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Background: The spectrum of clinical manifestations and pathogenetic mechanisms of bronchial asthma (BA) is very wide. Given the complex pathogenesis and syndromic nature of BA, it is not surprising that there is no single universal biomarker. The objective of this study was to evaluate levels of neuropeptide Y (NPY) and its association with levels of leptin, adiponectin, oxidative damage, antioxidant status, spirometry parameters, and asthma control in BA patients. Methods and Results: Overall, 140 patients [35(25%) men and 105(75%) women; mean age of 57.0±9.34 years] with moderate asthma participated in the study. According to body mass index, all patients were divided into three groups. The asthma diagnosis was based on the integral assessment of symptoms, medical history, health status, and spirometry values according to the Global Strategy for Asthma Management and Prevention. (GINA, 2017 REPORT). The Asthma Control Test (АСТ) was used to assess asthma control. NPY was measured in blood serum in EIA. The NPY level was significantly higher in overweight patients and patients with obesity than in patients with normal body weight. The NPY level significantly correlated with leptin (r=0.44; P

Background Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries. Results We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2. Conclusions On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y. pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.

Introduction. When conducting PCR (polymerase chain reaction) testing of biospecimens for SARS-CoV-2 RNA at the beginning of the COVID-19 pandemic, the laboratory service in Russia and foreign countries encountered problems related to the accuracy of diagnostics and obtaining false negative, false positive, and dubious results. The objective of this work was to analyze current literature on the problem of false positive and dubious results of RT-PCR testing for COVID-19. Material and methods. We selected Russian and foreign English-language publications devoted to organization of laboratory diagnostics of the novel coronavirus disease, challenges of PCR testing for SARS and MERS, and general issues of DNA contamination in a PCR laboratory for 2012–2020. We also reviewed current regulations and guidelines for COVID-19 diagnostic testing. Results. The analysis of factors leading to contamination of specimens with nucleic acids in the laboratories performing massive COVID-19 PCR testing during the pandemic showed that the main reasons for contamination included a large number of tests, accumulation of samples in the laboratory, and the increased amount of wastes containing amplification products. Cross-contamination occurs due to technical errors in the course of laboratory manipulations at the stages of sample preparation and inactivation, RNA isolation, and addition of cDNA/RNA or positive control samples to the reaction mixture. Pollution of laboratory working areas with amplicons arising from the opening of tubes and plates containing PCR products is the main cause of total contamination in the laboratory. Signs of cross-contamination include the increase in the proportion of positive samples with low threshold cycle values and detection of a positive signal from negative control samples at RNA isolation and amplification stages. A positive result for all samples in a round, including negative control samples, is a marker of “total contamination” in the laboratory. In addition to contamination, formation of nonspecific PCR products at late reaction cycles and nonspecific fluorescence of the reaction mixture, which occurs when reagent storage temperatures are not observed, may also lead to false positive results. Conclusion. To prevent contamination in a PCR laboratory, strict control over the flow of test samples and medical wastes, regular analysis of the frequency of positive test results, and mandatory laboratory quality control of testing and DNA/RNA contamination are compulsory.

In this report, we present new data on the diversity and geographical distribution of genetic variants in Crimean-Congo hemorrhagic fever virus (CCHFV) in Russia. Partial S, M, and L segment sequences of the CCHFV genome were obtained from 500 serum samples from CCHF patients and 103 pools of ticks collected in the south of the European region of Russia in 2007–2017. The investigated viral strains belonged to the lineages Europe 1 (596 samples), Africa 3 (1 sample) and a new genetic lineage, Europe 3 (6 samples). The Russian CCHFV strains of the Europe 1 lineage formed four subgroups (Va-Vd) correlated with the geographical site of virus isolation. Segment reassortment events between strains of different subgroups within lineage Europe 1 were revealed. The complete S, M and L genome segments of 18 CCHFV strains belonging to different subgroups of the Europe 1 lineage and the complete S segments of 3 strains of the Europe 3 lineage and 1 strain of the Africa 3 lineage were sequenced. The analysis of the geographical distribution of CCHFV genetic variants in southern Russia revealed local viral populations with partially overlapping boundaries.

