tRNAGlu Increases the Affinity of Glutamyl-tRNA Synthetase for Its Inhibitor Glutamyl-Sulfamoyl-Adenosine,an Analogue of the Aminoacylation Reaction Intermediate Glutamyl-AMP: Mechanistic and Evolutionary Implications

For tRNA-dependent protein biosynthesis, amino acids are first activated by aminoacyl-tRNA synthetases (aaRSs) yielding the reaction intermediates aminoacyl-AMP (aa-AMP). Stable analogues of aa-AMP, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aaRSs. Glutamyl-sulfamoyl-adenosine (Glu-AMS) is the best known inhibitor of Escherichia coli glutamyl-tRNA synthetase (GluRS). Thermodynamic parameters of the interactions between Glu-AMS and E. coli GluRS were measured in the presence and in the absence of tRNA by isothermal titration microcalorimetry. A significant entropic contribution for the interactions between Glu-AMS and GluRS in the absence of tRNA or in the presence of the cognate tRNA^Glu or of the non-cognate tRNA^Phe is indicated by the negative values of –TΔS_b, and by the negative value of ΔC_p. On the other hand, the large negative enthalpy is the dominant contribution to ΔG_b in the absence of tRNA. The affinity of GluRS for Glu-AMS is not altered in the presence of the non-cognate tRNA^Phe, but the dissociation constant K _d is decreased 50-fold in the presence of tRNA^Glu; this result is consistent with molecular dynamics results indicating the presence of an H-bond between Glu-AMS and the 3’-OH oxygen of the 3’-terminal ribose of tRNA^Glu in the Glu-AMS•GluRS•tRNA^Glu complex. Glu-AMS being a very close structural analogue of Glu-AMP, its weak binding to free GluRS suggests that the unstable Glu-AMP reaction intermediate binds weakly to GluRS; these results could explain why all the known GluRSs evolved to activate glutamate only in the presence of tRNA^Glu, the coupling of glutamate activation to its transfer to tRNA preventing unproductive cleavage of ATP.     

Divergence Times and the Evolutionary Radiation of New World Monkeys (Platyrrhini,Primates): An Analysis of Fossil and Molecular Data

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27–31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21–29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade.     

Potential causes of enhanced transfer of mercury to St. Lawrence River Biota: implications for sediment management strategies at Cornwall, Ontario, Canada

We examined factors and pathways involved in the transfer of mercury (Hg) to the food web in St. Lawrence River embayments near Cornwall, Ontario, where natural remediation of contaminated sediments (eventual burial by settling of cleaner sediments) has been adopted as a management strategy. Yellow perch (Perca flavescens) from one of the study zones (Zone 1) along the river by Cornwall contained significantly higher total mercury (THg) concentrations than perch from other equally contaminated zones. While THg concentrations in benthic invertebrates did not vary among contaminated zones, THg concentrations in yellow perch and invertebrate prey recovered from the perch stomachs were 1.5–2.5 times higher in Zone 1 than those from other zones, suggesting that prey selection affects THg accumulation more than habitat location. No significant differences were found in THg concentrations among different prey species within Zone 1, although there were significant differences in THg concentrations in the same prey species within Zone 1. In contrast, THg concentrations among different prey species increased significantly with trophic level in other contaminated and reference zones. The lack of correspondence between trophic position and THg accumulation in Zone 1 suggests two possibilities: (1) yellow perch in Zone 1 are highly mobile and are assimilating THg from a wide range of prey across Zone 1 with variable THg concentrations and (2) there may be an important non-dietary source of THg to the Zone 1 food web. Potential waterborne Hg sources to Zone 1 were investigated. Whereas THg and MeHg values in discharges from a disused canal were similar to Zone 1 surface water values (0.97 and 0.04 ng l^?1, respectively), concentrations in storm sewer and combined sewer overflows discharging in the vicinity of Zone 1 were 19–45-fold (THg) and 2–4-fold (MeHg) higher than upstream river water. Contributions of Hg to the water column from sediment–water diffusion, estimated using a simple, well-mixed reactor model, ranged 0.05–0.1% of the surface water THg concentration and 1–2% of the MeHg concentration measured in summer months in Zone 1. Although not investigated in the other zones, a strong correlation (r ² = 0.82) was found between MeHg in porewater and amphipod concentrations in Zone 1, indicating that the sediment porewater is bioavailable and likely an important pathway for transfer of sediment Hg to the foodweb. Large areas of Zone 1 contain bark deposits and produce high rates of gas ebullition, and may not provide favourable conditions for progressive burial with clean sediments and attenuation of Hg transfer to biota through natural remediation. Careful monitoring of surface sediment concentrations and biota is required in these areas. Failure to reduce concentrations of Hg in these media would indicate alternative or additional management measures are required.     

A nucleic acid sequence-based amplification (NASBA) system for Listeria monocytogenes and simple method for detection of amplimers

A NASBA system amplifying specific sequences of the Listeria monocytogenes hlyA gene and an immunoenzymatic assay for the detection of amplimers was developed. The immunoenzymatic assay utilized a simple microtiter plate format and an anti-RNA:DNA hybrid antibody for the detection of NASBA product (predominantly RNA) hybridized to an immobilized DNA probe. This highly sensitive isothermal amplification and detection system was reactive with genomic DNA from various L. monocytogenes isolates but not with other Listeria or non-Listeria species.     

Thiophene and bioisostere derivatives as new MMP12 inhibitors

A new MMP12 inhibitor series has been identified containing a thiophene moiety. Different approaches have been considered to replace this potential toxicophore. α-Fluorothiophene derivatives were the most interesting compounds. Their synthesis is presented.     

Chylopericardial tamponade masquerading as hemopericardium: an uncommon complication of cardiac surgery

Chylopericardial tamponade occurs very rarely after heart surgery. It may be the result of lymphatic duct interruption during mammary artery harvest, division of a large thymic remnant, or thrombosis of the subclavian or internal jugular vein by an indwelling central line. Although relatively straightforward when the pericardial aspirate has the usual milky appearance, the correct diagnosis can easily be overlooked particularly early after surgery when the patient is still fasting. We present a case report that illustrates the importance of sending all aspirates for chemical analysis irrespective of their color to arrive at the correct diagnosis and institute the appropriate medical management of this rare condition.