Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats.

We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers.

Characterization of Arabidopsis FPS isozymes and FPS gene expression analysis provide insight into the biosynthesis of isoprenoid precursors in seeds

Arabidopsis thaliana contains two genes encoding farnesyl diphosphate (FPP) synthase (FPS), the prenyl diphoshate synthase that catalyzes the synthesis of FPP from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In this study, we provide evidence that the two Arabidopsis short FPS isozymes FPS1S and FPS2 localize to the cytosol. Both enzymes were expressed in E. coli, purified and biochemically characterized. Despite FPS1S and FPS2 share more than 90% amino acid sequence identity, FPS2 was found to be more efficient as a catalyst, more sensitive to the inhibitory effect of NaCl, and more resistant to thermal inactivation than FPS1S. Homology modelling for FPS1S and FPS2 and analysis of the amino acid differences between the two enzymes revealed an increase in surface polarity and a greater capacity to form surface salt bridges of FPS2 compared to FPS1S. These factors most likely account for the enhanced thermostability of FPS2. Expression analysis of FPS::GUS genes in seeds showed that FPS1 and FPS2 display complementary patterns of expression particularly at late stages of seed development, which suggests that Arabidopsis seeds have two spatially segregated sources of FPP. Functional complementation studies of the Arabidopsis fps2 knockout mutant seed phenotypes demonstrated that under normal conditions FPS1S and FPS2 are functionally interchangeable. A putative role for FPS2 in maintaining seed germination capacity under adverse environmental conditions is discussed.

LKB1 regulates polarity remodeling and adherens junction formation in the Drosophila eye.

The serine-threonine kinase LKB1 regulates cell polarity from Caenorhabditis elegans to man. Loss of lkb1 leads to a cancer predisposition, known as Peutz-Jeghers Syndrome. Biochemical analysis indicates that LKB1 can phosphorylate and activate a family of AMPK- like kinases, however, the precise contribution of these kinases to the establishment and maintenance of cell polarity is still unclear. Recent studies propose that LKB1 acts primarily through the AMP kinase to establish and/or maintain cell polarity. To determine whether this simple model of how LKB1 regulates cell polarity has relevance to complex tissues, we examined lkb1 mutants in the Drosophila eye. We show that adherens junctions expand and apical, junctional, and basolateral domains mix in lkb1 mutants. Surprisingly, we find LKB1 does not act primarily through AMPK to regulate cell polarity in the retina. Unlike lkb1 mutants, ampk retinas do not show elongated rhabdomeres or expansion of apical and junctional markers into the basolateral domain. In addition, nutrient deprivation does not reveal a more dramatic polarity phenotype in lkb1 photoreceptors. These data suggest that AMPK is not the primary target of LKB1 during eye development. Instead, we find that a number of other AMPK-like kinase, such as SIK, NUAK, Par-1, KP78a, and KP78b show phenotypes similar to weak lkb1 loss of function in the eye. These data suggest that in complex tissues, LKB1 acts on an array of targets to regulate cell polarity.

Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: A network-level analysis of selective pressures

Complexity of biological function relies on large networks of interacting molecules. However, the evolutionary properties of these networks are not fully understood. It has been shown that selective pressures depend on the position of genes in the network. We have previously shown that in the Drosophila insulin/target of rapamycin (TOR) signal transduction pathway there is a correlation between the pathway position and the strength of purifying selection, with the downstream genes being most constrained. In this study, we investigated the evolutionary dynamics of this well-characterized pathway in vertebrates. More specifically, we determined the impact of natural selection on the evolution of 72 genes of this pathway. We found that in vertebrates there is a similar gradient of selective constraint in the insulin/TOR pathway to that found in Drosophila. This feature is neither the result of a polarity in the impact of positive selection nor of a series of factors affecting selective constraint levels (gene expression level and breadth, codon bias, protein length, and connectivity). We also found that pathway genes encoding physically interacting proteins tend to evolve under similar selective constraints. The results indicate that the architecture of the vertebrate insulin/TOR pathway constrains the molecular evolution of its components. Therefore, the polarity detected in Drosophila is neither specific nor incidental of this genus. Hence, although the underlying biological mechanisms remain unclear, these may be similar in both vertebrates and Drosophila.

