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Comparison of symbol sequences: No editing, no alignment [Text] / M. G. Sadovsky // Open Syst. Inf. Dyn. - 2002. - Vol. 9, Is. 1. - P. 19-36, DOI 10.1023/A:1014278811727. - Cited References: 12 . - ISSN 1230-1612

РУБ Thermodynamics + Computer Science, Information Systems + Mathematics, Applied + Mechanics + Physics, Mathematical + Statistics & Probability
Рубрики:
MULTIPLE
Аннотация: The new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires no string editing or other transformations of the compared objects. The comparison is provided through a calculation of the specific entropy of a frequency dictionary against the special dictionary called the hybrid one; the latter is the statistical ancestor of the group of sequences to be compared. Some applications of the method developed to genetics, bioinformatics, and linguistics axe discussed.

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

Доп.точки доступа:
Sadovsky, M.G.

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On the problem of genome redundancy in viruses and prokaryotes [Text] / M. G. Sadovsky // Russ. J. Genet. - 2002. - Vol. 38, Is. 5. - P. 575-581, DOI 10.1023/A:1015503617023. - Cited References: 10 . - ISSN 1022-7954

РУБ Genetics & Heredity

Аннотация: A specific index of nucleotide sequence redundancy, the specific restriction length of a finite frequency dictionary, was determined for a complete set of genes in some viral genomes and a genome of a bacterium, Bacillus subtilis. The distribution of the gene number over the specific restriction length was shown to be bimodal for viral genomes and unimodal for the Bac. subtilis genome. These results agree with earlier data.

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

Доп.точки доступа:
Sadovsky, M.G.

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The method to compare nucleotide sequences based on the minimum entropy principle [Text] / M. G. Sadovsky // Bull. Math. Biol. - 2003. - Vol. 65, Is. 2. - P. 309-322, DOI 10.1016/S0092-8240(02)00107-6. - Cited References: 20 . - ISSN 0092-8240

РУБ Biology + Mathematical & Computational Biology
Рубрики:
GENOME
Аннотация: A new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires neither string editing, nor other transformations of the compared objects. The comparison is executed through a calculation of the specific entropy of a frequency dictionary against the special dictionary called the hybrid one; this latter is the statistical ancestor of the group of sequences under comparison. Some applications of the developed method in the fields of genetics and bioinformatics are discussed. (C) 2003 Society for Mathematical Biology. Published by Elsevier Science Ltd. All rights reserved.

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

Доп.точки доступа:
Sadovsky, M.G.

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Information capacity of symbol sequences [Text] / M. G. Sadovsky // Open Syst. Inf. Dyn. - 2002. - Vol. 9, Is. 1. - P. 37-49, DOI 10.1023/A:1014230928565. - Cited References: 23 . - ISSN 1230-1612

РУБ Thermodynamics + Computer Science, Information Systems + Mathematics, Applied + Mechanics + Physics, Mathematical + Statistics & Probability
Рубрики:
REDUNDANCY
INTRONS
Аннотация: The information capacity of sequences is considered through the calculation of specific entropy of their frequency dictionary. The specific entropy was calculated against the reconstructed dictionary which bears the most probable continuations of shorter strings. The measure developed allows to distinguish the sequences both from the random ones, and those with high level of (rather simple) order. Some applications of the developed methodology to genetics, bioinformatics, and linguistics axe discussed.

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

Доп.точки доступа:
Sadovsky, M.G.

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High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH [Text] / Z. . Wawrzak [et al.] // Proteins. - 1999. - Vol. 35, Is. 4. - P. 425-439, DOI 10.1002/(SICI)1097-0134(19990601)35:4425::AID-PROT63.0.CO;2-1. - Cited References: 33 . - ISSN 0887-3585

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
MAGNAPORTHE-GRISEA
   HEMAGGLUTININ
   GLYCOPROTEIN
   REFINEMENT
   MELANIN
   DISEASE
   SITE
Кл.слова (ненормированные):
structure-based design -- enzyme inhibitors -- X-ray crystallography -- fungicides -- melanin biosynthesis
Аннотация: Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at preventing the fungal disease caused by Magnaporthe grisea. A method for cocrystallization of enzyme with inhibitors at neutral pH has produced several crystal structures of enzyme-inhibitor complexes at resolutions ranging from 1.5 to 2.2 Angstrom Four high resolution structures of different enzyme-inhibitor complexes are described. In contrast to the original X-ray structure of the enzyme, the four new structures have well-defined electron density for the loop region comprising residues 115-119 and a different conformation between residues 154 and 160. The structure of the enzyme complex with an aminoquinazoline inhibitor showed that the inhibitor is in a position to form a hydrogen bond with the amide of the Asn131 side chain and with two water molecules in a fashion similar to the salicylamide inhibitor in the original structure, thus confirming design principles. The aminoquinazoline structure also allows for a more confident assignment of donors and accepters in the hydrogen bonding network, The structures of the enzyme complexes with two dichlorocyclopropane carboxamide inhibitors showed the two chlorine atoms nearly in plane with the amide side chain of Asn131. The positions of Phe53 and Phe158 are significantly altered in the new structures in comparison to the two structures obtained from crystals grown at acidic pH, The multiple structures help define the mobility of active site amino acids critical for catalysis and inhibitor binding. Proteins 1999;35:425-439. (C) 1999 Wiley-Liss, Inc.

