Proceedings of the Scientific-Practical Conference "Research and Development - 2016"

This open access book relates to the III Annual Conference hosted by the Russian Federal Ministry of Education and Science in December 2016. This event has summarized, analyzed and discussed the interim results, academic outputs and scientific achievements of the Russian Federal Targeted Programme for Research and Development in priority areas of development of the Russian Scientific and Technological Complex for 2014-2020. It contains 75 selected papers from 6 areas considered priority by the Federal programme: computer science, ecology & environment sciences; energy and energy efficiency; life sciences; nanoscience & nanotechnology; and transport & communications. The chapters report the results of the 3-years research projects supported by the Programme and finalized in 2016

Bacteriophages of soil bacilli: A new multivalent phage of Bacillus altitudinis

© 2017, Allerton Press, Inc. Bacillus are soil saprophytes, facultative anaerobes developing in the temperature range of 28–37°С. 16S rRNA cataloging shows that these bacteria form a coherent class with broad variability of virulence. Bacillus phages can be extensively used for phagotyping bacteria in the process of soil, water, and food monitoring. Bacillus phages can also be used as vectors in horizontal gene transfer and potential therapeutic agents. Thus, description of the biological diversity of the Bacillus phages is useful for further development of tools used in molecular biology and biomedicine. In this work, the scheme for isolation of soil bacteriophages was unified, which allowed ten bacillus phages to be isolated from different types of soil. It was shown that the number of phages depended on the soil fertility, decreasing as the soil changed from black soil to chestnut soil to gray forest soil to uncontaminated urban soil to oil-contaminated urban soil. A new polyvalent DNA-containing bacteriophage SRT01hs of B. altitudinis (it is also able to infect B. subtilis, B. cereus, and B. pumilus, but not B. licheniformis and B. atrophaeus) was described in detail. It has a typical structure: a total length of 360 nm and an icosahedron-shaped head 100 nm in diameter. Several phages simultaneously attack a B. altitudinis cell by increasing the level of intracellular low-molecular RNA. Infection with the phage virtually eliminates the stationary growth phase of infected bacilli and leads to a permanent increase in the number of phages in cultural liquor, with the exception of the time period of high activity of the secreted ribonuclease

IMPROVING THE THERMAL-HYDRAULIC EFFICIENCY OF BOILERS AND HEAT EXCHANGERS USING COMPACT TUBE BUNDLES

Проведен сравнительный анализ интенсивности теплообмена и гидравлического сопротивления трубных пучков различной конфигурации в котлах и теплообменных аппаратах. Применительно к змеевикам с пружинно-витыми каналами разработана геометрическая модель поверхности теплообмена для расчетов термомасляных и прямоточных паровых котлов в среде ANSYS.A comparative analysis of the heat exchange intensity and hydraulic resistance of tube bundles of different configurations in boilers and heat exchangers is carried out. In relation to coils with spring-twisted channels, a geometric model of the heat exchange surface has been developed for calculations of thermal oil and direct-flow steam boilers in the ANSYS environment

Polarization Dependence of Anomalous X-ray Scattering in Orbital Ordered Manganites

In order to determine types of the orbital ordering in manganites, we study theoretically the polarization dependence of the anomalous X-ray scattering which is caused by the anisotropy of the scattering factor. The general formulae of the scattering intensity in the experimental optical system is derived and the atomic scattering factor is calculated in the microscopic electronic model. By using the results, the X-ray scattering intensity in several types of the orbital ordering is numerically calculated as a function of azimuthal and analyzer angles.Comment: 9 pages, 7 figure

Resonant X-ray Scattering in Manganites - Study of Orbital Degree of Freedom -

Orbital degree of freedom of electrons and its interplay with spin, charge and lattice degrees of freedom are one of the central issues in colossal magnetoresistive manganites. The orbital degree of freedom has until recently remained hidden, since it does not couple directly to most of experimental probes. Development of synchrotron light sources has changed the situation; by the resonant x-ray scattering (RXS) technique the orbital ordering has successfully been observed . In this article, we review progress in the recent studies of RXS in manganites. We start with a detailed review of the RXS experiments applied to the orbital ordered manganites and other correlated electron systems. We derive the scattering cross section of RXS where the tensor character of the atomic scattering factor (ASF) with respect to the x-ray polarization is stressed. Microscopic mechanisms of the anisotropic tensor character of ASF is introduced and numerical results of ASF and the scattering intensity are presented. The azimuthal angle scan is a unique experimental method to identify RXS from the orbital degree of freedom. A theory of the azimuthal angle and polarization dependence of the RXS intensity is presented. The theoretical results show good agreement with the experiments in manganites. Apart from the microscopic description of ASF, a theoretical framework of RXS to relate directly to the 3d orbital is presented. The scattering cross section is represented by the correlation function of the pseudo-spin operator for the orbital degree of freedom. A theory is extended to the resonant inelastic x-ray scattering and methods to observe excitations of the orbital degree of freedom are proposed.Comment: 47 pages, 24 figures, submitted to Rep. Prog. Phy

Analysis of the Key Directions of Low-Carbon Transformation of the Moscow Economy for the Period until 2035

