Étude de l’évolution des génomes par duplications, pertes et réarrangements

La duplication est un des évènements évolutifs les plus importants, car elle peut mener à la création de nouvelles fonctions géniques. Durant leur évolution, les génomes sont aussi affectés par des inversions, des translocations (incluant des fusions et fissions de chromosomes), des transpositions et des délétions. L'étude de l'évolution des génomes est importante, notamment pour mieux comprendre les mécanismes biologiques impliqués, les types d'évènements qui sont les plus fréquents et quels étaient les contenus en gènes des espèces ancestrales. Afin d'analyser ces différents aspects de l'évolution des génomes, des algorithmes efficaces doivent être créés pour inférer des génomes ancestraux, des histoires évolutives, des relations d'homologies et pour calculer les distances entre les génomes. Dans cette thèse, quatre projets reliés à l'étude et à l'analyse de l'évolution des génomes sont présentés : 1) Nous proposons deux algorithmes pour résoudre des problèmes reliés à la duplication de génome entier : un qui généralise le problème du genome halving aux pertes de gènes et un qui permet de calculer la double distance avec pertes. 2) Nous présentons une nouvelle méthode pour l'inférence d'histoires évolutives de groupes de gènes orthologues répétés en tandem. 3) Nous proposons une nouvelle approche basée sur la théorie des graphes pour inférer des gènes in-paralogues qui considère simultanément l'information provenant de différentes espèces afin de faire de meilleures prédictions. 4) Nous présentons une étude de l'histoire évolutive des gènes d'ARN de transfert chez 50 souches de Bacillus.Gene duplication is one of the most important types of events affecting genomes during their evolution because it can create novel gene function. During the evolution process, genomes are also affected by inversions, translocations (including chromosome fusions and fissions), transpositions and deletions. Studying the evolution of genomes is important to get a better understanding of the biological mechanisms involved, which types of events are more frequent than others and what was the gene content in the ancestral species just to name a few. In order to analyze these different aspects of genome evolution, efficient algorithms need to be developed to infer ancestral genomes, evolutionary histories, homology relationships between genes and to compute distances between genomes. In this thesis, four different projects related to the study and analysis of genome evolution are presented: 1) We developed two algorithms to solve problems related to whole genome duplication: one that generalizes the genome halving problem to gene losses, and one that allows to compute the double distance with losses. 2) We developed a new method to infer evolutionary histories of orthologous tandemly arrayed gene clusters. 3) We proposed a new graph-theoretic approach to infer inparalogs that simultaneously considers the information given by multiple species in order to make better inferences of inparalogous gene pairs. 4) We studied the evolutionary history of the tRNA genes of 50 Bacillus strains

Synthèse diastéréosélective de monofluoroalcènes

Cette thèse traite du développement de nouvelles méthodes de synthèse diastéréosélective de monofluoroalcènes diversement substitués. Le premier chapitre présente la place du fluor dans les molécules organiques et son impact sur leurs propriétés. Ensuite, un résumé des méthodes de synthèse existantes de monofluoroalcènes di- et trisubstitués est présenté. L’introduction se termine par un survol des travaux précurseurs du laboratoire Paquin dans le domaine de la synthèse diastéréosélective de monofluoroalcènes tri- et tétrasubstitués. Le second chapitre présente la séquence de synthèse diastéréosélective des 1,1-diaryle-2-fluoroéthènes. Premièrement, les 1-aryle-1-bromo-2-fluoroéthènes sont générés par une réaction d’addition d’hydrure/élimination à partir des β, β-difluorostyrènes-α-silylés, suivie d’une séquence réactionnelle de bromation/désilicobromation. Pour terminer, un couplage de Suzuki-Miyaura avec une variété d’acides boroniques donne accès aux 1,1-diaryle-2-fluoroéthènes. Le troisième chapitre présente la séquence de synthèse diastéréosélective menant à chacun des isomères cis et trans des dérivés β-fluorostyrènes à partir d’intermédiaires réactionnels communs : les (Z)-1-aryle-2-fluoro-1-(triméthylsilyl)éthènes. Les isomères trans sont obtenus par remplacement stéréospécifique du groupement silylé en présence d’eau et de fluorures. Les isomères cis sont accessibles via une séquence de bromation/désilicobromation, suivie par la réduction du nouveau lien C-Br vinylique. Le quatrième chapitre traite d’une nouvelle séquence synthétique permettant la préparation de dérivés silylés des 2,2-difluorostyrènes. Cette nouvelle route présente de nombreux avantages sur la route originale, incluant une étendue réactionnelle plus vaste, des rendements plus élevés, une facilité de purification accrue et l’absence de produits secondaires désilylés. Pour conclure, le cinquième chapitre résume les précédents et aborde aussi les perspectives futures découlant de mes travaux.This thesis focuses on the developpement of novel stereoselective methods to access diversely substituted monofluoroalkenes. The first chapter introduces the fluorine atom and its properties when found within organic molecules. Then, a summary of the existing synthetic methods found in the literature for the synthesis of di- and trisubstituted monofluoroalkenes is presented. The last section of the introduction is an overview of the previous work from the Paquin’s group in the field of tri- and tetrasubstituted monofluoroalkene synthesis. The second chapter presents the diastereoselective synthetic sequence leading to 1,1-diaryl-2-fluoroethenes. First, 1-bromo-1-aryl-2-fluoroethenes are generated by an addition of hydride/elimination sequence on α-trialkylsilyl-β, β-difluorostyrenes, followed by a bromination/desilicobromination sequence. The last step is a Suzuki-Miyaura cross-coupling reaction with various aryl or heteroarylboronic acids, giving access to 1,1-diaryl-2-fluoroethenes. The third chapter describes the diastereoselective synthetic sequences leading to both (Z) and (E)-β-fluorostyrenes from a common intermediate: (Z)-1-aryle-2-fluoro-1-(trialkylsilyl)ethenes. The E isomers are obtained by stereospecific replacement of the silyl group in the presence of a fluoride source and water. The Z isomers are accessible by a bromination/desilicobromination sequence followed by the reduction of a vinylic C-Br bond. The fourth chapter describes a new synthetic sequence allowing the preparation of trialkylsilylated derivatives of 2,2-difluorostyrenes. This new synthetic route shows significant improvements over the original method, including broader reaction scope, ease of purification, and absence of undesirable side-products. To conclude, the fifth chapter summarizes the thesis and opens-up on synthetic perspectives

