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Article ; Online: Differential expression of Dusp1 and immediate early response genes in the hippocampus of rats, subjected to forced swim test.

Vlasov, Ivan / Filatova, Elena / Slominsky, Petr / Shadrina, Maria

2023 Volume 13, Issue 1, Page(s) 9985

Abstract: The forced swim test (FST) is widely used to screen for potential antidepressant drugs and treatments. Despite this, the nature of stillness during FST and whether it resembles "depressive-like behavior" are widely debated issues. Furthermore, despite ... ...

Abstract	The forced swim test (FST) is widely used to screen for potential antidepressant drugs and treatments. Despite this, the nature of stillness during FST and whether it resembles "depressive-like behavior" are widely debated issues. Furthermore, despite being widely used as a behavioral assay, the effects of the FST on the brain transcriptome are rarely investigated. Therefore, in this study we have investigated changes in the transcriptome of the rat hippocampus 20 min and 24 h after FST exposure. RNA-Seq is performed on the hippocampus tissues of rats 20 min and 24 h after an FST. Differentially expressed genes (DEGs) were identified using limma and used to construct gene interaction networks. Fourteen differentially expressed genes (DEGs) were identified only in the 20-m group. No DEGs were identified 24 h after the FST. These genes were used for Gene Ontology term enrichment and gene-network construction. Based on the constructed gene-interaction networks, we identified a group of DEGs (Dusp1, Fos, Klf2, Ccn1, and Zfp36) that appeared significant based on multiple methods of downstream analysis. Dusp1 appears especially important, as its role in the pathogenesis of depression has been demonstrated both in various animal models of depression and in patients with depressive disorders.
MeSH term(s)	Rats ; Animals ; Antidepressive Agents/pharmacology ; Brain/metabolism ; Swimming/physiology ; Hippocampus/metabolism ; Depression/genetics ; Depression/metabolism ; Dual Specificity Phosphatase 1/genetics ; Dual Specificity Phosphatase 1/metabolism ; Kruppel-Like Transcription Factors/metabolism
Chemical Substances	Antidepressive Agents ; Dusp1 protein, rat (EC 3.1.3.48) ; Dual Specificity Phosphatase 1 (EC 3.1.3.48) ; Klf2 protein, rat ; Kruppel-Like Transcription Factors
Language	English
Publishing date	2023-06-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-36611-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Differential expression of Dusp1 and immediate early response genes in the hippocampus of rats, subjected to forced swim test

Ivan Vlasov / Elena Filatova / Petr Slominsky / Maria Shadrina

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract The forced swim test (FST) is widely used to screen for potential antidepressant drugs and treatments. Despite this, the nature of stillness during FST and whether it resembles “depressive-like behavior” are widely debated issues. Furthermore, ... ...

Abstract	Abstract The forced swim test (FST) is widely used to screen for potential antidepressant drugs and treatments. Despite this, the nature of stillness during FST and whether it resembles “depressive-like behavior” are widely debated issues. Furthermore, despite being widely used as a behavioral assay, the effects of the FST on the brain transcriptome are rarely investigated. Therefore, in this study we have investigated changes in the transcriptome of the rat hippocampus 20 min and 24 h after FST exposure. RNA-Seq is performed on the hippocampus tissues of rats 20 min and 24 h after an FST. Differentially expressed genes (DEGs) were identified using limma and used to construct gene interaction networks. Fourteen differentially expressed genes (DEGs) were identified only in the 20-m group. No DEGs were identified 24 h after the FST. These genes were used for Gene Ontology term enrichment and gene-network construction. Based on the constructed gene-interaction networks, we identified a group of DEGs (Dusp1, Fos, Klf2, Ccn1, and Zfp36) that appeared significant based on multiple methods of downstream analysis. Dusp1 appears especially important, as its role in the pathogenesis of depression has been demonstrated both in various animal models of depression and in patients with depressive disorders.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptome Profiling Reveals Differential Expression of Circadian Behavior Genes in Peripheral Blood of Monozygotic Twins Discordant for Parkinson's Disease.

