Dissecting the role of salicylic acid in mediating stress response in mungbean cultivars concurrently exposed to Macrophomina phaseolina infection and drought stress.

The combined stress studies provide fundamental knowledge that could assist in producing multiple stress resilient crops. The fungal phytopathogen, Macrophomina phaseolina is a major limiting factor in the productivity of the crop, Vigna radiata (mungbean). This fungal species tends to flourish under hot and dry conditions. Therefore, in this study the salicylic acid (SA) mediated stress responses in contrasting mungbean cultivars (Shikha and RMG-975) exposed to combined M. phaseolina infection (F) and drought stress (D) have been elucidated. The combined stress was applied to ten days seedlings in three orders i.e. drought followed by fungal infection (DF), drought followed by fungal infection with extended water deficit (DFD) and fungal infection followed by drought stress (FD). The severity of infection was analyzed using ImageJ analysis. Besides, the concentration of SA has been correlated with the phenylpropanoid pathway products, expression of pathogenesis-related proteins (ß-1,3-glucanase and chitinase) and the specific activity of certain related enzymes (phenylalanine ammonia lyase, lipoxygenase and glutathione-S-transferase). The data revealed that the cultivar RMG-975 was relatively more tolerant than Shikha under individual stresses. However, the former became more susceptible to the infection under DFD treatment while the latter showed tolerance. Otherwise, the crown rot severity was reduced in both the cultivars under other combined treatments. The stress response analysis suggested that enhanced chitinase expression is vital for tolerance against both, the pathogen and drought stress. Also, it was noted that plants treat each stress combination differently and the role of SA was more prominently visible under individual stress conditions.

Insilico screening to identify novel inhibitors targeting 30S ribosomal protein S12 in meningitis-causing organism 'Elizabethkingia meningoseptica'.

The current trend in biomedical research is on prioritizing infections based on multidrug resistance. Elizabethkingia meningoseptica, a nosocomial infection-causing organism emerging from Neonatal Intensive Care Units (NICUs), leads to neonatal meningitis and sepsis resulting in severe illness, and, in some cases, fatal. Finding a solution remains challenging due to limited prior work. Translational S12 ribosomal proteins play a crucial role in decoding the codon-anticodon helix, which is essential for the survival of E. meningoseptica. These proteins do not exhibit significant similarity with humans, making them potential drug targets. An in silico study aims to identify specific inhibitors for E. meningoseptica ribosomal proteins among known bioactive compounds targeting prokaryotic 30S ribosomal protein. A 3D model of the 7JIL_h protein from Flavobacterium johnsoniae, showing 90% sequence similarity with the target protein was generated using SWISS-MODEL software. The model was validated through Molprobity v4.4, VERIFY 3D, Errata, and ProSA analysis, confirming conserved residues of the target protein. Insilico screening of known bioactive compounds and their analogs identified potential ligands for the target protein. Molecular Docking and post-docking analysis assessed the stability of the protein-ligand complexes among the shortlisted compounds. The top two compounds with high Gold fitness scores and low predicted binding energy underwent MD simulation and further estimation of free binding energy using the MM_PBSA module. These computationally shortlisted compounds, namely chEMBL 1323619 and chEMBL 312490 may be considered for future in-vivo studies as potential inhibitors against the modeled 30S ribosomal protein S12 of E. meningoseptica.Communicated by Ramaswamy H. Sarma.

Salt stress in plants and amelioration strategies: alleviation of agriculture and livelihood risks after the Covid-19 pandemic.

