Genomic Bayesian Prediction Model for Count Data with Genotype x Environment Interaction

Genomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size (nT ) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size (nT ). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment G x E interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data

Evaluating the influence of environmental variables on fish assemblages along Tropical Andes: considerations from ecology to conservation

The lack of knowledge about freshwater biodiversity in remote areas like montane Andean rivers is noticeable and hinder the development of efficient conservation plans for aquatic ecosystems. Habitat requirements of tropical Andean fishes have been poorly analysed, despite the relevance of these ecological features on the fish conservation strategies. The present study aimed to examine fish assemblages along the altitudinal gradient in tropical Andean rivers and their relationship to habitat features to detect the most relevant abiotic factors and their implication on conservation. This study was conducted on a regional scale, along six basins located in tropical Andes (500 to 2,692 m a.s.l.). We studied fish diversity and distribution and their habitats along these elevation gradients. We found 6,320 specimens from 53 genera. Our analysis for the six most common and widely distributed genera (Astroblepus, Brycon, Bryconamericus, Chaetostoma, Pimelodella and Trichomycterus) underlines the relevance of hydromorphological variables on fish community structure in the Andean montane rivers, whereas human alterations seem to be less significant. These findings could be useful for current management and conservation strategies considering present threats over tropical montane rivers

Blanqueo de la fibra de celulosa de paja de caña de azúcar (Saccharum spp.) con peróxido de hidrógeno

Objective: Optimize the treatment of cellulose bleaching, replacing the use of sodium hypochlorite with hydrogen peroxide. Design/methodology/approach: A completely randomized design was used, the treatments were six processes of cellulose bleaching, which were carried out with 18 repetitions. To extract the cellulose, the artisanal method and 40 g of straw were used per treatment. The extraction and yield of cellulose and cellulose fiber, whiteness, crystallinity, granule size, purity of the cellulose and an economic analysis of the cost of the bleaching process were evaluated. Results: The average cellulose fiber extracted was 14 g, meaning that the yield of cellulose fiber was 35%. The average cellulose was 8 g, which represents a yield of 39.9% cellulose. The whiteness with sodium hypochlorite was 86.6 %, with a crystallinity of 65.9% and the cellulose granule size was 2.6 nm, and with hydrogen peroxide whiteness was 83%, the crystallinity was 68 % and the average granule size was 2.7 nm, according to the XRD method. This means similarity in both bleaching process. According to the FTIR analysis, the cellulose bleached in both processes is similar to the cellulose structure. Limitations on study/implications: Cellulose bleaching is more expensive with hydrogen peroxide process. Findings/conclusions: The cellulose extracted from the sugar cane straw, bleached with hydrogen peroxide presents acceptable characteristics to produce artisanal paperObjetivo: Optimizar el tratamiento de blanqueo de celulosa, sustituyendo el uso de hipoclorito de sodio por peróxido de hidrógeno. Diseño/metodología/aproximación: Se utilizó un diseño completamente al azar, donde los tratamientos fueron seis procesos de blanqueo de celulosa, que se realizaron con 18 repeticiones. Para extraer la celulosa se usó el método artesanal y 40 g de paja por tratamiento. Se evaluó la extracción y rendimiento de fibra de celulosa y celulosa, blancura, cristalinidad, tamaño de gránulo, pureza de la celulosa y un análisis económico del costo del proceso de blanqueo. Resultados: El promedio de fibra de celulosa extraída fue de 14 g, esto significa que el rendimiento de fibra de celulosa fue 35 %. El promedio de celulosa fue de 8 g que representa un rendimiento de 39.9 % de celulosa. La blancura con hipoclorito de sodio fue del 86.6%, la cristalinidad de 65.9 % y un tamaño de granulo de celulosa de 2.6 nm, y con peróxido de hidrógeno fue del 83 %, la cristalinidad del 68% y el tamaño de granulo promedio fue 2.7 nm, según el método de XRD, indicando resultados similares. De acuerdo al análisis de FTIR, la celulosa blanqueada en ambos procesos, es similar a la estructura de celulosa reportada en la literatura. Limitaciones del estudio/implicaciones: Se observó un costo más elevado en el blanqueo de la celulosa con el peróxido de hidrógeno. Hallazgos/conclusiones: La celulosa de la paja de caña de azúcar blanqueada con peróxido de hidrógeno presenta características adecuadas para elaborar papel artesanal

Implications of noncoding regulatory functions in the development of insulinomas

Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in β cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of β cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations

Protection of Spanish Ibex (Capra pyrenaica) against Bluetongue Virus Serotypes 1 and 8 in a Subclinical Experimental Infection

Many wild ruminants such as Spanish ibex (Capra pyrenaica) are susceptible to Bluetongue virus (BTV) infection, which causes disease mainly in domestic sheep and cattle. Outbreaks involving either BTV serotypes 1 (BTV-1) and 8 (BTV-8) are currently challenging Europe. Inclusion of wildlife vaccination among BTV control measures should be considered in certain species. In the present study, four out of fifteen seronegative Spanish ibexes were immunized with a single dose of inactivated vaccine against BTV-1, four against BTV-8 and seven ibexes were non vaccinated controls. Seven ibexes (four vaccinated and three controls) were inoculated with each BTV serotype. Antibody and IFN-gamma responses were evaluated until 28 days after inoculation (dpi). The vaccinated ibexes showed significant (P<0.05) neutralizing antibody levels after vaccination compared to non vaccinated ibexes. The non vaccinated ibexes remained seronegative until challenge and showed neutralizing antibodies from 7 dpi. BTV RNA was detected in the blood of non vaccinated ibexes from 2 to the end of the study (28 dpi) and in target tissue samples obtained at necropsy (8 and 28 dpi). BTV-1 was successfully isolated on cell culture from blood and target tissues of non vaccinated ibexes. Clinical signs were unapparent and no gross lesions were found at necropsy. Our results show for the first time that Spanish ibex is susceptible and asymptomatic to BTV infection and also that a single dose of vaccine prevents viraemia against BTV-1 and BTV-8 replication

