Des mutations germinales dans les gènes majeurs du cancer du sein BRCA1 et BRCA2 sont responsables de la maladie chez les patientes cumulant histoire familiale et apparition du cancer à un jeune âge. Environ 15% des femmes testées pour les mutations de BRCA1 et BRCA2 sont porteuses d’une mutation clairement pathogénique dans un des deux gènes. Cependant, des variants de signification clinique incertaine (VUS pour "variants of uncertain clinical significance") sont détectés dans 5% à 15% des cas testés. Pour évaluer la signification clinique des VUS, le Breast cancer Infomation Core (BIC) a développé un modèle Bayésien intégré, basé sur des données d'observations. Align-GVGD, un algorithme d'évaluation des substitutions faux-sens basé sur l'histoire évolutionnaire de la protéine fournit la probabilité a priori du modèle. Cependant, lorsqu'une substitution silencieuse est détectée, elle sera jugée comme neutre par l'évaluation in silico. Pourtant, une mutation au niveau de l'ARNm peut perturber la mécanique de l'épissage, par deux moyens principaux: endommagement des sites sauvages d'épissage, ou la création de sites exoniques d'épissage de novo. Notre premier objectif est de rassembler les variants déjà publiés, de les re-analyser avec le modèle d'évaluation intégrée. Nous voulons extraire le plus de variants publiés premièrement sous le statut de VUS vers un statut plus informatif, avec des recommandations cliniques associées. Par la suite, nous voulons étendre le modèle pour évaluer plus de variants, plus précisément, en intégrant l'évaluation des perturbations de l'épissage. Finalement, nous serons capable de présenter et de fournir ces informations librement sur Internet, via une interface web populaire, une Leiden Open Variation Database (LOVD) / Germline mutations in major breast cancer susceptibility genes BRCA1 and BRCA2 are responsible for the disease for high-risk patients (patients with early onset and familial history of breast cancer). Around 15% of screened women for BRCA1 and BRCA2 mutations carry one clearly pathogenic mutation in one of those two genes. However, variants of uncertain clinical significance (VUS) are detected in 5% to 15% of tested patients. To assess clinical significance of VUS, the Breast cancer Information Core (BIC) has developed a Bayesian integrated model, based on observational data. Align-GVGD, an algorithm evaluating damage of missense substitutions based on the evolutionary history of the protein, is providing the prior probability of the model. However, whenever a silent substitution arise, it is firstly treated as neutral by the in silico assessment. Indeed, a mutation at the mRNA level can disrupt the splicing machinery by two main means: damaging wild-type splice sites, or creating exonic de novo splice sites. Our first goal is to be a central repository of already published variants, to re-analyze them using the unified integrated evaluation model. We would like to extract the most variants from the original published status of VUS to a more informative status, with associated clinical recommendations. Then we would like to extend the model to be able to evaluate more variants more precisely by adding the splicing damages assessment in the integrated evaluation. In the end, we will be able to provide these informations freely on Internet, via a widely use web interface, a Leiden Open Variation Database (LOVD)