Semenova, Ekaterina I / Vlasov, Ivan N / Partevian, Suzanna A / Rosinskaya, Anna V / Rybolovlev, Ivan N / Slominsky, Petr A / Shadrina, Maria I / Alieva, Anelya Kh

Cells

2022 Volume 11, Issue 16

Abstract: Parkinson's disease (PD) is one of the most common neurodegenerative diseases. Investigating individuals with the most identical genetic background is optimal for minimizing the genetic contribution to gene expression. These individuals include ... ...

Abstract	Parkinson's disease (PD) is one of the most common neurodegenerative diseases. Investigating individuals with the most identical genetic background is optimal for minimizing the genetic contribution to gene expression. These individuals include monozygotic twins discordant for PD. Monozygotic twins have the same genetic background, age, sex, and often similar environmental conditions. The aim of this study was to carry out a transcriptome analysis of the peripheral blood of three pairs of monozygotic twins discordant for PD. We identified the metabolic process "circadian behavior" as a priority process for further study. Different expression of genes included in the term "circadian behavior" confirms that this process is involved in PD pathogenesis. We found increased expression of three genes associated with circadian behavior, i.e.,
MeSH term(s)	Gene Expression Profiling ; Humans ; Parkinson Disease/genetics ; Repressor Proteins/genetics ; Trans-Activators/genetics ; Twins, Monozygotic/genetics
Chemical Substances	MTA1 protein, human ; Repressor Proteins ; Trans-Activators
Language	English
Publishing date	2022-08-20
Publishing country	Switzerland
Document type	Journal Article ; Twin Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11162599
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Article ; Online: Benzo[a]pyrene in Moscow road dust: pollution levels and health risks.

Kosheleva, Natalia E / Vlasov, Dmitry V / Timofeev, Ivan V / Samsonov, Timofey E / Kasimov, Nikolay S

Environmental geochemistry and health

2022 Volume 45, Issue 5, Page(s) 1669–1694

Abstract: Benzo[a]pyrene (BaP) is one of the priority pollutants in the urban environment. For the first time, the accumulation of BaP in road dust on different types of Moscow roads has been determined. The average BaP content in road dust is 0.26 mg/kg, which is ...

Abstract	Benzo[a]pyrene (BaP) is one of the priority pollutants in the urban environment. For the first time, the accumulation of BaP in road dust on different types of Moscow roads has been determined. The average BaP content in road dust is 0.26 mg/kg, which is 53 times higher than the BaP content in the background topsoils (Umbric Albeluvisols) of the Moscow Meshchera lowland, 50 km east of the city. The most polluted territories are large roads (0.29 mg/kg, excess of the maximum permissible concentration (MPC) in soils by 14 times) and parking lots in the courtyards (0.37 mg/kg, MPC excess by 19 times). In the city center, the BaP content in the dust of courtyards reaches 1.02 mg/kg (MPC excess by 51 times). The accumulation of BaP depends on the parameters of street canyons formed by buildings along the roads: in short canyons (< 500 m), the content of BaP reaches maximum. Relatively wide canyons accumulate BaP 1.6 times more actively than narrow canyons. The BaP accumulation in road dust significantly increases on the Third Ring Road (TRR), highways, medium and small roads with an average height of the canyon > 20 m. Public health risks from exposure to BaP-contaminated road dust particles were assessed using the US EPA methodology. The main BaP exposure pathway is oral via ingestion (> 90% of the total BaP intake). The carcinogenic risk for adults is the highest in courtyard areas in the south, southwest, northwest, and center of Moscow. The minimum carcinogenic risk is characteristic of the highways and TRR with predominance of nonstop traffic.
MeSH term(s)	Dust/analysis ; Benzo(a)pyrene ; Polycyclic Aromatic Hydrocarbons/analysis ; Air Pollutants/analysis ; Moscow ; Environmental Monitoring/methods ; Carcinogens/analysis ; Risk Assessment
Chemical Substances	Dust ; Benzo(a)pyrene (3417WMA06D) ; Polycyclic Aromatic Hydrocarbons ; Air Pollutants ; Carcinogens
Language	English
Publishing date	2022-05-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	52039-1
ISSN	1573-2983 ; 0142-7245 ; 0269-4042
ISSN (online)	1573-2983
ISSN	0142-7245 ; 0269-4042
DOI	10.1007/s10653-022-01287-9
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Article ; Online: A new algorithm for the identification of sinusoidal signal frequency with constant parameters

