The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.     

The genome sequence of the filamentous fungus Neurospora crassa

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.     

A gravitationally lensed quasar with quadruple images separated by 14.62 arcseconds

Gravitational lensing is a powerful tool for the study of the distribution of dark matter in the Universe. The cold-dark-matter model of the formation of large-scale structures (that is, clusters of galaxies and even larger assemblies) predicts the existence of quasars gravitationally lensed by concentrations of dark matter so massive that the quasar images would be split by over 7 arcsec. Numerous searches for large-separation lensed quasars have, however, been unsuccessful. All of the roughly 70 lensed quasars known, including the first lensed quasar discovered, have smaller separations that can be explained in terms of galaxy-scale concentrations of baryonic matter. Although gravitationally lensed galaxies with large separations are known, quasars are more useful cosmological probes because of the simplicity of the resulting lens systems. Here we report the discovery of a lensed quasar, SDSS J1004 + 4112, which has a maximum separation between the components of 14.62 arcsec. Such a large separation means that the lensing object must be dominated by dark matter. Our results are fully consistent with theoretical expectations based on the cold-dark-matter model.     

Shorebird predation on benthic macroinvertebrates in an irrigation reservoir

American Falls Reservoir in southeastern Idaho is an irrigation reservoir used as an inland feeding stopover by many shorebird species. Six exclosure experiments were conducted during the 1990 drawdown period to investigate shorebird predation impact on benthic macroinvertebrate populations. The study sites differed in sediment composition, sediment slope, invertebrate densities, and shorebird abundance. Shorebird predation significantly affected invertebrate densities in only 1 of 6 experiments (Aberdeen Mouth). This site had higher sediment slope and a lower water recedence than other study sites, resulting in concentration of shorebird predation on a small area of newly exposed sediment. Shorebird predation had the greatest impact on medium size class chironomid larvae at Aberdeen Mouth. Our results suggest that inland sites such as American Falls Reservoir represent viable shorebird habitat and may be managed to insure consistent prey availability. Drawdown rate, sediment slope, invertebrate densities, and shorebird abundance are all important factors influencing shorebird predation. Monitoring shorebird abundance and predation impact on invertebrate densities may help in manipulating drawdown rate to provide adequate shorebird prey. Management of inland sites for shorebird use may become more important in the future as human encroachment in coastal areas continues.     

Spawning chronology and larval emergence of June sucker ( Chasmistes liorus )

June sucker ( Chasmistes liorus ) spawned in the Provo River, Utah, over a 2-wk period in early June during both 1987 and 1988. Emergent larvae emigrated from the river to Utah Lake over a 2- to 3-wk period. Drift into the lake peaked between 1200 and 0400. During daylight hours, emergent larvae tended to occur in pools. Peak emergence of larval drift was approximately 1.2 larvae/m 3 during late June in 1987 and 1988. Recruitment failure of June sucker is not due to reproductive failure.     

Genome-wide recombination in Chlamydia trachomatis

A new study reports comparative genomic analysis of 52 geographically diverse strains of Chlamydia trachomatis. The authors reconstruct a genome-wide phylogeny of the species and report extensive genome-wide recombination across multiple lineages of this intracellular bacterial pathogen.     

Survivorship and cause-specific mortality in five populations of mule deer

We used retrospective analyses to investigate cause-specific mortality and survivorship among 5 populations of mule deer ( N = 168 telemetered animals) wintering in the western Great Basin during 1986-1994. These populations existed under similar environmental conditions, but survivorship functions differed among them. Monthly survival ranged from 0.964 to 0.990, and annual survival ranged from 0.643 to 0.884. The proportion of deaths attributed to predation and malnutrition or anthropogenic causes did not differ among the 5 populations. Predation was the leading cause of mortality; mountain lions were responsible for approximately 90% of the deer killed by predators. No difference existed among these populations in the proportion of telemetered deer that were killed by mountain lions, but proportionally more females than males were killed by these large fields. Predation by mountain lions is the primary source of mortality and a widespread phenomenon among the populations of mule deer we investigated.