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

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Systems Biology and Biomedicine symposium

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Systems Biology and Biomedicine symposiumCorrelation between Cytokines Lymph and Mesenteric Lymph Nodes on Breast Cancer in Rat

Correlation between Cytokines Lymph and Mesenteric Lymph Nodes on Breast Cancer in Rat

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/14.pdf”]
Kazakov Oleg1, Poveshchenko Alexander2, Orlov Nikolai3, Kabakov Alexey4, Lykov Alexander5, Strunkin Dmitry6, Konenkov Vladimir7
1Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, kazakoff_oleg@mail.ru
2Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, poveshchenkoa200@mail.ru
3Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, nbo@ngs.ru
4Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, kabakov_av85@mail.ru
5Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, aplykov2@mail.ru
6Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Strunkind@mail.ru
7Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, vikonenkov@gmail.com

The correlation analysis of the morphometry of mesenteric lymph nodes and cytokines of the chest duct lymph in chemically induced breast cancer was carried out. The study showed that in breast cancer, the activity of the local immune response in the lymph nodes is aimed at antitumor protection. In breast cancer, the area of the paracortical zone remains at the level of the intact group, the area of lymphoid nodules with germinative centers and the area of medullary substance are increased, the number of macrophages in the thymus-dependent zone and zone responsible for humoral immunity is increased. In breast cancer positive correlation were revealed: in the germinative centers and medullary substance – mitotically dividing cells with cytokine IL-5, medium lymphocytes with chemokine MIP-1О±, in the germinative centers – immunoblasts with cytokine GRO/KC, in the paracortical zone – chemokine MCP-1 with macrophages, reticular cells with IL-6 and M-CSF, in medullary substance – small lymphocytes and mature cells plasma cells (the number of which is decrease) with chemokine Gro/KC, that can be caused by their migration from lymph nodes.В 

Systems Biology and Biomedicine symposiumToxicity of Fucoxanthin on Balb/c Mice Splenocytes and Thymocytes

Toxicity of Fucoxanthin on Balb/c Mice Splenocytes and Thymocytes

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/13.pdf”]
Alexander Lykov1, Lubov Rachkovskaya2, Olga Poveshchenko3, Maria Surovtseva4, Irina Kim5, Edmund Rachkovsky6, Maxim Korolev7, Ruslan Gevorgiz8, Svetlana Zheleznova9, Anastasiya Kotlyarova10, Andrey Letyagin11
1Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, aplykov2@mail.ru
2Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, lymphology@niikel.ru
3Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, poveschenkoov@yandex.ru
4Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, mfelde@ngs.ru
5Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, kii5@yandex.ru
6Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, lymphology@niikel.ru
7Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, kormax@bk.ru
8A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, r.gevorgiz@yandex.ru
9A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, zheleznovasveta@yandex.ru
10Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, kotlyarova.anastasiya@yandex.ru
11Research Institute of Clinical ans Experimental Lymphology- Branch of the Institute of Cytology and Genetics SB RAS, letyaginay@bionet.nsc.ru

This work described toxicity of composition of fucoxanthin with particles of porous aluminum oxide with polydimethylsiloxane (Fx@Al/PDMS) in mice lymphocytes. Effects of Fx@Al/PDMS on Balb/c mice splenocytes and thymocytes viability, and proliferation, and intracellular myeloperoxidase activity, and nitric oxide (NO) production, and apoptosis were studied. It was shown that short-term (24 h) and long-term (129 h) incubation lymphocytes with Fx@Al/PDMS did not have any adverse effect on functional properties of splenocytes and thymocytes.

Systems Biology and Biomedicine symposiumThe rs12255372 and rs7903146 polymorphisms of the TCF7L2 gene among Buryats and Russians of Eastern Siberia.

The rs12255372 and rs7903146 polymorphisms of the TCF7L2 gene among Buryats and Russians of Eastern Siberia.

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/171.pdf”]
Ludmila Tabikhanova1, Ludmila Osipova2, Tatiana Churkina3, Daria Lichman4, Elena Voronina5, Maxim Filipenko6
1Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk State University, tabikhan@bionet.nsc.ru
2Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk State University, ludos77@yandex.ru
3Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk State University, tan646464@gmail.com
4Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk State University, daria.lichman@gmail.com
5Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, voronina_l@mail.ru
6Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, max@niboch.nsc.ru

