CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance

Salt-sensitive yeast mutants were deployed to characterize a gene encoding a C2H2 zinc finger protein (CaZF) that is differentially expressed in a drought-tolerant variety of chickpea (Cicer arietinum) and provides salinity-tolerance in transgenic tobacco. In Saccharomyces cerevisiae most of the cellular responses to hyper-osmotic stress is regulated by two interconnected pathways involving high osmolarity glycerol mitogen-activated protein kinase (Hog1p) and Calcineurin (CAN), a Ca(2+)/calmodulin-regulated protein phosphatase 2B. In this study, we report that heterologous expression of CaZF provides osmotolerance in S. cerevisiae through Hog1p and Calcineurin dependent as well as independent pathways. CaZF partially suppresses salt-hypersensitive phenotypes of hog1, can and hog1can mutants and in conjunction, stimulates HOG and CAN pathway genes with subsequent accumulation of glycerol in absence of Hog1p and CAN. CaZF directly binds to stress response element (STRE) to activate STRE-containing promoter in yeast. Transactivation and salt tolerance assays of CaZF deletion mutants showed that other than the transactivation domain a C-terminal domain composed of acidic and basic amino acids is also required for its function. Altogether, results from this study suggests that CaZF is a potential plant salt-tolerance determinant and also provide evidence that in budding yeast expression of HOG and CAN pathway genes can be stimulated in absence of their regulatory enzymes to provide osmotolerance.

SubCellProt: predicting protein subcellular localization using machine learning approaches

High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Two machine learning algorithms, k Nearest Neighbor (k-NN) and Probabilistic Neural Network (PNN) were used to classify an unknown protein into one of the 11 subcellular localizations. The final prediction is made on the basis of a consensus of the predictions made by two algorithms and a probability is assigned to it. The results indicate that the primary sequence derived features like amino acid composition, sequence order and physicochemical properties can be used to assign subcellular localization with a fair degree of accuracy. Moreover, with the enhanced accuracy of our approach and the definition of a prediction domain, this method can be used for proteome annotation in a high throughput manner. SubCellProt is available at www.databases.niper.ac.in/SubCellProt.

Sensitive biomarker of polycyclic aromatic hydrocarbons (PAHs): urinary 1-hydroxyprene glucuronide in relation to smoking and low ambient levels of exposure

The study was conducted in a Chinese population with occupational or environmental exposures to polycyclic aromatic hydrocarbons (PAHs). A total of 106 subjects were recruited from coke-oven workers (workers), residents in a metropolitan area (residents) and suburban gardeners (gardeners). All subjects were monitored twice for their personal exposures to PAHs. The biological samples were collected for measurements of 1-hydroxypyrene (1-OHP) and cotinine in urine. The geometric means of personal exposure levels of pyrene, benz(a)anthracene (BaA) and benzo(a)pyrene (BaP) in workers were 1.470, 0.978 and 0.805 microg m-3, respectively. The corresponding levels in residents were 0.050, 0.034 and 0.025 microg m-3; and those in gardeners were 0.011, 0.020 and 0.008 microg m-3, respectively. The conjugate of 1-OHP with glucuronide (1-OHP-G) is the predominant form of pyrene metabolite in urine and it showed strong associations with exposures not only to pyrene, but also to BaA, BaP and total PAHs. Most importantly, a significant difference in 1-OHP-G was even detected between the subgroups with exposures to BaP at < 0.010 and > 0.010 but < 0.020 microg m-3, suggesting that 1-OHP-G is a good marker that can be used for the risk assessment of BaP exposure at levels currently encountered in ambient air. Furthermore, multiple regression analyses of 1-OHP-G on PAHs exposure indicated that cigarette smoke was a major confounding factor and should be considered and adjusted for while using 1-OHP to estimate PAHs exposure.

