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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bashmakova E. E., Krasitskaya V. V., Bondar A. A., Kozlova A. V., Ruksha T. G., Frank L. A.
Заглавие : A bioluminescent assay for detecting melanocortin-1 receptor (MC1R) gene polymorphisms R160W, R151C, and D294H
Место публикации : Mol. Biol. - 2015. - Vol. 49, Is. 6. - С. 852-857. - ISSN 00268933 (ISSN) , DOI 10.1134/S0026893315050039
Ключевые слова (''Своб.индексиров.''): bioluminescent assay--mc1r receptor--melanoma--single nucleotide polymorphisms
Аннотация: Several polymorphisms in the melanocortin-1 receptor gene (MC1R) have been associated with melanoma risk. In particular, rs1805007, rs1805008, and rs1805009 mutations, which result in R151C, R160W, and D294H amino acid substitutions, respectively, and are associated with the phenotype of red-hair mutations, have also been connected with melanoma and nonmelanoma skin cancer risks. This work describes a method of detecting these polymorphisms using primer extension with subsequent dual bioluminescent assay. Model plasmids carrying polymorphic MC1R fragments, as well as several clinical DNA samples, were tested using the proposed technique. The results agreed well with those obtained by Sanger sequencing. © 2015, Pleiades Publishing, Inc.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Makhrov A. A.
Заглавие : A narrowing of the phenotypic diversity range after large rearrangements of the karyotype in salmonidae: The relationship between saltational genome rearrangements and gradual adaptive evolution
Место публикации : Genes: MDPI AG, 2017. - Vol. 8, Is. 11. - ISSN 20734425 (ISSN) , DOI 10.3390/genes8110297
Ключевые слова (''Своб.индексиров.''): ecology--evolution--genome--karyotype--morphology--ecology--gene rearrangement--genome--karyotype--morphology--nonhuman--salmonid
Аннотация: The problem of how a gradual development of ecological and morphological adaptations combines with large genome rearrangements, which have been found to occur in the phylogeny of many groups of organisms, is a matter of discussion in the literature. The objective of this work was to study the problem with the example of salmonids, whose evolution included at least six events of multiple chromosome fusions. Large karyotype rearrangements are associated with a decrease in ecological and morphological diversity in salmonids. In the above example, genome rearrangements seem to distort the function of the genetic systems that are responsible for the occurrence of certain ecological forms in salmonids. © 2017 by the authors; Licensee MDPI, Basel, Switzerland.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorban' A.N., Mirkes Ye.M., Popova T.G., Sadovskii M.G.
Заглавие : A new approach to the study of the statistical properties of gene sequences
Место публикации : Biophysics. - 1993. - Vol. 38, Is. 5. - P783-787. - ISSN 00063509 (ISSN)
Аннотация: An essentially new method is proposed for studying the statistical properties of gene sequences (g.s.) based on construction of a frequency-correlation dictionary (f.c.d.) for the g.s. being investigated (the f.c.d. is the set of all subsequences (words) with a length from 1 to N together with the frequencies of their encounter in the g.s. studied). It is shown that a measure of the redundancy of the g.s. is the characteristic length of the word d* starting from which all the words in the g.s. are unique, i.e. have the frequency 1. В© 1994.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Popova L.Y., Kargatova T.V., Maksimova E.E., Belyavskaya V.A.
Заглавие : A study on the possibility of environmental adaptation of a Bacillus subtilis strain containing a recombinant plasmid with the gene of human interferon alpha 2
Колич.характеристики :5 с
Место публикации : Microbiology: MAIK NAUKA/INTERPERIODICA, 1997. - Vol. 66, Is. 6. - P637-641. - ISSN 0026-2617
Примечания : Cited References: 13
Предметные рубрики: GENETICALLY-MODIFIED MICROORGANISMS
Ключевые слова (''Своб.индексиров.''): microecosystem--bacillus subtilis--recombinant plasmid--interferon--adaptation
Аннотация: Adaptation of the Bacillus subtilis strain 2335/105 (Km(r)Inf(+)) containing a recombinant plasmid encoding the extracellular human interferon alpha 2 was studied under various conditions. Stability of the plasmid in the population of B. subtilis 2335/105 was estimated under nonselective conditions. The plasmid-free cells and cells with a low number of plasmid copies were found to accumulate progressively, constituting 80% of the population after 10 culture passages, indicating the poor competitiveness of cells carrying a high number of plasmid copies. The behavior of vegetative cells of the recombinant strain introduced into aquatic microcosms differing in trophic chain length was studied. Within the first 10 days, the lysis of vegetative cells of B. subtilis 2335/105 occurred; the number of viable spores was very low but remained constant for half a year.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Hellweger F.L., Kravchuk E.S., Novotny V., Gladyshev M.I.
