Phosphatidylinositol 5-Phosphate Links Dehydration Stress to the Activity of ARABIDOPSIS TRITHORAX-LIKE Factor ATX1

Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) tri-methylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 contains a PtdIns5P interaction domain (PHD finger) and thus, phosphoinositide signaling, may link environmental stress to changes in gene transcription.Using the plant Arabidopsis as a model system, we demonstrate a link between PtdIns5P and the activity of the chromatin modifier ATX1 in response to dehydration stress. We show for the first time that dehydration leads to an increase in cellular PtdIns5P in Arabidopsis. The Arabidopsis homolog of myotubularin (AtMTM1) is capable of generating PtdIns5P and here, we show that AtMTM1 is essential for the induced increase in PtdIns5P upon dehydration. Furthermore, we demonstrate that the ATX1-dependent gene, WRKY70, is downregulated during dehydration and that lowered transcript levels are accompanied by a drastic reduction in H3K4me3 of its nucleosomes. We follow changes in WRKY70 nucleosomal K4 methylation as a model to study ATX1 activity at chromatin during dehydration stress. We found that during dehydration stress, the physical presence of ATX1 at the WRKY70 locus was diminished and that ATX1 depletion resulted from it being retained in the cytoplasm when PtdIns5P was elevated. The PHD of ATX1 and catalytically active AtMTM1 are required for the cytoplasmic localization of ATX1.The novelty of the manuscript is in the discovery of a mechanistic link between a chromatin modifying activity (ATX1) and a lipid (PtdIns5P) synthesis in a signaling pathway that ultimately results in altered expression of ATX1 dependent genes downregulated in response to dehydration stress

State support of stability in Coal-Donbas regions

Purpose. To develop a new approach to feasibility assessment mechanism of supporting production facilities of loss-making mines in Donetsk and Dnipropetrovsk regions. Methods. To solve the objective set, a complex approach was used including as-sessment of enterprise investment attractiveness, determination of production potential, definition of the ability to switch to a break-even mode. The process for planning ways to save the industrial potential of coal-mining regions may be considered as the reflection of multidimensional space (initial and design values) into the one-dimensional (amount of investment money). Findings. It has been established that on the stage of building a model for managing mine unprofitability decrease processes, it is necessary to overview 8-10 factorial features, which may determine the formation of economic potential, taking into consideration peculiarities of remaining deposit bedding and their quality, as integral assessment of mine potential in terms of (state and non-state) investment perception. The objective set comes down to selection of the mini-mum number of factors, which would the most adequately reflect the mine internal potential expressed by economic value added – as a consequence of interaction of factors of coal mine economic activities in specific mining, geological and technological conditions. Originality. The academic novelty is that as a complex component of the state of the loss-making mine, it is reasonable to use an indicator of economic reliability, which synthesizes the capacity of links, economic level of technical and economic indicators and the amount of remaining deposits. The latter determine the residual life of the mine, physical content of the proposed indicators is not identical, and it is this fact, which allows for their joint use to obtain a more complete estimate than when using any single indicator. Practical implications. Practical significance includes actual assessment of the state of Donbass coal enterprises and determination of marginal break-even indicators, which allowed for the formation of recommendations for attracting financial resources

Organization of production activities of a regional coal-mining complex

Objective is to propose a new approach to investment allocation in the group of coal-mining enterprises. Methods. To solve the specified objective, a complex approach has been applied including assessment of enterprise investment attractiveness, determination of production potential, and definition of the possibility to switch to a break-even mode. The process of planning the ways to save industrial potential of coal-mining regions may be considered as the representation of multidimensional space (initial and design values) in terms of the one-dimensional (amount of investment money) one. Findings. It has been established that the stage dealing with the development of a model for managing processes for mine unprofitability reduction should involve consideration of 8-10 factorial features, which may determine the formation of economic potential, taking into account peculiarities of the remaining deposits and their quality, as the integral assessment of mine potential in terms of both state and non-state investments. The formulated objective means selection of the minimum number of factors, which would reflect in the most adequate way the internal potential of a mine expressed by economic added value – as a consequence of interaction of factors of coal mine economic activities in specific mining, geological, and technological conditions. Originality of the research is in the fact that it is expedient to use an indicator of economic reliability, which synthesizes the capacity of links, economic level of technical and economic indicators, and the amount of remaining deposits, as a complex component of the level of an unprofitable mine. The mentioned indicators determine the residual life of the mine. Their physical content is not identical; and it is the fact that helps (in terms of their joint use) obtain more complete estimate than when using any single indicator. Practical implications. Practical significance includes actual assessment of the state of Donbas coal enterprises and determination of marginal break-even indicators, which has made it possible to elaborate recommendations for attracting financial resources

Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses

Analysis of shotgun proteomics datasets requires techniques to distinguish correct peptide identifications from incorrect identifications, such as linear discriminant functions and target/decoy protein databases. We report an efficient, flexible proteomic analysis workflow pipeline that implements these techniques to control both peptide and protein false discovery rates. We demonstrate its performance by analyzing two-dimensional liquid chromatography separations of lens proteins from human, mouse, bovine, and chicken lenses. We compared the use of International Protein Index databases to UniProt databases and no-enzyme SEQUEST searches to tryptic searches. Sequences present in the International Protein Index databases allowed detection of several novel crystallins. An alternate start codon isoform of βA4 was found in human lens. The minor crystallin γN was detected for the first time in bovine and chicken lenses. Chicken γS was identified and is the first member of the γ-crystallin family observed in avian lenses

PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx

Flexural performance of concrete beams reinforced with steel–FRP composite bars

YesFlexural performance of concrete beams reinforced with steel–FRP composite bar (SFCB) was investigated in this paper. Eight concrete beams reinforced with different bar types, namely one specimen reinforced with steel bars, one with fiber-reinforced polymer (FRP) bars and four with SFCBs, while the last two with hybrid FRP/steel bars, were tested to failure. Test results showed that SFCB/hybrid reinforced specimens exhibited improved stiffness, reduced crack width and larger bending capacity compared with FRP-reinforced specimen. According to compatibility of strains, materials’ constitutive relationships and equilibrium of forces, two balanced situations, three different failure modes and balanced reinforcement ratios as well as analytical technique for predicting the whole loading process are developed. Simplified formulas for effective moment of inertia and crack width are also proposed. The predicted results are closely correlated with the test results, confirming the validity of the proposed formulas for practical use.National Natural Science Foundation of China (51678514), China Postdoctoral Science Foundation (2018M642335), the Science and Technology Project of Jiangsu Construction System (2018ZD047), the Cooperative Education Project of Ministry of Education, China (201901273053), the Blue Project Youth Academic Leader of Colleges and Universities in Jiangsu Province (2020), the Six Talent Peaks Project of Jiangsu Province (JZ038, 2016) and the Yangzhou University Top Talents Support Projec