[Текст] : статья / Е.Ю. Бушмелев и др. // 8-th European conf. on Mathematical and Theoretical Biology. - 2011. - p. 78
Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.
Труды сотрудников ИВМ СО РАН
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Найдено документов в текущей БД: 34
System Biology on Mitochondrion Genomes
[Text] : статья / M.G. Sadovskii, N.A. Zaitseva, Yu.A. Putintseva // Proceedings of The Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies. - 2011. - p. 61-66
. - ISBN 978-1-61208-007-9
Полный текст
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zaitseva, N.A.; Putintseva, Yu.A.; Путинцева Ю.А.; Садовский, Михаил Георгиевич
Полный текст
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zaitseva, N.A.; Putintseva, Yu.A.; Путинцева Ю.А.; Садовский, Михаил Георгиевич
System biology of mitochondrial genomes based on their statistical analysis
[Текст] : статья / Н.А. Зайцева и др. // Functional Genomics. Next Generation Applications & Technologies. - 2011. - p. 76
Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.
Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.
Comparative analysis of phytoplankton of the Baikal and Khanka lakes
[Text] / L.A. Shchur, N.A. Bondarenko // Hydrobiological Journal. - 2012. - Vol. 48, Is. 3. - pp. 14-23, DOI 10.1615/HydrobJ.v48.i3.20
. - ISSN 0018-8166
Кл.слова (ненормированные):
Biomass -- Numbers -- Phytoplankton -- Primary and specific production -- alga -- biomass -- community composition -- comparative study -- dominance -- environmental conditions -- functional group -- hydrological regime -- lake ecosystem -- phytoplankton -- primary production -- vegetation structure -- Khanka Lake -- Lake Baikal -- Russian Federation -- algae
Аннотация: The structure and production potential of phytoplankton were studied in two large lakes of Asia, including the Baikal and Khanka lakes differing in their hydrological conditions. It has been found that the studied algae flora is saturated. The environmental conditions in the lakes are rather favorable to the development of algae. The functional characteristics of phytoplankton depended mainly on the regime of illumination, dimensional composition of algae, intensity of their development, vegetation stage, and also on the peculiarities of dominant forms biology. В© 2012 Begell House, Inc.
Scopus
Доп.точки доступа:
Shchur, L.A.; Щур, Людмила Александровна; Bondarenko, N.A.
Кл.слова (ненормированные):
Biomass -- Numbers -- Phytoplankton -- Primary and specific production -- alga -- biomass -- community composition -- comparative study -- dominance -- environmental conditions -- functional group -- hydrological regime -- lake ecosystem -- phytoplankton -- primary production -- vegetation structure -- Khanka Lake -- Lake Baikal -- Russian Federation -- algae
Аннотация: The structure and production potential of phytoplankton were studied in two large lakes of Asia, including the Baikal and Khanka lakes differing in their hydrological conditions. It has been found that the studied algae flora is saturated. The environmental conditions in the lakes are rather favorable to the development of algae. The functional characteristics of phytoplankton depended mainly on the regime of illumination, dimensional composition of algae, intensity of their development, vegetation stage, and also on the peculiarities of dominant forms biology. В© 2012 Begell House, Inc.
Scopus
Доп.точки доступа:
Shchur, L.A.; Щур, Людмила Александровна; Bondarenko, N.A.
Dynamical modeling of microRNA action on the protein translation process
[Text] / A.Zinovyev [et al.] // BMC Syst. Biol. - 2010. - Vol. 4. - Ст. 13, DOI 10.1186/1752-0509-4-13. - Cited References: 66. - We acknowledge support from Agence Nationale de la Recherche (project ANR-08-SYSC-003 CALAMAR) and from the Projet Incitatif Collaboratif "Bioinformatics and Biostatistics of Cancer" at Institut Curie. AZ and EB are members of the team "Systems Biology of Cancer" Equipe labellis'ee par la Ligue Nationale Contre le Cancer. This work was supported by the European Commission Sixth Framework Programme Integrated Project SIROCCO contract number LSHG-CT-2006-037900. We thank Vitaly Volpert and Laurence Calzone for inspiring and useful discussions.
. - ISSN 1752-0509
РУБ Mathematical & Computational Biology
Аннотация: Background: Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation. Results: In contrary to the study by Nissan and Parker, we show that dynamical data allow discriminating some of the mechanisms of microRNA action. We demonstrate this using the same models as developed by Nissan and Parker for the sake of comparison but the methods developed (asymptotology of biochemical networks) can be used for other models. We formulate a hypothesis that the effect of microRNA action is measurable and observable only if it affects the dominant system (generalization of the limiting step notion for complex networks) of the protein translation machinery. The dominant system can vary in different experimental conditions that can partially explain the existing controversy of some of the experimental data. Conclusions: Our analysis of the transient protein translation dynamics shows that it gives enough information to verify or reject a hypothesis about a particular molecular mechanism of microRNA action on protein translation. For multiscale systems only that action of microRNA is distinguishable which affects the parameters of dominant system (critical parameters), or changes the dominant system itself. Dominant systems generalize and further develop the old and very popular idea of limiting step. Algorithms for identifying dominant systems in multiscale kinetic models are straightforward but not trivial and depend only on the ordering of the model parameters but not on their concrete values. Asymptotic approach to kinetic models allows putting in order diverse experimental observations in complex situations when many alternative hypotheses co-exist.