Background Brucellosis is a bacterial zoonotic disease. Annually in the world more than 500,000 new cases of brucellosis in humans are registered. In this study, we propose an evolutionary model of the historical distribution of B. melitensis based on the full-genomic SNP analysis of 98 strains. Results We performed an analysis of the SNP of the complete genomes of 98 B. melitensis strains isolated in different geographical regions of the world to obtain relevant information on the population structure, genetic diversity and the evolution history of the species. Using genomic sequences of 21 strains of B. melitensis isolated in Russia and WGS data from the NCBI database, it was possible to identify five main genotypes and 13 species genotypes for analysis. Data analysis based on the Bayesian Phylogenetics and Phylogeography method allowed to determine the regions of geographical origin and the expected pathways of distribution of the main lines (genotypes and subgenotypes) of the pathogen. Conclusions Within the framework of our study, the model of global evolution and phylogeography of B. melitensis strains isolated in various regions of the planet was proposed for the first time. The sets of unique specific SNPs described in our study, for all identified genotypes and subgenotypes, can be used to develop new bacterial typing and identification systems for B. melitensis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4762-2) contains supplementary material, which is available to authorized users.

Background Anthrax is a zoonotic disease caused by the gram-positive bacterium Bacillus anthracis. The most anthrax-endemic regions of Russia are Siberia and North Caucasus. Previously, genotyping of Russian B.anthracis isolates was carried out using canSNP and MLVA data; these methods yield lower resolution results compared to whole genome SNP analysis (wgSNP). In this research, we have used wgSNP method for genotyping of 10 B.anthracis isolates, obtained during 1961–2016 in Russia on territory of Western Siberia. Results We have analyzed 185 B.anthracis genomes available in GenBank database and genomes of 10 isolates obtained in this study to determine the place of Russian isolates in the global phylogeny of B.anthracis. For the studied genomes we have detected 7203 SNPs, which were used for building a phylogenetic reconstruction with Maximum Likelihood Method. Results of the phylogenetic analysis indicate that Russian strains belong to three different genetic groups. Three strains belong to genetic group “Ames”, two strains – to “STI” group. Five strains belong to the main genetic line B, and four of them form a subcluster, described for the first time, which we have named “Siberia”. Conclusions In this study, the data on genetic diversity of B.anthracis strains on the territory of Western Siberia is presented for the first time. As a result of complex phylogenetic analysis, the place of these isolates was determined in the global phylogenetic structure of the B.anthracis population. We describe a new cluster in the main genetic line B for the first time. Electronic supplementary material The online version of this article (10.1186/s12864-019-6060-z) contains supplementary material, which is available to authorized users.

One of the new promising candidate genes defining productive qualities of sheep is MEF2B. Protein from the MEF2 group encoded by it affects the production of myostatin and the expression of the genes responsible for the growth of skeletal muscle fibers. Thus, the knowledge of the MEF2B gene structure is important for genomic selection. We have studied the structure of the MEF2B gene at sheep of Severokavkazskaya breed bred in Russia. To detect alleles we use NimbleGen sequencing technology by Roche (USA). As a result, it was revealed 14 single nucleotide polymorphisms (SNP) at the given breed. The discovered SNPare located in not coding areas. From them 7 polymorphisms are in the area of 5' upstream gene in loci: c.-1713, c.-1319, c.-839, c.-321, c.-246, c.-161, c.-3; 6 polymorphisms are in introns, loci: c.55-51, c.258+312, c.258+380, c.259-52, c.452+95, c.452+ 103, 1 SNP is in 3' downstream gene, c.*252. Two of the identified SNPs are significantly connected with high indices of meat productivity: c.55-51 and c.259-52. At the same time it was not possible to find out the impact on productivity of c.-1713 polymorphism. Our investigation is a base of next research of affection of different MEF2B gene alleles on meat quality and can be used to prepare PCR test-system for genomic selection.

