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A Highly Sensitive and Rapid Method for the Detection of DNA Fragments Using the Photoprotein Obelin as a Reporter [Text] / V. V. Borisova [et al.] // Russ. J. Bioorg. Chem. - 2008. - Vol. 34, Is. 6. - P709-715, DOI 10.1134/S1068162008060101. - Cited References: 13. - This work was supported the program Molecular and Cellular Biology (project no. 10.6), integration grants of the Siberian Division of the Russian Academy of Sciences (73 and 55), CRDF, and the Russian Foundation for Basic Research (project nos. 06-04-49263-a and 06-04-08076-ofi). . - ISSN 1068-1620

РУБ Biochemistry & Molecular Biology + Chemistry, Organic
Рубрики:
BIOLUMINESCENT IMMUNOASSAY
Кл.слова (ненормированные):
obelin -- bioluminescent hybridization assay -- PCR
Аннотация: The recombinant Ca(2+)-activated photoprotein obelin was used as a reporter protein in a solid-phase bioluminescent hybridization DNA assay. Oligonucleotide probes were immobilized on the surface of polymer methacrylate beads or microbiological plates of different types. A 30-mer oligonucleotide or its derivative with the biotin residue on the 3'-terminus, as well as a denatured double-stranded PCR fragment of the hepatitis C virus with the sequence of the 30-mer oligonucleotide was used as a DNA template. The probe in the hybridization complex was labeled by the elongation of the chain using a Taq DNA polymerase in the presence of biotinylated deoxyuridine triphosphate. The results of the bioluminescent assay were compared with the results of colorimetric analysis obtained with alkaline phosphatase as a reporter protein. It was shown that the use of the bioluminescent obelin label substantially accelerates the DNA detection procedure, provides a high sensitivity of the assay (no less than 10(-15) mol of DNA template), and ensures a quantitative determination of the amount of DNA template in the tested sample.

Держатели документа:
[Borisova, V. V.
Frank, L. A.] Russian Acad Sci, Inst Biophys, Siberian Branch, Krasnoyarsk 660036, Russia
[Pyshnaya, I. A.
Pyshnyi, D. V.] Russian Acad Sci, Siberian Branch, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Borisova, V.V.; Pyshnaya, I.A.; Pyshnyi, D.V.; Frank, L.A.

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Ca2+-Regulated Photoproteins: Effective Immunoassay Reporters [Text] / L. A. Frank // Sensors. - 2010. - Vol. 10, Is. 12. - P11287-11300, DOI 10.3390/s101211287. - Cited References: 70. - This work was supported by the grant No. 76 of the Russian Academy of Sciences, Siberian Branch. . - ISSN 1424-8220

РУБ Chemistry, Analytical + Electrochemistry + Instruments & Instrumentation
Рубрики:
POLYMERASE-CHAIN-REACTION
   CYTOKINE MESSENGER-RNA
   BIOLUMINESCENT IMMUNOASSAY
   MYCOBACTERIUM-TUBERCULOSIS
   BIOTINYLATED AEQUORIN
   RECOMBINANT AEQUORIN
   ANGSTROM RESOLUTION
   FUSION PROTEIN
   PCR ASSAY
   OBELIN
Кл.слова (ненормированные):
bioluminescence -- Ca2+-regulated photoprotein -- immunoassay -- PCR-ELISA -- multiplex assay -- re-engineered photoproteins
Аннотация: Ca2+-regulated photoproteins of luminous marine coelenterates are of interest and a challenge for researchers as a unique bioluminescent system and as a promising analytical instrument for both in vivo and in vitro applications. The proteins are comprehensively studied as to biochemical properties, tertiary structures, bioluminescence mechanism, etc. This knowledge, along with available recombinant proteins serves the basis for development of unique bioluminescent detection systems that are "self-contained", triggerable, fast, highly sensitive, and non-hazardous. In the paper, we focus on the use of photoproteins as reporters in binding assays based on immunological recognition element-bioluminescent immunoassay and hybridization immunoassay, their advantages and prospects.

Держатели документа:
Russian Acad Sci, Inst Biophys, Siberian Branch, Krasnoyarsk 660036, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Frank, L.A.

