Promoter expression landscape in skeletal muscle in hindlimb suspension and recovery model in rat

Poster (download) Guzel Gazizova1, Ruslan Deviatiiarov2, Islam Nigmetzyanov3, Oksana Tyapkina4, Leniz Nurullin5, Oleg Gusev61Kazan Federal University, grgazizova@gmail.com2Kazan Federal University, ruselusalbus@gmail.com3Kazan Federal University, islamka32@gmail.com4Federal Research Center “Kazan Scientific Center of the RAS\”, antitoxin@icloud.com5Federal Research Center “Kazan Scientific Center of the RAS\”, leniz2009@gmail.com6Kazan Federal University, RIKEN, oleg.gusev@riken.jp Loss of muscle mass and function during long period of physical inactivity still remains a clinical problem for humanity because the significant reducing of life quality and increasing mortality. In recent studies global gene expression in atrophied and recovered skeletal muscles on different animal models was analyzed. However, previously whole-genome regulation of atrophy and following recovery at promoter and enhancer level has not been studied. To identify transcription initiation sites (TSS), and evaluate full-genome RNA expression at the level of individual promoters and enhancers during unloading and subsequent recovery in rats two types of muscles, \”slow\” (m. Soleus) and \”fast\” (m. EDL), were examined in rats in normal conditions, after 1, 3 and 7 days of hindlimb suspension and following 1, 3 and 7 days of recovery using CAGE (Cap Analysis of Gene Expression) method followed by Illumina HiSeq 2500 sequencing. We obtained 9971 unique CAGE clusters, among which 6377 were promoters associated with genes. Differential expression of genes and their promoter activity were strongly varied in m. EDL and m. soleus within suspension-recovery time course. This study provides the first systematic annotation of promoters landscape and genes activated in \”fast\” and \”slow\” muscle types under induced atrophy and following recovery in rats.

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Molecular basis of phosphoryl guanidine oligonucleotides elongation by Taq DNA polymerase

Video (download) Alexander Lomzov11ICBFM SB RAS, lomzov@niboch.nsc.ru Phosphoryl guanidine oligonucleotides (PGO) become essential tools for basic research in molecular biology, molecular diagnostics and perspective for the therapeutics. To determine molecular basis of the observed effects of PG modification on elongation efficiency we performed molecular dynamics simulation of Taq polymerase / PGO complexes. The data obtained shows most important points for the analysis of protein / PGO interaction and gives useful information for development of improved PCR analysis.

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New germline mutations in PTEN and RAD51D genes among the Buryat Mongol breast cancer patients

Polina Gervas1, Aleksey Molokov2, Nadezda Cherdyntseva31Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia, pgervas@yandex.ru2Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia, amolokov@inbox.ru3Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia, nvch@tnimc.ru Breast cancer is the most prevalent female malignancy worldwide. In recent decades, breast cancer has been the most common malignancy in the regions of Siberia and Russian Far East, which occupy about 70% of the Russian Federation. The population is descended primarily from newcomers (Slavic ancestors) and indigenous population (Mongolian). More than 13.8 million women inhabit these regions. Currently, little information has been reported regarding the molecular factors associated with increased risk of developing hereditary breast cancer in the indigenous population (Buryats, Evenks, Altaians, Tuvinians, Khakassians). For the indigenous population, there are no standards for the treatment of inherited breast cancer. Breast cancer prevention models for indigenous population have not been developed yet. For \”slavic\” patients with a family history, the BRCA1/2 mutation testing is the standard of care. In addition, the development of new antitumour drugs has resulted in improved survival rates. More than 1000 mutations of the BRCA1 gene have been identified. Recent research is focused on the confirmation the beneficial effect of identified mutations. In our previous study we did not find \”slavic\” mutations of the BRCA1 gene in Mongoloid breast cancer patients having family history. Pathological mutations in the BRCA1 gene among indigenous people have not been identified using Sanger sequencing (RFBR grant 12-04-90830). Thus, the advances in molecular oncology for the treatment of hereditary breast cancer are not available for the indigenous population of the Siberian and Far Eastern region.

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Genome distance between regulatory elements of growth-related genes may determine morpho-physiological traits in mammals

Dmitriy11Southern federal university, rdme@yandex.ru The problem of growth regulation in mammals is one of the long-standing mysteries in biology. We found significant correlation between morpho-physiological traits and genome distances between conserved elements in neighborhoods of growth-related genes Mycn, Plagl1 and Ezh2 in mammals. Given these conserved elements may be regulatory as well, we propose that genome distance between them may evolutionary modulate gene expression of these genes and eventually affects phenotype. It opens intriguing prospect to control morpho-physiological traits of mammals (i.e. adult body mass or longevity) just simply editing genome distance between these elements.

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Potential of Whole Genome Sequencing in the Assessment of Sensitivity of Clinical Isolate M.tuberculosis to Antibiotics

OLGA BERDYUGINA11Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, berolga73@rambler.ru To study the potential of whole genome sequencing in assessing the sensitivity of the clinical isolate of M.tuberculosis is an important research task. The data obtained can be used when choosing antibiotics in the treatment of a patient.

