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

Poster (download) Video (download) Mikhail A. Kulyashov1, Semyon K. Kolmykov2, Ivan S. Yevshin3, Fedor A. Kolpakov41BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, m.kulyashov@mail.ru2BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, kolmykovsk@gmail.com3BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, ivan@developmentontheedge.com4BIOSOFT.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.

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PCR dependent biases could significantly affect quantitative estimation of plant mix composition

Valeriia Kaptelova1, Maria Logacheva2, Anna Speranskaya3, Denis Omelchenko4, Anna Fedotova5, Anastasia Krinitsina6, Andrey Ayginin7, Kamil Khafizov8, Elena Korneenko9, Andrei Samoilov101Central Research Institute of Epidemiology, Moscow, Russia, valeriia.kaptelova@gmail.com2Skolkovo Institute of Science and Technology, Skolkovo, Russia, maria.log@gmail.com3Central Research Institute of Epidemiology, Moscow, Russia, hanna.s.939@gmail.com4Institute of Information Transmission Problems, Moscow, Russia, omdeno@gmail.com5Skolkovo Institute of Science and Technology, Skolkovo, Russia, mikrobiomsu@list.ru6Lomonosov Moscow State University, Moscow, Russia, ankrina@gmail.com7FSBI “Center of Strategic Planning” of the Ministry of Health, Moscow, Russia, ayginin75@gmail.com8FSBI “Center of Strategic Planning” of the Ministry of Health, Moscow, Russia, kkhafizov@gmail.com9Central Research Institute of Epidemiology, Moscow, Russia, lennatta@yandex.ru10Central Research Institute of Epidemiology, Moscow, Russia, andrei.samoilov@gmail.com Metagenomic analysis using high-throughput sequencing is an intensively developing approach nowadays. One of its problems is the adequate quantification of components in metagenomic samples.

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Short sequence repeats (SSR) under selection pressure: Cyprinidae fish case study

Mikhail Orlov1, Andrey Tykhonov21ICB RAS, orlovmikhailanat@gmail.com2Aqua Logo group company, andrew693@mail.ru Short sequence repeats (SSR) were earlier shown to have length well correlated with various genomic hotspots including intense selection pressure, chromosome rearrangement, etc. We approach this by considering SSR sets for numerous Cyprinidae fish representatives. Analysis of length of SSR as well as their oligonucleotide composition revealed difference between domesticated vs free-living fish.

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Automatic Annotation of Operons Responsible for O-antigen Synthesis

Danil Zilov1, Polina Chesnokova2, Alexey Komissarov31Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, zilov@scamt-itmo.ru2Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, chesnokova@scamt-itmo.ru3Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, komissarov@scamt-itmo.ru Unfortunately, the most ready-made tools for serotype determination are limited to genome E. Coli only. However, there is a problem due to the low accuracy of Рћ-antigen cluster identification in the genome. Pipeline, which was created due the work, solves this problem and can be used to find and annotate a cluster of genes in genome of the most gram-negative bacteria.

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Genome-wide Association Study Reveals Novel Genetic Variants Associated with HIV-1C Infection in Botswana Population

Andrey Shevchenko1, Sergey V. Malov2, Alexey Antonik31Theodosius Dobzhansky Center for Genome Bioinformatics St.-Petersburg State University St-Petersburg, Russia, andrey.k.shevchenko@gmail.com2Theodosius Dobzhansky Center for Genome Bioinformatics St.-Petersburg State University St-Petersburg, Russia, malovs@sm14820.spb.edu3Theodosius Dobzhansky Center for Genome Bioinformatics St.-Petersburg State University St-Petersburg, Russia, alexey.antonik@gmail.com Genome wide association studies (GWAS) allow to identify common variants associated with the trait in question. In order to efficiently search for the genetic associations we have previously developed Genome-Wide AssociationВ Tracks Chromosome Highway (GWATCH). The broad goal of the Botswana GWAS project is to identify genetic determinants of susceptibility and resistance to infection by HIV-1 subtype C among people severely affected by HIV/AIDS in Botswana. By conducting GWAS analysis on HIV1C case/control dataset consisting of 762 Tswana people (combined from two partly overlapping datasets of 809 microarray and 362 WGS samples), we found several gene regions slightly below significance level.

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  • June 29, 2020
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Detection of alphacoronavirus in bat fecal samples from Volgograd regions

Korneenko Elena11Central Research Institute of Epidemiology, Moscow, Russia, lennatta@yandex.ru Bats are natural reservoirs of many emerging viruses and their virome can differ according to the regions. In this study we have found a genome fragment of Coronaviridae which was 99% percent identical to Alphacoronavirus N.las/C/Spain/2007В in bat fecal sample from Volgograd region

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Metavirome analysis of Baikal sponges

