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

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Genomics, transcriptomics, bioinformatics symposium

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Genomics, transcriptomics, bioinformatics symposiumA study of genes controlling carcinogenesis in a regenerative model flatworm Macrostomum lignano

A study of genes controlling carcinogenesis in a regenerative model flatworm Macrostomum lignano

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Poster (download)

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Kitill Ustyantsev1, Valeriya Vavilova2, Mikhail Biryukov3, Eugene Berezikov4
1Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia, ustyantsev@bionet.nsc.ru
2Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia, valeriya-vavilova@bionet.nsc.ru
3Interinstitutional laboratory of molecular paleogenetics and paleogenomics ICG SB RAS Novosibirsk, Russia, birykov@bionet.nsc.ru
4Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia European Research Institute for the Biology of Ageing Groningen, The Netherlands, eberez@bionet.nsc.ru

В Free-living flatworm Macrostomum lignano is a novel model organism that provides a genetically tractable experimental system to specifically study the interplay between regulation of regeneration and cancer. Here, we tested two chemical carcinogens (MMS and CsA) and short wavelength ultraviolet irradiation (UVC) in M. lignano in order to identify genes and molecular pathways underlying carcinogenic response in this flatworms. For the first time, sensitivity of M. lignano to hard UV was evaluated, and it was shown that the worm can easily tolerate sterilization-level doses of higher than 100 mJ/cm2. Using differential gene expression analysis based on generated RNA-Seq data, common and individual patterns of M. lignano transcriptional response to the induced carcinogenesis by the tested stimuli were determined. This allowed us to select promising candidate genes for functional studies using RNAi knock-down screens and for determination of their role in stem cells regulation under regeneration and homeostasis in M. lignano.

Genomics, transcriptomics, bioinformatics symposiumTranscriptional profiling of ventral tegmental area of male mice with alternative patterns of social behaviors

Transcriptional profiling of ventral tegmental area of male mice with alternative patterns of social behaviors

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Olga Redina1, Vladimir Babenko2, Vadim Efimov3, Dmitry Smagin4, Irina Kovalenko5, Anna Galyamina6, Natalia Kudryavtseva7
1Laboratory of Neuropathology Modeling, Laboratory of Evolutional Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, oredina@bionet.nsc.ru
2Laboratory of Neuropathology Modeling, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, bob@bionet.nsc.ru
3Laboratory of Molecular Genetic Systems Modeling, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, efimov@bionet.nsc.ru
4Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, smagin@bionet.nsc.ru
5Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, koir@bionet.nsc.ru
6Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, galyamina@bionet.nsc.ru
7Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, n.n.kudryavtseva@gmail.com

The activity of ventral tegmental area (VTA) neurons plays a crucial role in the reward circuit, emotional and addictive behaviors in animals and humans. To elucidate the molecular mechanisms underlying the functional changes in VTA neurons under stress arising from social interactions, RNA-Seq analysis was used to compare the transcriptome profiles in the VTA of three groups of male mice: chronically winning mice with positive social experience in daily agonistic interactions, chronically defeated mice with negative social experience in daily agonistic interactions, and control mice having no experience of agonistic interactions. The data obtained showed that both winning and defeated mice experience stress, however, in defeated animals, the repeated agonistic interactions have a stronger effect and cause more significant changes in the levels of gene transcription. Several genes have been identified that may be involved in the determination of alternative behavioral phenotypes in groups of male mice with alternative social experience.

Genomics, transcriptomics, bioinformatics symposiumGenetic mapping of QTLs controlling the ISIAH hypertensive rat behavior in an open field tests

Genetic mapping of QTLs controlling the ISIAH hypertensive rat behavior in an open field tests

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Olga Redina1, Svetlana Smolenskaya2, Arcady Markel3
1Laboratory. of Evolutional Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, oredina@bionet.nsc.ru
2Laboratory of Evolutional Genetics, Wheat Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, svsmol@ngs.ru
3Laboratory. of Evolutional Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, markel@bionet.nsc.ru

Genetic mapping of QTLs controlling the ISIAH hypertensive rat behavior in an open field tests evaluating research behavior, the level of anxiety and motor activity of animals was performed. The work was carried out using two groups of male hybrid rats F2(ISIAHxWAG) of different ages – 3-4 months (n = 103) and 6 months (n = 126) obtained by crossing hypertensive ISIAH and normotensive WAG rats whose behaviors are significantly different in all six tests in an open field taken in the analysis: the latency, the motor activity at 1-st minute of the test, motor activity on the periphery, grooming on the periphery, rearing on the periphery, defecation score. In both groups of rats, genetic loci associated with the studied traits of behavior were found and the common loci associated with both the behavioral traits and traits related to the hypertension development were identified. The results of our work suggest that genes that control behavioral patterns of ISIAH rats can either be closely linked to genes involved in the control of traits associated with the hypertensive status of these rats, or, in some loci, may have a pleiotropic effect on both behavioral traits and on the traits associated with the hypertensive status of ISIAH rats.

