RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

BACKGROUND: The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. RESULTS: The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. CONCLUSION: We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3622-9) contains supplementary material, which is available to authorized users

GEOLOGIC FRAMEWORK AND HYDROGEOLOGIC CHARACTERISTICS OF THE EDWARDS AQUIFER RECHARGE ZONE, BEXAR COUNTY, TEXAS

In Bexar County, residential and commercial development on the Edwards aquifer recharge zone is increasing. The aquifer possibly can be contaminated by spills, leakage of hazardous materials, or runoff from the rapidly developing urban areas that surround, or are built on, the intensely faulted and fractured, karstic limestone outcrops characteristic of the recharge zone. Furthermore, some of the hydrogeologic subdivisions that compose the Edwards aquifer have greater effective porosity than others. The areas where the most porous subdivisions crop out might provide efficient avenues for contaminants to enter the aquifer. The Edwards aquifer recharge zone has relatively large permeability resulting, in part, from the development or redistribution of secondary porosity. Lithology, stratigraphy, diagenesis, and karstification account for the effective porosity and permeability in the Edwards aquifer outcrop. Karst features that greatly enhance effective porosity in the outcrop area include sinkholes and caves. Hydrogeologic subdivision VI, the Kirschberg evaporite member, appears to be the most porous and permeable subdivision within the Kainer Formation. Hydrogeologic subdivision HI, the leached and collapsed members, undivided, is the most porous and permeable subdivision within the Person Formation. Hydrogeologic subdivision II, the cyclic and marine members, undivided, is moderately permeable, with both fabric- and notfabric-selective porosity. The faults in northern Bexar County are part of the Balcones fault zone. Although most of the faults in this area trend northeast, a smaller set of cross-faults trend northwest. Generally, the faults are en echelon and normal, with the downthrown blocks typically toward the coast

GEOLOGIC FRAMEWORK AND HYDROGEOLOGIC CHARACTERISTICS OF THE EDWARDS AQUIFER RECHARGE ZONE, BEXAR COUNTY, TEXAS

In Bexar County, residential and commercial development on the Edwards aquifer recharge zone is increasing. The aquifer possibly can be contaminated by spills, leakage of hazardous materials, or runoff from the rapidly developing urban areas that surround, or are built on, the intensely faulted and fractured, karstic limestone outcrops characteristic of the recharge zone. Furthermore, some of the hydrogeologic subdivisions that compose the Edwards aquifer have greater effective porosity than others. The areas where the most porous subdivisions crop out might provide efficient avenues for contaminants to enter the aquifer. The Edwards aquifer recharge zone has relatively large permeability resulting, in part, from the development or redistribution of secondary porosity. Lithology, stratigraphy, diagenesis, and karstification account for the effective porosity and permeability in the Edwards aquifer outcrop. Karst features that greatly enhance effective porosity in the outcrop area include sinkholes and caves. Hydrogeologic subdivision VI, the Kirschberg evaporite member, appears to be the most porous and permeable subdivision within the Kainer Formation. Hydrogeologic subdivision HI, the leached and collapsed members, undivided, is the most porous and permeable subdivision within the Person Formation. Hydrogeologic subdivision II, the cyclic and marine members, undivided, is moderately permeable, with both fabric- and notfabric-selective porosity. The faults in northern Bexar County are part of the Balcones fault zone. Although most of the faults in this area trend northeast, a smaller set of cross-faults trend northwest. Generally, the faults are en echelon and normal, with the downthrown blocks typically toward the coast

Escenario ONG's: Proyecto de playas

El municipio de Cabo Corrientes es uno de los municipios del estado de Jalisco, específicamente de la región Costa-Sierra Occidental, que cuenta con un alto desarrollo del medio ambiente en comparación al resto de otros municipios de la entidad. El Í ndice Municipal de Medio Ambiente, 2013, destaca que Cabo Corrientes se ubica en un acuífero no sobreexplotado. El í ndice del medio ambiente atiende aspectos como la generación de residuos sólidos, deforestación, explotación de acuíferos, cobertura forestal, á reas naturales protegidas, entre otros. Los principales problemas que presenta este municipio son la falta de infraestructura pública que contempla puentes vehiculares, centros de salud, escuelas, alumbrado público y calles pavimentadas. Otro de los principales problemas es la poca gestión que existe sobre el turismo, ya que esto conlleva a que exista un uso desordenado en las playas. El presente trabajo busca dar cuenta de los resultados obtenidos en la investigación realizada en el municipio de Cabo Corrientes sobre sus recursos e infraestructura, así como si es un lugar que cuenta con el suficiente potencial para desarrollar proyectos ecoturísticos que fomenten la economía siempre cuidando al medio ambiente.ITESO, A.C

Reconnaissance investigation of the geology and hydrogeology of Lackland Air Force Base, San Antonio, Texas /

Shipping list no.: 93-0650-P.Includes bibliographical references (p. 20).Mode of access: Internet

Diversification of the celiac disease α-gliadin complex in wheat: a 33-mer peptide with six overlapping epitopes, evolved following polyploidization

The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6–8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: p31–43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. Next-generation sequencing (NGS) and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1–6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31–43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only type 1 α-gliadins contained 33-mer epitopes. Moreover, the full immunodominant 33-mer fragment was only present in hexaploid wheat at low abundance, probably as the result of allohexaploidization events from subtype 1.2 α-gliadins found only in Aegilops tauschii, the D-genome donor of hexaploid wheat. Type 3 α-gliadins seem to be the ancestral type as they are found in most of the α-gliadin-expressing Triticeae species. These findings are important for reducing the incidence of CD by the breeding/selection of wheat varieties with low stimulatory capacity of T cells. Moreover, advanced genome-editing techniques (TALENs, CRISPR) will be easier to implement on the small group of α-gliadins containing only immunogenic peptides.The Spanish Ministry of Economy and Competitiveness (Project AGL2013-48946-C3-1-R), the European Regional Development Fund (FEDER), and Junta de Andalucía (Project P11-AGR-7920) supported this work.Peer reviewe