Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation.

The Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, SARS-CoV-2, has recently emerged as a pandemic. Here, an attempt has been made through in-silico high throughput screening to explore the antiviral compounds from traditionally used plants for antiviral treatments in India namely, Tea, Neem and Turmeric, as potential inhibitors of two widely studied viral proteases, main protease (Mpro) and papain-like protease (PLpro) of the SARS-CoV-2. Molecular docking study using BIOVIA Discovery Studio 2018 revealed, (-)-epicatechin-3-O-gallate (ECG), a tea polyphenol has a binding affinity toward both the selected receptors, with the lowest CDocker energy - 46.22 kcal mol-1 for SARS-CoV-2 Mpro and CDocker energy - 44.72 kcal mol-1 for SARS-CoV-2 PLpro, respectively. The SARS-CoV-2 Mpro complexed with (-)-epicatechin-3-O-gallate, which had shown the best binding affinity was subjected to molecular dynamics simulations to validate its binding affinity, during which, the root-mean-square-deviation values of SARS-CoV-2 Mpro-Co-crystal ligand (N3) and SARS-CoV-2 Mpro- (-)-epicatechin-3-O-gallate systems were found to be more stable than SARS-CoV-2 Mpro system. Further, (-)-epicatechin-3-O-gallate was subjected to QSAR analysis which predicted IC50 of 0.3281 nM against SARS-CoV-2 Mpro. Overall, (-)-epicatechin-3-O-gallate showed a potential binding affinity with SARS-CoV-2 Mpro and could be proposed as a potential natural compound for COVID-19 treatment.

Molecular characterization of porcine group A rotavirus to contain piglet diarrhea for productivity enhancement in North East India.

Gastrointestinal tract infections with acute diarrhea are indeed a serious cause of concern that held back the swine industry of North East India and among the various etiological agents causing the disease, group A rotavirus is the most common. In this regard, molecular characterization of the viral strains circulating in the region is of utmost importance for a strategic approach to control the disease. Thus, in the present study, diarrheic fecal samples from piglets of Tripura and Assam were evaluated for genotypic characterization of VP7 and VP4 gene of the virus. The samples positive for group A rotavirus were subjected to G and P type determination by nested- multiplex RT PCR as well as nucleotide sequencing of VP7 and VP4 gene. Nested- multiplex RT PCR revealed the presence of porcine group A rotavirus in the genotypic combination of G1P[6], G3P[6], G8P[6] and G4P[6] in the two states of North East India. Nucleotide sequencing of VP7 and VP4 genes however, revealed emergence of an unusual genotypic combination G26P[13]. VP7 and VP4 nucleotide and its deduced amino acid sequences when compared with global isolates, showed that the present strains shared closest similarity to the porcine rotavirus strain TJ4-1from Japan and hp140 from Eastern India. Identification of a novel genotype G26P[13] in the RVA infected pig population of Tripura and Assam, suggested presence of a greater diversity in rotavirus strains in the region. Thus, it evokes the need for continuous monitoring to assess and consider the strain variability in the design of a suitable vaccine candidate against the virus. Supplementary Information: The online version of this article (10.1007/s13337-021-00659-6) contains supplementary material, which is available to authorized users.

Defense Response in Chickpea Pod Wall due to Simulated Herbivory Unfolds Differential Proteome Profile.

The pod wall of legumes is known to protect the developing seeds from pests and pathogens. However, the mechanism of conferring defense against insects has not yet been deciphered. Here, we have utilized 2-dimensional gel electrophoresis (2D-GE) coupled with mass spectrometry (MS/MS) to identify over expressed proteins in the pod wall of two different cultivars (commercial cultivar: JG 11 and tolerant cultivar: ICC 506-EB) of chickpea after 12 h of application of Helicoverpa armigera oral secretions (simulated herbivory). The assays were performed with a view that larvae are a voracious feeder and cause substantial damage to the pod within 12 h. A total of 600 reproducible protein spots were detected on gels, and the comparative analysis helped identify 35 (12 up-regulated, 23 down-regulated) and 20 (10 up-regulated, 10 down-regulated) differentially expressed proteins in JG 11 and ICC 506-EB, respectively. Functional classification of protein spots of each cultivar after MS/MS indicated that the differentially expressed proteins were associated with various metabolic activities. Also, stress-related proteins such as mannitol dehydrogenase (MADH), disease resistance-like protein-CSA1, serine/threonine kinase (D6PKL2), endoglucanase-19 etc. were up-regulated due to simulated herbivory. The proteins identified with a possible role in defense were further analyzed using the STRING database to advance our knowledge on their interacting partners. It decoded the involvement of several reactive oxygen species (ROS) scavengers and other proteins involved in cell wall reinforcement. The biochemical analysis also confirmed the active role of ROS scavengers during simulated herbivory. Thus, our study provides valuable new insights on chickpea-H.armigera interactions at the protein level.

Antifungal properties of rhamnolipid produced by Pseudomonas aeruginosa DS9 against Colletotrichum falcatum.

