Sialic acids acquired by Pseudomonas aeruginosa are involved in reduced complement deposition and siglec mediated host-cell recognition

The opportunism of Pseudomonas aeruginosa (PA) in immunocompromised hosts prompted us to explore the potential role of sialic acids (Sia) in this phenomenon. Culture of PA in the presence of exogenous Sia resulted in linkage-specific incorporation of Sia which was associated with decreased complement deposition on the bacteria. Sia acquired by PA mediated enhanced binding of bacteria to recombinant-CHO cells expressing human siglec-7 or siglec-9, as well as to human NK-cells and monocytes naturally expressing these siglecs. Therefore, Sia may be acquired by PA in the host and contribute to bacterial pathogenicity and host-cell interactions via reduction of complement deposition and siglec-dependent recognition.     

Alternative models of cancer stem cells: The stemness phenotype model, 10 years later

The classical cancer stem cell (CSCs) theory proposed the existence of a rare but constant subpopulation of CSCs. In this model cancer cells are organized hierarchically and are responsible for tumor resistance and tumor relapse. Thus, eliminating CSCs will eventually lead to cure of cancer. This simplistic model has been challenged by experimental data. In 2010 we proposed a novel and controversial alternative model of CSC biology (the Stemness Phenotype Model, SPM). The SPM proposed a non-hierarchical model of cancer biology in which there is no specific subpopulation of CSCs in tumors. Instead, cancer cells are highly plastic in term of stemness and CSCs and non-CSCs can interconvert into each other depending on the microenvironment. This model predicts the existence of cancer cells ranging from a pure CSC phenotype to pure non-CSC phenotype and that survival of a single cell can originate a new tumor. During the past 10 years, a plethora of experimental evidence in a variety of cancer types has shown that cancer cells are indeed extremely plastic and able to interconvert into cells with different stemness phenotype. In this review we will (1) briefly describe the cumulative evidence from our laboratory and others supporting the SPM; (2) the implications of the SPM in translational oncology; and (3) discuss potential strategies to develop more effective therapeutic regimens for cancer treatment.     

Effect of nutritional conditions on dye removal from textile effluent by <Emphasis Type="Italic">Aspergillus lentulus</Emphasis>

The nutritional conditions supporting growth and maximum dye removal by Aspergillus lentulus have been investigated. Initially a composite media containing yeast extract, glucose and mineral components was used and the effect of various components on dye removal was studied. For maximum dye removal (≈100%), ≥0.5% (w/v) glucose and ≥0.25% (w/v) yeast extract were essential. While glucose played an important role in pellet formation, which in turn was important for dye removal, yeast extract contributed towards higher biomass production. Mineral components (except NH₄NO₃) did not affect dye removal significantly. Next the alternate sources of carbon (molasses, jaggery, starch and sodium acetate) and nitrogen (peptone, urea, ammonium nitrate, sodium nitrate and ammonium chloride) were tested. Among carbon sources, all the sources produced almost complete dye removal in 48 h (more than 97% in 24 h), except sodium acetate (64% in 48 h). All the tested nitrogen sources resulted in >90% dye removal in 48 h. Yeast extract and peptone gave best results with high dye removal rate (9.8 and 8.1 mg/l/h, respectively). However, among the low cost alternates, urea and NH₄Cl came out to be suitable sources due to the high uptake capacity of the biomass produced coupled with high dye removal rate in case of NH₄Cl. Therefore, a combination of urea and NH₄Cl was tested, which produced complete dye removal with a high dye removal rate (10 mg/l/h). Finally the modified composite media containing urea and NH₄Cl as nitrogen sources and glucose as carbon source was utilized for effluent treatment. Results indicated that performance of modified composite media was at par with composite media for supporting growth of A. lentulus and dye removal from the textile effluent.     

Exome sequencing followed by large-scale genotyping fails to identify single rare variants of large effect in idiopathic generalized epilepsy

