http://lod.bco-dmo.org/id/dataset/984849
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-09-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Prevalence of PcaFV in Apostichopus californicus specimens collected in Southeast Alaska from Jun to Nov 2021
2025-10-06
publication
2025-10-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-10-07
publication
https://doi.org/10.26008/1912/bco-dmo.984849.1
Ian Hewson
Cornell University
principalInvestigator
Kyle Hebert
Alaska Department of Fish and Game
principalInvestigator
Em G Lim
Simon Fraser University
principalInvestigator
Joel Markis
University of Alaska Southeast
principalInvestigator
Megan Schwartz
University of Washington
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Crandell, J., Altera, A., DeRito, C., Hebert, K., Lim, E. G., Markis, J., Philipp, K. H., Rede, J., Schwartz, M., Vilanova-Cuevas, B., Wang, E., Hewson, I. (2025) Prevalence of PcaFV in Apostichopus californicus specimens collected in Southeast Alaska from Jun to Nov 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.984849.1 [access date]
PcaFV Prevalence Dataset Description: Methods and Sampling: <p>Sea cucumbers were collected at 3 locations (near Juneau, Alaska, near Sitka, Alaska, and Nanoose, British Columbia) to assess the presence and load of PcaFV and other aquatic invertebrate flaviviruses.</p>
<p>Twenty individual <em>Apostichopus californicus</em> specimens were collected by SCUBA divers during routine fisheries surveys by Alaska Department of Fish and Game from near southeastern Alaska (Juneau) in June/July 2021. Specimens were immediately placed into a refrigerated hold on the ship in zip-lock bags before transport to the lab in Juneau later in the day. There, specimens were frozen at -20°C and couriered overnight to Cornell University (Ithaca, NY, USA) where they were frozen at -80°C on arrival.</p>
<p>Thirty-two specimens of <em>Apostichopus californicus</em> were collected by SCUBA divers in Sitka Sound (57.1273 N, 135.4042 W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Specimens were immediately sampled for tube feet by pulling them off and placing into RNALater, before freezing at -20<sup>o</sup>C for transport to the lab at the University of Alaska Southeast.</p>
<p>Five specimens of <em>Apostichopus californicus</em> were collected from Nanoose, British Columbia, Canada in September 2021 and transported on wet ice to the lab at Cornell University for further analysis.&nbsp;</p>
<p>RT-LAMP was performed in duplicate in 25 µL reactions containing 1X WarmStart Colorimetric RT-LAMP Master Mix (New England Biolabs), 0.5 µL of fluorescent dye, 2.5 µL primers designed using the New England BioLabs primer tool around a portion of the PcaFV NS5 amplicon (GenBank accession MT949664), and 5 µL of extracted RNA. The primer master mix comprised 16 μL of the 100uM PcaFV_NS5_FIP and PcaFV-NS5_BIP primers, 2 μL of 100uM PcaFV_NS5_F3 and PcaFV_NS5_B3 primers, 4 μL of the 100uM PcaFV_NS5_LoopF and PcaFV_NS5_Loop B primers, as well as 56 μL of nuclease-free water (diH<sub>2</sub>O). Reactions were performed in optically clear quantitative PCR tubes (Applied Biosystems). Negative controls comprised 5 μL of diH<sub>2</sub>O, while positive controls used 5 μL of PcaFV synthetic gene fragment. The tube strips were incubated in a water bath at 65°C for 30&nbsp;min. After incubation, tubes were removed from the bath and scored based on color change. Positive detections were scored when the reaction appeared yellow and negative detections were scored when the reaction appeared red. Positive controls were consistently yellow, and negative controls were consistently red. When positive controls had not turned yellow, reactions were further incubated for 15&nbsp;min in the bath, and then reassessed. Possible detections were scored when the reactions turned orange.</p>