The objective of the present study was to investigate the polymorphism of metabolism genes in indigenous populations of Siberia. To this end, we have studied the ethnic features of allele frequency distribution for polymorphic variants in gene TCF7L2 G103894T (rs12255372) and C53341T (rs7903146) in the samples taken from Buryats, and Russians of Eastern Siberia, and compared it with data on world populations. Samples of Eastern (N = 132) and Western (N = 278) Buryats, Russians (N = 122) and persons of mixed Buryat-Russian origin (N = 56) were genotyped by real-time PCR using competitive TaqMan- probes. Compared to the Russians, the Buryats showed a statistically significantly lower incidence of the TCF7L2 103894T and TCF7L2 53341T alleles associated with metabolic diseases and Type 2 diabetes mellitus (T2DM). Buryats are intermediate between Caucasian and East Asian populations. This agrees with the lower susceptibility of Buryats to metabolic disorders compared to the Caucasian population described in the literature. Intermediate frequencies alleles in the group of mixed origin may indicate a higher risk of the associated metabolic disorders in the descendants of mixed marriages compared to the Buryats.

Systems Biology and Biomedicine symposiumLYVE-1 expression in liver cells of mice with functional pinealectomy

LYVE-1 expression in liver cells of mice with functional pinealectomy

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/222.pdf”]
Irina Yurievna Ishchenko1, Svetlana Viktorovna Michurina2, Sergey Alekseevich Arkhipov3, Andrey Yurievich Letyagin4, Maxim Aleksandrovich Korolev5, Evgenii Leonidovich Zavjalov6
1Group of experimental pharmacology SRICEL – a branch of ICG SB RAS Novosibirsk, Russia, irenisch@mail.ru
2Group of experimental pharmacology SRICEL – a branch of ICG SB RAS Novosibirsk, Russia, s.michurina@ngs.ru
3Group of experimental pharmacology SRICEL – a branch of ICG SB RAS Novosibirsk, Russia, arhipowsergei@yandex.ru
4Laboratory of pharmaceutical technologies SRICEL – a branch of ICG SB RAS Novosibirsk, Russia, letyagin-andrey@yandex.ru
5Laboratory of connective tissue pathology SRICEL – a branch of ICG SB RAS Novosibirsk, Russia, kormax@bk.ru
6Center of genetis resources of laboratory animals ICG SB RAS Novosibirsk, Russia, zavjalov@bionet.nsc.ru

The expression of the lymphatic vessel endothelial receptor-1 hyaluronan-1 (LYVE-1) was studied in the liver cells of male C57BL / 6 mice, which were kept for 14 days under 24-hour illumination (mice with functional pinealectomy). Used immunohistochemical analysis (indirect avidin-biotin-ABC-peroxidase method) and morphometric evaluation. A 2-fold decrease in the LIVE-1 expression area was detected against a 2% increase in the optical density of LIVE-1 staining in mouse liver cells after chronic continuous illumination. Weak expression of LYVE-1 on the membranes of endothelial cells of the sinusoids of the liver may indicate a violation of the functioning of the fields of fenestration of these cells. This can lead to a decrease in the endocytotic activity of the latter, difficulty in the exchange of hematotissue tissues, deterioration of lymphatic drainage and the development of tissue hypoxia in the liver of mice with functional pinealectomy.

Systems Biology and Biomedicine symposiumReconstruction and Analysis of Regulatory Gene Networks Involving Human Genes Associated with Main Forms of Pathozoospermia

Reconstruction and Analysis of Regulatory Gene Networks Involving Human Genes Associated with Main Forms of Pathozoospermia

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/216.pdf”]
Elena V. Ignatieva1, Alexander V. Osadchuk2, Maxim A Kleshev3, Ludmila V. Osadchuk4
1The Federal Research Center Institute of Cytology and Genetics, SB RAS, eignat@bionet.nsc.ru
2The Federal Research Center Institute of Cytology and Genetics, SB RAS, osadchuk@bionet.nsc.ru
3The Federal Research Center Institute of Cytology and Genetics, SB RAS, max82cll@bionet.nsc.ru
4The Federal Research Center Institute of Cytology and Genetics, SB RAS, losadch@bionet.nsc.ru

The study of the molecular-genetic mechanisms predisposing to decline in male reproductive potential (spermatogenic failure) is an actual problem of reproductive biology. Most often in laboratory studies evaluating male fertility, a study of the quality of ejaculate is used. Thus, a pathological condition called pathozoospermia can be detected if the quality indicators of the ejaculate are decreased. Pathozoospermia can manifest itself in several distinct forms, may occur in many diseases and can be caused by many factors, including genetic ones. To reveal regulatory interactions between genes associated with pathozoospermia, we reconstructed gene regulatory network involving genes harboring allelic variants associated with pathozoospermia. Regulatory network comprised seven genes encoding transcription factors (TFs) for which a set of target genes were predicted by MoLoTool web-service. We identified three key regulatory transcription factors (WT1, AHR, NR0B1) that have the greatest number of target genes in the network. Genes encoding these factors can be considered as the most promising candidate genes for identifying genetic variants associated with pathozoospermia.