WOS
Держатели документа:
Dupont Co, Stine Haskell Res Ctr, Agr Prod, Newark, DE 19714 USA
Dupont Co, Expt Stn, Life Sci, Wilmington, DE USA
Karolinska Inst, Dept Med Biochem & Biophys, Stockholm, Sweden
Russian Acad Sci, Inst Biophys, Krasnoyarsk, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Wawrzak, Z...; Sandalova, T...; Steffens, J.J.; Basarab, G.S.; Lundqvist, T...; Lindqvist, Y...; Jordan, D.B.

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Green flavoprotein from P. leiognathi: purification, characterization and identification as the product of the lux G(N) gene / A. A. Raibekas // Journal of bioluminescence and chemiluminescence. - 1991. - Vol. 6, Is. 3. - P. 169-176 . - ISSN 0884-3996
Кл.слова (ненормированные):
bacterial protein -- flavoprotein -- amino acid sequence -- article -- bacterial gene -- chemistry -- genetics -- isolation and purification -- luminescence -- molecular genetics -- molecular weight -- Photobacterium -- Amino Acid Sequence -- Bacterial Proteins -- Flavoproteins -- Genes, Bacterial -- Luminescence -- Molecular Sequence Data -- Molecular Weight -- Photobacterium -- Support, U.S. Gov't, P.H.S.
Аннотация: A green flavoprotein (GFP) was isolated and purified to homogeneity from Photobacterium leiognathi, strain 208. GFP is a homodimer of molecular weight 54,000 and contains two molecules of an unusual flavin per molecule of protein. Various biochemical characteristics including isoelectric point, trypsin and chymotrypsin degradation, SDS and temperature influence on subunit dissociation and the dissociation of the flavin chromophore, were investigated. The sequence of 23 N-terminal amino acids was determined and found to be concurrent with the N-terminal amino acid sequence encoded by the lux G(N) gene of P. leiognathi. This fact suggests that GFP is a structural component of the Photobacterium luminescence system.

Scopus
Держатели документа:
Institute of Biophysics, USSR Academy of Sciences, Krasnoyarsk. : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Raibekas, A.A.

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Ca(2+)-activator of the luminescence system of the earthworms Henlea sp., (Annelida: Clitellata: Oligochaeta: Enchytraeidae) / N. S. Rodionova, V. S. Bondar, V. N. Petushkov // Doklady. Biochemistry and biophysics. - 2002. - Vol. 386. - P260-263 . - ISSN 1607-6729
Кл.слова (ненормированные):
calcium -- divalent cation -- edetic acid -- luciferase -- luciferin -- metal -- animal -- annelid worm -- article -- chemistry -- dose response -- enzymology -- genetics -- kinetics -- luminescence -- metabolism -- Animals -- Calcium -- Cations, Divalent -- Dose-Response Relationship, Drug -- Edetic Acid -- Firefly Luciferin -- Kinetics -- Luciferases -- Luminescent Measurements -- Metals -- Oligochaeta

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036 Russia. : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Rodionova, N.S.; Bondar, V.S.; Petushkov, V.N.

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The comparative redundancy of genes of various organisms and viruses / A. N. Gorban [и др.] // Genetika. - 1993. - Vol. 29, Is. 9. - P. 1413-1419 . - ISSN 0016-6758
Кл.слова (ненормированные):
article -- dna content -- evolution -- genome -- nonhuman -- restriction mapping -- virus -- amino acid sequence -- comparative study -- gene frequency -- human -- molecular genetics -- nucleotide sequence -- restriction mapping -- virus gene -- Amino Acid Sequence -- Base Sequence -- Comparative Study -- English Abstract -- Gene Frequency -- Genes, Viral -- Human -- Molecular Sequence Data -- Restriction Mapping

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Gorban, A.N.; Mirkes, E.M.; Popova, T.G.; Sadovsky, M.G.

