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Naumova NB, Barsukov PA, Baturina OA, Kabilov MR. Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage. Vavilovskii Zhurnal Genet Selektsii 2023; 27:703-711. [PMID: 38023813 PMCID: PMC10643539 DOI: 10.18699/vjgb-23-81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. We studied alveolate diversity in soil under the undisturbed steppe (US) and cropped for wheat using two tillage practices (conventional, CT, and no-till, NT) by amplifying the ITS2 marker with ITS3_KYO2/ITS4 primers and sequencing amplicons using Illumina MiSeq. A total of 198 Alveolata OTUs were identified, with 158 OTUs attributed to the Ciliophora phylum, containing five classes: Litostomatea, Spirotrichea and Oligohymenophorea, Nassophorea and Phyllopharyngea. Litostomatea and Phyllopharyngea were more abundant in US as compared with CT and NT. The observed OTU richness was higher in US than in CT and NT. The β-biodiversity of soil ciliates also very distinctly differentiated the US field from CT and NT. In the US, Nassophorea and Spirotrichea correlated positively with sand and negatively with clay, silt and SOM contents. This is the first report about soil ciliates diversity in Siberia as assessed by metabarcoding technique. The revealed clear effect of land use on the relative abundance of some taxa and a lack of tillage effect suggest the importance of the quantity and quality of plant material input for shaping the prey for ciliates. The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.
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Affiliation(s)
- N B Naumova
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P A Barsukov
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O A Baturina
- Institute of Soil Science and Agrochemistry of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Kiselev IS, Kulakova OG, Baturina OA, Kabilov MR, Boyko AN, Favorova OO. [DNA Methylation Profile of CD14+ Monocytes Changes in Primary Progressive Multiple Sclerosis]. Mol Biol (Mosk) 2023; 57:819-826. [PMID: 37752647 DOI: 10.31857/s002689842305004x, edn: gvhyat] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 09/28/2023]
Abstract
Multiple sclerosis (MS) is a chronic autoimmune inflammatory and neurodegenerative disease of the central nervous system, which is characterized by significant clinical heterogeneity. Primary progressive MS (PPMS) develops in 10-15% of patients. Unlike the most common relapsing-remitting form of MS, PPMS involves steady progress of neurodegeneration and, as a consequence, a persistent gradual increase in neurological symptoms. The peculiarities of epigenetic regulation of gene expression may be one of the reasons for the differences in the pathogenesis of the two MS forms. DNA methylation is one of the key epigenetic mechanisms, which remains almost unexplored in different cell populations of PPMS patients. The goal of this work was to identify differential methylation profiles of the CpG sites in the CD14+ monocyte DNA, which characterize PPMS. A genome-wide analysis of DNA methylation in PPMS patients and healthy individuals has identified 169 differentially methylated positions (DMPs), 90.5% of which were hypermethylated in PPMS patients. More than half of all DMPs are located in/near known genes and within CpG islands and their neighboring regions, which indicates their high functional significance. We have found six differentially methylated regions (DMRs) in the OR2L13, CAT, LCLAT1, HOXA5, RNF39, and CRTAC1 genes involved in inflammation and neurodegeneration, which indicates active epigenetic regulation of their expression.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- Federal Center for Brain and Neurotechnology, Federal Medical-Biological Agency, Moscow, 117997 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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Kiselev IS, Kulakova OG, Baturina OA, Kabilov MR, Boyko AN, Favorova OO. [A comparison of DNA methylation profiles of blood mononuclear cells in patients with multiple sclerosis in remission and relapse]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:60-64. [PMID: 37560835 DOI: 10.17116/jnevro202312307260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
