Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.

Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.

An investigation of the role of transition metal ions impurities in CdO: Local structure and electronic properties.

According to the high-order perturbation formulae of 3d5 (Mn2+ ) and 3d9 (Cu2+ ) ions in octahedron, the local structures and electron paramagnetic resonance (EPR) parameters (g factors and hyperfine structure constants A) for Cu2+ and Mn2+ in CdO are theoretically studied in a consistent way. Due to the Jahn-Teller effect, both the substituted sites of Cu2+ and Mn2+ show the tetragonally elongated distortion with different elongation τ. Meanwhile, the crystal field and covalency around doped Cu2+ and Mn2+ are obtained, which can account for the electronic properties in doped CdO. In order to make further investigation of the potential optical and electrical properties, the band structure and density of states (DOS) of pure and transition metal ions (TMs) doped CdO are comparably calculated through density functional theory (DFT). The results show that the band gap of Mn2+ - and Cu2+ -doped CdO can be effectively reduced, due to the improved covalency between the central ions and ligand ions.

[Invasive ductal carcinomas of breast showing partial reversed cell polarity are associated with lymphatic tumor spread].

OBJECTIVE: To investigate the relationship between partial reversed cell polarity (PRCP) and lymphatic tumor spread in invasive ductal carcinoma (IDC), not othervise specified (NOS). METHODS: Immunohistochemistry (EnVision method) was used to examine the expression of epithelial membrane antigen (EMA) and the reversed cell polarity in 199 cases of IDC. RESULTS: Of the 199 cases, including five cases with micropapillary differentiation,30 cases with PRCP and 164 cases of IDC-NOS (without micropapillary differentiation and/or PRCP), lymphovascular invasion was seen in four (4/5), 13(43.3%) and 30 cases (18.3%) respectively; nodal metastasis was seen in four (4/5), 19 (63.3%) and 56 cases (34.1%) respectively. The rates of lymphovascular invasion and nodal metastasis were significantly higher in IDC with PRCP or IMPC than IDC-NOS (P = 0.00); there was however no significant difference between IDC with PRCP and IMPC for lymphovascular invasion and nodal metastasis (P = 0.18, P = 0.64). CONCLUSIONS: IDC with PRCP, similar to IMPC, is more likely to show lymphovascular invasion and nodal metastasis. Complete or partial reversal of cell polarity may play a significant role in lymphatic tumor spread.

[Expression characteristics of prolactin gene in Eastern Zhejiang white geese].

This study was conducted to clone the prolactin gene (PRL) in Eastern Zhejiang White Geese and to investigate the PRL gene expression characteristics during egg-laying, out-of-lay and incubating periods by real time PCR. Comparisons were made respectively of concentration of prolactin mRNA in the hypothalamus, pituitary gland and ovary of the adult female geese at different reproductive periods. The result indicated that there were significant differences (P<0.05) in PRL mRNA expression between different reproductive periods of the geese. The lowest level of PRL expression was found in out-of-lay geese, higher in the egg-laying geese, and the highest in incubating geese. Furthermore, the analysis of PRL expression in different tissues indicated that the highest levels of PRL was expressed in the pituitary gland, followed in hypothalamus, and the least in ovary of the geese. There were significant difference (P<0.01) expression of PRL between the pituitary gland/hypothalamus and ovary of the geese, whereas no any difference was observed between the pituitary gland and hypothalamus (P>0.05). In summary, the PRL mRNA expression had variance in different reproductive periods of the geese.