Copy number variation mapping and genomic variation of autochthonous and commercial turkey populations

This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d\u2019Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix\uae. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362\u2014189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting

7th Drug hypersensitivity meeting: part two

No abstract availabl

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival

MgCo2-D2 and MgCoNi-D2 systems synthesized at high pressures and interaction mechanism during the HDDR processing

MgCo2 and MgNiCo crystallize with hexagonal Laves type intermetallic structures of the C14 type and do not form hydrides at ambient hydrogen pressures. However, applying high hydrogen pressures in the GPa range forces the hydrogen absorption and leads to the formation of multi-phase compositions, which contain approximately 2.5 atoms H per formula unit of MgCo2 or MgNiCo and remain thermally stable under normal conditions. The hydrogenation of MgCo2 resulted in its decomposition to a ternary Mg2CoD5 deuteride and metallic cobalt. Phase-structural transformations accompanying the vacuum desorption of deuterium in the temperature range of 27–500 °C were studied using in situ neutron powder diffraction. The investigation showed a complete recovery of the initial MgCo2 intermetallic via a Hydrogenation-Disproportionation-Desorption-Recombination process. At 300 °C, the Mg2CoD5 deuteride first decomposed to elementary Mg and hexagonal Co. At 400 °C, a MgCo phase was formed by interaction between Mg and Co. At the highest processing temperature of 500 °C, a solid-state interaction of MgCo and Co resulted in the recovery of the initial MgCo2. The interaction of MgNiCo with deuterium under the synthesis conditions of 2.8 GPa and 200 °C proceeded in a more complex way. A very stable ternary deuteride MgNi2D3 was leached away while Co was separated in the form of Mg2CoD5 and the remaining nickel formed a solid solution with Co with the approximate composition Ni0.7Co0.3. The thermal desorption of deuterium from MgCo2D2.5 and from MgNiCoD2.5 has been studied by Thermal Desorption Spectroscopy with deuterium released into a closed volume. The observed effects nicely correlate with changes in the phase structural composition of the hydrides formed. MgCo2 is a new example of the hydrogen storage alloy, in which a successful HDDR processing results in the reversible formation of the initial intermetallic at much lower temperatures than in the equilibrium phase diagram of the Mg-Co system