Библиотека института физики им. Л.В. Киренского СО РАН

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Каталог книг и брошюр библиотеки ИФ СО РАН

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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Begunovich L. V., Kovaleva E. A., Korshunov M. M., Shabanov V. F.
Заглавие : Absorption spectra of the purple nonsulfur bacteria light-harvesting complex: A DFT study of the B800 part
Колич.характеристики :7 с
Место публикации : J. Photochem. Photobiol. A: Chem. - 2024. - Vol. 450. - Ст.115454. - ISSN 10106030 (ISSN), DOI 10.1016/j.jphotochem.2023.115454. - ISSN 18732666 (eISSN)
Примечания : Cited References: 42. - This work was supported by the state assignment of the Ministry of Science and Higher Education of the Russian Federation. Authors would like to thank Information Technology Centre, Novosibirsk State University for providing access to their supercomputers. L.V.B. would like to thank Irkutsk Supercomputer Center of SB RAS for providing the access to HPC-cluster «Akademik V.M. Matrosov» (Irkutsk Supercomputer Center of SB RAS, Irkutsk: ISDCT SB RAS; http://hpc.icc.ru, accessed 20.10.2023)
Аннотация: We’ve studied the B800 part of Rhodoblastus acidophilus light-harvesting complex (LH2) by several quantum chemical techniques based on the density functional theory (DFT) and determined the specific method and a minimal reliable model suitable for further studies of the LH2. In addition to bacteriochlorophyll a molecules, the minimal model includes two α and one β chain amino acids. Within the model, we are able to reproduce the contribution of the B800 ring of nine bacteriochlorophyll a molecules to the near infrared Qy absorption band. We also discuss the use of hybrid DFT calculations for precise energy and optical estimations and DFT-based tight binding (DFTB) method for the large-scale calculations. Crucial importance of Hartree-Fock exchange interaction for the correct description of B800 peak position was shown.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Yehia M. R., Smolyarova T. E., Shabanov A. V., Sushko E. S., Badun G. A., Kudryasheva N. S.
Заглавие : Adaptation of a bacterial bioluminescent assay to monitor bioeffects of gold nanoparticles
Место публикации : Bioengineering. - 2022. - Vol. 9, Is. 2. - Ст.61. - ISSN 2306-5354(eISSN), DOI 10.3390/bioengineering9020061
Примечания : Cited References: 91. - This research was funded by RFBR, N18-29-19003; RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science, N20-44-243001; and partly supported by the Program of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Fundamental Study 2020–2025 (Russian Federation)
Аннотация: Our current study aimed to adapt a bioluminescent bacteria-based bioassay to monitor the bioeffects of gold nanoparticles (AuNPs). Luminous marine bacteria Photobacterium phosphoreum and AuNPs modified with polyvinylpyrrolidone were employed; low-concentration (≤10−3 g/L) bioeffects of AuNPs were studied. Bioluminescence intensity was used as an indicator of physiological activity in bacteria. Two additional methods were used: reactive oxygen species (ROS) content was estimated with a chemiluminescent luminol method, and bacterial size was monitored using electron microscopy. The bacterial bioluminescent response to AuNPs corresponded to the “hormesis” model and involved time-dependent bioluminescence activation, as well as a pronounced increase in the number of enlarged bacteria. We found negative correlations between the time courses of bioluminescence and the ROS content in bacterial suspensions, demonstrating the relationship between bioluminescence activation and bacterial ROS consumption. The combined effects of AuNPs and a beta-emitting radionuclide, tritium, revealed suppression of bacterial bioluminescent activity (as compared to their individual effects) and a reduced percentage of enlarged bacteria. Therefore, we demonstrated that our bacteria-based bioluminescence assay is an appropriate tool to study the bioeffects of AuNPs; the bioeffects can be further classified within a unified framework for rapid bioassessment.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Boyandin A. N., Prudnikova S. V., Filipenko M. L., Khrapov E. A., Vasil'ev A. D., Volova T. G.
