Environmental and Technological Problems of Rational Use of Secondary Resources for Processing Grapes

Rational use of grapes processing resources is among environmental problems of AIC of Republics of the North Caucasus and Krasnodar Territory. Currently, waste from grapes processing is not practically used and worsen the ecological state of environment. The research subject is a technology based on the production of cryo-powder from pulp, squeeze, seeds and grapes skin grown in the foothill and mountainous regions. The prerequisites for research were previously performed author works on related topics. The data on vacuum SHF-drying of grape raw materials and subsequent grinding in a cryomiller are given. Modes of preparation of grape raw materials and its subsequent dehydration and cryo-grinding, which provide the possibility of successful use in the dried state in the production technology of wine beverages, are proposed. The principal feature is the use of whole grapes as a raw material, with skin and seeds. Physico-chemical parameters, the content of phenolic substances and organoleptic characteristics of wine beverages made according to the traditional technology and the beverage made from grape cryo-powders are studied. A comparative assessment is made. It is established that vacuum SHF-drying contributes to better preservation of the properties of raw materials and finished products. The organoleptic assessment has shown that wine beverages developed according to the proposed technology had a more intense color and a more pronounced taste of sweetness and acid than traditional wine beverages. The advantage of this technology is the ability to transport grape cryo-powders in unregulated temperature conditions to any point close to the consumer and carry out the production of nutritional food there

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance

Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. These DEFLs, in concert with other defense molecules, are suggested to determine enhanced resistance of elicitor-pretreated wheat seedlings. In addition to providing a better understanding of the mode of action of the elicitors from FS-94 in controlling diseases, up-regulated IR-specific DEFL genes represent novel candidates for genetic transformation of plants and development of pathogen-resistant crops

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

<p>Abstract</p> <p>Background</p> <p>Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, <it>Fagopyrum esculentum </it>and <it>F. tataricum</it>, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. <it>F. esculentum </it>(common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations <it>Fagopyrum </it>species have not been the subject of large-scale sequencing projects.</p> <p>Results</p> <p>Normalized cDNA corresponding to genes expressed in flowers and inflorescences of <it>F. esculentum </it>and <it>F. tataricum </it>was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for <it>F. esculentum</it>) and 229 (<it>F. tataricum</it>) thousands of reads with average length of 341-349 nucleotides. <it>De novo </it>assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences.</p> <p>Conclusions</p> <p>454 transcriptome sequencing and <it>de novo </it>assembly was performed for two congeneric flowering plant species, <it>F. esculentum </it>and <it>F. tataricum</it>. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.</p

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns of DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that Treg-specific DNA hypomethylated regions were closely associated with Treg up-regulated transcriptional start site clusters, whereas Foxp3 binding regions had no significant correlation with either up- or down-regulated clusters in nonactivated Treg cells. However, in activated Treg cells, Foxp3 binding regions showed a strong correlation with down-regulated clusters. In accordance with these findings, the above two features of activation-dependent gene regulation in Treg cells tend to occur at different locations in the genome. The results collectively indicate that Treg-specific DNA hypomethylation is instrumental in gene up-regulation in steady state Treg cells, whereas Foxp3 down-regulates the expression of its target genes in activated Treg cells. Thus, the two events seem to play distinct but complementary roles in Treg-specific gene expression

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Modelowanie sterowania w hierarchicznym aktywnym systemie z wykorzystaniem paradygmatu entropii analizy subiektywnej

Authors presented and considered a example and algorithms of modeling of control in an active system. The examples analyzed two of subjects and two alternatives. The calculated an entropies and ratings of the subjects. Shaw in investigating the role of the parameter “subjective temperature” a changes in the phase portraits.Autorzy przedstawili i wykazali na przykładzie algorytm modelowania hierarchicznej kontroli nad aktywnym systemem. Przykłady analizują zachowanie dwóch subiektów i dwóch alternatyw. Obliczono entropię i rankingi podmiotów systemu aktywnego. W badaniu pokazano rolę parametru „subiektywnej temperatury” na zmiany portretów fazowych

Zarządzanie hierarchicznym aktywnym systemem na podstawie paradygmatu entropii analizy subiektywnej

The theory of conflicts, as conflicts of preferences distributions, is developed on the basis of this model. A classification of conflicts that reflects, to a significant degree, the existing knowledge in this field is proposed. A conflict transformation from one phase into another is connected with overcoming certain entropy thresholds is considered to be. The dynamics of conflicts, intrapersonal and interpersonal conflicts. The authors discuss a hierarchical system control tasks, diagnostic and preventive measures of a conflict. A control at the stage of the conflict being such a cold conflict. Productive conflicts having often form of a competition, opposition and they stop the destructive conflicts. A subjective analysis provides a method for a formalization of a cold conflict when "muses are silent" go to the hot conflict, when the "cannons thunder", as well as models of the dynamics of mental processes within a paradigm of entropy.Konflikty rozkładów preferencji, zostały opracowane na podstawie modelu konfliktów. Zaproponowano klasyfikację konfliktów, które w znacznym stopniu odzwierciedlają istniejący stan wiedzy w tej dziedzinie. Uważa się, że przechodzenie konfliktów z jednego etapu do drugiego jest połączone z przezwyciężeniem pewnych progów entropii. Omówiona została dynamika konfliktów, konflikty interpersonalne i intrapersonalne. Autorzy omawiają zadania kontroli hierarchicznej systemu, podają niektóre środki diagnostyczne i profilaktyczne rozwoju konfliktu. Kontrola na danym etapie chłodnego konfliktu ma wpływ na konkurencję i często konkurencja, opozycja zatrzymuje destrukcyjne konflikty. Subiektywna analiza dostarcza sposobu na sformalizowania chłodnego konfliktu, oraz przejścia do gorącego konfliktu – gdy „muzy milczą” to „armaty grzmią”. Przedstawiono również modele dynamiki procesów umysłowych w ramach paradygmatu entropii

Узагальнення нерівності Крамера-Рао в разі існуючих апріорних зв'язків між оцінюваними параметрами

It is shown, that the lowest Cramer-Rao bound for statistical estimation could be changed to accounting a priori links between estimated parameters and the residual variances could be essentially reduced. The case of two parameters being linked with algebraic linear equation to be estimated is considered. In the second part of the paper the results of “concordance” of flight information on the base of use of a centre motion and kinematics Euler relationships as a priori links are representedПоказано, что нижняя граница Крамера-Рао для статистических оценок изменена, если алгоритмы оценивания строятся с учетом априорных связей между оцениваемыми величинами и остаточные дисперсии могут быть существенно уменьшены. Рассмотрен случай оценки двух параметров, между которыми существует линейная алгебраическая априорная связь. Представлены результаты согласования полетной информации на основе использования избыточности, содержащейся в уравнениях движения центра масс летательного аппарата и кинематических уравнениях ЭйлераПоказано, що нижня межа Крамера-Рао для статистичних оцінок змінена, якщо алгоритми оцінювання будуються з урахуванням апріорних зв'язків між оцінюваними величинами і залишкові дисперсії можуть бути істотно зменшені. Розглянуто випадок оцінки двох параметрів, між якими існує лінійна алгебраїчна апріорна зв'язок. Представлені результати "узгодження" польотної інформації на основі використання надмірності, що міститься в рівняннях руху центру мас літального апарату і кінематичних рівняннях Ейлер