Filters: Tags: Polymerase Chain Reaction (X)
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The dataset contains Esherichia coli and quantitative polymerase chain reaction data for microbial source tracking markers in the Chattahoochee River and streams within the Chattahoochee River National Recreation area from samples collected in the winter and summer of the federal fiscal years 2016 and 2017. Six water samples were collected from three sites on the Chattahoochee River each season. Eleven stream sites and one additional site on the Chattahoochee River were sampled once each season, with the exception of two sites, which were not sampled in winter FY16.
Categories: Data;
Tags: Atlanta,
Chattahoochee,
Environmental Health,
USGS Science Data Catalog (SDC),
Water Resources,
This dataset includes quantifications of bigheaded carp DNA found in water samples collected from the Wabash River along transects at 3 sites over time. The samples were collected at 18 equidistant points in a transect across the river at each site. Samples were collected in 2013 on May 29, 30, 31, June 5, 6, 7, 8, 9, 10, 11, 16, 17, 19, 20, 21, and 22. Quantitative polymerase chain reaction (qPCR) was performed to determine the DNA concentrations in two replicates using the bigheaded carp assay defined in Merkes and others 2014.
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Americus,
Asian carp,
Bigheaded carps,
Environmental DNA,
French Post,
Avian botulism toxicity is a common cause of death to water and shore birds that live near or migrate through Lake Michigan. The botulism neuro-toxin type E (bontE) gene is responsible for the production of botulinum neurotoxin type E. Quantitative Polymerase Chain Reaction (qPCR) was performed using a Step One Plus Thermocycler (Applied Biosystems) and protocol described in Getchell and others, 2011, Journal of Aquatic Animal Health. The assay was used to assess microbial community DNA obtained from environmental samples that were collected by Great Lakes Science Center and by National Park Service from 2011 to 2014 for the bontE gene. Samples were obtained by ponar grab or by divers and matrices collected...
These data were collected as part of a voluntary initiative to create a White-Nose Syndrome Diagnostic Laboratory Network among laboratories participating in research and surveillance for Pseudogymonascus destructans (Pd) - the fungal pathogen causing White-Nose Syndrome in bats. Pd_qPCR_InterlaboratoryLODdata.xlsx is raw qPCR data from multiple laboratories running serial dilutions of Pd gBlock in known concentrations for the collectively used Muller (2013) Pd qPCR assay. Pd_qPCR_InterlaboratoryResults_LOD.xlsx contains the data output for each laboratory from running a generic LOD/LOQ calculator script. the generic LOD/LOQ calculator script is available at:https://github.com/cmerkes/qPCR_LOD_Calc. Pd_qPCR_InterlaboratoryPTResults_PanelData.xlsx...
Categories: Data;
Tags: USGS Science Data Catalog (SDC),
Wildlife Disease,
biota,
health,
microbiology,
Water samples from the Platte River were collected and analyzed for environmental DNA (eDNA). The U.S. Geological Survey (USGS) Nebraska Water Science Center (NEWSC) collected samples monthly from November 2019 to September 2022 at the Platte River near Ashland, Nebraska (USGS: 06801000). The USGS, in cooperation with the City of Lincoln, collected these samples. Water from the Platte River was collected as a series of weighted bottle subsamples that were taken from equal width increments across the river and composited into a sterilized 1-liter bottle. An aliquot of this composited sample was extracted using a sterile syringe and then filtered by the USGS NEWSC staff using filters provided by Jonah Ventures. These...
These are genetic data collected from replicated samples of 21 Enteroctopus (E. dofleini or a cryptic lineage) in Prince William Sound Alaska to evaluate tissue type, DNA extraction method, and time until analyses are completed on data reliability. Data collected from all samples include two microsatellites identified as possible lineage indicators, and nine microsatellite loci previously identified as polymorphic in both lineages. DNA sequence data from 528 bp of the octopine dehydrogenase (OCDE) gene were also collected.