<p>Quantitative reverse transcriptase PCR (qRT-PCR) using primers PcaFV_NS5_F3 (5’- CCA GCC ATG GAT GAG TAA TG-3’) and PcaFV_NS5_R3 (5’- GCT GAA CTG CTC CTG AAA CC-3’), and probe PcaFV_NS5_Pr3 (5’-[FAM]CAC GAA TGT ACG GCA ACG GAC G[TAMRA]-3’) was used to determine PcaFV load within individual tissue RNA extracts. qRT-PCR reactions were performed in duplicate for each specimen and compared against duplicate reactions of oligonucleotide standards spanning the amplicon region (from 10<sup>2</sup> to 10<sup>7</sup> copies µl<sup>-1</sup>) and using 4 negative controls (nuclease free H<sub>2</sub>O only). PCR reactions (20 µL) contained 1 X Luna Universal Probe One-Step Reaction Mix (New England Biolabs), 1X Luna WarmStart RT Enzyme Mix (New England Biolabs), 8 µmol each of primers and probes, and 1 µL of template RNA. Reactions were thermal cycled in an ABI StepOne qPCR machine. Reactions were initially held at 55°C for 10&nbsp;min, followed by an initial denaturation step at 95°C for 1&nbsp;min. Reactions were then subject to 45 cycles of denature at 95°C and anneal at 56°C, with fluorescence data collected after the annealing step. Linearity of standards was checked during downstream analysis of qPCR data.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049225 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049225
completed
Ian Hewson
Cornell University
1-607-255-0151
Department of Microbiology Wing Hall 403
Ithaca
NY
14853
USA
hewson@cornell.edu
pointOfContact
Kyle Hebert
Alaska Department of Fish and Game
kyle.hebert@alaska.gov
pointOfContact
Em G Lim
Simon Fraser University
em_lim@sfu.ca
pointOfContact
Joel Markis
University of Alaska Southeast
jamarkis@alaska.edu
pointOfContact
Megan Schwartz
University of Washington
megansc@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
Sample_Identity
Geographic_Location
Tissue_Type
PcaFV_Quantity_qRTPCR
LAMP_Detection
Date_of_Collection
Latitude
Longitude
ABI Step One Real Time PCR machine
SCUBA
theme
None, User defined
sample type
species scientific name (binomial)
region
No BCO-DMO term
date
latitude
longitude
featureType
BCO-DMO Standard Parameters
qPCR Thermal Cycler
Self-Contained Underwater Breathing Apparatus
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics
https://osprey.bco-dmo.org/project/863960
Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics
<p>NSF Award Abstract:</p>
<p>Marine diseases pose considerable risks to invertebrates, such as sea cucumbers, in the face of changing ocean conditions. While many invertebrate diseases are driven by pathogens, the interplay between animal biology and environmental conditions often mediates the outcome of the pathogen-host relationship. Sea cucumbers are ecologically and economically important animals that occur in a wide range of marine habitats. This project aims to decipher how the interaction between the biology of sea cucumbers, environmental conditions, and a newly-discovered type of virus, seemingly innocuous under typical conditions, may lead to lethal disease in giant Pacific sea cucumbers in the U.S. West Coast. The study includes surveys in coastal regions in southeast Alaska, Washington, and California as well as laboratory experiments manipulating seawater oxygen concentrations, temperature, and simulated microalgal blooms. The project engages community scientists, fishers, high school students, and indigenous groups, and supports training of one graduate and several undergraduate students. A workshop that brings together scientists across marine ecology, disease, and veterinary disciplines is planned to prepare a handbook of best practices in marine disease investigation.</p>
<p>Metagenomic and community-level sequencing efforts have revealed an astonishing diversity of viruses associated with grossly normal marine invertebrates. The vast majority of detected viruses likely represents asymptomatic infections under typical conditions but may generate pathology in hosts under changing environmental conditions. This project investigates the ecology of a group of enveloped positive sense single-stranded RNA viruses (flaviviruses) that this research team has recently discovered in the giant California sea cucumber Apostichopus californicus by addressing three hypotheses: 1) Aquatic insect-only Flaviviruses (aiFVs) do