Analysis of epistasis in linked regions in the Irish study of high-density schizophrenia families

Epistasis may be important in the etiology of schizophrenia. Analysis of epistasis has been important in the positional cloning of a gene involved in the etiology of type II diabetes mellitus. We investigated the importance of epistasis among six linked regions in 268 multiplex pedigrees in the Irish Study of High-Density Schizophrenia Families (ISHDSF) by computing pairwise correlations between nonparametric linkage scores for narrow, intermediate, and broad diagnostic definitions. The linked regions were on chromosomes 2, 4, 5, 6, 8, and 10. No correlation reached our a priori level of statistical significance. Using this statistical approach, we did not find evidence of important epistatic effects among these six regions in the ISHDSF.

Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases.

Using numerical simulations, we compare properties of knotted DNA molecules that are either torsionally relaxed or supercoiled. We observe that DNA supercoiling tightens knotted portions of DNA molecules and accentuates the difference in curvature between knotted and unknotted regions. The increased curvature of knotted regions is expected to make them preferential substrates of type IIA topoisomerases because various earlier experiments have concluded that type IIA DNA topoisomerases preferentially interact with highly curved DNA regions. The supercoiling-induced tightening of DNA knots observed here shows that torsional tension in DNA may serve to expose DNA knots to the unknotting action of type IIA topoisomerases, and thus explains how these topoisomerases could maintain a low knotting equilibrium in vivo, even for long DNA molecules.

Analyse de la localisation génomique et identification de nouvelles fonctions des sous-unités Rpb4/Rpb7 de l’ARN polymérase II et des facteurs TFIIF, TFIIS et UBR5

Grâce à un grand nombre d’études biochimiques, génétiques et structurales effectuées dans les dernières années, des avancements considérables ont été réalisés et une nouvelle vision du processus par lequel la machinerie transcriptionnelle de l’ARN polymérase II (Pol II) décode l’information génétique a émergé. De nouveaux indices ont été apportés sur la diversité des mécanismes de régulation de la transcription, ainsi que sur le rôle des facteurs généraux de transcription (GTFs) dans cette diversification. Les travaux présentés dans cette thèse amènent de nouvelles connaissances sur le rôle des GTFs humains dans la régulation des différentes étapes de la transcription. Dans la première partie de la thèse, nous avons analysé la fonction de la Pol II et des GTFs humains, en examinant de façon systématique leur localisation génomique. Les patrons obtenus par immunoprécipitation de la chromatine (ChIP) des versions de GTFs portant une étiquette TAP (Tandem-Affinity Purification) indiquent de nouvelles fonctions in vivo pour certains composants de cette machinerie et pour des éléments structuraux de la Pol II. Nos résultats suggèrent que TFIIF et l’hétérodimère Rpb4–Rpb7 ont une fonction spécifique pendant l’étape d’élongation transcriptionnelle in vivo. De plus, notre étude amène une première image globale de la fonction des GTFs pendant la réaction transcriptionnelle dans des cellules mammifères vivantes. Deuxièmement, nous avons identifié une nouvelle fonction de TFIIS dans la régulation de CDK9, la sous-unité kinase du facteur P-TEFb (Positive Transcription Elongation Factor b). Nous avons identifié deux nouveaux partenaires d’interaction pour TFIIS, soit CDK9 et la E3 ubiquitine ligase UBR5. Nous montrons que UBR5 catalyse l’ubiquitination de CDK9 in vitro. De plus, la polyubiquitination de CDK9 dans des cellules humaines est dépendante de UBR5 et TFIIS. Nous montrons aussi que UBR5, CDK9 and TFIIS co-localisent le long du gène  fibrinogen (FBG) et que la surexpression de TFIIS augmente les niveaux d’occupation par CDK9 de régions spécifiques de ce gène, de façon dépendante de UBR5. Nous proposons que TFIIS a une nouvelle fonction dans la transition entre les étapes d’initiation et d’élongation transcriptionnelle, en régulant la stabilité des complexes CDK9-Pol II pendant les étapes précoces de la transcription.

