Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)

Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons.We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene.Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.

A nuclear defect in the 4p16 region predisposes to multiple mitochondrial DNA deletions in families with Wolfram syndrome.

Wolfram syndrome is a progressive neurodegenerative disorder transmitted in an autosomal recessive mode. We report two Wolfram syndrome families harboring multiple deletions of mitochondrial DNA. The deletions reached percentages as high as 85-90% in affected tissues such as the central nervous system of one patient, while in other tissues from the same patient and from other members of the family, the percentages of deleted mitochondrial DNA genomes were only 1-10%. Recently, a Wolfram syndrome gene has been linked to markers on 4p16. In both families linkage between the disease locus and 4p16 markers gave a maximum multipoint lod score of 3.79 at theta = 0 (Pi<0.03) with respect to D4S431. In these families, the syndrome was caused by mutations in this nucleus-encoded gene which deleteriously interacts with the mitochondrial genome. This is the first evidence of the implication of both genomes in a recessive disease.

A nuclear defect in the 4p16 region predisposes to multiple mitochondrial DNA deletions in families with Wolfram syndrome.

Wolfram syndrome is a progressive neurodegenerative disorder transmitted in an autosomal recessive mode. We report two Wolfram syndrome families harboring multiple deletions of mitochondrial DNA. The deletions reached percentages as high as 85-90% in affected tissues such as the central nervous system of one patient, while in other tissues from the same patient and from other members of the family, the percentages of deleted mitochondrial DNA genomes were only 1-10%. Recently, a Wolfram syndrome gene has been linked to markers on 4p16. In both families linkage between the disease locus and 4p16 markers gave a maximum multipoint lod score of 3.79 at theta = 0 (Pi<0.03) with respect to D4S431. In these families, the syndrome was caused by mutations in this nucleus-encoded gene which deleteriously interacts with the mitochondrial genome. This is the first evidence of the implication of both genomes in a recessive disease.

A new classification of the Turkish terranes and sutures and its implication for the paleotectonic history of the region

The Turkish part of the Tethyan realm is represented by a series of terranes juxtaposed through Alpine convergent movements and separated by complex suture zones. Different terranes can be defined and characterized by their dominant geological background. The Pontides domain represents a segment of the former active margin of Eurasia, where back-arc basins opened in the Triassic and separated the Sakarya terrane from neighbouring regions. Sakarya was re-accreted to Laurasia through the Balkanic mid-Cretaceous orogenic event that also affected the Rhodope and Strandja zones. The whole region from the Balkans to the Caucasus was then affected by a reversal of subduction and creation of a Late Cretaceous arc before collision with the Anatolian domain in the Eocene. If the Anatolian terrane underwent an evolution similar to Sakarya during the Late Paleozoic and Early Triassic times, both terranes had a diverging history during and after the Eo-Cimmerian collision. North of Sakarya, the Küre back-arc was closed during the Jurassic, whereas north of the Anatolian domain, the back-arc type oceans did not close before the Late Cretaceous. During the Cretaceous, both domains were affected by ophiolite obduction, but in very different ways: north directed diachronous Middle to Late Cretaceous mélange obduction on the Jurassic Sakarya passive margin; Senonian synchronous southward obduction on the Triassic passive margin of Anatolia. From this, it appears that the Izmir-Ankara suture, currently separating both terranes, is composite, and that the passive margin of Sakarya is not the conjugate margin of Anatolia. To the south, the Cimmerian Taurus domain together with the Beydağları domain (part of the larger Greater Apulian terrane), were detached from north Gondwana in the Permian during the opening of the Neotethys (East-Mediterranean basin). The drifting Cimmerian blocks entered into a soft collision with the Anatolian and related terranes in the Eo-Cimmerian orogenic phase (Late Triassic), thus suturing the Paleotethys. At that time, the Taurus plate developed foreland-type basins, filled with flysch-molasse deposits that locally overstepped the lower plate Taurus terrane and were deposited in the opening Neotethys to the south. These olistostromal deposits are characterized by pelagic Carboniferous and Permian material from the Paleotethys suture zone found in the Mersin mélange. The latter, as well as the Antalya and Mamonia domains are represented by a series of exotic units now found south of the main Taurus range. Part of the Mersin exotic material was clearly derived from the former north Anatolian passive margin (Huğlu-type series) and re-displaced during the Paleogene. This led us to propose a plate tectonic model where the Anatolian ophiolitic front is linked up with the Samail/Baër-Bassit obduction front found along the Arabian margin. The obduction front was indented by the Anatolian promontory whose eastern end was partially subducted. Continued slab roll-back of the Neotethys allowed Anatolian exotics to continue their course southwestward until their emplacement along the Taurus southern margin (Mersin) and up to the Beydağları promontory (Antaya-Mamonia) in the latest Cretaceous-Paleocene. The supra-subduction ocean opening at the back of the obduction front (Troodos-type Ocean) was finally closed by Eocene north-south shortening between Africa and Eurasia. This brought close to each other Cretaceous ophiolites derived from the north of Anatolia and those obducted on the Arabian promontory. The latter were sealed by a Maastrichtian platform, and locally never affected by Alpine tectonism, whereas those located on the eastern Anatolian plate are strongly deformed and metamorphosed, and affected by Eocene arc magmatism. These observations help to reconstruct the larger frame of the central Tethyan realm geodynamic evolution.

