhaust catalyst over -Al2O3 coated cordierite honeycomb. The process consists of (a) growing  -Al2O3 on cordierite by solution combustion of Al(NO3)3 and oxylyldihydrazide (ODH) at 600 0C. Active catalyst phase, Ce0.98Pd0.02O2- is coated on - Al2O3 coated cordierite again by combustion of ceric ammonium nitrate and ODH with 1.2  10-3 M PdCl2 solution at 500 0C. In this way a coat layer over cordierite ceramic has been achieved and catalyst has the active sites in the form of Pd2+ ions rather than Pd metal. Weight of the active catalyst can be varied from 0.02 to 2 wt% which is sufficient but can be loaded even up to 12 wt% by repeating dip dry combustion [1]. Adhesion of catalyst to cordierite surface is via oxide growth on oxide ceramic which is very strong. 100 % conversion of CO is achieved below 80 oC at a space velocity of 880 h-1. At much higher space velocity of 21000h-1, 100 % conversion is obtained below 245 oC. Activation energy for CO oxidation is 8.4 kcal/mol. At a space velocity of 880 h-1 100% NO conversion is attained below 185 oC and 100 % conversion of ‘HC’(C2H2) below 220 oC. At the same space velocity 3-way catalytic performance over Ce0.98Pd0.02O2- coated monolith shows 100% conversion of all the pollutants below 220 o C with 15% excess oxygen. Catalytic activity of cordierite honeycomb coated by this new coating method for the oxidation of major hydrocarbons in exhaust gas is discussed further in this chapter. ‘HC’ oxidation over the monolith catalyst is carried out with a mixture having the composition, 470 ppm of both propene and propane and 870 ppm of both ethylene and acetylene with the varying amount of O2. 3-way catalytic test is done by putting hydrocarbon mixture along with CO (10000ppm), NO (2000ppm) and O2 (15000ppm). Below 350 oC full conversion is achieved [2]. A comparison of the results shows that Ce1-xPdxO2-δ far superior to other catalysts. In this method, handling of nano material powder is avoided. In the 4th chapter we present a detailed study on the catalytic combustion of hydrogen by oxygen (hydrogen oxygen recombination reaction). Ever since Michel Faraday showed H2 + O2 recombination reaction over platinum metal plates, Pt metal has remained the only room temperature recombination catalyst. In search of an alternative catalyst, we discovered a new Pt free Ti0.99Pd0.01O2- compound which shows high rates of this reaction above 45 oC compared to Ce0.98Pt0.02O2-, Pt/Al2O3 and Pd/Al2O3. High rates of H2+O2 recombination over Pt and Pd ion respectively in CeO2 and TiO2 is due to the protonic type H2+ adsorption on Pt2+ or Pd2+ and dissociative chemisorption of O2 on the electron rich oxide ion vacancies [3]. In the case of Ce0.98Pt0.02O2-, H2/Pt ratio in a TPR experiment is ~2.3 at 0 oC. In the case of Ti0.99Pd0.01O2- also, H2 adsorption occurs below 0 oC and H2 / Pd ratio is ~2.2. Thus, more than 4-5 H atoms are adsorbed per metal ion. This is attributed to hydrogen spillover. H2 is known to be adsorbed as hydride ion (H-) over Pt, Pd, Rh, Ru, Os and Ir metals. Proton NMR studies of H2 adsorbed on Pd metal have shown upfield i.e. negative shift of 12 ppm with respect to TMS. We have studied proton NMR of Ti0.99Pd0.01O2- + H2 which show a downfield shift of 11.35 ppm confirming H+ or H2+ kind of species over Pd2+ ion in Ti0.99Pd0.01O2-. In Ce0.98Pt0.02O2- also H2 adsorption led to H2+ like species observed at 8 ppm and DFT calculations indeed showed H2+ kind species. H2+ is a precursor for dissociation and can readily induce O2 dissociation leading to high rates of recombination. In the 5th chapter we report water gas shift reaction (WGS) and preferential oxidation of CO (PROX) over Ti0.99Pt0.01O2-, Ce0.83Ti0.15Pt0.02O2- and Ce0.98Pt0.02O2-δ. The water gas shift reaction (WGS) is an important reaction to produce hydrogen. In this study, we have synthesized nano crystalline catalysts where Pt ion is substituted in the +2 state in TiO2, CeO2 and Ce1-xTixO2-δ. The catalysts have been characterized by X-ray diffraction and X-ray photoelectron spectroscopy (XPS) and it has been shown that Pt2+ ions in these reducible oxides of the form Ti0.99Pt0.01O2-, Ce0.83Ti0.15Pt0.02O2- and Ce0.98Pt0.02O2-δ are highly active. These catalysts were tested for the water gas shift reaction both in presence and absence of hydrogen. It is shown that Ti0.99Pt0.01O2- exhibits higher catalytic activity than Ce0.83Ti0.15Pt0.02O2- and Ce0.98Pt0.02O2-δ [4]. Further, experiments were conducted to determine the deactivation of these catalysts by performing the daily startup and shutdown of the reactor for over 24 hours. There was no sintering of Pt and no carbonate formation and, therefore, the catalyst did not deactivate even after prolonged reaction. There was no carbonate formation because of the highly acidic nature of Ce4+, Ti4+ ions in the catalysts. Further, PROX activity of these catalysts has been studied. Ce0.83Ti0.15Pt0.02O2- and Ce0.98Pt0.02O2-δ showed high activity, large operating temperature window and low working temperature proving them to be highly effective PROX catalysts. In the 6th chapter we study the electrocatalysis of formic acid electro-oxidation and simultaneously mapping the electronic states of the electrodes by X-ray photoelectron spectroscopy (XPS). Ionically dispersed platinum in Ce1-xPtxO2-δ and Ce1-x-yTiyPtxO2-δ is very active towards oxygen evolution and formic acid oxidation. Higher electro-catalytic activity of Pt2+ ions in CeO2 and Ce1-xTixO2 compared to Pt0 in Pt/C is due to Pt2+ ion interaction with the supports, CeO2 and Ce1-xTixO2 respectively [5]. Further, ionic platinum does not suffer from CO poisoning effect unlike Pt0 in Pt/C. Utilization of lattice oxygen from the electrodes during the reaction has been demonstrated. This lattice oxygen exchange is responsible to convert CO to CO2 in the lower potential region to remove CO poisoning effect. In 7th chapter we repeat our study on the noble metal ion reducible oxide interaction in Ce1-xPtxO2- and Ce1-xPdxO2- (x= 0.02) system by a novel electrochemical method combined with XPS. Working electrodes made of CeO2 and Ce0.98Pt0.02O2- mixed with 30% carbon are cycled between 0.0-1.2 V in potentio-static (chronoamperometry) and potentio-dynamic (cyclic voltametry) mode with reference to saturated calomel electrode (SCE). Reversible oxidation of Pt0 to Pt2+ and Pt4+ state due to the applied positive potential is coupled to simultaneous reversible reduction of Ce4+ to Ce3+ state. CeO2 reduces to CeO2-y (y= 0.35) after applying +1.2 V which is not reversible. But Ce0.98Pt0.02O2- reaches a steady state with Pt2+: Pt4+ in the ratio of 0.60: 0.40 and Ce4+: Ce3+ in the ratio of 0.55: 0.45 giving a composition Ce0.98Pt0.02O1.74 at 1.2 V which is reversible [6]. Composition of Pt ion substituted compound is reversible between Ce0.98Pt0.02O1.95 to Ce0.98Pt0.02O1.74 within the potential range of 0.0-1.2 V. Thus, Ce0.98Pt0.02O2- forms a stable electrode for oxidation of H2O to O2 unlike CeO2. A linear relation between oxidation of Pt2+ to Pt4+ with simultaneous reduction of Ce4+ to Ce3+ is observed demonstrating Pt-CeO2 metal support interaction is due to reversible Pt0/Pt2+/Pt4+ interaction with Ce4+/Ce3+ redox couple. Similar studies have been performed with Ce0.98Pd0.02O2- catalyst to show the redox coupling between Pd2+/Pd0 and Ce4+/Ce3+ redox couples. We expect similar redox coupling for Pd, Pt ions substituted TiO2, and Ce1-xTixO2. In the final chapter 8, a critical review and conclusion on the results presented in the thesis is presented. The combustion synthesized catalysts reported in this thesis stabilizes the Pt and Pd metals in their ionic state rather than zero valent metallic state. Thus, the catalysts are uniform solid catalysts. High activity and stability of these catalysts are shown to be due to the electronic interaction between noble metal ions and the reducible oxide. Redox couples Pt0/Pt2+, Pt2+/Pt4+ and Pd0/Pd2+ interact with Ce4+/Ce3+, Ti4+/Ti3+ couples such that metal is oxidized and the support is reduced. This has been established in the thesis by a combined use of electrochemistry and XPS thus solving a long standing problem of metal support interaction in catalysis. We hope that the results presented in the thesis is a worthwhile contribution to catalysis. (For mathematical equations pl refer pdf file.)