Alliance Politics in Hybrid Regimes : Political Stability and Instability since World War II

Cette thèse étudie la stabilité et l’instabilité politique des régimes hybrides. Elle pose la question suivante : dans quelles conditions l’autorité des élites au pouvoir est-elle reconnue ou contestée? Notre réponse s’articule en lien avec le caractère inclusif ou exclusif de la coalition dirigeante : c’est-à-dire, l’alliance stratégique des élites dirigeantes avec les groupes sociaux dominants. L’inclusion de ces derniers favorise le consentement et la stabilité; leur exclusion entraîne l’affrontement et l’instabilité politique. Sa composition dépend (i) du degré de violence organisée extra-légale et (ii) du degré de pénétration de l’État sur le territoire et dans l’économie. La première variable permet d’identifier quel groupe social au sein de l’État (militaires) ou du régime (partis d’opposition) est dominant et influence les formes de communication politique avec les élites dirigeantes. La deuxième variable permet d’identifier quel groupe social au sein de l’État (fonctionnaires) ou de la société (chefs locaux) est dominant et oriente les rapports entre les régions et le pouvoir central. L’apport de la recherche est d’approfondir notre compréhension des institutions politiques dans les régimes hybrides en mettant l’accent sur l’identité des groupes sociaux dominants dans un contexte donné. La thèse propose un modèle simple, flexible et original permettant d’appréhender des relations causales autrement contre-intuitives. En ce sens, la stabilité politique est également possible dans un pays où l’État est faible et/ou aux prises avec des mouvements de rébellion; et l’instabilité dans un contexte inverse. Tout dépend de la composition de la coalition dirigeante. Afin d’illustrer les liens logiques formulés et d’exposer les nuances de notre théorie, nous employons une analyse historique comparative de la coalition dirigeante en Malaisie (1957-2010), en Indonésie (1945-1998), au Sénégal (1960-2010) et au Paraguay (1945-2008). La principale conclusion est que les deux variables sont incontournables. L’une sans l’autre offre nécessairement une explication incomplète des alliances politiques qui forgent les conditions de stabilité et d'instabilité dans les régimes hybrides.

Teleconnections between Ethiopian summer rainfall and sea surface temperature: part II. Seasonal forecasting

A seasonal forecasting system that is capable of skilfully predicting rainfall totals on a regional scale would be of great value to Ethiopia. Here, we describe how a statistical model can exploit the teleconnections described in part 1 of this pair of papers to develop such a system. We show that, in most cases, the predictors selected objectively by the statistical model can be interpreted in the light of physical teleconnections with Ethiopian rainfall, and discuss why, in some cases, unexpected regions are chosen as predictors. We show that the forecast has skill in all parts of Ethiopia, and argue that this method could provide the basis of an operational seasonal forecasting system for Ethiopia.

Predictability and skill of boreal winter forecasts made with the ECMWF Seasonal Forecasting System II

The performance of boreal winter forecasts made with the European Centre for Medium-Range Weather Forecasts (ECMWF) System 11 Seasonal Forecasting System is investigated through analyses of ensemble hindcasts for the period 1987-2001. The predictability, or signal-to-noise ratio, associated with the forecasts, and the forecast skill are examined. On average, forecasts of 500 hPa geopotential height (GPH) have skill in most of the Tropics and in a few regions of the extratropics. There is broad, but not perfect, agreement between regions of high predictability and regions of high skill. However, model errors are also identified, in particular regions where the forecast ensemble spread appears too small. For individual winters the information provided by t-values, a simple measure of the forecast signal-to-noise ratio, is investigated. For 2 m surface air temperature (T2m), highest t-values are found in the Tropics but there is considerable interannual variability, and in the tropical Atlantic and Indian basins this variability is not directly tied to the El Nino Southern Oscillation. For GPH there is also large interannual variability in t-values, but these variations cannot easily be predicted from the strength of the tropical sea-surface-temperature anomalies. It is argued that the t-values for 500 hPa GPH can give valuable insight into the oceanic forcing of the atmosphere that generates predictable signals in the model. Consequently, t-values may be a useful tool for understanding, at a mechanistic level, forecast successes and failures. Lastly, the extent to which t-values are useful as a predictor of forecast skill is investigated. For T2m, t-values provide a useful predictor of forecast skill in both the Tropics and extratropics. Except in the equatorial east Pacific, most of the information in t-values is associated with interannual variability of the ensemble-mean forecast rather than interannual variability of the ensemble spread. For GPH, however, t-values provide a useful predictor of forecast skill only in the tropical Pacific region.