The region makes the difference: disparities in management of acute myocardial infaction within Switzerland

Purpose: To assess geographical differences within Switzerland regarding management and revascularization procedures for acute myocardial infarction (AMI). Methods: Swiss hospital discharge database for period 2007-2008. The main inclusion criterion was AMI as a primary discharge diagnosis. AMI revascularization procedures were identified and seven Swiss regions (Leman, Mittelland, Northwest, Zurich, Central, Eastern and Ticino) were analyzed. Results: Data from 25,674 AMI discharges were analyzed. Almost half (53.6%) of them were managed in a single hospital, the values ranging from 63.1% (Leman) to 31.4% (Ticino) see table. Relative to the total number of discharges, the highest Intensive Care Unit admission rate was in Leman (69.7%), the lowest (16.4%) in Ticino (Swiss average: 35.8%). Intracoronary revascularization rates were highest in Leman (51.6%) and lowest (30.8%) in Central Switzerland (Swiss average: 41.4%). Bare (non-drug-eluting) stents use was highest in Leman (33.1%) and lowest (7.0%) in Ticino (Swiss average: 15.8%), while drug eluting stent use was highest (32.8%) in Ticino and lowest (13.9%) in Central Switzerland (Swiss average: 24.0%). Coronary artery bypass graft rates were highest (4.6%) in Ticino and lowest (0.4%) in Eastern Switzerland (Swiss average: 2.6%). Mechanical circulatory assistance rates were highest (4.1%) in Zurich and lowest (0.4%) in Ticino (Swiss average: 1.7%). The differences in revascularization procedures remained after adjusting for age, single or multiple hospital management and gender. Conclusion: In Switzerland, significant geographical differences in management and revascularization procedures for AMI were found.

Integrative analysis of the Regulatory Region of the FGFR3 Oncogene

The study of transcriptional regulation often needs the integration of diverse yet independent data. In the present work, sequence conservation, predic-tion of transcription factor binding sites (TFBS) and gene expression analysis have been applied to the detection of putative transcription factor (TF) modules in the regulatory region of the FGFR3 oncogene. Several TFs with conserved binding sites in the FGFR3 regulatory region have shown high positive or negative corre-lation with FGFR3 expression both in urothelial carcinoma and in benign nevi. By means of conserved TF cluster analysis, two different TF modules have been iden-tified in the promoter and first intron of FGFR3 gene. These modules contain acti-vating AP2, E2F, E47 and SP1 binding sites plus motifs for EGR with possible repressor function.

