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 Widespread Colonization Island of Actinobacillus actinomycetemcomitans

Genomic islands, such as pathogenicity islands, contribute to the evolution and diversification of microbial life. Here we report on the Widespread Colonization Island, which encompasses the tad (tight adherence) locus for colonization of surfaces and biofilm formation by the human pathogen Actinobacillus actinomycetemcomitans. At least 12 of the 14 genes at the tad locus are required for tenacious biofilm formation and synthesis of bundled Flp pili (fibrils) that mediate adherence. The pilin subunit, Flp1, remains inside the cell in tad-locus mutants, indicating that these genes encode a secretion system for export and assembly of fibrils. We found tad-related regions in a wide variety of Bacterial and Archaeal species, and their sequence characteristics indicate possible horizontal transfer. To test the hypothesis of horizontal transfer, we compared the phylogeny of the tad locus to a robust organismal phylogeny using statistical tests of congruence and tree reconciliation techniques. Our analysis strongly supports a complex history of gene shuffling by recombination and multiple horizontal transfers, duplications and losses. We present evidence for a specific horizontal transfer event leading to the establishment of this region as a determinant of disease.     

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.     

A multiple intelligent agent system for credit risk prediction via an optimization of localized generalization error with diversity

Company bankruptcies cost billions of dollars in losses to banks each year. Thus credit risk prediction is a critical part of a bank＇s loan approval decision process. Traditional financial models for credit risk prediction are no longer adequate for describing today＇s complex relationship between the financial health and potential bankruptcy of a company. In this work, a multiple classifier system （embedded in a multiple intelligent agent system） is proposed to predict the financial health of a company. In our model, each individual agent （classifier） makes a prediction on the likelihood of credit risk based on only partial information of the company. Each of the agents is an expert, but has limited knowledge （represented by features） about the company. The decisions of all agents are combined together to form a final credit risk prediction. Experiments show that our model out-performs other existing methods using the benchmarking Compustat American Corporations dataset.     

Black-tailed prairie dog populations one year after treatment with rodenticides

Three rodenticide treatments, zinc phosphide with prebait, strychnine with prebait, and strychnine without prebait, were applied to black-tailed prairie dog Cynomys ludovicianus colonies in west central South Dakota. Results were compared immediately posttreatment and for one year after application. Zinc phosphide was the most effective for reducing prairie dog numbers immediately. When burrow activity levels of prairie dogs were initially reduced by 45% with strychnine only, they returned to untreated levels within ten months. When initial reductions were 95% with zinc phosphide, however, the number of active burrows was still reduced 77% in September the following year. Strychnine with prebait treatment showed initial reductions of 83% in burrow activity. Bait consumption by prairie dogs was highest for zinc phosphide.     

Field study of plant survival as affected by amendments to bentonite spoil

Efforts to reclaim amended and raw bentonite spoils with six plant species (two forbs, three shrubs, and one tree) were evaluated over a 4-year period. Plant species included fourwing saltbush ( Atriplex canescens [Pursh] Nutt.), big sagebrush ( Artemisia tridentata tridentata Nutt.), Rocky Mountain Juniper ( Juniperus scopulorum Sarg.), Russian olive ( Elaeagnus angustifolia L.) common yarrow ( Achillea millifolium L.) and scarlet globemallow ( Sphaeralcea coccinea [Pursh] Rydb.). Spoil treatments included addition of gypsum, sawdust, perlite, straw, and vermiculite; the control treatment was amended. Fourwing saltbush had 52% survival across all spoil treatments, with greatest survival occurring on perlite-treated spoil (80%), followed by gypsum (70%) and vermiculite amendments (70%). Survival of other plant species ranged from 0 to 2% averaged across all treatments after 4 years. No differences in plant survival occurred among amendments when all species were considered.     

Response of understory species to changes in ponderosa pine stocking levels in the Black Hills

The objective of this study was to test the hypothesis that there are no differences in understory production, by species, due to stocking levels of Pinus ponderosa (ponderosa pine). Understory production was estimated, by species, on 3 replicates each of 8 growing stock levels, ranging from clearcuts to unthinned stands, in both sapling- and pole-sized pine stands (48 plots) over 3 nonconsecutive years. All stands were approximately 70 yr old when thinning treatments were applied. Production of many herbaceous species, especially Agropyron spp. (wheatgrasses) and Carex spp. (sedges), declined as growing stock levels (measured in terms of basal area) of ponderosa pine increased. While trends in total production were similar, there were specific differences between sapling and pole stands. Sedges and Oryzopsis asperfolia (roughleaf ricegrass) produced more in sapling stands, whereas Danthonia intermedia (timber oatgrass) was more abundant in pole stands. Shrub production, dominated by Acrtostaphylos uva-ursi (bearberry), was relatively consistent across all stocking levels except unthinned. Although the total number of species declined as pine basal area increased, a few species, such as Linnaea borealis (twinflower) and Shepherdia canadensis (buffaloberry), were found only under relatively dense pine canopies. While floristic species richness was greater at lower stocking levels of ponderosa pine, the total number of species would be greater if all stocking levels were present.