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Jason Ferrante , Ph.D. (Former Employee)

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Community for data integration 2019 project report

The U.S. Geological Survey Community for Data Integration annually supports small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 14 projects supported in fiscal year 2019 and outlines their goals, activities, and accomplishments. Proposals in 2019 were encouraged to addre
Authors
Amanda N. Liford, Caitlin M. Andrews, Aparna Bamzai, Joseph A. Bard, David S. Blehert, John B. Bradford, Wesley M. Daniel, Sara L. Caldwell Eldridge, Frank Engel, Jason A. Ferrante, Amy K. Gilmer, Margaret E. Hunter, Jeanne M. Jones, Benjamin Letcher, Frances L. Lightsom, Richard R. McDonald, Leah E. Morgan, Sasha C. Reed, Leslie Hsu
By
Ecosystems Mission Area, Water Resources Mission Area, Science Analytics and Synthesis (SAS) Program, Volcano Hazards Program, Community for Data Integration (CDI), Geology, Geophysics, and Geochemistry Science Center, Geosciences and Environmental Change Science Center, National Wildlife Health Center, Oklahoma-Texas Water Science Center, Southwest Biological Science Center, Volcano Science Center, Western Geographic Science Center, Wetland and Aquatic Research Center , Woods Hole Coastal and Marine Science Center, Science Data Management

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for t
Authors
Jason Ferrante, Wesley Daniel, Jonathan (Contractor) Adam Freedman, Katy E. Klymus, Matthew Neilson, Yale Passamaneck, Christopher B. Rees, Adam J. Sepulveda, Margaret Hunter
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Ecosystems Mission Area, Northern Rocky Mountain Science Center, Wetland and Aquatic Research Center

A framework to integrate innovations in invasion science for proactive management

Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches ha
Authors
Charles B. van Rees, Brian K. Hand, Sean C. Carter, Charles Bargeron, Timothy Joseph Cline, Wesley Daniel, Jason A. Ferrante, Keith Gaddis, Margaret E. Hunter, Catherine S. Jarnevich, Melodie A. McGeoch, Jeffrey T. Morisette, Matthew E. Neilson, Helen E. Roy, Mary Ann Rozance, Adam J. Sepulveda, Rebekah D. Wallace, Diane Whited, Taylor Wilcox, John S. Kimball, Gordon Luikart
By
Ecosystems Mission Area, Fort Collins Science Center, Northern Rocky Mountain Science Center, Wetland and Aquatic Research Center

Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by seque
Authors
Jason Ferrante, Chase H. Smith, Laura Thompson, Margaret Hunter
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Lipidomics reveals specific lipid molecules associated with cold stress syndrome in the Florida manatee (Trichechus manatus latirostris)

Cold stress syndrome (CSS) in the Florida manatee (Trichechus manatus latirostris) results in perturbations to many physiological pathways, often leading to further illness or death. In this study, we applied a non-targeted lipidomics approach with ultra-high performance liquid chromatography and high-resolution tandem mass spectrometry to characterize changes related to CSS in the lipidomic profi
Authors
Emily K. Griffin, Kaylie Anne Costa, Juan J. Aristizabal-Henao, Michael P. Napolitano, Margaret Hunter, Jason Ferrante, John A. Bowden
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Environmental DNA (eDNA) detection of nonnative bullseye snakehead in southern Florida

Bullseye Snakehead Channa marulius (Hamilton 1822) was first detected in the southern Florida town of Tamarac in 2000 and has been expanding its geographic range since. Environmental DNA (eDNA) analysis is a newly-developed technique used to noninvasively detect cryptic or low-density species or those that are logistically difficult-to-study. Genetic material shed into the environment through tis
Authors
Margaret Hunter, Pam Schofield, Gaia Meigs-Friend, Mary Brown, Jason Ferrante
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Efficacy of eDNA as an early detection indicator for Burmese pythons in the ARM Loxahatchee National Wildlife Refuge in the Greater Everglades Ecosystem

Environmental DNA (eDNA) detection of invasive species can be used to delimited occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades i
Authors
Margaret Hunter, Gaia Meigs-Friend, Jason Ferrante, Brian Smith, Kristen Hart
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Wetland and Aquatic Research Center

Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques

To inform management and conservation decisions, environmental DNA (eDNA) methods are used to detect genetic material shed into the water by imperiled and invasive species. Methodological enhancements are needed to reduce filter clogging, PCR inhibition, and false-negative detections when eDNA is at low concentrations. In the first of three simple experiments, we sought to ameliorate filter cloggi
Authors
Margaret Hunter, Jason Ferrante, Gaia Meigs-Friend, Amelia Ulmer
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation

ObjectiveWe use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA
Authors
Jason A. Ferrante, Michelle R. Giles, Emily Benzie, Margaret Hunter
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome bquantitative PCR and droplet digital PCR eDNA assays were develop
Authors
Margaret Hunter, Gaia Meigs-Friend, Jason A. Ferrante, Aristide Takoukam Kamla, Robert Dorazio, Lucy Keith Diagne, Fabia Luna, Janet M. Lanyon, James P. Reid
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Development and validation of quantitative PCR assays to measure cytokine transcript levels in the Florida manatee (Trichechus manatus latirostris)