Доп.точки доступа:
Zinovyev, A.; Morozova, N.; Nonne, N.; Barillot, E.; Harel-Bellan, A.; Gorban, A.N.; Горбань, Александр Николаевич
Рубрики:
MESSENGER-RNAS
CHEMICAL-KINETICS
HUMAN-CELLS
MAMMALIAN-CELLS
LET-7 MICRORNA
INITIATION
REPRESSION
INHIBITION
GENE
MANIFOLDS
MESSENGER-RNAS
CHEMICAL-KINETICS
HUMAN-CELLS
MAMMALIAN-CELLS
LET-7 MICRORNA
INITIATION
REPRESSION
INHIBITION
GENE
MANIFOLDS
Аннотация: Background: Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation. Results: In contrary to the study by Nissan and Parker, we show that dynamical data allow discriminating some of the mechanisms of microRNA action. We demonstrate this using the same models as developed by Nissan and Parker for the sake of comparison but the methods developed (asymptotology of biochemical networks) can be used for other models. We formulate a hypothesis that the effect of microRNA action is measurable and observable only if it affects the dominant system (generalization of the limiting step notion for complex networks) of the protein translation machinery. The dominant system can vary in different experimental conditions that can partially explain the existing controversy of some of the experimental data. Conclusions: Our analysis of the transient protein translation dynamics shows that it gives enough information to verify or reject a hypothesis about a particular molecular mechanism of microRNA action on protein translation. For multiscale systems only that action of microRNA is distinguishable which affects the parameters of dominant system (critical parameters), or changes the dominant system itself. Dominant systems generalize and further develop the old and very popular idea of limiting step. Algorithms for identifying dominant systems in multiscale kinetic models are straightforward but not trivial and depend only on the ordering of the model parameters but not on their concrete values. Asymptotic approach to kinetic models allows putting in order diverse experimental observations in complex situations when many alternative hypotheses co-exist.
Доп.точки доступа:
Zinovyev, A.; Morozova, N.; Nonne, N.; Barillot, E.; Harel-Bellan, A.; Gorban, A.N.; Горбань, Александр Николаевич
How much non-coding DNA do eukaryotes require?
[Текст] : статья / S. Ahnert, T. Fink, A. Zinovyev // Journal of Theoretical Biology. - 2008. - Vol. 252, Iss. 4. - p. 587–592DOI 10.1016/j.jtbi.2008.02.005
. -
Аннотация: Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic genomes, which indicates that eukaryotes require a certain minimum amount of non-coding DNA (ncDNA). This minimum increases quadratically with the amount of DNA located in exons. Based on a simple model of the growth of regulatory networks, we derive a theoretical prediction of the required quantity of ncDNA and find it to be in excellent agreement with the data. The amount of additional ncDNA (in basepairs) which eukaryotes require obeys Ndef=1/2 (Nc/Np) (Nc−Np), where Nc is the amount of exonic DNA, and Np is a constant of about 10 Mb. This value Ndef corresponds to a few percent of the genome in Homo sapiens and other mammals, and up to half the genome in simpler eukaryotes. Thus, our findings confirm that eukaryotic life depends on a substantial fraction of ncDNA and also make a prediction of the size of this fraction, which matches the data closely.
Полный текст на сайте издательства
Доп.точки доступа:
Fink, Thomas M.A.; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич
Аннотация: Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic genomes, which indicates that eukaryotes require a certain minimum amount of non-coding DNA (ncDNA). This minimum increases quadratically with the amount of DNA located in exons. Based on a simple model of the growth of regulatory networks, we derive a theoretical prediction of the required quantity of ncDNA and find it to be in excellent agreement with the data. The amount of additional ncDNA (in basepairs) which eukaryotes require obeys Ndef=1/2 (Nc/Np) (Nc−Np), where Nc is the amount of exonic DNA, and Np is a constant of about 10 Mb. This value Ndef corresponds to a few percent of the genome in Homo sapiens and other mammals, and up to half the genome in simpler eukaryotes. Thus, our findings confirm that eukaryotic life depends on a substantial fraction of ncDNA and also make a prediction of the size of this fraction, which matches the data closely.
