Restorative Effect of Kalpaamruthaa, an Indigenous Preparation, on Oxidative Damage in Mammary Gland Mitochondrial Fraction in Experimental Mammary Carcinoma

Cancer prevention and treatment using phytochemicals have attracted increased interest. Recent studies have shown that Semecarpus anacardium Linn nut milk extract (SA), a promising antioxidant and anticancer drug, exerts its anticancer effect through reducing or quenching reactive oxygen species under different conditions. The present study examined whether Phyllanthus emblica Linn fruit, rich in vitamin C content synergistically in combination can enhance both the antioxidant and anticancer activity of S. anacardium nut milk extract in 7, 12-dimethyl benz[a]anthracene (DMBA)-induced experimental mammary carcinoma in rat model. Female Sprague Dawley rats of 180 ± 10g were categorized into six groups. Three groups were administered DMBA (25mg/rat, orally) dissolved in olive oil to induce mammary carcinoma. One of these groups received Kalpaamruthaa (KA) (300mg/kg b.wt, orally) and other group received SA (200mg/kg b.wt, orally) for 14 days after 90 days of DMBA induction. A vehicle treated control and drug control groups were also included. The mitochondrial fraction of untreated DMBA-induced mammary gland showed 2.61-fold increase in lipid peroxidation level and abnormal changes in the activities/levels of mitochondrial enzymic (superoxide dismutase, glutathione peroxidase and glutathione reductase) and non-enzymic (glutathione, vitamin C and vitamin E) antioxidants were observed. DMBA treated rats also showed decline in the activities of mitochondrial enzymes such as succinate dehydrogenase, malate dehydrogenase, α-ketoglutarate dehydrogenase and isocitrate dehydrogenase. In contrast, rats treated with Kalpaamruthaa showed normal lipid peroxide level and antioxidant defenses. The results of the present study highlight the improved antioxidant property of KA than sole treatment of S. anacardium nut milk extract.     

Ethnic differences in key candidate genes for spontaneous preterm birth: TNF-alpha and its receptors

OBJECTIVES: Spontaneous preterm birth (PTB) has a significant ethnic disparity with people of African descent having an almost 2-fold higher incidence than those of European descent in the United States. This disparity may be caused by differences in the distribution of genetic risk factors. The objective of this study is to examine genetic differences between African-Americans and European Americans for single nucleotide polymorphisms (SNPs) in candidate genes for PTB. METHODS: We examined patterns of variation in 19 SNPs in 3 candidate genes for preterm birth: TNF-alpha, TNF-receptor 1 and TNF-receptor 2. Allele, genotype and haplotype frequencies were compared between African-Americans (AA) and European-Americans (EA) in cases and controls separately. Both maternal and fetal genotypes were studied, as it is unclear whether one or both of these are important in the etiology of PTB. RESULTS: The vast majority of the SNPs differed significantly between ethnic groups, although there are only a few suggestive results comparing cases and controls within an ethnic group. For TNF-alpha, four of six SNPs; for TNF-R1, 5/6; and for TNF-R2, 6/7 showed significant differences between ethnic groups in either allele and/or genotype frequency. CONCLUSIONS: Our data demonstrate highly significant genetic differences between ethnic groups in genes that may play a role in the risk of PTB.     

Synthesis,stereochemistry and antimicrobial studies of novel oxime ethers of aza/diazabicycles

Two series of bicyclic oxime ethers viz, 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-one O-benzyloximes 13–24 and 2,4,6,8-tetraaryl-3,7-diazabicyclo[3.3.1]nonan-9-one O-benzyloximes 31–36 were synthesized and stereochemistry was established by their spectral (1D and 2D NMR) and crystal studies. Synthesized oxime ethers were screened for their in vitro antimicrobial activity against a set of pathogenic bacteria (Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi, Escherichia coli and Klebsiella pneumoniae) and fungi (Candida albicans, Candida-51, Rhizopus sp., Aspergillus niger and Aspergillus flavus) by twofold serial dilution method, respectively, using Ciprofloxacin and Amphotericin B as standards. Most of the molecules expressed promising antimicrobial profile against the tested pathogens and even a few compounds 16, 21, 22, 33 and 34 were better than standard drugs.     

Induction of HIV-1 resistance: cell susceptibility to infection is an inverse function of globotriaosyl ceramide levels

To examine the role of the glycosphingolipid (GSL), globotriaosylceramide(Gb₃, CD77, p^k blood group antigen) in HIV-1 infection, we havepharmacologically modulated Gb₃ metabolism in an X4 HIV-1 infectablemonocytic cell line (THP-1) that naturally expresses Gb₃ andin a Gb₃-expressing glioblastoma cell line (U87) transfectedto express both CD4 and CCR5 to permit R5 HIV-1 infection. THP-1and U87 cells were treated with either a competitive inhibitorof -galactosidase A, 1-deoxygalactonojirimycin (DGJ) to induceGb₃ accumulation, or a glucosylceramide synthase inhibitor,phenyl-2-palmitylamino-3-pyrrolidino-1-propanol (P4) to depletecells of Gb₃. HIV susceptibility was determined via measurementof p24^gag antigen production by ELISA. In addition, total cellularGb₃ content was determined using thin layer chromatography followedby Verotoxin1 overlay binding. The cell surface expression ofGb₃ was verified by FACS analysis. We found that DGJ significantlydecreased THP-1 and U87 cell susceptibility to HIV-1_IIIB andHIV-1_BaL infection, respectively, at a concentration of approximately100 µM. In contrast, P4 (2 µM) substantiallyincreased cellular susceptibility to HIV-1 infection. Totalcellular GSL analysis verified increased Gb₃ expression in cellstreated with DGJ and considerable reduction of Gb₃ in P4-treatedcells as compared to controls. These results show a reciprocalrelationship between Gb₃ expression and infection with eitherX4 HIV-1_IIIB or R5 HIV-1_Ba-L. These results support previousstudies that Gb₃ provides resistance to HIV infection. VariableGb₃ expression may provide a natural HIV resistance factor inthe general population, and pharmacological manipulation ofGb₃ levels may provide an approach to induction of HIV resistance.     