Recently Whole Genome Sequencing (WGS) has become the new high-resolution tool used to trace the source of foodborne outbreaks. There are often only a few genetic differences that can distinguish closely related bacterial isolates, and variability in data quality between different laboratories may influence the results. In this project, a data set from ten laboratories where the same bacterial samples were sequenced using different library preparation kits and sequencing methods in an interlaboratory study, has been used. Factors that could be responsible for the different performance in terms of how well the raw WGS data from the different labs assembles were investigated. The raw data from the different labs assembled very differently. One lab showed adapter sequences in their reads and filtering them improved the assembly substantially. All labs utilizing the transposase-based library preparation kit Nextera, had base composition bias in the beginning of the reads. For many labs, as the coverage was increased, the number of contigs first increased and then decreased. This was due to low number of contaminating reads from other species. However, these contaminations were barely visible in the plots generated by Kraken/Krona. Filtering out contigs with very low coverage removed this problem. Two labs performed much worse than the others. Some of their reads showed quality drop towards the ends, whereas their data also had the longest read length. However, quality trimming the read ends did not improve the assembly. These two labs had higher GC content in their reads compared to the other labs, the reason for this needs further investigation.

La digoxine est un cardiotonique largement employé pour contrôler les symptômes de l'insuffisance cardiaque et de la fibrillation auriculaire. Il est connu depuis les années 1980 que le métabolite principal de la digoxine, la dihydrodigoxine, est produit exclusivement par le microbiome intestinal (métabolisme de premier passage) et plus précisément la bactérie Eggerthella lenta. Aux États-Unis, c'est 14% des participants à une étude qui excrétaient 40% et plus de la dose sous la forme de ce métabolite rapidement éliminable et ayant perdu son affinité pour sa cible. De plus, chaque année, la digoxine est le médicament qui engendre le plus d'hospitalisations pour effets secondaires toxiques. Les effets secondaires très problématiques de la digoxine sont souvent déclenchés par l'ajout d'antibiotiques (surtout les macrolides) à la prescription de digoxine. La théorie explorée ici explique les évènements de toxicité chez les patients métabolisateurs. Ces derniers ont une dose quotidienne de maintien de digoxine plus élevée pour compenser l'action de la bactérie et, lorsque ces patients reçoivent un antibiotique pour une infection non reliée à leur condition cardiaque, l'arrêt du métabolisme par le microbiome engendre une augmentation de la biodisponibilité de la digoxine. Si la concentration plasmatique du médicament augmente trop, les effets secondaires peuvent aller jusqu'à causer la mort. Dans le présent projet, nous avons vérifié la sensibilité de E. lenta à deux antibiotiques de la famille des céphalosporines de seconde génération, in vivo et in vitro. Pour les 18 volontaires qui ont été exposés à 2x500mg de céfprozil durant une semaine, il y a une tendance à la baisse de l'abondance de la bactérie d'intérêt (par 58,3% par rapport au niveau initial), mais pas de significativité au niveau des tests statistiques. Pour les échantillons complets de microbiome fécal, mis en culture avec et sans antibiotiques, il y a une différence statistiquement significative avec une valeur-p de 0,0457, alors que la croissance de E. lenta a été impactée négativement par l'ajout de céfprozil au milieu de culture. Les