Полный текст на сайте издательства
Доп.точки доступа:
Fink, Thomas M.A.; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич
A comprehensive modular map of molecular interactions in RB/E2F pathway
[Text] : статья / L. Calzone [et al.] // Molecular Systems Biology. - 2008. - Vol. 4. - p. 174-178DOI 10.1038/msb.2008.7
. -
Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel
Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel
Robust simplifications of multiscale biochemical networks
[Text] : статья / O. Radulescu [et al.] // BMC Systems Biology. - 2008. - Vol. 2. - Ст. 86DOI 10.1186/1752-0509-2-86
. -
Полный текст на сайте правообладателя
Доп.точки доступа:
Radulescu, Ovidiu; Gorban, A.N.; Горбань, Александр Николаевич; Zinovyev, A.; Зиновьев, Андрей Юрьевич; Lilienbaum, Alain
Полный текст на сайте правообладателя
Доп.точки доступа:
Radulescu, Ovidiu; Gorban, A.N.; Горбань, Александр Николаевич; Zinovyev, A.; Зиновьев, Андрей Юрьевич; Lilienbaum, Alain
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
[Text] : статья / A. Zinovyev [et al.] // Bioinformatics. - 2008. - Vol. 24, Iss. 6. - p. 876-877DOI 10.1093/bioinformatics/btm553
. -
Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Аннотация: BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of ‘interfaces’ for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others.
Полный текст на сайте журнала
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel
Collective dynamics: when one plus one does not make two
[Text] : статья / A. N. Gorban, S. Petrovskii // Mathematical Medicine and Biology. - 2011. - Vol. 28, Iss. 2. - p. 85-88DOI 10.1093/imammb/dqr003
. -
Кл.слова (ненормированные):
population dynamics -- biological evolution -- pattern formation -- nonlinear dynamics
Аннотация: A brief introduction into the interdisciplinary field of collective dynamics is given, followed by an overview of ‘Mathematical Models of Collective Dynamics in Biology and Evolution’ (University of Leicester, 11–13 May 2009).
Полный текст на сайте правообладателя
Доп.точки доступа:
Petrovskii, Sergei; Горбань, Александр Николаевич
Кл.слова (ненормированные):
population dynamics -- biological evolution -- pattern formation -- nonlinear dynamics
Аннотация: A brief introduction into the interdisciplinary field of collective dynamics is given, followed by an overview of ‘Mathematical Models of Collective Dynamics in Biology and Evolution’ (University of Leicester, 11–13 May 2009).
Полный текст на сайте правообладателя
Доп.точки доступа:
Petrovskii, Sergei; Горбань, Александр Николаевич
Law of the Minimum paradoxes
[Text] : статья / A. N. Gorban [et al.] // Bulletin of Mathematical Biology. - 2011. - Vol. 73, Iss. 9. - p. 2013-2044DOI 10.1007/s11538-010-9597-1
. -
Аннотация: The “Law of the Minimum” states that growth is controlled by the scarcest resource (limiting factor). This concept was originally applied to plant or crop growth (Justus von Liebig, 1840, Salisbury, Plant physiology, 4th edn., Wadsworth, Belmont, 1992) and quantitatively supported by many experiments. Some generalizations based on more complicated “dose-response” curves were proposed. Violations of this law in natural and experimental ecosystems were also reported. We study models of adaptation in ensembles of similar organisms under load of environmental factors and prove that violation of Liebig’s law follows from adaptation effects. If the fitness of an organism in a fixed environment satisfies the Law of the Minimum then adaptation equalizes the pressure of essential factors and, therefore, acts against the Liebig’s law. This is the the Law of the Minimum paradox: if for a randomly chosen pair “organism–environment” the Law of the Minimum typically holds, then in a well-adapted system, we have to expect violations of this law. For the opposite interaction of factors (a synergistic system of factors which amplify each other), adaptation leads from factor equivalence to limitations by a smaller number of factors. For analysis of adaptation, we develop a system of models based on Selye’s idea of the universal adaptation resource (adaptation energy). These models predict that under the load of an environmental factor a population separates into two groups (phases): a less correlated, well adapted group and a highly correlated group with a larger variance of attributes, which experiences problems with adaptation. Some empirical data are presented and evidences of interdisciplinary applications to econometrics are discussed.
Полный текст на сайте правообладателя
Доп.точки доступа:
Gorban, A.N.; Горбань, Александр Николаевич; Pokidysheva, L.I.; Smirnova, E.V.; Tyukina, T.A.
