Изучение множественного встраивания модифицированных нуклеотидов в растущую цепь ДНК

Objectives. This study investigated the substrate properties of the modified derivatives of triphosphates of purine and pyrimidine deoxynucleosides (5-propynyl-2’-deoxyuridine-5’-triphosphate, 5-propynyl2’-deoxycytidine-5’-triphosphate, 5-methyl-2’-deoxycytidine-5’-triphosphate, and N6-methyl-2’-deoxyadenosine-5’-triphosphate) during their simultaneous incorporation in enzymatic reactions (polymerase chain and primer extension reactions).Methods. The real-time polymerase chain and primer extension reactions were used to study the substrate efficiency of modified deoxynucleotide triphosphates. Various pairwise combinations of modified derivatives were used; specially designed synthetic DNA fragments and libraries for the Systematic Evolution of Ligands by Exponential Enrichment technology were used as templates. Reactions were conducted using DNA polymerases: Taq, Vent (exo-), DeepVent (exo-), and KOD XL.Results. In each case, a pair of compounds (modified dUTP + dCTP, dUTP + dATP, and dCTP + dATP) was selected to study the simultaneous incorporation into the growing DNA strand. The most effective combinations of nucleotides for simultaneous insertion were dU and dC, having 5-propynyl substitution. The Vent (exo-) DNA polymerase was found as the most effective for the modified substrates.Conclusions. The selected compounds can be used for the enzymatic preparation of modified DNA, including aptamers with extended physicochemical properties. Цели. Целью данной работы является изучение субстратных свойств модифицированных производных трифосфатов дезоксинуклеозидов пуриновой и пиримидиновой природы (5-пропинил-2’-дезоксиуридин-5’-трифосфат, 5-пропинил-2’-дезоксицитидин-5’-трифосфат, 5-метил-2’-дезоксицитидин-5’-трифосфат, N6-метил-2’-дезоксиаденозин-5’-трифосфат) при их одновременном встраивании в процессе ферментативных реакций (полимеразной цепной реакции и реакции удлинения праймера).Методы. В работе для изучения субстратной эффективности модифицированных трифосфатов дезоксинуклеозидов использовали методы полимеразной цепной реакции в режиме реального времени и реакции удлинения праймера. Использовали различные попарные сочетания модифицированных производных, в качестве матриц применяли специальным образом сконструированные синтетические фрагменты ДНК и библиотеки для SELEX. Реакции проводили с применением ДНК-полимераз: Taq, Vent (exo-), DeepVent (exo-) и KOD XL.Результаты. В каждом случае из исследуемых соединений выбирали пару соединений (модифицированные dUTP + dCTP, dUTP + dATP, dCTP + dATP) для изучения одновременного встраивания в растущую цепь ДНК. Найдены наиболее эффективные сочетания нуклеотидов для одновременного встраивания, а именно: dU и dC, имеющие 5-пропинильный заместитель. Также найдена наиболее эффективная (из протестированных) ДНК-полимераза: Vent (exo-).Выводы. Выбранные соединения можно использовать для ферментативного получения модифицированных ДНК, в частности аптамеров с расширенными физико-химическими свойствами.

Scaling Analysis of Defect Induced Structure of A6061 Alloy at Dynamic Strain Localization

Plastic strain localization and fracture of dynamically loaded metallic samples, occurred during plug formation, are investigated. These processes are closely related to the instability of plastic flow and can be attributed to structural-scaling transitions in mesodefect ensembles. The multiscale nature of defect structure allows us to use the fractal concept for quantitative analysis of both the fracture surface and the inner structure of a deformed material. The scaling properties of fracture surfaces are established in terms of the roughness index (Hurst exponent) as the characteristics of strain localization and fracture

Дизайн и синтез производных 4-нитроимидазола с потенциальной антитуберкулезной активностью