A developmental framework for endodermal differentiation and polarity.

The endodermis is a root cell layer common to higher plants and of fundamental importance for root function and nutrient uptake. The endodermis separates outer (peripheral) from inner (central) cell layers by virtue of its Casparian strips, precisely aligned bands of specialized wall material. Here we reveal that the membrane at the Casparian strip is a diffusional barrier between the central and peripheral regions of the plasma membrane and that it mediates attachment to the extracellular matrix. This membrane region thus functions like a tight junction in animal epithelia, although plants lack the molecular modules that establish tight junction in animals. We have also identified a pair of influx and efflux transporters that mark both central and peripheral domains of the plasma membrane. These transporters show opposite polar distributions already in meristems, but their localization becomes refined and restricted upon differentiation. This "central-peripheral" polarity coexists with the apical-basal polarity defined by PIN proteins within the same cells, but utilizes different polarity determinants. Central-peripheral polarity can be already observed in early embryogenesis, where it reveals a cellular polarity within the quiescent center precursor cell. A strict diffusion block between polar domains is common in animals, but had never been described in plants. Yet, its relevance to endodermal function is evident, as central and peripheral membranes of the endodermis face fundamentally different root compartments. Further analysis of endodermal transporter polarity and manipulation of its barrier function will greatly promote our understanding of plant nutrition and stress tolerance in roots.

Influence of sample processing on the analysis of carotenoids in maize

We performed a number of tests with the aim to develop an effective extraction method for the analysis of carotenoid content in maize seed. Mixtures of methanol–ethyl acetate (6:4, v/v) and methanol–tetrahydrofuran (1:1, v/v) were the most effective solvent systems for carotenoid extraction from maize endosperm under the conditions assayed. In addition, we also addressed sample preparation prior to the analysis of carotenoids by liquid chromatography (LC). The LC response of extracted carotenoids and standards in several solvents was evaluated and results were related to the degree of solubility of these pigments. Three key factors were found to be important when selecting a suitable injection solvent: compatibility between the mobile phase and injection solvent, carotenoid polarity and content in the matrix.

Maladie des griffes du chat et autres bartonelloses [Cat scratch disease and other human infections caused by Bartonella species].

The different Bartonella species can cause various human infections such as cat scratch disease, chronic bacteremia (homeless patient with nonspecific symptom), endocarditis, bacillary angiomatosis, peliosis, and Carrion's disease. Diagnostic approaches include serology, culture and molecular approaches. PCR is especially useful on lymph nodes biopsies from patients with cat-scratch disease and on valvular samples taken from culture-negative endocarditis. Serology exhibits a very high sensitivity in the latter situation. The treatment should be chosen according to the clinical presentation.

An update on EMU sovereign yield spread drivers in times of crisis: A panel data analysis

We empirically investigate the determinants of EMU sovereign bond yield spreads with respect to the German bund. Using panel data techniques, we examine the role of a wide set of potential drivers. To our knowledge, this paper presents one of the most exhaustive compilations of the variables used in the literature to study the behaviour of sovereign yield spreads and, in particular, to gauge the effect on these spreads of changes in market sentiment and risk aversion. We use a sample of both central and peripheral countries from January 1999 to December 2012 and assess whether there were significant changes after the outbreak of the euro area debt crisis. Our results suggest that the rise in sovereign risk in central countries can only be partially explained by the evolution of local macroeconomic variables in those countries.

An update on EMU sovereign yield spread drivers in times of crisis: A panel data analysis

We empirically investigate the determinants of EMU sovereign bond yield spreads with respect to the German bund. Using panel data techniques, we examine the role of a wide set of potential drivers. To our knowledge, this paper presents one of the most exhaustive compilations of the variables used in the literature to study the behaviour of sovereign yield spreads and, in particular, to gauge the effect on these spreads of changes in market sentiment and risk aversion. We use a sample of both central and peripheral countries from January 1999 to December 2012 and assess whether there were significant changes after the outbreak of the euro area debt crisis. Our results suggest that the rise in sovereign risk in central countries can only be partially explained by the evolution of local macroeconomic variables in those countries.