Effect of improving representation of horizontal and vertical cloud structure on the Earth's global radiation budget. Part II: The global effects

Reliably representing both horizontal cloud inhomogeneity and vertical cloud overlap is fundamentally important for the radiation budget of a general circulation model. Here, we build on the work of Part One of this two-part paper by applying a pair of parameterisations that account for horizontal inhomogeneity and vertical overlap to global re-analysis data. These are applied both together and separately in an attempt to quantify the effects of poor representation of the two components on radiation budget. Horizontal inhomogeneity is accounted for using the “Tripleclouds” scheme, which uses two regions of cloud in each layer of a gridbox as opposed to one; vertical overlap is accounted for using “exponential-random” overlap, which aligns vertically continuous cloud according to a decorrelation height. These are applied to a sample of scenes from a year of ERA-40 data. The largest radiative effect of horizontal inhomogeneity is found to be in areas of marine stratocumulus; the effect of vertical overlap is found to be fairly uniform, but with larger individual short-wave and long-wave effects in areas of deep, tropical convection. The combined effect of the two parameterisations is found to reduce the magnitude of the net top-of-atmosphere cloud radiative forcing (CRF) by 2.25 W m−2, with shifts of up to 10 W m−2 in areas of marine stratocumulus. The effects of the uncertainty in our parameterisations on radiation budget is also investigated. It is found that the uncertainty in the impact of horizontal inhomogeneity is of order ±60%, while the uncertainty in the impact of vertical overlap is much smaller. This suggests an insensitivity of the radiation budget to the exact nature of the global decorrelation height distribution derived in Part One.

Technological change and the challenges for regional development: building social capital in less-favoured regions

The relevance of regional policy for less favoured regions (LFRs) reveals itself when policy-makers must reconcile competitiveness with social cohesion through the adaptation of competition or innovation policies. The vast literature in this area generally builds on an overarching concept of ‘social capital’ as the necessary relational infrastructure for collective action diversification and policy integration, in a context much influenced by a dynamic of industrial change and a necessary balance between the creation and diffusion of ‘knowledge’ through learning. This relational infrastructure or ‘social capital’ is centred on people’s willingness to cooperate and ‘envision’ futures as a result of “social organization, such as networks, norms and trust that facilitate action and cooperation for mutual benefit” (Putnam, 1993: 35). Advocates of this interpretation of ‘social capital’ have adopted the ‘new growth’ thinking behind ‘systems of innovation’ and ‘competence building’, arguing that networks have the potential to make both public administration and markets more effective as well as ‘learning’ trajectories more inclusive of the development of society as a whole. This essay aims to better understand the role of ‘social capital’ in the production and reproduction of uneven regional development patterns, and to critically assess the limits of a ‘systems concept’ and an institution-centred approach to comparative studies of regional innovation. These aims are discussed in light of the following two assertions: i) learning behaviour, from an economic point of view, has its determinants, and ii) the positive economic outcomes of ‘social capital’ cannot be taken as a given. It is suggested that an agent-centred approach to comparative research best addresses the ‘learning’ determinants and the consequences of social networks on regional development patterns. A brief discussion of the current debate on innovation surveys has been provided to illustrate this point.

The unsteady flow of a weakly compressible fluid in a thin porous layer II: three-dimensional theory

We consider the problem of determining the pressure and velocity fields for a weakly compressible fluid flowing in a three-dimensional layer, composed of an inhomogeneous, anisotropic porous medium, with vertical side walls and variable upper and lower boundaries, in the presence of vertical wells injecting and/or extracting fluid. Numerical solution of this three-dimensional evolution problem may be expensive, particularly in the case that the depth scale of the layer h is small compared to the horizontal length scale l, a situation which occurs frequently in the application to oil and gas reservoir recovery and which leads to significant stiffness in the numerical problem. Under the assumption that $\epsilon\propto h/l\ll 1$, we show that, to leading order in $\epsilon$, the pressure field varies only in the horizontal directions away from the wells (the outer region). We construct asymptotic expansions in $\epsilon$ in both the inner (near the wells) and outer regions and use the asymptotic matching principle to derive expressions for all significant process quantities. The only computations required are for the solution of non-stiff linear, elliptic, two-dimensional boundary-value, and eigenvalue problems. This approach, via the method of matched asymptotic expansions, takes advantage of the small aspect ratio of the layer, $\epsilon$, at precisely the stage where full numerical computations become stiff, and also reveals the detailed structure of the dynamics of the flow, both in the neighbourhood of wells and away from wells.