Заглавие : Biodegradation of polyhydroxyalkanoates by soil microbial communities of different structures and detection of PHA degrading microorganisms
Место публикации : Appl. Biochem. Microbiol.: MAIK Nauka-Interperiodica / Springer, 2012. - Vol. 48, Is. 1. - P.28-36. - ISSN 0003-6838, DOI 10.1134/S0003683812010024
Примечания : Cited References: 39. - The work was supported by the project initiated by the Government of the Russian Federation for governmental support of scientific research conducted under the guidance of leading scientists at Russian institutions of higher learning (Agreement No. 11.G34.31.0013) and the Program of Integrated Research of the Presidium of the Siberian Branch of Russian Academy of Sciences (project no. 96).
Предметные рубрики: POLY-BETA-HYDROXYBUTYRATE
CHAIN-LENGTH POLYHYDROXYALKANOATES
DEGRADATION
FILMS
POLY(3-HYDROXYBUTYRATE-CO-3-HYDROXYVALERATE)
BACTERIA
ACID
Аннотация: Biodegradation of microbial linear polymers of hydroxyalkanoic acids (polyhydroxyalkanoates, PHAs) by soil microbial communities of different structures has been studied during two field seasons in different weather conditions. This process was shown to be influenced by the polymer chemical composition, temperature, humidity, and the microbial soil component. The PHA degradation was accompanied by a decrease in the polymer molecular weight and an increase in the degree of crystallinity, indicating the preferential destruction of the amorphous phase compared to the crystalline one. The quantity of the true PHA destructors developing at the surface of the polymer samples was lower than the quantity of accompanying bacteria. The dominant PHA degrading microorganisms under the test conditions were identified as bacteria of the genera Variovorax, Stenotrophomonas, Acinetobacter, Pseudomonas, Bacillus, and Xanthomonas and as micromycetes from Penicillium, Paecilomyces, Acremonium, Verticillium, and Zygosporium.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Balasoiu M., Kuklin A. I., Arzumanian G. M., Murugova T. N., Stolyar S. V., Iskhakov R. S., Ishchenko L. A., Raikher Yu. L.
Заглавие : Biogenic nanoparticles produced by bacteria Klebsiella Oxytoca: structure investigations : Chapter
Место публикации : Modern trends of nanoscience/ ed.: M. Balasoiu, G. M. Arzumanian. - Bucharest: Publishing House of Romanian Academy, 2012. - Chapter. - P.179-186. - ISBN 978-973-27-2230-5
Аннотация: A promising new dimension in this field is the use of microorganisms for the production of inorganic nanoscale particles. The clean, nontoxic and environmentally friendly ability of eukaryotic and prokaryotic microorganisms to form nanoparticles either intra- or extra-cellularly is particularly important in the development of nanobiotechnology. The development of techniques for the synthesis of nanoparticles of well-defined size, shape and composition is a challenge and an important area of research. Steps in the methodological work for structural properties determination of biogenic ferrihydrite nanoparticles by means of small angle techniques are reviewed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Vysotski E. S., Zavoruev V. V., Mezhevikin V. V., Rodicheva E. K., Fish A. M., Gitelzon I. I.
Заглавие : Bioluminescence of cell-free-extracts of luminous bacteria
Место публикации : Doklady Akademii Nauk. - 1981. - Vol. 261, Is. 1. - P.216-219. - ISSN 0002-3264
Примечания : Cited References: 8
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kudryasheva, Nadezhda S., Kovel, Ekaterina S., Sachkova, Anna S., Vorobeva, Anna A., Isakova V. G., Churilov G. N.
Заглавие : Bioluminescent enzymatic assay as a tool for studying antioxidant activity and toxicity of bioactive compounds
Коллективы : Russian Foundation for Basic Research [15-03-06786, 15-43-04377-sibir]; Russian Academy of Sciences [01201351504]
Место публикации : Photochem. Photobiol.: Wiley, 2017. - Vol. 93, Is. 2. - P.536-540. - ISSN 0031-8655, DOI 10.1111/php.12639. - ISSN 1751-1097(eISSN)
Примечания : Cited References:40. - The work was supported by the Russian Foundation for Basic Research, Grants 15-03-06786 and 15-43-04377-sibir; the state budget allocated to the fundamental research at the Russian Academy of Sciences (project 01201351504).