Принятие федеральной Стратегии социально-экономического развития Российской Федерации с низким уровнем выбросов парниковых газов до 2050 года определяет необходимость учета климатического аспекта в стратегическом планировании, в том числе на уровне отдельных регионов и городов. Цель статьи заключается в анализе ключевых и наиболее эффективных направлений низкоуглеродной трансформации экономики города Москвы. Исследование опирается на методы математического моделирования и сценарного прогнозирования, модельный инструментарий разработан для оценки прямых эмиссий парниковых газов, обусловленных потреблением топливноэнергетических ресурсов. Москва является регионом-лидером в части снижения эмиссий парниковых газов: за 2012-2019 гг. они сократились на 9 % благодаря модернизации сектора энергоснабжения, приоритезации когенерации, развитию городского транспорта. На период до 2035 г. реалистичной и достижимой является цель снижения эмиссий еще на 7-11 %. Для этого необходимо активизировать меры по следующим ключевым направлениям: энергоэффективные капитальные ремонты и новое строительство (включая программу реновации), автоматизация центральных тепловых пунктов и узлов управления системами теплоснабжения в сфере зданий и ЖКХ, полная электрификация общественного транспорта, стимулирование топливной эффективности и использования электромобилей (личных, а также в сфере такси, каршеринга, доставки, коммерческих перевозок) в сфере транспорта. В сфере энергетики следует отказаться от форсированного наращивания собственной электрогенерации: альтернативой должны стать поддержание существующих эффективных генерирующих мощностей и закупка недостающих объемов на профицитном оптовом рынке электроэнергии. Для обеспечения условий низкоуглеродной трансформации Москвы целесообразно внедрить критерий влияния принимаемых мер на объем эмиссий при планировании всех городских программ, схем развития и инвестиционных проектов. Результаты и выводы статьи могут быть полезны при разработке документов стратегического планирования города Москвы.The adoption of the Strategy for the socio-economic development of the Russian Federation with low greenhouse gas emissions until 2050 requires considering the climate aspect of strategic planning, including at the regional and city levels. The article analyses key areas of low-carbon transformation of the Moscow economy. The study is based on the methods of mathematical modelling and scenario forecasting, utilised to estimate direct greenhouse gas emissions from energy and fuel consumption. Moscow is the leading region in terms of reducing greenhouse gas emissions, as they decreased by 9 % in 20122019 due to the modernisation of the energy sector, use of cogeneration, and development of urban transport. For the period until 2035, a realistic and achievable goal is to reduce emissions by another 7-11 %. To this end, it is necessary to strengthen measures in the following areas: energy-efficient capital repairs and construction (including the renovation programme); automation of central heating systems and heat supply units of buildings and housing and communal services; full electrification of public transport; promotion of fuel efficiency and the use of electric vehicles (personal and commercial transport, taxi, carsharing, delivery). In the energy sector, we recommend to maintain the existing generating capacities and purchase the rest on the surplus energy market rather than forcibly increase power generation. To ensure low-carbon transformation of Moscow, the criterion of the impact of adopted measures on emissions should be introduced and considered when planning city programmes, development schemes and investment projects. The research findings may be used to create strategic planning documents for Moscow.Авторы выражают признательность С. Р. Милякину, А. А. Галингеру, Н. Д. Курдюковой (ИНП РАН), А. О. Миронович, С. Н. Щукину (ЦНП) за значимый вклад в результаты исследования.The authors would like to express their gratitude to S. R. Milyakin, A. A. Galinger, N. D. Kurdyukova (Institute of Economic Forecasting of RAS,), A. O. Mironovich and S. N. Shchukin (Tax Policy Center) for their valuable contributions to the study

Effect of Strain Magnitude on the Tissue Properties of Engineered Cardiovascular Constructs

Mechanical loading is a powerful regulator of tissue properties in engineered cardiovascular tissues. To ultimately regulate the biochemical processes, it is essential to quantify the effect of mechanical loading on the properties of engineered cardiovascular constructs. In this study the Flexercell FX-4000T (Flexcell Int. Corp., USA) straining system was modified to simultaneously apply various strain magnitudes to individual samples during one experiment. In addition, porous polyglycolic acid (PGA) scaffolds, coated with poly-4-hydroxybutyrate (P4HB), were partially embedded in a silicone layer to allow long-term uniaxial cyclic mechanical straining of cardiovascular engineered constructs. The constructs were subjected to two different strain magnitudes and showed differences in biochemical properties, mechanical properties and organization of the microstructure compared to the unstrained constructs. The results suggest that when the tissues are exposed to prolonged mechanical stimulation, the production of collagen with a higher fraction of crosslinks is induced. However, straining with a large strain magnitude resulted in a negative effect on the mechanical properties of the tissue. In addition, dynamic straining induced a different alignment of cells and collagen in the superficial layers compared to the deeper layers of the construct. The presented model system can be used to systematically optimize culture protocols for engineered cardiovascular tissues

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p>Abstract</p> <p>Background</p> <p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it>Quercus robur</it>, its characterization and an analysis of BAC end sequences.</p> <p>Results</p> <p>The <it>Eco</it>RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it>ab initio </it>repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it>Arabidopsis thaliana</it>, <it>Vitis vinifera </it>and <it>Populus trichocarpa</it>. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it>V. vinifera.</it></p> <p>Conclusions</p> <p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p

Considering Transposable Element Diversification in De Novo Annotation Approaches

Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species