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Microbial community of the chemocline of the meromictic Lake Shunet (Khakassia, Russia) during summer stratification / D. Y. Rogozin [et al.] // Microbiology. - 2010. - Vol. 79, Is. 2. - P253-261, DOI 10.1134/S0026261710020189 . - ISSN 0026-2617
Кл.слова (ненормированные):
Chemocline -- Cyanobacteria -- Green sulfur bacteria -- Meromictic lakes -- Microstratification -- PCR-DGGE -- Phytoflagellates -- Purple sulfur bacteria -- Bacteria (microorganisms) -- Chlorobi -- Chromatiaceae -- Cryptomonas -- Cyanobacteria -- Lamprocystis purpurea -- Phytomastigophorea -- Proteobacteria -- Synechococcus
Аннотация: The spatio-temporal organization of the bacterial community inhabiting the chemocline of the stratified meromictic Lake Shunet (Khakassia, Russia) was investigated from May to September 2005 by means of microscopy, analysis of photosynthetic pigments, and PCR-DGGE with subsequent 16S rDNA analysis. The samples were collected with a multisyringe stratification sampler, sampling being performed every 5 cm. It was demonstrated that, during the period of investigation, there were no large changes in the bacterial community of the chlemocline, at least among the detected forms. During the whole period of study, purple sulfur bacteria related to Lamprocystis purpurea (Chromatiaceae) were predominant in the chemocline. Beneath the layer of purple bacteria, green sulfur bacteria were revealed that were phylogenetically distant from strain ShNPel02, which was previously isolated from this lake. Development of phytoflagellates of the genus Cryptomonas was observed in the upper zone of the chemocline. In the chemocline of Lake Shunet, the numbers of picoplankton cyanobacteria of the genus Synechococcus increased from May to September. It was demonstrated that the application of universal bacterial primers for DGGE resulted in the same qualitative distributional pattern of predominant species as microscopic studies. В© Pleiades Publishing, Ltd., 2010.

Scopus
Держатели документа:
Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk 660036, Russian Federation
Siberian Federal University, pr. Svobodnyi, 79, Krasnoyarsk 660041, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Rogozin, D.Y.; Trusova, M.Y.; Khromechek, E.B.; Degermendzhy, A.G.

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Seasonal features of consumption of lysine by uncultivated bacterial plankton of Eutrophic water reservoir / M. Y. Trusova, O. V. Kolmakova, M. I. Gladyshev // Contemporary Problems of Ecology. - 2012. - Vol. 5, Is. 4. - P391-398, DOI 10.1134/S1995425512040154 . - ISSN 1995-4255
Кл.слова (ненормированные):
16S ribosomal RNA -- biogeochemical function -- denaturing gradient gel electrophoresis -- eutrophic water reservoir -- lysine -- microecosystem (MES) -- uncultivated bacterial plankton -- amino acid -- bacterioplankton -- bacterium -- biogeochemistry -- electrokinesis -- eutrophication -- laboratory method -- microbial community -- polymerase chain reaction -- reservoir -- seasonal variation -- specialization -- Bacteria (microorganisms)
Аннотация: Dynamics of bacterial plankton community of eutrophic water reservoir in laboratory microecosystems with amino acid lysine was studied using PCR-DGGE technique. The addition of lysine to the microecosystems resulted in changes in the composition of the bacterial plankton in summer; in particular, a number of Lys1 and Lys2 species (genotypes) that consume this amino acid grew fast in the bacterial community. The plank tonic bacterial communities did not respond to the addition of lysine in spring and late summer. The obtained data confirm the hypothesis for the narrow specialization of bacterial plankton species to the consumption of individual organic substances. В© 2012 Pleiades Publishing, Ltd.

Scopus
Держатели документа:
Institute of Biophysics of Siberian Branch of Russian Academy of Sciences, Akademgorodok 50-50, Krasnoyarsk 660036, Russian Federation
Siberian Federal University, Svobodnii prosp. 79, Krasnoyarsk 660041, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Trusova, M.Y.; Kolmakova, O.V.; Gladyshev, M.I.

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Bioluminescent reporters for identification of gene allelic variants / V. V. Krasitskaya [et al.] // Russ. J. Bioorg. Chem. - 2012. - Vol. 38, Is. 3. - P298-305, DOI 10.1134/S1068162012030090. - Cited References: 13. - The authors thank the staff of Hematology Research Center (Krasnoyarsk Branch of Russian Academy of Medical Sciences) for providing DNA samples. The work was supported by the Integration Interdisciplinary Project of Siberian Branch of the Russian Academy of Sciences No. 76 and the Krasno yarsk Regional Fund for the support of scientific and technological activities. . - ISSN 1068-1620

