N V Tikunova

Institute of Chemical Biology and Fundamental Medicine, Novo-Nikolaevsk, Novosibirsk, Russia

Are you N V Tikunova?

Claim your profile

Publications (76)70.24 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: This study used geological, geochemical, and microbiological data to examine the Uzon oils and conditions within the Uzon caldera. The trace-element compositions of crude oils and solutions from boreholes and hydrothermal springs were determined by ICP-MS. The majority of hydrothermal manifestations within the Uzon caldera are controlled by three trends of faults. The major fault zone, trending nearly E–W, is located between Kikhpinych and Taunshits volcanoes. It acts as a magma conduit and hosts numerous oval-shaped hydrothermal vents. The Oil site is situated on the periphery of the hottest area of highest hydrothermal activity within the Eastern thermal field. On the Eh–pH diagram, most solutions of the Uzon caldera define distinct fields and trends which correlate with the stability fields for sulfur and iron. The Oil site is characterized by very wide variations in temperature and Eh–pH parameters of pore solutions. The geochemical signatures of the solutions at this site are broadly similar to those from other areas of the Uzon caldera, but differ in their sulfide ion and sulfate ion concentrations. These differences can be explained by mixing of deep chloride-sodium hydrothermal solutions and solutions produced during surface oxidation of sulfide-containing material. With respect to the average continental crust, the Uzon oil is enriched in S, As, and Hg. The crude oil and solutions have broadly similar concentrations of B, S, Cl, As, Se, Br, Cd, I, Hg, and Pb and highly variable concentrations of Ti, V, Cr, Co, Ni, Cu, Cd, Nb, and Sn. The community structure of archaeal assemblages in springs and test pits at the Eastern thermal field was analyzed by 16S rRNA library and pyrosequencing methods. It was found that the proportion of archaea in the microbial communities of the Uzon caldera ranges from 2 to over 70% of the total sequences identified. Crenarchaeota were found in large proportions in all samples except one. The majority of the sequences in four samples were affiliated with Euryarchaeota, which comprise methanogenic archaea, extreme halophiles, and some extreme thermophiles. The results of geological, mineralogical-geochemical, microbiological and physicochemical studies of oil seeps in the Uzon caldera reveal distinctive geochemical characteristics of crude oil and the complexity of oil formation. © 2015, V.S. Sobolev IGM, Siberian Branch of the RAS. Published by Elsevier B.V. All rights reserved.
    Russian Geology and Geophysics 02/2015; 56(1-2):39-63. DOI:10.1016/j.rgg.2015.01.003 · 1.41 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Noroviruses (NoVs) are an important cause of acute gastroenteritis worldwide. To monitor the molecular epidemiology of NoVs genogroup II (GII) in Novosibirsk, Russia, a total of 10,198 stool samples from young children hospitalized with acute gastroenteritis and two asymptomatic comparison groups were collected from 2003 to 2012. All samples were screened for the presence of NoV GII, rotavirus, and astrovirus by RT-PCR. The prevalence of NoV in gastroenteritis cases was 13.1%, varying from 7.1% to 21.3% in different seasons. Rotavirus and/or astrovirus were detectable in 25% of the NoV-positive samples. NoV was detected throughout the year with a seasonal increase during winter months. Based on sequence analysis of regions D and/or C within the VP1 gene, 892 identified NoV strains were divided into nine genotypes-GII.3 (51%), GII.4 (44%), GII.6 (2%), as well as GII.1, GII.2, GII.5, GII.7, GII.16, and GII.21 (totally, 3%). The prevalence of NoV in the comparison groups was considerably lower (∼2.5%); only GII.4 (n = 6), GII.21 (n = 2) and GII.1 (n = 1) genotypes were revealed. Based on phylogenetic analysis of the ORF1/ORF2 junction region sequences, GII.P21/GII.3 recombinant and GII.P4/GII.4 were prevalent genotypes (totally, 93%) and their ratio changed every season. The median age of children with NoV infection was 6.6 months (range, <1-35 months), but it was different depending on NoV genotype. Children infected with the NoV GII.3 were younger (median 6.2 months) than GII.4-positive patients (median 9.1 months). This is the first long-term systematic study of NoV molecular epidemiology in Russia. J. Med. Virol. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
