A Case of Laying Hens Mycosis Caused by Fusarium proliferatum.

In this article, we present the first case report of a chicken mycosis caused by F. proliferatum occurred on a private farm in the Russian Federation. Lesions on the skin of the legs and scallops were reported. The object of this study was samples of feed and pathological material from sick hens-layers. Mycological analysis included determination of the total number of fungi (TNF) and identification and determination of the toxicity and pathogenicity of the isolates. The identification of the isolate was carried out taking into account direct microscopy, morphological features, and the method of molecular genetic analysis. Microscopic fungi of the genus Penicillium and Rhizopus were isolated by mycological analysis of the feed. The test feed was nontoxic. Mycological examination of pathological material (scrapings from the combs and affected legs) identified an isolate of Fusarium proliferatum, which showed toxicity on biological objects (protozoa, rabbits) and pathogenicity (white mice). Dermal application of F. proliferatum suspension was accompanied by reddening of the rabbit skin. Intraperitoneal injection of fungal spores caused mycosis in white mice. Polymerase chain reaction (PCR) made it possible to identify this type of microscopic fungus (F. proliferatum) with high accuracy in the samples under study. The research results allow us to consider F. proliferatum as a cause of poultry disease against the background of predisposing factors in the form of desquamation of the stratum corneum of the skin against the background of immunosuppression and metabolic disorders caused by an imbalance in the diet.

Assessment of Irrigation Efficiency by Coupling Remote Sensing and Ground-Based Data: Case Study of Sprinkler Irrigation of Alfalfa in the Saratovskoye Zavolgie Region of Russia.

Nowadays, the leading role of data from sensors to monitor crop irrigation practices is indisputable. The combination of ground and space monitoring data and agrohydrological modeling made it possible to evaluate the effectiveness of crop irrigation. This paper presents some additions to recently published results of field study at the territory of the Privolzhskaya irrigation system located on the left bank of the Volga in the Russian Federation, during the growing season of 2012. Data were obtained for 19 crops of irrigated alfalfa during the second year of their growing period. Irrigation water applications to these crops was carried out by the center pivot sprinklers. The actual crop evapotranspiration and its components being derived with the SEBAL model from MODIS satellite images data. As a result, a time series of daily values of evapotranspiration and transpiration were obtained for the area occupied by each of these crops. To assess the effectiveness of irrigation of alfalfa crops, six indicators were used based on the use of data on yield, irrigation depth, actual evapotranspiration, transpiration and basal evaporation deficit. The series of indicators estimating irrigation effectiveness were analyzed and ranked. The obtained rank values were used to analyze the similarity and non-similarity of indicators of irrigation effectiveness of alfalfa crops. As a result of this analysis, the opportunity to assess irrigation effectiveness with the help of data from ground and space-based sensors was proved.

Investigation of Hafnium Thin Films for Design of TES Microcalorimeters.

Hafnium is a superconductor with a transition temperature slightly above 100 mK. This makes it attractive for such applications as microcalorimeters with high energy resolution. We report the superconducting properties of Hf films of thicknesses ranging from 60 to 115 nm, deposited on Si and Al2O3 substrates by electron beam evaporation. Besides that, we fabricated and measured combinations of hafnium with thin layers of normal metals, decreasing the critical temperature by the proximity effect. The critical temperature of the studied films varied from 56 to 302 mK. We have observed a significant change in the critical temperature of some films over time, which we propose to prevent by covering hafnium films with a thin layer of titanium.

Spatial Interpolation of Gravimetric Soil Moisture Using EM38-mk Induction and Ensemble Machine Learning (Case Study from Dry Steppe Zone in Volgograd Region).

The implementation of the sustainable management of the interaction between agriculture and the environment requires an increasingly deep understanding and numerical description of the soil genesis and properties of soils. One of the areas of application of relevant knowledge is digital irrigated agriculture. During the development of such technologies, the traditional methods of soil research can be quite expensive and time consuming. Proximal soil sensing in combination with predictive soil mapping can significantly reduce the complexity of the work. In this study, we used topographic variables and data from the Electromagnetic Induction Meter (EM38-mk) in combination with soil surface hydrological variables to produce cartographic models of the gravimetric soil moisture for a number of depth intervals. For this purpose, in dry steppe zone conditions, a test site was organized. It was located at the border of the parcel containing the irrigated soybean crop, where 50 soil samples were taken at different points alongside electrical conductivity data (ECa) measured in situ in the field. The modeling of the gravimetric soil moisture was carried out with the stepwise inclusion of independent variables, using methods of ensemble machine learning and spatial cross-validation. The obtained cartographic models showed satisfactory results with the best performance R2cv 0.59-0.64. The best combination of predictors that provided the best results of the model characteristics for predicting gravimetric soil moisture were geographical variables (buffer zone distances) in combination with the initial variables converted into the principal components. The cartographic models of the gravimetric soil moisture variability obtained this way can be used to solve the problems of managed irrigated agriculture, applying fertilizers at variable rates, thereby optimizing the use of resources by crop producers, which can ultimately contribute to the sustainable management of natural resources.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse.

Eukaryotic genomes contain many nongenic elements that function in gene regulation, chromosome organization, recombination, repair, or replication, and mutation of those elements can affect genome function and cause disease. Although numerous epigenomic studies provide high coverage of gene regulatory regions, those data are not usually exposed in traditional genome annotation and can be difficult to access and interpret without field-specific expertise. The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature. The curated data set is comprised of richly annotated sequence records, descriptive records in the NCBI Gene database, reference genome feature annotation, and activity-based interactions between nongenic regions, target genes, and each other. The data set provides succinct functional details and transparent experimental evidence, leverages data from multiple experimental sources, is readily accessible and adaptable, and uses a flexible data model. The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation; as known positive controls for epigenomic data evaluation; and as reference standards for functional interactions. Comparisons to other gene regulatory data sets show that the RefSeqFE data set includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data selection biases. RefSeqFEs thus provide an alternative and complementary resource for experimentally assayed functional elements, with future data set growth expected.

Artificial Dense Lattices of Magnetic Skyrmions.

Multilayer Co/Pt films with perpendicular magnetic anisotropy are irradiated by focused a He+ ion beam to locally reduce the anisotropy value. The irradiated spots with the diameters of 100 and 200 nm are arranged in square lattices with the periods of 200 and 300 nm. The formation of nonuniform magnetic states within the spots was observed by magnetic force microscopy methods. We use the concentric distribution of the irradiation fluence within the spot to obtain the radial modulation of the anisotropy constant. This allows us to induce magnetic skyrmions during magnetization reversal of the system. The skyrmions remained stable at zero external magnetic field at room temperature. Magnetization hysteresis loops of the samples were investigated by magnetooptical methods and the results are in good agreement with micromagnetic simulations.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Gene: a gene-centered information resource at NCBI.

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP.

RefSeq: an update on mammalian reference sequences.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI's eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI's eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.