Systems Biology and Biomedicine symposiumCalcium Signaling Dynamics in Single Platelets during Optically-induced Activation.

Calcium Signaling Dynamics in Single Platelets during Optically-induced Activation.

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Darya V. Spiryova1, Alexander E. Moskalensky2, Alexei Vorob’ev3
1NSU, gerd.raz@yandex.ru
2NSU, a.mosk@nsu.ru
3NSU, vor@nioch.nsc.ru

Activation of blood platelets is the main process in normal hemostasis. Unfortunately, it also makes a great contribution to the development of cardiovascular diseases. In this work, we study activation dynamics using cytosolic calcium probe. To increase the accuracy of dynamic measurements, we present a method for optical activation of single platelets in suspension. It is achieved by the use of photolabile “caged” activation agonists. Futhermore, a mathematical model was developed that allows to detect individual calcium peaks and derive their dynamic parameters.

Systems Biology and Biomedicine symposiumMitochondrial dysfunction and redox balance alterations in the development of AD-like pathology in OXYS rats

Mitochondrial dysfunction and redox balance alterations in the development of AD-like pathology in OXYS rats

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Mikhail Tyumentsev1, Natalia Muraleva2, Yulia Polienko3, Artyom Gorodetsky4, Elena Bagryanskaya5
1ICG SB RAS, landselur@bionet.nsc.ru
2ICG SB RAS, Myraleva@bionet.nsc.ru
3NIOCH SB RAS, polienko@nioch.nsc.ru
4NIOCH SB RAS, gorodaa@nioch.nsc.ru
5NIOCH SB RAS, egbagryanskaya@nioch.nsc.ru

This study focuses on the relationship between mitochondrial dysfunction and redox-status in the context of the development of signs of Alzheimer’s disease (AD). Mitochondrial dysfunction is considered the missing link between brain aging and AD [1], the most common type of age-related dementia worldwide, but the exact causal relationship between mitochondrial dysfunction and the transition from healthy aging to AD remains to be fully understood. Oxidative stress is thought to play a significant role in this mitochondrial dysfunction, leading to cellular damage in redox imbalance. However, the extent of these processes and timing of their occurrence within the scope of AD remain hard to study, especially so in the early, pre-clinical stages of the disease. We explored the mechanisms underlying the disruption of mitochondrial function, their impact on the initiation and progression of pathological molecular cascades of AD, and assessed the changes in redox status as one of the main consequences of oxidative stress. This investigation was conducted using senescence-accelerated OXYS rats, which spontaneously develop all major signs of AD and largely reproduce the stages of the disease. We concluded that mitochondrial dysfunction appears to mediate or possibly even initiate AD-like pathology in OXYS rats. Importantly this takes place with no apparent connection to redox imbalance as on both transcriptional and biochemical levels OXYS rats display no significant changes in redox-status and ROS production as compared to controls.

Systems Biology and Biomedicine symposiumA new method for the diagnosis of osteoporosis using standing waves

A new method for the diagnosis of osteoporosis using standing waves

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/199.pdf”]
Video (download)

Konstantin Fedin1, Olga Fazullina2, Vadim Klimontov3, Yuriy Kolesnikov4
1Laboratory of seismic dynamic analysis Trofimuk Institute of Petroleum Geology and Geophysics of Siberian Branch Russian Academy of Sciences; IPGG SB RAS, fedin.konstantin@gmail.com
2Laboratory of Endocrinology Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, fazullina@ngs.ru
3Laboratory of Endocrinology Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, klimontov@mail.ru
4Laboratory of seismic dynamic analysis Trofimuk Institute of Petroleum Geology and Geophysics of Siberian Branch Russian Academy of Sciences; IPGG SB RAS, KolesnikovYI@ipgg.sbras.ru

Osteoporosis is a non-infectious epidemic with severe medical and economic consequences. The main complication of reducing bone mineral density is the occurrence of fractures due to minimal trauma. Fractures, in turn, require long-term treatment, subsequent rehabilitation, and can often lead to disability. In addition, cases of fractures of the proximal femur are aggravated by the presence of deaths during the first year in a large number of patients. Thus, early diagnosis of osteoporosis is important for verifying the diagnosis and timely prescribing anti-osteoporotic therapy to reduce the risk of low-energy fractures.
Currently, there are three main methods used for densitometry. Quantitative computed tomography is very accurate, but requires significant material costs, also the disadvantages include the long duration of the procedure, the received dose of x-ray radiation and the inability to evaluate the dynamics in the future. Quantitative computed tomography can only be performed in a specialized center, as performed using tomography equipment having stringent requirements for installation and operation.

