Improving the quality of barley transcriptome <i>de novo</i> assembling by using a hybrid approach for lines with varying spike and stem coloration

De novo transcriptome assembly is an important stage of RNA-seq data computational analysis. It allows the researchers to obtain the sequences of transcripts presented in the biological sample of interest. The availability of accurate and complete transcriptome sequence of the organism of interest is, in turn, an indispensable condition for further analysis of RNA-seq data. Through years of transcriptomic research, the bioinformatics community has developed a number of assembler programs for transcriptome reconstruction from short reads of RNA-seq libraries. Different assemblers makes it possible to conduct a de novo transcriptome reconstruction and a genome-guided reconstruction. The majority of the assemblers working with RNA-seq data are based on the De Bruijn graph method of sequence reconstruction. However, specif ics of their procedures can vary drastically, as do their results. A number of authors recommend a hybrid approach to transcriptome reconstruction based on combining the results of several assemblers in order to achieve a better transcriptome assembly. The advantage of this approach has been demonstrated in a number of studies, with RNA-seq experiments conducted on the Illumina platform. In this paper, we propose a hybrid approach for creating a transcriptome assembly of the barley Hordeum vulgare isogenic line Bowman and two nearly isogenic lines contrasting in spike pigmentation, based on the results of sequencing on the IonTorrent platform. This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. It was shown that, based on the summation of these metrics, transcriptome meta-assembly surpasses individual transcriptome assemblies it consists of

Evaluation of Electronic Spectra of Unsaturated Organic Compounds Using the Pariser-Parr-Pople Method with Adaptation of Parameters

The possibility of quantitative predictions of absorption maxima in electronic spectra of unsaturated organic compounds by means of the Pariser-Parr-Pople method with adaptation of parameters is examined. A schematic classification of quantum chemical methods is proposed which is based on the idea of extrapolation from elementary particles (physical constants) to the molecule, from atoms to the molecule and, finally, from fragments to the molecule

In situ X-ray diffraction investigation of nitride coatings at high-temperature oxidation

Structural and phase researches of the multicomponent nanocrystalline coatings synthesized by plasma-assisted vacuum arc method at high-temperature influence by method of X-ray diffraction with the use of synchrotron radiation in situ have been carried out. The main features of these coatings are the superhardness (39 - 45 GPa) and nanocrystalline structure (5 - 20 nm). The analysis of results of structural and phase researches, physical and mechanical characteristics after oxidation of multicomponent nitride coatings at high-temperature heating in open air is presented

Somatic embryogenesis in Larix: the state of art and perspectives

Clonal propagation of conifers using somatic embryogenesis is essential for the selection of tree species, and for the implementation of afforestation and reforestation. In combination with cryopreservation, somatic embryogenesis creates the basis for the development of economically valuable lines of clones and elite genotypes. The industrial use of such genetically verified clone lines in forestry can significantly increase forest productivity compared to any conventional methods for improving tree crops that are available. Larch is considered as one of the main conifer candidates for large-scale reforestation, not only due to the vastness of its habitat, but also due to the unique quality of its wood, rapid growth and high ecological plasticity. However, the vast majority of larch species are characterized by uneven yields and extremely low seed quality. In this regard, obtaining planting material for reforestation from larch seeds on seed plantations is not advisable, but can be successfully implemented in afforestation programs using somatic embryogenesis technologies. Research on the somatic embryogenesis of larch has been conducted for over 30 years, which allowed considerable experience in this field to be accumulated. To date, the conditions for the initiation and maintenance of embryogenic cultures, as well as for the formation and development of somatic embryos have been determined. Significant progress has been made in the study of both the factors affecting these processes and the molecular mechanisms that underlie the various stages of embryogenesis. Nevertheless, despite the successes achieved, knowledge available today on the somatic embryogenesis of representatives of the genus Larix is still not enough to develop technologies for producing valuable plant-breeding material in vitro. This review analyzes the current state of research on the problem of somatic embryogenesis of representatives of the genus Larix. Particular attention is paid to the choice of explants for somatic embryogenesis, the composition of the media for cultivation, the dependence of the potential of somatic embryogenesis on the duration of cultivation, and the genetic control of somatic embryogenesis

Condensation of a tetrahedra rigid-body libration mode in HoBaCo4O7 : the origin of phase transition at 355 K

Rietveld profiles, Moessbauer spectra and x-ray absorption fine structure (XAFS) were analyzed through the structural phase transition at Ts = 355 K in HoBaCo4O7. Excess of the oxygen content over O7 was avoided via annealing the samples in argon flow at 600 degree C. Space groups (S.G.) Pbn21c and P63mc were used to refine the structure parameters in the low- and high-temperature phases, respectively. Additionally, the Cmc21 symmetry was considered as a concurrent model of structure of the low-temperature phase. In the high-temperature phase, severe anisotropy of thermal motion of the major part of the oxygen atoms was observed. This anisotropic motion turns to be quenched as the sample is cooled below Ts. The variation of quadrupole splitting near Ts is not similar to a steplike anomaly frequently seen at the charge-ordering transition. We observe instead a dip-like anomaly of the average quadrupole splitting near Ts. Narrow distribution of the electric field gradient (EFG) over different cobalt sites is observed and explained on the basis of point-charge model. XAFS spectra show no evidence of significant difference between YBaCo4O7 (T > Ts) and HoBaCo4O7 (T < Ts). The origin of the transition at Ts is ascribed to the condensation of the libration phonon mode associated with the rigid-body rotational movements of the starlike tetrahedral units, the building blocks of kagome network. It is shown that the condensation of the libration mode is not compatible with translation symmetry for the hexagonal S.G., but compatible for the orthorhombic S.G. The orthorhombic lattice parameters and EFG components (Vxx, Vyy, Vzz) vary smoothly with temperature at approaching Ts and closely follow each other.Comment: 13 figure