Objectives. To develop the procedures for synthesis of hybrid molecules with potential anti-tubercular activity containing heterocyclic cores of 4-nitroimidazole and 1,3,4-thiadiazole within the framework of a double-drug strategy and predict bioactivity of target structures and drug-likeness physicochemical parameters.Methods. Target compounds were prepared by classical organic synthesis methods. The structure of the obtained compounds was characterized by melting points, 1H and 13C nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry. The calculation of the physicochemical parameters of the target compounds and prediction of their biological activity were carried out using publicly available software for cheminformatics and molecular modeling.Results. Acylation of propargylamine with (2-methyl-4-nitro-1H-imidazol-1-yl)acetic and (4-nitro-1H-imidazol-1-yl)acetic acids provided the corresponding amides, which were cyclized with seven different benzylamines in the presence of zinc triflate. In this way, seven new compounds were obtained at 20–30% yields. Ten arylamines were acylated with chloroacetyl chloride and the resulting chloroacetamides were converted into corresponding thio-oxahydrazides by the Willgerodt–Kindler reaction. Following acylation by (4-nitro-1H-imidazol-1-yl)acetic acid, these compounds were converted into the target hybrid imidazolyl-thiadiazoles at 29–54% yields.Conclusions. Two series of new heterocyclic compounds with a hybrid structure including a privileged 4-nitroimidazole moiety linked to the second heterocycle, imidazole, or thiadiazole, were obtained. The synthesis and characterization of compounds by physicochemical methods was aimed at searching for anti-tuberculosis activity. The bioactivity potential of target compounds was demonstrated by preliminary calculations performed using public prognostic programs.Цели. Разработка синтеза гибридных молекул c потенциальной противотуберкулезной активностью, содержащих гетероциклические системы 4-нитроимидазола и 1,3,4-тиадиазола, в рамках стратегии «double drug». Анализ соответствия их расчетных физико-химических параметров интервалам значений для лекарственно-подобных («drug-likeness») соединений.Методы. Целевые соединения были получены классическими методами органического синтеза. Структура полученных соединений была охарактеризована температурами плавления, спектроскопией ядерного магнитного резонанса 1H и 13C, масс-спектрометрией высокого разрешения. Расчет физико-химических параметров целевых соединений и прогнозирование их биологической активности проводили с использованием общедоступного программного обеспечения для хемоинформатитки и молекулярного моделирования.Результаты. Ацилированием пропаргиламина (2-метил-4-нитро-1Н-имидазол-1-ил)уксусной и (4-нитро-1Н-имидазол-1-ил)уксусной кислотами были получены пропаргиламиды, которые циклизовали с 7 различными бензиламинами в присутствии трифлата цинка. Таким способом с выходами 20–30% от теоретического была получена серия из 7 новых 2-[(4-нитро-1Н-имидазол-1-ил)метил]-1-бензил-5-метил-1Н-имидазолов. 10 ариламинов были ацилированы хлорацетилхлоридом. Полученные хлорацетамиды реакцией Вильгеродта–Киндлера превратили в соответствующие тиооксагидразиды. Эти соединения после ацилирования (4-нитро-1Н-имидазол-1-ил)уксусной кислотой были превращены циклодегидратацией в целевые гибридные имидазолил-тиадиазолы, с выходами 29–54%.Выводы. Получены две серии новых гетероциклических соединений с гибридной структурой, включающей привилегированный фрагмент 4-нитроимидазола, соединенный алкильным линкером со вторым гетероциклом – имидазолом или тиадиазолом. Соединения сконструированы с целью поиска противотуберкулезной активности, синтезированы и охарактеризованы физико-химическими методами. Предварительные расчеты, выполненные с помощью общедоступных прогностических программ, показали возможный потенциал биологической активности целевых структур

Особенности оптимизации мультипраймерной ПЦР для выявления возбудителей инфекционной пневмонии человека

Objectives. The objectives of this work are the development of a multi-primer system based on the polymerase chain reaction (PCR) aimed at the simultaneous detection of six bacterial pathogens that cause human pneumonia and the determination of the parameters important for the optimization of this multi-primer system, including solid-phase PCR systems (biological microarrays).Methods. To determine the optimal parameters of the system, PCR methods were used in monoplex and multiplex formats.Results. Primers for Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenza, Legionella pneumophila, Klebsiella pneumoniae, and Streptococcus pneumoniae detection were designed, and the PCR cycling conditions were optimized. The patterns of primer design for solidphase PCR were revealed.Conclusions. The developed prototype of a system specifically identifies six clinically significant bacterial pathogens. It could be expanded for the analysis of viral and fungal pathogens and used in clinical diagnostics. A prototype of a system for pathogenic agent detection in the immobilized phase (biological microarray) was created.Цели. Разработка мультипраймерной системы на основе полимеразной цепной реакции (ПЦР), направленной на одновременное выявление шести основных бактериальных возбудителей пневмонии человека; выявление параметров и закономерностей, имеющих важное значение для оптимизации мультипраймерной системы, в том числе для разработки систем ПЦР в иммобилизованной фазе (на биологическом микрочипе).Методы. Для определения оптимальных параметров системы использовали методы ПЦР в т.н. «моноплексном» и мультиплексном форматах.Результаты. Сконструированы праймеры, и оптимизирован температурно-временной профиль проведения ПЦР в объеме для выявления Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenza, Legionella pneumophila, Klebsiella pneumoniae и Streptococcus pneumoniae. Выявлены закономерности конструирования праймеров для ПЦР в иммобилизованной фазе.Выводы. Изученные закономерности особенностей оптимизации мультипраймерных систем позволили разработать прототип системы, способной специфично выявлять шесть клинически значимых возбудителей пневмонии человека. Прототип системы может быть расширен для анализа вирусных и грибковых патогенов и применяться в клинической диагностике. Результаты изучения особенностей мультиплексной ПЦР в иммобилизованной фазе привели к созданию прототипа системы для выявления патогенных агентов на биологическом микрочипе

