A comparative study on the reactivity of electrogenerated bromine with cyclohexene in acetonitrile and the room temperature ionic liquid, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide

The reactivity of electrogenerated bromine with cyclohexene has been studied on a platinum microelectrode by linear sweep and cyclic voltammetry in both the room temperature ionic liquid, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, and the conventional aprotic solvent, acetonitrile. Variation in the voltammetric response was observed in the two solvents, indicating that the bromination reaction proceeded via separate mechanisms. To identify the different products, electrolysis was conducted on the preparative scale and NMR spectroscopy confirmed that while bromination of the organic substrate in the ionic liquid yields trans-1,2-dibromocyclohexane, in acetonitrile, trans-1-(N-acetylamino)-2-bromocyclohexane is instead obtained as the major product. The reaction mechanism for bromination in acetonitrile has been modeled using digital simulation.

CO oxidation on Pd(100) and Pd(111): A comparative study of reaction pathways and reactivity at low and medium coverages

We have performed density functional theory calculations with the generalized gradient approximation to investigate CO oxidation on a close-packed transition metal surface, Pd(lll), and a more open surface, Pd(100), aiming to shed light on surface structure effects on reaction pathways and reactivity, an important issue in catalysis. Reaction pathways on both surfaces at two different coverages have been studied. It is found that the reaction pathways on both surfaces possess crucial common features despite the fact that they have different surface symmetries. Having determined reaction barriers in these systems, we find that the reaction on Pd(lll) is strongly coverage dependent. Surface coverages, however, have little effect on the reaction on Pd(100). Calculations also reveal that the low coverage reactions are structure sensitive while the medium coverage reactions are not. Detailed discussions on these results are given.

Comparative analysis of dna methylation profiles in peripheral blood leukocytes versus lymphoblastoid cell lines

Previous reports have shown that DNA methylation profiles within primary human malignant tissues are altered when these cells are transformed into cancer cell lines. However, it is unclear if similar differences in DNA methylation profiles exist between DNA derived from peripheral blood leukocytes (PBLs) and corresponding Epstein-Barr Virus transformed lymphoblastoid cell lines (LCLs). To assess the utility of LCLs as a resource for methylation studies we have compared DNA methylation profiles in promoter and 5' regions of 318 genes in PBL and LCL sample pairs from patients with type 1 diabetes with or without nephropathy. We identified a total of 27 (similar to 8%) genes that revealed different DNA methylation profiles in PBL compared with LCL-derived DNA samples. In conclusion, although the profiles for most promoter regions were similar between PBL-LCL pairs, our results indicate that LCL-derived DNA may not be suitable for DNA methylation studies at least in diabetic nephropathy.

Kassina senegalensis skin tachykinins: Molecular cloning of kassinin and (Thr2, Ile9)-kassinin biosynthetic precursor cDNAs and comparative bioactivity of mature tachykinins on the smooth muscle of rat urinary bladder

Tachykinins are among the most widely-studied families of regulatory peptides characterized by a highly-conserved C-terminal -Phe-X-Gly-Leu-Met.amide motif, which also constitutes the essential bioactive core. The amphibian skin has proved to be a rich source of these peptides with physalaemin from the skin of Physalaemus fuscomaculatus representing the archetypal aromatic tachykinin (X = Tyr or Phe) and kassinin from the skin of Kassina senegalensis representing the archetypal aliphatic tachykinin in which X = Val or Ile. Despite the primary structures of both mature peptides having been known for at least 30 years, neither the structures nor organizations of their biosynthetic precursors have been reported. Here we report the structure and organization of the biosynthetic precursor of kassinin deduced from cDNA cloned from a skin secretion library. In addition, a second precursor cDNA encoding the novel kassinin analog (Thr2, Ile9)-kassinin was identified as was the predicted mature peptide in skin secretion. Both transcripts exhibited a high degree of nucleotide sequence similarity and of open-reading frame translated amino acid sequences of putative precursor proteins. The translated preprotachykinins each consisted of 80 amino acid residues encoding single copies of either kassinin or its site-substituted analog. Synthetic replicates of each kassinin were found to be active on rat urinary bladder smooth muscle at nanomolar concentrations. The structural organization of both preprotachykinins differs from that previously reported for those of Odorrana grahami skin indicating a spectrum of diversity akin to that established for amphibian skin preprobradykinins.

Effect of pooling samples on the efficiency of comparative studies using microarrays

Motivation: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large.