Forecasting financial weather - can we foresee market sentiment? Spectrum of stock price behavior - NYSE case study

The desire to create a statistical or mathematical model, which would allow predicting the future changes in stock prices, was born many years ago. Economists and mathematicians are trying to solve this task by applying statistical analysis and physical laws, but there are still no satisfactory results. The main reason for this is that a stock exchange is a non-stationary, unstable and complex system, which is influenced by many factors. In this thesis the New York Stock Exchange was considered as the system to be explored. A topological analysis, basic statistical tools and singular value decomposition were conducted for understanding the behavior of the market. Two methods for normalization of initial daily closure prices by Dow Jones and S&P500 were introduced and applied for further analysis. As a result, some unexpected features were identified, such as a shape of distribution of correlation matrix, a bulk of which is shifted to the right hand side with respect to zero. Also non-ergodicity of NYSE was confirmed graphically. It was shown, that singular vectors differ from each other by a constant factor. There are for certain results no clear conclusions from this work, but it creates a good basis for the further analysis of market topology.

Comparative sequence analysis of the P-, M- and L-coding region of the measles virus CAM-70 live attenuated vaccine strain

Measles virus is a highly contagious agent which causes a major health problem in developing countries. The viral genomic RNA is single-stranded, nonsegmented and of negative polarity. Many live attenuated vaccines for measles virus have been developed using either the prototype Edmonston strain or other locally isolated measles strains. Despite the diverse geographic origins of the vaccine viruses and the different attenuation methods used, there was remarkable sequence similarity of H, F and N genes among all vaccine strains. CAM-70 is a Japanese measles attenuated vaccine strain widely used in Brazilian children and produced by Bio-Manguinhos since 1982. Previous studies have characterized this vaccine biologically and genomically. Nevertheless, only the F, H and N genes have been sequenced. In the present study we have sequenced the remaining P, M and L genes (approximately 1.6, 1.4 and 6.5 kb, respectively) to complete the genomic characterization of CAM-70 and to assess the extent of genetic relationship between CAM-70 and other current vaccines. These genes were amplified using long-range or standard RT-PCR techniques, and the cDNA was cloned and automatically sequenced using the dideoxy chain-termination method. The sequence analysis comparing previously sequenced genotype A strains with the CAM-70 Bio-Manguinhos strain showed a low divergence among them. However, the CAM-70 strains (CAM-70 Bio-Manguinhos and a recently sequenced CAM-70 submaster seed strain) were assigned to a specific group by phylogenetic analysis using the neighbor-joining method. Information about our product at the genomic level is important for monitoring vaccination campaigns and for future studies of measles virus attenuation.

PERFORMANCE ANALYSIS OF A TACTICAL ASSET ALLOCATION – Evidence from the Black–Litterman model based fixed income portfolio

Over time the demand for quantitative portfolio management has increased among financial institutions but there is still a lack of practical tools. In 2008 EDHEC Risk and Asset Management Research Centre conducted a survey of European investment practices. It revealed that the majority of asset or fund management companies, pension funds and institutional investors do not use more sophisticated models to compensate the flaws of the Markowitz mean-variance portfolio optimization. Furthermore, tactical asset allocation managers employ a variety of methods to estimate return and risk of assets, but also need sophisticated portfolio management models to outperform their benchmarks. Recent development in portfolio management suggests that new innovations are slowly gaining ground, but still need to be studied carefully. This thesis tries to provide a practical tactical asset allocation (TAA) application to the Black–Litterman (B–L) approach and unbiased evaluation of B–L models’ qualities. Mean-variance framework, issues related to asset allocation decisions and return forecasting are examined carefully to uncover issues effecting active portfolio management. European fixed income data is employed in an empirical study that tries to reveal whether a B–L model based TAA portfolio is able outperform its strategic benchmark. The tactical asset allocation utilizes Vector Autoregressive (VAR) model to create return forecasts from lagged values of asset classes as well as economic variables. Sample data (31.12.1999–31.12.2012) is divided into two. In-sample data is used for calibrating a strategic portfolio and the out-of-sample period is for testing the tactical portfolio against the strategic benchmark. Results show that B–L model based tactical asset allocation outperforms the benchmark portfolio in terms of risk-adjusted return and mean excess return. The VAR-model is able to pick up the change in investor sentiment and the B–L model adjusts portfolio weights in a controlled manner. TAA portfolio shows promise especially in moderately shifting allocation to more risky assets while market is turning bullish, but without overweighting investments with high beta. Based on findings in thesis, Black–Litterman model offers a good platform for active asset managers to quantify their views on investments and implement their strategies. B–L model shows potential and offers interesting research avenues. However, success of tactical asset allocation is still highly dependent on the quality of input estimates.

