Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

<p>Abstract</p> <p>Background</p> <p>'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (F_ST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle.</p> <p>Results</p> <p>We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian F_ST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme F_STvalues were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant F_STvalues were found in regions of some relevant genes such as SMCP and FGF1.</p> <p>Conclusions</p> <p>Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and F_STsuggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation.</p

Comparative assessment of the performance of long period fiber grating-based biosensors

Evanescent wave-based optical fiber biosensors consisting of long period grating (LPG) are presented. A chemical or a biochemical interaction taking place on a conveniently treated surface causes a refractive index (RI) change that can be evaluated using optical approaches. By implementing the same antibody/antigen (IgG/anti-IgG) assay protocol in the same experimental conditions, a comparative assessment of the biosensor performance was carried out by using different types of LPGs (standard, turn-around point and coated) in which the coupling occurred with different cladding modes. These sensors were firstly characterized in terms of volume (or bulk) RI sensitivity, which just provides an indication of the biosensor performance, and then of detection limit (LOD), which in turn represents a real and effective analytical parameter of biosensors extrapolated from their calibration curves. LODs of the order of μg L-1 (10-11 M) were achieved for turn-around point and coated LPGs both in buffer and in serum as real and complex matrix, thus also proving the biosensor specificity

Growth of Ta₂SnO₆ Films, a Candidate Wide-Band-Gap p‑Type Oxide

In an effort to discover a high-mobility p-type oxide, recent computational studies have focused on Sn2+-based ternary oxides. Ta2SnO6 has been suggested as a potentially useful p-type material based on the prediction of simultaneously high hole mobility and a wide range of synthesis conditions over which it is the energetically favored phase. In this study, we synthesized this material epitaxially for the first time and evaluated its properties experimentally. We measured the band gap to be 2.4 eV and attempted to substitutionally dope titanium for tantalum (TiTa’) and potassium for tin (KSn’) but found that both doped and undoped films were insulating. Amorphous Ta2SnO6 films were also grown via thermal atomic layer deposition (ALD) at 175 °C. Electrical characterization of the ALD-fabricated amorphous films found them to be insulating with an optical band gap of 2.24 eV. Density functional theory calculations indicate that, under MBE growth conditions, oxygen vacancies have a negative energy of formation in crystalline Ta2SnO6 when the Fermi energy lies near the valence band edge. These oxygen vacancies would lead to compensation of holes generated by TiTa’ or KSn’ dopants, which is consistent with our observations. We conclude that the direct growth of epitaxial p-type Ta2SnO6 films using MBE-accessible growth conditions is thwarted by the spontaneous formation of oxygen vacancies. While our growth conditions do not yield p-type films, we calculate that there are conditions under which Ta2SnO6 is the thermodynamically stable phase and spontaneous formation of compensating defects does not occur, motivating further studies with different synthesis techniques

Cladocera of Malaysia and Singapore with new records, redescriptions, and remarks on some species

An intensive and extensive sampling of the zooplankton from East and West Malaysia and Singapore yielded 63 cladoceran species of which 26 are recorded for this region for the first time. Redescriptions of a few species are given together with remarks on some others. The records include the first known occurrence of Alonella nana, Chydorus faviformis and Streblocercus pygmaeus in the tropics. The most diverse fauna was found in rice fields and ponds. The species composition is typical for a tropical region and lacks the families Polyphemidae, Leptodoridae and Holopedidae. Also Daphnia was extremely rare