Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity.

Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.

Groundwater vulnerability mapping using the modified DRASTIC model: the metaheuristic algorithm approach.

Vulnerability assessment and mapping is a significant tool for sustainable management of the precious natural groundwater resources. DRASTIC is an extensively used index model to map groundwater vulnerable zones. However, the original DRASTIC model rates and weights used in most of the research depict the poor correlation between nitrate concentration and groundwater vulnerability index. Wilcoxon test and five population-based metaheuristic (MH) algorithms, namely, firefly algorithm (FA), invasive weed optimization (IWO), teaching learning-based optimization (TLBO), shuffled frog leaping algorithm (SFLA), and particle swarm optimization (PSO), were used to optimize the rates and weights of the DRASTIC model to improve its accuracy. The performance of all the employed metaheuristic algorithms converges to a global optimal solution at different iterations, and to choose the best algorithm for DRASTIC weights optimization, a ranking methodology was proposed. The algorithms were ranked by calculating the relative closeness of alternatives with computational speed and the number of iterations as attributes in the TOPSIS method. This study identifies FA as the outperforming algorithm among the employed for this specified weight optimization problem based on ranking. The result of the optimization model proposed depicts significant improvement in the correlation coefficient between the groundwater vulnerability index and nitrate concentration from 0.0545 for the original DRASTIC model to 0.7247 for the Wilcoxon-MH- DRASTIC. Hence, this ranking approach can be adopted when global optimal solution is found by all employed algorithms in DRASTIC weight optimization.

A snapshot of gut microbiota of an adult urban population from Western region of India.

The human gut microbiome contributes to a broad range of biochemical and metabolic functions that directly or indirectly affect human physiology. Several recent studies have indicated that factors like age, geographical location, genetic makeup, and individual health status significantly influence the diversity, stability, and resilience of the gut microbiome. Of the mentioned factors, geographical location (and related dietary/socio-economic context) appears to explain a significant portion of microbiome variation observed in various previously conducted base-line studies on human gut microbiome. Given this context, we have undertaken a microbiome study with the objective of cataloguing the taxonomic diversity of gut microbiomes sampled from an urban cohort from Ahmedabad city in Western India. Computational analysis of microbiome sequence data corresponding to 160 stool samples (collected from 80 healthy individuals at two time-points, 60 days apart) has indicated a Prevotella-dominated microbial community. Given that the typical diet of participants included carbohydrate and fibre-rich components (predominantly whole grains and legume-based preparations), results appear to validate the proposed correlation between diet/geography and microbiome composition. Comparative analysis of obtained gut microbiome profiles with previously published microbiome profiles from US, China, Finland, and Japan additionally reveals a distinct taxonomic and (inferred) functional niche for the sampled microbiomes.

Localized multiple cemental excrescences: a rare presentation of hypercementosis.

Hypercementosis is an abnormal thickening of cementum which may be generalized or localized. Localized hypercementosis is usually characterized by nodular enlargement of apical third of root. Hypercementosis in the form of multiple cemental spikes distributed throughout the entire length of root is a very rare finding. In this article, we report such a rare manifestation of localized hypercementosis affecting right maxillary third molar in a 24-year-old male. This finding was an accidental observation following a difficult extraction procedure as the spikes were not evident in the orthopantamogram. It is imperative that every dental practitioner be aware of several presentations of hypercementosis and ensure that such an entity is considered in the differential diagnosis of difficult extraction procedures as an Intraoral Periapical (IOPA) radiograph or even an Orthopantamogram (OPG) could not differentiate the root morphology.