    Journal of Medical Virology 02/2015; DOI:10.1002/jmv.24068 · 2.22 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The complete genomes of two human bocavirus 4 (HBoV4) isolates recovered in 2011 in Novosibirsk, Russia have been determined. A set of primers was designed based on the determined and previously published HBoV sequences; this primer pair was able to detect all possible HBoV replicative intermediates. This primer set was used to assay all HBoV genotypes and detected only those structures that correspond to an episomal form of this viral genome. Also, for the first time, head-to-tail nucleotide sequences have been determined for HBoV4. Secondary structures of the terminal noncoding regions (NCRs) of episomal forms have been computed for all HBoV genotypes, as well as for the canine bocavirus. Conserved secondary structures in episomal NCRs, which are likely to play an important part in the replication of bocaviruses, were found. NCR heterogeneity in the genomes of individual HBoV isolates has been shown for the first time. Copyright © 2014 Elsevier B.V. All rights reserved.
    Virus Research 01/2015; 195C:196-202. DOI:10.1016/j.virusres.2014.10.019 · 2.83 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Ixodid ticks were assayed for the presence of Babesia spp. using nested PCR.•Babesia 18S rRNA gene sequences were determined for all of the positive ticks.•New Babesia genetic variants and earlier known Babesia species were found.•The newly identified Babesia genetic variants belonged to distinct phylogenetic clusters.
    Infection Genetics and Evolution 12/2014; 28. DOI:10.1016/j.meegid.2014.10.010 · 3.26 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The mechanisms triggering most of autoimmune diseases are still obscure. Autoreactive B cells play a crucial role in the development of such pathologies and, in particular, production of autoantibodies of different specificities. The combination of deep-sequencing technology with functional studies of antibodies selected from highly representative immunoglobulin combinatorial libraries may provide unique information on specific features in the repertoires of autoreactive B cells. Here, we have analyzed cross-combinations of the variable regions of human immunoglobulins against the myelin basic protein (MBP) previously selected from a multiple sclerosis (MS)-related scFv phage-display library. On the other hand, we have performed deep sequencing of the sublibraries of scFvs against MBP, Epstein–Barr virus (EBV) latent membrane protein 1 (LMP1), and myelin oligodendrocyte glycoprotein (MOG). Bioinformatics analysis of sequencing data and surface plasmon resonance (SPR) studies have shown that it is the variable fragments of antibody heavy chains that mainly determine both the affinity of antibodies to the parent autoantigen and their cross-reactivity. It is suggested that LMP1-cross-reactive anti-myelin autoantibodies contain heavy chains encoded by certain germline gene segments, which may be a hallmark of the EBV-specific B cell subpopulation involved in MS triggering.
    Molecular Immunology 12/2014; DOI:10.1016/j.molimm.2014.01.013 · 3.00 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Whole genome sequencing of Novosibirsk human bocavirus (HBoV) isolates has detected an isolate that emerged via recombination between HBoV3 and HBoV4 genotypes. The recombination site is located between regions with abnormally low and abnormally high GC contents in the genome. This site is a bocavirus recombination hotspot and coincides with one of two parvovirus recombination hotspots. The Novosibirsk recombinant isolate, which is similar to a previously studied isolate from Thailand, utilizes the strategy of borrowing ORF3, which encodes structural proteins, of a rare genotype HBoV4. The role of recombination in HBoV evolution is discussed.
    Infection Genetics and Evolution 12/2014; DOI:10.1016/j.meegid.2014.08.026 · 3.26 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Lyme disease, caused by bacteria of the Borrelia burgdorferi sensu lato complex, is the most frequent tick-borne infection in Eurasia. Here, we report the complete genome sequence of the Borrelia valaisiana Tom 4006 and Borrelia afzelii Tom 3107 strains isolated from Ixodes persulcatus ticks in western Siberia. Copyright © 2014 Kurilshikov et al.