Заглавие : Agent-based modeling of the complex life cycle of a cyanobacterium (Anabaena) in a shallow reservoir
Место публикации : Limnology and Oceanography. - 2008. - Vol. 53, Is. 4. - С. 1227-1241. - ISSN 00243590 (ISSN)
Ключевые слова (''Своб.индексиров.''): algal bloom--annual variation--cyanobacterium--ecological modeling--eulerian analysis--experimental study--lagrangian analysis--life cycle--nutrient availability--phytoplankton--population dynamics--reservoir--shallow water--survival--water column--bugach reservoir--eurasia--krasnoyarsk [russian federation]--russian federation--anabaena--anabaena flos-aquae
Аннотация: The cyanobacterium Anabaena flos-aquae and many other phytoplankton species have a complex life cycle that includes a resting stage (akinete). We present a new agent-based (also known as individual-based) model of Anabaena that includes the formation and behavior of akinetes. The model is part of a coupled Eulerian-Lagrangian model and can reproduce the main features of the observed seasonal and interannual population dynamics in Bugach Reservoir (Siberia), including an unexpectedly large bloom in a year with low nutrient concentrations. Model analysis shows that the internal loading of phosphorus (P) due to germination from the sediment bed is ?10% of the total input. However, most of the long-term nutrient uptake for Anabaena occurs in the sediment bed, which suggests that the sediment bed is not just a convenient overwintering location but may also be the primary source of nutrients. An in silico tracing experiment showed that most water column cells (?90%) originated from cells located in the sediment bed during the preceding winter. An in silico gene knockout experiment (akinete formation is prohibited) showed that the formation of resting stages is of critical importance to the survival of the population on an annual basis. A nutrient-reduction management scenario indicates that Anabaena densities increase because they are less sensitive to water column nutrient levels (because of the sediment bed source) than other species. В© 2008, by the American Society of Limnology and Oceanography, Inc.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Chiu H.H., Rogozin D.Y., Huang S.P., Degermendzhy A.G., Shieh W.Y., Tang S.L.
Заглавие : Aliidiomarina shirensis sp nov., a halophilic bacterium isolated from Shira Lake in Khakasia, southern Siberia, and a proposal to transfer Idiomarina maris to the genus Aliidiomarina
Колич.характеристики :6 с
Коллективы : National Science Council, Taiwan [NSC 99-2923-B-001-001-MY3]; Russian Foundation for Basic Research [14-04-01060-a]; Siberian Branch of Russian Academy of Sciences, joint Taiwan-Siberian Project [11]
Место публикации : Int. J. Syst. Evol. Microbiol.: SOC GENERAL MICROBIOLOGY, 2014. - Vol. 64. - С. 1334-1339. - ISSN 1466-5026, DOI 10.1099/ijs.0.057851-0. - ISSN 1466-5034
Примечания : Cited References: 22. - We thank Dr Egor S. Zadereev and Dr Vladimir V. Zykov at the Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, for assistance with sampling. This study was supported by Russia Taiwan joint project funding (NSC 99-2923-B-001-001-MY3) from the National Science Council, Taiwan, the Russian Foundation for Basic Research, Grant No. 14-04-01060-a and Siberian Branch of Russian Academy of Sciences, joint Taiwan-Siberian Project No. 11.
Предметные рубрики: SHALLOW COASTAL WATER
RIBOSOMAL-RNA GENE
EMENDED DESCRIPTION
PSEUDIDIOMARINA
PHYLOTYPES
SEQUENCE
TAIWAN
Аннотация: Strain AIS(T), an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that 'Aliidiomarina haloalkalitolerans', 'Allidiomarina sanyensis', Idiomarina maris and AIS(T) formed a distinct lineage. The sequence similarities between AIS(T) and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6-95.1 % and 94.0-96.9 %, respectively. The major isoprenoid quinone of AIS(T) was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C-17:0, iso-C-15:0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIS(T) represents a novel species of the genus Aliidiomarina, and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIST (=JCM 17761(T)=BCRC 80327(T)). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina mans be transferred to the genus Aliidiomarina.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Chiu H.-H., Rogozin D.Y., Huang S.-P., Degermendzhy A.G., Shieh W.Y., Tang S.-L.