Sustained release nanoparticulate formulation containing antioxidant-ellagic acid as potential prophylaxis system for oral administration

The aim of the present work was to develop ellagic acid (EA) loaded poly(d,l-lactide-co-glycolide) (PLGA) nanoparticles for oral administration. PLGA nanoparticles were prepared by a method based on the concept of emulsion-diffusion-evaporation by using polyethylene glycol (PEG) 400 as a cosolvent for solubilizing the drug. While developing this method, didodecyldimethylammomium bromide (DMAB) and polyvinyl alcohol (PVA), alone and in combination with chitosan (CS) were employed. DMAB stabilized particles were the smallest of all the formulations with a particle size of 148.5 nm. PVA alone gave particles of 269.7 nm but a blend with CS (80:20) resulted in an increase in particle size (359.6 +/- 23.6 nm). Initial release of EA from nanoparticles in pH 7.4 phosphate buffer was rapid, followed by a slower sustained release. Release rates followed the order PVA > PVA-CS > DMAB. Release rate from the PLGA-DMAB particles was slowest, which is attributed to higher hydrophobicity of DMAB as compared to PVA, preventing diffusion of drug out of polymeric matrix. Insolubility of CS at alkaline pH could have retarded the release in case of PVA-CS system. In situ intestinal permeability study of pure drug and the drug encapsulated in nanoparticles prepared using PVA, PVA-CS blend and DMAB as stabilizer in rats showed 66, 75, 73 and 87% permeation, respectively. EA showed good free radical scavenging effect in a yeast cell culture model as well as in a cell free system.

Target-specific anti-fungal discovery by targeting Geotrichum candidum histidinol dehydrogenase: a hybrid approach

This study describes a hybrid approach of screening substrate analogue inhibitors of histidinol dehydrogenase. Imidazole derivative library of approximately 400 compounds classified using Hierarchical cluster analysis, representative compounds of each class were tested in enzymatic assay and used for the development of quantitative structure-activity relationship models. Rest of the compounds in the library were screened using developed models and compounds predicted active were retested. 60% of the predicted compounds showed enzyme inhibition activity with IC(50) values ranged between 5.2 and 58.0 microm range and have fungistatic activity.

Selectivity-based QSAR approach for screening and evaluation of TRH analogs for TRH-R1 and TRH-R2 receptors subtypes

Design and development of therapeutically useful CNS selective thyrotropin-releasing hormone (TRH) analogs acting on TRH-R2 receptor subtype, exerting weak or no TRH-R1-mediated TSH-releasing side effects has gained imagination of researchers in the recent past. The present study reports the development and implementation of a selectivity-based QSAR approach for screening selective agonists of TRH-R2 receptor subtype. The statistically significant predictive models were thoroughly validated using an external validation set whose activity was previously unknown. The model was able to predict preference for either of the receptor subtypes successfully.

Nicotinamide inhibits Plasmodium falciparum Sir2 activity in vitro and parasite growth

Plasmodium falciparum sirtuin, PfSir2, contains histone deacetylase (HDAC) activity that may be central to the regulation of virulence gene expression in the parasites. Although a few reports have been published recently regarding in vitro and in vivo function of PfSir2, expression of the endogenous protein (c. 30 kDa) has not been shown yet. Here we report the presence of PfSir2 in the parasite at the protein level by specific antibodies. HDAC activity of PfSir2 can be inhibited by nicotinamide, a product of sirtuin reaction. Surprisingly, we find that nicotinamide also delays parasite growth significantly in culture. These findings further our knowledge on PfSir2 and raise the possibility of using an inexpensive agent like nicotinamide as an antimalarial in combination with other antiparasitic drugs.

Portability of tag SNPs across isolated population groups: an example from India

Isolated population groups are useful in conducting association studies of complex diseases to avoid various pitfalls, including those arising from population stratification. Since DNA resequencing is expensive, it is recommended that genotyping be carried out at tagSNP (tSNP) loci. For this, tSNPs identified in one isolated population need to be used in another. Unless tSNPs are highly portable across populations this strategy may result in loss of information in association studies. We examined the issue of tSNP portability by sampling individuals from 10 isolated ethnic groups from India. We generated DNA resequencing data pertaining to 3 genomic regions and identified tSNPs in each population. We defined an index of tSNP portability and showed that portability is low across isolated Indian ethnic groups. The extent of portability did not significantly correlate with genetic similarity among the populations studied here. We also analyzed our data with sequence data from individuals of African and European descent. Our results indicated that it may be necessary to carry out resequencing in a small number of individuals to discover SNPs and identify tSNPs in the specific isolated population in which a disease association study is to be conducted.