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Conflict: induction-inhibition of transgene bacteria luminescence in studying expression of lux-genes / D. V. Lesniak, L. I. Popova // Biofizika. - 2002. - Vol. 47, Is. 6. - P. 1059-1063 . - ISSN 0006-3029
Кл.слова (ненормированные):
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.

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk-36, Akademgorodok, 660036 Russia. : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Lesniak, D.V.; Popova, L.I.

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10.

Comparison of real frequencies of strings vs. the expected ones reveals the information capacity of macromoleculae [Text] / M. G. Sadovsky // J. Biol. Phys. - 2003. - Vol. 29, Is. 1. - P. 23-38, DOI 10.1023/A:1022554613105. - Cited References: 45 . - ISSN 0092-0606

РУБ Biophysics
Рубрики:
DNA-SEQUENCE
ENTROPY
REDUNDANCY
Кл.слова (ненормированные):
dictionary -- entropy -- information capacity -- Markov model -- ordered sequence -- random sequence -- reconstructed dictionary -- specific entropy
Аннотация: The information capacity of nucleotide sequences is defined through the calculation of specific entropy of their frequency dictionary. The specific entropy of the frequency dictionary is calculated against the reconstructed dictionary; this latter bears the most probable continuations of the shorter strings. This developed measure allows to distinguish the sequences both from the randons ones, and from those with high level of (rather simple) order. Some implications of the developed methodology in the fields of genetics, bioinformatics, and molecular biology are discussed.

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

Доп.точки доступа:
Sadovsky, M.G.

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11.

Global data set of long-term summertime vertical temperature profiles in 153 lakes / R. M. Pilla, E. M. Mette, C. E. Williamson [et al.] // Sci. Data. - 2021. - Vol. 8, Is. 1. - Ст. 200, DOI 10.1038/s41597-021-00983-y . - ISSN 2052-4463
Аннотация: Climate change and other anthropogenic stressors have led to long-term changes in the thermal structure, including surface temperatures, deepwater temperatures, and vertical thermal gradients, in many lakes around the world. Though many studies highlight warming of surface water temperatures in lakes worldwide, less is known about long-term trends in full vertical thermal structure and deepwater temperatures, which have been changing less consistently in both direction and magnitude. Here, we present a globally-expansive data set of summertime in-situ vertical temperature profiles from 153 lakes, with one time series beginning as early as 1894. We also compiled lake geographic, morphometric, and water quality variables that can influence vertical thermal structure through a variety of potential mechanisms in these lakes. These long-term time series of vertical temperature profiles and corresponding lake characteristics serve as valuable data to help understand changes and drivers of lake thermal structure in a time of rapid global and ecological change. © 2021, The Author(s).

