Fair sharing of network resources among workflow ensembles

Cluster Computing - Computational science depends on complex, data intensive applications operating on datasets from a variety of scientific instruments. A major challenge is the integration of...     

First example of 5/6-O-linked pseudosaccharides: synthesis of bicyclic nucleosides containing azido or extended carbohydrate moiety

Treatment of the d-glucose-derived substrate 1 with sodium hydride in tetrahydrofuran provided 3,6-anhydro monosaccharide 2, along with the 5,6-ether linked pseudodisaccharide 3, and pseudotrisaccharide 4. However, reaction of 1 with sodium ethoxide in ethanol afforded 2 as the sole product, elaborated to the bicyclic azidonucleosides 9 and 16. Acetylated bicyclic nucleosides 17-19 with extended carbohydrate residues have been synthesized from 3.     

Characterisation of Pseudomonas aeruginosa isolated from freshwater culture systems

Members of the genus Pseudomonas are important phytopathogens and agents of human infections, while other strains and species exhibit bioremediation and biocontrol activities. Species-specific detection of Pseudomonas species in the environment may help to gain a more complete understanding of the ecological significance of these microorganisms. The objective of present study was comparative analysis of biochemically and PCR based confirmed 10 isolates of Pseudomonas aeruginosa (6 from fish intestine and 4 from pond sediment). PCR-ribotyping and PAGE revealed that there was extensive heterogeneity at the genetic and protein levels. Both genetic and phenotypic heterogeneity were more in the sediment isolates compared to the fish isolates. SDS-PAGE clearly demonstrated the differences between fish and sediment isolates as evident from the higher range of protein profiling. In antibiotic sentivity test no habitat specific antibiogram was obtained. Zinc adversely affected the DNA of all the isolates to be amplified by PCR as DNA banding pattern was different from normal DNA in stressed DNA. Thus stress, particularly, zinc may interfere monitoring of Pseudomonas by PCR.     

A Recurrent Mutation in PARK2 Is Associated with Familial Lung Cancer

PARK2, a gene associated with Parkinson disease, is a tumor suppressor in human malignancies. Here, we show that c.823C>T (p.Arg275Trp), a germline mutation in PARK2, is present in a family with eight cases of lung cancer. The resulting amino acid change, p.Arg275Trp, is located in the highly conserved RING finger 1 domain of PARK2, which encodes an E3 ubiquitin ligase. Upon further analysis, the c.823C>T mutation was detected in three additional families affected by lung cancer. The effect size for PARK2 c.823C>T (odds ratio = 5.24) in white individuals was larger than those reported for variants from lung cancer genome-wide association studies. These data implicate this PARK2 germline mutation as a genetic susceptibility factor for lung cancer. Our results provide a rationale for further investigations of this specific mutation and gene for evaluation of the possibility of developing targeted therapies against lung cancer in individuals with PARK2 variants by compensating for the loss-of-function effect caused by the associated variation.     

Protection by protein A of apoptotic cell death caused by anti-AIDS drug zidovudine.

Zidovudine, the anti-AIDS drug, caused inhibition of mitogen-induced proliferation and perturbation of cell-cycle progression of cultured bone marrow cells of mice. There was significant hypoploidy observed in flow cytometric analysis of AZT-treated bone marrow cells. In apo-direct analysis, cells showed apoptosis in G0/G1 phase. In DNA gel analysis, characteristic laddering of apoptosis was observed in AZT-treated bone marrow cells. We demonstrated that, when the animals were pretreated with protein A (PA) of Staphylococcus aureus, the apoptotic changes could be prevented in bone marrow cells of AZT-treated animals. There is a significant (p < 0.05) increase in proliferation of bone marrow cells subjected to mitogen treatment in PA+AZT-treated animals, compared to only AZT-treated animals. However, cell-cycle phase distribution was not hampered and no laddering in DNA gel analysis was also observed in this group. In apo-direct analysis, PA treatment showed significant (p < 0.001) inhibition of AZT-induced apoptosis. These observations indicate that by using a suitable agent such as protein A the toxic side effects of AZT could be minimized.     

The Bovine Ruminal Fluid Metabolome

The rumen is a unique organ that serves as the primary site for microbial fermentation of ingested plant material for domestic livestock such as cattle, sheep and goats. The chemical composition of ruminal fluid is thought to closely reflect the healthy/unhealthy interaction between rumen microflora and diet. Just as diet and feed quality is important for livestock production, rumen health is also critical to the growth and production of high quality milk and meat. Therefore a detailed understanding of the chemical composition of ruminal fluid and the influence of diet on its composition could help improve the efficiency and effectiveness of farming and veterinary practices. Consequently we have undertaken an effort to comprehensively characterize the bovine ruminal fluid metabolome. In doing so, we combined NMR spectroscopy, inductively coupled plasma mass-spectroscopy (ICP-MS), gas chromatography-mass spectrometry (GC-MS), direct flow injection (DFI) mass spectrometry and lipidomics with computer-aided literature mining to identify and quantify essentially all of the metabolites in bovine ruminal fluid that can be routinely detected (with today’s technology). The use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these techniques. Tables containing the set of 246 ruminal fluid metabolites or metabolite species, their concentrations, related literature reference and links to their known diet associations for the bovine rumen metabolome are freely available at http://www.rumendb.ca.     

Thorough investigation of epileptic behavioral characterization of caffeine in adult zebrafishes in correlation with drug brain concentration

Our present research aimed to perform a detailed behavioral characterization of caffeine-induced seizure activity in zebrafish. Epileptic activity was observed by immersing individuals in different concentrations of caffeine solution at 250, 350, and 500 mg/l, respectively. Higher concentrations of caffeine rapidly induced intense behavioral activity resembling tonic seizures. Lower concentrations resulted in behavior that was less intense but sustained for longer periods. Significant attenuation of seizure severity was observed in zebrafish pretreated with the barbiturate phenobarbitone. Finally, brain caffeine levels were measured using HPLC-UV methodology in fish immersed in different concentrations of caffeine. Brain caffeine levels increased with higher concentrations of caffeine treatment; however, they were not significantly altered by pretreatment with phenobarbitone.