De l’aller-retour au point de non-retour : Étude comparative de l’expérience interculturelle et du sentiment d’épuisement culturel des expatriés occidentaux en Inde

Afin de saisir le contexte du phénomène de l’expatriation d’Occidentaux en Inde, nous relevons d’abord certains traits de la modernité occidentale, tels le sentiment d’aliénation, le tournant subjectiviste, la globalisation et les principaux mythes-modèles de l’Inde qui circulent dans les pays occidentaux et donnent naissance aux projets d’expatriation. Une approche expérientielle facilite la compréhension de l’expatriation telle qu’elle est vécue par les acteurs. La collecte de données ethnographiques permet de saisir ces expériences à partir de récits recueillis dans trois zones frontière : 1) à Rishikesh, auprès d’expatriés spirituels; 2) à Calcutta, auprès d’expatriés humanitaires; 3) à Goa, auprès d’expatriés hédonistes-expressifs cherchant à améliorer leur style de vie. Ces données ethnographiques sont présentées dans trois chapitres distincts. Un chapitre comparatif met ensuite en relief quelques points de convergence dans l’expérience des expatriés, soit l’insertion locale au sein de communautés spécifiques, fortement associées à des mythes-modèles de l’Inde; le renouveau identitaire découlant de l’expérience interculturelle; et finalement, l’impact du transnationalisme sur la consolidation du malaise face à la modernité. La discussion théorique présente les solutions mises en branle par les expatriés pour tempérer leur malaise par rapport à l’Occident, soit : 1) l’engagement en profondeur dans un mode de vie permettant de se réaliser selon ses propres aspirations; 2) le regroupement par affinités et l’adoption d’un rôle social clair; 3) l’affranchissement de la pression sociale et l’adoption de pratiques transnationales permettant de préserver une continuité affective avec les proches tout en endossant un statut d’étranger. L’étude révèle aussi qu’on ne peut faire abstraction de l’histoire des relations de l’Occident avec le sous-continent pour comprendre les relations interculturelles des expatriés occidentaux avec les Indiens locaux. Enfin, les privilèges socioéconomiques des Occidentaux en Inde sont clairement identifiés comme étant une condition essentielle de leurs projets d’expatriation, ceux-ci étant néanmoins motivés principalement par un sentiment d’épuisement culturel face à l’Occident et à son mode de vie. Faisant suite à l’analyse des points de vue critiques sur la modernité (renforcés par l’expérience d’altérité), la thèse s’achève sur l’évocation de quelques pistes de recherche pour une anthropologie de l’Occident, tout en interrogeant, implicitement, le projet anthropologique.

Contribution du cortex pariétal postérieur au contrôle de la locomotion sous guidage visuel chez le chat