Genomics, transcriptomics, bioinformatics symposiumGenome-Centered Integrated Instrumental Information System Modeling and Interpretation of Human and Virus Omics

Genome-Centered Integrated Instrumental Information System Modeling and Interpretation of Human and Virus Omics

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Anatoliy Shlikht1, Natalia Kramorenko2
1Far Eastern Federal University, schliht@mail.ru
2Far Eastern Federal University, kramnat@mail.ru

Creating an integrated genome-centered intellectual system based on highly structured databases and knowledge bases for modeling and interpreting human and virus omics. The system allows you to automatically find functionally significant structures (templates, motifs, epitopes) for genomic and proteomic data in the formation of nucleo-protein complexes and antigen-antibody complexes, determine protein functions, and model spatio-temporal biochemical and physiological processes.

Genomics, transcriptomics, bioinformatics symposiumResults of the whole-genomic sequencing and annotation of the Listeria phenotype

Results of the whole-genomic sequencing and annotation of the Listeria phenotype

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Marina Terekhova1
1St. Petersburg State University of Information Technologies, Mechanics and Optics, Saint-Petersburg, Russia
, n.mim@mail.ru

The incidence of Listeriosis in recent years is constantly 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. welshimeriare most often distinguished. And if earlier it was believed that representatives of the species L. monocytogenespossess the largest set of pathogenicity factors, then the possibilities of molecular and bioinformatics research methods provide a reliable picture with respect to other representatives of the genus Listeria, in particular L. innocua.

Genomics, transcriptomics, bioinformatics symposiumAllelic drop-out is a common phenomenon reducing the diagnostic yield of PCR-based target sequencing

Allelic drop-out is a common phenomenon reducing the diagnostic yield of PCR-based target sequencing

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Anna Shestak1, Anna Bukaeva2, Siamak Saber3, Elena Zaklyazminskaya4
1Petrovsky National Research Center of Surgery, Moscow, Russia, anna.shestak87@gmail.com
2Petrovsky National Research Center of Surgery, Moscow, Russia, 16_anna_02@mail.ru
3Cardiac Electrophysiology Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran, s_saber2002@yahoo.com
4Petrovsky National Research Center of Surgery, Moscow, Russia, helenezak@gmail.com

Abstract Allelic drop-out (ADO) is a known phenomenon of selective allele amplification representing the potential problem of correct DNA diagnostics. The results demonstrate the incidence of ADO reducing the diagnostic yield of PCR-based target sequencing.В 

Motivation and aim: Allelic drop-out (ADO) is a known phenomenon of selective allele amplification representing the potential problem of correct DNA diagnostics. Both NGS and Sanger sequencing are PCR-based methods, Sanger sequencinq is used to verify NGS results. The aim of this study is to demonstrate the incidence of ADO reducing the diagnostic yield in primary cardiomyopathy genetic testing via semiconductor NGS and Sanger sequencing of target gene panels.

Methods: We have developed 3 AmpliSeq custom gene panels for mutational screening: “K+/Na+ ion channels”, “Desmosomal proteins”, “Sarcomeric proteins”, contains 1049 primer pairs (37 genes) totally, 152 kb. About 140 probands were screened with at least one of these gene panels. AmpliSeq sequences were analyzed in silico and visually compared with Sanger control sequences, noting the facts of heterozygosity loss.

Results: We have detected 12 ADO cases both in Sanger (5 cases) and AmpliSeq (7 cases) sequencing data. All ADO events happened due to frequent or rare SNVs in the oligoprimer annealing sites and were detected due to mismatch in frequent SNPs zygosity nearby. Three pathogenic variants would be missed if were not revealed by re-sequencing with alternative method and alternative oligos.

Conclusion: All PCR-based methods have a risk of ADO leading to a decrease of diagnostic yield of genetic testing.В ADO can theoretically affect 1% amplicons.В It seems that real scope of ADO might be much higher and depends on numbers of primer pairs. The software for ADO detection is needed.

Acknowledgment: В This work was supported by Russian Science Foundation grant в„–16-15-10421.