OBJECTIVE To study the whole-genome DNA methylation profiles of peripheral blood mononuclear blood cells (PBMCs) of patients with relapsing-remitting multiple sclerosis (RRMS) in remission and relapse in order to assess the contribution of this epigenetic mechanism of gene expression regulation to the activity of the pathological process. MATERIAL AND METHODS Eight patients with RRMS in remission and 6 patients in relapse were included in the study. Methylation levels of DNA CpG sites in PBMCs were analyzed using Infinium HumanMethylation450 BeadChip DNA microarrays. RESULTS Seven differentially methylated positions (DMPs) were identified, of which 3 were hypermethylated (cg02981003, cg18486102, cg19533582) and 4 were hypomethylated (cg16814680, cg1964802, cg18584440, cg08291996) during RRMS relapse. Five DMPs are located in protein-coding genes (GPR123, FAIM2, BTNL2, ZNF8, ASAP2), one in microRNA gene (MIR548N), and one in an intergenic region. For all identified DMPs, we observed a change in DNA methylation levels of more than 20% (range 20.2-57.5%). Hierarchical clustering of DNA samples on the heatmap shows their clear aggregation into separate clusters corresponding to RRMS patients in the stages of relapse and remission. CONCLUSION For the first time it was shown that during relapse and remission of RRMS there are differences in the DNA methylation profile that allow discrimination between these clinical stages. These data indicate the involvement of the epigenetic mechanism of DNA methylation in the activation of the pathological process in RRMS.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine - Genomics Core Facility, Novosibirsk, Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, Russia
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Kiselev IS, Kulakova OG, Danilova LV, Baturina OA, Kabilov MR, Popova EV, Boyko AN, Favorova OO. Genome-Wide Analysis of DNA Methylation in Cd4+ T Lymphocytes of Patients with Primary Progressive Multiple Sclerosis Indicates Involvement of This Epigenetic Process in the Disease Immunopathogenesis. Mol Biol 2022. [DOI: 10.1134/s0026893322030074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kiselev IS, Kulakova OG, Danilova LV, Baturina OA, Kabilov MR, Popova EV, Boyko AN, Favorova OO. [Genome-Wide Analysis of DNA Methylation in Cd4+ T Lymphocytes of Patients with Primary Progressive Multiple Sclerosis Indicates Involvement of This Epigenetic Process in the Disease Immunopathogenesis]. Mol Biol (Mosk) 2022; 56:468-475. [PMID: 35621102 DOI: 10.31857/s0026898422030089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 06/15/2023]
Abstract
The pathogenesis of multiple sclerosis (MS), a chronic disease of the CNS, includes autoimmune and neurodegenerative components. In most cases, patients develop relapsing-remitting MS (RRMS), while 10-15% of patients develop primary progressive MS (PPMS), which differs from RRMS in the mechanisms of the pathological process, some demographic, and some clinical characteristics. These differences may be explained by the epigenetic regulation of gene expression in PPMS including DNA methylation as one of the key epigenetic processes. The features of DNA methylation in various cell populations in PPMS patients remain understudied. The goal of this study is to identify differentially methylated CpG sites (DMSs) of the genome of CD4+ T lymphocytes, which characterize PPMS. The study included eight treatment-naive PPMS patients and eight healthy controls. Genome-wide analysis of DNA methylation of CD4+ T lymphocytes was performed using high-density DNA microarrays. We have identified 108 DMSs, which distinguish PPMS patients from healthy controls. In PPMS patients 81% of the DMSs are hypermethylated. More than a half of the identified DMSs are located in known genes in CpG islands and adjacent regions, which indicates a high functional significance of these DMSs in PPMS development. Analysis of the overrepresentation of DMS-containing genes in the main biological processes demonstrates their involvement in the regulation of cell adhesion to the extracellular matrix and the development of the immune response, i.e., antigen processing and presentation, and development of the immune system. Genome-wide analysis of DNA methylation in CD4+ T lymphocytes of PPMS patients indicates the involvement of this epigenetic process in the immunopathogenesis of the disease. These results may help better understand the pathogenesis of this severe form of MS.