Agriculture sustains the livelihoods of over 2.5 billion people worldwide. The growing nature of disasters, the systemic nature of risk, a more recent pandemic along with abiotic stress factors are endangering our entire food system. In these stressful environment, it is widely reprimanded that strategies should be encompassed to attain increased crop yield and economic returns which would alleviate food and nutritional scarcity in developing countries. To study the physiological responses to salt stress, Vigna radiata seedlings subjected to varying levels of salt stress (0, 25, 50, 100 and 200 mM NaCl) were evaluated by tracking changes in Chl a fluorescence, pigment content, free proline and carotenoids content by HPLC. The ability of plants to adapt to salt stress is related with the plasticity and resilience of photosynthesis. As salt concentration increased, chlorophyll fluorescence indices decreased and a reduction in the PSII linear electron transport rate was observed. Chlorophyll fluorescence parameters can be used for in vitro non-invasive monitoring of plants responses to salt stress. Overall, Vigna responded to salt stress by the changes in avoidance mechanism and protective systems. Chl fluorescence indices, enzymatic contents of POD, CAT and free proline were sensitive to salt stress. The study is significant to evaluate the tolerance mechanisms of plants to salt stress and may develop insights for breeding new salt-tolerant varieties.

Computational characterization and analysis of molecular sequence data of Elizabethkingia meningoseptica.

OBJECTIVE: Elizabethkingia meningoseptica is a multidrug resistance strain which primarily causes meningitis in neonates and immunocompromised patients. Being a nosocomial infection causing agent, less information is available in literature, specifically, about its genomic makeup and associated features. An attempt is made to study them through bioinformatics tools with respect to compositions, embedded periodicities, open reading frames, origin of replication, phylogeny, orthologous gene clusters analysis and pathways. RESULTS: Complete DNA and protein sequence pertaining to E. meningoseptica were thoroughly analyzed as part of the study. E. meningoseptica G4076 genome showed 7593 ORFs it is GC rich. Fourier based analysis showed the presence of typical three base periodicity at the genome level. Putative origin of replication has been identified. Phylogenetically, E. meningoseptica is relatively closer to E. anophelis compared to other Elizabethkingia species. A total of 2606 COGs were shared by all five Elizabethkingia species. Out of 3391 annotated proteins, we could identify 18 unique ones involved in metabolic pathway of E. meningoseptica and this can be an initiation point for drug designing and development. Our study is novel in the aspect in characterizing and analyzing the whole genome data of E. meningoseptica.

A systematic review on iron-based nanoparticle-mediated clean-up of textile dyes: challenges and prospects of scale-up technologies.

The projected increase of the global textile industry to USD1002.84 billion in 2027 indicates a simultaneous increase in water pollution due to textile dye-rich voluminous effluents highlighting the requirement of source clean-up. This review analyzes the colossal amount of literature on lab-scale nanoremediation technologies involving iron-based nanoparticles and the mechanistic aspects. However, not many studies are in place with regard to execution because there are several bottlenecks in the scale-up of the technology. This review attempts to identify the limitations of scale-up by focusing on each step of nanoremediation from synthesis of iron-based nanoparticles to their applications. The most prominent appears to be the low economic viability of physico-chemical synthesis of nanoparticles, lack of appropriate toxicity studies of iron-based nanoparticles, and dearth of studies on field applications. It is recommended that above studies should be made not only on lab scale but also on field samples preferably utilizing microbial products based green synthesized iron-based nanoparticles and conducting toxicity studies. Besides, immobilization of the nanoparticles on renewable material greatly enhances the sustainability and economic value of the process. Furthermore, since the chemical composition of dye-rich effluents varies among industries, effluent specific optimization of process parameters and kinetics thereof is also a major prerequisite for scale-up. The value of this review lies in the fact that it brings, for the first time, a comprehensive and critical systematization of various aspects needing attention in order to scale-up such effective nanoremediation processes.

Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel.

BACKGROUND: Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS: The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION: These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice.

Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenarios: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. Trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments.

Phytoremediation efficiency of Brassica juncea cultivars at vegetative and reproductive growth stages under individual and combined treatment of fluoride and aluminium.