La vision fournit des informations essentielles sur la surface de marche, ainsi que sur la taille, la forme et la position d’obstacles potentiels dans notre environnement. Dans le cas d’un prédateur, la vision fournit également des informations sur la vitesse d’une proie potentielle. Les mécanismes neuronaux impliqués dans l’exécution des modifications de la marche sous guidage visuel sont relativement bien connus, mais ceux impliqués dans la planification de ces modifications de la marche sont peu étudiés. Le cortex pariétal postérieur (CPP) semble être un candidat approprié si l’on considère les propriétés du CPP lors des mouvements d’atteinte vers une cible. Le but des présents travaux est de déterminer la contribution du CPP au contrôle de la locomotion sous guidage visuel. La première étude présentée dans cette thèse a pour hypothèse que le CPP du chat est impliqué dans la planification du placement précis du pied lors des modifications volontaires de la marche. Nous avons entraîné les animaux à enjamber des obstacles en mouvement attachés à la ceinture d’un tapis roulant. Afin d’augmenter la nécessité d’intégrer les informations visuelles et proprioceptives, nous avons dissocié la vitesse des obstacles de celle du tapis roulant. Nous avons observé que plus la vision devient critique pour la tâche, plus les déficits sont importants. Notre analyse démontre que ceux-ci résultent d’un placement inapproprié du pied dans le cycle de marche précédant l’enjambement de l’obstacle. Ceci suggère que le CPP est impliqué dans la planification du placement précis du pied pendant la locomotion sous guidage visuel. La vision directe est disponible lors de la modification de l’activité des membres antérieurs, mais n’est plus disponible lorsque l’obstacle passe sous le corps. Par conséquent, la modification de l’activité des membres postérieurs doit être basée sur l’information gardée en mémoire et coordonnée avec celle des membres antérieurs. Notre deuxième étude a pour but de caractériser les mécanismes neuronaux responsables de cette coordination. Nous avons proposé que le CPP soit impliqué dans la coordination des membres antérieurs et postérieurs lors de l’enjambement d’obstacles. Pour tester cette hypothèse, nous avons enregistré l’activité de neurones de l’aire 5 pendant la même tâche. Nous avons découvert deux populations: une qui décharge lors du passage de l’obstacle entre les membres antérieurs et postérieurs et une autre qui décharge lors du passage de l’obstacle par les membres postérieurs. Dans la tâche de dissociation visuelle, la décharge est modifiée en fonction du temps de passage de l’obstacle sous le corps et reflète la modification du couplage entre les membres lors du changement dans la stratégie d’enjambement. De plus, ces mêmes neurones maintiennent une décharge soutenue lorsqu’un obstacle fixe se trouve entre les membres antérieurs et postérieurs ou les deux membres postérieurs (limite testée : 1-2min). Ces neurones pourraient être responsables de l’emmagasinage à plus long terme des caractéristiques d’un obstacle pour le guidage des mouvements des membres postérieurs. Nos résultats suggèrent que le CPP est impliqué dans l’intégration des informations visuelles et proprioceptives pour la planification du placement précis du pied devant un obstacle. Le patron de décharge de nos populations neuronales suggère qu’il encode également l’information temporelle et spatiale concernant la vitesse et la position de l’obstacle afin de coordonner l’activité des quatre membres pendant la tâche. Finalement, nous proposons qu’une des fonctions du CPP soit d’estimer la position des membres par rapport à l’obstacle en mouvement.

Le sentiment de surqualification chez les diplômés

La majorité des auteurs qui s’intéressent à la surqualification la comprennent et l’analysent habituellement comme une situation de suréducation ou de déclassement scolaire. Ce mémoire fait l’hypothèse que le sens qu’accordent les individus au fait d’être surqualifié est beaucoup plus large. Même s’il est raisonnable de croire que la majorité des diplômés espèrent pouvoir obtenir un emploi à la hauteur de leur diplôme, le fait de définir le sentiment de surqualification de façon substantialiste, en ne considérant que le niveau de diplôme obtenu par le travailleur et exigé par l’employeur, semble quelque peu réducteur. Le sentiment de surqualification naît d’un jugement social : il est empirique, contextualisé et dynamique. À la croisée des mesures objectives et subjectives, nous explorons ainsi les facteurs explicatifs du sentiment de surqualification chez les diplômés canadiens à partir d’une analyse statistique des déterminants de ce sentiment dans les premières années qui suivent l’obtention de leur diplôme d’études postsecondaires. Nous montrons d’abord que l’utilisation de compétences en emploi et le lien entre le diplôme obtenu et l’emploi expliquent bien plus le sentiment de surqualification que la suréducation objective. Nous montrons aussi que l’impact du niveau d’utilisation d’une compétence donnée sur le sentiment de surqualification varie substantiellement selon le domaine d’études du diplômé et la nature de cette compétence.