Particulate inputs to Dublin Bay and to the South Lagoon,Bull Island

There are substantial riverine and sewage particulate inputs into Dublin Bay. The main river, the R. Liffey, accounts for almost 85% of the riverine input, which amounts to 37.1 t d^–1 of SPM. The sewage input, which is discharged into the estuary, is slightly less at 35.3 t d^–1. The combined inputs deliver 17.4 t d^–1, 2.9 t d^–1and 1.2 t d^–1of particulate C, N and P, respectively, to the Bay as a whole. Although the particulate N load accounts for just 20% of the total N input, the retention of particulates within the system, and the subsequent remobilisation of N from the sediments is heavily implicated in the macroalgal blooms. A particulate mass balance of SPM, and of C, N and P for the South Lagoon showed no consistent pattern of import/export except that the fluxes of the individual elements reflected SPM load and varied with quantity rather than quality. The molar C:N ratio was around 6:1 although on occasion values approaching 3:1 were obtained, indicating very high quality and potentially labile SPM. The controlling factors in the budget appeared to be the water velocities and to a lesser extent, the SPM load, which surprisingly was no greater on a spring tide than on a neap. In this shallow, and primarily intertidal, system, wind- or wave-driven resuspension may exert more influence than predictable factors such as tidal range.     

Chemoreceptor VfcA Mediates Amino Acid Chemotaxis in Vibrio fischeri

Flagellar motility and chemotaxis by Vibrio fischeri are important behaviors mediating the colonization of its mutualistic host, the Hawaiian bobtail squid. However, none of the 43 putative methyl-accepting chemotaxis proteins (MCPs) encoded in the V. fischeri genome has been previously characterized. Using both an available transposon mutant collection and directed mutagenesis, we isolated mutants for 19 of these genes, and screened them for altered chemotaxis to six previously identified chemoattractants. Only one mutant was defective in responding to any of the tested compounds; the disrupted gene was thus named vfcA (Vibrio fischeri chemoreceptor A; locus tag VF_0777). In soft-agar plates, mutants disrupted in vfcA did not exhibit the serine-sensing chemotactic ring, and the pattern of migration in the mutant was not affected by the addition of exogenous serine. Using a capillary chemotaxis assay, we showed that, unlike wild-type V. fischeri, the vfcA mutant did not undergo chemotaxis toward serine and that expression of vfcA on a plasmid in the mutant was sufficient to restore the behavior. In addition to serine, we demonstrated that alanine, cysteine, and threonine are strong attractants for wild-type V. fischeri and that the attraction is also mediated by VfcA. This study thus provides the first insights into how V. fischeri integrates information from one of its 43 MCPs to respond to environmental stimuli.     

Novel quinoline derivatives as inhibitors of bacterial DNA gyrase and topoisomerase IV

A structurally novel set of inhibitors of bacterial type II topoisomerases with potent in vitro and in vivo antibacterial activity was developed. Dual-targeting ability, hERG inhibition, and pharmacokinetic properties were also assessed.     

Microsomal and cytosolic cytochrome P450 mediated benzo(a)pyrene hydroxylation in Pleurotus pulmonarius

Summary Microsomal and soluble fractions of Pleurotus pulmonarius exhibited a reduced carbon monoxide difference spectrum with P450 maxima at 448nm and 450–452nm respectively. Substrate induced Type I spectra were observed on addition of benzo(a)pyrene to both fractions. Benzo(a)pyrene hydroxylation was measured using the aryl hydrocarbon hydroxylase assay and was observed to be P450 dependent as indicated by carbon monoxide inhibition together with the substrate binding characteristics. The activity of the fractions were observed to give K_m of 200mM and 660mM and V_max of 1.25 nmol/min/nmol P450 and 0.57 nmol/min/nmol P450 for the microsomal and cytosolic fractions respectively.     