Microbiological Implications of Periurban Agriculture and Water Reuse in Mexico City

BACKGROUND: Recycled treated or untreated wastewater represents an important health challenge in developing countries due to potential water related microbiological exposure. Our aim was to assess water quality and health implications in a Mexico City periurban agricultural area. METHODOLOGY/PRINCIPAL FINDINGS: A longitudinal study in the Xochimilco wetland area was conducted, and 42 sites were randomly selected from 211, including irrigation water canals and effluents of treatment plants. Sample collection took place during rainy and dry seasons (2000-2001). Microbiological parameters (total coliforms, fecal coliforms, streptococci/enterococci, and bacteria other than Vibrio grown on TCBS), Helicobacter pylori, and physicochemical parameters including trihalomethanes (THM) were determined. Fecal coliforms and fecal streptococci are appropriate indicators of human or animal fecal contamination. Fecal coliform counts surpass Mexican and World Health Organization irrigation water guidelines. Identified microorganisms associated with various pathologies in humans and domestic animals comprise Escherichia coli, Klebsiella spp., Salmonella spp., Enterobacter spp., Enterococcus spp., and Pseudomonas spp; H. pylori was also present in the water. An environmental characteristic of the canal system showed high Total Organic Carbon content and relatively low dissolved oxygen concentration; residual chlorine as a disinfection control is not efficient, but THMs do not represent a problem. During the rainy season, temperature and conductivity were higher; in contrast, pH, dissolved oxygen, ammonia, and residual chlorine were lower. This is related with the continuous load of feces from human and animal sources, and to the aquatic systems, which vary seasonally and exhibit evidence of lower water quality in effluents from treatment plants. CONCLUSIONS/SIGNIFICANCE: There is a need for improvement of wastewater treatment systems, as well as more efficient monitoring, regulation, and enforcement procedures for wastewater disposal into bodies of water

Spatial distribution and risk factors of Brucellosis in Iberian wild ungulates

<p>Abstract</p> <p>Background</p> <p>The role of wildlife as a brucellosis reservoir for humans and domestic livestock remains to be properly established. The aim of this work was to determine the aetiology, apparent prevalence, spatial distribution and risk factors for brucellosis transmission in several Iberian wild ungulates.</p> <p>Methods</p> <p>A multi-species indirect immunosorbent assay (iELISA) using <it>Brucella </it>S-LPS antigen was developed. In several regions having brucellosis in livestock, individual serum samples were taken between 1999 and 2009 from 2,579 wild bovids, 6,448 wild cervids and4,454 Eurasian wild boar (<it>Sus scrofa</it>), and tested to assess brucellosis apparent prevalence. Strains isolated from wild boar were characterized to identify the presence of markers shared with the strains isolated from domestic pigs.</p> <p>Results</p> <p>Mean apparent prevalence below 0.5% was identified in chamois (<it>Rupicapra pyrenaica</it>), Iberian wild goat (<it>Capra pyrenaica</it>), and red deer (<it>Cervus elaphus</it>). Roe deer (<it>Capreolus capreolus</it>), fallow deer (<it>Dama dama</it>), mouflon (<it>Ovis aries</it>) and Barbary sheep (<it>Ammotragus lervia</it>) tested were seronegative. Only one red deer and one Iberian wild goat resulted positive in culture, isolating <it>B. abortus </it>biovar 1 and <it>B. melitensis </it>biovar 1, respectively. Apparent prevalence in wild boar ranged from 25% to 46% in the different regions studied, with the highest figures detected in South-Central Spain. The probability of wild boar being positive in the iELISA was also affected by age, age-by-sex interaction, sampling month, and the density of outdoor domestic pigs. A total of 104 bacterial isolates were obtained from wild boar, being all identified as <it>B. suis </it>biovar 2. DNA polymorphisms were similar to those found in domestic pigs.</p> <p>Conclusions</p> <p>In conclusion, brucellosis in wild boar is widespread in the Iberian Peninsula, thus representing an important threat for domestic pigs. By contrast, wild ruminants were not identified as a significant brucellosis reservoir for livestock.</p

Genomic Bayesian Prediction Model for Count Data with Genotype × Environment Interaction

Genomic tools allow the study of the whole genome, and facilitate the study of genotype-environment combinations and their relationship with phenotype. However, most genomic prediction models developed so far are appropriate for Gaussian phenotypes. For this reason, appropriate genomic prediction models are needed for count data, since the conventional regression models used on count data with a large sample size (nT) and a small number of parameters (p) cannot be used for genomic-enabled prediction where the number of parameters (p) is larger than the sample size (nT). Here, we propose a Bayesian mixed-negative binomial (BMNB) genomic regression model for counts that takes into account genotype by environment (G×E) interaction. We also provide all the full conditional distributions to implement a Gibbs sampler. We evaluated the proposed model using a simulated data set, and a real wheat data set from the International Maize and Wheat Improvement Center (CIMMYT) and collaborators. Results indicate that our BMNB model provides a viable option for analyzing count data