O Transtorno de Déficit de Atenção e Hiperatividade (TDAH) é a doença do neurodesenvolvimento mais comum na infância, afetando cerca de 5,8% de crianças e adolescentes no mundo. Muitos estudos vêm tentando investigar a suscetibilidade genética em TDAH, mas sem muito sucesso. Este estudo teve como objetivo analisar variantes raras e comuns contribuindo para a arquitetura genética do TDAH. Foram gerados os primeiros dados de exoma de TDAH de 30 trios brasileiros em que o filho foi diagnosticado com TDAH esporádico. Foram analisados tanto variações de único nucleotídeo (ou SNVs, single-nucleotide variants) quanto variações de número de cópias (ou CNVs, copy-number variants), tanto nesses trios quanto em outros conjuntos de dados, incluindo uma amostra brasileira de 503 crianças/adolescentes controles, bem como resultados previamente publicados em quatro estudos com variação de número de cópias e uma meta-análise de estudos de associação ao longo do genoma. Tanto os trios quanto os controles fazem parte da Coorte de Escolares de Alto Risco para o desenvolvimento de Psicopatologia e Resiliência na Infância do Instituto Nacional de Psiquiatria do Desenvolvimento (INPD). Os resultados de trios brasileiros mostraram três padrões marcantes: casos com variações herdadas e somente SNVs de novo ou CNVs de novo, e casos somente com variações herdadas. Embora o tamanho amostral seja pequeno, pudemos ver que diferentes comorbidades são mais frequentes em casos somente com variações herdadas. Após explorarmos a composição de variações nos probandos brasileiros, foram selecionados genes recorrentes entre amostras do nosso estudo ou em bancos de dados públicos. Além disso, usando somente genes expressos no cérebro (amostras pós-mortem dos projetos Brain Atlas e Genotype-Tissue Expression), construímos uma rede de interação proteína-proteína \"in silico\" com interações físicas confirmadas por pelo menos duas fontes. Análises topológicas e funcionais dos genes da rede mostraram genes relacionados a sinapse, adesão celular, vias glutamatérgicas e serotonérgicas, o que confirma achados de trabalhos independentes na literatura indicando ainda novos genes e variantes genéticas nessas vias. / Attention-Deficit/Hyperactivity Disorder (ADHD) is the most common neuro-developmental disorder in children, affecting 5.8% of children and adolescents in the world. Many studies have attempted to investigate the genetic susceptibility of ADHD without much success. The present study aimed to analyze rare and common variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios where the children were diagnosed with sporadic ADHD. We analyzed both single-nucleotide variants (SNVs) and copy-number variants (CNVs) in these trios and across multiple datasets, including a Brazilian sample of 503 children/adolescent controls from the High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of four CNV studies of ADHD involving children/adolescent Caucasian samples. The results from the Brazilian trios showed 3 major patterns: cases with inherited variations and de novo SNVs or de novo CNVs and cases with only inherited variations. Although the sample size is small, we could see that various comorbidities are more frequent in cases with only inherited variants. After exploring the rare variant composition in our 30 cases we selected genes with variations (SNVs or located in CNV regions) in our trio analysis that are recurrent in the families analyzed or in public data sets. Moreover, using only genes expressed in brain (post-mortem samples from Brain Atlas and The Genotype-Tissue Expression project), we constructed an in silico protein-protein interaction (PPI) network, with physical interactions confirmed by at least two sources. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

Detta självständiga arbete fokuserar på att utforska hur gymnasieelever som läser ett nationellt program med musik som tillval uppfattar ensemblespel. Syftet med arbetet är att bidra med kunskap om hur dessa elever ser på och upplever ensemblespel. För att besvara frågeställningarna användes en kvalitativ metod med fokusgruppsintervjuer för att samla in data från ett homogent urval av elever. Resultatet som besvarar frågeställningarna visar att eleverna beskriver ensemblespel som en möjlighet att utveckla färdigheter i social interaktion, samarbete och ledarskap. Eftersom musik inte är elevernas huvudämne har de sällan samma tid för övning och musikalisk ambition som elever med musik som huvudämne har, vilket gör att en stark gruppdynamik värdesätts högre än speltekniska färdigheter. Det förekommer även gruppdynamiska svårigheter, och resultatet visar på att processen för att ta ett demokratiskt beslut ibland är en orsak till stress inom gruppen. Trots dessa svårigheter är elevernas inställning till ensemblespel positiv och ensemble ses som ett roligt och engagerande komplement till den annars teoretiska skolveckan. Resultatet av detta arbete ger en större inblick i elevernas syn på ensembleundervisning, vilket kan hjälpa musikpedagoger som vill förbättra kvaliteten och tillgängligheten för musikutbildning i gymnasieskolor. / This study focuses on exploring how high school students who are studying a national program with music as an optional subject perceive ensemble classes. The aim of this research is to contribute with knowledge about how these students view and experience ensemble classes. The study employed a qualitative approach, using focus group interviews to collect data from a homogenous sample of students. Findings show that ensemble classes provide the students with opportunities for developing skills in social interaction and teamwork as well as leadership. Since music isn’t their primary subject, they rarely have the same musical competence or time for practice as students with music as primary subject do, which is why a strong group dynamic is highly valued. However, the students also expressed difficulties about said group dynamic, finding the process of a democratic decision to sometimes be a cause of distress within the group. Despite these difficulties the students view ensemble classes in a positive light, seeing them as a fun and engaging complement to the otherwise theoretical school week. The findings of this study focus of the students’ perception of ensemble, which can benefit music educators who seek to improve the quality and accessibility of music education in high schools.

No description available.

Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics. Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper II on generating strand specific RNA-seq libraries. Paper III and IV deal with current biological issues. In paper III, whole exomes of cancer patients undergoing chemotherapy are sequenced and their genetic variants associ- ated to their toxicity induced adverse drug reactions. In paper IV a comprehensive view of the gene expression of the endometrium is assessed from two time points of the menstrual cycle. Together these papers show relevant aspects of contemporary sequencing technologies and how it can be applied to diverse biological topics. / <p>QC 20160329</p>

Les cystéinyl-leucotriènes (cysLTs) sont des médiateurs lipidiques pro-inflammatoires impliqués dans l'asthme, liant trois récepteurs couplés aux protéines G: CysLT[indice inférieur 1], CysLT[indice inférieur 2] et GPR99. Des polymorphismes de deux de ces récepteurs, CysLT[indice inférieur 1]-G300S et CysLT[indice inférieur 2]-M201V, ont été fortement associés à l’atopie, une prédisposition aux allergies, alors que le polymorphisme CysLT[indice inférieur 1]-I206S n’y est pas significativement associé. Il a été montré précédemment que le variant CysLT[indice inférieur 2]-M201V avait une signalisation diminuée. L'objectif du projet était d'étudier la signalisation cellulaire des variants CysLT[indice inférieur 1]-G300S et CysLT[indice inférieur 1]-I206S, ainsi que l’interaction du variant CysLT[indice inférieur 1]-G300S avec le récepteur CysLT[indice inférieur 2]-M201V. La lignée cellulaire HEK-293 a été transfectée avec les ADNs plasmidiques codant pour des récepteurs de type sauvage et mutants. L’expression de surface des récepteurs a été vérifiée par cytométrie en flux. La production d’inositol phosphates (IPs) et la transactivation des promoteurs de l’IL-8 et de l’IL-13 ont été mesurées par essai IP-1 et essai luciférase, respectivement, en réponse au LTD[indice inférieur 4] et LTC[indice inférieur 4]. Ensuite, la phosphorylation de principaux effecteurs de signalisation (Erk1/2, p65, p38 et c-Jun) suite à l’activation des récepteurs par le LTD[indice inférieur 4], a été évaluée par immunobuvardage Western. Enfin, l’interaction entre les récepteurs a été étudiée par des expériences de BRET (Bioluminescence Resonance Energy Transfer) et BiFC (Bimolecular Fluorescent Complementation), en plus d’expériences de type fonctionnel en co-expression. L’expression de surface des récepteurs mutants et de type sauvage est équivalente. Le variant CysLT[indice inférieur 1]-G300S induit une plus forte production d’IPs et une plus grande transactivation des promoteurs de l’IL-8 et de l'IL-13 que le récepteur de type sauvage. De plus, la phosphorylation de Erk1/2 est également augmentée par l’activation de ce variant. Par contre, le récepteur CysLT[indice inférieur 1]-I206S ne montre pas de différence significative dans sa transduction de signal. La co-expression des récepteurs CysLT[indice inférieur 1]-G300S et CysLT[indice inférieur 2]-M201V n’affecte pas leur expression de surface, mais résulte en une faible transactivation du promoteur de l’IL-8 et une production réduite d’IPs en réponse au LTD[indice inférieur 4]. Enfin, les récepteurs ont la capacité d’interagir et de dimériser entre eux. En conclusion, ces résultats suggèrent que le variant CysLT[indice inférieur 1]-G300S induit une plus forte réponse que le récepteur de type sauvage. Cependant, bien qu’il puisse dimériser et interagir avec le variant CysLT[indice inférieur 2]-M201V, ce dernier domine la réponse combinée lorsqu’il est co-exprimé avec le variant CysLT[indice inférieur 1]-G300S.

This thesis presents a design and implementation of a long-range communication subsystem for a UAV and a ground control station. The subsystem is a low-cost alternative employing a line of sight, local communication network for optimal communications between a low-altitude UAV and a portable ground control station. In this thesis, real world experiments are conducted to model the time-variant wireless channel between a low-altitude micro-UAV and a portable ground control station operating in an urban environment. The large-scale and small-scale fading coefficients are calculated and analyzed for this dynamic channel. The channel properties, along with the fading distribution parameters, are computed and analyzed for two most popular antenna configurations for UAV systems (Yagi to omnidirectional and omnidirectional to omnidirectional). For the Yagi-to-omnidirectional link, the effects of three major impacting factors i.e. propagation distance, antenna gains in specific spherical angles and polarization mismatch factor on the overall fading distribution is investigated. Through regression analysis, a multiple-regression model is derived that estimates the instantaneous fading parameter, given these channel conditions. For this model, a modified particle-swarm optimization algorithm is designed and implemented to estimate the underlying model coefficients, given the instantaneous fading information. The implementation of this algorithm, along with the regression model, demonstrates that a sufficient approximation of the fading parameter can be provided for any given wireless channel when the impacting factors and instantaneous fading information is available. / February 2016