V. TRUKHACHEV, V. BELYAEV, A. KVOCHKO, A. KULICHENKO, D. KOVALEV, S. PISARENKO, A. VOLYNKINA, M. SELIONOVA, M. AYBAZOV, S. SHUMAENKO, A. OMAROV, T. MAMONTOVA, N. GOLOVANOVA, O. YATSYK & A. KRIVORUCHKO Faculty of Veterinary Medicine, Stavropol State Agrarian University, Stavropol, Russian Federation; Stavropol Research Anti-plague Institute, Stavropol, Russian Federation; All-Russian Research Institute of Sheep and Goat Breeding; Stavropol, Russian Federation

Summary Background: marker assisted selection methods of sheep require the identification of genes that positively and negatively affect meat quality. Genes with high expression levels could have the greatest impact on growth and structure of muscle fibers. Objective: this study evaluated the expression of genes in the loin muscle of Dzhalginsky Merino sheep. Methods: reverse transcription-quantitative real-time PCR (RT-qPCR) was used to investigate the expression of 48 genes in the loin muscle of Dzhalginsky Merino sheep bred in Russia. Results: genes GAPDH, PYGM, CAST, ATP5G1, CAPN3, SOD1, VEGFA, CALM2, YWHAZ, ASIP, MYOD1, CAPN1, GHR, OXTR, BEGAIN, SLC2A3, and SS18L2 showed the highest expression. The group of genes with a medium level of expression included ATOX1, BAMBI, TLR6, IGF2, FOS, FST, GGTA2P, C-MET, FGF5, ACVR2A, CAPN2, GH, DGAT1, and IGF1. Low levels of expression were identified for genes ABCG2, SPP2, PYGL, PPARG2, TGFB1, CXCR4, MSTN, CYP2J, LEPR, CDKN1A, IGFBP4, and SERT. Trace expression was detected in genes SST, TSHR, GDF9, FGF7 and BMP15. Significant correlation between expression level and live weight was observed for most of the investigated genes. Conclusion: our results demonstrate the feasibility of using these newly identified candidate genes as genetic markers in sheep. Keywords: growth traits, marker assisted selection (MAS), microarray analysis, transcription. Resumen Antecedentes: los metodos de seleccion asistida de ovejas a traves de marcadores requieren la identificacion de los genes que afectan positiva o negativamente la calidad de la carne. Los genes con niveles mas altos de expresion podrian tener mayor impacto en el crecimiento y estructura de las fibras musculares. Objetivo: evaluar la expresion de los genes en el musculo del lomo de carneros de la raza Dzhalginsky Merino. Metodos: se utilizo RT-PCR cuantitativa en tiempo real (RT-qPCR) para investigar la expresion de 48 genes en el musculo del lomo de ovejos raza Merino Dzhalginsky criados en Rusia. Resultados: los genes GAPDH, PYGM, CAST, ATP5G1, CAPN3, SOD1, VEGFa, CALM2, YWHAZ, ASIP, MYOD1, CAPN1, GHR, OXTR, BEGAIN, SLC2A3 y SS18L2 mostraron la mas alta expresion. El grupo de genes con un nivel medio de expresion incluyo ATOX1, BAMBI, TLR6, IGF2, FOS, FST, GGTA2P, C-MET, FGF5, ACVR2A, CAPN2, GH, DGAT1 y IGF1. Se identificaron bajos niveles de expresion en los genes ABCG2, SPP2, PYGL, PPARG2, TGFB1, CXCR4, NTCR, CYP2J, LEPR, CDKN1A, IGFBP4 y SERT. Expresion traza fue detectada en los genes SST, TSHR, GDF9, FGF7 y BMP15. Para la mayoria de los genes investigados hubo una correlacion significativa entre el nivel de expresion y el peso vivo de los carneros. Conclusion: los resultados demuestran la factibilidad del uso de estos genes candidatos identificados recientemente como marcadores geneticos en ovejas. Palabras clave: analisis de micromatrices, caracteristicas de crecimiento, seleccion asistida por marcadores (MAS), transcripcion. Resumo Antecedentes: metodos que utilizam marcadores de selecao assistida em ovelhas exigem a identificacao de novos genes que afetam a qualidade da carne. Genes com maiores niveis de expressao podem ter maior impacto sobre o crescimento e a estrutura das fibras musculares. Objetivo: avaliar a expressao de genes no musculo lombar de ovinos da raca Merino Dzhalginsky. Metodos: foi utilizada a reacao em cadeia da polimerase-transcriptase reversa e em tempo real (RT-qPCR) para investigar a expressao de 48 genes em musculo do lombo da raca de ovinos Merino Dzhalginsky, que foram criados na Russia. Resultados: os genes GAPDH, PYGM, CAST, ATP5G1, CAPN3, SOD1, VEGFA, CALM2, YWHAZ, ASIP, MYOD1, CAPN1, GHR, OXTR, BEGAIN, SLC2A3 e SS18L2 apresentaram a maior expressao. O grupo de genes com um nivel medio de expressao incluiram ATOX1, BAMBI, TLR6, IGF2, FOS, FST, GGTA2P, C-MET, FGF5, ACVR2A, CAPN2, GH, DGAT1 e IGF1. Foram identificados baixos niveis de expressao para os genes ABCG2, SPP2, PYGL, PPARG2, TGFB1, CXCR4, MSTN, CYP2J, LEPR, CDKN1A, IGFBP4 e SERT. Foi detectado rastreamento de expressao nos genes SST, TSHR, GDF9, FGF7 e BMP15. Para a maioria dos genes investigados, houve uma correlacao significativa entre o nivel de expressao e o peso vivo dos carneiros Dzhalginsky Merino. Conclusao: os resultados demonstram a viabilidade do uso desses genes candidatos recentemente identificados como marcadores geneticos no desenvolvimento de novas racas de ovinos. Palavras chave: caracteristicas de crescimento, microarray analise, selecao assistida por marcadores (MAS), transcricao.