Заглавие : Aliidiomarina shirensis sp. nov., a halophilic bacterium isolated from Shira Lake in Khakasia, southern Siberia, and a proposal to transfer Idiomarina maris to the genus Aliidiomarina
Место публикации : Int. J. Syst. Evol. Microbiol. - 2014. - Vol. 64, Is. PART 4. - Ст.057851. - С. 1334-1339. - ISSN 14665026 (ISSN) , DOI 10.1099/ijs.0.057851-0
Аннотация: Strain AIST, an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that 'Aliidiomarina haloalkalitolerans', 'Aliidiomarina sanyensis', Idiomarina maris and AIST formed a distinct lineage. The sequence similarities between AIST and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6-95.1 % and 94.0-96.9 %, respectively. The major isoprenoid quinone of AIST was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C17: 0, iso-C15: 0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIST represents a novel species of the genus Aliidiomarina, and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIST (= JCM 17761T = BCRC 80327T). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina. © 2014 IUMS.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lunina O.N., Bryantseva I.A., Akimov V.N., Rusanov I.I., Barinova E.S., Lysenko A.M., Rogozin D.Yu., Pimenov N.V.
Заглавие : Anoxygenic phototrophic bacterial community of Lake Shira (Khakassia)
Место публикации : Microbiology. - 2007. - Vol. 76, Is. 4. - С. 469-479. - ISSN 00262617 (ISSN) , DOI 10.1134/S0026261707040133
Ключевые слова (''Своб.индексиров.''): anoxygenic photosynthesis--anoxygenic phototrophic bacteria--meromictic brackish lakes--ahrensia kielensis--bacteria (microorganisms)--chlorobi--chlorobium--chlorobium limicola--chromatiaceae--lamprocystis purpurea--photobacteria--proteobacteria--rhodomicrobium--rhodovulum--rhodovulum strictum--thiocapsa roseopersicina
Аннотация: The anoxygenic phototrophic bacterial community of the brackish meromictic Lake Shira (Khakassia) was investigated in August 2001, July 2002, and February-March 2003. In all the periods of investigation, the prevailing microorganisms were purple sulfur bacteria similar to Lamprocystis purpurea in morphology and pigment composition. Their highest number (3 ? 10 5 cells/ml) was recorded in July 2002 at the depth of 15 m. According to 16S rRNA gene analysis, the strain of purple sulfur bacteria isolated in 2001 and designated ShAm01 exhibited 98.6% similarity to the type strain of Thiocapsa roseopersicina and 97.1-94.4% similarity to the type strains of Tca. pendens, Tca. litoralis, and Tca. rosea. The minor microorganisms of the anoxygenic phototrophic bacterial community within the period of investigation were nonsulfur purple bacteria phylogenetically close to Rhodovulum strictum (98.3% similarity, strain ShRb01), Ahrensia kielensis (of 93.9% similarity, strain ShRb02), Rhodomicrobium vannieli (of 99.7% similarity, strain ShRmc01), and green sulfur bacteria, phylogenetically close to Chlorobium limicola (of 98.7% similarity, strain ShCl03). В© 2007 Pleiades Publishing, Ltd.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Medvedeva S.E., Boyandin A., Lankin Y., Kotov D., Rodicheva E., Popova L.
