Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Local influence for spatial analysis of soil physical properties and soybean yield using student's t-distribution

The modeling and estimation of the parameters that define the spatial dependence structure of a regionalized variable by geostatistical methods are fundamental, since these parameters, underlying the kriging of unsampled points, allow the construction of thematic maps. One or more atypical observations in the sample data can affect the estimation of these parameters. Thus, the assessment of the combined influence of these observations by the analysis of Local Influence is essential. The purpose of this paper was to propose local influence analysis methods for the regionalized variable, given that it has n-variate Student's t-distribution, and compare it with the analysis of local influence when the same regionalized variable has n-variate normal distribution. These local influence analysis methods were applied to soil physical properties and soybean yield data of an experiment carried out in a 56.68 ha commercial field in western Paraná, Brazil. Results showed that influential values are efficiently determined with n-variate Student's t-distribution.

The impact of navigator timing parameters and navigator spatial resolution on 3D coronary magnetic resonance angiography.

The impact of navigator spatial resolution and navigator evaluation time on image quality in free-breathing navigator-gated 3D coronary magnetic resonance angiography (MRA), including real-time motion correction, was investigated in a moving phantom. Objective image quality parameters signal-to-noise ratio (SNR) and vessel sharpness were compared. It was found that for improved mage quality a short navigator evaluation time is of crucial importance. Navigator spatial resolution showed minimal influence on image quality.

Spatial weights : constructing weight-compatible exchange matrices from proximity matrices

Exchange matrices represent spatial weights as symmetric probability distributions on pairs of regions, whose margins yield regional weights, generally well-specified and known in most contexts. This contribution proposes a mechanism for constructing exchange matrices, derived from quite general symmetric proximity matrices, in such a way that the margin of the exchange matrix coincides with the regional weights. Exchange matrices generate in turn diffusive squared Euclidean dissimilarities, measuring spatial remoteness between pairs of regions. Unweighted and weighted spatial frameworks are reviewed and compared, regarding in particular their impact on permutation and normal tests of spatial autocorrelation. Applications include tests of spatial autocorrelation with diagonal weights, factorial visualization of the network of regions, multivariate generalizations of Moran's I, as well as "landscape clustering", aimed at creating regional aggregates both spatially contiguous and endowed with similar features.

Do habitat suitability models reliably predict the recovery areas of threatened species?

1. Identifying those areas suitable for recolonization by threatened species is essential to support efficient conservation policies. Habitat suitability models (HSM) predict species' potential distributions, but the quality of their predictions should be carefully assessed when the species-environment equilibrium assumption is violated.2. We studied the Eurasian otter Lutra lutra, whose numbers are recovering in southern Italy. To produce widely applicable results, we chose standard HSM procedures and looked for the models' capacities in predicting the suitability of a recolonization area. We used two fieldwork datasets: presence-only data, used in the Ecological Niche Factor Analyses (ENFA), and presence-absence data, used in a Generalized Linear Model (GLM). In addition to cross-validation, we independently evaluated the models with data from a recolonization event, providing presences on a previously unoccupied river.3. Three of the models successfully predicted the suitability of the recolonization area, but the GLM built with data before the recolonization disagreed with these predictions, missing the recolonized river's suitability and badly describing the otter's niche. Our results highlighted three points of relevance to modelling practices: (1) absences may prevent the models from correctly identifying areas suitable for a species spread; (2) the selection of variables may lead to randomness in the predictions; and (3) the Area Under Curve (AUC), a commonly used validation index, was not well suited to the evaluation of model quality, whereas the Boyce Index (CBI), based on presence data only, better highlighted the models' fit to the recolonization observations.4. For species with unstable spatial distributions, presence-only models may work better than presence-absence methods in making reliable predictions of suitable areas for expansion. An iterative modelling process, using new occurrences from each step of the species spread, may also help in progressively reducing errors.5. Synthesis and applications. Conservation plans depend on reliable models of the species' suitable habitats. In non-equilibrium situations, such as the case for threatened or invasive species, models could be affected negatively by the inclusion of absence data when predicting the areas of potential expansion. Presence-only methods will here provide a better basis for productive conservation management practices.

