http://lod.bco-dmo.org/id/dataset/984803
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)
Dynamics of the Apostichopus californicus-associated flavivirus under suboxic conditions and organic matter amendment in mesocosm experiment
2025-09-20
publication
2025-09-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-10-07
publication
https://doi.org/10.26008/1912/bco-dmo.984803.1
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) Dynamics of the Apostichopus californicus-associated flavivirus under suboxic conditions and organic matter amendment in mesocosm experiment. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-09-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.984803.1 [access date]
Physicochemical Experimental Data and PcaFV Loads in Experiment Dataset Description: Methods and Sampling: <p>Forty-two specimens of <em>Apostichopus californicus</em> (urn:lsid:marinespecies.org:taxname:529363)&nbsp;were collected by SCUBA divers in Thimbleberry Bay (57.031861N, 135.250972W), 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 weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel.</p>
<p>Two mesocosms served as controls (no amendment), 4 mesocosms were subject to daily organic matter (20 µM) amendment, and 1 mesocosm was continuously sparged with N<sub>2</sub> (Airgas, medical grade; the other 6 mesocosms were bubbled continuously with air). Seawater was subject to 50% volume water change daily and specimens were not fed during captivity. Mesocosms were covered while not sampled (i.e., they were light limited). We selected two organic matter substrates (glucose and peptone) based on their ability to stimulate microbial activity in prior work in addition to two common constituents of dissolved organic matter in coastal environments (N-acetylglucosamine and fucose + rhamnose). We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers. Logger data is included as a supplemental file attached to this dataset. Loggers began collecting data on 9 November 2021.</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>
<p>Relative microbial activity was measured in each mesocosm and from the surface of 2 specimens per mesocosm by bromodeoxyuridine (BrDU) incorporation. Five 2 mL water samples were retrieved from each mesocosm by pipette and placed into 2&nbsp;ml cryovials. Water samples (5 replicates) were collected from the surface of each of two haphazardly chosen specimens by pressing the pipette tip against the dorsal epidermis and slowly retrieving sample, which was then placed into 2 mL cryovials. Water samples were inoculated with 0.04 nmol BrDU and incubated in the mesocosm for 8&nbsp;h. Incubations were then retrieved, and flash frozen in liquid N<sub>2</sub>.</p>
<p>A standard for comparison between BrDU blots was made by amending 50 mL of water collected from an aquarium with 0.04 nmol BrDU. A single sheet of chromatography paper was placed in a Tupperware container soaked with 6X SSC Buffer with a nylon transfer membrane on top and allowed to soak for 10 minutes. The nylon transfer filter was then mounted in a slot blot manifold. Samples (0.5 mL) were pipetted into slot wells, where each membrane included 6 standards, then vacuum filtered through the membrane. The membrane was placed sample side down onto a stack of 3 sheets of chromatography paper with the lysis solution, then immediately turned sample side up and incubated for 10&nbsp;min. This was repeated in the same fashion for neutralization solution. The membrane was then placed sample-side down on a piece chromatography paper soaked in FixDenat for 15 s, followed by 30&nbsp;min incubation on the FixDenat stack. The membrane was placed between two sheets of chromatography paper and baked at 80°C for ~1 h.</p>
<p>The dried membrane was placed in a plastic tray, 25 mL Blocking Solution was added, and the apparatus incubated on a rotating incubator at 30 rev min<sup>-1</sup> for 1&nbsp;h. After this time, the blocking solution was poured off and 6 mL of Antibody Incubation Solution was added to the tray, which was placed on a rotating incubator at 30 rev min<sup>-1</sup> for 3&nbsp;h. The antibody incubation solution was poured off and 25 mL wash solution was added, which was incubated on rotating incubator for 5&nbsp;min. The wash step was repeated. After washing, the wash solution was poured off, and 25 mL of maleic acid buffer was added and incubated on rotating incubator for 5&nbsp;min. This maleic acid buffer treatment then was repeated. The nylon transfer membrane was placed in a plastic tray, sample side up, to which 4 mL of the Supersignal West Femto was added and incubated for 2 minutes. The membrane was visualized in a BioRad ChemiDoc system at high sensitivity and 4 x 4 binning with an exposure time of 600 s.</p>
