Poster (download) Video (download) Ivan Petrushin1, Yuri Konstantinov2, Igor Gorbenko31LIN SB RAS, ivan.kiel@gmail.com2SIPPB SB RAS, yukon@sifibr.irk.ru3SIPPB SB RAS, gravov.chemistry@gmail.com In the nuclear genome of Arabidopsis thaliana some cas genes and CRISPR cassettes were found by in silico methods. It is hypothesized that CRISPR-Cas-like elements appeared in plant genome as a result of endosymbiosis of ancient alphaproteobacteria.
Read MorePoster (download) Elena Voropaeva1, Yuriy Orlov2, Olga Beresina3, Tatyana Pospelova4, Viktoria Karpova5, Vladimir Maximov6, Elizaveta Melnikova7, Anastasia Ivanova8, Anna Gurageva9, Maria Churkina101IITPM – Branch of ICG SB RAS, vena.81@mail.ru2I.M.Sechenov First Moscow State Medical University, orlov_yury@yahoo.com3NSMU,, ovb-mail@ya.ru4NSMU, postatgem@mail.ru5State Regional Clinical Hospital, vicka-34@ngs.ru6IITPM – Branch of ICG SB RAS, medik11@mail.ru7IITPM – Branch of ICG SB RAS, jarinaleksi@list.ru8IITPM – Branch of ICG SB RAS, ivanova_a_a@mail.ru9IITPM – Branch of ICG SB RAS, annapalna1@mail.ru10NSMU, nats.sagan@yandex.ru In this study, based on the information presented in the specialized resource CBioPortal for Cancer Genomics database, the data on the diffuse large B-cell lymphoma (DLBCL) mutation profile detected by next generation sequencing (NGS) methods have been analyzed. The features associated with a high risk of secondary central nervous system (CNS) involvement have been highlighted. In patients with DLBCL and secondary CNS involvement, the most frequently mutated genes were MYD88, PIM1, CARD11 and CD79B. These genes related to the BCR/NF-kB signaling pathway. The MYD88, PIM1 and CD79B genes mutations were often combined and, in total, occurred in 39.6% of cases in patients with CNS relapsed DLBCL.
Read MorePoster (download) Alla Saksaganskaia1, Viktoria Muntyan2, Alexey Afonin3, Marina Roumiantseva41ARRIAM, Saint-Petersburg, Pushkin, Russia, allasaksaganskaya@mail.ru2ARRIAM, Saint-Petersburg, Pushkin, Russia, vucovar@yandex.ru3ARRIAM, Saint-Petersburg, Pushkin, Russia, afoninalexeym@gmail.com4ARRIAM, Saint-Petersburg, Pushkin, Russia, mroumiantseva@yandex.ru Abundance of plasmids in genomes of root nodule nitrogen fixing bacteria (rhizobia) is their common feature. Plasmids harboring genes related to symbiosis are usually called symbiotic plasmids, while rhizobia can contain differing number of cryptic plasmids, which sizes are varied from 7 kbp to 600 kbp. Cryptic plasmids were predicted to be important both for the existence of rhizobia in soil and for formation of effective nitrogen-fixing symbiosis with particular host plant. Nevertheless, assemble and annotation of such replicons became possible only in the postgenomic era. In this work a structural and functional analysis of cryptic plasmids of Sinorhizobium meliloti which forming symbiosis with alfalfa was done. Native isolates of S. meliloti were recovered from nodules of alfalfa plants adapted to salinized soils at the Aral Sea region. The sequence analysis was done for four plasmids ranging in size from 31.2 kbp to 453.7 kbp. A large number of ORFs of cryptic plasmids of S. meliloti are associated with metabolic processes as it was established. For the first time prophage sequences were identified in cryptic plasmids. Data proving that cryptic plasmids of native strains are related to horizontal gene transfer and could be essential for rhizobia fitness.
Read MoreAlexey Boyko1, Igor Dolmatov21NSCMB FEB RAS, Vladivostok, Russia, Alteroldis@gmail.com2NSCMB FEB RAS, Vladivostok, Russia, idolmatov@mail.ru The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. It has been repeatedly confirmed that regeneration is only due to the transformation of terminally differentiated cells. In this study, we examined changes in gene expression during gut regeneration of the holothurian E. fraudatrix and found 11 TFs, which are candidates for the role of transdifferentiation regulators.
Read MoreEkaterina Vodiasova1, Aleksandra Andreyeva2, Рђnastasiya Lantushenko3, Yakov Meger4, Irina Deghtyar5, Dmitry Afonnikov61IBSS RAS, Sevastopol, Russia, eavodiasova@gmail.com2IBSS RAS, Sevastopol, Russia, andreevaal@gmail.com3SSU, Sevastopol, Russia, lantushenko@mail.ru4SSU, Sevastopol, Russia, meger_yakov@mail.ru5SSU, Sevastopol, Russia, skuratovskaya95@mail.ru6ICG SB RAS, Novosibirsk, Russia, ada@bionet.nsc.ru Despite that mussel is an important object of mariculture and can play the role of an ecosystem bio-indicator, the study of the effect of hypoxia on these mollusСЃs is limited only by biochemical and RT-PCR experiments for individual genes (enzymes). There is no data on changes in the expression profile of all genes based on RNA sequencing. At the same time, an understanding of physiological processes requires comprehensive studies based on the study of the expression of all genes in target tissues. At this work, the transcriptomes of the gills of Mytilus galloprovincialis exposed to hypoxic stress (DO 0.3 mg/l) for 24h were sequenced using Illumina technology for the first time. The raw reads assembled into 255,302 transcripts with an N50 value of 1,273 nt. A total of 65 transcripts that differed in abundance in the hypoxia-exposed mussels were identified. Their putative function was assigned using BLAST. The data obtained will allow further large-scale studies for other targeted tissues and to study all aspects of the physiological response of M. galloprovincialis to the emerging oxygen deficiency in the environment.