    Genome Announcements 11/2014; 2(6). DOI:10.1128/genomeA.01315-14
  • [Show abstract] [Hide abstract]
    ABSTRACT: Anaplasma phagocytophilum is a causative agent of granulocytic anaplasmosis in different mammals. The presence of A. phagocytophilum was assayed in Ixodes persulcatus, Ixodes trianguliceps ticks and Myodes spp. voles from two I. persulcatus/I. trianguliceps sympatric areas in the Omsk region (Western Siberia, Russia). In total, A. phagocytophilum was found in 42/108 (38.9%) of vole blood samples, 13/34 (38.2%) of I. trianguliceps ticks removed from voles, 1/12 (8.3%) of I. persulcatus removed from voles, and 18/279 (7.2%) of questing I. persulcatus. GroESL operon sequence analysis of positive samples revealed three distinct A. phagocytophilum genetic groups previously identified in ticks and mammals in Russia. Genetic group 1 was found in 6/36 (16.7%) of sequenced positive blood samples; this group was previously revealed in I. persulcatus and Myodes spp. voles in different regions of Russia. Genetic group 2 was found in 30/36 (83.3%) of sequenced positive blood samples and all positive I. trianguliceps; this group was previously revealed only in Myodes spp. voles and common shrews (Sorex araneus) in I. persulcatus/I. trianguliceps sympatric areas in the Northern Ural. Genetic group 3 was found in all positive questing I. persulcatus and one blood sample; this group was previously revealed in I. persulcatus and Siberian chipmunks (Tamias sibiricus). We suppose that I. trianguliceps is the most probable vector for A. phagocytophilum of group 2. Analysis of the msp4 gene, intergenic region DOV1, and some other genetic loci has shown that isolates from different genetic groups significantly differ in all studied loci and that A. phagocytophilum of group 2 is closely related to A. phagocytophilum isolates revealed in voles and I. trianguliceps in Europe. A. phagocytophilum of groups 1 and 2 are the most similar to each other, while A. phagocytophilum of group 3 clusters with European A. phagocytophilum isolates from I. ricinus and various mammalian species.
    Ticks and Tick-borne Diseases 10/2014; 5(6). DOI:10.1016/j.ttbdis.2014.07.008 · 2.88 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The efficiency of several mouse monoclonal antibodies (mAbs) specific to the tick-borne encephalitis virus (TBEV) glycoprotein E in post-exposure prophylaxis was assessed, and mAb14D5 was shown to be the most active of all those studied. It was proven that the hybridoma cell line 14D5 produced one immunoglobulin H chain and two L chains. They were used to construct chimeric antibodies ch14D5a and ch14D5b, the affinity constants of which were 2.6×10(10)M(-1) and 1.0×10(7)M(-1), respectively, according to the SPR-based ProteOn biosensor assay. The neutralization index (IC50) of ch14D5a was 0.04μg/ml in the focus reduction neutralization test. In in vivo experiments, ch14D5a at a dose of 10μg/mouse resulted in a 100% survival of the mice infected with 240 LD50 of TBEV. This chimeric antibody is promising for further development of prevention and therapeutic drugs against TBEV.
