Salinity tolerance in different cultivars of barley (Hordeum vulgare L.)

Seven barley(Hordeum vulgäre L.) cultivars tested varied greatly in their responses to root medium salinity (electrical conductivity of 3, 5, 10, 15 and 20 dS nr^-1)-lant growth was relatively more adversely affected than seed germination. Dry/fresh mass ratio increased at higher salinity levels in all barley cultivars indicating reduced water uptake. Higher K/Na ratio in plant shoots compared to that in the root medium solution indicated selective uptake of K that seems to be among processes involved in tolerance of cultivars to salinity stress.     

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

The analysis of single-cell genomics data presents several statistical challenges, and extensive efforts have been made to produce methods for the analysis of this data that impute missing values, address sampling issues and quantify and correct for noise. In spite of such efforts, no consensus on best practices has been established and all current approaches vary substantially based on the available data and empirical tests. The k-Nearest Neighbor Graph (kNN-G) is often used to infer the identities of, and relationships between, cells and is the basis of many widely used dimensionality-reduction and projection methods. The kNN-G has also been the basis for imputation methods using, e.g., neighbor averaging and graph diffusion. However, due to the lack of an agreed-upon optimal objective function for choosing hyperparameters, these methods tend to oversmooth data, thereby resulting in a loss of information with regard to cell identity and the specific gene-to-gene patterns underlying regulatory mechanisms. In this paper, we investigate the tuning of kNN- and diffusion-based denoising methods with a novel non-stochastic method for optimally preserving biologically relevant informative variance in single-cell data. The framework, Denoising Expression data with a Weighted Affinity Kernel and Self-Supervision (DEWÄKSS), uses a self-supervised technique to tune its parameters. We demonstrate that denoising with optimal parameters selected by our objective function (i) is robust to preprocessing methods using data from established benchmarks, (ii) disentangles cellular identity and maintains robust clusters over dimension-reduction methods, (iii) maintains variance along several expression dimensions, unlike previous heuristic-based methods that tend to oversmooth data variance, and (iv) rarely involves diffusion but rather uses a fixed weighted kNN graph for denoising. Together, these findings provide a new understanding of kNN- and diffusion-based denoising methods. Code and example data for DEWÄKSS is available at https://gitlab.com/Xparx/dewakss/-/tree/Tjarnberg2020branch.     

Association of Genetic Structure and Diversity in Iranian Wild Germplasms of Mentha longifolia L. Based on Phenotypical,Biochemical, and Molecular Markers

Mentha longifolia L. is well-known to be one of the most pervasive wild-growing species of the Lamiaceae family, which has extensive beneficial properties in the fields of pharmacology and biological products. In the present study, the correlation between Inter-simple sequence repeat (ISSR) markers and morpho-chemical parameters of twenty different M. longifolia accessions (MLACs) were assessed. The geographic information system (GIS) has been employed to interpret the original habitat of the accessions in Iran. ISSR analysis indicated a remarkable difference in the studied accessions, segregated them into three main groups, constructed by an unweighted pair-group method with arithmetic (UPGMA) and principal coordinate analysis (PCoA). A total of 89 bands were generated by 12 ISSR primers, among which 82 (91.97 %) of them were polymorphic. The cluster analysis based on agro-morphological data scattered MLACs into two main groups. The essential oils (EOs) were analyzed through GC/FID/MS, and four chemotypes were characterized according to the major constituents. Pulegone ranged from 0.17 to 69.50 % was the main oil constituent with the highest content. Also, HPLC-PDA was employed to identify and to quantify the phenolic compounds in the MeOH extracts of MLACs. Heatmap cluster based on phenolic compounds produced three main categories of accessions. The components identified in the extracts were rosmarinic acid, rutin, vanillic acid, ferulic acid, chlorogenic acid, caffeic acid, 3,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid, and p-coumaric acid, which among them rosmarinic acid (RA) varied from 39.16 to 261.55 mg/100 g (DW) as a predominant constituent. Subsequently, multiple regression analyses between ISSR fragments and morpho-chemical data illustrated considerable relationships in the plant materials. The high variation and correlation observed in metabolic and phenotypic traits of MLACs establish an adequate source to conduct reserves conservation programs.     

Community-Based Network Study of Protein-Carbohydrate Interactions in Plant Lectins Using Glycan Array Data

Lectins play major roles in biological processes such as immune recognition and regulation, inflammatory responses, cytokine signaling, and cell adhesion. Recently, glycan microarrays have shown to play key roles in understanding glycobiology, allowing us to study the relationship between the specificities of glycan binding proteins and their natural ligands at the omics scale. However, one of the drawbacks in utilizing glycan microarray data is the lack of systematic analysis tools to extract information. In this work, we attempt to group various lectins and their interacting carbohydrates by using community-based analysis of a lectin-carbohydrate network. The network consists of 1119 nodes and 16769 edges and we have identified 3 lectins having large degrees of connectivity playing the roles of hubs. The community based network analysis provides an easy way to obtain a general picture of the lectin-glycan interaction and many statistically significant functional groups.     

