Search

The paper presents the results on the development of an optical coating for a single-crystal ZnGeP2 substrate based on a selenide-oxide pair of materials (ZnSe/Al2O3). The obtained coating ensures the operation of OPO in the mid-IR range up to 5 μm wavelengths. The possibility of ZnSe sputtering by the IBS method is shown. The obtained optical coating has a high laser-induced damage threshold (LIDT) value at a 2097 µm wavelength: WoE=3.51 J/cm2 in energy density and WoP= 101 W/cm2 in power density at a 10 KHz pulse repetition frequency and a pulse duration of 35 ns. Thus, it is shown for the first time that the pair of materials ZnSe/Al2O3 can be used for the deposition of optical coatings by the IBS method with high LIDT values for ZnGeP2 optical elements operating in the mid-IR range.

Zinc germanium phosphide (ZGP) crystals have garnered significant attention for their nonlinear properties, making them good candidates for powerful mid-IR optical parametric oscillators and second-harmonic generators. A ZnGeP2 single crystal was treated by deep magnetorheological processing (MRP) until an Angstrom level of roughness. The studies presented in this article are devoted to the experimental evaluation of the influence of deep removal (up to 150 μm) from the surface of a ZnGeP2 single crystal by magnetorheological polishing on the parameters of optical breakdown. It was shown that the dependence of the ZnGeP2 laser-induced damage threshold on MRP depth is a smooth monotonically decreasing logarithmic function. The obtained logarithmic dependence indicates the thermal nature of optical breakdown and the dependence of the ZnGeP2 laser-induced damage threshold on the concentration of surface absorbing defects.

Terahertz wave generation through the optical rectification of 780 nm femtosecond laser pulses in ZnGeP2 crystals has been studied. All of the possible interactions of types I and II were analyzed by modeling and experimentally. We demonstrate the possibility of broadband “low-frequency” terahertz generation by an ee–e interaction (with two pumping waves and a generated terahertz wave; all of these had extraordinary polarization in the crystal) and “high-frequency” terahertz generation by an oe–e interaction. The arising possibility of achieving the narrowing of the terahertz generation bandwidth at the oe–e interaction using thicker ZnGeP2 crystals is experimentally confirmed. It has been found that the thermal annealing of as-grown ZnGeP2 crystals and their doping with a 0.01 mass % of Sc reduces the absorption in the “anomalous absorption” region (λ = 0.62–3 μm). The terahertz generation by the oo–e interaction in (110) ZnGeP2:Sc and the as-grown ZnGeP2 crystals of equal thicknesses was compared. It has been found that ZnGeP2:Sc is more efficient for 780 nm femtosecond laser pulses optical rectification.

A multispectral anti-reflective coating of high radiation strength for laser applications in the IR spectrum for nonlinear ZnGeP2 crystals has been developed for the first time. The coating was constructed using YbF3/ZnS. The developed coating was obtained by a novel approach using ion-beam deposition of these materials on a ZnGeP2 substrate. It has a high LIDT of more than 2 J/cm2. Optimal layer deposition regimes were found for high film density and low absorption, and good adhesion of the coating to the substrate was achieved. At the same time, there was no dissociation of the double compound under high-energy ions.

Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional F ST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4 , COX17 , MAATS1 , UPK1B , IFNGR1 , DDX23 , PPT1 , THBS1 , CCL5 , ATF1 , PLA1A , PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.

The opportunities and special features of using a multi-purpose digital holographic camera (DHC) adapted for particle research for various diagnostic tasks, such as plankton investigation in its habitat, optical glass diagnostics, and study of defects in single crystals, are investigated. Experimental research with the DHC carried out and described in this paper has demonstrated the universality of the DHC measurement technology and its effectiveness for solving a number of diagnostic tasks in the study of small particles of different natures in various media.

