Rapid and precise detection of cryptic tea pathogen Exobasidium vexans: RealAmp validation of LAMP approach.

This work embodies the development of a real time loop mediated isothermal amplification (RealAmp) assay for the rapid detection of the cryptic tea phytopathogen, Exobasidium vexans, the causal organism of blister blight disease. Due to the widespread popularity of tea as a beverage and the associated agro-economy, the rapid detection and management of the fast-spreading blister blight disease have been a longstanding necessity. Loop-mediated isothermal amplification (LAMP) primers were designed targeting the E. vexans ITS rDNA region and the reaction temperature was optimized at 62 °C with a 60 min reaction time. Amplification of the E. vexans isolates in the initial LAMP reactions was confirmed by both agarose gel electrophoresis and SYBR Green I dye based colour change visualization. The specificity of the LAMP primers for E. vexans was validated by negative testing of seven different phytopathogenic test fungi using LAMP and RealAmp assay. The positive findings in RealAmp assay for E. vexans strain were corroborated via detecting fluorescence signals in real-time. Further, the LAMP assays performed with gDNA isolated from infected tea leaves revealed positive amplification for the presence of E. vexans. The results demonstrate that this rapid and precise RealAmp assay has the potential to be applied for field-based detection of E. vexans in real-time.

Integrated pretreatment of banana agrowastes: Structural characterization and enhancement of enzymatic hydrolysis of cellulose obtained from banana peduncle.

An integrated treatment coupling alkali, steam explosion and ammonia/chlorine-free bleaching with sequential mild acid pretreatment were performed to isolate and characterize cellulose from banana agrowastes followed by optimized enzymatic hydrolysis to glucose. The cellulose yield, compositional, microstructural, and morphological analysis initially obtained from three post-harvest banana agrowastes (peel, pseudostem, and peduncle) were surveyed. Isolation parameters for banana peduncle agrowastes, the most efficient precursor, were reconfigured for acid hydrolysis by applying an orthogonal L9 array of Taguchi design. Effects of solution-to-pulp ratio, acid concentration, temperature, and reaction time on physicochemical parameters were assessed resulting in ~81% cellulose recovery. Subsequently, cellulase driven enzymatic conversion to glucose was modelled using response surface methodology (RSM), where the mutual influences of incubation time, enzyme concentration, substrate concentration, and surfactant concentration were investigated. Artificial Neural Network (ANN) modelling further improved upon RSM optimizations ensuing ~97% optimized glucose yield, verified experimentally.

Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus.

Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. vexans, to address the problem of molecular identification within the background of cryptic speciation. The isolation of E. vexans strain was confirmed through morphological studies followed by molecular identification utilizing the developed ITS barcode. Phylogenetic analysis based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) confirmed the molecular identification of the pathogen as E. vexans strain. Further, BI analysis using BEAST mediated the estimation of the divergence time and evolutionary relationship of E. vexans within genus Exobasidium. The speciation process followed the Yule diversification model wherein the genus Exobasidium is approximated to have diverged in the Paleozoic era. The study thus sheds light on the molecular barcode-based species delimitation and evolutionary relationship of E. vexans within its genus Exobasidium.

Enhancing arsenic sequestration on ameliorated waste molasses nanoadsorbents using response surface methodology and machine-learning frameworks.

The development of a novel nanobiosorbent derived from waste molasses for the adsorptive removal of arsenic (As) has been attempted in this study. Waste molasses were chemically ameliorated through a solvothermal route for the incorporation of iron oxide, thereby producing iron oxide incorporated carbonaceous nanomaterial (IOCN). Synthesis of IOCN was confirmed through transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and atomic emission spectroscopy (AES) analysis. The surface area and porous behavior of IOCN were elucidated by Brunauer-Emmett-Teller (BET) assessments. The experimental conditions for adsorption were first modeled using response surface methodology (RSM) based on the central composite design (CCD), considering the parameters: adsorbate dosage, adsorbent dosage, pH, and contact time. RSM optimizations were improved upon using a three-layer feed-forward multilayer perceptron (MLP) based Artificial Neural Network (ANN) model. Optimization through ANN model resulted in the increase of the maximal As adsorption efficiency to ~ 96% for IOCN. The IOCN isotherm plots show the best fit for the Sips isotherm, and the reaction kinetics follows the pseudo-second-order model, indicating the chemisorption mechanism for As adsorption. Evidence for direct coordination of As to the surface of adsorbents was further confirmed by FTIR spectroscopic studies before and after As adsorption. The high adsorption efficiencies and the low-cost facile synthesis of the IOCN nanosorbent from agro-industrial waste indicate their potential for commercial applications.