The rhamnolipid biosurfactant (RL-DS9) extracted from the bacterial strain Pseudomonas aeruginosa DS9 was evaluated for its antifungal activity against Colletotrichum falcatum that causes red rot in sugarcane. The surface tension (ST) reduction, biosurfactant production, and antifungal activity of biosurfactant against C. falcatum were investigated by using the medium with different carbon sources and it was found to be maximum in glucose. Moreover, highest reduction of ST and production of biosurfactant was achieved at 4.5% (w/v) concentration of glucose. The efficacy of RL-DS9 was compared with a commercially available rhamnolipid (RL-R95) using microtitre plate assay. Results showed that at 100 µg ml(-1) concentration RL-DS9 exhibited 86.6% inhibition against C. falcatum spore germination, and in the same concentration RL-R95 showed 83.3% inhibition. From liquid chromatography-mass spectrometry (LC-MS) analysis, it was revealed that only two similar congeners Rha-(C10 ) and Rha-Rha-(C10:1 ) were found to be in common among both the rhamnolipids. In the plant bioassay test, it was noted that red rot incidence was reduced on the sugarcane plants treated with RL-DS9. This is the first report that rhamnolipid biosurfactant produced by Pseudomonas aeruginosa DS9 could be able to control red rot disease of sugarcane caused due to the infection with the fungus Colletotrichum falcatum.

Antioxidant properties, physico-chemical characteristics and proximate composition of five wild fruits of Manipur, India.

Antioxidant properties, physico-chemical characteristics and proximate composition of five wild fruits viz., Garcinia pedunculata, Garcinia xanthochymus, Docynia indica, Rhus semialata and Averrhoa carambola grown in Manipur, India were presented in the current study. The order of the antioxidant activity and reducing power of the fruit samples was found as R. semialata > D. indica > G. xanthochymus > A. carambola > G. pedunculata. Good correlation coefficient (R(2) > 0.99) was found among the three methods applied to determine antioxidant activity. Total phenolic content was positively correlated (R(2) = 0.960) with the antioxidant activity however, total flavonoid content was not positively correlated with the antioxidant activity. Physico-chemical and proximate composition of these fruits is documented for the first time.

Rhamnolipid biosurfactant against Fusarium sacchari--the causal organism of pokkah boeng disease of sugarcane.

Pokkah boeng disease on sugarcane caused by the fungus Fusarium sacchari results considerable damage to the crop leading to top rot, the most serious and advanced stage of pokkah boeng, where the growing point is killed and the entire top of the plant dies. In the present study, the effect of rhamnolipid biosurfactant as an antifungal agent against F. sacchari to control pokkah boeng disease was investigated. On the basis of surface tension reduction, 12 bacterial isolates were selected as potent biosurfactant producers and eight of them showed antagonistic effect against F. sacchari. Among the eight, the isolate DS9 was found as the effective inhibitor of the fungus in vitro which was further evaluated using its biosurfactant present in whole culture, cell-free culture supernatant and crude biosurfactant at various concentrations. Reductions of fungal growths were found more with crude biosurfactant. By sequencing 16S rRNA, DS9 was identified as P. aeruginosa and the produced biosurfactant was characterized as rhamnolipid by Liquid Chromatography-Mass Spectrometry (LC-MS) analysis. The rhamnolipid biosurfactant inhibits phytopathogenic fungi F. sacchari and therefore seems to be a good biocontrol agent to control pokkah boeng disease of sugarcane.

DEBDOM: Database Exploring Banana Diversity of Manipur.

UNLABELLED: : Being poor man's apple, banana has a wide popularity worldwide. It's one of the important horticultural crops used irrespective of rich and poor alike. Manipur along with the other states of Northeast India harboured with plenty of wild and cultivated species of banana that are not fully explored. A data base named DEBDOM has been developed here describing the diversity of banana resources of Manipur and it comprises twenty eight genotypes of Musaceae. The database DEBDOM provides a sophisticated web base access to the details of the taxonomy, morphological characteristics, utility as well as sites of collection of Musa genotypes, and it would have contribute as a potential gene pool sources for the conservation, sustainability as well as for crop improvement in the future breeding programmes. AVAILABILITY: http://ibsd.gov.in/debdom/

CIBMAN: Database exploring Citrus biodiversity of Manipur.

UNLABELLED: The rich wealth of Citrus genetic resources makes India to enjoy a remarkable position in the "Citrus belt of the world". We have developed CIBMAN, a unique database on Citrus biodiversity of Manipur which comprises 33 accessions collected through extensive survey for more than three years. CIBMAN provides integrated access to Citrus species through sophisticated web interface which has following capabilities a) morphological details, b) socio-economic details, c) taxonomic details and d) geographical distribution. Morphological variability among Citrus accessions is due to variance in their genome which contributes to diverse agronomical traits and diverse bioactive compounds of high value. This diverse gene pool can be potential source for genetic improvement of existing cultivars and rootstocks. Systematic collection, characterization and conservation of the underutilized or lesser exploited varieties is required for incorporating in breeding program and conserve the germplasm from ever going on genetic erosion. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects especially industrialization of Citrus found in the state. Further, the features will be suited for detailed investigation on potential medicinal and edible Citrus that make CIBMAN a powerful tool for sustainable management. AVAILABILITY: http://ibsd.gov.in/cibman.