résultats valident une prémisse importante pour la démonstration du rôle du microbiome dans la pharmacocinétique de la digoxine et la gestion clinique du médicament cardiotonique. / Digoxin is a widely used cardiotonic drug in the management of heart failure and atrial fibrillation. It has been known since the early 1980's that the main metabolite of digoxin, dihydrodigoxin, is synthesized by the gut microbiome during first pass metabolism and is exclusively produced by the bacteria Eggerthella lenta. In a clinical study done in the U.S.A., there were 14% of high metabolizers, for whom over 40% of the oral digoxin dose is transformed to the inactive metabolite and rapidly eliminated. Digoxin toxicity is the leading cause of hospitalization from medication's secondary effects. The toxicity events are often associated with the addition of an antibiotic (mostly from the macrolides class) to the patient's drugs regiments. The theory explored in this project could help explain the toxicity events in metabolizers. These patients have a higher daily digoxin maintenance dose to counteract the effects of the microbiome and are then prescribed antibiotics for an infection unrelated to their heart condition. The antibiotic alters E. lenta negatively, which cannot metabolize digoxin anymore and therefore augments the bioavailability of the cardiotonic. If the plasmatic concentration reaches dangerous levels (over 2ng/ml of plasma), the patients face adverse effects that include death. In the present project, we evaluated the susceptibility of E. lenta to two second generation cephalosporins, in vivo and in vitro. With the 18 healthy volunteers that were exposed to 2x500mg of cefprozil daily for 7 days, we observed a diminution of the abundance of the bacteria of interest by 58,3% from the initial levels. This change did not however produce statistically significant tests results. For the complete fecal microbiome that were cultivated in vitro, with or without cefprozil, the difference between the two conditions resulted in a statistically significant p-value of 0.0457, confirming the sensitivity of E. lenta to this cephalosporin. These results validate an important premise for the demonstration of the importance of the gut microbiome in the pharmacokinetics of digoxin and the clinical management of the drug to avoid toxicity events in clinical practice.

Rare diseases are estimated to affect 3.75% of the global population, which roughly translates to 300 million affected individuals. A large proportion of patients still do not have their diagnosis and current approaches such as chromosomal microarray (CMA), whole exome sequencing (WES), and whole genome sequencing (WGS) that targets DNA and the exome aims to resolve that very first step. RNA-seq serves as a powerful approach complementing the aforementioned methods that have reached a plateau in the diagnostic yield. RNA-seq can facilitate the finding of aberrant events that appear during transcription e.g., splicing, changes in gene expression and monoallelic expression. In this study, we aimed to establish RNA-seq analysis pipelines and evaluate whether RNA-seq could be utilized to enhance diagnostic yield. A total of 47 clinical samples were analysed along with the publicly controlled GEAUVADIS dataset to evaluate the potential of RNA-seq in a clinical setting. The pilot pipeline used, an RNA-seq analysis wrapper around Detection of RNA Outlier Pipeline (DROP), used detected a highly ranked splicing variant in a positive control control  sample that was hard to identify in a WGS analysis. The remaining two other positive control other two control samples with aberrant expression were also detected by the pipeline. Additionally, the pipeline gave a manageable list of candidate genes per affected sample in the population along with corroborating graphs that can support the decision-making for clinicians. The results of this pipeline proved successful for integrating RNA-seq and thustherefore, we expect anticipate an increase in diagnosis.

