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We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.
Real-time PCR results of a round robin evaluation of 5 assays that target dreissenid mussel DNA. Water samples collected from waters with and without dreissenid mussels were analyzed using these five assays in four USGS laboratories. Samples from waters without dreissenid mussels were spiked with known amounts of dreissend DNA.
Data were collected as part of an investigation developed by Leetown Science Center to investigate the comparative detection of avian influenza viruses from waterfowl and potential environmental reservoirs such as aquatic sediment from waterfowl habitat. This dataset identifies positive or negative test results for qRT-PCR (quantitative reverse transcriptase polymerase chain reaction) for avian influenza virus through identification of the Type A influenza virus matrix gene from aquatic sediment samples. Sediment samples were collected from waterfowl habitat so as to determine if temporal and spatial differences in virus detection by qRT-PCR were evident among test sites.
Categories: Data;
Tags: Delmarva Peninsula,
Dorchester County, Maryland,
USGS Science Data Catalog (SDC),
avian influenza,
molecular biology,
Oil and gas (OG) wastewaters are commonly disposed of by underground injection and previous research showed that activities at a disposal facility in West Virginia affected stream biogeochemistry and sediment microbial communities downstream from the facility. Microorganisms can control the fate and transport of organic and inorganic components of OG wastewater highlighting the need to characterize the effects of OG wastewater components on microbial activity. We conducted a series of aerobic microcosm experiments to assess the influence of high total dissolved solids (TDS) and hydraulic fracturing fluid additives (2,2-dibromo-3-nitrilopropionamide (DBNPA), a biocide, and ethylene glycol, an anti-scaling additive),...
Categories: Data;
Tags: Biochemistry,
DNA sequencing,
Energy Resources,
Environmental Health,
Fayette County,
We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.
Categories: Data;
Types: Citation;
Tags: California,
Idaho,
Montana,
PCR,
Proliferative Kidney Disease,
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes Proliferative Kidney Disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. We present data that was used to determine assay sensitivity, specificity and to define the limits of detection and quantification.
Categories: Data;
Types: Citation;
Tags: East Gallatin River,
Montana,
Sypes Canyon Creek,
Tetracapsuloides bryosalmonae,
Yellowstone River,
These data were compiled to provide seed transfer and native plant materials development guidance to managers and practitioners across the Colorado Plateau and in adjacent regions. This data release contains empirical seed transfer zones derived from molecular genetic data for Cleome serrulata (syn. Peritoma serrulata), Heliomeris multiflora, and Astragalus lonchocarpus. These species show distinct population structure (i.e., genetic differentiation) across their ranges; as such, seed transfer zones reflect both patterns of genetic differentiation and information on each species' unique adaptations to climatic gradients. These shapefile data may support successful restoration outcomes if, for example, seed transfer...
Categories: Data;
Types: Downloadable,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
Shapefile;
Tags: Arizona,
Astragalus lonchocarpus,
Botany,
Cleome serrulata (syn. Peritoma serrulata),
Colorado,
These data were compiled for a mtDNA (CO1 gene) analysis of net-spinning caddisflies (Hydropsyche oslari) in the Colorado River Basin of the western United States. They were incorporated in a study that investigated the genetic diversity and population structure of H. oslari relative to the river network structure in the Upper and Lower Colorado River Basins. The data were collected from 2015 to 2016 through a collaboration with river runners. These citizen scientists collected insects by deploying light traps for one hour each night of their expedition. Light trap contents were preserved in ethanol on site and returned to the Southwest Biological Science Center in Flagstaff, Arizona for analysis in the laboratory.
The files in this data release are RNA seq datafiles from a study that examined the effects of the synthetic anabolic steroid 17β hydroxyestra 4,9,11 trien-3-one, trenbolone (17βT - CAS 10161-33-8), a common contaminant of wastes from confined animal feeding operations (CAFOs). Japanese quail (Coturnix japonica) were exposed in the egg and through feed to multiple doses of 17βT and liver transcriptomes were examined to identify genes and pathways directly affected by this androgenic compound. RNA was extracted from liver of adults and embryos and analyzed (1x50 bp) on an Illumina HiSeq 2000. NCBI Biosample accessions and the raw counts that were input into the differential expression analysis are provided in this...
Categories: Data;
Tags: Environmental Health,
Patuxent,
RNA sequencing,
USGS Science Data Catalog (SDC),
ecotoxicology,
Upper Klamath Lake, located in southern Oregon, is a hypereutrophic lake where cyanobacterial blooms, dominated by Aphanizomenon flos-aquae (AFA), occur every summer. The decay of excess biomass after AFA senescence leads to problematic water quality conditions including high pH ( > 9) and anoxia. Water samples from the photic zone and bottom of the water column, and the flocculation layer of the bottom sediments were collected weekly at four sites within Upper Klamath Lake, Oregon during summer 2016. This data release reports the chemical and microbiological analysis of these samples.
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