РУБ Biochemistry & Molecular Biology + Chemistry, Organic
Рубрики:
COELENTERAZINE-BINDING PROTEIN
   RENILLA-MUELLERI
   LUCIFERASE
   PURIFICATION
   SUBSTRATE
   CLONING
   CDNA
Кл.слова (ненормированные):
SNP -- PEXT reaction -- obelin -- luciferase -- bioluminescent microassay
Аннотация: A method for single nucleotide polymorphism identification was developed, which was based on the primer extension reaction (PEXT) followed by bioluminescent solid-phase microassay. Recombinant Ca2+-regulated photoprotein obelin and coelenterazine-dependent Renilla muelleri luciferase were used as reporters. The study was performed as an example of SNP genotyping of the human F5 gene encoding human Factor V Leiden polymorphism 1691 G -> A (R506Q). Genomic DNA was amplified by PCR using primers flanking polymorphic site of 140 base pairs. PCR products were used as templates for two PEXT reactions using two primers containing 3'-terminal nucleotides, which were complementary to either normal or mutant alleles. If the template and allele-specific primer were completely complementary, the latter was elongated with DNA polymerase. The resulting extension product contained biotin residue due to the presence of biotinylated deoxyuridine triphosphate (B-dUTP) in the reaction mixture. The products were analyzed using obelin-streptavidin conjugates. The optimal PEXT-reaction conditions were found, which ensured a high reliability of SNP genotyping. A new approach to simultaneously revealing both alleles in one well was developed using two bioluminescent reporters. The efficiency of the proposed approach was shown in the study of clinical DNA samples.

Держатели документа:
[Krasitskaya, V. V.
Burakova, L. P.
Frank, L. A.] Russian Acad Sci, Inst Biophys, Siberian Branch, Krasnoyarsk 660036, Akademgorodok, Russia
[Pyshnaya, I. A.] Russian Acad Sci, Siberian Branch, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Krasitskaya, V.V.; Burakova, L.P.; Pyshnaya, I.A.; Frank, L.A.

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Simultaneous genotyping of four single nucleotide polymorphisms associated with risk factors of hemostasis disorders / E. E. Bashmakova, V. V. Krasitskaya, L. A. Frank // Comb. Chem. High Throughput Screen. - 2015. - Vol. 18, Is. 10. - P930-936 . - ISSN 1386-2073
Кл.слова (ненормированные):
Bioluminescent microassay -- Multiplex PCR -- PEXT reaction -- Photoprotein obelin -- SNP detection
Аннотация: Multiplex simultaneous genotyping technique was developed for four polymorphisms in genes coding for blood coagulation factors and homocysteine metabolism which are considered as thrombophilia related mutations: FV Leiden, FII G20210A, MTHFR C677T, and FVII G10976A. It is based on primer extension reaction with the following bioluminescent solid-phase microassay. At that, two different in bioluminescence obelin mutants were applied to simultaneous detection of two gene allelic variants. The assay is carried out in microtiter plate format and provides fast and reliable genotyping of four single nucleotide polymorphisms in four different genes within 2.5 hours. A large number of clinical samples were analyzed and the obtained results were found to be in complete correlation with those obtained by using conventional RT-PCR techniques. © 2015 Bentham Science Publishers.

Scopus
Держатели документа:
Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, Russian Federation
Siberian Federal University, Svobodnii Ave., 79, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Bashmakova, E. E.; Krasitskaya, V. V.; Frank, L. A.

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Simultaneous Genotyping of Four Single Nucleotide Polymorphisms Associated with Risk Factors of Hemostasis Disorders [Text] / E. E. Bashmakova, V. V. Krasitskaya, L. A. Frank // Comb. Chem. High Throughput Screen. - 2015. - Vol. 18, Is. 10. - P930-936, DOI 10.2174/1386207318666150917095903. - Cited References:20. - The study was supported by the grant 14-14-01119 of the Russian Science Foundation. . - ISSN 1386-2073. - ISSN 1875-5402

РУБ Biochemical Research Methods + Chemistry, Applied + Pharmacology &
Рубрики:
ALLELE-SPECIFIC PCR
FACTOR-V-LEIDEN
BIOLUMINESCENT IMMUNOASSAY
Кл.слова (ненормированные):
SNP detection -- PEXT reaction -- photoprotein obelin -- bioluminescent -- microassay -- multiplex PCR
Аннотация: Multiplex simultaneous genotyping technique was developed for four polymorphisms in genes coding for blood coagulation factors and homocysteine metabolism which are considered as thrombophilia related mutations: FV Leiden, FII G20210A, MTHFR C677T, and FVII G10976A. It is based on primer extension reaction with the following bioluminescent solid-phase microassay. At that, two different in bioluminescence obelin mutants were applied to simultaneous detection of two gene allelic variants. The assay is carried out in microtiter plate format and provides fast and reliable genotyping of four single nucleotide polymorphisms in four different genes within 2.5 hours. A large number of clinical samples were analyzed and the obtained results were found to be in complete correlation with those obtained by using conventional RT-PCR techniques.

WOS
Держатели документа:
Russian Acad Sci, Siberian Branch, Inst Biophys, Photobiol Lab, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.