Lipopolysaccharide bound structures of the active fragments of fowlicidin-1, a cathelicidin family of antimicrobial and antiendotoxic peptide from chicken, determined by transferred nuclear Overhauser effect spectroscopy

Cathelicidins comprise a major family of host-defense antimicrobial peptides in vertebrates. The C-terminal part of the cathelicidins is bestowed with antimicrobial and lipopolysaccharide (LPS) neutralizing activities. In this work, we repot high resolution solution structures of two nontoxic active fragments, residues 1-16 or RG16 and residues 8-26 or LK19, of fowlicidin-1, a cathelicidin family of peptide from chicken, as a complex with LPS using two-dimensional transferred nuclear Overhauser effect (Tr-NOE) spectroscopy. Both peptides are highly flexible and do not assume any preferred conformations in their free states. Upon complexation with endotoxin or LPS, peptides undergo structural transitions towards folded conformations. Structure calculations reveal that the LK19 peptide adopts a well defined helical structure with a bend at the middle. By contrast, the first seven amino acids of RG16 are found to be flexible followed by a helical conformation for the residues L8-A15. In addition, a truncated version of LK19 encompassing residues A15-K26 or AK12 displays an amphipathic helical structure in LPS. Saturation transfer difference (STD) NMR studies demonstrate that all peptides, RG16, LK19, and AK12, are in close proximity with LPS, whereby the aromatic residues showed the strongest STD effects. Fluorescence studies with fluorescein isothiocyanate (FITC) labeled LPS in the presence of full-length fowlicidin-1, LK19, RG16, and AK12 indicated that LPS-neutralization property of these peptides may result from plausible dissociation of LPS aggregates. The helical structures of peptide fragments derived from fowlicidin-1 in LPS could be utilized to develop nontoxic antiendotoxic compounds.     

Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth

Background

The use of biological annotation such as genes and pathways in the analysis of gene expression data has aided the identification of genes for follow-up studies and suggested functional information to uncharacterized genes. Several studies have applied similar methods to genome wide association studies and identified a number of disease related pathways. However, many questions remain on how to best approach this problem, such as whether there is a need to obtain a score to summarize association evidence at the gene level, and whether a pathway, dominated by just a few highly significant genes, is of interest.

Methods

We evaluated the performance of two pathway-based methods (Random Set, and Binomial approximation to the hypergeometric test) based on their applications to three data sets of Crohn's disease. We consider both the disease status as a phenotype as well as the residuals after conditioning on IL23R, a known Crohn's related gene, as a phenotype.

Results

Our results show that Random Set method has the most power to identify disease related pathways. We confirm previously reported disease related pathways and provide evidence for IL-2 Receptor Beta Chain in T cell Activation and IL-9 signaling as Crohn's disease associated pathways.

Conclusions

Our results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight.     

Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome

Subminimum inhibitory concentrations (sub-MICs) of antibiotics can be therapeutically effective, but the underlying molecular mechanisms are not well-characterized. We analyzed the Pasteurella multocida proteome response to sub-MICs of amoxicillin, chlortetracycline, and enrofloxacin using isotope-coded affinity tags (ICAT). There were parallel effects on inhibition of growth kinetics and suppression of protein expression by clusters of orthologous groups (COG) categories. Potential compensatory mechanisms enabling antibiotic adaptation were identified, including increased RecA expression caused by enrofloxacin.     

Detailed comparison of the protein-ligand docking efficiencies of GOLD, a commercial package and ArgusLab, a licensable freeware

Molecular docking and virtual screening based on molecular docking have become an integral part of many modern structure-based drug discovery efforts. Hence, it becomes a useful endeavor to evaluate existing docking programs, which can assist in the choice of the most suitable docking algorithm for any particular study. The objective of the current study was to evaluate the ability of ArgusLab 4.0, a relatively new molecular modeling package in which molecular docking is implemented, to reproduce crystallographic binding orientations and to compare its accuracy with that of a well established commercial package, GOLD. The study also aimed to evaluate the effect of the nature of the binding site and ligand properties on docking accuracy. The three dimensional structures of a carefully chosen set of 75 pharmaceutically relevant protein-ligand complexes were used for the comparative study. The study revealed that the commercial package outperforms the freely available docking engine in almost all the parameters tested. However, the study also revealed that although lagging behind in accuracy, results from ArgusLab are biologically meaningful. This taken together with the fact that ArgusLab has an easy to use graphical user interface, means that it can be employed as an effective teaching tool to demonstrate molecular docking to beginners in this area.