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5Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.

Streams integrate biogeochemical processes operating at broad to local spatial scales and long term to short term time scales. Humans have extensively altered those processes in North America, with serious consequences for aquatic ecosystems. We collected data on Upper Tennessee River tributaries in North Carolina to: (1) compare landuse and landscape geomorphology with respect to their ability to explain variation in water quality, sedimentation measures, and large woody debris; (2) determine if landscape change over time contributed significantly to explaining present stream conditions; and (3) assess the importance of spatial scale in examining landuse influences on streams. Stream variables were related to both landuse and landscape geomorphology. Forest cover accounted for the most variation in nearly all models, supporting predictions of nutrient enrichment, thermal pollution, and sedimentation caused by landscape disturbance. Legacy effects from past catchment disturbance were apparent in sedimentation measures. Nitrogen and phosphorus concentrations, as well as stream temperature, were lower where riparian buffers had reforested. Models of stream physicochemistry fit better when predictors were catchment wide rather than more localized (i.e., within 2 km of a site). Cumulative impacts to streams due to changes in landuse must be managed from a watershed perspective with quantitative models that integrate across scales.

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Abstract-This ecological risk assessment was designed to characterize risk of copper and cadmium exposure in the Chesapeake Bay watershed by comparing the probability distributions of environmental exposure concentrations with the probability distributions of species response data determined from laboratory studies. The overlap of these distributions was a measure of risk to aquatic life. Dissolved copper and cadmium exposure data were available from six primary data sources covering 102 stations in 18 basins in the Chesapeake Bay watershed from 1985 through 1996. Highest environmental concentrations of copper (based on 90th percentiles) were reported in the Chesapeake and Delaware (C and D) Canal, Choptank River, Middle River, and Potomac River; the lowest concentrations of copper were reported in the lower and middle mainstem Chesapeake Bay and Nanticoke River. Based on the calculation of 90th percentiles, cadmium concentrations were highest in the C and D Canal, Potomac River, Upper Chesapeake Bay, and West Chesapeake watershed. Lowest environmental concentrations of cadmium were reported in the lower and middle mainstem Chesapeake Bay and Susquehanna River. The ecological effects data used for this risk assessment were derived primarily from acute copper and cadmium laboratory toxicity tests conducted in both fresh water and salt water; chronic data were much more limited. The 10th percentile (concentration protecting 90% of the species) for all species derived from the freshwater acute copper toxicity database was 8

Smallmouth bass Micropterus dolomieu and spotted bass M. punctulatus are sympatric in riverine and impounded sections of the New River, Virginia. Resource use (habitat and food) by the two species was investigated to determine patterns and extent of resource partitioning and how those patterns might differ between lotic and lentic environments. Growth and body condition were also measured to assess performance of populations of the two species in the study areas. Diet analyses showed that similar prey were consumed by the two species. Habitat use differed along a lotic-lentic gradient; spotted bass were predominant in the impoundment, and smallmouth bass were more abundant in the river. Spatial segregation also occurred within river and impoundment habitats. In the impoundment, smallmouth bass were concentrated in areas with steep dropoffs and rocky substrates, and in the river, they used shoreline areas more than midriver areas. Spotted bass were widely distributed in the impoundment but were most common in areas featuring fine substrate that had woody debris and bank vegetation as cover types. In the river, spotted bass were largely restricted to the banks, to areas away from high current velocities, and to areas with fine substrate, woody debris, and overhanging bank vegetation. We observed higher catch rates for spotted bass in the river section downstream from the impoundment than in the section upstream of the lake, whereas the converse was true for smallmouth bass. Measures of physiological well-being for both species were near regional norms in both river and impoundment. Normal condition in populations of the two fishes, combined with the similarity in diets, indicated that food availability was adequate in the study area and that competitive pressures were not intense during the study period. Ecological segregation of the species appeared to be along the spatial rather than the trophic axis.

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