Influence of Celery on the Remediation of PAHs-contaminated Farm Soil

Polycyclic aromatic hydrocarbons (PAHs) contamination has been considered as one of the major environmental concerns for farmland soil all over the world including China. Due to small per capita land area, to find crops or vegetable, which could not only degrade the PAHs contaminants but also would not concentrate PAHs, was particularly important. Celery was selected as the phytoremediator in this experiment, and the soil enzyme activity, PAHs-degrading microorganisms, and the speciation of PAHs in soil were studied. The results showed that celery could significantly enhance the remediation of PAHs compared with the controlled experiment after 90 days (p< 0.01), and the removal efficiency were 31.29%, 30.79%, and 50.21% in the soil, non-rhizosphere soil, and rhizosphere soil, respectively. The soil enzyme activity and PAHs-degrading microorganisms significantly increased in rhizosphere soil compared with non-rhizosphere soil (p< 0.05), and the bioaccessibility of PAHs in soil could have been enhanced in the presence of celery root exudates. Those would help the bioremediation of PAHs by soil microorganisms. Meanwhile, the concentration of PAHs in the edible portion of celery was only 17.13 ± 1.24 μg/kg, and the bioconcentration factors in the aboveground part of celery were only 0.025. This study provides a potential in-site farmland soil phytoremediation technology that could have practical utility.     

Recent Advances of Using Ionic Liquids for Biopolymer Extraction and Processing

The evolution of petroleum‐derived polymers is one of the crowning accomplishments of the past century. Although the significant economic gains from this industrial model of resource utilization are achieved, the environmental impacts are fatal. One of the principles of sustainable development is to replace such polymers with potential alternatives derived from renewable materials. Biopolymers derived from natural resources afford a new, versatile, environmentally benign feedstock that could exhibit closed‐loop life cycles as part of a future material's industrial ecology. However, the solubility and processability of biopolymer materials provoke a serious bottleneck owing to their dense networks of inter ‐ and intramolecular bondings and structural heterogeneity. Recently, ionic liquids (ILs) have emerged as promising green solvents and acquired augmented appreciation for their peerless power of biopolymer processing. Among the fourteen principle of green chemistry, the two key elements encourage the exploitation of renewable raw materials by using environmentally benign solvents that cover in dissolution of biopolymers using ILs. This mini review represents a brief overview of the comprehensive ILs assisted extraction and processing of various biopolymeric materials for value‐added applications.     

Phorate triggers oxidative stress and mitochondrial dysfunction to enhance micronuclei generation and DNA damage in human lymphocytes

Herein, we studied phorate for its toxicological effects in human lymphocytes. Phorate treatment for 3 h has induced significant increase in the lymphocytic DNA damage. Compared to control, comet data from highest concentration of phorate (1000 µM) showed 8.03-fold increase in the Olive tail moment (OTM). Cytokinesis blocked micronucleus (CBMN) assay revealed 6.4-fold increase in binucleated micronucleated (BNMN) cells following the exposure with phorate (200 µM) for 24 h. The nuclear division index (NDI) in phorate (200 µM) treated cells reduced to 1.8 vis-à-vis control cells showed NDI of 1.94. Comparative to untreated control, 60.43% greater DCF fluorescence was quantitated in lymphocytes treated with phorate (500 µM), affirming reactive oxygen species (ROS) generation and oxidative stress. Flow cytometric data of phorate (200 µM) treated lymphocytes showed 81.77% decline in the fluorescence of rhodamine 123 (Rh123) dye, confirming the perturbation of mitochondrial membrane potential (ΔΨm). Calf thymus DNA (ct-DNA) treated with phorate (1000 µM) exhibited 2.3-fold higher 8-Hydroxy-2′-deoxyguanosine (8-oxodG) DNA adduct formation, signified the oxidative DNA damage. The alkaline unwinding assay revealed 4.0 and 6.5 ct-DNA strand breaks when treated to phorate and phorate-Cu (II) complex. Overall, the data unequivocally suggests the cyto- and genotoxic potential of phorate in human lymphocytes, which may induce comparable toxicological consequences in persons occupationally or non-occupationally exposed to insecticide phorate.     

Physical and chemical mutagens improved Sporotrichum thermophile,strain ST20 for enhanced Phytase activity

ObjectivePhosphorous is an essential micronutrient of plants and involved in critical biological functions. In nature, phosphorous is mostly present in immobilized inorganic mineral and in the fixed organic form including phytic acid and phosphoesteric compounds. However, the bioavailability of bound phosphorous could be enhanced by the use of phosphate solubilizing microorganisms such as bacteria and fungi. The phytases are widespread in an environment and have been isolated from different sources comprising bacteria and fungi.MethodologyIn current studies, we show the successful use of gamma rays and EMS (Ethyl Methane Sulphonate) mutagenesis for enhanced activity of phytases in a fungal strain Sporotrichum thermophile.ResultsWe report an improved strain ST2 that could produce a clear halo zone around the colony, up to 24 mm. The maximum enzymatic activity was found of 382 U/mL on pH 5.5. However, the phytase activity was improved to 387 U/ml at 45 °C. We also report that the mutants produced through EMS showed the greater potential for phytase production.ConclusionThe current study highlights the potential of EMS mutagenesis for strain improvement over physical mutagens.