Заглавие : BIOLUMBASE - The database of natural and transgenic bioluminescent organisms
Место публикации : Luminescence. - 2005. - Vol. 20, Is. 2. - С. 90-96. - ISSN 15227235 (ISSN) , DOI 10.1002/bio.809
Ключевые слова (''Своб.индексиров.''): bioluminescence--database--luminous bacteria--lux gene--marine--article--bacterial strain--bacterium culture--bacterium isolation--bioluminescence--data base--gene construct--medical information--transgenics--wide area network--bacteria--bacterial proteins--databases, factual--ecology--luminescence--luminescent proteins--marine biology--organisms, genetically modified--photobacterium--transgenes
Аннотация: The Institute of Biophysics SB RAS hosts and maintains a specialized collection of luminous bacteria (CCIBSO 836) containing over 700 strains isolated in various regions of the world's oceans. The culture collection is a source of lux genes and biologically active substances. The wide application of bioluminescence in medicine and ecology has given importance to analys-ing information on the structure and functioning of bioluminescence systems in natural and transgenic microorganisms, as well as on their features that are closely interrelated with bioluminescence. The aims of our BIOLUMBASE database are: gathering information on microorganisms with lux genes, their analysis and free access, and distribution of this data throughout the global network. The database includes two sections, natural and transgenic luminous microorganisms, and is updated by our own experimental results, the published literature and internet resources. For the future, a publicly available internet site for BIOLUMBASE is planned. This will list the strains and provide comprehensive information on the properties and functions of luminous bacteria, the mechanisms of regulation of bioluminescence systems, constructs with lux genes, and applications of bioluminescence in microbiology, ecology, medicine and biotechnology. It is noteworthy that this database will also be useful for evaluation of biological hazards of transgenic strains. Users will be able to carry out bibliographic and strain searches starting from any feature of interest. Copyright В© 2005 John Wiley & Sons, Ltd.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Krasitskaya V.V., Burakova L.P., Pyshnaya I.A., Frank L.A.
Заглавие : Bioluminescent reporters for identification of gene allelic variants
Колич.характеристики :8 с
Место публикации : Russ. J. Bioorg. Chem.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2012. - Vol. 38, Is. 3. - С. 298-305. - ISSN 1068-1620, DOI 10.1134/S1068162012030090
Примечания : 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.
Предметные рубрики: COELENTERAZINE-BINDING PROTEIN
RENILLA-MUELLERI
LUCIFERASE
PURIFICATION
SUBSTRATE
CLONING
CDNA
Ключевые слова (''Своб.индексиров.''): 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.
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bashmakova E. E., Krasitskaya V. V., Bondar A. A., Eremina E. N., Slepov E. V., Zukov R. A., Frank L. A.
Заглавие : Bioluminescent SNP genotyping technique: Development and application for detection of melanocortin 1 receptor gene polymorphisms
Место публикации : Talanta: Elsevier B.V., 2018. - Vol. 189. - С. 111-115. - ISSN 00399140 (ISSN) , DOI 10.1016/j.talanta.2018.06.057
Ключевые слова (''Своб.индексиров.''): ca2+-regulated photoprotein obelin--genotyping--melanocortin 1 receptor gene--single nucleotide polymorphisms (snp)--bioluminescence--clinical research--curricula--diagnosis--genes--oncology--biomedical research--clinical characteristics--development and applications--genotyping--healthy individuals--photoproteins--receptor genes--single-nucleotide polymorphisms--dermatology
Аннотация: SNP genotyping based on the reaction of specific primer extension with the following bioluminescent detection of its products was shown to be potentially applicable for biomedical exploration. The paper describes its elaboration and first application in extensive biomedical research concerning MC1R gene variants’ frequency and associations with clinical characteristics in melanoma patients of Eastern Siberia (Krasnoyarsk region, Russia). Polymorphisms rs 1805007 (R151C), rs 1805008 (R160W), and rs 1805009 (D294H) were detected in 174 DNA samples from patients with histologically proved diagnosis of cutaneous melanoma and in 200 samples from healthy individuals. All the results on bioluminescent SNP genotyping were confirmed by Sanger sequencing. Some features characteristic of the population were found, i.e. melanoma is mostly associated with R160W or R151C while variant D294H is extremely rare; simultaneous carriage of any two investigated variants is also strongly associated with melanoma; R151C is associated with ulceration and consequently the disease course is more aggressive, etc. The design of the technique allows fast evaluation of any known diagnostically important SNP frequencies and associations across population. © 2018 Elsevier B.V.
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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bauer S..., Schott A.K., Illarionova V..., Bacher A..., Huber R..., Fischer M...