Khac Tung Nguyen / Sergey M. Vlasov / Anton A. Pyrkin / Ivan V. Popkov

Naučno-tehničeskij Vestnik Informacionnyh Tehnologij, Mehaniki i Optiki, Vol 22, Iss 1, Pp 18-

2022 Volume 24

Abstract: The paper presents a solution for identifying the frequency of a sinusoidal signal with constant parameters. The issue can be relevant for compensation of disturbances, control of dynamic objects, and other tasks. The authors propose a method to improve ... ...

Abstract	The paper presents a solution for identifying the frequency of a sinusoidal signal with constant parameters. The issue can be relevant for compensation of disturbances, control of dynamic objects, and other tasks. The authors propose a method to improve the quality of the estimation of the sinusoidal signal frequency and to ensure exponential convergence to zero of the estimation errors. At the first stage, the sinusoidal signal is presented as an output signal of a linear generator of finite dimension. The signal parameters (amplitude, phase, and frequency) are unknown. At the second stage, the Jordan form of the matrix and the delay operator are applied to parameterize the sinusoidal signal. After a series of special transformations, the simplest equation is obtained containing product of one frequency-dependent unknown parameter and a known function of time. To find the unknown parameter, the authors used the methods of gradient descent and least squares. A new algorithm for the parametrization of a sinusoidal signal is presented. The solution is based on transforming the signal model to a linear regression equation. The problem is solved using gradient descent and least squares tuning methods based on a linear regression equation obtained by parametrizing a sinusoidal signal. The results involve the analysis of the capabilities of the proposed estimation method using computer modeling in the Matlab environment (Simulink). The results confirmed the convergence of the frequency estimation errors to the true values. The developed method can be effectively applied to a wide class of tasks related to compensating or suppressing disturbances described by sinusoidal or multisinusoidal signals, for example, to control a surface vessel with compensation of sinusoidal disturbances.
Keywords	sinusoidal signal ; identification ; jordan form of the matrix ; linear regression model ; Optics. Light ; QC350-467 ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	310
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Plasmon-Enhanced Ultraviolet Luminescence in Colloid Solutions and Nanostructures Based on Aluminum and ZnO Nanoparticles.

Lizunova, Anna A / Malo, Dana / Guzatov, Dmitry V / Vlasov, Ivan S / Kameneva, Ekaterina I / Shuklov, Ivan A / Urazov, Maxim N / Ramanenka, Andrei A / Ivanov, Victor V

Nanomaterials (Basel, Switzerland)

2022 Volume 12, Issue 22

Abstract: Aluminum nanoparticles attract scientific interest as a promising low-cost material with strong plasmon resonance in the ultraviolet region, which can be used in various fields of photonics. In this paper, for the first time, ultraviolet luminescence of ... ...