Предметные рубрики: LUMINOUS MARINE-BACTERIA
HUMIC SUBSTANCES
DETOXIFICATION PROCESSES
Аннотация: A bioluminescent assay based on a system of coupled enzymatic reactions catalyzed by bacterial luciferase and NADH:FMN-oxidoreductase was developed to monitor toxicity and antioxidant activity of bioactive compounds. The assay enables studying toxic effects at the level of biomolecules and physicochemical processes, as well as determining the toxicity of general and oxidative types. Toxic and detoxifying effects of bioactive compounds were studied. Fullerenols, perspective pharmaceutical agents, nanosized particles, water-soluble polyhydroxylated fullerene-60 derivatives were chosen as bioactive compounds. Two homologous fullerenols with different number and type of substituents, C60O2–4(OH)20–24 and Fe0.5C60(OH) xOy (x + y = 40–42), were used. They suppressed bioluminescent intensity at concentrations 0.01 g L−1 and 0.001 g L−1 for C60O2–4(OH)20-24 and Fe0.5C60(OH)xOy, respectively; hence, a lower toxicity of C60O2–4(OH)20–24 was demonstrated. Antioxidant activity of fullerenols was studied in model solutions of organic and inorganic oxidizers; changes in toxicities of general and oxidative type were determined; detoxification coefficients were calculated. Fullerenol C60O2–4(OH)20–24 revealed higher antioxidant ability at concentrations 10−17−10−5 g L−1. The difference in the toxicity and antioxidant activity of fullerenols was explained through their electron donor/acceptor properties and different catalytic activity. Principles of bioluminescent enzyme assay application for evaluating the toxic effect and antioxidant activity of bioactive compounds were summarized and the procedure steps were described.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Semenov S. V., Knyazev Yu. V., Balaev D. A., Karnachuk O. V., Ikkert O. P.
Заглавие : Biosyntesis of magnetic nanocomposites using sulfate-reducing bacteria
Коллективы : Байкальская международная конференция "Магнитные материалы. Новые технологии", "Магнитные материалы. Новые технологии", Байкальская международная конференция, "Magnetic materials. New tecnologies", Baikal International Conference, Иркутский государственный университет
Место публикации : Магнитные материалы. Новые технологии: тез. докл. IX Байкал. междунар. конф. BICMM-2023/ чл. прогр. ком.: S. S. Aplesnin [et al.] ; чл. орг. ком. R. S. Iskhakov [et al.]. - Иркутск, 2023. - P.170. - ISBN 978-5-00133-051-6, DOI 10.26516/978-5-9624-2178-0.2023.1-207
Примечания : Библиогр.: 2
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Вид документа : Статья из сборника (выпуск продолж. издания)
Шифр издания :
Автор(ы) : Balasoiu M., Kichanov S., Pantelica A., Pantelica D., Stolyar S. V., Iskhakov R. S., Aranghel D., Ionescu P., Badita C. R., Kurkin S., Orelovich O., Tiutiunikov S.
Заглавие : Characterization of biogenic ferrihydrite nanoparticles by means of SAXS, SRD and IBA methods
Коллективы : International School and Workshop on Complex and Magnetic Soft Matter Systems: Structure and Physico - Mechanical Properties
Место публикации : J. Phys.: Conf. Ser. - 2018. - Vol. 994: 3rd International School and Workshop on Complex and Magnetic Soft Matter Systems: Structure and Physico - Mechanical Properties, CMSMS 2017 (28 - 30 June 2017), Is. 1. - Ст.012012. - , DOI 10.1088/1742-6596/994/1/012012
Примечания : Cited References: 20. - The work was accomplished in the frame of IFIN-HH User Beam schedule at the 3 MV Tandetron accelerator and partially was supported by the Joint Institute for Nuclear Research (JINR) Dubna Theme No. 04-4-1121-2015/2017, RO-JINR Projects Nos. 95/15.02.2016 and 96/15.02.2016, items 77, 82; Nos. 219/10.04.2017 and 220/10.04.2017 item 38; RFBR and Krasnoyarsk region Project No. 17-43-240527. Support by the Special Program for Siberian Federal University of the Ministry of Education and Science of the Russian Federation is acknowledged.
