Identification of Small-Molecule Inhibitors against Meso-2, 6-Diaminopimelate Dehydrogenase from Porphyromonas gingivalis

Species-specific antimicrobial therapy has the potential to combat the increasing threat of antibiotic resistance and alteration of the human microbiome. We therefore set out to demonstrate the beginning of a pathogen-selective drug discovery method using the periodontal pathogen Porphyromonas gingivalis as a model. Through our knowledge of metabolic networks and essential genes we identified a “druggable” essential target, meso-diaminopimelate dehydrogenase, which is found in a limited number of species. We adopted a high-throughput virtual screen method on the ZINC chemical library to select a group of potential small-molecule inhibitors. Meso-diaminopimelate dehydrogenase from P. gingivalis was first expressed and purified in Escherichia coli then characterized for enzymatic inhibitor screening studies. Several inhibitors with similar structural scaffolds containing a sulfonamide core and aromatic substituents showed dose-dependent inhibition. These compounds were further assayed showing reasonable whole-cell activity and the inhibition mechanism was determined. We conclude that the establishment of this target and screening strategy provides a model for the future development of new antimicrobials.     

MiST: A new approach to variant detection in deep sequencing datasets

MiST is a novel approach to variant calling from deep sequencing data, using the inverted mapping approach developed for Geoseq. Reads that can map to a targeted exonic region are identified using exact matches to tiles from the region. The reads are then aligned to the targets to discover variants. MiST carefully handles paralogous reads that map ambiguously to the genome and clonal reads arising from PCR bias, which are the two major sources of errors in variant calling. The reduced computational complexity of mapping selected reads to targeted regions of the genome improves speed, specificity and sensitivity of variant detection. Compared with variant calls from the GATK platform, MiST showed better concordance with SNPs from dbSNP and genotypes determined by an exonic-SNP array. Variant calls made only by MiST confirm at a high rate (>90%) by Sanger sequencing. Thus, MiST is a valuable alternative tool to analyse variants in deep sequencing data.     

Inoculation of Cucumber (Cucumis sativus L.) Seedlings with Salt-Tolerant Plant Growth Promoting Bacteria Improves Nutrient Uptake,Plant Attributes and Physiological Profiles

Journal of Plant Growth Regulation - Salinity is one of the major abiotic stresses that cause retarded plant growth and crop production. It has been reported that harmful effects of salinity could...     

Overexpression of Extracellular Superoxide Dismutase Protects against Brain Injury Induced by Chronic Hypoxia

Extracellular superoxide dismutase (EC-SOD) is an isoform of SOD normally found both intra- and extra-cellularly and accounting for most SOD activity in blood vessels. Here we explored the role of EC-SOD in protecting against brain damage induced by chronic hypoxia. EC-SOD Transgenic mice, were exposed to hypoxia (FiO2.1%) for 10 days (H-KI) and compared to transgenic animals housed in room air (RA-KI), wild type animals exposed to hypoxia (H-WT or wild type mice housed in room air (RA-WT). Overall brain metabolism evaluated by positron emission tomography (PET) showed that H-WT mice had significantly higher uptake of ¹⁸FDG in the brain particularly the hippocampus, hypothalamus, and cerebellum. H-KI mice had comparable uptake to the RA-KI and RA-WT groups. To investigate the functional state of the hippocampus, electrophysiological techniques in ex vivo hippocampal slices were performed and showed that H-KI had normal synaptic plasticity, whereas H-WT were severely affected. Markers of oxidative stress, GFAP, IBA1, MIF, and pAMPK showed similar values in the H-KI and RA-WT groups, but were significantly increased in the H-WT group. Caspase-3 assay and histopathological studies showed significant apoptosis/cell damage in the H-WT group, but no significant difference in the H-KI group compared to the RA groups. The data suggest that EC-SOD has potential prophylactic and therapeutic roles in diseases with compromised brain oxygenation.     

Natural regulation of white grub (Holotrichia sp: Scarabidae) by birds in agroecosystem

The white grub (Holotrichia sp: Scarabidae) is an important subterranean pest damaging root systems of several crops. Experiments conducted during I985 and I986 showed that at least I4 species of birds picked up the grubs exposed during ploughing operation. The important bird predators were mynasAcridotheres tristis (Linnaeus) andAcridotheres ginginianus (Latham), crowsCorvus splendens (Vieillot),Corvus macrorhynchos (Sykes), drongoDicrurus adsimilis (Hodgson) and cattle egretBubulcus ibis. The birds were found to reduce 45 to 65% grub population during 3 subsequent ploughings. The plant stand of second crop raised in bird exposed field was higher in experimental plot compared to the control. The number of birds attracted to the plough was not consistent with the density of grubs exposed but oh many extraneous factors. Factors affecting the extent of bird predation were presence of insectivorous birds in the surroundings, proximity to their breeding sites and timing of ploughing. White grub control by birds is economically cheaper and environmentally safe compared to the chemical control.     

Technical Note: Degradation of Phenanthrene and Anthracene by Pseudomonas Strain,Isolated From Coastal Area

A bacterial strain was isolated from a Mumbai coastal area. It was dosed with anthracene and phenanthrene, and, after 14 days of incubation, it had degraded 90% and 93% of the anthracene and phenanthrene, respectively. The metabolites were extracted and identified by ultraviolet (UV)-visible light absorption, high-performance liquid chromatography, mass spectrometry, and by comparing with actual compounds and data. Neutral extracts from anthracene showed four metabolites, viz 1,2-dihydroxyanthracene, 6,7-benzocoumarin, 1-methoxy-2-hydroxyanthracene, and 9,10 anthraquinone. When Pseudomonas were grown in the presence of phenanthrene, two metabolites, viz 9,10-dihydroxyphenanthrene and 3,4-dihydroxyphenanthrene were identified.     