Abstract	Aluminum nanoparticles attract scientific interest as a promising low-cost material with strong plasmon resonance in the ultraviolet region, which can be used in various fields of photonics. In this paper, for the first time, ultraviolet luminescence of zinc oxide nanoparticles in colloid solutions and nanostructure films in the presence of plasmonic aluminum nanoparticles 60 nm in size with a metal core and an aluminum oxide shell were studied. Mixture colloids of ZnO and Al nanoparticles in isopropyl alcohol solution with concentrations from 0.022 to 0.44 g/L and 0.057 to 0.00285 g/L, correspondingly, were investigated. The enhancement of up to 300% of ZnO emission at 377 nm in colloids mixtures with metal nanoparticles due to formation of Al-ZnO complex agglomerates was achieved. Plasmon nanostructures with different configurations of layers, such as Al on the surface of ZnO, ZnO on Al, sandwich-like structure and samples prepared from a colloidal mixture of ZnO and Al nanoparticles, were fabricated by microplotter printing. We demonstrated that photoluminescence can be boosted 2.4-fold in nanostructures prepared from a colloidal mixture of ZnO and Al nanoparticles, whereas the sandwich-like structure gave only 1.1 times the amplification of luminescence. Calculated theoretical models of photoluminescence enhancement of ideal and weak emitters near aluminum nanoparticles of different sizes showed comparable results with the obtained experimental data.
Language	English
Publishing date	2022-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano12224051
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Article ; Online: Transcriptome Analysis of Induced Pluripotent Stem Cells and Neuronal Progenitor Cells, Derived from Discordant Monozygotic Twins with Parkinson's Disease.

Vlasov, Ivan N / Alieva, Anelya Kh / Novosadova, Ekaterina V / Arsenyeva, Elena L / Rosinskaya, Anna V / Partevian, Suzanna A / Grivennikov, Igor A / Shadrina, Maria I

Cells

2021 Volume 10, Issue 12

Abstract: Parkinson's Disease (PD) is a widespread severe neurodegenerative disease that is characterized by pronounced deficiency of the dopaminergic system and disruption of the function of other neuromodulator systems. Although heritable genetic factors ... ...

Abstract	Parkinson's Disease (PD) is a widespread severe neurodegenerative disease that is characterized by pronounced deficiency of the dopaminergic system and disruption of the function of other neuromodulator systems. Although heritable genetic factors contribute significantly to PD pathogenesis, only a small percentage of sporadic cases of PD can be explained using known genetic risk factors. Due to that, it could be inferred that changes in gene expression could be important for explaining a significant percentage of PD cases. One of the ways to investigate such changes, while minimizing the effect of genetic factors on experiment, are the study of PD discordant monozygotic twins. In the course of the analysis of transcriptome data obtained from IPSC and NPCs, 20 and 1906 differentially expressed genes were identified respectively. We have observed an overexpression of
MeSH term(s)	Aged ; Cell Differentiation ; Dopamine/genetics ; Female ; Gene Expression Profiling ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Induced Pluripotent Stem Cells/pathology ; Neural Stem Cells/metabolism ; Neural Stem Cells/pathology ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Neurons/metabolism ; Parkinson Disease/genetics ; Parkinson Disease/pathology ; Transcriptome/genetics ; Twins, Monozygotic/genetics
Chemical Substances	Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2021-12-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10123478
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Article ; Online: Targeted exome analysis of Russian patients with hypertrophic cardiomyopathy.

Filatova, Elena V / Krylova, Natalia S / Vlasov, Ivan N / Maslova, Maria S / Poteshkina, Natalia G / Slominsky, Petr A / Shadrina, Maria I

Molecular genetics & genomic medicine

2021 Volume 9, Issue 11, Page(s) e1808

Abstract: Background: Hypertrophic cardiomyopathy (HCM), described as the presence of hypertrophy of left ventricular, is the most prevalent heritable cardiovascular disease with predominantly an autosomal dominant type of inheritance. However, pathogenic alleles ...