Заглавие : Biosynthesis of tetrahydrofolate in plants: Crystal structure of 7,8-dihydroneopterin aldolase from Arabidopsis thaliana reveals a novel adolase class
Колич.характеристики :13 с
Место публикации : J. Mol. Biol.: ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, 2004. - Vol. 339, Is. 4. - P967-979. - ISSN 0022-2836, DOI 10.1016/j.jmb.2004.04.034
Примечания : Cited References: 66
Предметные рубрики: GTP CYCLOHYDROLASE-I
GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE
6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
ESCHERICHIA-COLI
DIHYDRONEOPTERIN ALDOLASE
FOLIC-ACID
ENZYMATIC SYNTHESIS
DIHYDROPTEROATE SYNTHASE
REACTION-MECHANISM
3-DIMENSIONAL STRUCTURE
Ключевые слова (''Своб.индексиров.''): tetrahydrofolate biosynthesis--aldolase classes--retroaldol reaction--purin binding--schiff base
Аннотация: Dihydroneopterin aldolase (DHNA) catalyses a retroaldol reaction yielding 6-hydroxymethyl-7,8-dihydropterin, a biosynthetic precursor of the vitamin, tetrahydrofolate. The enzyme is a potential target for antimicrobial and anti-parasite chemotherapy. A gene specifying a dihydroneopterin aldolase from Arabidopsis thaliana was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified to apparent homogeneity and crystallised using polyethylenglycol as the precipitating agent. The crystal structure was solved by X-ray diffraction analysis at 2.2 Angstrom resolution. The enzyme forms a D-4-symmetric homo-octamer. Each polypeptide chain is folded into a single domain comprising an antiparallel four-stranded beta-sheet and two long alpha-helices. Four monomers are arranged in a tetrameric ring, and two of these rings form a hollow cylinder. Well defined purine derivatives are found at all eight topologically equivalent active sites. The subunit fold of the enzyme is related to substructures of dihydroneopterin triphosphate epimerase, GTP cyclohydrolase I, and pyruvoyltetrahydropterin synthase, which are all involved in the biosynthesis of pteridine type cofactors, and to urate oxidase, although some members of that superfamily have no detectable sequence similarity Due to structural and mechanistical differences of DHNA in comparison with class I and class II aldolases, a new aldolase class is proposed. (C) 2004 Elsevier Ltd. All rights reserved.
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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Markova S.V., Golz S..., Frank L.A., Kalthof B..., Vysotski E.S.
Заглавие : Cloning and expression of cDNA for a luciferase from the marine copepod Metridia longa - A novel secreted bioluminescent reporter enzyme
Колич.характеристики :6 с
Место публикации : J. Biol. Chem.: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2004. - Vol. 279, Is. 5. - С. 3212-3217. - ISSN 0021-9258, DOI 10.1074/jbc.M309639200
Примечания : Cited References: 37
Предметные рубрики: VARGULA-HILGENDORFII LUCIFERASE
GREEN FLUORESCENT PROTEIN
GENE-EXPRESSION
FIREFLY LUCIFERASE
PROMOTER ACTIVITY
MAMMALIAN-CELLS
RECEPTOR
CANCER
PHOTOPROTEINS
LUMINESCENCE
Аннотация: Metridia longa is a marine copepod from which a blue bioluminescence originates as a secretion from epidermal glands in response to various stimuli. We demonstrate that Metridia luciferase is specific for coelenterazine to produce blue light (lambda(max)=480 nm). Using an expression cDNA library and functional screening, we cloned and sequenced the cDNA encoding the Metridia luciferase. The cDNA is an 897-bp fragment with a 656-bp open reading frame, which encodes a 219-amino acid polypeptide with a molecular weight of 23,885. The polypeptide contains an N-terminal signal peptide of 17 amino acid residues for secretion. On expression of the Metridia luciferase gene in mammalian Chinese hamster ovary cells the luciferase is detected in the culture medium confirming the existence of a naturally occurring signal peptide for secretion in the cloned luciferase. The novel secreted luciferase was tested in a practical assay application in which the activity of A2a and NPY2 G-protein-coupled receptors was detected. These results clearly suggest that the secreted Metridia luciferase is well suited as a reporter for monitoring gene expression and, in particular, for the development of novel ultra-high throughput screening technologies.
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14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kozhevnikov I.V., Volova T.G., Hai T., Steinbuchel A.