Optimizing In vitro Culture Conditions for the Biotrophic Fungi Exobasidium vexans Through Response Surface Methodology.

The blister blight disease caused by the fungus, Exobasidium vexans has serious implications on the quality of tea production. The disease however, has been poorly studied and hence there is very limited information on the pathogen and as such the pathogenesis of blister blight infection. One of the major roadblocks in understanding E. vexans is the obligate and biotrophic nature of the fungus which limits the establishment and maintenance of in vitro cultures. To address this issue, a Central Composite Design based Response Surface Methodology (RSM) was adopted to study the modification of three fungal culture media viz. czapek dox, potato dextrose, and v8 juice, and the effect of altered media composition on growth conditions and media compositions were assessed. The response parameter for the RSM experiments was the mycelial biomass produced under different culture conditions. The uni and bi-parametric interactions among the experimental variables provided the basis for the statistically optimized conditions for maximal fungal growth. The study thus presents the recommended modifications of existing media that can lead to the successful establishment and maintenance of E. vexans in vitro cultures.

Greener production of microcrystalline cellulose (MCC) from Saccharum spontaneum (Kans grass): Statistical optimization.

In this study, microcrystalline cellulose (MCC) was isolated from Saccharum spontaneum by integrating alkaline delignification, chlorine-free bleaching, and acid hydrolysis treatments, through an environment friendly and sustainable method. To minimize acid concentrations, the acid hydrolysis conditions were optimized using Taguchi orthogonal L9 design that evaluated the influences of reaction time, temperature, acid concentration and solution to pulp ratio on the physical and chemical characteristics of MCC. The cellulose source at its different stages of processing was submitted to various analytical techniques for morphological and physiochemical investigations. The highest MCC yield optimized was 83%. This process is favorable due to the use of very low (5% H2SO4) acid concentration, low corrosivity, effluent reduction, and cost-effectiveness. Detailed analyses showed that the isolated MCC has good crystallinity and thermal stability and hence expected as a high-value precursor for the production of polymer biocomposites for diverse applications.

Detoxification and eco-friendly recycling of brick kiln coal ash using Eisenia fetida: A clean approach through vermitechnology.

Brick kiln coal ashes (BKCAs) are one of the major toxic byproducts of the rapidly growing construction industry in developing countries. However, eco-friendly recycling avenues for BKCAs are yet to be explored. The major objectives of the present research were to evaluate the viability of vermitechnology in transforming BKCAs into valuable products, and to examine the metal detoxification potential of Eisenia fetida BKCA-based feedstocks. BKCAs were mixed in large scale with cow dung (CD) in 1:1 and 2:1 ratios, for vermicomposting and aerobic composting; performance was assessed in comparison with CD. Vermiconverted-BKCA was then used as organic fertilizer for rice grown in poorly fertile soil. Acidic nature of BKCA feedstocks was neutralized by 30-86% in the vermireactors. Total N and available P concentrations significantly increased in the vermireactors supplemented with considerable mineralization of total organic C. Exorbitantly high K and S contents were pacified to a normal range after vermicomposting. Greater improvement in microbial biomass, respiration, fungal and bacterial growth was observed under vermicomposting against aerobic composting. Consequently, urease and phosphatase activity increased by 1-4 folds in the BKCA based vermibeds. Bioavailability of toxic metals reduced by 41-74% in the vermicomposted BKCAs. High metal accumulation by the earthworms resulted in substantial reduction of pollution load in the finished product. The field experiment demonstrated that vermiconverted-BKCA could be utilized as potential organic fertilizer for rice production, soil fertility rejuvenation, and metal detoxification. Overall, the study reveals that E. fetida could be used as an efficient contender for sanitization of toxic BKCAs.