Dans le noyau des cellules eucaryotes, l'ADN est compacté sous forme de chromosome, ultime forme de compaction. La chromatine est le second niveau d'organisation de l'ADN. C'est une structure variable et dynamique elle-même issue de la compaction de chapelets de nucléosomes. Le nucléosome est donc l'unité de base de la chromatine. Cette structure nucléoprotéique sert de barrière empêchant l'accès de complexes protéiques à l'ADN. Différents facteurs protéiques remodèlent la chromatine, modifient les histones de manière covalente, remplacent les histones canoniques par des variants d'histones ou participent à l'assemblage des nucléosomes. Lors de ce travail de thèse, nous avons travaillé sur deux variants : macroH2A et H2A.Bbd. Ces variants s'incorporent dans une particule nucléosomale et remplacent l'histone canonique H2A. Leur présence crée un nucléosome possédant une structure, une organisation et des caractéristiques particulières. Ainsi la présence de l'un ou l'autre de ces deux variants au sein d'une particule nucléosomale inhibent l'action des facteurs de remodelage SWI/SNF et ACF. Par contre, le variant H2A.Bbd permet de dissocier les différents mécanismes d'action du complexe SWI/SNF. Des expériences de transcription in vitro nous permettent de montrer que le variant macroH2A inhibe la transcription grâce à son domaine macro tandis que le variant H2A.Bbd active la transcription. De la même façon nous montrons que la présence de macroH2A inhibe l'acétylation des histones alors que H2A.Bbd stimule ce phénomène. Le variant H2A.Bbd est associé à des zones actives en transcription, le variant macroH2A à des zones inactives en transcription.

Trypanosoma brucei is a protozoan parasite that is the causative agent of sleeping sickness in sub-Saharan Africa. T. brucei has a complex life cycle involving passage between a mammalian host and the tsetse fly. The parasite evades the mammalian immune system via expression of Variant Surface Glycoprotein (VSG) on the cell surface. VSG genes are expressed at telomeric expression sites and at these sites are a number of Expression Site Associated Genes (ESAGs). One unusual ESAG, ESAG9, is developmentally regulated: RNA for these genes accumulates during the transition from slender to stumpy cells in the mammalian bloodstream and cellassociated protein is only detected transiently in stumpy and differentiating cells. Transgenic cell lines were generated which ectopically express one or more members of the ESAG9 gene family. Biochemical and cytological analyses using these cell lines indicated that some members of this family are glycosylated and GPI-anchored, and also that one gene, ESAG9-K69, is secreted. ESAG9-K69 is also secreted by wild-type stumpy parasites. In vivo experiments with tsetse flies did not conclusively show whether ESAG9 proteins play a role in the establishment of a tsetse fly mid-gut infection by transgenic trypanosomes. However, In vivo and ex vivo experiments using the mouse model of trypanosomiasis indicated that expression of ESAG9 proteins may alter parasitaemia in the mouse and results in a significant decrease in the proportion of CD4+ T cells in the mouse spleen.

Serpins are a unique breed of proteins due to their enzymatic mechanism. Two systems were closely monitored during fluorescent binding studies, the ACT-CHY along with the AT:TRY interaction. Four different conformational variants of each system were studied including the native, cleaved, latent and complex forms. Three different fluorescent dyes were used to identify the conformations including ANS, TNS, and bis-ANS. SI studies and protease assays utilizing both Suc-AAPF-pNA and L-BAPNA were instrumental in determining conformations along with gel electrophoresis studies. The hydrophobic dyes bound to the different serpins with varying KD and ΔFmax due to structural variations among the conformers and the complex. Both TNS and bis-ANS gave higher ΔFmax values than ANS. Bis-ANS gave significantly higher ΔFmax values for the ACT:CHY than the other conformations, while also exhibiting relatively low KD value. KD values for the bis-ANS complexes are relatively low when compared to other fluorophores. Bis-ANS is more specific for the AT system than either TNS or ANS. Bis-ANS displays a ΔFmax of 36 fold for the ACT:CHY complex, while TNS displays a 27 fold increase for AT:TRY system. Modulation studies using bis-ANS to alter the kinetics of latent ACT formation proved unsuccessful, suggesting that fluorescent dyes have little, if any effect on serpin variant formation.