Аннотация: The “Law of the Minimum” states that growth is controlled by the scarcest resource (limiting factor). This concept was originally applied to plant or crop growth (Justus von Liebig, 1840, Salisbury, Plant physiology, 4th edn., Wadsworth, Belmont, 1992) and quantitatively supported by many experiments. Some generalizations based on more complicated “dose-response” curves were proposed. Violations of this law in natural and experimental ecosystems were also reported. We study models of adaptation in ensembles of similar organisms under load of environmental factors and prove that violation of Liebig’s law follows from adaptation effects. If the fitness of an organism in a fixed environment satisfies the Law of the Minimum then adaptation equalizes the pressure of essential factors and, therefore, acts against the Liebig’s law. This is the the Law of the Minimum paradox: if for a randomly chosen pair “organism–environment” the Law of the Minimum typically holds, then in a well-adapted system, we have to expect violations of this law. For the opposite interaction of factors (a synergistic system of factors which amplify each other), adaptation leads from factor equivalence to limitations by a smaller number of factors. For analysis of adaptation, we develop a system of models based on Selye’s idea of the universal adaptation resource (adaptation energy). These models predict that under the load of an environmental factor a population separates into two groups (phases): a less correlated, well adapted group and a highly correlated group with a larger variance of attributes, which experiences problems with adaptation. Some empirical data are presented and evidences of interdisciplinary applications to econometrics are discussed.
Полный текст на сайте правообладателя
Доп.точки доступа:
Gorban, A.N.; Горбань, Александр Николаевич; Pokidysheva, L.I.; Smirnova, E.V.; Tyukina, T.A.
Seasonal and interannual dynamics of phytoplankton of the Yenisei River in the area of the Gremyachii Log water-intake facilities
[Text] / Y. A. Ponomareva, L. A. Schure // Inland Water Biol. - 2014. - Vol. 7, Is. 1. - P34-36, DOI 10.1134/S1995082914010118. - Cited References: 14
. - ISSN 1995-0829. - ISSN 1995-0837
РУБ Marine & Freshwater Biology
Кл.слова (ненормированные):
phytoplankton -- composition -- abundance -- biomass -- Yenisei River -- trophic state -- water quality
Аннотация: A total of 81 taxa of algae of the rank below the genus of five divisions have been recorded in phytoplankton of the Yenisei River in the area of the Gremyachii Log water-intake facilities. Diatoms dominate in the structure of algocenoses in abundance and biomass. The trophic status of the area, estimated according to the average biomass of phytoplankton 1.92 +/- 0.09 mg/L, corresponds to the mesotrophic state; the water quality corresponds to the third class: "satisfactory clean.".
WOS
Держатели документа:
Russian Acad Sci, Inst Computat Modeling, Siberian Branch, Krasnoyarsk 660036, Russia
ИВМ СО РАН
Доп.точки доступа:
Ponomareva, Y.A.; Schure, L.A.; Щур, Людмила Александровна
Кл.слова (ненормированные):
phytoplankton -- composition -- abundance -- biomass -- Yenisei River -- trophic state -- water quality
Аннотация: A total of 81 taxa of algae of the rank below the genus of five divisions have been recorded in phytoplankton of the Yenisei River in the area of the Gremyachii Log water-intake facilities. Diatoms dominate in the structure of algocenoses in abundance and biomass. The trophic status of the area, estimated according to the average biomass of phytoplankton 1.92 +/- 0.09 mg/L, corresponds to the mesotrophic state; the water quality corresponds to the third class: "satisfactory clean.".
WOS
Держатели документа:
Russian Acad Sci, Inst Computat Modeling, Siberian Branch, Krasnoyarsk 660036, Russia
ИВМ СО РАН
Доп.точки доступа:
Ponomareva, Y.A.; Schure, L.A.; Щур, Людмила Александровна
Long-term dynamics of chlorophyll concentration in the ocean surface layer (by space data)
/ A. Shevyrnogov, G. Vysotskaya // Advances in Space Research. - 2007. - Vol. 39, Is. 1. - P. 197-202, DOI 10.1016/j.asr.2006.10.015
. - ISSN 0273-1177
Кл.слова (ненормированные):
Dynamics -- Ocean -- Phytopigment -- Climatology -- Concentration (process) -- Hydrology -- Marine biology -- Ocean currents -- Plants (botany) -- Biosphere -- Ocean -- Phytopigments -- Chlorophyll
Аннотация: To preserve the biosphere and to use it efficiently, it is necessary to gain a deep insight into the dynamics of the primary production process on our planet. Variability of chlorophyll concentration in the ocean is one of the most important components of this process. These investigations are, however, very labor-consuming, because of the difficulties related to the accessibility of the water surface and its large size. In this work long-term changes in chlorophyll concentration in the surface layer of the ocean have been analyzed on the basis of the CZCS data for 7.5 years from 1979 to 1986 and the SeaWiFS data from 1997 to 2004. It has been shown that the average chlorophyll concentration calculated in all investigated areas varies moderately. However, when analyzing spatially local trends, the areas have been detected that have significant rise and fall of chlorophyll concentrations. Some interesting features of the long-term dynamics of chlorophyll concentration have been found. The opposite directions of long-term trends (essential increase or decrease) cannot be explained only by large-scale hydrological phenomena in the ocean (currents, upwellings, etc.). The measured chlorophyll concentration results from the balance between production and destruction processes. Which process dominates is determined by various hydrophysical, hydrobiological, and climatic processes, leading to sharp rises or falls of the concentration. It is important to estimate the scale of the areas in which this or that process dominates. Therefore, the study addresses not only the dynamics of the mean value but also the dynamics of the areas in which the dominance of certain factors has led to a sharp fall or rise in chlorophyll concentration. Thus, the obtained results can be used to estimate long-term changes in the ocean biota. В© 2006 COSPAR.