An understanding of what effects particular genes can have on body parameters in productive animals is particularly significant for the process of marker-assisted selection. The gene of transcriptional factor CCAAT/enhancer-binding protein delta (CEBPD gene) is involved in the process of growth in animals and is known to be a promising candidate for use as a genomic marker. The structure of the CEBPD gene locus was determined using NimbleGen sequencing technology (Roche, USA). The effect of polymorphisms, which were identified using the aforementioned technology, was investigated in 30 rams of the Manych Merino sheep breed. Twenty-two single nucleotide polymorphisms (SNP) were detected in the CEBPD gene locus. Significantly, two SNPs, namely, g.315TG and g.327CT, have been identified for the first time. It was demonstrated that the complex of linked SNPs, consisting of g.301AT, g.426TC, and g.1226TC, had a negligible effect on body parameters in Manych Merino sheep. Animals with the heterozygous type of SNP g.1142CT exhibited changes solely in the chest and croup width. The newly discovered SNP g.327CT was proven to have a negative effect on live weight and body size (p 0.05) in Manych Merino sheep. Sheep with the heterozygous type of g.562GA and g.3112CG SNP complex showed an increase in live weight and dimensions (p 0.05) compared with those of wild homozygous type. Consequently, SNPs g.327CT, g.562GA, and g.3112CG in the CEBPD gene locus can be successfully used as markers in sheep breeding. Future research will evaluate the influence of the aforementioned SNPs on slaughter indicators for sheep meat production.