<p>Protein content was measured in body wall tissues using RIPA buffer extraction and Bradford reagent spectrophotometry. Two biopsy punch (5&nbsp;mm) tissue samples were harvested from frozen animal carcasses and placed into 2 mL microcentrifuge tubes. RIPA buffer (2 mL; 150mM NaCl, 10 mM Tris, 1 mM EDTA, 1% Triton X-100, 0.01% sodium dodecyl sulfate, and 0.01% sodium deoxycholate) was added to each sample, and samples were homogenized in a mortar and pestle for 2&nbsp;min or until the tissue was completely homogenized. Samples were incubated at room temperature in a shaking incubator for 2&nbsp;h. Following this, tubes were centrifuged at 16,000 x g at 4°C for 20&nbsp;min, and supernatant removed into a new microcentrifuge tube. Protein quantity was determined against a bovine serum albumin standard. Bradford reagent (1500 µL) was added to 30 µL sample, allowed to incubate at room temperature for&nbsp;15&nbsp;min, then absorbance at 595 nm measured on a spectrophotometer.</p>
<p>Lipid content was assessed. Two biopsy punch (5&nbsp;mm) tissue samples were harvested from animal carcass dorsal body wall and placed into 15 mL centrifuge tubes. Tissue samples were weighed, amended with 12 mL chloroform:methanol, then homogenized in a mortar and pestle until the tissue had completely disintegrated and resembled a paste. The homogenates were centrifuged at 3,000 x g for 10&nbsp;min in a benchtop centrifuge and the solvent fraction removed into fresh centrifuge tubes. Three microcentrifuge tubes per sample were weighed, and then 2 mL of the solvent fraction from each tissue sample homogenate was placed into the tubes. Tubes were then placed into a rotating vacuum desiccator until they were dry. Sample tubes were then re-weighed, and mass difference calculated on aggregate for all replicate tubes per sample as a percentage of wet weight.</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
Specimen_No
Treatment
Animal_Surf_Productivity
Mesocosm_Water_Productivity
Tissue_Lipid_pct
Tissue_Protein_Concentration
Animal_Mass_loss
Tube_Foot_PcaFV_Load_Day_0
Tube_Foot_PcaFV_Load_Day_7
Resp_Tree_PcaFV_Load_Day_7
Gonad_PcaFV_Load_Day_7
Intestine_PcaFV_Load_Day_7
Date_of_Animal_Sampling
Date_of_Specimen_Collection
Photographed
Centrifuge
Mortar and pestle
Continuous submersible HOBO logger
ABI StepOne qPCR
Scale
SCUBA
Shaking incubator
Spectrophotometer
theme
None, User defined
sample identification
treatment
growth
lipids in biota
protein concentration
mass
cell_concentration
date
featureType
BCO-DMO Standard Parameters
Camera
Centrifuge
Homogenizer
Oxygen Sensor
qPCR Thermal Cycler
scale or balance
Self-Contained Underwater Breathing Apparatus
Shaker
Spectrometer
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
-135.250972
-135.250972
57.031861
57.031861
2021-11-09
2021-11-18
Northeastern Pacific Ocean
0
BCO-DMO catalogue of parameters from Dynamics of the Apostichopus californicus-associated flavivirus under suboxic conditions and organic matter amendment in mesocosm experiment
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/985034.rdf
Name: Specimen_No
Units: unitless
Description: <p>Specimen Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/985035.rdf
Name: Treatment
Units: unitless
Description: <p>Experimental Treatment Type: Control (1 and 2), Fucose/Rhamnose, Glucose, N-Acetylglucosamine, N2, Peptone</p>
http://lod.bco-dmo.org/id/dataset-parameter/985036.rdf
Name: Animal_Surf_Productivity
Units: unitless
Description: <p>Relative microbial productivity on animal surface</p>
http://lod.bco-dmo.org/id/dataset-parameter/985037.rdf
Name: Mesocosm_Water_Productivity
Units: unitless
Description: <p>Relative microbial productivity in plankton in mesocosm</p>
http://lod.bco-dmo.org/id/dataset-parameter/985038.rdf
Name: Tissue_Lipid_pct
Units: percent
Description: <p>Body Wall Lipid content</p>
http://lod.bco-dmo.org/id/dataset-parameter/985039.rdf
Name: Tissue_Protein_Concentration
Units: ug/mL
Description: <p>Body Wall Protein content</p>
http://lod.bco-dmo.org/id/dataset-parameter/985040.rdf
Name: Animal_Mass_loss
Units: percent per day
Description: <p>Animal weight loss from start of experiment to end of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/985041.rdf
Name: Tube_Foot_PcaFV_Load_Day_0
Units: copies / ng RNA
Description: <p>PcaFV Load in Tube Feet Tissues at T = 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/985042.rdf
Name: Tube_Foot_PcaFV_Load_Day_7