    Vaccine 05/2014; DOI:10.1016/j.vaccine.2014.05.012 · 3.49 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Complete genome sequences of previously unstudied human astrovirus subgenotypes - HAstV-2a and HAstV-2c - and two isolates of a rare genotype HAstV-4 have been determined. These isolates were recovered from fecal samples of young children hospitalized with acute intestinal infections in Novosibirsk (Russia). Three of the four sequenced isolates (HAstV-2a, HAstV-2c, and HAstV-4) are recombinants. It has been shown that all known HAstV-2 genomes have emerged via recombination; the HAstV-1 and HAstV-4 genotypes contain both recombinant and non-recombinant isolates; and all HAstV-3, HAstV-5, and HAstV-6 whole-genome sequences display no reliable signs of recombination. The average mutation accumulation rate has been determined based on an extended ORF2 fragment and amounts to 1.0×10(-3) substitutions per site per year. The evolutionary chronology of current HAstV genotypes has been reconstructed.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2014; DOI:10.1016/j.meegid.2014.01.010 · 3.22 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Штамм энтеровируса Коксаки В6, селективно инфицирующий и лизирующий опухолевые клетки человека in vitro и депонированный в Государственной коллекции Роспотребнадзора возбудителей вирусных инфекций и риккетсиозов Федерального бюджетного учреждения науки Государственный научный центр вирусологии и биотехнологии «Вектор» под регистрационным номером V-576.
    Ref. No: 2496873, Year: 10/2013
  • [Show abstract] [Hide abstract]
    ABSTRACT: The regulatory region of the Escherichia coli yfiA gene was reconstructed by using the SITECON web resource and mathematical modeling; the complexity of its expression under oxidative stress was assessed. Simulation of the response of E. coli cells transformed with the pYfi-gfp plasmid to oxidative stress indicated that the maximum agreement with experimental data was achieved in a model implying complex action, apparently mediated by several transcription factors (TFs). The regulatory region of the yfiA gene was inspected for potential TF binding sites, and highly reliable predictions were made for TFs MarA, IscR, MetJ, PurR, and SoxS, which directly or indirectly participate in the response of the gene to oxidative stress, and for CRP, a global regulator of carbohydrate catabolism. The presence of binding sites for CRP, MarA, and SoxS in the E. coli yfiA promoter was confirmed by a electrophoretic mobility-shift assay with purified recombinant TFs. This fact explains the sensitivity of yfiA to mitomycin and radical-forming agents.
    07/2013; 3(4). DOI:10.1134/S2079059713040059
  • [Show abstract] [Hide abstract]
    ABSTRACT: Silver nanoparticles possess antibacterial effect for various bacteria; however mechanisms of the interaction between Ag-NPs and bacterial cells remain unclear. The aim of our study was to obtain direct evidence of Ag-NPs penetration into cells of Gram-negative bacterium S. typhimurium and Gram-positive bacterium S. aureus, and to study cell responses to Ag-NPs. The Ag-NPs (most 8-10 nm) were obtained by gas-jet method. S. typhimurium (7.81 × 10(7) CFU), or S. aureus (8.96 × 10(7) CFU) were treated by Ag-NPs (0.05 mg/l of silver) in orbital shaker at 190 rpm, 37 °C. Bacteria were sampled at 0.5, 1, 1.5, 2, 5 and 23 h of the incubation for transmission electron microscopy of ultrathin sections. The Ag-NPs adsorbed on outer membrane of S. typhimurium and cell wall of S. auereus; penetrated and accumulated in cells without aggregation and damaging of neighboring cytoplasm. In cells of S. aureus Ag-NPs bound with DNA fibers. Cell responses to Ag-NPs differed morphologically in S. typhimurium and S. aureus, and mainly were presented by damage of cell structures. The cytoplasm of S. aureus became amorphous, while S. typhimurium showed lumping and lysis of cytoplasm which led to formation of "empty" cells. Other difference was fast change of cell shape in S. typhimurium, and late deformation of S. aureus cells. The obtained results showed how different could be responses induced by the same NPs in relatively simple prokaryotic cells. Evidently, Ag-NPs directly interact with macromolecular structures of living cells and are exert an active influence on their metabolism.