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Affiliation(s)
- I S Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
| | - L V Danilova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia
- Johns Hopkins School of Medicine, Baltimore, MD 21205 USA
| | - O A Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - E V Popova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- Federal Center for Brain and Neurotechnology, Federal Medical and Biological Agency of the Russian Federation, Moscow, 117997 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
- National Medical Research Center for Cardiology, Moscow, 121552 Russia
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Kolmakova OV, Trusova MY, Baturina OA, Kabilov MR. Bacteria of Lake Pyasino and Adjacent Rivers after an Accidental Diesel Spill in 2020. CONTEMP PROBL ECOL+ 2021. [DOI: 10.1134/s1995425521040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rogozin DY, Bulkhin AO, Zykov VV, Ivanova EA, Darin AV, Kalugin IA, Baturina OA, Kabilov MR. Long-Chain Alkenones in Saline Meromictic Lakes of the North Minusinsk Depression (Southern Siberia): First Knowledge and Possible Correlation with Water-Level Dynamics. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s199542552006013x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Mirzaev KB, Ivashchenko DV, Volodin IV, Grishina EA, Akmalova KA, Kachanova AA, Skripka AI, Minnigulov RM, Morozova TE, Baturina OA, Levanov AN, Shelekhova TV, Kalinkin AI, Napalkov DA, Sokolova AA, Andreev DA, Sychev IN, Bochkov PO, Sychev DA. New Pharmacogenetic Markers to Predict the Risk of Bleeding During Taking of Direct Oral Anticoagulants. Racionalʹnaâ farmakoterapiâ v kardiologii 2020. [DOI: 10.20996/1819-6446-2020-10-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aim. To search for new pharmacogenetic biomarkers of bleeding risk in patients taking rivaroxaban and dabigatran for different indications: atrial fibrillation, endoprosthesis of large joints of lower limbs.Material and methods. The study enrolled 29 patients (17 patients received dabigatran and 12 –rivaroxaban), who had hemorrhagic complications during taking direct oral anticoagulants. To find new pharmacogenetic biomarkers of bleeding risk, a next generation sequencing (NGS) was performed for selected candidate genes.Results. Among the patients with bleeding who received dabigatran, 13 variants of the nucleotide sequence showed statistically significant deviation from the population values: 11 in the CES1 gene and 2 in the ABCB1 gene. Among the patients with bleeding who received rivaroxaban, 7 variants of nucleotide sequence showed significant deviation: 4 in the ABCG2 gene, 2 in the CYP3A4 gene, and 1 in the ABCB1 gene.Conclusion. The identified in this study polymorphisms of candidate genes ABCB1, ABCG2, CES1, CYP3A4 were associated with the risk of bleeding in patients taking rivaroxaban and dabigatran. It makes an important contribution to the pharmacogenetics of direct oral anticoagulants and require additional assessment of clinical significance in further studies.
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Affiliation(s)
- K. B. Mirzaev
- Russian Medical Academy of Continuous Professional Education
| | | | - I. V. Volodin
- Russian Medical Academy of Continuous Professional Education;
Research Centre for Medical Genetics
| | - E. A. Grishina
- Russian Medical Academy of Continuous Professional Education
| | - K. A. Akmalova
- Russian Medical Academy of Continuous Professional Education
| | - A. A. Kachanova
- Russian Medical Academy of Continuous Professional Education
| | - A. I. Skripka
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - R. M. Minnigulov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - T. E. Morozova
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - O. A. Baturina
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - A. N. Levanov
- Saratov State Medical University named after V.I. Razumovsky
| | | | | | - D. A. Napalkov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - A. A. Sokolova
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - D. A. Andreev
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - I. N. Sychev
- Russian Medical Academy of Continuous Professional Education
| | - P. O. Bochkov
- Russian Medical Academy of Continuous Professional Education
| | - D. A. Sychev
- Russian Medical Academy of Continuous Professional Education
