Orbital parameters and evolutionary status of the highly-peculiar binary system HD 66051

The spectroscopic binary system HD 66051 (V414 Pup) consists of a highlypeculiar CP3 (HgMn) star and an A-type component. It also shows out-of-eclipsevariability that is due to chemical spots. This combination allows thederivation of tight constraints for the testing of time-dependent diffusionmodels. We analysed radial velocity and photometric data using two differentmethods to determine astrophysical parameters and the orbit of the system.Appropriate isochrones were used to derive the age of the system. The orbitalsolution and the estimates from the isochrones are in excellent agreement withthe estimates from a prior spectroscopic study. The system is very close to thezero-age main sequence and younger than 120 Myr. HD 66051 is a most importantspectroscopic binary system that can be used to test the predictions of thediffusion theory explaining the peculiar surface abundances of CP3 stars.Fil: Paunzen, E.. Masaryk University; República ChecaFil: Fedurco, M.. Masaryk University; República ChecaFil: Helminiak, K.G.. Masaryk University; República ChecaFil: Pintado, Olga Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Correlación Geológica. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Departamento de Geología. Cátedra Geología Estructural. Instituto Superior de Correlación Geológica; Argentin

Periodic variable A-F spectral type stars in the northern TESS continuous viewing zone. I. Identification and classification

Context. In the time of large space surveys that provide tremendous amounts of precise data, it is highly desirable to have a commonly accepted methodology and system for the classification of variable stars. This is especially important for A-F stars, which can show intrinsic brightness variations due to both rotation and pulsations. Aims: The goal of our study is to provide a reliable classification of the variability of A-F stars brighter than 11 mag located in the northern TESS continuous viewing zone. We also aim to provide a thorough discussion about issues in the classification related to data characteristics and the issues arising from the similar light-curve shape generated by different physical mechanisms. Methods: We used TESS long- and short-cadence photometric data and corresponding Fourier transform to classify the variability type of the stars. We also used spectroscopic observations to determine the projected rotational velocity of a few stars. Results: We present a clear and concise classification system that is demonstrated on many examples. We find clear signs of variability in 3025 of 5923 studied stars (51%). For 1813 of these 3025 stars, we provide a classification; the rest cannot be unambiguously classified. Of the classified stars, 64.5% are pulsating stars of g-mode γ Doradus (GDOR) and p-mode δ Scuti types and their hybrids. We realised that the long- and short-cadence pre-search data conditioning simple aperture photometry data can differ significantly not only in amplitude but also in the content of instrumental and data-reduction artefacts, making the long-cadence data less reliable. We identified a new group of stars that show stable light curves and characteristic frequency spectrum patterns (8.5% of the classified stars). According to the position in the Hertzsprung-Russell diagram, these stars are likely GDOR stars but are on average about 200 K cooler than GDORs and have smaller amplitudes and longer periods. With the help of spectroscopic measurements of v sin i, we show that the variability of stars with unresolved groups of peaks located close to the positions of the harmonics in their frequency spectra (16% of the classified stars) can be caused by rotation rather than by pulsations. We show that without spectroscopic observations it can be impossible to unambiguously distinguish between ellipsoidal variability and rotational variability. We also applied our methodology to three previous studies and find significant discrepancies in the classification. Conclusions: We demonstrate how difficult the classification of variable A-F stars can be when using only photometric data, how the residual artefacts can produce false positives, and that some types cannot actually be distinguished without spectroscopic observations. Our analysis provides collections that can be used as training samples for automatic classification. Full Table 5 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/cat/J/A+A/666/A14

Biochemical applications of surface-enhanced infrared absorption spectroscopy

An overview is presented on the application of surface-enhanced infrared absorption (SEIRA) spectroscopy to biochemical problems. Use of SEIRA results in high surface sensitivity by enhancing the signal of the adsorbed molecule by approximately two orders of magnitude and has the potential to enable new studies, from fundamental aspects to applied sciences. This report surveys studies of DNA and nucleic acid adsorption to gold surfaces, development of immunoassays, electron transfer between metal electrodes and proteins, and protein–protein interactions. Because signal enhancement in SEIRA uses surface properties of the nano-structured metal, the biomaterial must be tethered to the metal without hampering its functionality. Because many biochemical reactions proceed vectorially, their functionality depends on proper orientation of the biomaterial. Thus, surface-modification techniques are addressed that enable control of the proper orientation of proteins on the metal surface. [Figure: see text

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model

Abstract Background Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh throughput genomic sequencing both provide rapid, robust, and comprehensive methods to identify CNVs on a whole-genome scale. Results We developed a Bayesian statistical analysis algorithm for the detection of CNVs from both types of genomic data. The algorithm can analyze such data obtained from PCR-based bacterial artificial chromosome arrays, high-density oligonucleotide arrays, and more recently developed high-throughput DNA sequencing. Treating parameters--e.g., the number of CNVs, the position of each CNV, and the data noise level--that define the underlying data generating process as random variables, our approach derives the posterior distribution of the genomic CNV structure given the observed data. Sampling from the posterior distribution using a Markov chain Monte Carlo method, we get not only best estimates for these unknown parameters but also Bayesian credible intervals for the estimates. We illustrate the characteristics of our algorithm by applying it to both synthetic and experimental data sets in comparison to other segmentation algorithms. Conclusions In particular, the synthetic data comparison shows that our method is more sensitive than other approaches at low false positive rates. Furthermore, given its Bayesian origin, our method can also be seen as a technique to refine CNVs identified by fast point-estimate methods and also as a framework to integrate array-CGH and sequencing data with other CNV-related biological knowledge, all through informative priors.</p

Addressing challenges in the production and analysis of illumina sequencing data

Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq) represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.</p> <p>Results</p> <p>More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.</p> <p>Conclusion</p> <p>We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.</p