Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs.

Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by VB7 and TK towards the suppression of root-knot nematode under field conditions.

Unlabelled: The plant-parasitic Root Knot Nematodes ( spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach.

Molecular Docking of Nimbolide Extracted from Leaves of with Protein Targets to Confirm the Antifungal, Antibacterial and Insecticidal Activity.

Unlabelled: Nimbolide, a tetranortriterpenoid (limonoid) compound isolated from the leaves of , was screened both in vitro and in silico for its antimicrobial activity against f. sp. , , , pv.

Triamcinolone Acetonide Produced by Bacillus velezensis YEBBR6 Exerts Antagonistic Activity Against Fusarium oxysporum f. sp. Cubense: A Computational Analysis.

Fusarium oxysporum f. sp. cubense is one of the most severe and threatening pathogens of bananas, causing "Panama wilt" worldwide.

Thyromegaly: Not The Usual Cause.

Non-Hodgkin lymphoma (NHL) of the thyroid is a very rare condition. Swelling of the neck is the usual presentation among patients. Of all thyroid malignancies, only a very small portion accounts for NHL of the thyroid.

Nematicidal Property of Clindamycin and 5-hydroxy-2-methyl Furfural (HMF) from the Banana Endophyte (YEBBR6) Against Banana Burrowing Nematode .

Unlabelled: Radopholus similis is a burrowing nematode which causes banana toppling disease and is of major economic threat for the banana production. Bacterial endophyte Bacillus velezensis (YEBBR6) produce biomolecules like 5-hydroxy-2-methyl furfural (HMF) and clindamycin in during interaction with Fusarium oxysporum f.sp.

Mining the Genome of 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.

Optimization of adsorption process parameters by response surface methodology for hexavalent chromium removal from aqueous solutions using Annona reticulata Linn peel microparticles.

Fruit peel microparticles of Annona reticulata Linn were used as biosorbent for the sequestration of hexavalent chromium (CR(VI)). Characterization of the biosorbent was done using scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDXS), Fourier transfer infrared spectroscopy (FTIR), gas chromatography-mass spectrometry (GCMS), carbon, hydrogen, nitrogen and sulphur (CHNS) elemental analysis, mercury intrusion porosimetry and point of zero charge. Influential parameters were optimized using response surface methodology (RSM) with a total of 17 experimental runs based on the Box-Behnken design and found to be pH 1.

Hexavalent chromium removal from aqueous solutions by a novel powder prepared from Colocasia esculenta leaves.

In this study, batch removal of hexavalent chromium from aqueous solutions by powdered Colocasia esculenta leaves was investigated. Batch experiments were conducted to study the effects of adsorption of Cr(VI) at different pH values, initial concentrations, agitation speeds, temperatures, and contact times. The biosorbent was characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectrometer analysis.

Analysis of secondary structural and physicochemical changes in protein-protein complexes.

Conformation switching in protein-protein complexes is considered important for the molecular recognition process. Overall analysis of 123 protein-protein complexes in a benchmark data-set showed that 6.8% of residues switched over their secondary structure conformation upon complex formation.

Discovery of adamantane based highly potent HDAC inhibitors.

Herein, we report the development of highly potent HDAC inhibitors for the treatment of cancer. A series of adamantane and nor-adamantane based HDAC inhibitors were designed, synthesized and screened for the inhibitory activity of HDAC. A number of compounds exhibited GI50 of 10-100 nM in human HCT116, NCI-H460 and U251 cancer cells, in vitro.

Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein-ligand complexes.

The importance of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking has been studied in 48 protein-ligand complexes belonging to eight protein families. In continuation of our earlier study on protein flexibility in relationship to PCV and LV, this study analyzes the importance of PCV and LV in the scoring and ranking of ligands in docking experiments. Crystal structures of protein-ligand complexes with varied PCV were chosen for docking ligands of varied volume in each protein family.

An alphabetic code based atomic level molecular similarity search in databases.

Atomic level molecular similarity and diversity studies have gained considerable importance through their wide application in Bioinformatics and Chemo-informatics for drug design. The availability of large volumes of data on chemical compounds requires new methodologies for efficient and effective searching of its archives in less time with optimal computational power. We describe an alphabetic algorithm for similarity searching based on atom-atom bonding preference for ligands.