Ключевые слова (''Своб.индексиров.''): bacteria--data handling--ion beams--mechanical properties--nanoparticles--synchrotron radiation
Аннотация: Investigations of biogenic ferrihydrite nanoparticles produced by bacteria Klebsiella oxytoca by applying small angle X-ray scattering, synchrotron radiation diffraction and ion beam analysis methods are reviewed. Different experimental data processing methods are used and analyzed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorban A., Popova T., Zinovyev A.
Заглавие : Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences
Разночтения заглавия :авие SCOPUS: Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences
Место публикации : Physica A: ELSEVIER SCIENCE BV, 2005. - Vol. 353. - P365-387. - ISSN 0378-4371, DOI 10.1016/j.physa.2005.01.043
Примечания : Cited References: 46
Предметные рубрики: DNA-BASE COMPOSITION
ASYMMETRIC SUBSTITUTION PATTERNS
PROTEIN-CODING REGIONS
MICROBIAL GENOMES
GENE IDENTIFICATION
MARKOV-MODELS
G+C CONTENT
BIAS
PREDICTION
SELECTION
Ключевые слова (''Своб.индексиров.''): genome--cluster--codon usage--correlations--entropy--mean field--cluster--codon usage--correlations--entropy--genome--mean field--approximation theory--correlation methods--database systems--entropy--functions--genes--mathematical models--clusters--codon usage--genomes--mean field--bacteria
Аннотация: Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon us-age of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/similar to zinovyev/7clusters. (c) 2005 Elsevier B.V. All rights reserved.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shabanova O. V., Nemtsev I. V., Shabanov A. V.
Заглавие : Development of SEM method for analysis of organ-containing objects using inverse opals
Место публикации : Sib. J. Sci. Technol. - 2020. - Vol. 21, Is. 4. - P.565-573. - ISSN 2587-6066, DOI 10.31772/2587-6066-2020-21-4-565-573; \b Сибирский журнал науки и технологий
Примечания : Cited References: 25
Аннотация: The purpose of this study is to test the possibility of using inorganic macroporous structures of inverse opal in sample preparation for scanning electron microscopy of biological objects. As an absorbent substrate we used silica inverse opals prepared by a sol-gel method to study the biological objects.The process of manufacturing the inverse opal involves a complex multi-stage technological process. First, we synthesized submicron spherical particles from polymethylmethacrylate by the method of emulsifier-free emulsion polymerization of methylmethacrylate in an aqueous medium in the presence of a diazoinitiator. This method can be used to obtain an ensemble of particles with high monodispersity, the average size of which can vary in the range from 100 to 500 nm. Then, by self-assembly technique, we deposited the beads of polymethylmethacrylate into ordered matrices (templates), mainly with a face-centered cubic lattice. The resulting mesoporous structures, called artificial opals or colloidal crystals, had lateral dimensions of about 10 × 10 × 2 mm. Then we heat-treated the opals to 120 °C to harden the template before being impregnated with the precursor. Further, we impregnated the opals with silica sol with a particle size distribution from 1 to 5 nm, obtained by hydrolysis of tetraethoxysilane in the presence of hydrochloric acid, and then, after curing and drying the impregnating composition in air at room temperature, we multi-stage fired them up to 550 °C at normal pressure in the air atmosphere to remove all organic components. As a result, the macroporous metamaterial (the so-called inverse opals) with an open system of pores up to 400 nm in size, occupying about 80 % of the volume, were obtained. We studied lactic acid bacteria of cucumber brine and human red blood cells with TM4000 Plus, SU3500 and S-5500 scanning electron microscopes. Auxiliary substance for the sample preparation was ionic liquid VetexQ EM (Interlab LLC). We showed that it is possible to use the inverse opal as an absorbent substrate for sample preparation and rapid analysis in scanning electron microscopy without pre-drying, chemical treatment, or temperature exposure. To improve imaging in the electron microscope, we used sputter coater to cover the inverse opal surface with