Доп.точки доступа:
Bashmakova, Eugenia E.; Krasitskaya, Vasilisa V.; Frank, Ludmila A.; Russian Science Foundation [14-14-01119]

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Adsorption of viral particles from the blood plasma of patients with viral hepatitis on nanodiamonds / A. V. Baron [et al.] // Doklad. Biochem. Biophys. - 2016. - Vol. 469, Is. 1. - P244-246, DOI 10.1134/S1607672916040037 . - ISSN 1607-6729
Аннотация: Adsorption of viral particles from the blood plasma of patients with viral hepatitis B and C on modified nanodiamonds (MNDs) was shown in the in vitro experiments. PCR method showed the treatment of plasma with MNDs leads to a decrease in the viral load by 2–3 orders of magnitude or more in both cases studied. These results make it possible to predict the applicability of MNDs for the development of new technologies of hemodialysis and plasmapheresis for binding and removal of viral particles from the blood of infected patients. © 2016, Pleiades Publishing, Ltd.

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Держатели документа:
Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, Russian Federation
Siberian Federal University, Svobodnyi pr. 79, Krasnoyarsk, Russian Federation
Krasnoyarsk Regional Center for Prevention and Control of AIDS, ul. Karla Marksa 47, Krasnoyarsk, Russian Federation
Voino-Yasenetskii State Medical University, Ministry of Health of the Russian Federation, ul. Partizana Zheleznyaka 1, Krasnoyarsk, Russian Federation
Krasnoyarsk Branch of Hematology Research Center, Ministry of Health of the Russian Federation, Krasnoyarsk, Russian Federation
Krasnoyarsk Research Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Baron, A. V.; Osipov, N. V.; Yashchenko, S. V.; Kokotukha, Y. A.; Baron, I. J.; Puzyr, A. P.; Olkhovskiy, I. A.; Bondar, V. S.

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Bacterial Communities of Three Saline Meromictic Lakes in Central Asia [Text] / B. Baatar [et al.] // PLoS One. - 2016. - Vol. 11, Is. 3. - Ст. e0150847, DOI 10.1371/journal.pone.0150847. - Cited References:65. - This study was supported by the thematic project funding of Taiwan-Russian Joint Project (NSC99- 2923-B-001-001-MY3 and NSC 102-2923-B-001-004) and Taiwan-Mongolian Joint Project (NSC101-2923-B-001-003-MY3) from the National Sciences Council of Taiwan and Biodiversity Research Center, Academia Sinica, Taiwan and the Russian Foundation for Basic Research, Grant No. 14-04-01060-a.; We thank our Russian and Mongolian colleagues in the Institute of Biophysics SB RAS and National University of Mongolia for assistance with providing samples and hydro-parameter data. This study was supported by the thematic project funding of Taiwan-Russian Joint Project (NSC99-2923-B-001-001-MY3 and NSC 102-2923-B-001-004) and Taiwan-Mongolian Joint Project (NSC101-2923-B-001-003-MY3) from the National Sciences Council of Taiwan and Biodiversity Research Center, Academia Sinica, Taiwan and the Russian Foundation for Basic Research, Grant No. 14-04-01060-a. . - ISSN 1932-6203

РУБ Multidisciplinary Sciences
Рубрики:
PURPLE SULFUR BACTERIA
REAL-TIME PCR
MICROBIAL COMMUNITIES
Аннотация: Meromictic lakes located in landlocked steppes of central Asia (similar to 2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (similar to 20.6% of relative abundance), Lake Shunet (similar to 27.1%) and Lake Oigon (similar to 9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

WOS,
Scopus
Держатели документа:
Acad Sinica, Taiwan Int Grad Program, Mol & Biol Agr Sci Program, Taipei 115, Taiwan.
Acad Sinica, Biodivers Res Ctr, Taipei 115, Taiwan.
Natl Chung Hsing Univ, Grad Inst Biotechnol, Taichung 40227, Taiwan.
SB RAS, Inst Biophys, Krasnoyarsk 660036, Russia.
Natl Pingtung Univ Sci & Technol, Pingtung 91201, Taiwan.
Natl Univ Mongolia, Sch Art & Sci, Ulaanbaatar 14201, Mongol Peo Rep.
Natl Chung Hsing Univ, Ctr Biotechnol, Taichung 40227, Taiwan.

Доп.точки доступа:
Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G.; Tang, Sen-Lin; National Sciences Council of Taiwan [NSC99- 2923-B-001-001-MY3, NSC 102-2923-B-001-004, NSC101-2923-B-001-003-MY3, NSC99-2923-B-001-001-MY3]; Biodiversity Research Center, Academia Sinica, Taiwan; Russian Foundation for Basic Research [14-04-01060-a]

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