Synthesis, characterization, and antimicrobial activity of nano-hydroxyapatite-zinc for bone tissue engineering applications.

The bone implants used in tissue repair are susceptible to infections caused by staphylococci, specifically Staphylococcus aureus. Hence, the development of better biological materials that provide antimicrobial activity in bone tissue engineering is required. The nanoparticles of hydroxyapatite (nHAp) and nHAp dopped with Zn (nHAp-Zn) were prepared by the wet chemical method and the ion exchange method, respectively.

Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes.

Background: Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology.

Methods: We have developed an energy based approach for identifying the binding site residues in protein-protein complexes.

QSAR studies on HIV-1 protease inhibitors using non-linearly transformed descriptors.

Human Immunodeficiency Virus (HIV)-1 protease is one of the key targets for Acquired Immunodeficiency Syndrome (AIDS). A large number of inhibitors are being designed for this target with the focus towards interactions with backbone atoms to combat drug resistance. In the present study, we have developed QSAR models for 99 inhibitors which include P₁/P₁' and P₂/P₂' substituents with diverse scaffolds.

Synthesis of 2-substituted 17β-hydroxy/17-methylene estratrienes and their in vitro cytotoxicity in human cancer cell cultures.

Synthesis of various types of 2-(alkylaminomethyl) and 2-(aroyl) 17β-estradiol analogs are reported. The synthesis of similar types of 2-substituted 17-methylene estratriene analogs was also achieved. Synthesis of chalcone derivatives of 17β-estradiol and 17-methylene estratriene were also realized.

Enhanced osteoblast adhesion on polymeric nano-scaffolds for bone tissue engineering.

Bone tissue engineering is an interdisciplinary field which is emerged for the development of viable substitutes that restore and maintain the function of human bone tissues. The success of bone tissue engineering depends on designing of the scaffolds. The polymer-based composite scaffolds containing micro- and nano-structures could provide a platform influencing osteoblastic cell adhesion, spreading, proliferation, and differentiation.

Role of interactions and volume variation in discriminating active and inactive forms of cyclin-dependent kinase-2 inhibitor complexes.

Molecular recognition process occurs through various non-bonded interactions in protein-ligand complexes. Analysis and visualization of interactions in a set of protein-ligand complexes provide insight for structure-based drug design. In the present study, we have made a comprehensive analysis on similarities and differences observed in hydrophobic interactions and hydrogen bond interactions of 170 X-ray crystal structures of active and inactive cyclin-dependent kinase-2 (CDK-2) ligand complexes obtained from the Protein Data Bank.

Synthesis and characterization of nanoscale-hydroxyapatite-copper for antimicrobial activity towards bone tissue engineering applications.

The bacterial infection is one of the major problems associated with implant and reconstructive surgery of bone. Hence, the aim of this study was to develop biomaterials having antibacterial activity for bone tissue engineering. The hydroxyapatite nanoparticles (nHAp) improve the mechanical properties and incorporate nanotopographic features that mimic the nanostructure of natural bone.

Chitosan and its derivatives for gene delivery.

Gene delivery can particularly be used for the treatment of diseases by the insertion of genetic materials (DNA and RNA) into mammalian cells either to express new proteins or to prevent the expression of existing proteins. Chitosan, a natural polymer is nontoxic, biocompatible, and biodegradable and it is used as a support material for gene delivery. However, practical use of chitosan has been mainly limited to its unmodified forms, and thus modified chitosans can be used for the wide range of biomedical applications including the interaction and intracellular delivery of genetic materials.

Variation of protein binding cavity volume and ligand volume in protein-ligand complexes.

We have systematically analyzed the variation of protein binding cavity volume of 200 protein-ligand complexes belonging to eight protein families. Wide variation in protein binding cavity volume for the same protein is observed on binding different ligands. Analysis of individual protein families shows high correlation between atom-atom interactions in binding site and ligand volume.

Arbitrarily primed PCR- a rapid and simple method for typing of leptospiral serovars.

Purpose: To investigate the use of arbitrarily primed polymerase chain reaction (AP-PCR) for typing of leptospiral serovars.

Methods: AP-PCR was adopted for identification of laboratory strains of leptospires and leptospiral cultures at serovar level. A primer of 12 bp was used for amplifying DNA of 13 laboratory strains of leptospires as well as culture pellets of leptospires.