Les progrès des technologies de séquençage ont joué un rôle important dans le diagnostic moléculaire des maladies rares, telles que les myopathies et les dystrophies musculaires. Cependant, plusieurs patients atteints de maladies neuromusculaires restent sans diagnostic. Ceci est dû à la grande hétérogénéité clinique et génétique ainsi qu'au caractère hautement polymorphique des gènes associés à ces troubles. L'interprétation des données génétiques est un grand défi et les tests génétiques aboutissent souvent à l'identification de variants de signification inconnue (VUSs). Plusieurs de ces variants peuvent perturber l'épissage normal de l'ARN ou affecter l'expression des gènes. À cet égard, nous proposons une approche bio-informatique. Notre objectif est de mettre en place un pipeline identifiant et caractérisant des variants d'intérêt dans un contexte pathologique. Afin de déterminer si les variants ont un impact fonctionnel, notre pipeline se concentre sur l'épissage alternatif ainsi que sur l'intégration des données génomiques et transcriptomiques. Nous émettons l'hypothèse qu'une partie des patients sans diagnostic pour leur maladie neuromusculaire s'explique par des variants introniques jouant un rôle régulateur ou affectant l'épissage et l'abondance de l'ARNm. Cette approche multi-omique permet de déterminer si les variants ont un impact fonctionnel. Pour ce faire, nous avons réalisé un séquençage de l'ARN et de l'ADN à partir de biopsies musculaires de quatre patients. Les données ont été alignées et annotées avec différents scores de pathogénicité. Les événements d'épissage sont analysés par SpliceAI et rMATS. L'analyse des gènes différentiellement exprimés a été réalisée par l'outil LPEseq. Les CNVs et les expansions de répétitions ont été analysés avec CNVkit et ExpansionHunter. Plusieurs scripts maison filtrent et intègrent les données ARN et ADN. Pour l'instant, un total de huit variants pathogéniques sont proposés pour nos patients, mais des investigations supplémentaires sont nécessaires. Les variants recherchés sont rares et nécessitent donc un pipeline cohérent et efficace. Ce projet apportera un bénéfice significatif pour les patients en leur permettant d'obtenir un diagnostic et ainsi d'avoir accès à un meilleur suivi clinique. / Advances in sequencing technologies have played an important role in the molecular diagnosis of rare diseases, such as myopathies and muscular dystrophies. However, several patients with these neuromuscular diseases remain undiagnosed. This is due to the great clinical and genetic heterogeneity as well as the highly polymorphic nature of the genes associated with myopathies and muscular dystrophies. The interpretation of genetic data is a great challenge and genetic testing often results in the identification of variants of uncertain significances (VUSs). Many of these variants can disrupt normal RNA splicing or affect gene expression. In this regard, we propose a bioinformatics approach. Our aim is to put in place a pipeline identifying and characterizing variants of interest in a pathological context. To determine if the variants have a functional impact, our pipeline focuses on alternative splicing as well as the integration of genomic and transcriptomic data. We hypothesize that a portion of patients without a diagnosis for their neuromuscular disorder is explained by intronic variants having a regulatory role or affecting mRNA splicing and abundance. This multi-omics approach will make it possible to determine whether the variants have a functional impact. To do so, we performed RNA and DNA sequencing using muscle biopsies from four patients. Data was aligned and annotated with different pathogenicity scores. Splicing events are analyzed by SpliceAI and rMATS. The analysis of the differentially expressed genes was carried out by the LPEseq tool. CNVs and repeat expansion were analyzed with CNVkit and ExpansionHunter. Several in-house scripts filter and integrate RNA and DNA data. For now, a total of eight pathogenic variants are proposed for our patients, but further investigations are needed. The variants sought are rare and therefore require a coherent and efficient pipeline to facilitate their characterization. This project will have a significant benefit for patients by allowing them to obtain a diagnosis and thus have access to better clinical follow-up.