    Biology of Metals 05/2013; DOI:10.1007/s10534-013-9633-3 · 2.69 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Human bocavirus (HBoV) is associated with acute gastroenteritis in humans, occurring mostly in young children and elderly people. Four bocavirus genotypes (HBoV1-HBoV4) have been found so far. Since there were no data on the contribution of HBoV to gastroenteritis in Russia, 1781 fecal samples collected from infants hospitalized with acute gastroenteritis in Novosibirsk, Russia during one year were tested for the presence of nucleic acids from HBoV and three major gastrointestinal viruses (rotavirus A, norovirus II, and astrovirus). HBoV was detected only in 1.9% of the samples: HBoV1 was detected in 0.6% and HBoV2, in 1.3%. Complete genome sequencing of three Novosibirsk isolates was performed. An evolutionary analysis of these sequences and the available sequences of human and great apes bocaviruses demonstrated that the current HBoV genotypes diverged comparatively recently, about 60-300 years ago. The independent evolution of bocaviruses from chimpanzees and gorillas commenced at the same time period. This suggests that these isolates of great apes bocaviruses belong to separate genotypes within the species of human bocavirus, which is actually the primate bocavirus. The rate of mutation accumulation in the genome of primate bocaviruses has been estimated as approximately 9×10(-4) substitutions/site/year. It has been demonstrated that HBoV1 diverged from the ancestor common with chimpanzee bocavirus approximately 60-80 years ago, while HBoV4 separated from great apes bocaviruses about 200-300 years ago. The hypothesis postulating independent evolution of HBoV1 and HBoV4 genotypes from primate bocaviruses has been proposed.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2013; DOI:10.1016/j.meegid.2012.12.023 · 3.22 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Anti-cytokine autoantibodies (auto-Abs) are ubiquitous both in patients suffering from infectious, inflammatory and autoimmune diseases and in healthy individuals. Particularly anti-IFN-γ auto-Abs are shown to be elevated in blood of multiple sclerosis (MS) patients.OBJECTIVE: The aim of present study was to investigate whether repertoires of anti-IFN-γ auto-Abs differ in MS patients and healthy donors. Using phage display technique we have compared repertoires of the genes encoding anti-IFN-γ single-chain variable fragments selected from MS and naïve phage display libraries.RESULTS: The panel of anti-IFN-γ auto-Abs selected from MS library includes (i) 'fetal' auto-Abs, encoded by the V _{H} 6-1 gene segment and the combination proximal D segments with distal J _{H} segments; (ii) naïve auto-Abs; (iii) affinity maturated antibodies; and (iv) abnormal single-domain antibodies. Meanwhile, the panel of anti-IFN-γ auto-Abs selected from naïve library mainly contains the naïve antibodies. Moreover, the overall antibody repertoire of MS library is skewed compared to the overall repertoire of naïve library and also contained the antibodies carrying a 'fetal' V _{H} 6 domain and the ratio of κ and λ chains was reversed. These results suggest existence of a special mechanism or trigger that provides for reconstitution of the immune system in MS.
    Human antibodies 01/2013; 22(1):31-49. DOI:10.3233/HAB-130269
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The objective. To determine various bacterial and viral causative agents of acute enteric infections (AEI) in hospitalized adults and to genotype the obtained isolated of viral pathogens. Patients and methods. Molecular and mictobiological methods were used to examine stool samples from 100 adult patients with AEI hospitalized in 2009 to CCH No 1 of Novosibirsk, for the presence of viral (human rota-, noro-, astro-, entero- and bocaviruses) and bacterial (Salmonella spp., Shigella spp., Escherichia coli, Staphylococcus spp., Klebsiella spp.) agents. Rotaviruses of group A were genotyped by the method of multiplex PCR. For genotyping other enteropathogenic viruses the appropriate variable gene segments were sequenced. Results. The studied microorganisms were found in 57% of patients: in 23% - bacteria, in 24% - viruses, in 10% - bacteria and viruses simultaneously. The most frequently Salmonella spp. (19%) and genotypes GII.4 and GII.3 noroviruses (15%) were detected. In 7%, group А rotavirus genotypes G1P [8], G2P [4], G3P [8], G4P [8], in 3% -genotype 1 astroviruses, also in 3% -Shigella spp were found. In single cases, group С rotavirus and genotype 6 astrovirus were detected. Conclusion. As is shown, viral and bacterial agents are detected in stools of adult patients with diarrhea with the approximately equal incidence - 23-24%.