Units: copies / ng RNA
Description: <p>PcaFV Load in Tube Feet Tissues at T = 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/985043.rdf
Name: Resp_Tree_PcaFV_Load_Day_7
Units: copies / ng RNA
Description: <p>PcaFV Load in Respiratory Tree Tissues at T = 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/985044.rdf
Name: Gonad_PcaFV_Load_Day_7
Units: copies / ng RNA
Description: <p>PcaFV Load in Gonad Tissues at T = 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/985045.rdf
Name: Intestine_PcaFV_Load_Day_7
Units: copies / ng RNA
Description: <p>PcaFV Load in Intestinal Tissues at T = 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/985046.rdf
Name: Date_of_Animal_Sampling
Units: unitless
Description: <p>Date of Initial Animal Sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/985047.rdf
Name: Date_of_Specimen_Collection
Units: unitless
Description: <p>Date of Specimen Collection (Thimbleberry Bay)</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
5523
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/cf0f2e56-1ffa-4549-9cd8-2b039194a4a9/content
download
https://doi.org/10.26008/1912/bco-dmo.984803.1
download
onLine
dataset
<p>Forty-two specimens of <em>Apostichopus californicus</em> (urn:lsid:marinespecies.org:taxname:529363)&nbsp;were collected by SCUBA divers in Thimbleberry Bay (57.031861N, 135.250972W), 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 weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel.</p>
<p>Two mesocosms served as controls (no amendment), 4 mesocosms were subject to daily organic matter (20 µM) amendment, and 1 mesocosm was continuously sparged with N<sub>2</sub> (Airgas, medical grade; the other 6 mesocosms were bubbled continuously with air). Seawater was subject to 50% volume water change daily and specimens were not fed during captivity. Mesocosms were covered while not sampled (i.e., they were light limited). We selected two organic matter substrates (glucose and peptone) based on their ability to stimulate microbial activity in prior work in addition to two common constituents of dissolved organic matter in coastal environments (N-acetylglucosamine and fucose + rhamnose). We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers. Logger data is included as a supplemental file attached to this dataset. Loggers began collecting data on 9 November 2021.</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>
<p>Relative microbial activity was measured in each mesocosm and from the surface of 2 specimens per mesocosm by bromodeoxyuridine (BrDU) incorporation. Five 2 mL water samples were retrieved from each mesocosm by pipette and placed into 2&nbsp;ml cryovials. Water samples (5 replicates) were collected from the surface of each of two haphazardly chosen specimens by pressing the pipette tip against the dorsal epidermis and slowly retrieving sample, which was then placed into 2 mL cryovials. Water samples were inoculated with 0.04 nmol BrDU and incubated in the mesocosm for 8&nbsp;h. Incubations were then retrieved, and flash frozen in liquid N<sub>2</sub>.</p>
<p>A standard for comparison between BrDU blots was made by amending 50 mL of water collected from an aquarium with 0.04 nmol BrDU. A single sheet of chromatography paper was placed in a Tupperware container soaked with 6X SSC Buffer with a nylon transfer membrane on top and allowed to soak for 10 minutes. The nylon transfer filter was then mounted in a slot blot manifold. Samples (0.5 mL) were pipetted into slot wells, where each membrane included 6 standards, then vacuum filtered through the membrane. The membrane was placed sample side down onto a stack of 3 sheets of chromatography paper with the lysis solution, then immediately turned sample side up and incubated for 10&nbsp;min. This was repeated in the same fashion for neutralization solution. The membrane was then placed sample-side down on a piece chromatography paper soaked in FixDenat for 15 s, followed by 30&nbsp;min incubation on the FixDenat stack. The membrane was placed between two sheets of chromatography paper and baked at 80°C for ~1 h.</p>