Заглавие : Cloning and molecular organization of the polyhydroxyalkanoic acid synthase gene (phaC) of Ralstonia eutropha strain B5786
Место публикации : Applied Biochemistry and Microbiology. - 2010. - Vol. 46, Is. 2. - С. 140-147. - ISSN 00036838 (ISSN) , DOI 10.1134/S0003683810020031
Ключевые слова (''Своб.индексиров.''): aeromonas punctata--cupriavidus necator--ectothiorhodospira shaposhnikovii--pseudomonas--pseudomonas sp. 61-3--rhodococcus--rhodococcus ruber--rhodospirillum rubrum--thiococcus pfennigii
Аннотация: Class I polyhydroxyalkanoic acid (PHA) synthase gene (phaC) of Ralstonia eutropha strain B5786 was cloned and characterized. R. eutropha B5786 features the ability to synthesize multicomponent PHAs with short- and medium-chain-length monomers from simple carbohydrate substrate. A correlation was made between the molecular structure of PHA synthase and substrate specificity and the ability of strain-producers to accumulate PHAs of this or that structure. A strong similarity of PHA synthase of R. eutropha strain B5786 with PHA synthase of R. eutropha strain H16, which, as opposed to strain B5786, enables to incorporate medium chain length PHAs if hexanoate is used as carbon source, exhibited 99%. A correlation between the structure of PHA synthase of B5786 strain with synthases of microorganisms which synthesize short and medium chain length PHAs similarly to B5786 strain, showed an identity level from 26 to 41% (homology with synthase of Rhodospirillum rubrum makes 41%, Ectothiorhodospira shaposhnikovii makes 26%, Aeromonas punctata makes 40%, Thiococcus pfennigii makes 28%, Rhodococcus ruber makes 38%, and with PhaCl and PhaC2 synthases of Pseudomonas sp. 61-3 makes 34 and 37%, respectively). This allows for speaking about the absence of a direct connection between the molecular organization of PHA synthases and their functional abilities, namely, the ability to synthesize PHAs of a particular composition. В© 2010 Pleiades Publishing, Ltd.
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15.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Stepanyuk G.A., Unch J..., Malikova N.P., Markova S.V., Lee J..., Vysotski E.S.
Заглавие : Coelenterazine-v ligated to Ca2+-triggered coelenterazine-binding protein is a stable and efficient substrate of the red-shifted mutant of Renilla muelleri luciferase
Колич.характеристики :9 с
Коллективы :
Место публикации : Anal. Bioanal. Chem.: SPRINGER HEIDELBERG, 2010. - Vol. 398, Is. 4. - С. 1809-1817. - ISSN 1618-2642, DOI 10.1007/s00216-010-4106-9
Примечания : Cited References: 39. - This work was supported by grant 09-04-12022 of the Russian Foundation for Basic Research, "Molecular and Cell Biology" program of Russian Academy of Sciences, by the SB RAS grant No. 2, and by the SB RAS Lavrentiev grant for Young Scientists.
Предметные рубрики: GREEN-FLUORESCENT PROTEIN
BIOLUMINESCENT REPORTER
CA2+-REGULATED PHOTOPROTEINS
RENIFORMIS LUCIFERASE
RECOMBINANT OBELIN
GENE-EXPRESSION
IN-VIVO
CDNA
CLONING
PURIFICATION
Ключевые слова (''Своб.индексиров.''): bioluminescence--coelenterazine--calcium--imaging
Аннотация: It has been shown that the coelenterazine analog, coelenterazine-v, is an efficient substrate for a reaction catalyzed by Renilla luciferase. The resulting bioluminescence emission maximum is shifted to a longer wavelength up to 40 nm, which allows the use of some "yellow" Renilla luciferase mutants for in vivo imaging. However, the utility of coelenterazine-v in small-animal imaging has been hampered by its instability in solution and in biological tissues. To overcome this drawback, we ligated coelenterazine-v to Ca2+-triggered coelenterazine-binding protein from Renilla muelleri, which apparently functions in the organism for stabilizing and protecting coelenterazine from oxidation. The coelenterazine-v bound within coelenterazine-binding protein has revealed a greater long-term stability at both 4 and 37 degrees C. In addition, the coelenterazine-binding protein ligated by coelenterazine-v yields twice the total light over free coelenterazine-v as a substrate for the red-shifted R. muelleri luciferase. These findings suggest the possibility for effective application of coelenterazine-v in various in vitro assays.
