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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Reconstruction of Dementia Gene Network Using Online Bioinformatics Tools

Poster (download) Oleg Fateev1, Sergey S. Kovalev2, Yuriy L. Orlov31I.M.Sechenov First Moscow State Medical University, Moscow, Russia, fodmr1997@gmail.com2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia, kovalev@bionet.nsc.ru3Institute of Digital Medicine I.M.Sechenov First Moscow State Medical University), Moscow, Russia, orlov@bionet.nsc.ru In this work, the set of genes associated with mental diseases such as dementia was examined and analyzed using previously developed gene ontology annotation tools and databases. The aim of the study is to describe the molecular mechanisms of dementia based on the analysis of the gene set as a whole, using available bioinformatics databases, annotation and recent publications. Dementia is a chronic, general, usually irreversible decrease in cognitive function that affects all aspects of cognitive activity. The enriched gene ontology categories for dementia genes are regulation of neuronal death, regulation of cell death, organization of cellular components, and cognition. The study of the structure of the gene network shows a high connectivity of genes and their products.

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Consideration of pathogenicity of nsSNVs in CDKN2A gene, as a new tumor marker for leukemia, using bioinformatics methods

Poster (download) Video (download) Farzaneh Ghasemi1, Mohammad Mehdi Heidari2, Mehri Khatami3, Yuriy L. Orlov41Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir2Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir3Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir4I.M.Sechenov First Moscow State Medical University, Moscow, Russia, orlov@bionet.nsc.ru CDKN2A as a tumor suppressor gene (TSG) encodes p14 and p16 that they are tumor suppressor proteins and cell cycle regulators. Downregulation of these proteins causes various cancers. Sequence deletions or promoter hypermethylation lead to downregulation of these proteins. Also, point mutations can be caused malfunction or dysfunction of proteins. The aim of this study is definition of pathogenicity of non-synonymous single nucleotide variants (nsSNVs). We study three nsSNVs including rs104894095, rs786204195 and rs104894098 from NCBI/dbSNP databank. Then, these nsSNVs are considered by bioinformatics tools such as SIFT, PolyPhen-2, I-Mutant2.0, PANTHER, P-Mut, ExPASy/ProtScale, PEPTIDE 2.0 web server and PyMOL software. Plot of hydrophobicity of rs104894098 (V126D) is significantly changed. Also, we study hydrogen bonds length and atom distances in Aspartic acid substituted Valine in position 126 by PyMOL software. These parameters are compared with wild type protein. Finally, we find that rs786204195 and rs104894095 have destructive effects. But, rs104894098 (V126D) is deleterious because polar contacts, protein stability and hydrophobicity are changed in mutant form. This theory should be proved with experimental studies.

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Nanobodies design for treatment of age-related diseases

Mohammad Mehdi Heidari1, Yuriy L. Orlov21Department of Biology, Faculty of science,Yazd University, Yazd, Iran, Heidarimm@yazd.ac.ir2Novosibirsk State University, Novosibirsk, Russia, orlov@bionet.nsc.ru The problem of the treatment of age related diseases such as Alzheimer disease demands development of new drug design strategies. Reagents that specifically recognize oligomeric morphologies of AОІ have potential diagnostic and therapeutic value. Nanobodies (Nbs) or Single-domain antibodies are the smallest antigen-binding fragments derived from heavy-chain-only antibodies. The E1 nanobody selectively recognizes naturally occurring AОІ aggregates produced in human AD brain tissue We discuss a method for the generation and binding optimization of VHHs that involves the grafting of the complementarity determining regions (CDRs) from already existing, non-camelid antibodies to VHH frameworks, followed by affinity maturation and target binding improvement using in silico site-directed mutagenesis.

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Computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data

Poster (download) Andrew Kropochev1, Alexandra Klimenko2, S.A. Lashin31Kurchatov Genomics Center, Institute of Cytology and Genetics, andrew.kropochev@gmail.com2Kurchatov Genomics Center, Institute of Cytology and Genetics, klimenko@bionet.nsc.ru3Kurchatov Genomics Center, Institute of Cytology and Genetics, lashin@bionet.nsc.ru Human gut microbiota is essential for human health. Under the recent avalanche of metagenomic high-throughput sequencing data methods for its bioinformatic analysis and ecological reconstruction gain particular relevance. In this study, we employ the trait-based ecology approach to create a method of computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data and apply it to the synthetic community comprised of the key representatives of the human gut microbiota. Using this structure allowed us to evaluate the abundance of respective functional groups and infer a knowledge about the processes associated with them. The developed method can be applied to analyze intestinal microbial communities of other related species.  

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