Viticulture under climate change : understanding vulnerability and adaptive capacity of wineries and growers. A case study in El Penedès region, Catalonia

Climate change may pose challenges and opportunities to viticulture, and much research has focused in studying the likely impacts on grapes and wine production in different regions worldwide. This study assesses the vulnerability and adaptive capacity of the viticulture sector under changing climate conditions, based on a case study in El Penedès region, Catalonia. Farm assets, livelihood strategies, farmer-market interactions and climate changes perceptions are analysed through semi-structured interviews with different types of wineries and growers. Both types of actors are equally exposed to biophysical stressors but unevenly affected by socioeconomic changes. While wineries are vulnerable because of the current economic crisis and the lack of diversification of their work, which may affect their income or production, growers are mainly affected by the low prices of their products and the lack of fix contracts. These socioeconomic stressors strongly condition their capacity to adapt to climate change, meaning that growers prioritize their immediate income problems, rather than future socioeconomic or climate threats. Therefore, growers undertake reactive adaptation to climate changing conditions, mainly based on ancient knowledge, whilst wineries combine both reactive and anticipatory adaptation practices. These circumstances should be addressed in order to allow better anticipatory adaptation to be implemented, thus avoiding future climate threats.

Identification of the minimal promoter region of the mouse NKX5-3, a transcription factor implicated in eye development.

Early ocular development is controlled by a complex network of transcription factors, cell cycle regulators, and diffusible signalling molecules. Together, these molecules regulate cell proliferation and apoptosis, and specify retinal fate. NKX5-3 is a homeobox transcription factor implicated in eye development. The analysis of the 5'-flanking region of the mouse Nkx5-3 gene revealed a predicted TATA-less promoter sequence between -416 and -166 of the translation start site. To functionally characterise Nkx5-3 promoter activity, serial deletions of the promoter sequence were introduced in pGL-3 basic vector and promoter activity of these 5'- and 3'-deleted constructions was tested in HeLa and CHO cells. Transactivation assays identified a region between -350 and -296 exhibiting promoter-like activity. Combined analysis by deletions and point mutations showed that this sequence, containing multiple Sp1 binding sites was necessary to promote transcriptional activity. Binding of Sp1 to this region was confirmed by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation, using an antibody specific for Sp1. Altogether, these results demonstrated that the immediate upstream region of Nkx5-3 gene possessed a strong intrinsic promoter activity in vitro, suggesting a potential role in Nkx5-3 transcription in vivo.

Occurrence of Symphyla (Myriapoda) in the region of the Upper Solimões River, Amazonas, Brazil

The present work aimed at identifying the Symphyla species diversity and abundance in various land-use systems under different degrees of intensification in western Amazonia. This is the first inventory of Symphyla in primary and secondary forest, crops, agroforestry systems and pastures which was carried out in Benjamin Constant municipality, in the region of the Upper Solimões River, Brazil. Samples (n = 101) were collected using a metal corer, and the symphylan extraction was carried out using Berlese-Tullgren funnels. Two genera and three species of symphylans were encountered. Considering the diversity encountered in Amazonian inventories, with only four genera and five known species overall, the three species found in the present study are considered a reasonable representation of the regional diversity. Two of the Hanseniella species found have been known to cause plant damage.

The earthworm fauna of regenerating forests and anthropogenic habitats in the coastal region of Paraná

The aim of this study was to evaluate abundance, biomass and diversity of earthworms in the southern coast region of the Mata Atlântica biodiversity hotspot. A total of 51 study sites in pastures, banana monocultures, mixed agroforestry systems, secondary forests in succession and old-growth forests near the coast of Paraná, Brazil, were evaluated. Each site was sampled once. Species richness of the earthworms was generally low and varied little between sites. At all sites except for one, the peregrine species Pontoscolex corethrurus (Glossoscolecidae) strongly dominated. Three other peregrine species, Amynthas corticis, Amynthas gracilis (Megascolecidae) and Ocnerodrilus occidentalis (Ocnerodrilidae), were frequent in moist sites. No autochthonous species were found. Abundance and biomass of earthworms varied strongly within and between sites (0-338 individuals m-2, 0-96 g m-2 fresh weight). Pastures had significantly lower abundance than all other sites. The forest sites had similar earthworm abundance and biomass, with a tendency to be higher in younger succession stages. The coastal plain region has been strongly altered by human activities. Reasons for the lack of any autochthonous species and the dominance of one peregrine species require further investigation.