Evaluation of Pseudomonas aeruginosa Deacetylase LpxC Inhibitory Activity of Dual PDE4−TNFα Inhibitors: A Multiscreening Approach

In this study, we have focused on the implication of a multiscreening approach in the evaluation of Pseudomonas aeruginosa deacetylase LpxC inhibitory activity of dual PDE4-TNFalpha inhibitors. A genetic function approximation (GFA) directed quantitative structure-activity relationship (QSAR) model was developed for LpxC inhibition on the basis of reported biological activity (Kline and Andersen, J. Med. Chem. 2002, 45, 3112-3129). Subsequently, reported PDE4-TNFalpha inhibitors (Klienman and Campbell, J. Med. Chem. 1998, 41, 266-270) were screened using the QSAR model. Whereby, the compounds were predicted to have equipotent activity with the most potent compound in reported LpxC inhibitor series. A docking analysis of these compounds carried out on the LpxC homology model corroborated the initial results. The compounds were then validated using surface electronic properties analysis and subjected to an adsorption, distribution, metabolism, excretion, and toxicity filter. Taken together, a multiscreening strategy was used to validate potential leads for LpxC inhibition.

Escherichia coli versus Pseudomonas aeruginosa Deacetylase LpxC Inhibitors Selectivity: Surface and Cavity-Depth-Based Analysis

Although Escherichia coli and Pseudomonas aeruginosa LpxC share sequence and functional similarity, E. coli LpxC inhibitiors are ineffective against P. aeruginosa LpxC. It was earlier speculated that inactivity of the inhibitors is due to intrinsic resistance possibly mediated by efflux pumps. However, a recent study has documented that the inactivity is due to failure of inhibitor(s) to inhibit the enzyme rather then intrinsic resistance. In this study, we carried out a surface and cavity-depth-based analysis on homology models of E. coli and P. aeruginosa LpxC to get some new insights into the ligand-binding features of these enzymes. The surface analysis of the P. aeruginosa LpxC model suggested that the LpxC catalytic domain (where inhibitors are supposed to bind) has several minor but potentially important structural differences as compared to E. coli LpxC. Molecular docking studies which could distinguish between the reported receptor affinities of the inhibitors additionally helped in the identification of key binding-site residues and interactions. These differences can be exploited for designing broad-spectrum LpxC inhibitors against this target.

A novel range based QSAR study of human neuropeptide Y (NPY) Y5 receptor inhibitors

A conventional QSAR study has been carried out using thermodynamic and other descriptors, on a set of arylsulfonamidomethylcyclohexyl derivatives as antagonists of potential obesity drug target human neuropeptide Y Y5 receptor. In addition, a novel range based method was applied to obtain a QSAR model so that the information contained in the compounds for which an approximate value instead of exact value of inhibitory activity was available could be included in the model. Analysis of models suggests that range based model is better in screening biologically active compounds from chemical library. The conventional model is able to predict activity accurately only for active compounds whereas the range based method is better in discriminating active and inactive compounds.

Pharmacophoric features of Pseudomonas aeruginosa deacetylase LpxC inhibitors: an electronic and structural analysis

Various electronic properties of structurally diverse synthetic LpxC inhibitors containing oxazoline, aroylserine and thiazoline rings were calculated and correlated with biological activity. These electronic features include the magnitude and locations of 3-dimensional molecular electrostatic potentials, hydrogen bond acceptor/donor density, lowest unoccupied molecular orbital, and highest occupied molecular orbital. Strong correlation of these stereo-electronic properties with LpxC inhibitory potency reveals the potential pharmacophoric features of specific LpxC inhibitors. Thus, these pharmacophoric features of LpxC inhibitors based on electronic and surface analysis could be successfully exploited for designing more potent LpxC inhibitors.

