single nucleotide polymorphism discovery in the avian tapasin gene

Abstract Tapasin is a transmembrane glycoprotein located in the endoplasmic reticulum. Its function is to assist the assembly of major histocompatibility complex class I molecules. The chicken Tapasin gene includes 8 exons and is localized inside the major histocompatibility complex between the 2 class IIβ genes. The aim of the current study was the estimation of single nucleotide polymorphism frequency within the avian Tapasin gene. The Tapasin gene sequence from exon 5 to exon 6 was amplified for the chicken, turkey, and pheasant, and sequences of different lengths were obtained. The sequence analysis based on PolyBayes identified 25 putative single nucleotide polymorphism sites when the 3 species were compared. The coding sequences were further translated and analyzed to identify amino acid substitutions. The results indicated that polymorphisms within this region of the gene was mainly observed in the heterozygous state. The level of conservation of the Tapasin gene sequence among species is likely to be related to the functional importance of the gene

Regional evaluation of three day snow depth for avalanche hazard mapping in Switzerland

The distribution of the maximum annual three day snow fall depth <i>H<sub>72</sub></i>, used for avalanche hazard mapping according to the Swiss procedure (<i>Sp</i>), is investigated for a network of 124 stations in the Alpine part of Switzerland, using a data set dating back to 1931. Stationarity in time is investigated, showing in practice no significant trend for the considered period. Building on previous studies about climatology of Switzerland and using an iterative approach based on statistical tests for regional homogeneity and scaling of <i>H<sub>72</sub></i> with altitude, seven homogenous regions are identified. A regional approach based on the index value is then developed to estimate the <i>T</i>-years return period quantiles of <i>H<sub>72</sub></i> at each single site <i>i</i>, <i>H<sub>72i</sub>(T)</i>. The index value is the single site sample average μ<sub><i>H<sub>72i</sub></i></sub>. The dimensionless values of <i>H<sup>*</sup><sub>72i</sub>=H<sub>72i</sub> / μ<sub>H<sub>72i</sub></sub></i> are grouped in one sample for each region and their frequency of occurrence is accommodated by a General Extreme Value, GEV, probability distribution, including Gumbel. The proposed distributions, valid in each site of the homogeneous regions, can be used to assess the <i>T</i>-years return period quantiles of <i>H<sup>*</sup><sub>72i</sub></i>. It is shown that the value of <i>H<sub>72i</sub>(T)</i> estimated with the regional approach is more accurate than that calculated by single site distribution fitting, particularly for high return periods. A sampling strategy based on accuracy is also suggested to estimate the single site index value, i.e. the sample average μ<sub><i>H<sub>72i</sub></i></sub>, critical for the evaluation of the distribution of <i>H<sub>72i</sub></i>. The proposed regional approach is valuable because it gives more accurate snow depth input to dynamics models than the present procedure based on single site analysis, so decreasing uncertainty in hazard mapping procedure

Molecular characterization of genes involved in chicken MHC class I antigen presentation pathway

Tapasin, TAP1 and TAP2 are involved in the assembly of MHC class I molecules. The genes encoding these three products belong to the Major Histocompatibility Complex: in chicken, Tapasin is located between the two class IIb genes, while TAP1 and TAP2 are found between the two class I genes. The current study aimed at the molecular characterization of these three genes. Starting from Single Nucleotide Polymorphisms (11 in Tapasin, 18 in TAP1 and 21 in TAP2) previously discovered by the authors within these genes, the nucleotide diversity was assessed at each locus. Moreover, the haplotypes were reconstructed for each individual and the genetic distances between the chicken lines and breeds were estimated. From the analysis of the nucleotide diversity values, variable polymorphism rates could be observed among the three genes. In the three analyzed loci the SNPs rates were higher than the reported chicken genome mean nucleotide diversity of 5 SNPs kb-1. The calculation of the genetic distances permitted, generally, the distinction of animals among the analyzed lines/breeds

Microarray analyses to identify differentially expressed genes for assessing meat quality in swine

In order to identify candidate genes and molecular mechanisms that influence meat quality and production in pigs, microarray experiments were carried out to find differences in gene expression levels between two pools of six individuals, constituting the extreme tails of the Gaussian distribution of seven adjusted phenotypes of 100 Landrace and Large White animals. The phenotypes considered in this study were: muscle compactness, marbling, colour uniformity, fat covering, colour, dorsal fat, thickness, ham fat thickness. 437 differentially expressed ESTs (Expressed Sequence Tags) were found, clustering in different pathways according to their ontology. In particular, 73 functional categories were identified and ten of them could have a role in meat quality. Among the ESTs belonging to these pathways, seven of them were selected to be validated in quantitative real-time RT-PCR