Scopus
Держатели документа:
Miami University, Department of Biology, Oxford, OH, United States
Belarusian State University, Faculty of Biology, Minsk, Belarus
Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Berlin, Germany
INRAE, University of Savoie Mont-Blanc, CARRTEL, Thonon-les-Bains, France
University of Comahue: INIBIOMA, CONICET, Neuquen, Argentina
University of Shiga Prefecture, Hikone, Shiga, Japan
University of Nevada, Reno, Global Water Center, Reno, NV, United States
Uppsala University, Department of Ecology and Genetics/Limnology, Uppsala, Sweden
University of Montana, Flathead Lake Biological Station, Polson, Montana, United States
Universidad del Valle de Guatemala Centro de Estudios Atitlan, Guatemala, Guatemala
University of Innsbruck, Research Department for Limnology Mondsee, Mondsee, Austria
Mohonk Preserve, Daniel Smiley Research Center, New Paltz, NY, United States
UK Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster, United Kingdom
Seqwater, Ipswich, QLD, Australia
Florida International University, Department of Biological Sciences and Institute of Environment, Miami, FL, United States
U.S. National Park Service, Crater Lake National Park, Crater Lake, OR, United States
University of Oklahoma, Department of Biology, Norman, OK, United States
Griffith University, Australian Rivers Institute, Nathan, Australia
University of Florida, Gainesville, FL, United States
University of Oslo, Department of Biosciences, Oslo, Norway
LUBW Landesanstalt fur Umwelt, Messungen und Naturschutz Baden-Wurttemberg, Institut fur Seenforschung, Langenargen, Germany
IISD Experimental Lake Area Inc., Winnipeg, MB, Canada
FAO, BELSPO, Brussels, Belgium
University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dubendorf, Switzerland
CSIRO, Land and Water, Canberra, Australia
Laurentian University, Cooperative Freshwater Ecology Unit, Sudbury, Ontario, Canada
Fairfield University, Biology Department, Fairfield, CT, United States
University of Minnesota, Itasca Biological Station and Laboratories, Lake Itasca, MN, United States
Finnish Environment Institute SYKE, Freshwater Center, Helsinki, Finland
A.N. Severtsov Institute of Ecology and Evolution of The Russian Academy of Sciences, Laboratory of Ecology of Water Communities and Invasions, Moscow, Russian Federation
Zurich Water Supply, City of Zurich, Zurich, Switzerland
University of Regina, Institute of Environmental Change and Society, Regina, SK, Canada
Milano-Bicocca University, Milan, Italy
University of Applied Sciences and Arts of Southern Switzerland, Department for Environment, Constructions and Design, Canobbio, Switzerland
Kamchatka Research Institute of Fisheries & Oceanography, now Kamchatka Branch of Russian Federal Research Institute of Fisheries and Oceanography, Petropavlovsk-Kamchatsky, Russian Federation
University of Wisconsin, Center for Limnology, Boulder Junction, WI, United States
Federal Agency for Water Management, Institute for Aquatic Ecology and Fisheries Management, Mondsee, Austria
University of California Santa Barbara, Department of Ecology, Evolution and Marine Biology, Santa Barbara, California, United States
University of Waikato, Environmental Research Institute, Hamilton, New Zealand
Ryerson University, Department of Chemistry and Biology, Toronto, ON, Canada
University of Hamburg, Department of Biology, Hamburg, Germany
Dominion Diamond Mines, Environment Department, Calgary, AB, Canada
Ontario Ministry of the Environment, Conservation and Parks, Dorset Environmental Science Centre, Dorset, ON, Canada
Irkutsk State University, Institute of Biology, Irkutsk, Russian Federation
University of Liege, Chemical Oceanography Unit, Institut de Physique (B5A), Liege, Belgium
SUNY New Paltz, Biology Department, New Paltz, NY, United States
The Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
CNR Water Research institute, Verbania, Verbania, Pallanza, Italy
Krasnoyarsk Scientific Center SB RAS, Institute of Biophysics, Krasnoyarsk, Russian Federation
University of California Davis, Department of Environmental Science and Policy, Davis, CA, United States
Fondazione Edmund Mach, Research and Innovation Centre, San Michele all’Adige, Italy
University of Maine, Climate Change Institute, Orono, ME, United States
University of Turku, Turku, Finland
Universite Laval, Departments of Biology and Geography, Quebec, Canada
University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, United States
The Technical University of Kenya, Department of Geosciences and the Environment, Nairobi, Kenya
University of Innsbruck, Department of Ecology, Innsbruck, Austria
University of Konstanz, Limnological Institute, Konstanz, Germany
Dickinson College, Department of Environmental Science, Carlisle, PA, United States
Archbold Biological Station, Venus, FL, United States
University of Michigan, Biological Station, Pellston, MI, United States
Vrije Universiteit Brussel, Department of Hydrology and Hydraulic Engineering, Brussels, Belgium
ETH Zurich, Institute for Atmospheric and Climate Science, Zurich, Switzerland
National Institute of Water & Atmospheric Research, Hamilton, New Zealand
University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
Cary Institute of Ecosystem Studies, Millbrook, NY, United States

Доп.точки доступа:
Pilla, R. M.; Mette, E. M.; Williamson, C. E.; Adamovich, B. V.; Adrian, R.; Anneville, O.; Balseiro, E.; Ban, S.; Chandra, S.; Colom-Montero, W.; Devlin, S. P.; Dix, M. A.; Dokulil, M. T.; Feldsine, N. A.; Feuchtmayr, H.; Fogarty, N. K.; Gaiser, E. E.; Girdner, S. F.; Gonzalez, M. J.; Hambright, K. D.; Hamilton, D. P.; Havens, K.; Hessen, D. O.; Hetzenauer, H.; Higgins, S. N.; Huttula, T. H.; Huuskonen, H.; Isles, P. D.F.; Joehnk, K. D.; Keller, W. B.; Klug, J.; Knoll, L. B.; Korhonen, J.; Korovchinsky, N. M.; Koster, O.; Kraemer, B. M.; Leavitt, P. R.; Leoni, B.; Lepori, F.; Lepskaya, E. V.; Lottig, N. R.; Luger, M. S.; Maberly, S. C.; MacIntyre, S.; McBride, C.; McIntyre, P.; Melles, S. J.; Modenutti, B.; Muller-Navarra, D. C.; Pacholski, L.; Paterson, A. M.; Pierson, D. C.; Pislegina, H. V.; Plisnier, P. -D.; Richardson, D. C.; Rimmer, A.; Rogora, M.; Rogozin, D. Y.; Rusak, J. A.; Rusanovskaya, O. O.; Sadro, S.; Salmaso, N.; Saros, J. E.; Sarvala, J.; Saulnier-Talbot, E.; Schindler, D. E.; Shimaraeva, S. V.; Silow, E. A.; Sitoki, L. M.; Sommaruga, R.; Straile, D.; Strock, K. E.; Swain, H.; Tallant, J. M.; Thiery, W.; Timofeyev, M. A.; Tolomeev, A. P.; Tominaga, K.; Vanni, M. J.; Verburg, P.; Vinebrooke, R. D.; Wanzenbock, J.; Weathers, K.; Weyhenmeyer, G. A.; Zadereev, E. S.; Zhukova, T. V.