Comparative protein modeling and surface analysis of Leishmania sirtuin: A potential target for antileishmanial drug discovery

Homology model of Leishmania SIR2 shed new light on the ligand binding features of this enzyme. The molecular electrostatic potentials (MESP), the cavity depth analysis, and LmSIR2-hSIRT2 models' superposition suggested that the nicotinamide binding catalytic domain has several minor but potentially important structural differences. These differences could be exploited for designing antileishmanial compounds.

Quantitative structure activity relationship studies of aryl heterocycle-based thrombin inhibitors

A quantitative structure activity relationship (QSAR) analysis has been performed on a data set of 42 aryl heterocycle-based thrombin inhibitors. Several types of descriptors including topological, spatial, thermodynamic, information content and E-state indices were used to derive a quantitative relationship between the anti thrombin activity and structural properties. Genetic algorithm based genetic function approximation method of variable selection was used to generate the model. Best model was developed when number of descriptors in the equation was set to five. Highly statistically significant model was obtained with atom type logP descriptors, logP and Shadow_YZ. The model is not only able to predict the activity of new compounds but also explained the important regions in the molecules in a quantitative manner.

Genetic variation of farrowing kinetics traits and their relationships with litter size and perinatal mortality in French Large White sows

Genetic parameters of litter traits and their relationships with farrowing kinetics traits were estimated in a Large White population to examine the impact of selection for litter size on perinatal mortality and one of its main determinants, farrowing kinetics. Data were collected on 2,947 farrowings from 1,267 sows between 1996 and 2004. Litter traits included the number born in total (NBT), number born alive (NBA), and the number (NSB) and proportion (PSB) of stillborn piglets. Four farrowing kinetics traits were considered: farrowing duration (FD), birth interval (BI = FD/NBT), heterogeneity of birth intervals (SDNB = SD of the number of piglets born each one-half hour), and birth assistance (BA) during the farrowing process. Genetic parameters were estimated using restricted maximum likelihood methodology. All traits were analyzed using a mixed linear animal model including year x month and parity as fixed effects; the additive genetic value of each animal and the sow permanent environment were treated as random effects. To normalize their distribution, kinetics traits were Box-Cox-transformed. Low heritability estimates were obtained for litter size and mortality traits, which was in agreement with literature results (i.e., 0.10 +/- 0.02, 0.08 +/- 0.02, 0.19 +/- 0.02, and 0.14 +/- 0.02 for NBT, NBA, NSB, and PSB, respectively). Heritability values were also low for kinetics traits: 0.10 +/- 0.02, 0.08 +/- 0.02, 0.01 +/- 0.01, and 0.05 +/- 0.03 for FD, BI, SDNB, and BA, respectively. The genetic correlation between NBT and NBA was strongly positive (ra = 0.90). On both phenotypic and genetic scales, NBT was positively associated with stillbirth (ra = 0.45 +/- 0.11, rp = 0.38 for NSB; ra = 0.46 +/- 0.13, rp = 0.17 for PSB). Conversely, NBA had low correlations with SB and PSB. Number born in total was moderately correlated to FD (ra = 0.34 +/- 0.15) and BI (ra = -0.37 +/- 0.15). A stronger relationship was found between NBA and BI (ra = -0.49 +/- 0.13), whereas the relationship with FD was lower (ra = 0.16 +/- 0.17). Moreover, FD was strongly correlated with stillbirth (ra = 0.42 +/- 0.12 with NSB), whereas BI was nearly independent of stillbirth. Contrary to selection on NBT, selection on NBA appears to be a good way to limit the negative side effects on stillbirth. Moreover, selection on NBA would lead to a small increase in FD and a faster and more regular birth process than would be obtained by selecting on NBT.