Solar radiation use efficiency by soybean under field conditions in the Amazon region

The objective of this work was to evaluate the efficiency of soybean (Glycine max) in intercepting and using solar radiation under natural field conditions, in the Amazon region, Brazil. The meteorological data and the values of soybean growth and leaf area were obtained from an agrometeorological experiment carried out in Paragominas, Pará state, during 2007 and 2008. The radiation use efficiency (RUE) was obtained from the ratio between the above-ground biomass production and the intercepted photosynthetically active radiation (PAR) accumulated to 99 and 95 days after sowing, in 2007 and 2008, respectively. Climatic conditions during the experiment were very distinct, with reduction in rainfall in 2007, which began during the soybean mid-cycle, due to the El Niño phenomenon. An important reduction in the leaf area index and biomass production was observed during 2007. Under natural field conditions in the Amazon region, the values of RUE were 1.46 and 1.99 g MJ-1 PAR in the 2007 and 2008 experiments, respectively. The probable reason for the differences found between these years might be associated to the water restriction in 2007 coupled with the higher air temperature and vapor pressure deficit, and also to the increase in the fraction of diffuse radiation that reached the land surface in 2008.

Energy balance measurements over a banana orchard in the Semiarid region in the Northeast of Brazil

The objective of this work was to evaluate the reliability of eddy covariance measurements, analyzing the energy balance components, evapotranspiration and energy balance closure in dry and wet growing seasons, in a banana orchard. The experiment was carried out at a farm located within the irrigation district of Quixeré, in the Lower Jaguaribe basin, in Ceará state, Brazil. An eddy covariance system was used to measure the turbulent flux. An automatic weather station was installed in a grass field to obtain the reference evapotranspiration (ET0) from the combined FAO-Penman-Monteith method. Wind speed and vapor pressure deficit are the most important variables on the evaporative process in both growing seasons. In the dry season, the heat fluxes have a similar order of magnitude, and during the wet season the latent heat flux is the largest. The eddy covariance system had acceptable reliability in measuring heat flux, with actual evapotranspiration results comparing well with those obtained by using the water balance method. The energy balance closure had good results for the study area, with mean values of 0.93 and 0.86 for the dry and wet growing seasons respectively.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.

Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders.

Proteoglycans (PGs) are a major component of the extracellular matrix in many tissues and function as structural and regulatory molecules. PGs are composed of core proteins and glycosaminoglycan (GAG) side chains. The biosynthesis of GAGs starts with the linker region that consists of four sugar residues and is followed by repeating disaccharide units. By exome sequencing, we found that B3GALT6 encoding an enzyme involved in the biosynthesis of the GAG linker region is responsible for a severe skeletal dysplasia, spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMD-JL1). B3GALT6 loss-of-function mutations were found in individuals with SEMD-JL1 from seven families. In a subsequent candidate gene study based on the phenotypic similarity, we found that B3GALT6 is also responsible for a connective tissue disease, Ehlers-Danlos syndrome (progeroid form). Recessive loss-of-function mutations in B3GALT6 result in a spectrum of disorders affecting a broad range of skeletal and connective tissues characterized by lax skin, muscle hypotonia, joint dislocation, and spinal deformity. The pleiotropic phenotypes of the disorders indicate that B3GALT6 plays a critical role in a wide range of biological processes in various tissues, including skin, bone, cartilage, tendon, and ligament.