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Dubrovin EV, Presnova GV, Rubtsova MY, Egorov AM, Grigorenko VG, Yaminsky IV. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays. Acta Naturae 2015; 7:108-14. [PMID: 26085952 PMCID: PMC4463420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.
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Egorov AM, Matyukhova SA. Kinetics and mechanism of the reaction of benzyl bromide with copper in dimethylacetamide in the presence of oxygen. RUSS J GEN CHEM+ 2014. [DOI: 10.1134/s1070363214090047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Presnova GV, Rubtsova MY, Presnov DE, Grigorenko VG, Yaminsky IV, Egorov AM. Streptavidin conjugates with gold nanoparticles for visualization of single DNA interactions on the silicon surface. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s1990750814020103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pobolelova YI, Ulyashova MM, Rubtsova MY, Egorov AM. Multiplex PCR for joint amplification of carbapenemase genes of molecular classes A, B, and D. BIOCHEMISTRY. BIOKHIMIIA 2014; 79:566-70. [PMID: 25100015 DOI: 10.1134/s0006297914060108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here we present a method for joint amplification of genes of carbapenemases of molecular classes A, B, and D for hybridization analysis on DNA microarrays. Using new-generation DNA polymerase KAPA2G Fast (KAPA Biosystems, USA) together with optimization of the conditions for the multiplex PCR with 20 primer pairs allowed us to carry out joint amplification of full-length genes of seven different types of carbapenemases (KPC, VIM, IMP, SPM, SIM, GIM, and OXA) with simultaneous inclusion of biotin as a label. Yield of the labeled PCR product sufficient for further analysis by microarray hybridization was achieved 40 min after the start of the reaction. This reduced the total duration of DNA identification techniques, including sample preparation stage, to 4 h. The method for gene identification by DNA microarrays with the improved stage of amplification of specific carbapenemase genes was tested with clinical strains of gram-negative bacteria Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae spp. with different sensitivity towards carbapenems according to phenotyping tests. All clinical strains of A. baumannii resistant to carbapenems were found to have genes of OXA-type carbapenemases (subtypes OXA-51, OXA-23, OXA-40, and OXA-58), and clinical strains of P. aeruginosa resistant to carbapenems were found to possess the gene of VIM-type metallo-beta-lactamase (subtype VIM-2). When testing clinical strains sensitive to carbapenems, carbapenemase genes were not detected. Thus, the method of identifying carbapenemase genes on DNA microarrays is characterized by high accuracy and can be used in clinical microbiology laboratories for express diagnostics of resistance to carbapenems.
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Bagratashvili VN, Egorov AM, Krotova LI, Mironov AV, Panchenko VY, Parenago OO, Popov VK, Revelsky IA, Timashev PS, Tsypina SI. Supercritical fluid micronization of risperidone pharmaceutical substance. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2013. [DOI: 10.1134/s1990793112070019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Egorov AM, Putsylov IA, Smirnov SE, Fateev SA. A study of electrodes based on fluorinated fullerene black. RUSS J APPL CHEM+ 2012. [DOI: 10.1134/s1070427212110110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Egorov AM, Matyukhova SA, Dashkova EA. Kinetics and mechanism of benzyl chloride reaction with zinc in dimethylacetamide. RUSS J GEN CHEM+ 2012. [DOI: 10.1134/s107036321210009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Ulyashova MM, Rubtsova MY, Egorov AM. Colorimetric detection of immobilized horseradish peroxidase based on the co-oxidation of benzidine derivatives and 4-chloro-1-naphthol. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0101-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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34
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Rubtsova MY, Ulyashova MM, Bachmann TT, Schmid RD, Egorov AM. Multiparametric determination of genes and their point mutations for identification of beta-lactamases. BIOCHEMISTRY (MOSCOW) 2011; 75:1628-49. [PMID: 21417998 DOI: 10.1134/s0006297910130080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
More than half of all currently used antibiotics belong to the beta-lactam group, but their clinical effectiveness is severely limited by antibiotic resistance of microorganisms that are the causative agents of infectious diseases. Several mechanisms for the resistance of Enterobacteriaceae have been established, but the main one is the enzymatic hydrolysis of the antibiotic by specific enzymes called beta-lactamases. Beta-lactamases represent a large group of genetically and functionally different enzymes of which extended-spectrum beta-lactamases (ESBLs) pose the greatest threat. Due to the plasmid localization of the encoded genes, the distribution of these enzymes among the pathogens increases every year. Among ESBLs the most widespread and clinically relevant are class A ESBLs of TEM, SHV, and CTX-M types. TEM and SHV type ESBLs are derived from penicillinases TEM-1, TEM-2, and SHV-1 and are characterized by several single amino acid substitutions. The extended spectrum of substrate specificity for CTX-M beta-lactamases is also associated with the emergence of single mutations in the coding genes. The present review describes various molecular-biological methods used to identify determinants of antibiotic resistance. Particular attention is given to the method of hybridization analysis on microarrays, which allows simultaneous multiparametric determination of many genes and point mutations in them. A separate chapter deals with the use of hybridization analysis on microarrays for genotyping of the major clinically significant ESBLs. Specificity of mutation detection by means of hybridization analysis with different detection techniques is compared.