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Lavrentyeva EV, Banzaraktsaeva TG, Radnagurueva AA, Buryukhaev SP, Dambaev VB, Baturina OA, Kozyreva LP, Barkhutova DD. Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425519060088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Lavrentyeva EV, Erdyneeva EB, Banzaraktsaeva TG, Kotsyurbenko OR, Baturina OA, Khakhinov VV, Kozyreva LP. Prokaryotic Diversity in the Biotopes of the Gudzhirganskoe Saline Lake (Barguzin Valley, Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Sychev DA, Baturina OA, Mirzaev KB, Rytkin E, Ivashchenko DV, Andreev DA, Ryzhikova KA, Grishina EA, Bochkov PO, Shevchenko RV. CYP2C19*17 May Increase the Risk of Death Among Patients with an Acute Coronary Syndrome and Non-Valvular Atrial Fibrillation Who Receive Clopidogrel and Rivaroxaban. Pharmgenomics Pers Med 2020; 13:29-37. [PMID: 32158254 PMCID: PMC6986167 DOI: 10.2147/pgpm.s234910] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/03/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The aim of this study is to assess the influence of gene CYP2C19, CYP3A4, CYP3A5 and ABCB1 polymorphisms on clopidogrel antiplatelet activity, rivaroxaban concentration equilibrium, and clinical outcomes among patients with acute coronary syndrome and non-valvular atrial fibrillation. METHODS In the multicenter prospective registry study of the efficacy and safety of a combined antithrombotic therapy 103 patients with non-valvular atrial fibrillation both undergoing or not a percutaneous coronary intervention were enrolled. The trial assessed the primary outcomes (major bleeding, in-hospital death, cardiovascular death, stroke\transient ischaemic attack, death/renal insufficiency) and secondary outcomes (platelet reactivity units (PRU), rivaroxaban concentration). RESULTS For none of the clinical outcomes when combined with other covariates, the carriership of polymorphisms CYP3A5*3 rs776746, CYP2C19*2 rs4244285;*17 rs12248560, ABCB1 3435 C>T, ABCB1 rs4148738 was significant. None of the markers under study (CYP3A5*3 rs776746, CYP2C19*2 rs4244285, *17 rs12248560, ABCB1 3435 C>T, ABCB1 rs4148738) has proven to affect rivaroxaban equilibrium concentration in blood plasma among patients with atrial fibrillation and acute coronary syndrome. CONCLUSION In situations of double or triple antithrombotic rivaroxaban and clopidogrel therapy among patients with atrial fibrillation and acute coronary syndrome, the genetic factors associated with bleeding complications risk (CYP2C19*17) may prove to be clinically relevant.
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Affiliation(s)
- D A Sychev
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | | | - K B Mirzaev
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - E Rytkin
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - D V Ivashchenko
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - D A Andreev
- Sechenov University, Moscow, Russian Federation
| | - K A Ryzhikova
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - E A Grishina
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - P O Bochkov
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - R V Shevchenko
- Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Moscow, Russian Federation
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Baturina OA, Chernonosov AA, Koval VV, Morozov IV. Assessment of the Phenylketonuria (PKU)-Associated Mutation p.R155H Biochemical Manifestations by Mass Spectrometry-Based Blood Metabolite Profiling. Acta Naturae 2019. [DOI: 10.32607/20758251-2019-11-2-] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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13
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Baturina OA, Chernonosov AA, Koval VV, Morozov IV. Assessment of the Phenylketonuria (PKU)-Associated Mutation p.R155H Biochemical Manifestations by Mass Spectrometry-Based Blood Metabolite Profiling. Acta Naturae 2019; 11:42-46. [PMID: 31413878 PMCID: PMC6643343 DOI: 10.32607/20758251-2019-11-2-42-46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homozygous siblings with different treatment histories represent an excellent
model to study both the phenotypic manifestation of mutations and the efficacy
of therapy. We compared phenylketonuria (PKU) manifestations in two different
gender siblings who were homozygous carriers of a rare phenylalanine
hydroxylase (PAH) mutation, p.R155H, subjected to different
treatments. PKU caused by mild mutations may be easily underdiagnosed if the
diagnosis is based solely on the phenylalanine (Phe) blood concentration. One
of the described patients is an example of this diagnostic error. For reducing
diagnostic errors, we suggest the use of more elaborate methods in screening
practice, in particular mass spectrometric analysis of blood metabolites, the
efficiency of which is demonstrated in the present study.