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The Rich Inner World of Colorado Potato Beetles – a Metagenomic Survey of Viral Diversity in Public Data

Maria Starchevskaya1, Yuri Vyatkin2, Denis Antonets3 1SRC VB Vector Rospotrebnadzor, Koltsovo, Russia, starchevskayamaria@mail.ru 2Novosibirsk State University, Novosibirsk, Russia; Novel Software Systems LLC, Novosibirsk, Russia, vyatkin@gmail.com 3SRC VB Vector Rospotrebnadzor, Koltsovo, Russia; Novel Software Systems LLC, Novosibirsk, Russia, antonec@yandex.ru Abstract Recent metagenomic studies of various environments revealed an enormous number of viruses, with hundreds of previously unknown species and even new virus families, and thus greatly expanded our understanding of the virosphere. Investigations of insect virome will provide new insights into ecology and evolution of viruses and their hosts. Colorado potato beetle is one of the most serious insect pests feeding on Solanaceae plants. The Colorado potato beetle virome has not been studied yet and, as far as we know, our work is the first attempt to discover viral material in DNA- and RNA-Seq data of L. decemlineata. We also hope that identification of new viruses will help to extend the arsenal of biopesticides.

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Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data

Andrew G. Matveenko1, Anton B. Matiiv2, Yury A. Barbitoff3, Evgenia M. Maksiutenko4, Svetlana E. Moskalenko5, Alexandra V. Beliavskaia6, Alexander V. Predeus7, Galina A. Zhouravleva81Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, a.matveenko@spbu.ru2Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, antonmatiiv@yandex.ru3Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Bioinformatics Institute, St. Petersburg, Russia, barbitoff@bk.ru4Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, jmrose@yandex.ru5Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, s.moskalenko@spbu.ru6University of Liverpool, Liverpool, UK, alex.beliavskaia@gmail.com7University of Liverpool, Liverpool, UK; Bioinformatics Institute, St. Petersburg, Russia, predeus@bioinf.me8Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, g.zhuravleva@spbu.ru The Peterhof genetic collection (PGC) of yeastВ SaccharomycesВ cerevisiae is one of the rareВ examplesВ of a large genetic collection established independently of reference S288C strain. We assembled genomes of two widely used PGC strains, 1A-D1628 and 74-D694, using Oxford Nanopore MinION sequencing data. Subsequent analysis of structural variations showed a number of differences between PGC strains and S288C.

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Analysis of short- and long-range interactions within potential binding sites notably extends the fraction of verified peaks in ChIP-seq data

Poster (download) Anton Tsukanov1, Victor Levitsky2, Tatyana Merkulova31ICG SB RAS, Novosibirsk, Russia, tsukanov@bionet.nsc.ru2ICG SB RAS, Novosibirsk, Russia, levitsky@bionet.nsc.ru3ICG SB RAS, Novosibirsk, Russia, merkulova@bionet.nsc.ru We developed pipeline for integrative application of various de novo motif search tools to massive sequencing data. While traditional position weight matrices (PWMs) neglect dependencies between positions of motifs, the short-range interactionsв markov models BAMM/InMode permit only local dependencies, the long-range interaction model SiteGA allows dependencies between arbitrary positions. The massive analysis of ChIP-seq data have shown that the models BAMM/InMode and PWMs recognized similar and significantly overlapped peaks; but the notable fractions of peaks predicted by SiteGA model were not predicted by other models.

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MicroRNA content of horse and human milk exosomes

Sergey Sedykh1, Kuleshova Anna2, Georgy Nevinsky31SB RAS ICBFM, NSU, sedyh@niboch.nsc.ru2SB RAS ICBFM, aekuleshova25@gmail.com3SB RAS ICBFM, NSU, nevinsky@niboch.nsc.ru Exosomes are 40-100 nm diameter natural vesicles, containing CD9, CD63 and CD81 tetraspanins on the surface. It was shown that milk obtained from different sources contain exosomes: human, horse, bovine, rat. Horse milk is a unique source of exosomes since is less allergenic than bovine and not prion prone. Also, horse milk can be obtained in larger amounts than human milk. According to the results, published by the other research groups, milk exosomes contain hundreds and thousands of proteins, mRNA and microRNA molecules. Our recent results show that these numbers may be significantly overestimated.В Isolation of exosomes from sediments obtained after ultracentrifugation with an additional step of gel-filtration allows decreasing the number of proteins, that co-isolate with vesicles. Many microRNAs are described in exosomes, obtained from human and bovine milk. Here we show the content of more than two dozens major microRNA molecules, isolated fromВ human and horse milk exosomes on different stages of centrifugations, ultracentrifugations, before and after gel-filtration. According to these data, several microRNAs may be used as indicators of milk exosomes\’ purity. The study was funded by the Russian Scientific Foundation (research project 187410055 to S. Sedykh) and by the Program of Fundamental Research of Government Academia (РђРђРђРђ-Рђ17-117020210023-1 to Prof. G. Nevinsky).

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Results of whole-genome sequencing and phenotype annotation of bacteria of the genus Listeria

Rogacheva Elizaveta11Saint-Petersburg Pasteur Institute, elizvla@yandex.ru The incidence of listeriosis in recent years is con- stantly increasing. So, in highly developed countries it ranges from 0.3 to 1.5%, while in Russia – only 0.04% [1]. Moreover, the indicators in Moscow and St. Petersburg exceed those in the whole country by 4 times, which is explained by the different quality of clinical and laboratory diagnostics. Moreover, mortality due to complications of listeriosis infection can reach 30% [2]. Therefore, the fact of contamination of food products with listeria is of great concern. In this case, the strains of the species L. monocytogenes, L. innocua, L. ivanovii, L. grayii, L. seeligeri, L. welshimeri are most often distinguished. And if earlier it was believed that representatives of the species L. monocytogenespossess the largest set of pathogenic factors, then the possibilities of molecular and bioinformatics research methods provide a reliable picture with respect to other representatives of the genusListeria, in particular L. innocua.

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