The objective of this study was to investigate phytoremediation ability of Brassica juncea cultivars for aluminium (Al) and fluoride (F) independently and in combination (Al + F). Out of 8 cultivars which were treated with Al, F, and (Al + F), 4 cultivars (Bio-902, Pusa-Tarak, CS-14, and Laxmi) were selected for further studies on the basis of growth parameters. These cultivars were exposed to soil (pH 5) supplemented with F (0, 25, 50, and 75 mg kg-1) and Al (0, 50, 100, and 150 mg kg-1) independently and in combination (Al + F) (0 + 0, 50 + 25, 100 + 50, and 150 + 75 mg kg-1). We found that the accumulation of F, Al, and (Al + F) was highest in the roots followed by grains, shoots, and leaves. When the plants were treated with Al or F separately, the accumulation of Al or F were less as compared to when treated in combination (Al + F). Conclusively, the results also showed that maximum tolerance index, uptake, and translocation factor for F were highest in CS-14, Al in Bio-902, and (Al+ F) in Pusa-Tarak, and were found to be the lowest in Laxmi.

Targeting the ß-clamp in Helicobacter pylori with FDA-approved drugs reveals micromolar inhibition by diflunisal.

The ß-clamp is the processivity-promoting factor for most of the enzymes in prokaryotic DNA replication; hence, it is a crucial drug target. In the present study, we investigated the ß-clamp from Helicobacter pylori, aiming to seek potential drug molecules against this gastric-cancer-causing bacterium. An in silico screening of Food and Drug Administration (FDA) approved drugs against the H. pylori ß-clamp, followed by its in vitro inhibition using a surface competition approach, yielded the drug diflunisal as a positive initial hit. Diflunisal inhibits the growth of H. pylori in the micromolar range. We determined the structure of diflunisal in complex with the ß-clamp to show that the drug binds at subsite I, which is a protein-protein interaction site. Successful identification of FDA-approved molecules against H. pylori may lead to better and faster drug development.

Structural insight into ß-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of ß-clamp from H. pylori (Hpß-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial ß-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of ß-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of ß-clamp binding regions in them and validated by SPR studies. Hpß-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of ß-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with ß-clamp.

Structural and functional alterations in photosynthetic apparatus of plants under cadmium stress.

Cadmium is a potentially toxic heavy metal that hampers plant productivity by interfering with their photochemistry. Cd causes disturbances in a range of physiological processes of plants such as photosynthesis, water relations, ion metabolism and mineral uptake. Cd pronouncedly affects photosynthesis by alteration of its vital machinery in all aspects. Photosynthesis is a well organised and sequential process fundamental to all green plants and microorganisms which involves various components, including photosynthetic pigments and photosystems, the electron transport system and CO2 reduction pathways. Any damage at any level caused by Cd, critically affects overall photosynthetic capacity. Present review focuses on key effects of Cd on photosynthetic apparatus including chloroplast structure, photosynthetic pigments, Chl-protein complexes and photosystems resulting in overall decrease in efficiency of carbon assimilation pathway.

Plasticity of photosynthetic performance of the Indian tree Butea monosperma TAUB at three sites with different microclimates.

The Fabaceae tree Butea monosperma (TAUB.; syn. Erythrina monosperma (LAM.)) is widely distributed in Central and West-India. We studied it at three sites, i.e. at two locations with contrasting exposure (NE and SW, respectively) in a small mountain range with poor soil on highly drained rocky slopes and at a third location in a plane with deeper soils and better water supply. The two mountain range sites differed in the light climate where the NE-slope obtained more day-integrated irradiance. Chlorophyll fluorescence was measured with a portable fluorometer and leaf samples for stable isotope analyses (δ(13)C, δ(15)N, δ(18)O) were collected. No differences were seen in carbon and nitrogen contents of leaves at the three sites. N and O isotope signatures of the leaves were similar at the two rocky hill slope sites. More positive values for both signatures were obtained in the leaves in the plane. For all sites saturation of ETR was only achieved well above a PPFD of 1,000 µmol m(-2) s(-1) indicating that the leaves were sun-type leaves. The photosynthetic performance of Butea at the plane was very similar to that at the SW-slope of the mountain range and higher ETRs were obtained at the NE-slope. Ecophysiological flexibility allows Butea to perform well in a variety of habitats and yet gives it particular fitness at specific sites. The best performance was observed in the highly insolated steep rocky hill site (NE-slope) underlining the suitability of the tree for reforestation.