Idiopathic generalized epilepsy (IGE) is a complex disease with high heritability, but little is known about its genetic architecture. Rare copy-number variants have been found to explain nearly 3% of individuals with IGE; however, it remains unclear whether variants with moderate effect size and frequencies below what are reliably detected with genome-wide association studies contribute significantly to disease risk. In this study, we compare the exome sequences of 118 individuals with IGE and 242 controls of European ancestry by using next-generation sequencing. The exome-sequenced epilepsy cases include study subjects with two forms of IGE, including juvenile myoclonic epilepsy (n = 93) and absence epilepsy (n = 25). However, our discovery strategy did not assume common genetic control between the subtypes of IGE considered. In the sequence data, as expected, no variants were significantly associated with the IGE phenotype or more specific IGE diagnoses. We then selected 3,897 candidate epilepsy-susceptibility variants from the sequence data and genotyped them in a larger set of 878 individuals with IGE and 1,830 controls. Again, no variant achieved statistical significance. However, 1,935 variants were observed exclusively in cases either as heterozygous or homozygous genotypes. It is likely that this set of variants includes real risk factors. The lack of significant association evidence of single variants with disease in this two-stage approach emphasizes the high genetic heterogeneity of epilepsy disorders, suggests that the impact of any individual single-nucleotide variant in this disease is small, and indicates that gene-based approaches might be more successful for future sequencing studies of epilepsy predisposition.     

Blind docking of pharmaceutically relevant compounds using RosettaLigand

It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method.     

Regulatory Interactions between a Bacterial Tyrosine Kinase and Its Cognate Phosphatase

The cyclic process of autophosphorylation of the C-terminal tyrosine cluster (YC) of a bacterial tyrosine kinase and its subsequent dephosphorylation following interactions with a counteracting tyrosine phosphatase regulates diverse physiological processes, including the biosynthesis and export of polysaccharides responsible for the formation of biofilms or virulence-determining capsules. We provide here the first detailed insight into this hitherto uncharacterized regulatory interaction at residue-specific resolution using Escherichia coli Wzc, a canonical bacterial tyrosine kinase, and its opposing tyrosine phosphatase, Wzb. The phosphatase Wzb utilizes a surface distal to the catalytic elements of the kinase, Wzc, to dock onto its catalytic domain (Wzc_CD). Wzc_CD binds in a largely YC-independent fashion near the Wzb catalytic site, inducing allosteric changes therein. YC dephosphorylation is proximity-mediated and reliant on the elevated concentration of phosphorylated YC near the Wzb active site resulting from Wzc_CD docking. Wzb principally recognizes the phosphate of its phosphotyrosine substrate and further stabilizes the tyrosine moiety through ring stacking interactions with a conserved active site tyrosine.     

Polymorphism of fecundity genes (BMPR1B, BMP15 and GDF9) in the Indian prolific Black Bengal goat

The Black Bengal is a prolific goat breed in India. Natural mutations in prolific sheep breeds have shown that the transforming growth factor beta (TGF-β) super family ligands such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15) and their type I receptor (bone morphogenetic protein receptor, BMPR1B) are crucial for ovulation and as well as for increasing litter size. Mutations in any of these genes increased prolificacy in sheep. Based on the known mutation information in sheep PCR primers were designed to screen known polymorphism in 88 random Black Bengal goats. Only the BMPR1B gene was polymorphic. Three genotypes of animals were detected in tested animals with mutant (FecB^B) and wild type (FecB⁺) alleles were 0.57 and 0.43, respectively. Non-carrier, heterozygous carrier and homozygous carrier Black Bengal does had 2.7, 3.04 and 3.11 kids, respectively. All known point mutations of BMP15 and GDF9 genes were monomorphic in the animals tested. These results preliminarily showed that the BMPR1B gene might be a major gene that influences prolificacy of Black Bengal goats.     

Physical exercise, body mass index, subcutaneous adiposity and body composition among Bengalee boys aged 10-17 years of Kolkata, India

A comparative study of 215 sedentary (no regular physical exercise undertaken) and 313 physically active (regular physical exercise undertaken) Bengalee boys aged 10-17 years was undertaken to investigate the differences in overall adiposity (body mass index), subcutaneous adiposity (skinfolds) and body composition (percent body fat, fat mass and fat mass index). Both groups had a similar age. The results revealed that boys who did not undertake regular physical exercise (NPE) had a significantly greater mean body mass index (BMI) compared with those who undertook regular physical exercise (PE); p < 0.001. The means for all the skinfolds as well as percent body fat (PBF), fat mass (FM) and fat mass index (FMI) were significantly higher among the NPE group. The percentile distributions of all these variables and indices were consistently higher among the NPE group. The results of ANOVA of physical exercise (PE = yes, NPE = no) and PBF, FM and FMI, with age as covariate, revealed that PE had a significant negative effect on all these measures of body composition even after controlling for the impact of age. The means in each case were greater among the NPE group. In conclusion, this study provided evidence that Bengalee boys, who undertook regular physical exercise, had significantly less adiposity compared with those who did not undertake regular physical exercise.