Scopus,
Полный текст
Доп.точки доступа:
Shevyrnogov, A.; Vysotskaya, G.; Высоцкая, Галина Степановна
Кл.слова (ненормированные):
Dynamics -- Ocean -- Phytopigment -- Climatology -- Concentration (process) -- Hydrology -- Marine biology -- Ocean currents -- Plants (botany) -- Biosphere -- Ocean -- Phytopigments -- Chlorophyll
Аннотация: To preserve the biosphere and to use it efficiently, it is necessary to gain a deep insight into the dynamics of the primary production process on our planet. Variability of chlorophyll concentration in the ocean is one of the most important components of this process. These investigations are, however, very labor-consuming, because of the difficulties related to the accessibility of the water surface and its large size. In this work long-term changes in chlorophyll concentration in the surface layer of the ocean have been analyzed on the basis of the CZCS data for 7.5 years from 1979 to 1986 and the SeaWiFS data from 1997 to 2004. It has been shown that the average chlorophyll concentration calculated in all investigated areas varies moderately. However, when analyzing spatially local trends, the areas have been detected that have significant rise and fall of chlorophyll concentrations. Some interesting features of the long-term dynamics of chlorophyll concentration have been found. The opposite directions of long-term trends (essential increase or decrease) cannot be explained only by large-scale hydrological phenomena in the ocean (currents, upwellings, etc.). The measured chlorophyll concentration results from the balance between production and destruction processes. Which process dominates is determined by various hydrophysical, hydrobiological, and climatic processes, leading to sharp rises or falls of the concentration. It is important to estimate the scale of the areas in which this or that process dominates. Therefore, the study addresses not only the dynamics of the mean value but also the dynamics of the areas in which the dominance of certain factors has led to a sharp fall or rise in chlorophyll concentration. Thus, the obtained results can be used to estimate long-term changes in the ocean biota. В© 2006 COSPAR.
Scopus,
Полный текст
Доп.точки доступа:
Shevyrnogov, A.; Vysotskaya, G.; Высоцкая, Галина Степановна
Genome structure of organelles strongly relates to taxonomy of bearers
/ M. Sadovsky [et al.] // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2015. - Vol. 9043: 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015; Granada; Spain; 15 April 2015 through 17 April 2015; Code 125929. - P481-490
. -
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
Аннотация: We studied the relations between the triplet frequency dictionaries of organelle genome, and the phylogeny of their bearers. The clusters in 63-dimensional space were identified through K-means, and the clade composition of those clusters has been investigated. Very high regularity in genomes distribution among the clusters was found, in terms of taxonomy. The strong synchrony in evolution of nuclear and organelle genomes manifests through this correlation: the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically. Similar effect is also found in the ensembles of other (say, yeast) genomes. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Putintseva, Y.; Chernyshova, A.; Fedotova, V.
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
Аннотация: We studied the relations between the triplet frequency dictionaries of organelle genome, and the phylogeny of their bearers. The clusters in 63-dimensional space were identified through K-means, and the clade composition of those clusters has been investigated. Very high regularity in genomes distribution among the clusters was found, in terms of taxonomy. The strong synchrony in evolution of nuclear and organelle genomes manifests through this correlation: the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically. Similar effect is also found in the ensembles of other (say, yeast) genomes. © Springer International Publishing Switzerland 2015.
Scopus
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Putintseva, Y.; Chernyshova, A.; Fedotova, V.
Observations of hydrophysical characteristics of stratified salt lake shira (Siberia) as an important part of its environmental monitoring
/ L. A. Kompaniets, T. V. Iakubailik // International Multidisciplinary Scientific GeoConference Surveying Geology and Mining Ecology Management, SGEM. - 2015. - Vol. 2: 15th International Multidisciplinary Scientific Geoconference and EXPO, SGEM 2015 (18 June 2015 through 24 June 2015, ) Conference code: 153969, Is. 3. - P635-642
. -
Кл.слова (ненормированные):
Ecological condition -- Measuring hydro-values in situ -- Salt lake -- Air -- Ecology -- Water quality -- Ecological conditions -- Ecological status -- Environmental Monitoring -- Measuring hydro-values in situ -- Measuring instruments -- Mechanisms of formation -- Salt lakes -- Water temperatures -- Lakes
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation. © SGEM2014.
