MIC database: A collection of antimicrobial compounds from literature

We describe a database named MIC database containing 2-dimensional structures of synthesized compounds/antibiotics, IUPAC name, smiles notation and the MIC values / zone of inhibition against a particular organism, strain and culture conditions. The data was collected from various literature sources such as Arkivoc, Bioorganic Medicinal Chemistry Letters, Antimicrobial Agents and Chemotherapy, Journal of Clinical Microbiology and Journal of Bacteriology. MIC Database can be accessed at www.trimslabs.com/mic/index.htm.     

Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors

Plants are sessile organisms that have evolved a variety of mechanisms to maintain their cellular homeostasis under stressful environmental conditions. Survival of plants under abiotic stress conditions requires specialized group of heat shock protein machinery, belonging to Hsp70:J-protein family. These heat shock proteins are most ubiquitous types of chaperone machineries involved in diverse cellular processes including protein folding, translocation across cell membranes, and protein degradation. They play a crucial role in maintaining the protein homeostasis by reestablishing functional native conformations under environmental stress conditions, thus providing protection to the cell. J-proteins are co-chaperones of Hsp70 machine, which play a critical role by stimulating Hsp70s ATPase activity, thereby stabilizing its interaction with client proteins. Using genome-wide analysis of Arabidopsis thaliana, here we have outlined identification and systematic classification of J-protein co-chaperones which are key regulators of Hsp70s function. In comparison with Saccharomyces cerevisiae model system, a comprehensive domain structural organization, cellular localization, and functional diversity of A. thaliana J-proteins have also been summarized.     

On the Charge and Molecule Based Summations of Solvent Electrostatic Potentials and the Validity of Electrostatic Linear Response in Water

Solvent-induced electrostatic potentials and field components at thesolute sites of model Na^+q–Cs^-q molecules were computed bysumming over either solvent charges (q-summation) or solventmolecular centers (M-summation) from molecular dynamics simulations.These were compared with values obtained by solving Poisson equation withthe dielectric boundary defined by R _eff = (R _atom +R _gmax )/2.q-summation using cut-offs that are 10 Å generallyunderestimates or overestimates the magnitude of (a) the potentials and field components atNa^+q and Cs^-q relative to the theoretical values and (b)electrostatic solvation free energies of the dipolar solutes assuminglinear solvent response relative to the respective values from free energysimulations. Furthermore, the q-summed electric potentials showedsignificant oscillations even beyond the second hydration shell. Incontrast, the corresponding M-summed potentials plateaued after thefirst hydration shell. Although the different water molecular centersyielded different converged potential values, the dipole center producedvalues in remarkable agreement with the theoretical values for solutecharges ranging from 1 to 0.1e, indicating the existence of an a convenient molecular center for computing these quantities. In contrast to theM-summed potentials, the electrostatic field components andelectrostatic solvation free energies from linear response relationshipswere found not to be sensitive to the choice of the molecular centerfor typical cut-off distances (8 to 12 Å) used in most simulations.     

Finger ridge count correlations among four tribes of Andhra Pradesh,India

The present paper reports the distribution of finger ridge count correlations among four tribal populations from Andhra Pradesh, India viz., Dulia, Kotia, Manne Dora and Manzai Mali, and examines the intra and inter population variation. Higher correlations are recorded in left hands compared to right hands, but they are not significant. The homologous fingers exhibit a stronger correlation. In all the tribes, the correlations between right hand fingers are relatively higher among women when compared to men. Regarding inter population variation Dulia men differ significantly from the men of Manne Dora and the Manzai Mali tribes, and Kotia women also differ from the women of the Manne Dora significantly. The average correlation coefficient of the present populations is similar to other Indian populations reported earlier but lower than African and European populations.     

Metabolic responses in discrete regions of rat brain following acute administration of glutamate

Glutamate is a major excitatory neurotransmitter in the mammalian brain. Nevertheless, high extracellular levels of this amino acid have been shown to be toxic to several neuronal populations, but no data are available to show how glutamate homeostasis is altered in response to local infusion of glutamate. In the present study, 1 M of glutamate was stereotactically injected into cerebral cortex, striatum, and hippocampus of adult rat brain, and the activities of key metabolic enzymes, lactate dehydrogenase, glutamate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase were evaluated by postmortem analysis in tissue homogenates. The results show that glutamate bolus, induced significant alterations in vivo glutamate and energy metabolism, as evidenced by marked alterations in these enzyme activities, whereas dizocilpine, a glutamate receptor antagonist, negated many of the effects induced by high glutamate. However, the degree of involvement of these observations in glutamate-induced neurotoxicity remains to be ascertained.     