Specific Features of Lluminescence of Oxygen-Deficient Centres in Nanostructured Silicon Dioxide

Specific features of radiative and non-radiative relaxations of oxygen-deficient centres (ODC's) in nanostructured silicon dioxide were studied using optically stimulated electron emission and time-resolved photoluminescence. It was found that modifications of oxygen-deficient centres in the form of surface analogues can exist in nanostructured samples prepared by thermal decomposition of polysilazane in air. Photoluminescence of these centres was efficiently excited in the optical absorption bands of surface Es′-centres and silicon clusters {triple bond, long} SiSiSi {triple bond, long} and could be associated with the intercentre energy transfer during their nonradiative relaxation. Specific features of thermally induced changes in the luminescence characteristics of the defects due to transformation of the structure of silica samples from amorphous to partially crystalline modification were established from analysis of the spectral composition and the decay kinetics of the photoluminescence. © 2007.This study was supported by RFBR (Projects Nos. 04-02-96073, 05-02-16448 and 05-02-16530) and the RF Ministry of Education (Project RNP.2.1.1.2948)

Regularities of fracture pattern formation in alumina ceramics subjected to dynamic indentation

In this paper the process of dynamic indentation, causing deformation and fracture of alumina ceramics, is investigated. The dynamic indentation experiments were carried out on the original setup based on the split Hopkinson bar technique. The regularities of structure evolution caused by indenter penetration are studied using the computer tomography data of the samples subjected to different loads. The investigation revealed the existence of comminuted area in the vicinity of the indenter and the formation of multiple cracks in the zone lying below. It was found that the higher is the applied indentation load, the denser is the crack pattern and larger are the cracks. A similarity of such a mechanical behavior between the examined material and dentin taken as a biocomposite is discussed

Regularities of fracture pattern formation in alumina ceramics subjected to dynamic indentation

In this paper the process of dynamic indentation, causing deformation and fracture of alumina ceramics, is investigated. The dynamic indentation experiments were carried out on the original setup based on the split Hopkinson bar technique. The regularities of structure evolution caused by indenter penetration are studied using the computer tomography data of the samples subjected to different loads. The investigation revealed the existence of comminuted area in the vicinity of the indenter and the formation of multiple cracks in the zone lying below. It was found that the higher is the applied indentation load, the denser is the crack pattern and larger are the cracks. A similarity of such a mechanical behavior between the examined material and dentin taken as a biocomposite is discussed

Genotypic and ecological variability of zinc content in the grain of spring bread wheat varieties in the international nursery KASIB

Spring bread wheat is the staple crop in Western Siberia and Kazakhstan, a significant portion of which goes for export. Wheat breeding with a high level of zinc in wheat grain is the most cost-effective and environmentally friendly way to address zinc de iciency in the diet. The purpose of this work was to evaluate the contribution of the factors ‘location’ and ‘genotype’ in the variability of zinc content in wheat grain, and to identify the best varieties as sources of this trait for breed-ing. The research on screening zinc content in the wheat grain of 49 spring bread wheat varieties from the Kazakhstan-Siberia Spring Wheat Trial (KASIB) nursery was carried out at 4 sites in Russia (Chelyabinsk, Omsk, Tyumen, Novosibirsk) and 2 sites in Kazakhstan (Karabalyk and Shortandy) in 2017–2018. The content of zinc in wheat grain was evaluated at the Ionomic Facility of University of Nottingham in the framework of the EU pro ject European Plant Phenotyping Network-2020. The analysis of variance showed that the main contribution into the general phenotypic variation of the studied trait, 38.7 %, was made by the factor ‘location’ due to different contents of zinc and moisture in the soil of trial sites; the effect of the factor ‘year’ was 13.5 %, and the effect of the factor ‘genotype’ was 8.0 %. The most favorable environmental conditions for accumulation of zinc in wheat grain were observed in the Omsk region. In Omsk, the average zinc content in all studied varieties was 50.4 mg/kg, with 63.7 mg/ kg in the best variety ‘OmGAU 100’. These values are higher than the target values of the international program Harvest Plus. ‘Novosibirskaya 16’ (49.4 mg/kg), ‘Silach’ (48.4 mg/kg), ‘Line 4-10-16’ (47.2 mg/ kg), ‘Element 22’ (46.3 mg/kg) and ‘Lutescens 248/01’ (46.0 mg/kg) were identi ied as being the best varieties. Significant possibilities for the production of wheat grain with high zinc content, which is in demand for the production of bread and pastry products with functional properties, were identified in the Western Siberian region