Abstract	Background: Hypertrophic cardiomyopathy (HCM), described as the presence of hypertrophy of left ventricular, is the most prevalent heritable cardiovascular disease with predominantly an autosomal dominant type of inheritance. However, pathogenic alleles are not identified in at least 25% of patients with HCM, and the spectrum of pathogenic variants that contribute to the development of HCM in Russia has not been fully described. Therefore, the goal of our study was to identify genetic variants associated with the etiopathogenesis of HCM in Russian patients. Methods: The study cohort included 98 unrelated adult patients with HCM. We performed targeted exome sequencing, an analysis using various algorithms for prediction of the impact of variants on protein structure and the prediction of pathogenicity using ACMG Guidelines. Results: The frequency of pathogenic and likely pathogenic variants in all HCM-related genes was 8% in our patients. We also identified 20 variants of uncertain significance in all HCM-related genes. Conclusions: The prevalence of individual pathogenic variants in HCM-related genes in Russian population appears to be lower than in general European population, which could be explained by ethnic features of Russian population, age characteristics of our sample, or unidentified pathogenic variants in genes previously not linked with HCM.
MeSH term(s)	Adult ; Cardiomyopathy, Hypertrophic/genetics ; Exome ; Female ; Gene Frequency ; Humans ; Male ; Mutation ; Russia
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2734884-2
ISSN	2324-9269 ; 2324-9269
ISSN (online)	2324-9269
ISSN	2324-9269
DOI	10.1002/mgg3.1808
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Article ; Online: Fraction of plasma exomeres and low-density lipoprotein cholesterol as a predictor of fatal outcome of COVID-19.

Usenko, Tatiana / Miroshnikova, Valentina / Bezrukova, Anastasia / Basharova, Katerina / Landa, Sergey / Korobova, Zoia / Liubimova, Natalia / Vlasov, Ivan / Nikolaev, Mikhael / Izyumchenko, Artem / Gavrilova, Elena / Shlyk, Irina / Chernitskaya, Elena / Kovalchuk, Yurii / Slominsky, Petr / Totolian, Areg / Polushin, Yurii / Pchelina, Sofya

PloS one

2023 Volume 18, Issue 2, Page(s) e0278083

Abstract: Transcriptomic analysis conducted by us previously revealed upregulation of genes involved in low-density lipoprotein particle receptor (LDLR) activity pathway in lethal COVID-19 caused by SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2) ...

Abstract	Transcriptomic analysis conducted by us previously revealed upregulation of genes involved in low-density lipoprotein particle receptor (LDLR) activity pathway in lethal COVID-19 caused by SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). Last data suggested the possible role of extracellular vesicles in COVID-19 pathogenesis. The aim of the present study was to retrospectively evaluate parameters of cholesterol metabolism and newly identified EVs, exomeres, as possible predictors of fatal outcome of COVID-19 patients infected by the Alpha and the Delta variants of SARS-CoV-2 virus. Blood from 67 patients with severe COVID-19 were collected at the time of admission to the intensive care unit (ICU) and 7 days after admission to the ICU. After 30 days patients were divided into two subgroups according to outcome-34 non-survivors and 33 survivors. This study demonstrated that plasma low- and high-density lipoprotein cholesterol levels (LDL-C and HDL-C) were decreased in non-survivors compared to controls at the time of admission to the ICU. The conjoint fraction of exomeres and LDL particles measured by dynamic light scattering (DLS) was decreased in non-survivors infected by the Alpha and the Delta variants compared to survivors at the time of admission to the ICU. We first showed that reduction of exomeres fraction may be critical in fatal outcome of COVID-19.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Cholesterol, LDL ; Retrospective Studies
Chemical Substances	Cholesterol, LDL
Language	English
Publishing date	2023-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0278083
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Assessing research productivity in university environment

Panikarova, Svetlana / Boyko, Ivan / Vlasov, Maxim

Journal of information & knowledge management : JIKM Vol. 16, No. 2 , p. 1750016-1-12

institutional approach

2017 Volume 16, Issue 2, Page(s) 1750016–1–12

Author's details	Svetlana Panikarova, Maxim Vlasov and Ivan Boyko
Keywords	Knowledge creation ; knowledge management tools ; university ; measurement ; transaction cost
Language	English
Publisher	IKMS
Publishing place	Singapore
Document type	Article
ZDB-ID	2225563-1
ISSN	0219-6492
Database	ECONomics Information System

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