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

Category

Genomics, transcriptomics, bioinformatics symposium

Showing: 1 - 10 of 71 RESULTS
Genomics, transcriptomics, bioinformatics symposiumTranscriptome (RNA-seq) analysis of human salivary gland cells with exogenous expression of human pancreas beta cells transcription factors PDX1, MAFA, NGN3.

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

No Comment on Transcriptome (RNA-seq) analysis of human salivary gland cells with exogenous expression of human pancreas beta cells transcription factors PDX1, MAFA, NGN3.

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/364.pdf”]
Olga Brovkina1, Alexander Artyuhov2, Yulia Kolesova3, Erdem Dashinimaev4, Mikhail Borisov5, Ekaterina Vorotelyak6, Andrey Vasiliev7
1Federal Research and Clinical Center, FMBA of Russia, brov.olia@gmail.com
2Center for Precision Genome Editing and Genetic Technologies, Pirogov Russian National Research Medical University, alexanderartyuhov@gmail.com
3Sechenov First Moscow State Medical University, Institute of Molecular Medicine, vasilenko-yuliya@mail.ru
41. 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.com
5Koltzov Institute of Developmental Biology, Russian Academy of Sciences, borisov.mikhail2011@yandex.ru
6Koltzov Institute of Developmental Biology, Russian Academy of Sciences, vorotelyak@idbras.ru
7Koltzov 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.

Genomics, transcriptomics, bioinformatics symposiumEPhIMM: computational workflow for fast phylogenetic inference based on multiple alignment of prokaryotic single-copy marker genes

EPhIMM: computational workflow for fast phylogenetic inference based on multiple alignment of prokaryotic single-copy marker genes

No Comment on EPhIMM: computational workflow for fast phylogenetic inference based on multiple alignment of prokaryotic single-copy marker genes

Aleksei Korzhenkov1
1NRC Kurchatov Institute, oscypek@ya.ru

EPhIMM a computational workflow for fast and accurate phylogenetic inference for prokaryotic genomes was developed and tested on bacterial and archaeal datasets. Source code is freely available at https://github.com/laxeye/EPhIMM.

Genomics, transcriptomics, bioinformatics symposiumBioinformatic Screening for Subtilisin-like Peptidases in Dikaryotic Fungi

Bioinformatic Screening for Subtilisin-like Peptidases in Dikaryotic Fungi

No Comment on Bioinformatic Screening for Subtilisin-like Peptidases in Dikaryotic Fungi

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/377.pdf”]
Nikita Alkin1, Yakov Dunaevsky2, Mikhail Belozersky3, Galina Beliakova4, Valeriia Tereshchenkova5, Elena Elpidina6
1MSU Faculty of Biology, Moscow, Russia, nikita9801@mail.ru
2MSU Belozersky IPCB, Moscow, Russia, dun@belozersky.msu.ru
3MSU Belozersky IPCB, Moscow, Russia, mbeloz@belozersky.msu.ru
4MSU Faculty of Biology, Moscow, Russia, adm-odo@yandex.ru
5MSU Faculty of Chemistry, Moscow, Russia, v.tereshchenkova@gmail.com
6MSU 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.

Genomics, transcriptomics, bioinformatics symposiumPCR dependent biases could significantly affect quantitative estimation of plant mix composition

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

No Comment on 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 Samoilov10
1Central Research Institute of Epidemiology, Moscow, Russia, valeriia.kaptelova@gmail.com
2Skolkovo Institute of Science and Technology, Skolkovo, Russia, maria.log@gmail.com
3Central Research Institute of Epidemiology, Moscow, Russia, hanna.s.939@gmail.com
4Institute of Information Transmission Problems, Moscow, Russia, omdeno@gmail.com
5Skolkovo Institute of Science and Technology, Skolkovo, Russia, mikrobiomsu@list.ru
6Lomonosov Moscow State University, Moscow, Russia, ankrina@gmail.com
7FSBI “Center of Strategic Planning” of the Ministry of Health, Moscow, Russia, ayginin75@gmail.com
8FSBI “Center of Strategic Planning” of the Ministry of Health, Moscow, Russia, kkhafizov@gmail.com
9Central Research Institute of Epidemiology, Moscow, Russia, lennatta@yandex.ru
10Central 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.