Read MorePoster (download) Ekaterina Shchapova11Irkutsk State University, shchapova.katerina@gmail.com A diverse number of studies indicates that the hemolymph of aquatic invertebrates, apparently healthy invertebrates, is non-sterile. In this study we for the first time characterized the bacterial diversity in hemolymph of endemic amphipods from Lake Baikal on the example of abundant littoral species Eulimnogammarus verrucosus.
Read MoreРаънохон11Автор, solieva_r@mail.ru The protection and strengthening of the reproductive health of mothers, children and adolescents is an important and priority area of health care in the Republic of Uzbekistan and is fully supported by state programs, the basis of which is the development of preventive medicine.
Read MorePoster (download) Anna Shestak1, Anna Bukaeva2, Siamak Saber3, Elena Zaklyazminskaya41Petrovsky National Research Center of Surgery, Moscow, Russia, anna.shestak87@gmail.com2Petrovsky National Research Center of Surgery, Moscow, Russia, 16_anna_02@mail.ru3Cardiac Electrophysiology Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran, s_saber2002@yahoo.com4Petrovsky National Research Center of Surgery, Moscow, Russia, helenezak@gmail.com Abstract Allelic drop-out (ADO) is a known phenomenon of selective allele amplification representing the potential problem of correct DNA diagnostics. The results demonstrate the incidence of ADO reducing the diagnostic yield of PCR-based target sequencing. Motivation and aim: Allelic drop-out (ADO) is a known phenomenon of selective allele amplification representing the potential problem of correct DNA diagnostics. Both NGS and Sanger sequencing are PCR-based methods, Sanger sequencinq is used to verify NGS results. The aim of this study is to demonstrate the incidence of ADO reducing the diagnostic yield in primary cardiomyopathy genetic testing via semiconductor NGS and Sanger sequencing of target gene panels. Methods: We have developed 3 AmpliSeq custom gene panels for mutational screening: “K+/Na+ ion channels”, “Desmosomal proteins”, “Sarcomeric proteins”, contains 1049 primer pairs (37 genes) totally, 152 kb. About 140 probands were screened with at least one of these gene panels. AmpliSeq sequences were analyzed in silico and visually compared with Sanger control sequences, noting the facts of heterozygosity loss. Results: We have detected 12 ADO cases both in Sanger (5 cases) and AmpliSeq (7 cases) sequencing data. All ADO events happened due to frequent or rare SNVs in the oligoprimer annealing sites and were detected due to mismatch in frequent SNPs zygosity nearby. Three pathogenic variants would be missed if were not revealed by re-sequencing with alternative method and alternative oligos. Conclusion: All PCR-based methods have a risk of ADO leading to a decrease of diagnostic yield of genetic testing. ADO can theoretically affect 1% amplicons. It seems that real scope of ADO might be much higher and depends on numbers of primer pairs. The software for ADO detection is needed. Acknowledgment:  This work was supported by Russian Science Foundation grant №16-15-10421.
Read MorePoster (download) A.I. Klimenko1, Yu.G. Matushkin2, D.A. Afonnikov31Kurchatov Genomics Center, Institute of Cytology and Genetics, klimenko@bionet.nsc.ru2ICG SB RAS, mat@bionet.nsc.ru3ICG SB RAS, NSU, ada@bonet.nsc.ru The gene expression levels for bacteria are largely determined by the efficiency of translation elongation. We have performed bioinformatic elongation efficiency analysis of NRP biosynthetic gene clusters (BGCs) obtained from ANTISMASH-DB using whole-genome sequences of bacterial genomes that are available at NCBI Genbank. The analysis has provided the information about distribution of nonribosomal peptide biosynthetic gene clusters in bacteria and their putative translation elongation efficiency.
Read MoreVideo (download) Alexander Nesmelov1, Sabina Kondratyeva2, Taisiya Voronina31IFMB KFU, Kazan, Russia, nesmelov@gmail.com2IFMB KFU, Kazan, Russia, sabinakondr@gmail.com3IFMB KFU, Kazan, Russia, vorotaisiya@gmail.com Anhydrobiosis is survival of complete body desiccation, tightly linked to the ability to cope with a massive DNA damage. However, in anhydrobiotic midge Polypedilum vanderplanki this ability is not accompanied by a huge induction of genes of DNA reparation system which is typical for many other anhydrobiosis-related genes in this insect.
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