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Affiliation(s)
- O. A. Baturina
- Joint Center for genomic, proteomic and metabolomics studies, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - A. A. Chernonosov
- Joint Center for genomic, proteomic and metabolomics studies, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - V. V. Koval
- Joint Center for genomic, proteomic and metabolomics studies, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, Novosibirsk, 630090 , Russia
| | - I. V. Morozov
- Joint Center for genomic, proteomic and metabolomics studies, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, Novosibirsk, 630090 , Russia
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Baturina OA, Andreev DA, Ananicheva NA, Gilyarov MY, Sychev DA, Syrkin AL, Shchekochihin DY. Prevalence of Atrial Fibrillation and use of Oral Antithrombotic Therapy in Patients with Acute Coronary Syndrome. Kardiologiia 2019; 59:40-48. [PMID: 30710988 DOI: 10.18087/cardio.2019.1.10213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 01/27/2019] [Indexed: 11/18/2022]
Abstract
PURPOSE To assess the prevalence of atrial fibrillation (AF) and use of antithrombotic agents in adult patients with acute coronary syndrome (ACS). MATERIALS AND METHODS We consecutively enrolled all ACS patients (n=1155) who were hospitalized in two Moscowbased percutaneous coronary intervention centers (each center performs over 500 PCIs a year) between October 2017 and February 2018. AF was diagnosed in 204 patients (17.7%). The risk of thromboembolic complications was assessed using the CHA2DS2-VASc Score. The risk of hemorrhagic complications was assessed using the HAS-BLED Score. The data were processed using StatSoft Statistica 10.0 and IBM SPSS Statistics v.23 software. RESULTS The prevalence of diagnosed AF was 13.6%, while the prevalence of undiagnosed AF was 4.1%. Of the 179 discharged patients with AF, only 2 had a low risk of ischemic stroke (IS). One hundred and fifty patients (83.8%) eligible for oral anticoagulant therapy received oral anticoagulants. Patients with diagnosed AF were administered oral anticoagulants (OACs) significantly more often than patients with undiagnosed AF [125 (91.9%) vs. 25 (58.1%), р<0.001]. Novel oral anticoagulants (NOACs) were administered four times more often than vitamin K antagonists [120 (80.0%) vs. 29 (19.3%), р<0.001]. Rivaroxaban was used in 51.3% of cases. Of the 29 patients treated with warfarin, only 3 (10.3%) achieved the target international normalized ratio (INR) at discharge. Of the 107 patients who underwent percutaneous coronary intervention (PCI), 77 patients (80%) received an OAC and two antiplatelet agents (with 74% receiving this three-agent therapy for one month), 11 patients (10.3%) received an OAC and an antiplatelet agent, and 18 patients (16.8%) received two antiplatelet agents. The only antiplatelet agent used as part of the three-agent therapy was clopidogrel. The three-agent therapy without PCI was administered in 43.1% of cases. CONCLUSION We found that the prevalence of AF in patients with ACS was high. The fact that doctors administered NOACs suggests that they are aware of the need to use these agents to prevent thromboembolic complications in AF patients.
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Affiliation(s)
- O A Baturina
- Sechenov First Moscow State Medical University (Sechenov University).
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Baturina OA, Tupikin AE, Goroshkevich SN, Petrova EA, Kabilov MR. The complete chloroplast genome sequences of Pinus sibirica Du Tour. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1542983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- O. A. Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A. E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S. N. Goroshkevich
- Institute of Monitoring of Climatic and Ecological Systems, Siberian Branch of the Russian Academy of Sciences, Tomsk, Russia
| | - E. A. Petrova
- Institute of Monitoring of Climatic and Ecological Systems, Siberian Branch of the Russian Academy of Sciences, Tomsk, Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Martemyanov VV, Podgwaite JD, Belousova IA, Pavlushin SV, Slavicek JM, Baturina OA, Kabilov MR, Ilyinykh AV. A comparison of the adaptations of strains of Lymantria dispar multiple nucleopolyhedrovirus to hosts from spatially isolated populations. J Invertebr Pathol 2017; 146:41-46. [PMID: 28392286 DOI: 10.1016/j.jip.2017.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/17/2017] [Accepted: 04/05/2017] [Indexed: 11/18/2022]
Abstract
The adaptation of pathogens to either their hosts or to environmental conditions is the focus of many current ecological studies. In this work we compared the ability of six spatially-distant Lymantria dispar (gypsy moth) multiple nucleopolyhedrovirus (LdMNPV) strains (three from eastern North America and three from central Asia) to induce acute infection in gypsy moth larvae. We also sequenced the complete genome of one Asian (LdMNPV-27/0) and one North American (LdMNPV-45/0) strain which were used for bioassay. We found that all of the North American virus strains, with the exception of one, demonstrated higher potency than the Asian virus strains, either in North American (Lymantria dispar) larvae or, in Asian (Lymantria dispar asiatica) larvae. Complete genome sequencing revealed two gene deletions in the LdMNPV-27/0 strain: the virus enhancin factor gene (vef-1) and the baculovirus repeated orf gene (bro-p). These deletions were not seen in the LdMNPV-45/0 strain nor in other American strains available in archiving systems. We also found deletions of the bro-e and bro-o genes in LdMNPV-45/0 strain but not in the LdMNPV-27/0 strain. The phylogenetic inference with an alignment of the 37 core gene nucleotide sequences revealed the close relationship of the LdMNPV-45/0 strain with other American strains accessed in GenBank (Ab-a624 and 5-6) while the LdMNPV-27/0 strain was clustered together with the LdMNPV-3054 strain (isolated in Spain) instead of predicted clustering with LdMNPV- 3029 (isolated in Asia). Our study demonstrated that first, different LdMNPV isolates from the same metapopulations of L. dispar exhibit little or no difference in the degree of virulence towards host larvae and second, that locality of host population is not an important driver of LdMNPV virulence. Virulence of LdMNPV is determined only by viral genetics. The genetic differences between North American and Central Asian virus strains are discussed.