Categories: Data;
Tags: Amino Acid Oxidoreductases,
Animals/Invertebrates,
Bald Head Chris Island,
Biodiversity,
Biodiversity,
It is unclear whether DNA lysis buffers used for preservation of whole blood samples from Hawaiian forest birds cause denaturation and loss of antigen binding capability of antibody molecules. If their antigen binding capability is not affected, then the samples can be used in serological assays to provide an independent assessment of the accuracy of PCR (polymerase chain reaction) diagnostic tests for avian malaria. This data set reports raw absorbance measurements that were collected with a BioRad Model 3550 ELISA plate reader at a wavelength setting of 405 nm for different dilutions of blood from an infected Hawaii Amakihi that were preserved in PBS (phosphate buffered saline), TEN (Tris-Ethylenediaminetetraacetic...
Categories: Data;
Tags: Chlorodrepanis virens,
ELISA,
Hakalau Forest National Wildlife Refuge,
Hawaii,
Hawaii Amakihi,
Physiological and molecular endpoints observed in juvenile largemouth bass in response to an estrogen (17α-ethinylestradiol) and subsequently a bacterial challenge (Edwardsiella piscicida) exposure under laboratory conditions. Also included are water quality and chemical concentration data.
It is unclear whether DNA lysis buffers used for preservation of whole blood samples from Hawaiian forest birds cause denaturation and loss of antigen binding capability of antibody molecules. If their antigen binding capability is not affected, then the samples can be used in serological assays to provide an independent assessment of the accuracy of PCR (polymerase chain reaction) diagnostic tests for avian malaria. This data set provides derived Percent ELISA (Enzyme linked Immunosorbant Assay) Values calculated from adjusted absorbance measurements that were collected with a BioRad Model 3550 ELISA plate reader at a wavelength setting of 405 nm.
Categories: Data;
Tags: Chlorodrepanis virens,
ELISA,
Hakalau Forest National Wildlife Refuge,
Hawaii,
Hawaii Amakihi,
An interdisciplinary and multiagency study was conducted in southern Florida to examine harmful algal bloom (HAB) dynamics on the Caloosahatchee River, which drains from Lake Okeechobee to the west into the Gulf of Mexico. Using in-situ mesocosm experiments, ammonium, nitrate, phosphate, and urea were altered from ambient conditions to determine the effects on cyanotoxin biosynthesis gene presence and quantity as measured via quantitative polymerase chain reaction (qPCR). Eight experiments were conducted seasonally from May 2019 through July 2021 at the W.P. Franklin Lock and Dam. The experimental installations consisted of three floating metal cradles each containing four opaque fiberglass chambers filled with...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Caloosahatchee,
Environmental Health,
Genetics,
Limnology,
USGS Science Data Catalog (SDC),
The dataset contains quantitative polymerase chain reaction data for microbial source tracking markers screened on water samples collected from streams and rivers within and bounding Congaree National Park from samples collected throughout the year from December 2017 through June 2019. The number of samples collected per event ranged from 4-16 over the span of 11 sample events.
Collection of microsatellite genetic data from multiple projects involving southern mule deer (Odocoileus hemionus fuliginatus) in San Diego County, California. Samples were collected 2005-2007, 2010, 2012-2013, 2015, and 2018-2020. These data support the following publication: Mitelberg, A., Smith, J.G., and Vandergast, A.G., 2019, DNA Fingerprinting of Southern mule deer (Odocoileus hemionus fuliginatus) in north San Diego County, California (2018–19): U.S. Geological Survey Open-File Report 2019–1138, 25 p., https://doi.org/10.3133/ofr20191138.