Among the advantages of quantitative ultrasonic densitometry, one can note the absence of contraindications associated with exposure to x-ray radiation, the short time spent on research, low cost. Disadvantages – there is no quantitative data that allows dynamic assessment, low accuracy, evaluation only in the peripheral parts of the skeleton (calcaneus and radius), which does not allow extrapolating data to all skeleton bones as a whole.

The \”gold standard\” of diagnosis is currently dual energy X-ray absorptiometry (DEXA). The method has good reproducibility, accuracy, there are quantitative indicators to assess the state of bone tissue in dynamics. In modern densitometers, it is also possible to study bone microarchitectonics using special software. Contraindications to the conduct are common to all x-ray research methods. The disadvantages include the x-ray principle, lack of mobility, high cost of equipment.

Systems Biology and Biomedicine symposiumStudy of serotonin transporter gene polymorphism Stin2 in two Siberian indigenous populations

Study of serotonin transporter gene polymorphism Stin2 in two Siberian indigenous populations

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/193.pdf”]
Mira Khantemirova1, Daria Lichman2, Daria Bazovkina3, Anatoly Bragin4, Vladimir Naumenko5, Ludmila Osipova6
1Laboratory of populational ethnogenetics, Institute of cytology and genetics; Laboratory of computer genomics, Novosibirsk State University Novosibirsk, Russia, hantemiramira@mail.ru
2Laboratory of populational ethnogenetics, Institute of cytology and genetics; Laboratory of computer genomics, Novosibirsk State University Novosibirsk, Russia, daria.lichman@gmail.com
3Laboratory of behavioral neurogenomics, Institute of cytology and genetics Novosibirsk, Russia, daryabazovkina@gmail.com
4Laboratory of computer genomics, Novosibirsk State University Novosibirsk, Russia, ibragim@bionet.nsc.ru
5Laboratory of behavioral neurogenomics, Institute of cytology and genetics Novosibirsk, Russia, naumenko2002@bionet.nsc.ru
6Laboratory of populational ethnogenetics, Institute of cytology and genetics; Laboratory of computer genomics, Novosibirsk State University Novosibirsk, Russia, ludos77@yandex.ru

Serotonin (5-HT) participates in regulation of emotions, mood, sleep, appetite, and cognitive processes. Serotonin transporter (5-HTT, SERT) modulates serotoninergic neurotransmission through reuptake of 5-HT from the synaptic cleft. A variable number tandem repeat polymorphism found in intron 2 of the 5-HTT gene (Stin2 polymorphism) influences 5-HTT expression and is associated with anxiety, depression, suicidal behavior, obsessive-compulsive disorder. The aim of the present study was to investigate Stin2 allele frequencies in populations of Tundra Nenets and Nganasans inhabiting north and east Siberia. The frequency of the STin2.10 allele was 72.1% in Tundra Nenets and 89.4% in Nganasans. The data obtained are consistent with the uniform geographic gradient of STin2 alleles, with low frequency of the STin2.10 allele in East Asia and its increase towards west.

Systems Biology and Biomedicine symposiumGenetic Polymorphism Associated with Infectious Pulmonary Diseases in Siberian Populations and Among Patients with Community Acquired Pneumonia

Genetic Polymorphism Associated with Infectious Pulmonary Diseases in Siberian Populations and Among Patients with Community Acquired Pneumonia

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/192.pdf”]
Svetlama V. Mikhailova1
1ICG SB RAS, mikhail@bionet.nsc.ru

Innate immune system is the first to respond to pathogen invasion; it activates adaptive immunity and regulates the intensity of inflammation. Two single nucleotide polymorphisms of the innate immunity genes: rs5743708 of the TLR2 and rs8177374 of the TIRAP were shown to be associated with pneumonia and tuberculosis, but the data are contradictory in different ethnic groups. We assessed the prevalence of these variants in Caucasoid and Asian population samples, and among patients with community acquired pneumonia (CAP). Carriage of the rs5743708 A allele was found to be predisposed to severe CAP (OR=2.77, p=0.021), GG/CT genotype for rs5743708 / rs8177374 is proved to be protective against it (OR=0.478, p=0.022) in Caucasoid patients. Both Caucasoid and Asian studied populations were turn to be different from European and neighboring Asian populations on the genotypes prevalence. Differentiation of CAP by the causative pathogen could help to eliminate the currently observed contradictions between different research groups.