Molecular cloning,sequence analysis and homology modeling of galE encoding UDP-galactose 4-epimerase of Aeromonas hydrophila

A. hydrophila, a ubiquitous gram-negative bacterium present in aquatic environments, has been implicated in illness in humans, fish and amphibians. Lipopolysaccharides (LPS), a surface component of the outer membrane, are one of the main virulent factors of gram-negative bacteria. UDP-galactose 4-epimerase (GalE) catalyses the last step in the Leloir pathway of galactose metabolism and provides precursor for the biosynthesis of extracellular LPS and capsule. Due to its key role in LPS biosynthesis, it is a potential drug target. The present study describes cloning, sequence analysis and prediction of three dimensional structure of the deduced amino acid sequence of the galE of A. hydrophila AH17. The cloned galE consists of the putative promoter-operator region, and an open reading frame of 338 amino acid residues. Sequence alignment and predicted 3Dstructure revealed that the GalE of A. hydrophila consists of the signature sequences of the epimerase super family. The present study reports the molecular modeling / 3D-structure prediction of GalE of A. hydrophila. Further, the potential regions of the enzyme that can be targeted for drug design are identified.     

Chromatographic separation of enantiomers of non-protein alpha-amino acids after derivatization with Marfey's reagent and its four variants

Some non-protein α-amino acids were derivatized with 1-fluoro-2,4-dinitrophenyl-5-l-alaninamide (Marfey’s reagent, MR, FDNP-l-Ala-NH₂,) and four of its structural variants FDNP-l-Phe-NH₂, FDNP-l-Val-NH₂, FDNP-l-Leu-NH₂ and FDNP-l-Pro-NH₂. The resultant diastereomers were separated by normal and reversed phase thin layer chromatography (TLC) and reversed phase HPLC. In normal phase TLC, best resolution was obtained with solvent combination of phenol-water (3:1) while in reversed phase TLC mixtures of acetonitrile with triethylammonium phosphate buffer were found successful for resolution of diastereomers. The separation behavior of diastereomers prepared with different reagents was compared. The diastereomers of most of the amino acids prepared with FDNP-l-Leu-NH₂ were best separated while those prepared with FDNP-l-Pro-NH₂ failed to separate in most of the cases. The diastereomers were also separated on a reversed phase C₈ column with gradient elution using mixture of aqueous-trifluoroacetic acid (TFA) and acetonitrile and with detection at 340 nm. The effects of TFA concentration, flow rate and run time on HPLC separation were studied.     

Regulation of DNA repair mechanism in human glioma xenograft cells both in vitro and in vivo in nude mice

Background

Glioblastoma Multiforme (GBM) is the most lethal form of brain tumor. Efficient DNA repair and anti-apoptotic mechanisms are making glioma treatment difficult. Proteases such as MMP9, cathepsin B and urokinase plasminogen activator receptor (uPAR) are over expressed in gliomas and contribute to enhanced cancer cell proliferation. Non-homologous end joining (NHEJ) repair mechanism plays a major role in double strand break (DSB) repair in mammalian cells.

Methodology/Principal Findings

Here we show that silencing MMP9 in combination with uPAR/cathepsin B effects NHEJ repair machinery. Expression of DNA PKcs and Ku70/80 at both mRNA and protein levels in MMP9-uPAR (pMU) and MMP9-cathepsin B (pMC) shRNA-treated glioma xenograft cells were reduced. FACS analysis showed an increase in apoptotic peak and proliferation assays revealed a significant reduction in the cell population in pMU- and pMC-treated cells compared to untreated cells. We hypothesized that reduced NHEJ repair led to DSBs accumulation in pMU- and pMC-treated cells, thereby initiating cell death. This hypothesis was confirmed by reduced Ku70/Ku80 protein binding to DSB, increased comet tail length and elevated γH2AX expression in treated cells compared to control. Immunoprecipitation analysis showed that EGFR-mediated lowered DNA PK activity in treated cells compared to controls. Treatment with pMU and pMC shRNA reduced the expression of DNA PKcs and ATM, and elevated γH2AX levels in xenograft implanted nude mice. Glioma cells exposed to hypoxia and irradiation showed DSB accumulation and apoptosis after pMU and pMC treatments compared to respective controls.

Conclusion/Significance

Our results suggest that pMU and pMC shRNA reduce glioma proliferation by DSB accumulation and increase apoptosis under normoxia, hypoxia and in combination with irradiation. Considering the radio- and chemo-resistant cancers favored by hypoxia, our study provides important therapeutic potential of MMP9, uPAR and cathepsin B shRNA in the treatment of glioma from clinical stand point.     

ADAMTS7 Cleavage and Vascular Smooth Muscle Cell Migration Is Affected by a Coronary-Artery-Disease-Associated Variant

Recent genome-wide association studies have revealed an association between variation at the ADAMTS7 locus and susceptibility to coronary artery disease (CAD). Furthermore, in a population-based study cohort, we observed an inverse association between atherosclerosis prevalence and rs3825807, a nonsynonymous SNP (A to G) leading to a Ser-to-Pro substitution in the prodomain of the protease ADAMTS7. In light of these data, we sought a mechanistic explanation for this association. We found that ADAMTS7 accumulated in smooth muscle cells in coronary and carotid atherosclerotic plaques. Vascular smooth muscle cells (VSMCs) of the G/G genotype for rs3825807 had reduced migratory ability, and conditioned media of VSMCs of the G/G genotype contained less of the cleaved form of thrombospondin-5, an ADAMTS7 substrate that had been shown to be produced by VSMCs and inhibit VSMC migration. Furthermore, we found that there was a reduction in the amount of cleaved ADAMTS7 prodomain in media conditioned by VSMCs of the G/G genotype and that the Ser-to-Pro substitution affected ADAMTS7 prodomain cleavage. The results of our study indicate that rs3825807 has an effect on ADAMTS7 maturation, thrombospondin-5 cleavage, and VSMC migration, with the variant associated with protection from atherosclerosis and CAD rendering a reduction in ADAMTS7 function.     

Preparation of poly(acrylamide-co-acrylic acid)-grafted gum and its flocculation and biodegradation studies

Biodegradation studies of Gum ghatti (Gg) and acrylamide-co-acrylic acid based flocculants [Gg-cl-poly(AAm-co-AA)] have been reported using the soil composting method. Gg-cl-poly(AAm-co-AA) was found to degrade 89.76% within 60 days. The progress of biodegradation at each stage was monitored through FT-IR and SEM. Polymer was synthesized under pressure using potassium persulphate-ascorbic acid as a redox initiator and N,N′-methylene-bis-acrylamide as a crosslinker. Synthesized polymer was found to show pH, temperature and ionic strength of the cations dependent swelling behavior. Gg-cl-poly(AAm-co-AA) was utilized for the selective absorption of saline from different petroleum fraction-saline emulsions. The flocculation efficiency of the polymer was studied as a function of polymer dose, temperature and pH of the solution. Gg-cl-poly(AAm-co-AA) showed maximum flocculation efficiency with 20 mol L⁻¹ polymer dose in acidic medium at 50 °C.