Scopus
Держатели документа:
ICM SB RAS, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Yakubaylik, T.V.; Якубайлик, Татьяна Валерьевна; Компаниец, Лидия Алексеевна
Кл.слова (ненормированные):
Ecological condition -- Measuring hydro-values in situ -- Salt lake -- Air -- Ecology -- Water quality -- Ecological conditions -- Ecological status -- Environmental Monitoring -- Measuring hydro-values in situ -- Measuring instruments -- Mechanisms of formation -- Salt lakes -- Water temperatures -- Lakes
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation. © SGEM2014.
Scopus
Держатели документа:
ICM SB RAS, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Yakubaylik, T.V.; Якубайлик, Татьяна Валерьевна; Компаниец, Лидия Алексеевна
OBSERVATIONS OF HYDROPHYSICAL CHARACTERISTICS OF STRATIFIED SALT LAKE SHIRA (SIBERIA) AS AN IMPORTANT PART OF ITS ENVIRONMENTAL MONITORING
[Text] / L. A. Kompaniets, T. V. Iakubailik // WATER RESOURCES, FOREST, MARINE AND OCEAN ECOSYSTEMS, SGEM 2015, VOL II : STEF92 TECHNOLOGY LTD, 2015. - 15th International Multidisciplinary Scientific Geoconference (SGEM) (JUN 18-24, 2015, Albena, BULGARIA). - P635-641. - (International Multidisciplinary Scientific GeoConference-SGEM). - Cited References:6
. -
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation.
WOS
Держатели документа:
ICM SB RAS, Krasnoyarsk, Russia.
Доп.точки доступа:
Kompaniets, Lidiya A.; Компаниец, Лидия Алексеевна; Iakubailik, Tatiana V.; Якубайлик, Татьяна Валерьевна
Аннотация: To understand the mechanisms of formation of water quality it is necessary to study both biological and chemical properties of a lake as well as its hydro regime. For many years researchers have focused on the study of chemistry and biology of Lake Shira (situated in Siberia), but a detailed investigation of its hydro regime has become possible only recently with the development of modern measuring instruments. Using the latest generation of measuring devices we have obtained the hydrophysical characteristics of the stratified salt lake in situ (air and water temperature, wind strength and direction, water velocity). Relationships between the measured data have allowed us to analyze the flow in the lake as a whole, thus outlining the problem of determining lake ecological status in the period under observation.
WOS
Держатели документа:
ICM SB RAS, Krasnoyarsk, Russia.
Доп.точки доступа:
Kompaniets, Lidiya A.; Компаниец, Лидия Алексеевна; Iakubailik, Tatiana V.; Якубайлик, Татьяна Валерьевна
Model of Prey-Predator Dynamics with Reflexive Spatial Behaviour of Species Based on Optimal Migration
[Text] / M. Sadovsky, M. Senashova // Bull. Math. Biol. - 2016. - Vol. 78, Is. 4. - P736-753, DOI 10.1007/s11538-016-0159-z. - Cited References:58
. - ISSN 0092-8240. - ISSN 1522-9602
РУБ Biology + Mathematical & Computational Biology
Аннотация: We consider the model of spatially distributed community consisting of two species with "predator-prey" interaction; each of the species occupies two stations. Transfer of individuals between the stations (migration) is not random, and migration stipulates the maximization of net reproduction of each species. The spatial distribution pattern is provided by discrete stations, and the dynamics runs in discrete time. For each time moment, firstly a redistribution of individuals between the stations is carried out to maximize the net reproduction, and then the reproduction takes place, with the upgraded abundances. Besides, three versions of the basic model are implemented where each species implements reflexive behaviour strategy to determine the optimal migration flow. It was found that reflexivity gives an advantage to the species realizing such strategy, for some specific sets of parameters. Nevertheless, the regular scanning of the parameters area shows that non-reflexive behaviour yields an advantage in the great majority of parameters combinations.
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Держатели документа:
Inst Computat Modelling SB RAS, Krasnoyarsk, Russia.
Доп.точки доступа:
Sadovsky, Michael; Senashova, Mariya
Рубрики:
PATTERN-FORMATION
POPULATION-DYNAMICS
DIFFUSION
SYSTEMS
SELECTION
Кл.слова (ненормированные):
Two-species community -- Targeted migration -- Maximization -- Evolution -- optimality
PATTERN-FORMATION
POPULATION-DYNAMICS
DIFFUSION
SYSTEMS
SELECTION
Кл.слова (ненормированные):
Two-species community -- Targeted migration -- Maximization -- Evolution -- optimality
Аннотация: We consider the model of spatially distributed community consisting of two species with "predator-prey" interaction; each of the species occupies two stations. Transfer of individuals between the stations (migration) is not random, and migration stipulates the maximization of net reproduction of each species. The spatial distribution pattern is provided by discrete stations, and the dynamics runs in discrete time. For each time moment, firstly a redistribution of individuals between the stations is carried out to maximize the net reproduction, and then the reproduction takes place, with the upgraded abundances. Besides, three versions of the basic model are implemented where each species implements reflexive behaviour strategy to determine the optimal migration flow. It was found that reflexivity gives an advantage to the species realizing such strategy, for some specific sets of parameters. Nevertheless, the regular scanning of the parameters area shows that non-reflexive behaviour yields an advantage in the great majority of parameters combinations.