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Koliasnikov OV, Grigorenko VG, Egorov AM, Lange S, Schmid RD. Recombinant Production of Horseradish Peroxidase Conjugates with Fab Antibodies in Pichia pastoris for Analytical Applications. Acta Naturae 2011. [DOI: 10.32607/20758251-2011-3-3-85-92] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Andreeva IP, Vorob'eva NT, Vinnitskiĭ LI, Bogush SS, Gavrilova EM, Egorov AM. [Enzyme-linked immunosorbent assay for determination of cyclosporin A in whole blood]. BIOMEDITSINSKAIA KHIMIIA 2011; 57:554-561. [PMID: 22629606 DOI: 10.18097/pbmc20115705554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A test-system based on enzyme-linked immunosorbent assay (ELISA) for quantitative determination of cyclosporin A (CSA) in human whole blood has been developed. The detection limit of the method was 25 ng/ml, the linearity of the method in the concentration range 60-1400 ng/ml varied from 94 to 105%, the variation coefficient did not exceed 8%. The novel method exhibited good correlation with radio-immunoassay and polarization fluoroimmunoassay methods; the linear regression coefficients were 0.965 and 0.983, respectively. The developed test system is stable for at least 9 months when stored at 4 degrees C and can be used in clinical practice.
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Koliasnikov OV, Grigorenko VG, Egorov AM, Lange S, Schmid RD. Recombinant Production of Horseradish Peroxidase Conjugates with Fab Antibodies in Pichia pastoris for Analytical Applications. Acta Naturae 2011; 3:85-92. [PMID: 22649698 PMCID: PMC3347603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Recombinant immunoconjugates of marker enzymes with antigens or antibodies present considerably more advantages than those obtained by conventional methods of chemical synthesis; i.e. they are homogeneous, have a strictly determined stoichiometry, and retain the functional activity of both a marker protein and an antigen/antibody. Based on the pPICZαB shuttle vector, we first managed to obtain a recombinant conjugate of key marker enzyme horseradish peroxidase (HRP) withFabfragments of antibodies against atrazine. The resulting genetic construction allows us to switch to any other antibody sequence, via the simple re-cloning of variable parts and an additional reporter enzyme. Conjugates were successfully produced in thePichia pastorismethylotrophic yeast expression system. The target activity of the conjugates (both enzymatic and antigen-binding) has been demonstrated by ELISA method.
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Fedorova MD, Andreeva IP, Vilegzhanina ES, Komarov AA, Rubtsova MY, Samsonova JV, Egorov AM. Enzyme-linked immunosorbent assay of chlorampenicol in foodstuff. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810080107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Ulyashova MM, Khalilova YI, Rubtsova MY, Edelstein MV, Alexandrova IA, Egorov AM. Oligonucleotide Microarray for the Identification of Carbapenemase Genes of Molecular Classes A, B, and D. Acta Naturae 2010. [DOI: 10.32607/20758251-2010-2-3-101-109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Egorov AM, Matyukhova SA, Kocherova IS, Novikova AA, Anisimov AV. Kinetics and mechanism of nickel reaction with benzyl bromide in dimethylformamide. RUSS J GEN CHEM+ 2009. [DOI: 10.1134/s1070363209030177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Presnova GV, Rybcova MY, Egorov AM. Electrochemical biosensors based on horseradish peroxidase. RUSS J GEN CHEM+ 2009. [DOI: 10.1134/s1070363208120293] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ivanov DV, Egorov AM. [Spreading and mechanisms of antimicrobial resistance of microorganisms, producing beta-lactamases. Phenotyping of potential AmpC-beta-lactamases producers of Enterobacteriaceae and molecular mechanisms of resistance to beta-lactams of Enterobacter cloacae strains, isolated in cases of nosocomial infections]. BIOMEDITSINSKAIA KHIMIIA 2009; 55:50-60. [PMID: 19351033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Susceptibility of nosocomial potential AmpC-beta-lactamases producers strains (n=128), isolated from patients admitted to 30 medical centers of 15 various regions of Russia has been investigated. The susceptibility testing was performed by the broth microdilution method. The most active antibacterial agents acting to the investigated strains remained carbapenems (imipenem and meropenem). PCR-based detection of beta-lactamase genes (TEM, SHV, CTX) was investigated in 51 E. cloacae strains. Alone or in various combinations TEM type beta-lactamases have been found in 31 (60.8%) isolates, SHV in 22 (43.1%), and CTX--in 22 (43.1%). There were negative results of TEM, SHV, CTX beta-lactamases genotyping in 13 (25.5%) E. cloacae suspect strains.