Frequency of microplastics in mesopelagic fishes from the Northwest Atlantic

Microplastics are a ubiquitous pollutant in our seas today and are known to have detrimental effects on a variety of organisms. Over the past decade numerous studies have documented microplastic ingestion by marine species with more recent investigations focussing on the secondary impacts of microplastic ingestion on ecosystem processes. However, few studies so far have examined microplastic ingestion by mesopelagic fish which are one of the most abundant pelagic groups in our oceans and through their vertical migrations are known to contribute significantly to the rapid transport of carbon and nutrients to the deep sea. Therefore, any ingestion of microplastics by mesopelagic fish may adversely affect this cycling and may aid in transport of microplastics from surface waters to the deep-sea benthos. In this study microplastics were extracted from mesopelagic fish under forensic conditions and analysed for polymer type utilising micro-Fourier Transform Infrared Spectroscopy (micro-FTIR) analysis. Fish specimens were collected from depth (300–600 m) in a warm-core eddy located in the Northwest Atlantic, 1,200 km due west of Newfoundland during April and May 2015. In total, 233 fish gut contents from seven different species of mesopelagic fish were examined. An alkaline dissolution of organic materials from extracted stomach contents was performed and the solution filtered over a 0.7 μm borosilicate filter. Filters were examined for microplastics and a subsample originating from 35 fish was further analysed for polymer type through micro-FTIR analysis. Seventy-three percent of all fish contained plastics in their gut contents with Gonostoma denudatum having the highest ingestion rate (100%) followed by Serrivomer beanii (93%) and Lampanyctus macdonaldi (75%). Overall, we found a much higher occurrence of microplastic fragments, mainly polyethylene fibres, in the gut contents of mesopelagic fish than previously reported. Stomach fullness, species and the depth at which fish were caught at, were found to have no effect on the amount of microplastics found in the gut contents. However, these plastics were similar to those sampled from the surface water. Additionally, using forensic techniques we were able to highlight that fibres are a real concern rather than an artefact of airborne contaminatio

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Search for new particles in events with energetic jets and large missing transverse momentum in proton-proton collisions at root s=13 TeV

A search is presented for new particles produced at the LHC in proton-proton collisions at root s = 13 TeV, using events with energetic jets and large missing transverse momentum. The analysis is based on a data sample corresponding to an integrated luminosity of 101 fb(-1), collected in 2017-2018 with the CMS detector. Machine learning techniques are used to define separate categories for events with narrow jets from initial-state radiation and events with large-radius jets consistent with a hadronic decay of a W or Z boson. A statistical combination is made with an earlier search based on a data sample of 36 fb(-1), collected in 2016. No significant excess of events is observed with respect to the standard model background expectation determined from control samples in data. The results are interpreted in terms of limits on the branching fraction of an invisible decay of the Higgs boson, as well as constraints on simplified models of dark matter, on first-generation scalar leptoquarks decaying to quarks and neutrinos, and on models with large extra dimensions. Several of the new limits, specifically for spin-1 dark matter mediators, pseudoscalar mediators, colored mediators, and leptoquarks, are the most restrictive to date.Peer reviewe

Combined searches for the production of supersymmetric top quark partners in proton-proton collisions at root s=13 TeV

A combination of searches for top squark pair production using proton-proton collision data at a center-of-mass energy of 13 TeV at the CERN LHC, corresponding to an integrated luminosity of 137 fb(-1) collected by the CMS experiment, is presented. Signatures with at least 2 jets and large missing transverse momentum are categorized into events with 0, 1, or 2 leptons. New results for regions of parameter space where the kinematical properties of top squark pair production and top quark pair production are very similar are presented. Depending on themodel, the combined result excludes a top squarkmass up to 1325 GeV for amassless neutralino, and a neutralinomass up to 700 GeV for a top squarkmass of 1150 GeV. Top squarks with masses from 145 to 295 GeV, for neutralino masses from 0 to 100 GeV, with a mass difference between the top squark and the neutralino in a window of 30 GeV around the mass of the top quark, are excluded for the first time with CMS data. The results of theses searches are also interpreted in an alternative signal model of dark matter production via a spin-0 mediator in association with a top quark pair. Upper limits are set on the cross section for mediator particle masses of up to 420 GeV