not cause gross pathology under typical conditions; 2) aiFVs proliferate and generate clinical and gross pathology under suboxic stress; and 3) Periodic increases in primary production and mean temperature excursions cause aiFV proliferation and subsequently exacerbate holothurian disease process. The study comprises a restricted survey of aiFV diversity via amplicon sequencing and their prevalence within and between populations, development of an antibody-based approach for aiFV detection, and examination of aiFV behavior in concert with host transcription and veterinary pathology. The study includes field surveys and in laboratory manipulative experiments.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Holothurian Flaviviruses
largerWorkCitation
project
eng; USA
biota
oceans
-135.4042
-124.1411
49.2907
58.3769
2021-06-29
2021-11-11
Northeastern Pacific Ocean
0
BCO-DMO catalogue of parameters from Prevalence of PcaFV in Apostichopus californicus specimens collected in Southeast Alaska from Jun to Nov 2021
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/985344.rdf
Name: Sample_Name
Units: unitless
Description: <p>Name of specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/985345.rdf
Name: Sample_Identity
Units: unitless
Description: <p>Species sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/985346.rdf
Name: Geographic_Location
Units: unitless
Description: <p>Geographic Location</p>
http://lod.bco-dmo.org/id/dataset-parameter/985347.rdf
Name: Tissue_Type
Units: unitless
Description: <p>Tissue Type</p>
http://lod.bco-dmo.org/id/dataset-parameter/985348.rdf
Name: PcaFV_Quantity_qRTPCR
Units: copies ng⁻¹ RNA
Description: <p>Quantity of PcaFV determined by quantitative reverse transcriptase PCR (qRT-PCR) targeting PcaFV</p>
http://lod.bco-dmo.org/id/dataset-parameter/985349.rdf
Name: LAMP_Detection
Units: unitless
Description: <p>Result of LAMP detection based on colorimetric change</p>
http://lod.bco-dmo.org/id/dataset-parameter/985350.rdf
Name: Date_of_Collection
Units: unitless
Description: <p>Date of specimen collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/985351.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of specimen collection, positive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/985352.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of specimen collection, negative is West</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
6451
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/148fbf03-f77c-42f2-9e1d-63e84e89205a/content
download
https://doi.org/10.26008/1912/bco-dmo.984849.1
download
onLine
dataset
<p>Sea cucumbers were collected at 3 locations (near Juneau, Alaska, near Sitka, Alaska, and Nanoose, British Columbia) to assess the presence and load of PcaFV and other aquatic invertebrate flaviviruses.</p>
<p>Twenty individual <em>Apostichopus californicus</em> specimens were collected by SCUBA divers during routine fisheries surveys by Alaska Department of Fish and Game from near southeastern Alaska (Juneau) in June/July 2021. Specimens were immediately placed into a refrigerated hold on the ship in zip-lock bags before transport to the lab in Juneau later in the day. There, specimens were frozen at -20°C and couriered overnight to Cornell University (Ithaca, NY, USA) where they were frozen at -80°C on arrival.</p>
<p>Thirty-two specimens of <em>Apostichopus californicus</em> were collected by SCUBA divers in Sitka Sound (57.1273 N, 135.4042 W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Specimens were immediately sampled for tube feet by pulling them off and placing into RNALater, before freezing at -20<sup>o</sup>C for transport to the lab at the University of Alaska Southeast.</p>
<p>Five specimens of <em>Apostichopus californicus</em> were collected from Nanoose, British Columbia, Canada in September 2021 and transported on wet ice to the lab at Cornell University for further analysis.&nbsp;</p>
