International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”
OLGA BERDYUGINA1
1Institute 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.
Polina Drozdova1, Alexandra Dolgikh2, Anna Nazarova3, Yulia Lubyaga4, Maxim Timofeyev5
1Institute of Biology, Irkutsk State University, Irkutsk, Russia, drozdovapb@gmail.com
2Dept. of Genetics and Biotechnology St. Petersburg State University, St. Petersburg, Russia, sqshadol@gmail.com
3Institute of Biology, Irkutsk State University, Irkutsk, Russia, annazarova1995@gmail.com
4Institute of Biology, Irkutsk State University, Irkutsk, Russia, yuliya.a.lubyaga@gmail.com
5Institute of Biology, Irkutsk State University, Irkutsk, Russia, m.a.timofeyev@gmail.com
In this work, we explored two groups of proteins, the carbohydrate-binding lectins and enzymes of carotenoid metabolism, in amphipods of the Lake Baikal region based on the available transcriptome data. We found that different species possess quite similar repertoires of these proteins. The obtained sequence data are instrumental for further molecular-level exploration of amphipod physiology.
Rogacheva Elizaveta1
1Saint-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.
Poster (download)
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Elena Voropaeva1, Yuriy Orlov2, Olga Beresina3, Tatyana Pospelova4, Viktoria Karpova5, Vladimir Maximov6, Elizaveta Melnikova7, Anastasia Ivanova8, Anna Gurageva9, Maria Churkina10
1IITPM – Branch of ICG SB RAS, vena.81@mail.ru
2I.M.Sechenov First Moscow State Medical University, orlov_yury@yahoo.com
3NSMU,, ovb-mail@ya.ru
4NSMU, postatgem@mail.ru
5State Regional Clinical Hospital, vicka-34@ngs.ru
6IITPM – Branch of ICG SB RAS, medik11@mail.ru
7IITPM – Branch of ICG SB RAS, jarinaleksi@list.ru
8IITPM – Branch of ICG SB RAS, ivanova_a_a@mail.ru
9IITPM – Branch of ICG SB RAS, annapalna1@mail.ru
10NSMU, 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.
Poster (download)
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Video (download)
Ivan Petrushin1, Yuri Konstantinov2, Igor Gorbenko3
1LIN SB RAS, ivan.kiel@gmail.com
2SIPPB SB RAS, yukon@sifibr.irk.ru
3SIPPB 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.
Poster (download)
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Alla Saksaganskaia1, Viktoria Muntyan2, Alexey Afonin3, Marina Roumiantseva4
1ARRIAM, Saint-Petersburg, Pushkin, Russia, allasaksaganskaya@mail.ru
2ARRIAM, Saint-Petersburg, Pushkin, Russia, vucovar@yandex.ru
3ARRIAM, Saint-Petersburg, Pushkin, Russia, afoninalexeym@gmail.com
4ARRIAM, 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.
Alexey Boyko1, Igor Dolmatov2
1NSCMB FEB RAS, Vladivostok, Russia, Alteroldis@gmail.com
2NSCMB 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.
Anton Tsukanov1, Victor Levitsky2, Tatyana Merkulova3
1ICG SB RAS, Novosibirsk, Russia, tsukanov@bionet.nsc.ru
2ICG SB RAS, Novosibirsk, Russia, levitsky@bionet.nsc.ru
3ICG 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 вЂshort-range interactions’ markov models BAMM/InMode permit only local dependencies, the вЂlong-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.
Poster (download)
[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/456.pdf”]
Ekaterina Shchapova1
1Irkutsk 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.
Sergey Sedykh1, Kuleshova Anna2, Georgy Nevinsky3
1SB RAS ICBFM, NSU, sedyh@niboch.nsc.ru
2SB RAS ICBFM, aekuleshova25@gmail.com
3SB 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).