WOS,
Смотреть статью
Держатели документа:
Inst Computat Modelling SB RAS, Krasnoyarsk, Russia.
Доп.точки доступа:
Sadovsky, Michael; Senashova, Mariya
Suppression of surface plasmon resonance in Au nanoparticles upon transition to the liquid state
/ V. S. Gerasimov [et al.] // Opt. Express. - 2016. - Vol. 24, Is. 23. - P26851-26856, DOI 10.1364/OE.24.026851
. - ISSN 1094-4087
Кл.слова (ненормированные):
Electron scattering -- Gold -- Lattice constants -- Liquids -- Melting -- Metal nanoparticles -- Nanoparticles -- Surface plasmon resonance -- Electron phonon couplings -- Experimental spectra -- Experimental values -- Gold Nanoparticles -- Nonlinear optical response -- Plasmonic nanoparticle -- Relaxation constants -- Surface plasmon frequency -- Plasmons
Аннотация: Significant suppression of resonant properties of single gold nanoparticles at the surface plasmon frequency during heating and subsequent transition to the liquid state has been demonstrated experimentally and explained for the first time. The results for plasmonic absorption of the nanoparticles have been analyzed by means of Mie theory using experimental values of the optical constants for the liquid and solid metal. The good qualitative agreement between calculated and experimental spectra support the idea that the process of melting is accompanied by an abrupt increase of the relaxation constants, which depends, beside electronphonon coupling, on electron scattering at a rising number of lattice defects in a particle upon growth of its temperature, and subsequent melting as a major cause for the observed plasmonic suppression. It is emphasized that observed effect is fully reversible and may underlie nonlinear optical responses of nanocolloids and composite materials containing plasmonic nanoparticles and their aggregates in conditions of local heating and in general, manifest itself in a wide range of plasmonics phenomena associated with strong heating of nanoparticles. © 2016 Optical Society of America.
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Держатели документа:
Siberian Federal University, Krasnoyarsk, Russian Federation
Institute of Computational Modeling, Federal Research Center KSC SB RAS, Krasnoyarsk, Russian Federation
Siberian State Aerospace University, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarskz, Russian Federation
Division of Theoretical Chemistry and Biology, Royal Institute of Technology, Stockholm, Sweden
Доп.точки доступа:
Gerasimov, V. S.; Ershov, A. E.; Gavrilyuk, A. P.; Karpov, S. V.; Agren, H.; Polyutov, S. P.
Кл.слова (ненормированные):
Electron scattering -- Gold -- Lattice constants -- Liquids -- Melting -- Metal nanoparticles -- Nanoparticles -- Surface plasmon resonance -- Electron phonon couplings -- Experimental spectra -- Experimental values -- Gold Nanoparticles -- Nonlinear optical response -- Plasmonic nanoparticle -- Relaxation constants -- Surface plasmon frequency -- Plasmons
Аннотация: Significant suppression of resonant properties of single gold nanoparticles at the surface plasmon frequency during heating and subsequent transition to the liquid state has been demonstrated experimentally and explained for the first time. The results for plasmonic absorption of the nanoparticles have been analyzed by means of Mie theory using experimental values of the optical constants for the liquid and solid metal. The good qualitative agreement between calculated and experimental spectra support the idea that the process of melting is accompanied by an abrupt increase of the relaxation constants, which depends, beside electronphonon coupling, on electron scattering at a rising number of lattice defects in a particle upon growth of its temperature, and subsequent melting as a major cause for the observed plasmonic suppression. It is emphasized that observed effect is fully reversible and may underlie nonlinear optical responses of nanocolloids and composite materials containing plasmonic nanoparticles and their aggregates in conditions of local heating and in general, manifest itself in a wide range of plasmonics phenomena associated with strong heating of nanoparticles. © 2016 Optical Society of America.
Scopus,
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Держатели документа:
Siberian Federal University, Krasnoyarsk, Russian Federation
Institute of Computational Modeling, Federal Research Center KSC SB RAS, Krasnoyarsk, Russian Federation
Siberian State Aerospace University, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarskz, Russian Federation
Division of Theoretical Chemistry and Biology, Royal Institute of Technology, Stockholm, Sweden
Доп.точки доступа:
Gerasimov, V. S.; Ershov, A. E.; Gavrilyuk, A. P.; Karpov, S. V.; Agren, H.; Polyutov, S. P.