Spatial relationships between soil attributes and corn yield in no-tillage system

Soil properties play an important role in spatial variability of crop yield. However, a low spatial correlation has generally been observed between maps of crop yield and of soil properties. The objectives of the present investigation were to assess the spatial pattern variability of soil properties and of corn yield at the same sampling intensity, and evaluate its cause-and-effect relationships. The experimental site was structured in a grid of 100 referenced points, spaced at 10 m intervals along four parallel 250 m long rows spaced 4.5 m apart. Thus, points formed a rectangle containing four columns and 25 rows. Therefore, each sampling cell encompassed an area of 45 m² and consisted of five 10 m long crop rows, in which the referenced points represented the center. Samples were taken from the layers 0-0.1 m and 0.1-0.2 m. Soil physical and chemical properties were evaluated. Statistical analyses consisted of data description and geostatistics. The spatial dependence of corn yield and soil properties was confirmed. The hypothesis of this study was confirmed, i.e., when sampling the soil to determine the values of soil characteristics at similar to sampling intensity as for crop yield assessments, correlations between the spatial distribution of soil characteristics and crop yield were observed. The spatial distribution pattern of soil properties explained 65 % of the spatial distribution pattern of corn yield. The spatial distribution pattern of clay content and percentage of soil base saturation explained most of the spatial distribution pattern of corn yield.

Visuo-spatial processing in a dynamic and a static working memory paradigm in schizophrenia.

Recent findings suggest that the visuo-spatial sketchpad (VSSP) may be divided into two sub-components processing dynamic or static visual information. This model may be useful to elucidate the confusion of data concerning the functioning of the VSSP in schizophrenia. The present study examined patients with schizophrenia and matched controls in a new working memory paradigm involving dynamic (the Ball Flight Task - BFT) or static (the Static Pattern Task - SPT) visual stimuli. In the BFT, the responses of the patients were apparently based on the retention of the last set of segments of the perceived trajectory, whereas control subjects relied on a more global strategy. We assume that the patients' performances are the result of a reduced capacity in chunking visual information since they relied mainly on the retention of the last set of segments. This assumption is confirmed by the poor performance of the patients in the static task (SPT), which requires a combination of stimulus components into object representations. We assume that the static/dynamic distinction may help us to understand the VSSP deficits in schizophrenia. This distinction also raises questions about the hypothesis that visuo-spatial working memory can simply be dissociated into visual and spatial sub-components.

Characterization and classification of soils in the Taquari river basin - Pantanal region, state of Mato Grosso do Sul, Brazil

Among the soils in the Mato Grosso do Sul, stand out in the Pantanal biome, the Spodosols. Despite being recorded in considerable extensions, few studies aiming to characterize and classify these soils were performed. The purpose of this study was to characterize and classify soils in three areas of two physiographic types in the Taquari river basin: bay and flooded fields. Two trenches were opened in the bay area (P1 and P2) and two in the flooded field (P3 and P4). The third area (saline) with high sodium levels was sampled for further studies. In the soils in both areas the sand fraction was predominant and the texture from sand to sandy loam, with the main constituent quartz. In the bay area, the soil organic carbon in the surface layer (P1) was (OC) > 80 g kg-1, being diagnosed as Histic epipedon. In the other profiles the surface horizons had low OC levels which, associated with other properties, classified them as Ochric epipedons. In the soils of the bay area (P1 and P2), the pH ranged from 5.0 to 7.5, associated with dominance of Ca2+ and Mg2+, with base saturation above 50 % in some horizons. In the flooded fields (P3 and P4) the soil pH ranged from 4.9 to 5.9, H+ contents were high in the surface horizons (0.8-10.5 cmol c kg-1 ), Ca2+ and Mg² contents ranged from 0.4 to 0.8 cmol c kg-1 and base saturation was < 50 %. In the soils of the bay area (P1 and P2) iron was accumulated (extracted by dithionite - Fed) and OC in the spodic horizon; in the P3 and P4 soils only Fed was accumulated (in the subsurface layers). According to the criteria adopted by the Brazilian System of Soil Classification (SiBCS) at the subgroup level, the soils were classified as: P1: Organic Hydromorphic Ferrohumiluvic Spodosol. P2: Typical Orthic Ferrohumiluvic Spodosol. P3: Typical Hydromorphic Ferroluvic Spodosol. P4: Arenic Orthic Ferroluvic Spodosol.

Spatial and linear correlations between soil and corn

The Technologies setting at Agricultural production system have the main characteristics the vertical productivity, reduced costs, soil physical, chemical and biological improvement to promote production sustainable growth. Thus, the study aimed to determine the variability and the linear and special correlations between the plant and soil attributes in order to select and indicate good representation of soil physical quality for forage productivity. In the growing season of 2006, on the Fazenda Bonança in Pereira Barreto (SP), the productivity of autumn corn forage (FDM) in an irrigated no-tillage system and the soil physical properties were analyzed. The purpose was to study the variability and the linear and spatial correlations between the plant and soil properties, to select an indicator of soil physical quality related to corn forage yield. A geostatistical grid was installed to collect soil and plant data, with 125 sampling points in an area of 2,500 m². The results show that the studied properties did not vary randomly and that data variability was low to very high, with well-defined spatial patterns, ranging from 7.8 to 38.0 m. On the other hand, the linear correlation between the plant and the soil properties was low and highly significant. The pairs forage dry matter versus microporosity and stem diameter versus bulk density were best correlated in the 0-0.10 m layer, while the other pairs - forage dry matter versus macro - and total porosity - were inversely correlated in the same layer. However, from the spatial point of view, there was a high inverse correlation between forage dry matter with microporosity, so that microporosity in the 0-0.10 m layer can be considered a good indicator of soil physical quality, with a view to corn forage yield.