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16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Wu, Yu-Ting, Yang, Cheng-Yu, Chiang, Pei-Wen, Tseng, Ching-Hung, Chiu, Hsiu-Hui, Saeed, Isaam, Baatar, Bayanmunkh, Rogozin, Denis, Halgamuge, Saman, Degermendzhi, Andrei, Tang, Sen-Lin
Заглавие : Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
Колич.характеристики :21 с
Коллективы : Ministry of Science and Technology in Taiwan [NSC 99-2923-B-001-001-MY3, NSC 102-2923-B-001-004]; Russian Foundation for Basic Research [16-05-00091-a]; Russian Federation [NSh-9249.2016.5]
Место публикации : Front. Microbiol.: FRONTIERS MEDIA SA, 2018. - Vol. 9. - Ст.1763. - ISSN 1664-302X, DOI 10.3389/fmicb.2018.01763
Примечания : Cited References:103. - This research was supported by the Ministry of Science and Technology in Taiwan through the Taiwan-Russia Joint Project Grant NSC 99-2923-B-001-001-MY3 and NSC 102-2923-B-001-004 and the Russian Foundation for Basic Research, Grant No. 16-05-00091-a. The research was partially supported by the Council on grants from the President of the Russian Federation for support of leading scientific schools (grant NSh-9249.2016.5).
Предметные рубрики: BACTERIOPLANKTON COMMUNITY COMPOSITION
RIBOSOMAL-RNA GENES
ANTARCTIC
Ключевые слова (''Своб.индексиров.''): lake shunet--metagenomics--archaeal--bacterial and viral assemblages--meromictic lake
Аннотация: Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
WOS,
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17.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lesniak D.V., Popova L.I.
Заглавие : Conflict: induction-inhibition of transgene bacteria luminescence in studying expression of lux-genes
Место публикации : Biofizika. - 2002. - Vol. 47, Is. 6. - P1059-1063. - ISSN 00063029 (ISSN)
Ключевые слова (''Своб.индексиров.''): naphthalene derivative--salicylic acid derivative--article--bacterial gene--chemistry--chemoluminescence--culture medium--escherichia coli--gene expression regulation--genetics--metabolism--pseudomonas fluorescens--transgene--chemiluminescent measurements--culture media--escherichia coli--gene expression regulation, bacterial--genes, bacterial--naphthalenes--pseudomonas fluorescens--salicylates--transgenes
Аннотация: The relationship between the induction of the luminescent operon of lux-genes fused with the naphthalene and salicylate degradation genes and the inhibition of light emission caused by these compounds was studied. The quantitative correlations between these processes manifest themselves in the fact that light intensity linearly increased in a narrow concentration range of the inductor and then decreased due to the inhibition of the luminescence reaction itself, which is not related to the regulation of expression of lux-genes.
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18.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Volova, Tatiana, Sapozhnikova, Kristina, Zhila, Natalia
Заглавие : Cupriavidus necator B-10646 growth and polyhydroxyalkanoates production on different plant oils
Колич.характеристики :10 с
Коллективы : Project "Agropreparations of the new generation: a strategy of construction and realization" [074-02-2018-328]; Government of the Russian Federation; State assignment of the Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]
Место публикации : Int. J. Biol. Macromol.: ELSEVIER, 2020. - Vol. 164. - С. 121-130. - ISSN 0141-8130, DOI 10.1016/j.ijbiomac.2020.07.095. - ISSN 1879-0003(eISSN)
Примечания : Cited References:52. - This studywas financially supported by Project "Agropreparations of the new generation: a strategy of construction and realization" (Agreement No 074-02-2018-328) in accordance with Resolution No 220 of the Government of the Russian Federation of April 9, 2010, "On measures designed to attract leading scientists to the Russian institutions of higher learning" (polymer synthesis fromplant oils), and by the State assignment of the Ministry of Science and Higher Education of the Russian Federation No. FSRZ-2020-0006 (polymer properties).