The effects of explicit versus parameterized convection on the MJO in a large-domain high-resolution tropical case study. Part II: Processes leading to differences in MJO development

High-resolution simulations over a large tropical domain (∼20◦S–20◦N and 42◦E–180◦E) using both explicit and parameterized convection are analyzed and compared during a 10-day case study of an active Madden-Julian Oscillation (MJO) event. In Part II, the moisture budgets and moist entropy budgets are analyzed. Vertical subgrid diabatic heating profiles and vertical velocity profiles are also compared; these are related to the horizontal and vertical advective components of the moist entropy budget which contribute to gross moist stability, GMS, and normalized GMS (NGMS). The 4-km model with explicit convection and good MJO performance has a vertical heating structure that increases with height in the lower troposphere in regions of strong convection (like observations), whereas the 12-km model with parameterized convection and a poor MJO does not show this relationship. The 4-km explicit convection model also has a more top-heavy heating profile for the troposphere as a whole near and to the west of the active MJO-related convection, unlike the 12-km parameterized convection model. The dependence of entropy advection components on moisture convergence is fairly weak in all models, and differences between models are not always related to MJO performance, making comparisons to previous work somewhat inconclusive. However, models with relatively good MJO strength and propagation have a slightly larger increase of the vertical advective component with increasing moisture convergence, and their NGMS vertical terms have more variability in time and longitude, with total NGMS that is comparatively larger to the west and smaller to the east.

Immunohistochemical, tomographic and histological study on onlay bone graft remodeling. Part II: calvarial bone

Objectives Little information is available on the molecular events that occur during graft incorporation over time. The calvarial bone (Cb) grafts have been reported to produce greater responses compared with other donor regions in maxillofacial reconstructions, but the scientific evidences for this are still lacking. The objectives of this study are (1) to study the morphological pattern of Cb onlay bone grafts and compare them with the biological events through immunohistochemical responses and (2) to establish the effects of perforations in maintaining the volume and bone density of the receptor bed. Material and methods Sixty New Zealand White rabbits were submitted to Cb onlay bone grafts on the mandible. In 30 rabbits, the receptor bed was perforated (perforated group), while for the remaining animals the bed was kept intact (non-perforated group). Six animals from each group were sacrificed at 5, 7, 10, 20 and 60 days after surgery. Histological sections from the grafted area were prepared for immunohistochemical and histological analyses. Immuno-labeling was found for proteins Osteoprotegerin (OPG), receptor activator of nuclear factor-kappa beta ligand (RANKL), alkaline phosphatase (ALP), osteopontin (OPN), vascular endothelial growth factor (VEGF), tartrate-resistant acid phosphatase (TRAP), Type I collagen (COL I) and osteocalcin (OC). The tomography examination [computerized tomography (CT) scan] was conducted just after surgery and at the sacrifice. Results The histological findings revealed that the perforations contributed to higher bone deposition during the initial stages at the graft-receptor bed interface, accelerating the graft incorporation process. The results of the CT scan showed lower resorption for the perforated group (P < 0.05), and both groups showed high bone density rates at 60 days. This set of evidences is corroborated by the immunohistochemical outcomes indicating that proteins associated with revascularization and osteogenesis (VEGF, OPN, TRAP and ALP) were found in higher levels in the perforated group. Conclusions These findings indicate that the bone volume of calvarial grafts is better maintained when the receptor bed is perforated, probably resulting from more effective graft revascularization and greater bone deposition. The process of bone resorption peaked between 20 and 60 days post-operatively in both groups although significantly less in the perforated group. To cite this article:Pedrosa Jr WF, Okamoto R, Faria PEP, Arnez MFM, Xavier SP, Salata LA. Immunohistochemical, tomographic and histological study on onlay bone grafts remodeling. Part II: calvarial bone.Clin. Oral Impl. Res. 20, 2009; 1254-1264.doi: 10.1111/j.1600-0501.2009.01747.x.