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genetic analysis of group A rotavirus recovered from fecal samples of children admitted to hospitals in Novosibirsk and Omsk during four epidemic seasons 2007, 2007/2008, 2009/2010, 2010/2011 was performed. A total of 1416 rotavirus isolates were genotyped using multiplex PCR. The isolates of the most common rotavirus genotypes G1P[8], G4P[8], G2P[4], G3P[8] co-circulated in Western Siberia during 2007-2011. In isolated cases G9P[8], G2P[8], G3P[9], and G4P[6] genotypes were detected. Change of dominant genotype from G1P[8] to G4P[8] occurred in 2008 in Omsk and in Novosibirsk in 2009 as well. Incidence and distribution of rotavirus genotypes differed and changed every epidemic season in both cities. The phylogenetic analysis based on VP4 (VP8*), VP7, and VP6 gene sequences showed that the majority of isolates from Novosibirsk and Omsk were clustered together and demonstrated high level homology with rotavirus isolates found in other regions of Eurasia. In addition, a rare P[8]b (OP354-like) subtype of the VP4 gene was identified in fourteen isolates (G9, G1, and G4) in Novosibirsk and in a single isolate Omsk08-381/G9P[8]b in Omsk. The results obtained in this study demonstrate the necessity of long-term monitoring of rotavirus isolates in Western Siberia. This is important for selection of rotavirus vaccine for immunization of infants, improvement of diagnostic kits and understanding of the epidemiology and the evolution of group A rotaviruses
    Molecular Genetics Microbiology and Virology 11/2012; DOI:10.3103/S0891416812040076 · 0.27 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Increasing information concerning molecular biology of viruses and virus-cell interactions makes possible to use viruses as a tool in effort to treat cancer diseases. As a rule, tumor cells are highly sensitive to viruses that may be used in cancer therapy. Therewith, applications of viral oncolysis in treatment of cancer diseases assume maximum possible safety of used viruses for patient and environment. Human enteroviruses are one of the convenient sources to generate oncolytic viruses. Many of enteroviruses are non-pathogenic for humans or cause mild disease. Progress in genetic engineering permits to develop attenuated enterovirus variants with high safety and selectivity. This review focuses on the main members of Enterovirus genus, such as Coxsackieviruses, and vaccine strains as promising source for development of oncolytic agents, applicable for cancer therapy. It reviews data concerning recently developed and tested oncolytic variants of enteroviruses and discusses perspectives of their application in cancer therapy and problems, concerning their improvement and practical use.
    Molecular Biology 09/2012; 46(5-6):712-725. DOI:10.1134/S0026893312050032 · 0.74 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Human astrovirus is one of the etiological agents of acute gastroenteritis in humans, mostly in young children and elderly people. Complete genome sequencing of four human astrovirus strains isolated in Novosibirsk, Russia was performed. Analysis of these sequences and the sequences available in GenBank database has detected numerous potential recombination breakpoints. For the first time the rate of human astrovirus evolution was estimated based on the genome fragments without recombination breakpoints; the determined rate is typical of the RNA viruses with high evolutionary rate, amounting to approximately 3.7 × 10(-3) nucleotide substitutions per site per year, and for the synonymous changes, 2.8 × 10(-3) nucleotide substitutions per site per year.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 03/2012; 12(2):435-42. DOI:10.1016/j.meegid.2012.01.019 · 3.22 Impact Factor
  • Source
    Infection Genetics and Evolution 02/2012; · 3.26 Impact Factor

Publication Stats

119 Citations
70.24 Total Impact Points

Institutions

  • 2011–2015
    • Institute of Chemical Biology and Fundamental Medicine
      Novo-Nikolaevsk, Novosibirsk, Russia
  • 2011–2014
    • Russian Academy of Sciences
      • Institute of Chemical Biology and Fundamental Medicine
      Moskva, Moscow, Russia
  • 1999–2010
    • State Research Center of Virology and Biotechnology VECTOR
      Novo-Nikolaevsk, Novosibirsk, Russia