Preliminary study on MC1R polymorphism in some cattle breeds raised in Italy

Ricerche preliminari sul polimorfismo del gene MC1R in alcune razze bovine allevate in Italia – Il gene MC1R è stato analizzato in 193 soggetti appartenenti a 8 razze bovine, tramite PCR, per la presenza di due mutazioni ad effetto fenotipico noto sulla pigmentazione del mantello: la delezione G310 e la sostituzione T296C, associate rispettivamente al fenotipo feomelanico (e) ed eumelanico nero (Ed). Sessanta soggetti di razza Limousine e Pezzata Rossa Italiana presentano genotipo e/e; 27 soggetti di razza Frisona Italiana mostrano genotipo Ed/Ed mentre 2 genotipo Ed/e. Gli 84 soggetti appartenenti alle razze Cabannina, Chianina, Marchigiana e Piemontese non presentano tali mutazioni, analogamente a 18 soggetti di razza Romagnola, nella quale però si sono anche osservati 2 soggetti portatori dell’allele e allo stato eterozigote

Horse bone marrow mesenchymal stem cells express embryo stem cell markers and show the ability for tenogenic differentiation by in vitro exposure to BMP-12

Background: Mesenchymal stem cells (MSCs) have been recently investigated for their potential use in regenerative medicine. MSCs, in particular, have great potential, as in various reports they have shown pluripotency for differentiating into many different cell types. However, the ability of MSCs to differentiate into tendon cells in vitro has not been fully investigated. Results: In this study, we show that equine bone marrow mesenchymal stem cells (BM-MSCs), defined by their expression of markers such as Oct4, Sox-2 and Nanog, have the capability to differentiate in tenocytes. These differentiated cells express tendon-related markers including tenomodulin and decorin. Moreover we show that the same BM-MSCs can differentiate in osteocytes, as confirmed by alkaline phosphatase and von Kossa staining. Conclusion: As MSCs represent an attractive tool for tendon tissue repair strategies, our data suggest that bone marrow should be considered the preferred MSC source for therapeutic approaches

Crystallization Process and Site-Selective Excitation of Nd3+ in LaF3/NaLaF4 Sol–Gel-Synthesized Transparent Glass-Ceramics

In this study, transparent oxyfluoride glass-ceramics (GCs) with NaLaF4 nanocrystals (NCs) were prepared by the sol–gel method for the first time. Three different molar ratios of La(CH3COO)3/Na(CH3COO) were used to obtain the GCs, which were sintered at 450, 550 and 650 °C for 1 min. X-ray diffraction (XRD) was employed to follow the evolution of the xerogel during the heat treatments and to study crystal growth for the three temperatures. In all cases, the LaF3 crystalline phase was present, but crystallization of NaLaF4 was only promoted at 650 °C. Thermogravimetric and thermodifferential analysis (TGA-DTA) and Fourier transform infrared spectroscopy (FTIR) were used to analyze the crystallization process. High-resolution transmission electron microscopy (HRTEM) was employed to confirm NaLaF4 crystallization and determine the size distribution. The incorporation of Nd3+ ion into NaLaF4 and LaF3 nanocrystals was confirmed by site-selective emission and excitation spectra. The Nd3+ emission intensities in both phases depend not only on the NaLaF4/LaF3 ratio but also on their emission efficiencies.The authors acknowledge financial support from MINECO under projects MAT2017-87035-C2-1-P/-2-P (AEI/FEDER, UE), and Basque Government PIBA2018-24. This article is a part of the dissemination activities of the project FunGlass, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 739566

Towards interoperability in the european poetry community: the standardization of philological concepts

This paper stems from the Poetry Standardization and Linked Open Data project (POSTDATA). As its name reveals, one of the main aims of POSTDATA is to provide a means to publish European poetry (EP) data as Linked Open Data (LOD). Thus, developing a metadata application profile (MAP) as a common semantic model to be used by the EP community is a crucial step of this project. This MAP will enhance interoperability among the community members in particular, and among the EP community and other contexts in general (e.g. bibliographic records). This paper presents the methodology followed in the process of defining the concepts of the domain model of this MAP, as well as some issues that arise when labeling philological terms.info:eu-repo/semantics/publishedVersio