Genomics, transcriptomics, bioinformatics symposiumUsing fast homology search tools for protein sequence functional annotation: a comparison

Using fast homology search tools for protein sequence functional annotation: a comparison

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Pronozin Artem1, Mikhail Genaev2, Dmitry Afonnikov3
1lInstitute of Cytology and Genetics SB RAS, pronozinartem95@gmail.com
2lInstitute of Cytology and Genetics SB RAS, mag@bionet.nsc.ru
3lInstitute of Cytology and Genetics SB RAS, ada@bionet.nsc.ru

Annotation of the protein sequences by homology search and GO term transfer from highly homologous sequences is an important task for current genome and transcriptome sequencing projects. However, large size of sequence databases make homologous sequence search difficult in reasonable time. There exist tools that apply fast and ultrafast database search algorithms to find sequence homologs. These tools usually apply various heuristics for fast determining possible sequence matches. This result in different results of these programs with respect to returned set of homologous sequences and their rankings. These differences may lead to differences in the sets of GO terms and lead to errors in query sequence function annotation.В We compare performance of the highly homologous sequence detection by several fast search tools (BLASTP fast, Diamond, Usearch ublast, Usearch local, Mmseq2) applied for A.thaliana protein sequences represented in OrthoDB database. We compared their results with the sequence ranking obtained by ClustalW program for various number k of returned best hits.

Genomics, transcriptomics, bioinformatics symposiumIntermediate and high-risk prostate cancer methylation analysis

Intermediate and high-risk prostate cancer methylation analysis

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Poster (download)

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Elena Pudova1
1EIMB RAS, pudova_elena@inbox.ru

Prostate cancer is one of the most important socially significant oncological diseases in men. To select an effective approach to therapy, prostate cancer is stratified into appropriate risk groups based on criteria such as TNM status, Gleason score and the level of prostate-specific antigen (PSA). However, to optimize therapy, additional informative markers are necessary, and the aim of this study is to search for these markers at the level of genome methylation. This work included methylation data of prostate cancer from The Cancer Genome Atlas project. The cohort involved patients with high (23 cases) and intermediate (103 cases) risk. As a result, 1,056 differentially methylated CpG sites were found between high and medium risk groups. CpG most interested sites: cg17687367 (chr13: 79936801), cg26874611 (chr5: 168147884), cg06989693 (chr5: 41409252), cg02226810 (chr6: 1605117), cg07736716 (regulation regions: 85): 85 to 91 (85): 85 858: 858: 858: 85: 86: 85: 86: 85: 86: 85: 86: 85: 86: 85: 85.

Genomics, transcriptomics, bioinformatics symposiumRTrans: a pipeline for multi-way analysis of differential gene expression profiles

RTrans: a pipeline for multi-way analysis of differential gene expression profiles

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George Sergeevich Krasnov1, Anastasiya Andreevna Kobelyatskaya2, Anastasiya Vladimirovna Snezhkina3, Vladislav Sergeevich Pavlov4, Elena Anatolevna Pudova5, Anna Victorovna Kudryavtseva6
1EIMB RAS, gskrasnov@mail.ru
2EIMB RAS, kaa.chel@mail.ru
3EIMB RAS, leftger@rambler.ru
4EIMB RAS, vladislav1pavlov@gmail.com
5EIMB RAS, pudova_elena@inbox.ru
6EIMB RAS, rhizamoeba@mail.ru

RNA-Seq is a widespread technique routinely used to reveal differentially expressed (DE) genes, splicing events and affected signaling pathways. Usually, RNA-Seq data analysis needs skills in programming and bioinformatics. We aimed at developing easy-to-use pipeline covering multiple aspects of DE analysis. Here we present RTrans pipeline aimed at evaluating differential gene expression, pathway enrichment, WGCNA co-expression analysis and visualization. It provides rapid analysis of read counts data including MANOVA, paired tests, non-parametric tests. RTrans represents a versatile pipeline facilitating DE analysis based on RNA-Seq and other quantitative data.

Genomics, transcriptomics, bioinformatics symposiumDifferentially expressed genes associated with TMPRSS2-ERG molecular subtype of prostate cancer

Differentially expressed genes associated with TMPRSS2-ERG molecular subtype of prostate cancer

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Anastasiya Andreevna Kobelyatskaya1, Elena Anatolevna Pudova2, George Sergeevich Krasnov3, Anna Victorovna Kudryavtseva4, Kirill Mikhailovich Nyushko5, Boris Yakovlevich Alekseev6
1EIMB RAS, kaa.chel@mail.ru
2EIMB RAS, pudova_elena@inbox.ru
3EIMB RAS, gskrasnov@mail.ru
4EIMB RAS, rhizamoeba@mail.ru
5FSBI NMRRC, kirandja@yandex.ru
6FSBI NMRRC, mnioi@mail.ru

Prostate cancer (PC) is one of the most common and socially significant oncological diseases in men. This study examined the transcriptome profile of the most common molecular genetic subtype of prostate cancer, TMPRSS2-ERG. As a result of bioinformatics analysis conducted on the basis of The Cancer Genome Atlas project data, 115 differentially expressed genes were identified for this study group, and in particular, the most over-expressing genes were identified: ALOX15, CACNA1D, EML6, HLA-DMB, NKAIN1, OGDHL, PLA1A, SYT13. Enrichment pathways analysis showed that these genes are participants in important oncologically significant pathways, which emphasizes the association of this molecular subtype with an unfavorable prognosis for prostate cancer.