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12.

Deeper waters are changing less consistently than surface waters in a global analysis of 102 lakes / R. M. Pilla, C. E. Williamson, B. V. Adamovich [et al.] // Sci. Rep. - 2020. - Vol. 10, Is. 1. - Ст. 20514, DOI 10.1038/s41598-020-76873-x . - ISSN 2045-2322
Аннотация: Globally, lake surface water temperatures have warmed rapidly relative to air temperatures, but changes in deepwater temperatures and vertical thermal structure are still largely unknown. We have compiled the most comprehensive data set to date of long-term (1970–2009) summertime vertical temperature profiles in lakes across the world to examine trends and drivers of whole-lake vertical thermal structure. We found significant increases in surface water temperatures across lakes at an average rate of + 0.37 °C decade?1, comparable to changes reported previously for other lakes, and similarly consistent trends of increasing water column stability (+ 0.08 kg m?3 decade?1). In contrast, however, deepwater temperature trends showed little change on average (+ 0.06 °C decade?1), but had high variability across lakes, with trends in individual lakes ranging from ? 0.68 °C decade?1 to + 0.65 °C decade?1. The variability in deepwater temperature trends was not explained by trends in either surface water temperatures or thermal stability within lakes, and only 8.4% was explained by lake thermal region or local lake characteristics in a random forest analysis. These findings suggest that external drivers beyond our tested lake characteristics are important in explaining long-term trends in thermal structure, such as local to regional climate patterns or additional external anthropogenic influences. © 2020, The Author(s).

Scopus
Держатели документа:
Department of Biology, Miami University, Oxford, OH, United States
Faculty of Biology, Belarusian State University, Minsk, Belarus
Department of Ecosystems Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
Freie Universitat Berlin, Berlin, Germany
CARRTEL, INRAE, Thonon-les-Bains, France
Global Water Center, University of Nevada, Reno, NV, United States
Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
Flathead Lake Biological Station, University of Montana, Polson, MT, United States
Instituto de Investigacones, Universidad del Valle de Guatemala, Guatemala, Guatemala
Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
Department of Biological Sciences, Florida International University, Miami, FL, United States
Crater Lake National Park, U.S. National Park Service, Crater Lake, OR, United States
Department of Biology, Plankton Ecology and Limnology Lab and Geographical Ecology Group, University of Oklahoma, Norman, OK, United States
Australian Rivers Institute, Griffith University, Nathan, Australia
Florida Sea Grant and UF/IFAS, University of Florida, Gainesville, FL, United States
Department of Biosciences, University of Oslo, Oslo, Norway
IISD Experimental Lake Area Inc, Winnipeg, MB, Canada
Freshwater Center, Finnish Environment Institute SYKE, Helsinki, Finland
Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, Switzerland
Land and Water, CSIRO, Canberra, Australia
Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
Cooperative Freshwater Ecology Unit, Laurentian University, Ramsey Lake Road, Sudbury, ON, Canada
Itasca Biological Station and Laboratories, University of Minnesota, Lake Itasca, MN, United States
Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada
Institute for Global Food Security, Queen’s University Belfast, Belfast Co., Antrim, United Kingdom
Department for Environment, Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland, Canobbio, Switzerland
Federal Agency for Water Management AT, Mondsee, Austria
Lake Ecosystems Group, UK Centre for Ecology & Hydrology, Lancaster, United Kingdom
Bren School of Environmental Science and Management, University of California, Santa Barbara, CA, United States
Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
Department of Biology, University of Hamburg, Hamburg, Germany
Institute of Biology, Irkutsk State University, Irkutsk, Russian Federation
University of Liege, Liege, Belgium
Department of Biology, SUNY New Paltz, New Paltz, NY, United States
The Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
CNR Water Research Institute, Verbania Pallanza, Italy
Dorset Environmental Science Centre, Ontario Ministry of the Environment, Conservation, and Parks, Dorset, ON, Canada
Department of Environmental Science and Policy, University of California Davis, Davis, CA, United States
Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele All’Adige, Italy
Climate Change Institute, University of Maine, Orono, ME, United States
Centre D’Etudes Nordiques, Universite Laval, Quebec, QC, Canada
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States
Surface Waters-Research and Management, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
Department of Geosciences and the Environment, The Technical University of Kenya, Nairobi, Kenya
Department of Ecology, University of Innsbruck, Innsbruck, Austria
Limnological Institute, University of Konstanz, Konstanz, Germany
Department of Environmental Science, Dickinson College, Carlisle, PA, United States
Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
Institute for Atmospheric and Climate Science, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
National Institute of Water and Atmospheric Research, Hamilton, New Zealand
Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
Institute of Biophysics, Krasnoyarsk Scientific Center Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Pilla, R. M.; Williamson, C. E.; Adamovich, B. V.; Adrian, R.; Anneville, O.; Chandra, S.; Colom-Montero, W.; Devlin, S. P.; Dix, M. A.; Dokulil, M. T.; Gaiser, E. E.; Girdner, S. F.; Hambright, K. D.; Hamilton, D. P.; Havens, K.; Hessen, D. O.; Higgins, S. N.; Huttula, T. H.; Huuskonen, H.; Isles, P. D.F.; Joehnk, K. D.; Jones, I. D.; Keller, W. B.; Knoll, L. B.; Korhonen, J.; Kraemer, B. M.; Leavitt, P. R.; Lepori, F.; Luger, M. S.; Maberly, S. C.; Melack, J. M.; Melles, S. J.; Muller-Navarra, D. C.; Pierson, D. C.; Pislegina, H. V.; Plisnier, P. -D.; Richardson, D. C.; Rimmer, A.; Rogora, M.; Rusak, J. A.; Sadro, S.; Salmaso, N.; Saros, J. E.; Saulnier-Talbot, E.; Schindler, D. E.; Schmid, M.; Shimaraeva, S. V.; Silow, E. A.; Sitoki, L. M.; Sommaruga, R.; Straile, D.; Strock, K. E.; Thiery, W.; Timofeyev, M. A.; Verburg, P.; Vinebrooke, R. D.; Weyhenmeyer, G. A.; Zadereev, E.