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Affiliation(s)
- V V Martemyanov
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; Biological Institute, National Research Tomsk State University, Lenin av. 36, 634050 Tomsk, Russia.
| | - J D Podgwaite
- USDA Forest Service, Northern Research Station, 51 Mill Pond Rd., Hamden, CT 06514, United States.
| | - I A Belousova
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; Institute of Biology, Irkutsk State University, Karl Marx str. 1, Irkutsk 664003, Russia.
| | - S V Pavlushin
- Laboratory of Ecological Parasitology, Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - J M Slavicek
- USDA Forest Service, Northern Research Station, 359 Main Rd., Delaware, OH 43015, United States.
| | - O A Baturina
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentyev av. 8, 630090 Novosibirsk, Russia.
| | - M R Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentyev av. 8, 630090 Novosibirsk, Russia.
| | - A V Ilyinykh
- Laboratory of Insect Pathology, Institute of Systematics and Ecology of Animal SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia.
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Kulakova OG, Kabilov MR, Danilova LV, Popova EV, Baturina OA, Tsareva EY, Baulina NM, Kiselev IS, Boyko AN, Favorov AV, Favorova OO, Vlassov VV. Whole-Genome DNA Methylation Analysis of Peripheral Blood Mononuclear Cells in Multiple Sclerosis Patients with Different Disease Courses. Acta Naturae 2016. [DOI: 10.32607/20758251-2016-8-3-103-110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple sclerosis (MS) is a severe neurodegenerative disease of polygenic etiology affecting the central nervous system. In addition to genetic factors, epigenetic mechanisms, primarily DNA methylation, which regulate gene expression, play an important role in MS development and progression. In this study, we have performed the first whole-genome DNA methylation profiling of peripheral blood mononuclear cells in relapsing-remitting MS (RRMS) and primary-progressive MS (PPMS) patients and compared them to those of healthy individuals in order to identify the differentially methylated CpG-sites (DMSs) associated with these common clinical disease courses. In addition, we have performed a pairwise comparison of DNA methylation profiles in RRMS and PPMS patients. All three pairwise comparisons showed significant differences in methylation profiles. Hierarchical clustering of the identified DMS methylation levels and principal component analysis for data visualization demonstrated a clearly defined aggregation of DNA samples of the compared groups into separate clusters. Compared with the control, more DMSs were identified in PPMS patients than in RRMS patients (67 and 30, respectively). More than half of DMSs are located in genes, exceeding the expected number for random distribution of DMSs between probes. RRMS patients mostly have hypomethylated DMSs, while in PPMS patients DMSs are mostly hypermethylated. CpG-islands and CpG-shores contain 60% of DMSs, identified by pairwise comparison of RRMS and control groups, and 79% of those identified by pairwise comparison of PPMS and control groups. Pairwise comparison of patients with two clinical MS courses revealed 51 DMSs, 82% of which are hypermethylated in PPMS. Overall, it was demonstrated that there are more changes in the DNA methylation profiles in PPMS than in RRMS. The data confirm the role of DNA methylation in MS development. We have shown, for the first time, that DNA methylation as an epigenetic mechanism is involved in the formation of two distinct clinical courses of MS: namely, RRMS and PPMS.