Differential response of salt stress on Brassica juncea: photosynthetic performance, pigment, proline, D1 and antioxidant enzymes.

To investigate the ability of sensitive and tolerant variety of Brassica juncea to adapt to a saline environment in a field, we examined the activities of antioxidant enzymes in relation to photosystem II, chlorophyll a fluorescence, photosynthetic pigment concentration, protein (D1) and proline in plants exposed to salt stress. We observed a greater decline in the photosynthetic rate (∆F/Fm') and electron transport rate (ETRsat) and saturating photosynthetically active photo flux density (PPFDsat) under salt stress in var. Urvashi (sensitive variety) than in var. Bio902 (tolerant variety). Var. Urvashi was found to be more sensitive to high salinity. In var. Bio902, chlorophyll a, chlorophyll b and total chlorophyll concentrations were higher than in the sensitive variety. Proline and protein contents were also higher in var. Bio902 as compared to their lower accumulation in var. Urvashi. The improved performance of the var. Bio902 under high salinity was accompanied by an increase in ascorbate peroxidase (APX, EC 1.11.1.11) and catalase (CAT, EC 1.11.1.6), though no salt-dependent increase in the activity of superoxide dismutase (SOD, EC 1.15.1.1) was observed. However, no such increase in APX and CAT was observed in var. Urvashi, though there was significant increase in SOD activity. These results suggest that var. Bio902 is potentially more tolerant to salt damage and is associated with better adaptive responses found in var. Bio902 than var. Urvashi. Increased photoinhibition in var. Urvashi as observed by its reduced thylakoid membrane protein, D1 probably results from the greater photosynthetic damage caused by salt stress than var. Bio902.

Stress-mediated alteration in V-ATPase and V-PPase of Butea monosperma.

The activity and subunit amounts of V-ATPase and V-PPase in various plants of Butea monosperma Taub. (Fabaceae) (ver. Dhak; Palas) growing as a natural inhabitant in varying stress conditions in southeast Rajasthan were studied. Western blot analysis followed by immunological quantification of V-ATPase subunits using specific polyclonal antibodies showed that the subunits A, B, D, E, and c are clearly detectable in all plants, with A, B, and c appearing as intense bands. The other subunits of V-ATPase, viz., C, a, and d, were also detected in majority of the plants. Various subunits exhibited variations in their protein amount in different plants. Besides, a few other clear bands were also detected. Of these, the 30- and 29-kD bands may possibly be Di and Ei. Furthermore, a clear band of V-PPase corresponding to 67-70 kD was also detected. A comparison of the V-ATPase and V-PPase activity revealed that Butea plants in the upper region of the study site showed 70% and 39% higher activity, respectively. Furthermore, the immunological quantification showed that the V-ATPase and V-PPase protein amounts are also higher in the upper Butea plants which have drought stress and, moreover, are also exposed to stronger light intensities for relatively longer duration.

Two proteins homologous to PsbQ are novel subunits of the chloroplast NAD(P)H dehydrogenase.

The PsbQ-like (PQL) proteins 1 and 2, previously shown to be located in the thylakoid lumen of Arabidopsis thaliana, are homologous to PSII oxygen-evolving complex protein PsbQ. Nevertheless, pql mutants showed no defects in PSII but instead the activity of the chloroplast NAD(P)H dehydrogenease (NDH) complex was severely impaired. In line with this observation, the NDH subunits were low in abundance in pql mutants, and, conversely, ndh mutants strongly down-regulated the accumulation of the PQL proteins. In addition, the PQL2 protein was up-regulated in mutant plants deficient in the PSI complex or the thylakoid membrane-bound ferredoxin-NADP(+) oxidoreductase, whereas in pql mutants the PSI complex was slightly up-regulated. Taken together, the two PQL proteins are shown to be novel subunits of the lumenal protuberance of the NDH complex.