Surfactant-induced lipid peroxidation in a tropical euryhaline teleost Oreochromis mossambicus (Tilapia) adapted to fresh water

Exposure to anionic (sodium dodecyl sulfate, SDS), cationic (cetyl trimethyl ammonium bromide CTAB) and non ionic (Triton X-100) surfactants at a sub lethal concentration of 1 ppm resulted in severe oxidative stress in the hepatic, renal and cardiac tissues of fresh water adapted Oreochromis mossambicus. Hepatic catalase showed significant increase (P<0.001) in all the surfactant exposed fish, but the renal enzyme was significantly increased only in CTAB dosed fish (P<0.001) and the cardiac enzyme showed significant increase in Triton (P<0.05) and CTAB dosed fish (P<0.001). SOD levels were significantly increased (P<0.001) in hepatic, renal and cardiac tissues of all the surfactant-treated fish. Glutathione reductase also was significantly increased (P<0.001) in the hepatic and renal tissues of surfactant dosed fish except cardiac tissues of CTAB exposed animals. Glutathione levels in the tissues studied were significantly higher in the surfactant treated animals (P<0.001) whereas malondialdehyde levels were significantly elevated only in the hepatic tissues of animals exposed to Triton (P<0.001). The surfactants based on their charge, antioxidant profile and in vivo metabolism may be arranged in the order of decreasing toxicity as CTAB > Triton > SDS. Thus it may be inferred from the present study that the antioxidant defenses and the in vivo metabolism of the surfactants are key factors in deciding the surfactant toxicity.     

GenCompass: a universal system for analysing gene expression for any genome

Microarrays have become indispensable tools for studying the gene expression of particular organisms on a genomic scale. However, despite its widespread use, there are several draw-backs to the current technology. First, it requires prior knowledge of the DNA sequence encoded in the organism of interest, and second, chips must be designed specifically for each genome, greatly increasing the initial cost incurred in manufacturing the arrays.     

Antioxidant-associated chemoprevention by sodium selenite in N-nitrosodiethylamine-induced and phenobarbital-promoted hepatocarcinogenesis in rats

The anticarcinogenic/antioxidant potential of sodium selenite (Se), a micronutrient, was evaluated on liver tumourigenesis induced by N-nitrosodiethylamine (DEN) and promoted by phenobarbital (PB; 0.05% in diet). Male, albino rats of the Wistar strain were exposed intravenously to a single dose of DEN (200 mg x kg(-1) body weight). Se (4 ppm in drinking water) was supplemented before initiation, or during initiation and/or during the promotion period of carcinogenesis. At the end of 16 weeks (after DEN administration) nodular incidence, the total number of nodules and non-enzymic antioxidants such as vitamin E, vitamin C, total thiol, protein thiol and non-protein thiol contents were measured in hepatoma, surrounding tissue and kidney tissue of control and experimental groups. In hepatoma-bearing animals the above biochemical changes were decreased when compared with normal control animals. On Se treatment throughout the study, (20 weeks) the above biochemical changes reverted to normal levels. Pre- and post-treatment with Se also shows a tendency to reverse the above changes. The results indicate that prior application of Se significantly reverses the adverse changes produced during the tumourigenesis. Furthermore, prior applications of Se significantly reduced the cumulative number of tumours per tumour-bearing animals. The present study reveals the antitumour potential of Se against DEN-induced liver carcinogenesis.     

Sequestosome 1/p62 is a polyubiquitin chain binding protein involved in ubiquitin proteasome degradation

Herein, we demonstrate that the ubiquitin-associated (UBA) domain of sequestosome 1/p62 displays a preference for binding K63-polyubiquitinated substrates. Furthermore, the UBA domain of p62 was necessary for aggregate sequestration and cell survival. However, the inhibition of proteasome function compromised survival in cells with aggregates. Mutational analysis of the UBA domain reveals that the conserved hydrophobic patch MGF as well as the conserved leucine in helix 2 are necessary for binding polyubiquitinated proteins and for sequestration-aggregate formation. We report that p62 interacts with the proteasome by pull-down assay, coimmunoprecipitation, and colocalization. Depletion of p62 levels results in an inhibition of ubiquitin proteasome-mediated degradation and an accumulation of ubiquitinated proteins. Altogether, our results support the hypothesis that p62 may act as a critical ubiquitin chain-targeting factor that shuttles substrates for proteasomal degradation.