Genomics, transcriptomics, bioinformatics symposiumShort sequence repeats (SSR) under selection pressure: Cyprinidae fish case study

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

No Comment on Short sequence repeats (SSR) under selection pressure: Cyprinidae fish case study

Mikhail Orlov1, Andrey Tykhonov2
1ICB RAS, orlovmikhailanat@gmail.com
2Aqua 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.

Genomics, transcriptomics, bioinformatics symposiumAutomatic Annotation of Operons Responsible for O-antigen Synthesis

Automatic Annotation of Operons Responsible for O-antigen Synthesis

No Comment on Automatic Annotation of Operons Responsible for O-antigen Synthesis

Danil Zilov1, Polina Chesnokova2, Alexey Komissarov3
1Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, zilov@scamt-itmo.ru
2Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, chesnokova@scamt-itmo.ru
3Laboratory 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.

Genomics, transcriptomics, bioinformatics symposiumGenome-wide Association Study Reveals Novel Genetic Variants Associated with HIV-1C Infection in Botswana Population

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

No Comment on Genome-wide Association Study Reveals Novel Genetic Variants Associated with HIV-1C Infection in Botswana Population

Andrey Shevchenko1, Sergey V. Malov2, Alexey Antonik3
1Theodosius Dobzhansky Center for Genome Bioinformatics St.-Petersburg State University St-Petersburg, Russia, andrey.k.shevchenko@gmail.com
2Theodosius Dobzhansky Center for Genome Bioinformatics St.-Petersburg State University St-Petersburg, Russia, malovs@sm14820.spb.edu
3Theodosius 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.

Genomics, transcriptomics, bioinformatics symposiumDetection of alphacoronavirus in bat fecal samples from Volgograd regions

Detection of alphacoronavirus in bat fecal samples from Volgograd regions

No Comment on Detection of alphacoronavirus in bat fecal samples from Volgograd regions

Korneenko Elena1
1Central 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

Genomics, transcriptomics, bioinformatics symposiumMetavirome analysis of Baikal sponges

Metavirome analysis of Baikal sponges

No Comment on Metavirome analysis of Baikal sponges

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/365.pdf”]
Tatyana Vladimirovna Butina1, Yurij Sergeevich Bukin2, Igor Veniaminovich Khanaev3
1Laboratory of Analytical and Bioorganic Chemistry LIN SB RAS Irkutsk, Russia, tvbutina@mail.ru
2Laboratory of Genosystematics LIN SB RAS Irkutsk, Russia, bukinyura@mail.ru
3Laboratory 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.

Genomics, transcriptomics, bioinformatics symposiumFunctioning of unique nitrile-detoxifying system in soil xenobiotic degrader Rhodococcus rhodochrous: a whole-genome transcriptomic approach

Functioning of unique nitrile-detoxifying system in soil xenobiotic degrader Rhodococcus rhodochrous: a whole-genome transcriptomic approach

No Comment on Functioning of unique nitrile-detoxifying system in soil xenobiotic degrader Rhodococcus rhodochrous: a whole-genome transcriptomic approach

Konstantin V Lavrov1, Andrey D Novikov2, Tatyana I Kalinina3, Artem S Kasianov4, Alexander S Yanenko5
1NRC “Kurchatov institute – GosNIIgenetika”, lavrov.ko@gmail.com
2NRC “Kurchatov institute – GosNIIgenetika”, alexm19@mail.ru
3NRC “Kurchatov institute – GosNIIgenetika”, tatyana.i.kalinina@googlemail.com
4Vavilov Institute of General Genetics, artem.kasianov@gmail.com
5NRC “Kurchatov institute – GosNIIgenetika”, yanenko@genetika.ru

Organic nitriles are significant participants of interactions between soil living organisms, thus their synthesis and degradation are of interest. Using transcriptomic approach, we revealed a genetic cascade, realizing nitrile degradation in powerful nitrile degrader – Rhodococcus rhodochrous. We also hypothesized a genetic “network” for nitrile/amide utilization, connected with cobalt homeostasis.