Предметные рубрики: FATTY-ACID-COMPOSITION
PHA SYNTHASE GENE
PALM KERNEL OIL
Аннотация: The study addresses the growth of the wild-type strain Cupriavidus necator B-10646 and synthesis of polyhydroxyalkanoates by this strain on media containing plant oils with different compositions of fatty acids: palm, Siberian oilseed, and refined and unrefined sunflower seed oils. The study showed that the best carbon substrate was palm oil. Comparison of fatty acid compositions of the starting oils and unutilized residual substrates showed that C. necator B-10646 cells consumed the fatty acids from palm oil evenly while in experiments with other oils, they utilized polyenoic fatty acids first. Higher production parameters of the culture were obtained by preparation of emulsified oil medium using Tween 80 and sodium cocoyl glutamate as emulsifiers. All polyhydroxyalkanoate specimens were terpolymers that contained 3-hydroxybutyrate as the major component and minor amounts of 3-hydroxyvalerate (0.9-1.9 mol%) and 3-hydroxyhexanoate (0.5-1.1 mol%). Molecular weight of polyhydroxyalkanoate specimens depended on the type of plant oil and emulsifier. (C) 2020 Elsevier B.V. All rights reserved.
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19.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Medvedeva S.E., Boyandin A.N., Lankin Yu.P., Kotov D.A., Kargatova T.V., Rodicheva E.K., Popova L.Yu.
Заглавие : Database on natural and transgenic luminous microorganisms: "BIOLUMBASE"
Место публикации : Mikrobiologiya. - 2005. - Vol. 74, Is. 2. - С. 278-286. - ISSN 00263656 (ISSN)
Ключевые слова (''Своб.индексиров.''): bioluminescence--database--natural and transgenic luminous microorganisms--photoprotein--article--bacterial gene--bacterium--biotechnology--chemistry--ecology--factual database--genetics--luminescence--transgene--bacteria--biotechnology--databases, factual--ecology--genes, bacterial--luminescence--luminescent proteins--transgenes--bacteria (microorganisms)
Аннотация: The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with live genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.
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20.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Bashmakova E. E., Kudryavtsev A. N., Frank L. A.
Заглавие : Development of the method to produce functionally active recombinant streptavidin in escherichia coli cells
Место публикации : J. Sib. Fed. Univ. - Biol.: Siberian Federal University, 2020. - Vol. 13, Is. 2. - С. 218-229. - ISSN 19971389 (ISSN), DOI 10.17516/1997-1389-0324
Аннотация: Streptavidin is a homotetrameric protein produced by Streptomyces avidinii, each subunit of which binds biotin (vitamin H), forming a stable complex (Kd = 10-15 M). Streptavidin-biotin coreaction is widely used in analytical systems, for targeted delivery of compounds, for affinity purification, etc. The aim of this study was to develop a rational technique to produce functionally active recombinant streptavidin. Recombinant Escherichia coli strains producing minimal core and full-sized streptavidin variants were obtained. The E. coli BL21 Codon Plus (DE3) RIPL, as host cells, and the pET19b plasmid carrying gene of minimally-sized core (miniSAV) or full-sized (SAV) streptavidin were used. Synthesis of miniSAV results in its localization as insoluble inclusion bodies. Denatured miniSAV yield was 130 mg per liter of E. coli c ulture. T he r enaturation g ives o nly 10- 15 % of the functionally active protein. Full-sized streptavidin localizes in the cytoplasm in a soluble state, but its toxicity causes low yield of the protein (10-13 mg per liter of the culture). The induction of SAV synthesis at the end of the logarithmic stage of cell growth was found to increase the yield of SAV approximately 2-fold. The yield of functionally active protein was 30 mg per liter culture. SAV was produced practically in individual state after affine chromatography on 2-iminobiotin agarose. One molecule of full-sized streptavidin bound 3.9 biotin molecules as was shown by colorimetric analysis using HABA (4-hydroxyazobenzene-2-carboxylic acid). Both streptavidins form sandwichtype complexes with biotinylated molecules in solid-phase microassay conditions. E. coli BL21 Codon Plus (DE3) RIPL/pET19bSAV strain was stable during storage with 20 % glycerol at -70 °C, which was shown by repeated two-year reseeding. The streptavidin producing strain (E. coli BL21 Codon Plus (DE3) RIPL/pET19bSAV) is deposited in the Collection for extremophile microorganisms and type cultures (Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk), No. 3505. The method for producing functionally active recombinant streptavidin developed in this study ensures its availability for biotechnological research. © Siberian Federal University. All rights reserved.
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