Further novel amido sugars within the glycopeptidolipid antigens of Mycobacterium avium

The individual serovars of the Mycobacterium avium complex, a source of serious and persistent infections in individuals with underlying immune deficiencies, also present an extraordinary set of novel sugar epitopes as part of their type-specific glycopeptidolipid surface antigens. Californium desorption-mass spectrometry has been successfully applied to the holistic glycopeptidolipid antigen of M. avium serovar 12 and its per-O-acetyl derivative, to arrive at the following structure, of molecular mass 1876: (Sequence: see text). The pentasaccharide hapten, released as the tetraglycosyl alditol, was subjected to methylation analysis, absolute configurational analysis, 1H NMR and fast atom bombardment-mass spectrometry to arrive at the structure: 4-(2'-Hydroxy) propionamido-4,6-dideoxy-3-O-Me-Glcp (beta 1----3)-4-O-Me-L-Rhap (alpha 1----3)-L-Rhap (alpha 1----3)-L-Rhap (alpha 1----2)-6-deoxytalitol. Two-dimensional proton correlation spectroscopy was also applied to determine the configuration of the unique distal segment of the oligosaccharide unit. The significance of this structure in the context of the fully elucidated structures of the antigens from 12 of the 31-member M. avium complex is discussed.     

Common Variation at 1q24.1 (ALDH9A1) Is a Potential Risk Factor for Renal Cancer

So far six susceptibility loci for renal cell carcinoma (RCC) have been discovered by genome-wide association studies (GWAS). To identify additional RCC common risk loci, we performed a meta-analysis of published GWAS (totalling 2,215 cases and 8,566 controls of Western-European background) with imputation using 1000 Genomes Project and UK10K Project data as reference panels and followed up the most significant association signals [22 single nucleotide polymorphisms (SNPs) and 3 indels in eight genomic regions] in 383 cases and 2,189 controls from The Cancer Genome Atlas (TCGA). A combined analysis identified a promising susceptibility locus mapping to 1q24.1 marked by the imputed SNP rs3845536 (P _combined =2.30x10^-8). Specifically, the signal maps to intron 4 of the ALDH9A1 gene (aldehyde dehydrogenase 9 family, member A1). We further evaluated this potential signal in 2,461 cases and 5,081 controls from the International Agency for Research on Cancer (IARC) GWAS of RCC cases and controls from multiple European regions. In contrast to earlier findings no association was shown in the IARC series (P=0.94; P _combined =2.73x10^-5). While variation at 1q24.1 represents a potential risk locus for RCC, future replication analyses are required to substantiate our observation.     

Species specificity of protein kinase r antagonism by cytomegalovirus TRS1 genes

The host antiviral protein kinase R (PKR) has rapidly evolved during primate evolution, likely in response to challenges posed by many different viral antagonists, such as the TRS1 gene of cytomegaloviruses (CMVs). In turn, viral antagonists have adapted to changes in PKR. As a result of this "arms race," modern TRS1 alleles in CMVs may function differently in cells derived from alternative species. We have previously shown that human CMV TRS1 (HuTRS1) blocks the PKR pathway and rescues replication of a vaccinia virus mutant lacking its major PKR antagonist in human cells. We now demonstrate that HuTRS1 does not have these activities in Old World monkey cells. Conversely, the rhesus cytomegalovirus homologue of HuTRS1 (RhTRS1) fulfills these functions in African green monkey cells, but not rhesus or human cells. Both TRS1 proteins bind to double-stranded RNA and, in the cell types in which they can rescue VVΔE3L replication, they also bind to PKR and prevent phosphorylation of the α-subunit of eukaryotic initiation factor 2. However, while HuTRS1 binds to inactive human PKR and prevents its autophosphorylation, RhTRS1 binds to phosphorylated African green monkey PKR. These studies reveal that evolutionary adaptations in this critical host defense protein have altered its binding interface in a way that has resulted in a qualitatively altered mechanism of PKR antagonism by viral TRS1 alleles from different CMVs. These results suggest that PKR antagonism is likely one of the factors that contributes to species specificity of cytomegalovirus replication.