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Martemyanov VV, Kabilov MR, Tupikin AE, Baturina OA, Belousova IA, Podgwaite JD, Ilynykh AV, Vlassov VV. The enhancin gene: One of the genetic determinants of population variation in baculoviral virulence. DOKL BIOCHEM BIOPHYS 2016; 465:351-3. [DOI: 10.1134/s1607672915060022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/22/2022]
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Baturina OA, Bondar AA, Tupikin AE, Zhabin SG, Morozov IV. Analysis of phenylalanine hydroxylase gene mutations in phenylketonuria patients from Kemerovo oblast and the Sakha Republic. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712040032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Baturina OA, Bondar' AA, Tupikin AE, Zhabin SG, Morozov IV. [Mutation analysis of the phenylalanine hydroxylase gene of phenylketonuria patients of Kemerovskaya Oblast' and Saha Republic]. Tsitol Genet 2012; 46:40-47. [PMID: 23074961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phenylketonuria (PKU) associated mutations in phenylalanine hydroxylase (PAH) gene were identified by direct DNA sequencing in 46 PKU patients and members of their families from Kemerovskaya Region and Saha Republic. Mutations found included both widespread known mutations (R158Q, R252W, R261Q, P281L, IVS10-11G>A, R408W, IVS12+1G>A) and several rare mutations (IVS2+5G>A, R155H, Y168H, W187R, E221_D222>Efs, A342T, Y386C, IVS11+1G>C). We observed the increase in diversity of PKU-associated alleles in the populations studied, probably due to their complex mixed ethnic structure.
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Sinyakov AN, Kostina EV, Maksakova GA, Baturina OA, Ryabinin VA. Oligonucleotide conjugates with minor groove ligands as probes for hybridization microarray chips. Russ J Bioorg Chem 2007. [DOI: 10.1134/s1068162007050111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Siniakov AN, Kostina EB, Maksakova GA, Baturina OA, Riabinin VA. [Oligonucleotide conjugates with minor groove ligands as probes for hybridization microarray chips]. Bioorg Khim 2007; 33:571-573. [PMID: 18050664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A possibility of using oligonucleotide conjugates with minor groove ligands as probes for hybridization microarray chips was studied. The oligonucleotide conjugates contain a hairpin ligand (MGB) composed of two tripyrrolcarboxamide residues with an aminocaproic acid residue as a linker and bound to the oligonucleotide duplex AT tract in a site-specific manner. We used as (5'-3') probes GACAAGAp, GACAAAAp, GACAAGA-MGB, and GACAAAA-MGB. The oligonucleotides labeled with Cy3 cyanine dye, Cy3-ACTAATTTTGTC and Cy3-ACTAATCTTGTC, were used as targets. The maximal MGB effect on the fluorescence level of microarray chip spots, which caused its fourfold increase as compared with the initial unmodified duplex, was observed for the duplex containing only AT pairs in the ligand binding site. The presence of A-C and G-T mutations in the binding site (imperfect duplexes) or a C-G pair (perfect duplex) affects the change in fluorescence level to a considerably lesser degree.
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Riabinin VA, Shundrin LA, Kostina EV, Laassri M, Chizhikov VE, Maksakova GA, Baturina OA, Pozdniakova LD, Feshchenko MV, Shchelkunov SN, Chumakov KM, Siniakov AN. [An oligonucleotide microarray for detection and discrimination of orthopoxviruses based on oligonucleotide sequences of two viral genes]. Mol Gen Mikrobiol Virusol 2006:23-30. [PMID: 17094655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An oligonucleotide microarray for detection and identification of orthopoxviruses was developed. Genus specific and orthopoxvirus species-specific regions of the genes encoding chemokine binding and alpha/beta-interferon binding proteins were used as a target. The developed microarray allows the variola, monkeypox, cowpox, vaccinia, camel-pox and ectromelia (mousepox) viruses to be distinguished with a high degree of reliability.
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Damaskin BB, Baturina OA. RUSS J ELECTROCHEM+ 2002; 38:478-483. [DOI: 10.1023/a:1015476825180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Damaskin BB, Baturina OA. RUSS J ELECTROCHEM+ 2001; 37:73-79. [DOI: 10.1023/a:1009083813408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Damaskin BB, Baturina OA. RUSS J ELECTROCHEM+ 2001; 37:121-126. [DOI: 10.1023/a:1009019605888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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