Substrate-mediated Fidelity Mechanism Ensures Accurate Decoding of Proline Codons

Aminoacyl-tRNA synthetases attach specific amino acids to cognate tRNAs. Prolyl-tRNA synthetases are known to mischarge tRNA^Pro with the smaller amino acid alanine and with cysteine, which is the same size as proline. Quality control in proline codon translation is partly ensured by an editing domain (INS) present in most bacterial prolyl-tRNA synthetases that hydrolyzes smaller Ala-tRNA^Pro and excludes Pro-tRNA^Pro. In contrast, Cys-tRNA^Pro is cleared by a freestanding INS domain homolog, YbaK. Here, we have investigated the molecular mechanism of catalysis and substrate recognition by Hemophilus influenzae YbaK using site-directed mutagenesis, enzymatic assays of isosteric substrates and functional group analogs, and computational modeling. These studies together with mass spectrometric characterization of the YbaK-catalyzed reaction products support a novel substrate-assisted mechanism of Cys-tRNA^Pro deacylation that prevents nonspecific Pro-tRNA^Pro hydrolysis. Collectively, we propose that the INS and YbaK domains co-evolved distinct mechanisms involving steric exclusion and thiol-specific chemistry, respectively, to ensure accurate decoding of proline codons.     

Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

Abstract. Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species‐area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m²) exhibit different species‐area relationships and different species abundance patterns. The species‐area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species‐area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small‐stature annual species in California and the lack of annuals in Australian heathlands. Species‐area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species‐area curves initially rise rapidly between 1 and 100 m². Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m² but more rapidly between 100 and 1000 m² due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species‐area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species‐area curves, and this may be tied to patterns of life form distribution.     

tRNA processing in human mitochondrial disorders

Many human mitochondrial disorders are associated with mutations in tRNA genes or with deletions of regions containing tRNA genes, all of which may be suspected to play a role in recognition by RNase P. Here we describe the analysis of five such mutations. The results presented here demonstrate that none of thse mutations result in errors in RNase P function. Further studies of mutations in tRNAs need to be pursued to elucidate the identity elements for RNase P function in mammalian mitochondria.     

Productivity and population density estimates of the dengue vector mosquito Aedes aegypti (Stegomyia aegypti) in Australia

New mosquito control strategies centred on the modifying of populations require knowledge of existing population densities at release sites and an understanding of breeding site ecology. Using a quantitative pupal survey method, we investigated production of the dengue vector Aedes aegypti (L.) (Stegomyia aegypti) (Diptera: Culicidae) in Cairns, Queensland, Australia, and found that garden accoutrements represented the most common container type. Deliberately placed ‘sentinel’ containers were set at seven houses and sampled for pupae over 10 weeks during the wet season. Pupal production was approximately constant; tyres and buckets represented the most productive container types. Sentinel tyres produced the largest female mosquitoes, but were relatively rare in the field survey. We then used field‐collected data to make estimates of per premises population density using three different approaches. Estimates of female Ae. aegypti abundance per premises made using the container‐inhabiting mosquito simulation (CIMSiM) model [95% confidence interval (CI) 18.5–29.1 females] concorded reasonably well with estimates obtained using a standing crop calculation based on pupal collections (95% CI 8.8–22.5) and using BG‐Sentinel traps and a sampling rate correction factor (95% CI 6.2–35.2). By first describing local Ae. aegypti productivity, we were able to compare three separate population density estimates which provided similar results. We anticipate that this will provide researchers and health officials with several tools with which to make estimates of population densities.     

THE DISTRIBUTION, ABUNDANCE AND SELECTED PREY OF THE HARBOR SEAL, PHOCA VITULINA CONCOLOR, IN SOUTHERN NEW ENGLAND

The seasonal distribution and abundance of harbor seals occurring south of Maine were documented by counting the number of seals at traditional haulout locations. The average number of seals counted during each survey in Massachusetts and New Hampshire was 3,560 ± 255 (95% CI), 1983–1987. The maximum number of seals counted on any individual survey was 4,736 individuals. Fifty percent of all the surveys since January 1985 have resulted in counts greater than 4,000 seals reflecting a 27% increase in the abundance of seals in our study area since that date. Seventy-five percent of the seals in southern New England are located at haulout sites on Cape Cod and Nantucket Island. The largest aggregation of seals in the eastern United States occurs mid-winter at Monomoy Island and adjacent shoals. A single high count of 1,672 seals occurred at this site during the study period. An additional 271–374 seals were also counted in Rhode Island, Connecticut and eastern Long Island Sound during surveys conducted in March 1986 and 1987. The American sandlance Ammodytes americanus was the single dominant prey item of harbor seals in waters adjacent to Cape Cod based on the modified frequency of occurrence of each prey species in scat samples collected from three haulout sites on Cape Cod between 1984–1987. During January and February sandlance was the near exclusive prey item at Monomoy (99%, n= 80). During March and April, the frequency of Atlantic herring Clupea harengus increased in the scat samples at this site. Regional differences in the diet of seals reflect distinct prey communities throughout the study area. Since 1986, the percent occurrence and importance of sandlance in the diet of seals has decreased, reflecting an overall decrease in abundance of this prey species in waters adjacent to Cape Cod. In spite of fluctuations in abundance, and regional differences in the diet of seals throughout the study area, sandlance still comprised a minimum 55% of the total prey species of harbor seals throughout the study area.     

Distribution and abundance of young fish in the St. Clair River and associated waters,Ontario

Fish larvae were sampled in 1986 in the St. Clair River, and adjacent waters. Species richness (9 taxa as larvae; 4 others as juveniles) and abundance was lowest in the river, where many larvae (e.g., burbot, rainbow smelt, and yellow perch) were in transit from Lake Huron. The most abundant, and localized, species was gizzard shad, which reached a peak mean density of 4600 larvae 100 m^-3 in an agricultural canal. Adjacent waters contribute greatly to the fish communities of the river and adjoining Lakes Huron and Erie, especially in terms of the number and quantity of forage species.