Protein-Protein Interaction Prediction from Language of Biological Coding

Protein-protein interactions in a cell are essential to the characterization and performance of various fundamental biological processes. Due to the tedious, resource-expensive, and time-consuming experimental processes, computational techniques to solve protein pair interaction difficulties have emerged as an active research area in bioinformatics. This research seeks to develop an innovative machine learning-based technique that predicts the interaction of a protein pair based on carefully selected input features and exploits information-rich evolutionary information. We developed a protein-protein interaction predictor, PPILS, that leverages the evolutionary knowledge from the protein language model. We examined several distinct neural network architectures: CNN+LSTM, Transformer, Encoder-Decoder, and FNN and found that the encoder-decoder architecture with light attention performs the best. The method is straightforward; there are only four learnable weight matrices. The model will receive protein representations from the language model, perform one convolution on them to get attention coefficients, and then normalize them along the length dimension using the SoftMax function to generate attention. A second convolution is applied to input features to create values. Then, take the element-wise product of attention and values to construct a representation of the protein. After calculating the sum over the length dimension, a fixed-size protein representation is obtained. This is then concatenated with the maximum length dimension of the data and fed to the decoder. The decoder is our classification engine to predict protein interactions. We found that the PPILS outperformed other cutting-edge techniques for PPI prediction. We believe the proposed method could serve as an essential tool in protein-protein interaction prediction, further accelerating the protein drug discovery process

Numerical fault simulation in Himalayas with 2 D finite element method

The nature of the stress field in the Himalaya is examined by the 2D finite element method where linear elastic rheology and plain strain condition are assumed. The Mohr-Coulomb failure criterion has been adopted to analyze the relationship between stress distribution and fault formation.Two profile models are prepared and convergent displacement is imposed on them along the NE-SW horizontal direction.The convergent displacement and physical properties of the rock layer control the distribution,orientation,magnitude and intensity of the stress and fault development.According to the calculated stress pattern,thrust faults are expected to develop in the central Himalaya (model A).Normal and some thrust faults take place in the north-western Himalaya (model B).The results from our numerical experiment are in agreement with those from the seismicity and focal mechanism solution of earthquakes and also with those of M.M.Alam and D.Hayashi (Bull.Fac.Sci.Univ. Ryukyus, 73, 15, 2002) in the central Himalaya

Effects of calcium paste as a seed coat on growth, yield and enzymatic activities in NaCl stressed-pea plants

The present study was conducted to study the effect of coating the seeds with calcium paste before sowing, on plant growth, yield, the contents of some antioxidants and the activities of carbonic anhydrase and nitrate reductase in the Pisum sativum L. leaves under the influence of NaCl stress. NaCl stress reduced plant growth, photosynthetic pigment levels, ascorbic acid and calcium contents, and the activities of carbonic anhydrase and nitrate reductase. In contrast, proline and sodium contents were increased. These results are negatively reflected in the yield components. However, seed coating with calcium paste reduced the toxic effects of NaCl on plant growth and yield by increasing leaf pigments, ascorbic acid, proline contents and enzymatic activities. This study clearly highlights the effects of calcium paste as a seed coat in mitigating the phytotoxicity of NaCl stress in pea plants.Keywords: Calcium paste, carbonic anhydrase, nitrate reductase, ascorbate, growth, yield, Pisum sativum

Impacts of Madhas Dam Construction on the Chemical Composition of Plant and Soil Samples from Upstream and Downstream Sites of the Dam

The aim of this study was to assess and compare the impacts of Madhas dam construction on the chemical composition of five plant species (Pluchea dioscoridis, Pulicaria crispa, Tarchonanthus camphoratus, Lavandula pubescens and Argemone ochroleuca) together with soil samples collected from upstream and downstream sites of the dam. Plant samples (stem and leaf) were analyzed for determining total soluble sugars, total free amino acids, free proline, polyphenols, flavonoids and elemental composition. Organic matter and element contents were determined in each soil sample. The studied plants collected from the two sites showed profound variations in their chemical and elemental composition. A significant reduction of sodium content was observed in all plant tissues collected from downstream site of the dam. All plant species from downstream site showed apparent increasing of total soluble sugar, free proline, total polyphenol, flavonoid, nitrogen and potassium contents. Results suggest that the accumulation of these components, in plant species collected from downstream site of the dam, may have an important role in the tolerance of these plants to water stress. Apparent increased of nitrogen, phosphorus, potassium, sodium, calcium, aluminum and manganese levels was noticed in soil samples collected from downstream site of the dam

