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Uvarova YE, Bryanskaya AV, Rozanov AS, Shlyakhtun VN, Demidov EA, Starostin KV, Goryachkovskaya TN, Shekhovtsov SV, Slynko NM, Peltek SE. An integrated method for taxonomic identification of microorganisms. Vavilovskii Zhurnal Genet Selektsii 2021; 24:376-382. [PMID: 33659820 PMCID: PMC7716526 DOI: 10.18699/vj20.630] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
For accurate species-level identification of microorganisms, researchers today increasingly use a
combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level
of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection
using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the
ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media
were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various
substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e.g., the relationship with oxygen,
type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms
analyzed were combined into separate groups based on the similarities of their phenotypic characteristics.
This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps,
may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and
quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other
collections
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Affiliation(s)
- Yu E Uvarova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Bryanskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V N Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T N Goryachkovskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S V Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N M Slynko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Starostin KV, Demidov EA, Ershov NI, Bryanskaya AV, Efimov VM, Shlyakhtun VN, Peltek SE. Creation of an Online Platform for Identification of Microorganisms: Peak Picking or Full-Spectrum Analysis. Front Microbiol 2020; 11:609033. [PMID: 33391232 PMCID: PMC7775396 DOI: 10.3389/fmicb.2020.609033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/30/2020] [Indexed: 11/25/2022] Open
Abstract
Identification of microorganisms by MALDI-TOF mass spectrometry is a very efficient method with high throughput, speed, and accuracy. However, it is significantly limited by the absence of a universal database of reference mass spectra. This problem can be solved by creating an Internet platform for open databases of protein spectra of microorganisms. Choosing the optimal mathematical apparatus is the pivotal issue for this task. In our previous study we proposed the geometric approach for processing mass spectrometry data, which represented a mass spectrum as a vector in a multidimensional Euclidean space. This algorithm was implemented in a Jacob4 stand-alone package. We demonstrated its efficiency in delimiting two closely related species of the Bacillus pumilus group. In this study, the geometric approach was realized as R scripts which allowed us to design a Web-based application. We also studied the possibility of using full spectra analysis (FSA) without calculating mass peaks (PPA), which is the logical development of the method. We used 74 microbial strains from the collections of ICiG SB RAS, UNIQEM, IEGM, KMM, and VGM as the models. We demonstrated that the algorithms based on peak-picking and analysis of complete data have accuracy no less than that of Biotyper 3.1 software. We proposed a method for calculating cut-off thresholds based on averaged intraspecific distances. The resulting database, raw data, and the set of R scripts are available online at https://icg-test.mydisk.nsc.ru/s/qj6cfZg57g6qwzN.
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Affiliation(s)
- Konstantin V Starostin
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeny A Demidov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita I Ershov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vadim M Efimov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
| | - Valeriya N Shlyakhtun
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Stakhneva EM, Meshcheryakova IA, Demidov EA, Starostin KV, Sadovski EV, Peltek SE, Voevoda MI, Chernyavskii AM, Volkov AM, Ragino YI. A Proteomic Study of Atherosclerotic Plaques in Men with Coronary Atherosclerosis. Diagnostics (Basel) 2019; 9:diagnostics9040177. [PMID: 31703357 PMCID: PMC6963888 DOI: 10.3390/diagnostics9040177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Received: 10/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/24/2022] Open
Abstract
Background: To study the changes in protein composition of atherosclerotic plaques at different stages of their development in coronary atherosclerosis using proteomics. Methods: The object of research consisted of homogenates of atherosclerotic plaques from coronary arteries at different stages of development, obtained from 15 patients. Plaque proteins were separated by two-dimensional electrophoresis. The resultant protein spots were identified by the matrix-assisted laser desorption ionization method with peptide mass mapping. Results: Groups of differentially expressed proteins, in which the amounts of proteins differed more than twofold (p < 0.05), were identified in pools of homogenates of atherosclerotic plaques at three stages of development. The amounts of the following proteins were increased in stable atherosclerotic plaques at the stage of lipidosis and fibrosis: vimentin, tropomyosin β-chain, actin, keratin, tubulin β-chain, microfibril-associated glycoprotein 4, serum amyloid P-component, and annexin 5. In plaques at the stage of fibrosis and calcification, the amounts of mimecan and fibrinogen were increased. In unstable atherosclerotic plaque of the necrotic–dystrophic type, the amounts of human serum albumin, mimecan, fibrinogen, serum amyloid P-component and annexin were increased. Conclusion: This proteomic study identifies the proteins present in atherosclerotic plaques of coronary arteries by comparing their proteomes at three different stages of plaque development during coronary atherosclerosis.
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Affiliation(s)
- Ekaterina M. Stakhneva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630089 Novosibirsk, Russia; (E.V.S.); (M.I.V.); (Y.I.R.)
- Correspondence: ; Tel.: +7-(383)-264-2516; Fax: +73832642516
| | - Irina A. Meshcheryakova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.A.M.); (E.A.D.); (K.V.S.); (S.E.P.)
| | - Evgeny A. Demidov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.A.M.); (E.A.D.); (K.V.S.); (S.E.P.)
| | - Konstantin V. Starostin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.A.M.); (E.A.D.); (K.V.S.); (S.E.P.)
| | - Evgeny V. Sadovski
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630089 Novosibirsk, Russia; (E.V.S.); (M.I.V.); (Y.I.R.)
| | - Sergey E. Peltek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.A.M.); (E.A.D.); (K.V.S.); (S.E.P.)
| | - Michael I. Voevoda
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630089 Novosibirsk, Russia; (E.V.S.); (M.I.V.); (Y.I.R.)
| | - Alexander M. Chernyavskii
- The Federal State Budgetary Institution “National Medical Research Center named academician E.N. Meshalkin” of the Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia; (A.M.C.); (A.M.V.)
| | - Alexander M. Volkov
- The Federal State Budgetary Institution “National Medical Research Center named academician E.N. Meshalkin” of the Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia; (A.M.C.); (A.M.V.)
| | - Yuliya I. Ragino
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630089 Novosibirsk, Russia; (E.V.S.); (M.I.V.); (Y.I.R.)
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Stakhneva EM, Meshcheryakova IA, Demidov EA, Starostin KV, Ragino YI, Peltek SE, Voevoda MI. Proteomic Study of Blood Serum in Coronary Atherosclerosis. Bull Exp Biol Med 2017; 162:343-345. [PMID: 28091899 DOI: 10.1007/s10517-017-3611-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 11/28/2022]
Abstract
Changes in the blood serum proteins were assessed in men with coronary atherosclerosis and without coronary heart disease. Proteins were separated by 2D-electrophoresis, protein fractions were identified by their peptide fingerprint by MALDI method; fractions with more than twofold increase in protein level were determined. In blood serum of patients with coronary atherosclerosis, the content of C4 complement protein increased and ceruloplasmin level decreased, which is typical of heart failure and coronary heart disease.
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Affiliation(s)
- E M Stakhneva
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - I A Meshcheryakova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu I Ragino
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M I Voevoda
- Research Institute of Internal and Preventive Medicine, Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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