ВЛИЯНИЕ ЗАБОЛЕВАНИЯ НА РАСХОД ЭНЕРГИИ У НОВОРОЖДЕННЫХ

Purpose. With the aid of indirect calorimetry, to evaluate whether the nosological factors affect energy exchange in severely ill newborns.Materials and methods. Indirect calorimetry was employed to determine the true energy expenditure in new borns under the mechanical ventilation because of intranatal postanoxia encephalopathy (n=19), severe sepsis (n=18), and urgent surgery (n=19). Energy expenditure at rest was estimated at the beginning of intensive therapy and in in 48 hours. Sedation in groups was similar.Results. At the first stage, the energy exchange in all newborns was characterized by hypometabolism. In cases of damage of the central nervous system the anaerobic metabolism was increased, and the principal used substrate was glucose; the most prolonged hypometabolism was revealed in newborns with sepsis, in which the utilization of lactate was decreased, and the main energetic substrate were lipids; in early postoperative period, the decrease in energy expenditure was not associated with preferential oxidation of glucose or lipids, and disappeared due to elimination of anesthetics.Conclusion. Energetic hypometabolism can be considered as a main reaction of the newborn organism to previous invasion. Acute posthypoxic brain damage in newborns is characterized by high activity of peroxidation associated with hypometabolism. For newborns with severe sepsis a slow recovery of aerobic metabolism and intensity of energy expenditure were evident. Early postoperative period in newborns was characterized by profound iatrogenic hypometabolism with fast normalization of energy expenditure.Цель. На основе непрямой калориметрии установить наличие, характер и значимость влияния нозологических факторов на обмен энергии у тяжелобольных новорожденных.Материалы и методы. Методом непрямой калориметрии провели определение истинного расхода энергии у новорожденных, получавших искусственную вентиляцию легких по поводу интранатальной постаноксической энцефалопатии (19 человек), тяжелого сепсиса (15 человек), оперированных по экстренным показаниям (19 человек). Потребление энергии в покое определяли на этапе начала интенсивной терапии и в динамике через 48 часов. Влияние фактора седации в группах было одинаковым.Результаты. Обмен энергии на первом этапе у всех новорожденных характеризовался гипометаболизмом. При поражении центральной нервной системы повышен анаэробный метаболизм, основной используемый субстрат — глюкоза; при сепсисе самый длительный гипометаболизм, снижена утилизация лактата, основной энергетический субстрат — липиды; в раннем послеоперационном периоде снижение расхода энергии исчезало по мере элиминации анестетиков и не связано с преимущественным окислением глюкозы или липидов.Заключение. Энергетический гипометаболизм может рассматриваться как типичный ответ организма новорожденного на перенесенную агрессию. Острые постгипоксические поражения головного мозга у новорожденных характеризовались высокой активностью перекисного окисления на фоне гипометаболизма. Для тяжелого сепсиса новорожденных было характерно замедленное восстановление аэробного метаболизма и интенсивности расхода энергии. Ранний послеоперационный период у новорожденных характеризовался глубоким ятрогенным гипометаболизмом с быстрой нормализацией расхода энергии

Конспект рода Anopteris (Pteridophyta, Pteridaceae)

In the article a synopsis of the genus Anopteris (Prantl) Diels is given. The synopsis of Anopteris includes three species. For each species, the Latin name, basionym, nomenclatural citation, synonyms, information on locus classicus, type, habitat, and distribution are given. An original key for identification of the species of Anopteris is also prepared. The localities of occurrence of each species are precisely given. Приведен конспект рода Anopteris (Prantl) Diels. Конспект включает три вида. Для каждого из них приводится латинское название, базионим, номенклатурная цитата, синонимы, откуда описан, информация о типе, данные о местообитании, распространение по странам с цитированием мест сбора и общее распространение. Для определения всех видов рода Anopteris составлен оригинальный ключ, указаны подробные места произрастания. Приведен конспект рода Anopteris (Prantl) Diels. Конспект включает три вида. Для каждого из них приводится латинское название, базионим, номенклатурная цитата, синонимы, откуда описан, информация о типе, данные о местообитании, распространение по странам с цитированием мест сбора и общее распространение. Для определения всех видов рода Anopteris составлен оригинальный ключ, указаны подробные места произрастания.

PLACE OF LOW-MOLECULAR-WEIGHT HEPARINS IN INTENSIVE THERAPY OF HEPATIC INSUFFICIENCY

The practical significance of heparin low-molecular fractions as inhibitors of inflammation and antithrombin III consumption reduction were studied. That is most critical in acute hepatic failure. The study was performed using the low-molecular-weight heparin (Nadroparin calcium) in low (prophylactic) doses of 2000 anti-factor Xa units daily per 1 meter squared in the form of continuous intravenous infusion. The cohort study proved the nadroparin positive effect on carbohydrate and protein metabolism in children with acute poisoning by hepatotoxic poisons, The significant decrease in the quantitative assessment of disseminated intravascular coagulation relative to the comparison group has been revealed, and the decrease in 28-day mortality from 42 to 13 % has been found in children receiving nadroparin. Conclusions are drawn on the feasibility of introducing low molecular weight heparins into the intensive care regimen of liver failure

Comparison of induction heating parameters of various billets

In this paper, we consider the induction heating of various forms of blanks using a laboratory Autoclave. The thermal and energy characteristics are compared.В данной работе рассматривается индукционный нагрев различных форм заготовок с помощью лабораторной установки Автоклав. Проводится сравнение тепловых и энергетических характеристик