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13.

Single-cell genomics-based analysis reveals a vital ecological role of thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia / Y.-T. Wu, P.-W. Chiang, K. Tandon [et al.] // Microb. Genomics. - 2021. - Vol. 7, Is. 12. - Ст. 000712, DOI 10.1099/mgen.0.000712 . - ISSN 2057-5858
Кл.слова (ненормированные):
Flow cytometry -- Lake Shunet -- Purple sulfur bacteria -- Single-cell genomics -- genomic DNA -- RNA 16S -- Article -- bioinformatics -- carbon metabolism -- Enterobacter -- fluorescence activated cell sorting -- gene amplification -- gene ontology -- high throughput sequencing -- metagenomics -- microbial community -- microbial diversity -- molecular genetics -- nitrogen metabolism -- nonhuman -- nucleotide sequence -- phylogenetic tree -- phylogeny -- polymerase chain reaction -- Sanger sequencing -- Thiocapsa
Аннотация: Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic–anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes. © 2021 The Authors.

Scopus
Держатели документа:
Department of Forestry, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan
Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
Institute of Biophysics, Siberian Division of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Wu, Y. -T.; Chiang, P. -W.; Tandon, K.; Rogozin, D. Y.; Degermendzhy, A. G.; Tang, S. -L.

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14.

FOXC1-Mediated Effects of miR-204-5p on Melanoma Cell Proliferation / I. Y. Dubovtseva, M. B. Aksenenko, E. D. Nikolaeva [и др.] // Mol Biol (Mosk). - 2021. - Vol. 55, Is. 4. - С. 667-675, DOI 10.31857/S0026898421030058 . - ISSN 0026-8984
Кл.слова (ненормированные):
BRO -- dormant cancer cells -- FOXC1 -- melanoma -- miR-204-5p -- miRNA -- siRNA -- SK-MEL-2 -- forkhead transcription factor -- FOXC1 protein, human -- microRNA -- MIRN204 microRNA, human -- cell motion -- cell proliferation -- genetics -- human -- melanoma -- tumor cell line -- Cell Line, Tumor -- Cell Movement -- Cell Proliferation -- Forkhead Transcription Factors -- Humans -- Melanoma -- MicroRNAs
Аннотация: MicroRNAs epigenetically regulate physiological and pathological processes. Previously, we found that miR-204-5p is expressed at low levels in melanoma cells, and an increase in its level leads to a change in proliferation, migration, and invasion of these cancer cells. Now, using bioinformatics analysis, it has been shown that the target of miR-204-5p is FOXC1 transcription factor, which is implicated in carcinogenesis. Using the luciferase reporter assay, it was found that miR-204-5p suppresses expression of the FOXC1 gene by binding to its 3' non-coding region. Transfection of small interfering RNA (siRNA) targeting FOXC1 into melanoma cells caused a decrease in miR-204-5p levels, which is consistent with the generally accepted concept of feedback regulation of miRNA expression by target genes. According to the results of the MTT test and fluorescence microscopy, the proliferation level of melanoma cells under the influence of siRNA to FOXC1 decreased 72 h after transfection. Changes in the ratio of cells by cell cycle phase were analyzed using flow cytometry. Regulatory relationships between FOXC1 and miR-204-5p, and an inhibitory effect of FOXC1 knockdown on melanoma cell proliferation were revealed. Based on the results, it can be assumed that miR-204-5p regulates proliferation of melanoma cells by affecting FOXC1 expression.