Empirical study on transformational leadership, deviant behaviour, job performance, and gender : evidence from a study in Bangladesh

This paper studies the relationships between transformational leadership, deviant behaviour, job performance, and gender. Data collected from 160 respondents from different organisations using the convenience sampling method was analysed using descriptive statistics, bivariate correlation, and regression analysis. Results reveal that there is a negative relationship between transformational leadership and deviant behaviour, while a positive association exists between transformational leadership and job performance, with a negative correlation between deviant workplace behaviour and job performance. Gender analysis shows that female ratings for different indicators, such as transformational leadership, deviant behaviour, and job performance were not significantly distinct from those of males. The main implication of this research is that it informs executives how transformational leadership and deviant behaviour affect job performance. Limitations and future research directions are discussed.info:eu-repo/semantics/publishedVersio

Molecular cloning and expression of a vacuolar Na⁺/H⁺ antiporter gene (AgNHX1) in fig (Ficus carica L.) under salt stress

Soil salinity can be a major limiting factor for productivity in agriculture and forestry and in order to fully utilize saline lands productively in plantation forestry for fig production, the genetic modification of tree species for salt tolerance may be required. Na+/H+ antiporters have been suggested to play important roles in salt tolerance in plants. Here, we isolated AgNHX1 a vacuolar Na+/H+ antiporter from a halophytic species Atriplex gmelini and introduced it into fig (Ficus carica L.) cv. Black Mission via Agrobacterium-mediated transformation. Leaf discs explants of fig were co-cultivated for 2 days with Agrobacterium tumefaciens strain LBA 4404 harboring the binary vector pBI121 containing the AgNHX1 gene and the hpt selectable marker gene which encodes hygromycin phosphotransferase. Explants were cultured on MS medium containing 30 mg L−1 hygromycin, 3 % sucrose, 0.2 mg L−1 kinetin and 2.0 mg L−1 2,4-dichlorophenoxyacetic acid solidified with 2.5 g L−1 phytagel in darkness for callus formation. The calli were cultured on MS medium containing 2.0 mg L−1 zeatin riboside in combination with 0.4 mg L−1 indole acetic acid in the light for plant regeneration. Putative regenerated transformant shoots were confirmed by polymerase chain reaction (PCR) and Southern hybridization for the AgNHX1 gene. Reverse transcriptase polymerase chain reaction analysis indicated that the gene was highly expressed in transgenic plants, but the degree of this expression varied among transformants. Overexpression of the AgNHX1 gene conferred high tolerance to salt stress and transgenic fig plants overexpressing AgNHX1 developed normally under salinity conditions compared to those of non-transgenic plants. Salt treated transgenic plants contained high proline and K+ but less Na+ compared to non-transgenic control plants

Growth, heavy metal status and yield of salt-stressed wheat (Triticum aestivum L.) plants as affected by the integrated application of bio-, organic and inorganic nitrogen-fertilizers

Efforts have been made to use the integrated application of bio-, organic and inorganic nitrogen (N)-fertilizers to decrease waste accumulation, and to minimize nutrient losses and yield contamination with heavy metals for human nutrition and health. Therefore, a field experiment was conducted to assess the effect of integrated applications of organic manures, bio-fertilizer and/or mineral-N fertilizers on growth, yield, some chemical constituents and shoot and yielded grain heavy metal contents of wheat (Triticum aestivum L. cv. Sakha 93) plants grown under salinity stress (ECe = 7.84 dS m-1). Results showed that, the treatment comprised of ⅓NH4NO3 (55 kg N ha-1) + Cerealine (bio-fertilizer; 4 Kg ha-1) + cattle manure (10 t ha-1) was found to be most effective, producing the best status of growth characteristics, osmoprotectants concentrations, essential nutrient contents, shoot heavy metal concentrations, and grain yield and its content of heavy metals compared to the all other treatments. The treatment comprised of Cerealine (4 Kg ha-1) + cattle manure (20 t ha-1) was occupied the second order. We can recommend to use the integrated treatment of ⅓NH4NO3 (55 kg N ha-1) + Cerealine (bio-fertilizer; 4 Kg ha-1) + cattle manure (10 t ha-1) effectively in saline soils to improve wheat growth and yield with minimum contents of heavy metals for human health and nutrition