Poster (download) Tatyana Vladimirovna Butina1, Yurij Sergeevich Bukin2, Igor Veniaminovich Khanaev31Laboratory of Analytical and Bioorganic Chemistry LIN SB RAS Irkutsk, Russia, tvbutina@mail.ru2Laboratory of Genosystematics LIN SB RAS Irkutsk, Russia, bukinyura@mail.ru3Laboratory of Ichthyology LIN SB RAS Irkutsk, Russia, igkhan@lin.irk.ru Sponges are the oldest multicellular invertebrates (phylum Porifera); they are ecologically important components of marine and freshwater benthic environments. Associated communities of sponges include a variety of microorganisms: fungi, algae, archaea, bacteria and viruses. The aim of this study was to elucidate the genetic diversity of viruses in the community of Baikal endemic sponges Baikalospongia bacillifera using metagenomic approach. We have shown for the first time a high genetic, potential taxonomic and functional diversity of dsDNA viruses in these Baikal sponges. Identified viral sequences belonged to 28 viral families that infect a wide range of organisms. The bacteriophages of the Myoviridae, Siphoviridae and Podoviridae families dominated in the samples. The viruses of the Phycodnaviridae, Poxviridae Mimiviridae, Herpesviridae, Baculoviridae, Polydnaviridae and Iridoviridae families were also the most numerous. Viral communities of visually healthy and diseased Baikal sponges were significantly different. Analysis of viral sequences has indicated 22 functional categories of proteins and revealed a wide variety of structural viral proteins and enzymes. Among those the genes of proteins involved in the metabolism of host cells were also identified. Thus, the role of viruses in sponges may be both in the regulation of the number and diversity and in the maintenance of the vital activity of their hosts and the associated community as a whole.

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Transcriptome (RNA-seq) analysis of human salivary gland cells with exogenous expression of human pancreas beta cells transcription factors PDX1, MAFA, NGN3.

Poster (download) Olga Brovkina1, Alexander Artyuhov2, Yulia Kolesova3, Erdem Dashinimaev4, Mikhail Borisov5, Ekaterina Vorotelyak6, Andrey Vasiliev71Federal Research and Clinical Center, FMBA of Russia, brov.olia@gmail.com2Center for Precision Genome Editing and Genetic Technologies, Pirogov Russian National Research Medical University, alexanderartyuhov@gmail.com3Sechenov First Moscow State Medical University, Institute of Molecular Medicine, vasilenko-yuliya@mail.ru41. Center for Precision Genome Editing and Genetic Technologies, Pirogov Russian National Research Medical University; 2. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, dashinimaev@gmail.com5Koltzov Institute of Developmental Biology, Russian Academy of Sciences, borisov.mikhail2011@yandex.ru6Koltzov Institute of Developmental Biology, Russian Academy of Sciences, vorotelyak@idbras.ru7Koltzov Institute of Developmental Biology, Russian Academy of Sciences, vasiliev@idbras.ru Treatment of diabetes patients with exogenously administered insulin linked with burdensome for patients and the possibility of fallible doses. The development of cell technologies providing new sources of beta-cells represents an attractive therapeutic strategy to treat patients with diabetes.В One of the promising technologies is reprogramming the cells by target changes in transcript factors regulating beta-cells development and differentiation. In this study, we used transduction with lentivirus particles carrying a cassette for PDX1, MAFA and NGN3 expression (or all three at once) and GFP cassette as a control. We have chosen salivary gland (SGC) and HuTu80 as initial cell lines for reprogramming into beta-cells. The results were analyzed by RNAseq (Illumina HiSeq 4000). A total of 195 and 385 mRNA genes appeared to be differentially expressed in SGC and HuTu80, accordingly. The analysis of significant pathways revealed changes in the regulation of the actin cytoskeleton, which can play a crucial role in reprogramming into beta-cells.

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Functional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

Semyon K. Kolmykov1, Nikita V. Ivanisenko2, Ivan S. Evshin3, Mikhail Kulyashov4, Tamara M. Khlebodarova5, Ilya R. Akberdin61Institute of Computational Technologies SB RAS, kolmykovsk@gmail.com2FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com3Institute of Computational Technologies SB RAS, ivan@biosoft.ru4Institute of Computational Technologies SB RAS, m.kulyashov@mail.ru5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru6FRC 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.

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Bioinformatic Screening for Subtilisin-like Peptidases in Dikaryotic Fungi

Poster (download) Nikita Alkin1, Yakov Dunaevsky2, Mikhail Belozersky3, Galina Beliakova4, Valeriia Tereshchenkova5, Elena Elpidina61MSU Faculty of Biology, Moscow, Russia, nikita9801@mail.ru2MSU Belozersky IPCB, Moscow, Russia, dun@belozersky.msu.ru3MSU Belozersky IPCB, Moscow, Russia, mbeloz@belozersky.msu.ru4MSU Faculty of Biology, Moscow, Russia, adm-odo@yandex.ru5MSU Faculty of Chemistry, Moscow, Russia, v.tereshchenkova@gmail.com6MSU Belozersky IPCB, Moscow, Russia, elp2@yandex.ru Subtilisin-like peptidases (SLPs) play an important role in digestion and host colonization of pathogenic fungi. Analysis of 42 fungal genomes from all major taxa of Ascomycota and Basidiomycota was performed. Homologs of enzymes from all 4 major families of SLPs were found is the examined genomes. The most abundant types of the SLP homologs found were those of kexin and proteinase K families; pyrolysin homologs were detected in the half of the observed species; in addition, several homologs of OSP family proteins were found. Alignments of homologous amino acid sequences with type SLPs indicated presence of intact conserved domains and active sites. Number of SLP homologs differ distinctly between species from different environmental niches with the highest variety of SLPs found in pathogenic and parasitic fungi.

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