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Rubtsova MY, Samsonova JV, Egorov AM, Schmid RD. Simultaneous determination of several pesticides with chemiluminescent immunoassay on a multi‐spot membrane strip. FOOD AGR IMMUNOL 2008. [DOI: 10.1080/09540109809354986] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Rubtsova MY, Wittmann C, Egorov AM, Schmid RD. Chemiluminescent immunoassay: Application of a portable scanning luminometer for the determination of 2,4‐dichlorophenoxyacetic acid in microtiter and membrane strip format. FOOD AGR IMMUNOL 2008. [DOI: 10.1080/09540109709354954] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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45
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Ulyashova MM, Rubtsova MY, Bachmann T, Egorov AM. Optimization of DNA hybridization analysis on microarrays with colorimetric detection. ACTA ACUST UNITED AC 2008. [DOI: 10.3103/s0027131408020065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Ivanov DV, Egorov AM. [Spreading and mechanisms of antibiotic resistance of microorganisms, producing beta-lactamases. Molecular mechanisms of resistance to beta-lactams of Klebsiella spp. strains, isolated in cases of nosocomial infections]. BIOMEDITSINSKAIA KHIMIIA 2008; 54:104-113. [PMID: 18421915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Antibiotic sensivity of nosocomial Klebsiella spp. strains (n = 212), isolated from patients treated in 30 medical centers of 15 various regions of Russia was investigated. The Klebsiella genus was represented by the following species: Klebsiella pneumoniae ss. pneumoniae--182 (85.8%), Klebsiella pneumoniae ss. ozaenae--1 (0.5%), Klebsiella oxytoca--29 (13.7%) isolates. The most active antibacterial agents against the investigated strains were carbapenems (imipenem and meropenem). Among 3rd generation cephalosporine the lowest MICs were observed for ceftazidime/clavulanic acid (MIC50--0.25 microg/ml, MIC90--64 microg/ml) and cefoperazone/sulbactam (MIC50--16 microg/ml, MIC90--64 microg/ml). Beta-lactamase genes (TEM, SHV, CTX) were detected in 42 Klebsiella pneumoniae ss. pneumoniae strains by PCR. Alone or in various combinations TEM type beta-lactamases have been found in 16 (38.1%) isolates, SHV--in 29 (69%), and CTX--in 27 (64.3%). Combinations of 2 different determinants were detected in 23.8% of the isolates, 3--in 26.2%. There were not isolates producing MBL class B among resistant to carbapenems nosocomial Klebsiella spp. strains.
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Ivanov DV, Egorov AM. [Spreading and mechanisms of antimicrobial resistance of microorganisms, producing beta-lactamases. Phenotypical screening for MBL producers (carbapenemases B1) among strains of Pseudomonas genus, isolated in cases of nosocomial infections]. BIOMEDITSINSKAIA KHIMIIA 2007; 53:653-661. [PMID: 18323150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Intrahospital strains (215) of the bacterial genus Pseudomonas isolated from patients of 30 Medical centers of 15 Russian regions have been investigated for antibiotic resistance. The bacterial cultures resistant to imipenem and/or meropenem were considered as metallo-beta-lactamase (MBL) producers. Production of subclass B1 MBL (carbapenemases) was evaluated by means of the double-disk approximation test using MBL inhibitor, EDTA. There were 55 P. aeroginosa strains (25.6%) resistant to imipenem and meropenem simultaneously; 19 isolates (8.8%) of P. aeroginosa were characterized by synergism between carbapenem and EDTA. The subclass B1 MBL producers are widely distributed in the intrahospital strain obtained from Moscow, Yaroslavl, Ekaterinburg, Omsk, and Tomsk hospitals.
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Eremin SA, Samsonova ZV, Egorov AM. Immunochemical methods for the assays of herbicides of the 1,3,5-triazine group. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1994v063n07abeh000107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Egorov AM. [The goals and objectives of the Association of Clinical Laboratory Diagnostic Means Manufacture]. Klin Lab Diagn 2006:43-4. [PMID: 17087250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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50
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Egorov AM, Shibanov AN. [Domestic manufacture of means for clinical laboratory diagnosis]. Klin Lab Diagn 2006:44-7. [PMID: 17087251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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