PLANETARY NEBULAE IN THE INNER MILKY WAY II: THE BULGE-DISK TRANSITION

In this work, a sample of planetary nebulae located in the inner-disk and bulge of the Galaxy is used in order to find the galactocentric distance which better separates these two populations, from the point of view of abundances. Statistical distance scales are used to study the distribution of abundances across the disk-bulge interface. A Kolmogorov-Smirnov test is used to find the distance at which the chemical properties of these regions better separate. The results of the statistical analysis indicate that, on the average, the inner population has lower abundances than the outer. Additionally, for the a-element abundances, the inner population does not follow the disk radial gradient towards the galactic center. Based on our results, we suggest a bulge-disk interface at 1.5 kpc, marking the transition between the bulge and inner-disk of the Galaxy as defined by the intermediate mass population.

Nuclear and extended spectra of NGC 1068-II. Near-infrared stellar population synthesis

We performed stellar population synthesis on the nuclear and extended regions of NGC 1068 by means of near-infrared spectroscopy to disentangle their spectral energy distribution components. This is the first time that such a technique is applied to the whole 0.8-2.4 mu m wavelength interval in this galaxy. NGC 1068 is one of the nearest and probably the most studied Seyfert 2 galaxy, becoming an excellent laboratory to study the interaction between black holes, the jets that they can produce and the medium in which they propagate. Our main result is that traces of young stellar population are found at similar to 100 pc south of the nucleus. The contribution of a power-law continuum in the centre is about 25 per cent, which is expected if the light is scattered from a Seyfert 1 nucleus. We find peaks in the contribution of the featureless continuum about 100-150 pc from the nucleus on both sides. They might be associated with regions where the jet encounters dense clouds. Further support to this scenario is given by the peaks of hot dust distribution found around these same regions and the H(2) emission-line profile, leading us to propose that the peaks might be associated to regions where stars are being formed. Hot dust also has an important contribution to the nuclear region, reinforcing the idea of the presence of a dense, circumnuclear torus in this galaxy. Cold dust appears mostly in the south direction, which supports the view that the south-west emission is behind the plane of the galaxy and is extinguished very likely by dust in the plane. Intermediate-age stellar population contributes significantly to the continuum, especially in the inner 200 pc.

Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-1 9), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus; promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-1 9 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-1 9 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-1 9 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group 11 NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group 11 had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60% of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

Structure and Mode of Action of Microplusin, a Copper II-chelating Antimicrobial Peptide from the Cattle Tick Rhipicephalus (Boophilus) microplus

Microplusin, a Rhipicephalus (Boophilus) microplus antimicrobial peptide (AMP) is the first fully characterized member of a new family of cysteine-rich AMPs with histidine-rich regions at the N and C termini. In the tick, microplusin belongs to the arsenal of innate defense molecules active against bacteria and fungi. Here we describe the NMR solution structure of microplusin and demonstrate that the protein binds copper II and iron II. Structured as a single alpha-helical globular domain, microplusin consists of five alpha-helices: alpha 1 (residues Gly-9 to Arg-21), alpha 2 (residues Glu-27 to Asn-40), alpha 3 (residues Arg-44 to Thr-54), alpha 4 (residues Leu-57 to Tyr-64), and alpha 5 (residues Asn-67 to Cys-80). The N and C termini are disordered. This structure is unlike any other AMP structures described to date. We also used NMR spectroscopy to map the copper binding region on microplusin. Finally, using the Gram-positive bacteria Micrococcus luteus as a model, we studied of mode of action of microplusin. Microplusin has a bacteriostatic effect and does not permeabilize the bacterial membrane. Because microplusin binds metals, we tested whether this was related to its antimicrobial activity. We found that the bacteriostatic effect of microplusin was fully reversed by supplementation of culture media with copper II but not iron II. We also demonstrated that microplusin affects M. luteus respiration, a copper-dependent process. Thus, we conclude that the antibacterial effect of microplusin is due to its ability to bind and sequester copper II.