Categories: Data;
Tags: DNA sequencing,
Ecology,
Genetics,
San Diego,
USGS Science Data Catalog (SDC),
Four microbial mat-forming, non-axenic, strains of the non-heterocystous, filamentous, cyanobacterial genus Microcoleus were maintained in culture and examined for the ability to fix atmospheric nitrogen (N2). Each was tested for nitrogenase activity using the acetylene reduction assay (ARA) and for the presence of the dinitrogenase reductase gene (nifH), an essential gene for N2 fixation, using the polymerase chain reaction (PCR). The Microcoleus spp. cultures were incapable of growth without an exogenous nitrogen source and never exhibited nitrogenase activity. Attempts to amplify a 360-bp segment of the nifH gene using DNA purified from the cyanobacterial cultures did not produce any cyanobacteria-specific nifH...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Cryptobiotic soil crust,
FEMS Microbiology Ecology,
Marine microbial mat,
Microbial consortia,
N2 fixation,
Tabular amplification data for individual technical replicates of tissue and water samples collected from Glacier National Park in 2020 and amplified with a Lednia tumana species-specific qPCR assay. Reported results include fractional detection rates, mean quantification cycles, and estimated gene copies per reaction.
Categories: Data;
Tags: Aquatic Biology,
Ecology,
Genetics,
Glacier National Park,
USGS Science Data Catalog (SDC),
This data set is associated with an examination of environmental DNA (eDNA) from the invasive round goby (Neogobius melanostomus) in parallel with traditional fish surveys in the Great Lakes. Data resulting from bottom trawling surveys and angler hook and line methods include round goby fish count and biomass at different depths and seasons at multiple sites of Lake Huron and Lake Michigan (trawls), and breakwall locations of Lake Michigan at Portage Lakefront, Portage, Indiana and Washington Park, Michigan City, Indiana (angling). Data from eDNA water samples targeting round goby were analyzed by two molecular methods: droplet digital PCR (ddPCR) and quantitative PCR (qPCR); eDNA copy numbers are presented for...
It is unclear whether DNA lysis buffers used for preservation of whole blood samples from Hawaiian forest birds cause denaturation and loss of antigen binding capability of antibody molecules. If their antigen binding capability is not affected, then the samples can be used in serological assays to provide an independent assessment of the accuracy of PCR (polymerase chain reaction) diagnostic tests for avian malaria. This data set provides raw absorbance measurements that were collected with a BioRad Model 3550 ELISA plate reader at a wavelength setting of 405 nm for different dilutions of blood from an uninfected Hawaii Amakihi. The blood was preserved in different lysis buffers or placed in phosphate buffered...
Categories: Data;
Tags: Chlorodrepanis virens,
ELISA,
Hakalau Forest National Wildlife Refuge,
Hawaii,
Hawaii Amakihi,
This environmental dataset consists of 56 sediment, 24 Cladophora and 22 water samples collected from beaches at Glen Haven, Good Harbor, Platte Bay and Esch road beach, located within The Sleeping Bear Dunes National Lakeshore, Leelanau and Benzie counties, Michigan. The dataset includes matrix type, location, data, time and the qPCR reported value for each sample collected.
This data set describes nuclear microsatellite genotypes derived from eleven autosomal loci (Lar24, Lar12, Lar26, Lar19, Rbg13, K16, Rbg18, Hg18, Hg16, Hg25, Rbg29). A total of 651 Larus gulls were examined for this study with samples collected throughout North America, Europe, Russia, and South America.
The files in this data release are the processed DNA consensus sequence alignment files for the chelonid herpesvirus 5 (ChHV-5) genome plus 66 open reading frames representing protien-coding genes. DNA was extracted from tumor biopsies from green sea turtles (Chelonias mydas) with fibropapillomatosis sampled from Florida and Hawaii coastal waters. We used high-throughput short-read sequencing (Illumina MiSeq and Ion Torrent Personal Genome Machine) of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. The raw sequence data is available at the NCBI Sequence Read Archive under bioproject number PRJNA360405, including...
This dataset includes quantifications of bigheaded carp DNA found in water samples collected from the Wabash River along transects at 3 sites over time. The samples were collected at 18 equidistant points in a transect across the river at each site. Samples were collected in 2013 on May 29, 30, 31, June 5, 6, 7, 8, 9, 10, 11, 16, 17, 19, 20, 21, and 22. Quantitative polymerase chain reaction (qPCR) was performed to determine the DNA concentrations in two replicates using the bigheaded carp assay defined in Merkes and others 2014.
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Americus,
Asian carp,
Bigheaded carps,
Environmental DNA,
French Post,
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