Scopus
Держатели документа:
Voino-Yasenetsky Krasnoyarsk State Medical University, Ministry of Health of the Russian Federation, Krasnoyarsk, 660022, Russian Federation
Siberian Branch of the Russian Academy of Sciences, Research Institute for Medical Problems in the North, Krasnoyarsk, 660022, Russian Federation
Biophysics Institute of the Siberian Branch of the RAS - Division of Federal Research Center "Krasnoyarsk Scientific Center of the Siberian Branch of the RAS", Krasnoyarsk, 660022, Russian Federation

Доп.точки доступа:
Dubovtseva, I. Y.; Aksenenko, M. B.; Nikolaeva, E. D.; Averchuk, A. S.; Moshev, A. V.; Savchenko, A. A.; Markova, S. V.; Ruksha, T. G.

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15.

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
COMET ASSAY
REPAIR
CELLS
Аннотация: The effect of gamma-radiation on the level of nuclear DNA damage in onion seedlings (Allium-test) was studied using the comet assay. DNA breaks were first found in cells of onion seedlings exposed to low-dose radiation (

WOS
Держатели документа:
Russian Acad Sci, Siberian Branch, Krasnoyarsk Sci Ctr, Inst Biophys, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Inst Cytol & Genet, Siberian Branch, Novosibirsk 630090, Russia.
Novosibirsk State Univ, Novosibirsk 630090, Russia.
Russian Acad Sci, Res Inst Med Genet, Tomsk Natl Res Med Ctr, Tomsk 634058, Russia.

Доп.точки доступа:
Bolsunovsky, A. Ya.; Dementyev, D. V.; Frolova, T. S.; Trofimova, E. A.; Iniatkina, E. M.; Vasilyev, S. A.; Sinitsyna, O. I.; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [18-44-240001]; Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences

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16.

Low doses of gamma-radiation induce SOS response and increase mutation frequency in Escherichia coli and Salmonella typhimurium cells / A. Bolsunovsky [et al.] // Ecotoxicol. Environ. Saf. - 2016. - Vol. 134. - P233-238, DOI 10.1016/j.ecoenv.2016.09.009 . - ISSN 0147-6513
Кл.слова (ненормированные):
Absorbed dose -- Ames test -- Dose rate -- Mutation rate -- SOS chromotest -- Ames test -- cell death -- DNA repair -- Escherichia coli -- experimental model -- gamma radiation -- limit of detection -- long term exposure -- mutation rate -- nonhuman -- SOS chromotest -- Bacteria (microorganisms) -- Escherichia coli -- Salmonella typhimurium
Аннотация: This study addresses use of two bacterial test systems (the Ames test and the SOS chromotest) to estimate the effects of low doses of γ-radiation. The most substantial increases in induction of SOS response and mutation frequencies were observed in the first 24 h of exposure to γ-radiation as compared to the cells in the exposure-free control. Gamma-radiation also impaired growth and survival of S. typhimurium cells in the first 24 h. The effects were attenuated at lower exposure doses and at longer exposure times. In the experiments conducted in this study, at 96 h of exposure, the values of some of the γ-radiation effects were lower than the MID (minimum inducing dose) detection limits and, thus, were neglected. Long-term exposure to γ-radiation could also result in combined effects of γ-radiation and the death of cells in the culture. © 2016 Elsevier Inc.

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Держатели документа:
Institute of Biophysics of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation
FRC Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
Novosibirsk State University, Novosibirsk, Russian Federation

Доп.точки доступа:
Bolsunovsky, A.; Frolova, T.; Dementyev, D.; Sinitsyna, O.

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17.