<p>RT-LAMP was performed in duplicate in 25 µL reactions containing 1X WarmStart Colorimetric RT-LAMP Master Mix (New England Biolabs), 0.5 µL of fluorescent dye, 2.5 µL primers designed using the New England BioLabs primer tool around a portion of the PcaFV NS5 amplicon (GenBank accession MT949664), and 5 µL of extracted RNA. The primer master mix comprised 16 μL of the 100uM PcaFV_NS5_FIP and PcaFV-NS5_BIP primers, 2 μL of 100uM PcaFV_NS5_F3 and PcaFV_NS5_B3 primers, 4 μL of the 100uM PcaFV_NS5_LoopF and PcaFV_NS5_Loop B primers, as well as 56 μL of nuclease-free water (diH<sub>2</sub>O). Reactions were performed in optically clear quantitative PCR tubes (Applied Biosystems). Negative controls comprised 5 μL of diH<sub>2</sub>O, while positive controls used 5 μL of PcaFV synthetic gene fragment. The tube strips were incubated in a water bath at 65°C for 30&nbsp;min. After incubation, tubes were removed from the bath and scored based on color change. Positive detections were scored when the reaction appeared yellow and negative detections were scored when the reaction appeared red. Positive controls were consistently yellow, and negative controls were consistently red. When positive controls had not turned yellow, reactions were further incubated for 15&nbsp;min in the bath, and then reassessed. Possible detections were scored when the reactions turned orange.</p>
<p>Quantitative reverse transcriptase PCR (qRT-PCR) using primers PcaFV_NS5_F3 (5’- CCA GCC ATG GAT GAG TAA TG-3’) and PcaFV_NS5_R3 (5’- GCT GAA CTG CTC CTG AAA CC-3’), and probe PcaFV_NS5_Pr3 (5’-[FAM]CAC GAA TGT ACG GCA ACG GAC G[TAMRA]-3’) was used to determine PcaFV load within individual tissue RNA extracts. qRT-PCR reactions were performed in duplicate for each specimen and compared against duplicate reactions of oligonucleotide standards spanning the amplicon region (from 10<sup>2</sup> to 10<sup>7</sup> copies µl<sup>-1</sup>) and using 4 negative controls (nuclease free H<sub>2</sub>O only). PCR reactions (20 µL) contained 1 X Luna Universal Probe One-Step Reaction Mix (New England Biolabs), 1X Luna WarmStart RT Enzyme Mix (New England Biolabs), 8 µmol each of primers and probes, and 1 µL of template RNA. Reactions were thermal cycled in an ABI StepOne qPCR machine. Reactions were initially held at 55°C for 10&nbsp;min, followed by an initial denaturation step at 95°C for 1&nbsp;min. Reactions were then subject to 45 cycles of denature at 95°C and anneal at 56°C, with fluorescence data collected after the annealing step. Linearity of standards was checked during downstream analysis of qPCR data.</p>
Specified by the Principal Investigator(s)
- Imported "PcaFV_NaturalLoads_LAMP.xlsx" into Excel
- Formatted "PcaFV Quantity (qRTPCR)" to show all numbers for 30 digits and formatted date field as YYYY-MM-DD and exported to "PcaFV_NaturalLoads_LAMP.csv"
- Imported "PcaFV_NaturalLoads_LAMP.csv" into the BCO-DMO system
- Formatted the lat and lon to remove the letters and convert to a numeric field (adding a negative for W values
- Renamed parameter names to comply with BCO-DMO parameter naming guidelines
- Replaced "Stellawagan Bank, Sitka, Alaska" location value with "Sitka Sound, Sitka, Alaska", upon submitter request
- Replaced "2015-07-05" with "2021-07-05", upon submitter request
- Exported file as "984849_v1_pcafv_natural_loads.csv"
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ABI Step One Real Time PCR machine
ABI Step One Real Time PCR machine
PI Supplied Instrument Name: ABI Step One Real Time PCR machine PI Supplied Instrument Description:Reactions were thermal cycled in an ABI StepOne qPCR machine. Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Twenty individual Apostichopus californicus specimens were collected by SCUBA divers during routine fisheries surveys by Alaska Department of Fish and Game from near southeastern Alaska (Juneau) in June/July 2021.
Thirty-two specimens of Apostichopus californicus were collected by SCUBA divers in Sitka Sound (57.1273 N, 135.4042 W), near Sitka, Alaska on 10 November 2021 and transported together in plastic tubs to the lab at the University of Alaska Southeast (Japonski Island, Sitka). Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html