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Background: Since processes in well-known model organisms have specific features different from those in Bos taurus, the organism under study, a good way to describe gene regulation in ruminant embryos would be a species-specific consideration of closely related species to cattle, sheep and pig. However, as highlighted by a recent report, gene dictionaries in pig are smaller than in cattle, bringing a risk to reduce the gene resources to be mined (and so for sheep dictionaries). Bioinformatics approaches that allow an integration of available information on gene function in model organisms, taking into account their specificity, are thus needed. Besides these closely related and biologically relevant species, there is indeed much more knowledge of (i) trophoblast proliferation and differentiation or (ii) embryogenesis in human and mouse species, which provides opportunities for reconstructing proliferation and/or differentiation processes in other mammalian embryos, including ruminants. The necessary knowledge can be obtained partly from (i) stem cell or cancer research to supply useful information on molecular agents or molecular interactions at work in cell proliferation and (ii) mouse embryogenesis to supply useful information on embryo differentiation. However, the total number of publications for all these topics and species is great and their manual processing would be tedious and time consuming. This is why we used text mining for automated text analysis and automated knowledge extraction. To evaluate the quality of this "mining", we took advantage of studies that reported gene expression profiles during the elongation of bovine embryos and defined a list of transcription factors (or TF, n = 64) that we used as biological "gold standard". When successful, the "mining" approach would identify them all, as well as novel ones., Methods: To gain knowledge on molecular-genetic regulations in a non model organism, we offer an approach based on literature-mining and score arrangement of data from model organisms. This approach was applied to identify novel transcription factors during bovine blastocyst elongation, a process that is not observed in rodents and primates. As a result, searching through human and mouse corpuses, we identified numerous bovine homologs, among which 11 to 14% of transcription factors including the gold standard TF as well as novel TF potentially important to gene regulation in ruminant embryo development. The scripts of the workflow are written in Perl and available on demand. They require data input coming from all various databases for any kind of biological issue once the data has been prepared according to keywords for the studied topic and species; we can provide data sample to illustrate the use and functionality of the workflow., Results: To do so, we created a workflow that allowed the pipeline processing of literature data and biological data, extracted from Web of Science (WoS) or PubMed but also from Gene Expression Omnibus (GEO), Gene Ontology (GO), Uniprot, HomoloGene, TcoF-DB and TFe (TF encyclopedia). First, the human and mouse homologs of the bovine proteins were selected, filtered by text corpora and arranged by score functions. The score functions were based on the gene name frequencies in corpora. Then, transcription factors were identified using TcoF-DB and double-checked using TFe to characterise TF groups and families. Thus, among a search space of 18,670 bovine homologs, 489 were identified as transcription factors. Among them, 243 were absent from the high-throughput data available at the time of the study. They thus stand so far for putative TF acting during bovine embryo elongation, but might be retrieved from a recent RNA sequencing dataset (Mamo et al. , 2012). Beyond the 246 TF that appeared expressed in bovine elongating tissues, we restricted our interpretation to those occurring within a list of 50 top-ranked genes. Among the transcription factors identified therein, half belonged to the gold standard (ASCL2, c-FOS, ETS2, GATA3, HAND1) and half did not (ESR1, HES1, ID2, NANOG, PHB2, TP53, STAT3)., Conclusions: A workflow providing search for transcription factors acting in bovine elongation was developed. The model assumed that proteins sharing the same protein domains in closely related species had the same protein functionalities, even if they were differently regulated among species or involved in somewhat different pathways. Under this assumption, we merged the information on different mammalian species from different databases (literature and biology) and proposed 489 TF as potential participants of embryo proliferation and differentiation, with (i) a recall of 95% with regard to a biological gold standard defined in 2011 and (ii) an extension of more than 3 times the gold standard of TF detected so far in elongating tissues. The working capacity of the workflow was supported by the manual expertise of the biologists on the results. The workflow can serve as a new kind of bioinformatics tool to work on fused data sources and can thus be useful in studies of a wide range of biological processes.