International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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Genomics, transcriptomics, bioinformatics symposium

Showing: 11 - 20 of 71 RESULTS
Genomics, transcriptomics, bioinformatics symposiumFunctional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

Functional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

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Semyon K. Kolmykov1, Nikita V. Ivanisenko2, Ivan S. Evshin3, Mikhail Kulyashov4, Tamara M. Khlebodarova5, Ilya R. Akberdin6
1Institute of Computational Technologies SB RAS, kolmykovsk@gmail.com
2FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com
3Institute of Computational Technologies SB RAS, ivan@biosoft.ru
4Institute of Computational Technologies SB RAS, m.kulyashov@mail.ru
5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru
6FRC Institute of Cytology and Genetics SB RAS, akberdinir@gmail.com

Methane is a promising carbon source for biosynthesis of biotechnologically useful compounds using aerobic methanotrophic bacteria as biocatalysts. Despite more than a century-long history of discovering and studying of methanotrophic microorganisms, knowledge of the molecular mechanisms of gene expression regulation by transcription factors in these bacteria is very limited with only a few isolated cases being published. Therefore, the identification of potential transcription factors for methanotrophic organisms and their target genes is not only a foreground fundamental problem in the research field of methanotrophy, but it is also especially relevant for the active development of biotechnological application of methane-oxidizing microorganisms. In this study a comparative genomics approach together with the structural modeling techniques were applied to reveal the TFs in the 20ZR genome and predict their target regulatory genes.

Genomics, transcriptomics, bioinformatics symposiumAdvanced data curation in GTRD database: hierarchical dictionaries of cell types and experimental factors

Advanced data curation in GTRD database: hierarchical dictionaries of cell types and experimental factors

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Mikhail A. Kulyashov1, Semyon K. Kolmykov2, Ivan S. Yevshin3, Fedor A. Kolpakov4
1BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, m.kulyashov@mail.ru
2BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, kolmykovsk@gmail.com
3BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, ivan@developmentontheedge.com
4BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, fkolpakov@gmail.com

Abstract GEO database contains a lot of different experiments about transcription regulation. Most part of such experiments (ChIP-seq, DNase-seq and Histone-ChIP-seq) for 9 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Arabidopsis thaliana) were annotated and uniformly processed in GTRD database. Here we are describing the latest advances in these data annotations for GTRD database to formalise experimental data: hierarchical dictionaries of cell types and experimental factors. This approach helps us to integrate experimental data by cell lines (cell types and tissues) and experimental conditions as well as simplifies searching for relevant information for a user.

Genomics, transcriptomics, bioinformatics symposiumPromoter expression landscape in skeletal muscle in hindlimb suspension and recovery model in rat

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

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/342.pdf”]
Guzel Gazizova1, Ruslan Deviatiiarov2, Islam Nigmetzyanov3, Oksana Tyapkina4, Leniz Nurullin5, Oleg Gusev6
1Kazan Federal University, grgazizova@gmail.com
2Kazan Federal University, ruselusalbus@gmail.com
3Kazan Federal University, islamka32@gmail.com
4Federal Research Center “Kazan Scientific Center of the RAS\”, antitoxin@icloud.com
5Federal Research Center “Kazan Scientific Center of the RAS\”, leniz2009@gmail.com
6Kazan 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.

Genomics, transcriptomics, bioinformatics symposiumMolecular basis of phosphoryl guanidine oligonucleotides elongation by Taq DNA polymerase

Molecular basis of phosphoryl guanidine oligonucleotides elongation by Taq DNA polymerase

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Alexander Lomzov1
1ICBFM 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.

Genomics, transcriptomics, bioinformatics symposiumNew germline mutations in PTEN and RAD51D genes among the Buryat Mongol breast cancer patients

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

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Polina Gervas1, Aleksey Molokov2, Nadezda Cherdyntseva3
1Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia, pgervas@yandex.ru
2Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia, amolokov@inbox.ru
3Cancer 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.

Genomics, transcriptomics, bioinformatics symposiumGenome distance between regulatory elements of growth-related genes may determine morpho-physiological traits in mammals

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

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Dmitriy1
1Southern 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.

Genomics, transcriptomics, bioinformatics symposiumThe Rich Inner World of Colorado Potato Beetles – a Metagenomic Survey of Viral Diversity in Public Data

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

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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.

Genomics, transcriptomics, bioinformatics symposiumWhole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data

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

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Andrew G. Matveenko1, Anton B. Matiiv2, Yury A. Barbitoff3, Evgenia M. Maksiutenko4, Svetlana E. Moskalenko5, Alexandra V. Beliavskaia6, Alexander V. Predeus7, Galina A. Zhouravleva8
1Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, a.matveenko@spbu.ru
2Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, antonmatiiv@yandex.ru
3Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Bioinformatics Institute, St. Petersburg, Russia, barbitoff@bk.ru
4Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, jmrose@yandex.ru
5Vavilov 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.ru
6University of Liverpool, Liverpool, UK, alex.beliavskaia@gmail.com
7University of Liverpool, Liverpool, UK; Bioinformatics Institute, St. Petersburg, Russia, predeus@bioinf.me
8Dpt. 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.

Genomics, transcriptomics, bioinformatics symposiumGenes expression related to the effects of hypoxia in the marine mussel, Mytilus galloprovincialis

Genes expression related to the effects of hypoxia in the marine mussel, Mytilus galloprovincialis

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Ekaterina Vodiasova1, Aleksandra Andreyeva2, Рђnastasiya Lantushenko3, Yakov Meger4, Irina Deghtyar5, Dmitry Afonnikov6
1IBSS RAS, Sevastopol, Russia, eavodiasova@gmail.com
2IBSS RAS, Sevastopol, Russia, andreevaal@gmail.com
3SSU, Sevastopol, Russia, lantushenko@mail.ru
4SSU, Sevastopol, Russia, meger_yakov@mail.ru
5SSU, Sevastopol, Russia, skuratovskaya95@mail.ru
6ICG 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.

Genomics, transcriptomics, bioinformatics symposium“Justification of measures for optimization and prevention with dysplasia of stratified squamous epithelium of the cervix in women of reproductive age”

“Justification of measures for optimization and prevention with dysplasia of stratified squamous epithelium of the cervix in women of reproductive age”

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Раънохон1
1Автор, 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.