Spatial variation in the temporal change of male and female melanic ornamentation in the barn owl.

Because the magnitude of selection can vary between sexes and in space and time, sexually antagonistic selection is difficult to demonstrate. In a Swiss population of barn owls (Tyto alba), a heritable eumelanic colour trait (size of black spots on ventral feathers) was positively selected with respect to yearling survival only in females. It remains unclear whether the absence of negative selection in males is typical in this species. To tackle this issue indirectly, we measured the size of black spots in 1733 skin specimens collected by museums from 1816 to 2001 in seven European countries and in the Middle-East. The temporal change in spot size was sex- and country-specific. In males, spots became smaller particularly in three countries (Middle-East, Italy and Switzerland). In females, the size of spots increased significantly in two countries (UK and Spain) and decreased in two others (Germany and Switzerland). Because migration and phenotypic plasticity cannot explain these results, selection is the most likely cause. The weaker temporal change in spot size in females than males may be because of the combined effect of strong genetic correlation between the sexes and stronger negative selection in males than positive selection in females. We thus suggest that in the barn owl, spot size (or genetically correlated traits) is sexually antagonistically selected and that its pattern of selection may account for the maintenance of its variation and sexual dimorphism.

Phase-field approach to spatial perturbations in normal Saffman-Taylor fingers

We make a numerical study of the effect that spatial perturbations have in normal Saffman-Taylor fingers driven at constant pressure gradients. We use a phase field model that allows for spatial variations in the Hele-Shaw cell. We find that, regardless of the specific way in which spatial perturbations are introduced, a lateral instability develops on the sides of the propagating Saffman-Taylor finger. Moreover, the instability exists regardless of the intensity of spatial perturbations in the cell as long as the perturbations are felt by the finger tip. If, as the finger propagates, the spatial perturbations felt by the tip change, the instability is nonperiodic. If, as the finger propagates, the spatial perturbations felt by the tip are persistent, the instability developed is periodic. In the later case, the instability is symmetrical or asymmetrical depending on the intensity of the perturbation.

Spatial correlations and cross sections of clusters in the A + B -> 0 reaction

We consider the distribution of cross sections of clusters and the density-density correlation functions for the A+B¿0 reaction. We solve the reaction-diffusion equations numerically for random initial distributions of reactants. When both reactant species have the same diffusion coefficients the distribution of cross sections and the correlation functions scale with the diffusion length and obey superuniversal laws (independent of dimension). For different diffusion coefficients the correlation functions still scale, but the scaling functions depend on the dimension and on the diffusion coefficients. Furthermore, we display explicitly the peculiarities of the cluster-size distribution in one dimension.

Uncertainties in the prediction of spatial variability of soil CO2 emissions and related properties

The soil CO2 emission has high spatial variability because it depends strongly on soil properties. The purpose of this study was to (i) characterize the spatial variability of soil respiration and related properties, (ii) evaluate the accuracy of results of the ordinary kriging method and sequential Gaussian simulation, and (iii) evaluate the uncertainty in predicting the spatial variability of soil CO2 emission and other properties using sequential Gaussian simulations. The study was conducted in a sugarcane area, using a regular sampling grid with 141 points, where soil CO2 emission, soil temperature, air-filled pore space, soil organic matter and soil bulk density were evaluated. All variables showed spatial dependence structure. The soil CO2 emission was positively correlated with organic matter (r = 0.25, p < 0.05) and air-filled pore space (r = 0.27, p < 0.01) and negatively with soil bulk density (r = -0.41, p < 0.01). However, when the estimated spatial values were considered, the air-filled pore space was the variable mainly responsible for the spatial characteristics of soil respiration, with a correlation of 0.26 (p < 0.01). For all variables, individual simulations represented the cumulative distribution functions and variograms better than ordinary kriging and E-type estimates. The greatest uncertainties in predicting soil CO2 emission were associated with areas with the highest estimated values, which produced estimates from 0.18 to 1.85 t CO2 ha-1, according to the different scenarios considered. The knowledge of the uncertainties generated by the different scenarios can be used in inventories of greenhouse gases, to provide conservative estimates of the potential emission of these gases.

Audit report on the Great River Regional Waste Authority for the year ended June 30, 2011

Audit report on the Great River Regional Waste Authority for the year ended June 30, 2011