Secret life of tiny blood vessels: Lactate, scaffold and beyond
/ V. Salmin [et al.] // (26 April 2017 through 28 April 2017 : Springer Verlag, 2017. - Vol. 10208 LNCS. - P591-601, DOI 10.1007/978-3-319-56148-6_53
. -
Кл.слова (ненормированные):
Angiogenesis in vitro -- Brain microvessel endothelial cells -- Form factor -- Fractal dimension -- Gelatin scaffold -- Bioinformatics -- Biomedical engineering -- Blood vessels -- Brain -- Cells -- Cytology -- Endothelial cells -- Fractal dimension -- Fractals -- Angiogenesis -- Bio-scaffolds -- Form factors -- In-vitro -- Microenvironments -- Microvessel -- Microvessels -- Primary culture -- Scaffolds (biology)
Аннотация: We studied the model of cerebral angiogenesis in vitro using lactate-releasing gelatin bioscaffolds and primary culture of brain endothelial cells. We found that development of microvessels from actively proliferating rat brain microvessels endothelial cells was greatly modified by the presence of lactate at the surface of the scaffold with different lactate-releasing ability. Fractal dimension of newly-established vessel loops allows precise characterizing the local microenvironment supporting cell growth on various types of gelatin scaffolds. © Springer International Publishing AG 2017.
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Держатели документа:
Research Institute of Molecular Medicine and Pathobiochemistry, Krasnoyarsk State Medical University, p. Zheleznyaka str., 1, Krasnoyarsk, Russian Federation
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Salmin, V.; Morgun, A.; Khilazheva, E.; Pisareva, N.; Boitsova, E.; Lavrentiev, P.; Sadovsky, M.G.; Садовский, Михаил Георгиевич; Salmina, A.
Кл.слова (ненормированные):
Angiogenesis in vitro -- Brain microvessel endothelial cells -- Form factor -- Fractal dimension -- Gelatin scaffold -- Bioinformatics -- Biomedical engineering -- Blood vessels -- Brain -- Cells -- Cytology -- Endothelial cells -- Fractal dimension -- Fractals -- Angiogenesis -- Bio-scaffolds -- Form factors -- In-vitro -- Microenvironments -- Microvessel -- Microvessels -- Primary culture -- Scaffolds (biology)
Аннотация: We studied the model of cerebral angiogenesis in vitro using lactate-releasing gelatin bioscaffolds and primary culture of brain endothelial cells. We found that development of microvessels from actively proliferating rat brain microvessels endothelial cells was greatly modified by the presence of lactate at the surface of the scaffold with different lactate-releasing ability. Fractal dimension of newly-established vessel loops allows precise characterizing the local microenvironment supporting cell growth on various types of gelatin scaffolds. © Springer International Publishing AG 2017.
Scopus,
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WOS
Держатели документа:
Research Institute of Molecular Medicine and Pathobiochemistry, Krasnoyarsk State Medical University, p. Zheleznyaka str., 1, Krasnoyarsk, Russian Federation
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Salmin, V.; Morgun, A.; Khilazheva, E.; Pisareva, N.; Boitsova, E.; Lavrentiev, P.; Sadovsky, M.G.; Садовский, Михаил Георгиевич; Salmina, A.
Lost strings in genomes: What sense do they make?
/ M. Sadovsky [et al.] // (26 April 2017 through 28 April 2017 : Springer Verlag, 2017. - Vol. 10209 LNCS. - P20-29, DOI 10.1007/978-3-319-56154-7_3
. -
Кл.слова (ненормированные):
Combinatorics -- Composition -- Diversity -- Evolution -- Order -- Selection -- Bioinformatics -- Biology -- Biomedical engineering -- Chemical analysis -- Combinatorics -- Diversity -- Evolution -- Order -- Selection -- Genes
Аннотация: We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found. © Springer International Publishing AG 2017.
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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Johannes Gutenberg-Universitat Mainz, Mainz, Germany
Institute of Space and Information Technologies, Siberian Federal University, Kirenskogo Str., 26, Krasnoyarsk, Russian Federation
Institute of Molecular Biology, Mainz, Germany
Доп.точки доступа:
Sadovsky, M.; Fontaine, J. -F.; Andrade-Navarro, M. A.; Yakubailik, Y.; Rudenko, N.
Кл.слова (ненормированные):
Combinatorics -- Composition -- Diversity -- Evolution -- Order -- Selection -- Bioinformatics -- Biology -- Biomedical engineering -- Chemical analysis -- Combinatorics -- Diversity -- Evolution -- Order -- Selection -- Genes
Аннотация: We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found. © Springer International Publishing AG 2017.
Scopus,
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WOS
Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Johannes Gutenberg-Universitat Mainz, Mainz, Germany
Institute of Space and Information Technologies, Siberian Federal University, Kirenskogo Str., 26, Krasnoyarsk, Russian Federation
Institute of Molecular Biology, Mainz, Germany
Доп.точки доступа:
Sadovsky, M.; Fontaine, J. -F.; Andrade-Navarro, M. A.; Yakubailik, Y.; Rudenko, N.