Glycans as Modulators of Plant Defense Against Filamentous Pathogens.

Plants and microbes utilize glycoconjugates as structural entities, energy reserves for cellular processes, and components of cellular recognition or binding events. The structural heterogeneity of carbohydrates in such systems is a result of the ability of the carbohydrate biosynthetic enzymes to reorient sugar monomers in a variety of forms, generating highly complex, linear, branched, or hierarchical structures. During the interaction between plants and their microbial pathogens, the microbial cell surface glycans, cell wall derived glycans, and glycoproteins stimulate the signaling cascades of plant immune responses, through a series of specific or broad spectrum recognition events. The microbial glycan-induced plant immune responses and the downstream modifications observed in host-plant glycan structures that combat the microbial attack have garnered immense interest among scientists in recent times. This has been enabled by technological advancements in the field of glycobiology, making it possible to study the ongoing co-evolution of the microbial and the corresponding host glycan structures, in greater detail. The new glycan analogs emerging in this evolutionary arms race brings about a fresh perspective to our understanding of plant-pathogen interactions. This review discusses the role of diverse classes of glycans and their derivatives including simple sugars, oligosaccharides, glycoproteins, and glycolipids in relation to the activation of classical Pattern-Triggered Immunity (PTI) and Effector-Triggered Immunity (ETI) defense responses in plants. While primarily encompassing the biological roles of glycans in modulating plant defense responses, this review categorizes glycans based on their structure, thereby enabling parallels to be drawn to other areas of glycobiology. Further, we examine how these molecules are currently being used to develop new bio-active molecules, potent as priming agents to stimulate plant defense response and as templates for designing environmentally friendly foliar sprays for plant protection.

Structural and functional analysis of Erwinia amylovora SrlD. The first crystal structure of a sorbitol-6-phosphate 2-dehydrogenase.

Sorbitol-6-phosphate 2-dehydrogenases (S6PDH) catalyze the interconversion of d-sorbitol 6-phosphate to d-fructose 6-phosphate. In the plant pathogen Erwinia amylovora the S6PDH SrlD is used by the bacterium to utilize sorbitol, which is used for carbohydrate transport in the host plants belonging to the Amygdaloideae subfamily (e.g., apple, pear, and quince). We have determined the crystal structure of S6PDH SrlD at 1.84 Šresolution, which is the first structure of an EC 1.1.1.140 enzyme. Kinetic data show that SrlD is much faster at oxidizing d-sorbitol 6-phosphate than in reducing d-fructose 6-phosphate, however, equilibrium analysis revealed that only part of the d-sorbitol 6-phosphate present in the in vitro environment is converted into d-fructose 6-phosphate. The comparison of the structures of SrlD and Rhodobacter sphaeroides sorbitol dehydrogenase showed that the tetrameric quaternary structure, the catalytic residues and a conserved aspartate residue that confers specificity for NAD+ over NADP+ are preserved. Analysis of the SrlD cofactor and substrate binding sites identified residues important for the formation of the complex with cofactor and substrate and in particular the role of Lys42 in selectivity towards the phospho-substrate. The comparison of SrlD backbone with the backbone of 302 short-chain dehydrogenases/reductases showed the conservation of the protein core and identified the variable parts. The SrlD sequence was compared with 500 S6PDH sequences selected by homology revealing that the C-terminal part is more conserved than the N-terminal, the consensus of the catalytic tetrad (Y[SN]AGXA) and a not previously described consensus for the NAD(H) binding.

Glycan Phosphorylases in Multi-Enzyme Synthetic Processes.

Glycoside phosphorylases catalyse the reversible synthesis of glycosidic bonds by glycosylation with concomitant release of inorganic phosphate. The equilibrium position of such reactions can render them of limited synthetic utility, unless coupled with a secondary enzymatic step where the reaction lies heavily in favour of product. This article surveys recent works on the combined use of glycan phosphorylases with other enzymes to achieve synthetically useful processes.