Genotoxicity assessment of low-level doses of gamma radiation with the SOS chromotest and the Ames test / A. Y. Bolsunovsky [et al.] // Doklad. Biochem. Biophys. - 2016. - Vol. 469, Is. 1. - P309-312, DOI 10.1134/S1607672916040190 . - ISSN 1607-6729
Аннотация: This is the first study to present data on the genotoxicity of low γ-irradiation doses for E. coli and S. typhimurium cells obtained using the SOS chromotest and the Ames test. The most pronounced effect was recorded in the first 24 h of γ-irradiation. After 72 h in the Ames test and after 96 h in the SOS chromotest, a significant effect of γ-irradiation on bacterial cells was detected. The absence of genotoxicity at the later stages can be explained by the adaptation of bacterial cells to the conditions of exposure. The findings allow the bacterial test system to be used for studying the effects of low doses at the early stages of exposure to radiation. © 2016, Pleiades Publishing, Ltd.

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Держатели документа:
Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, Russian Federation
Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Akademika Lavrent’eva 10, Novosibirsk, Russian Federation
Novosibirsk State University, ul. Pirogova 2, Novosibirsk, Russian Federation
Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, pr. Akademika Lavrent’eva 9, Novosibirsk, Russian Federation

Доп.точки доступа:
Bolsunovsky, A. Y.; Sinitsyna, O. I.; Frolova, T. S.; Vasyunina, E. A.; Dementyev, D. V.

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18.

Effects of Gamma-Radiation on DNA Damage in Onion (Allium cepa L.) Seedlings / A. Y. Bolsunovsky, D. V. Dementyev, T. S. Frolova [et al.] // Dokl. Biochem. Biophys. - 2019. - Vol. 489, Is. 1. - P362-366, DOI 10.1134/S1607672919060024 . - ISSN 1608-3091
Аннотация: The effect of ?-radiation on the level of nuclear DNA damage in onion seedlings (Allium-test) was studied using the comet assay. DNA breaks were first found in cells of onion seedlings exposed to low-dose radiation (? 0.1 Gy). Dose dependence of DNA damage parameters showed nonlinear behavior: a linear section in the low-dose region (below 0.1 Gy) and a dose-independent plateau in the dose range between 1 and 5 Gy. Thus, the comet assay can be used to estimate the biological effects of low-dose ?-radiation on Allium cepa seedlings.

Scopus
Держатели документа:
Institute of Biophysics, Krasnoyarsk Science Center, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, 660036, Russian Federation
Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russian Federation
Novosibirsk State University, Novosibirsk, 630090, Russian Federation
Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russian Federation

Доп.точки доступа:
Bolsunovsky, A. Y.; Dementyev, D. V.; Frolova, T. S.; Trofimova, E. A.; Iniatkina, E. M.; Vasilyev, S. A.; Sinitsyna, O. I.

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19.

Types of Cytogenetic Abnormalities in the Apical Root Meristem of Elodea canadensis from the Yenisei River Areas with Different Types of Anthropogenic Pollution / M. Y. Medvedeva, A. Y. Bolsunovsky // Russ. J. Genet. Appl. Res. - 2018. - Vol. 8, Is. 2. - P115-123, DOI 10.1134/S2079059718020089 . - ISSN 2079-0597
Кл.слова (ненормированные):
anthropogenic contamination of bottom sediments -- Elodea canadensis -- genotoxicity -- mitotic abnormalities -- Yenisei River
Аннотация: The change in the spectrum of chromosomal abnormalities in the apical root meristem of Elodea canadensis Michx. (elodea) growing in areas with different types of anthropogenic (radioactive and chemical) pollution of the bottom sediments of the Yenisei River is shown. In the samples of elodea collected in the zone of radioactive contamination of the river by discharges of the Rosatom Mining and Chemical Combine (MCC, Zheleznogorsk), the predominant type of abnormalities consist of chromosomal aberrations (bridges, stickiness, chromosomal fragmentation), as well as multiple abnormalities in one cell. The elodea samples from the areas of the Yenisei River with nonradioactive (chemical) contamination of bottom sediments by the enterprises of the city of Krasnoyarsk are predominantly characterized by abnormalities associated with the disturbance of the mitotic spindle of cell division. © 2018, Pleiades Publishing, Ltd.

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Держатели документа:
Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Medvedeva, M. Y.; Bolsunovsky, A. Y.

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20.

Database on natural and transgenic luminous microorganisms: "BIOLUMBASE" / S. E. Medvedeva [и др.] // Mikrobiologiya. - 2005. - Vol. 74, Is. 2. - С. 278-286 . - ISSN 0026-3656
Кл.слова (ненормированные):
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.

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Medvedeva, S.E.; Boyandin, A.N.; Lankin, Yu.P.; Kotov, D.A.; Kargatova, T.V.; Rodicheva, E.K.; Popova, L.Yu.

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