a thin film of platinum. The use of ionic liquid in combination with the absorbent porous medium allows preserving an original shape of the biological structures. Using the human red blood cells and lactic acid bacteria, we showed that it is possible to carry out of the morphological analysis of the cells using various scanning electron microscopes. We found that on the basis of the inverse opal, there is a fundamental possibility of creating the absorbent substrate suitable for repeated use in the study of the biological objects. At the same time, trace remnants of previous samples remaining after annealing the plate do not introduce significant distortions when conducting new series of observations. In this study, we obtained high-quality electronic micrographs of the biological objects with high resolution and contrast. At the same time, due to the use of the inverse opals as the absorbent substrate, time and financial costs for researchare reduced.Целью данного исследования является апробация возможности применения неорганических макропористых структур инверсного опала при пробоподготовке для сканирующей электронной микроскопии биообъектов. Изготовленные золь-гель способом инверсные опалы на основе кремнезёма применялись в качестве впитывающей подложки для изучения биологических образцов. Изготовление инверсного опала представляет собой сложный многоступенчатый технологический процесс. Сначала методом безэмульгаторной эмульсионной полимеризации метилметакрилата в водной среде в присутствии диазоинициатора были синтезированы субмикронные сферические частицы из полиметилметакрилата. Таким способом можно получать ансамбль частиц с высокой монодисперсностью, средний размер которых может варьироваться в диапазоне от 100 до 500 нм. Затем методом самосборки субмикросферы полиметилметакрилата осаждались в упорядоченные матрицы (шаблоны) преимущественно с гранецентрированной кубической решёткой. Полученные мезопористые структуры, называемые искусственными опалами или коллоидными кристаллами, имели размеры порядка 10 ×10 × 2 мм. Затем опалы подвергались термической обработке до 120 °С для упрочнения шаблона перед пропиткой прекурсором. Далее опалы пропитывались золем кремнезёма с размером частиц от 1 до 5 нм, полученным путём гидролиза тетраэтоксисилана в присутствии соляной кислоты и затем, после отверждения и сушки пропитывающего состава на воздухе при комнатной температуре, подвергались многоступенчатому обжигу до 550 °С при нормальном давлении в воздушной атмосфере для удаления всех органических компонентов. В результате получались образцы макропористых метаматериалов (так называемые, инверсные или инвертированные опалы) с открытой системой пор размером до 400 нм, занимающих около 80 % объёма. В сканирующих электронных микроскопах TM4000 Plus, SU3500 и S-5500 с использованием макропористых структур были исследованы молочнокислые бактерии и красные кровяные тельца. Для улучшения визуализации использовались системы напыления металлов для покрытия поверхности инверсного опала тонкой плёнкой платины. Вспомогательным веществом в пробоподготовке выступала ионная жидкость VetexQ EM (Interlab LLC). Показано, что инверсный опал можно использовать как впитывающую подложку для пробоподготовки и экспресс-анализа в сканирующей электронной микроскопии без предварительной сушки, химической обработки или температурного воздействия биообъектов. Использование ионной жидкости в сочетании с впитывающей пористой средой позволяет сохранить первоначальную форму биологических структур. Показана возможность изучения морфологических особенностей биоструктур на примере эритроцитов человека и молочнокислых бактерий. Экспериментально установлено, что впитывающую подложку на основе инверсного опала можно использовать многократно при исследовании биологических объектов. Следовые остатки предыдущих проб, оставшиеся после отжига пластины, не вносят существенных искажений при проведении новых серий наблюдений. В нашем исследовании были получены высококачественные электронные микрофотографии биообъектов с высоким разрешением и контрастом. При этом за счёт использования инверсных опалов в качестве впитывающей подложки обеспечивается сокращение временных и финансовых затрат на исследования.
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