Peroxiredoxin 6 phosphorylation and subsequent phospholipase A2 activity are required for agonist-mediated activation of NADPH oxidase in mouse pulmonary microvascular endothelium and alveolar macrophages

Peroxiredoxin 6 (Prdx6), a bifunctional enzyme with glutathione peroxidase and phospholipase A2 (PLA(2)) activities, participates in the activation of NADPH oxidase 2 (NOX2) in neutrophils, but the mechanism for this effect is not known. We now demonstrate that Prdx6 is required for agonist-induced NOX2 activation in pulmonary microvascular endothelial cells (PMVEC) and that the effect requires the PLA(2) activity of Prdx6. Generation of reactive oxygen species (ROS) in response to angiotensin II (Ang II) or phorbol 12-myristate 13-acetate was markedly reduced in perfused lungs and isolated PMVEC from Prdx6 null mice. Rac1 and p47(phox), cytosolic components of NOX2, translocated to the endothelial cell membrane after Ang II treatment in wild-type but not Prdx6 null PMVEC. MJ33, an inhibitor of Prdx6 PLA(2) activity, blocked agonist-induced PLA(2) activity and ROS generation in PMVEC by >80%, whereas inhibitors of other PLA(2)s were ineffective. Transfection of Prx6 null cells with wild-type and C47S mutant Prdx6, but not with mutants of the PLA(2) active site (S32A, H26A, and D140A), "rescued" Ang II-induced PLA(2) activity and ROS generation. Ang II treatment of wild-type cells resulted in phosphorylation of Prdx6 and its subsequent translocation from the cytosol to the cell membrane. Phosphorylation as well as PLA(2) activity and ROS generation were markedly reduced by the MAPK inhibitor, U0126. Thus, agonist-induced MAPK activation leads to Prdx6 phosphorylation and translocation to the cell membrane, where its PLA(2) activity facilitates assembly of the NOX2 complex and activation of the oxidase.     

Characterization of 2T engine oil degrading indigenous bacteria,isolated from high altitude (Mussoorie), India

The biodegradability of petroleum hydrocarbons such as polycyclic aromatic hydrocarbons (PAHs) and n-branched alkanes etc. of 2T engine oil were studied in aqueous media using bacterial strain isolated from petroleum contaminated soil of high altitude. Out of five petroleum degrading bacterial strain one of the most growing bacteria was identified as Enterobacter strain by morphological, physiological, biochemical and partial sequencing of 16S rDNA. This strain was capable of degrading 75 ± 3% of n-alkanes, 32 ± 5% PAHs, and the abiotic loss was 24 ± 6% during 10 days incubation period. 85 ± 2% of n-alkanes and 51 ± 3% PAHs were biodegraded in 20 days. The abiotic loss during this period was 15 ± 3%. In 30 days of incubation period 98% ± 1% n-alkanes and 75 ± 3% PAHs were degraded. As expected abiotic losses were smaller with increasing long chain alkanes and PAH’s concentration. An increment in oil degradation was correlated to an increase in cell number indicating that the bacterial isolate was responsible for the oil degradation. The hydrocarbon contents were measured by Shimadzu QP-2000 Gas chromatography/mass spectrometry by ULBON HR-1 column.     

Numerical Simulation of Extinction Spectra of Plasmonically Coupled Nanospheres Using Discrete Dipole Approximation: Influence of Compositional Asymmetry

We demonstrate plasmon coupling phenomenon between equivalent (homodimer) and non-equivalent (heterodimer) spherical shape noble metal nanoparticle (Ag, Au and Al). A systematic comparison of surface plasmon resonance (SPR) and extinction properties of various configurations (monomer, homodimer and heterodimer) has been investigated to observe the effect of compositional asymmetry. Numerical simulation has been done by using discrete dipole approximation method to study the optical properties of plasmonically coupled metal nanoparticles (MNPs). Plasmon coupling between similar nanoparticles allows only higher wavelength bonding plasmon mode while both the plasmon modes lower wavelength antibonding mode as well as higher wavelength bonding mode in the case of heterodimer. Au monomer of radius 50 nm shows resonance peak at 518 nm while plasmon coupling between Au-Au homodimer results in a spectral red shift around 609 nm. Au-Ag plasmonic heterodimer (radius 50 nm) reveals two resonant modes corresponding to higher energy antibonding mode (422 nm) as well as lower energy bonding mode (533 nm). Further, we have shown that interparticle edge-to-edge separation is the most significant parameter affecting the surface plasmon resonances of MNPs. As the inter particle separation decreases, resonance wavelength shows red spectral shift which is maximum for the touching condition. It is shown that plasmon coupling is a reliable strategy to tune the SPR.

     

Synthesis and binary QSAR study of antitubercular quinolylhydrazides

In continuation with our previous work in anti-TB research area, in the present study we have demonstrated the structural diversity of quinolylhydrazides as potent anti-tuberculars. The compound library was synthesized by molecular hybridization approach and tested in vitro against Mycobacterium tuberculosis H₃₇Rv strains. Among the designed conjugates, the most promising molecules were found to exhibit 100% Growth Inhibition (GI) at MIC <6.25 μg/mL. Moreover, several analogs in the designed series were also turned out as excellent anti-tuberculars. To probe the structural characteristics influencing on the SAR, the classification model was generated using a binary QSAR approach termed recursive partitioning (RP) analysis. The significant features outlined by the RP model act as a guide in order to design the ‘lead’ compound.