Removal of Chlorophenols Compounds Using Treated Jatropha Seed Shells Adsorbents: Characterization and Thermodynamic

In this study, Jatropha seed shells from Yemeni plant have been tested for studying adsorption of treated seeds shells to remove chlorophenol compounds. The resulting adsorbents were designated as JAT1, JAT2 and JAT3. Most of the acidic groups on the surface were found to be phenolic in nature (37.5% in the case of JAT1 and 60% in the case of JAT). The adsorption of chlorophenol on JAT1, JAT2 and JAT3 was investigated in the temperature range 35–70 °C for initial chlorophenols concentrations ranging from 20 to 100 ppm. JAT2 was thereby found to be the best with respect to its capability to remove chlorophenols from solution indicating that thermal treatment at 500 °C is suitable to produce a good adsorbent. JAT3 is the worst in removing DCP even at high temperatures. It was also found that the removal efficiencies were in general enhanced at lower pH for all three adsorbents and for the two chlorophenols. For DCP, the corresponding heats of adsorption were found to be + 5.3, − 10.75 and − 14.4 kJ/mol. The small values for the heat of adsorption indicate that the interaction of chlorophenols with the adsorbent surface does not differ significantly from its interaction with water molecules in solution

The Role of Silicon in Antiherbivore Phytohormonal Signalling

The role of plant silicon (Si) in the alleviation of abiotic and biotic stress is now widely recognised and researched. Amongst the biotic stresses, Si is known to increase resistance to herbivores through biomechanical and chemical mechanisms, although the latter are indirect and remain poorly characterised. Chemical defences are principally regulated by several antiherbivore phytohormones. The jasmonic acid (JA) signalling pathway is particularly important and has been linked to Si supplementation, albeit with some contradictory findings. In this Perspectives article, we summarise existing knowledge of how Si affects JA in the context of herbivory and present a conceptual model for the interactions between Si and JA signalling in wounded plants. Further, we use novel information from the model grass Brachypodium distachyon to underpin aspects of this model. We show that Si reduces JA concentrations in plants subjected to chemical induction (methyl jasmonate) and herbivory (Helicoverpa armigera) by 34% and 32%, respectively. Moreover, +Si plants had 13% more leaf macrohairs than −Si plants. From this study and previous work, our model proposes that Si acts as a physical stimulus in the plant, which causes a small, transient increase in JA. When +Si plants are subsequently attacked by herbivores, they potentially show a faster induction of JA due to this priming. +Si plants that have already invested in biomechanical defences (e.g. macrohairs), however, have less utility for JA-induced defences and show lower levels of JA induction overall

Phytoremediation of heavy metal-contaminated sites: Eco-environmental concerns, field studies, sustainability issues and future prospects

Environmental contamination due to heavy metals (HMs) is of serious ecotoxicological concern worldwide because of their increasing use at industries. Due to non-biodegradable and persistent nature, HMs cause serious soil/water pollution and severe health hazards in living beings upon exposure. HMs can be genotoxic, carcinogenic, mutagenic, and teratogenic in nature even at low concentration. They may also act as endocrine disruptors and induce developmental as well as neurological disorders and thus, their removal from our natural environment is crucial for the rehabilitation of contaminated sites. To cope with HM pollution, phytoremediation has emerged as a low-cost and eco-sustainable solution to conventional physico-chemical cleanup methods that require high capital investment and labor alter soil properties and disturb soil microflora. Phytoremediation is a green technology wherein plants and associated microbes are used to remediate HM-contaminated sites to safeguard the environment and protect public health. Hence, in view of the above, the present paper aims to examine the feasibility of phytoremediation as a sustainable remediation technology for the management of metals-contaminated sites. Therefore, this paper provides an in-depth review on both the conventional and novel phytoremediation approaches, evaluate their efficacy to remove toxic metals from our natural environment, explore current scientific progresses, field experiences and sustainability issues and revise world over trends in phytoremediation research for its wider recognition and public acceptance as a sustainable remediation technology for the management of contaminated sites in 21st century