Cytokines have important roles in the mammalian response to viral and bacterial infections, trauma, and wound healing. Because of early cytokine production after physiologic stresses, the regulation of messenger RNA (mRNA) transcripts can be used to assess immunologic responses before changes in protein production. To detect and assess early immune changes in endangered Florida manatees (Trichechu
Authors
Jason A. Ferrante, Margaret Hunter, James F.X. Wellehan
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA

A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjec
Authors
Margaret Hunter, Robert M. Dorazio, John S. Butterfield, Gaia Meigs-Friend, Leo Nico, Jason A. Ferrante
By
Ecosystems Mission Area, Wetland and Aquatic Research Center
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Chronic Wasting Disease (CWD) Detection in Cervids Using MicroRNA Biomarkers from Blood

WARC scientists are testing and developing methods for the isolation of cervid exosomes from blood samples, followed by microRNA extraction and next generation sequencing.
By
Biological Threats and Invasive Species Research Program, Wetland and Aquatic Research Center
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Chronic Wasting Disease (CWD) Detection in Cervids Using MicroRNA Biomarkers from Blood

WARC scientists are testing and developing methods for the isolation of cervid exosomes from blood samples, followed by microRNA extraction and next generation sequencing.
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USGS science for a changing world logo

Implementing FAIR practices: Storing and displaying eDNA data in the USGS Nonindigenous Aquatic Species database

We are working to incorporate environmental DNA (eDNA) data into the Nonindigenous Aquatic Species (NAS) database, which houses over 570,000 records of nonindigenous species nationally, and already is used by a broad user-base of managers and researchers regularly for invasive species monitoring. eDNA studies have allowed for the identification and biosurveillance of numerous invasive and threaten
By
Community for Data Integration (CDI)
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Implementing FAIR practices: Storing and displaying eDNA data in the USGS Nonindigenous Aquatic Species database

We are working to incorporate environmental DNA (eDNA) data into the Nonindigenous Aquatic Species (NAS) database, which houses over 570,000 records of nonindigenous species nationally, and already is used by a broad user-base of managers and researchers regularly for invasive species monitoring. eDNA studies have allowed for the identification and biosurveillance of numerous invasive and threaten
Learn More
link
USGS science for a changing world logo

Establishing standards and integrating environmental DNA (eDNA) data into the USGS Nonindigenous Aquatic Species database

Environmental DNA (eDNA) testing allows for high sensitivity monitoring efforts of cryptic species in large, remote systems and is performed by investigating water and soil samples for sloughed DNA. Having access to eDNA datasets across multiple taxa and ecosystems is necessary for improved coordination among researchers and management. Additionally, quality control protocols are needed to vet inc
By
Community for Data Integration (CDI)
link

Establishing standards and integrating environmental DNA (eDNA) data into the USGS Nonindigenous Aquatic Species database

Environmental DNA (eDNA) testing allows for high sensitivity monitoring efforts of cryptic species in large, remote systems and is performed by investigating water and soil samples for sloughed DNA. Having access to eDNA datasets across multiple taxa and ecosystems is necessary for improved coordination among researchers and management. Additionally, quality control protocols are needed to vet inc
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Single Nucleotide Polymorphism (SNP) genomic data of moose (Alces alces) from the contiguous United States, 2009-2017

We analyzed the single nucleotide polymorphisms (SNPs) present in the genomes of moose representing 3 subspecies in the contiguous United States. Blood samples were collected opportunistically from collaborators during field efforts or were supplied to our lab from collaborators' archives, and represented moose sampling occurring between 2009-2017. DNA was extracted, sequenced using next generatio
By
Wetland and Aquatic Research Center

Burmese python environmental DNA data, and associated attributes, collected from ARM Loxahatchee NWR and surrounding areas, from 2014-2016

Environmental DNA (eDNA) detection of invasive species can be used to delimit occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades in
By
Biological Threats and Invasive Species Research Program, Wetland and Aquatic Research Center

Droplet digital PCR data from method testing to improve eDNA yield and reduce inhibitors from environmental water samples

Data files for manuscript "Improving eDNA yield and inhibitor reduction through increased water volumes and modified multi-filter isolation techniques". These include the results of different treatments for inhibitor removal from a water sample and DNA yield quantities from such tests. Environmental DNA (eDNA) methods detect genetic material that is shed into the environment through skin cells
By
Wetland and Aquatic Research Center

Novel protocol for moose DNA extraction from Tempus blood tube supernatant following RNA extraction

Data were collected to validate the use of supernatant from the isolation of RNA from Tempus blood RNA tubes to obtain genomic DNA in the associated blood sample from moose. Data represent the metrics measured to validate the novel technique for isolating DNA from the supernatant of an RNA isolation protocol using blood collected into Tempus blood RNA tubes.
By
Wetland and Aquatic Research Center

Manatee environmental DNA data, and associated attributes, collected from the United States, Cuba, and Cameroon, from 2013-2015

Environmental DNA (eDNA) detection is a rapidly expanding technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of targeted eDNA. To help delineate manatee habitat ranges, high use
By
Wetland and Aquatic Research Center

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