<p>The dried membrane was placed in a plastic tray, 25 mL Blocking Solution was added, and the apparatus incubated on a rotating incubator at 30 rev min<sup>-1</sup> for 1&nbsp;h. After this time, the blocking solution was poured off and 6 mL of Antibody Incubation Solution was added to the tray, which was placed on a rotating incubator at 30 rev min<sup>-1</sup> for 3&nbsp;h. The antibody incubation solution was poured off and 25 mL wash solution was added, which was incubated on rotating incubator for 5&nbsp;min. The wash step was repeated. After washing, the wash solution was poured off, and 25 mL of maleic acid buffer was added and incubated on rotating incubator for 5&nbsp;min. This maleic acid buffer treatment then was repeated. The nylon transfer membrane was placed in a plastic tray, sample side up, to which 4 mL of the Supersignal West Femto was added and incubated for 2 minutes. The membrane was visualized in a BioRad ChemiDoc system at high sensitivity and 4 x 4 binning with an exposure time of 600 s.</p>
<p>Protein content was measured in body wall tissues using RIPA buffer extraction and Bradford reagent spectrophotometry. Two biopsy punch (5&nbsp;mm) tissue samples were harvested from frozen animal carcasses and placed into 2 mL microcentrifuge tubes. RIPA buffer (2 mL; 150mM NaCl, 10 mM Tris, 1 mM EDTA, 1% Triton X-100, 0.01% sodium dodecyl sulfate, and 0.01% sodium deoxycholate) was added to each sample, and samples were homogenized in a mortar and pestle for 2&nbsp;min or until the tissue was completely homogenized. Samples were incubated at room temperature in a shaking incubator for 2&nbsp;h. Following this, tubes were centrifuged at 16,000 x g at 4°C for 20&nbsp;min, and supernatant removed into a new microcentrifuge tube. Protein quantity was determined against a bovine serum albumin standard. Bradford reagent (1500 µL) was added to 30 µL sample, allowed to incubate at room temperature for&nbsp;15&nbsp;min, then absorbance at 595 nm measured on a spectrophotometer.</p>
<p>Lipid content was assessed. Two biopsy punch (5&nbsp;mm) tissue samples were harvested from animal carcass dorsal body wall and placed into 15 mL centrifuge tubes. Tissue samples were weighed, amended with 12 mL chloroform:methanol, then homogenized in a mortar and pestle until the tissue had completely disintegrated and resembled a paste. The homogenates were centrifuged at 3,000 x g for 10&nbsp;min in a benchtop centrifuge and the solvent fraction removed into fresh centrifuge tubes. Three microcentrifuge tubes per sample were weighed, and then 2 mL of the solvent fraction from each tissue sample homogenate was placed into the tubes. Tubes were then placed into a rotating vacuum desiccator until they were dry. Sample tubes were then re-weighed, and mass difference calculated on aggregate for all replicate tubes per sample as a percentage of wet weight.</p>
Specified by the Principal Investigator(s)
- Imported "PcaFV_Ancillary.txt" into the BCO-DMO system
- Converted "Date of Collection" to ISO 8601 format YYYY-MM-DD
- Renamed "Date_of_Collection" to "Date_of_Animal_Sampling" and added "Date_of_Specimen_Collection" to differentiate those dates
- Removed Latitude and Longitude since all samples were from same location, noted in the methods, and dataset is experimental data
- Removed special characters from parameter names in compliance with BCO-DMO guidelines
- Exported file as "984803_v1_exp_data_pcafv_loads.csv"
Scientific names in the data were checked using World Register of Marine Species (WoRMS) Taxon Match. All scientific names in the data are valid and accepted names as of 2025-09-20.
Apostichopus californicus (urn:lsid:marinespecies.org:taxname:529363)
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
Photographed
Photographed
PI Supplied Instrument Name: Photographed PI Supplied Instrument Description:Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Centrifuge
Centrifuge
PI Supplied Instrument Name: Centrifuge PI Supplied Instrument Description:Following this, tubes were centrifuged at 16,000 x g at 4°C for 20 min, and supernatant removed into a new microcentrifuge tube. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Mortar and pestle
Mortar and pestle
PI Supplied Instrument Name: Mortar and pestle PI Supplied Instrument Description:RIPA buffer (2 mL; 150mM NaCl, 10 mM Tris, 1 mM EDTA, 1% Triton X-100, 0.01% sodium doecyl sulfate, and 0.01% sodium deoxycholate) was added to each sample, and samples were homogenized in a mortar and pestle for 2 min or until the tissue was completely homogenized. Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Continuous submersible HOBO logger
Continuous submersible HOBO logger
PI Supplied Instrument Name: Continuous submersible HOBO logger PI Supplied Instrument Description:We monitored dissolved oxygen levels in each mesocosm using continuous submersible HOBO loggers. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
ABI StepOne qPCR
ABI StepOne qPCR
PI Supplied Instrument Name: ABI StepOne qPCR 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).
Scale
Scale
PI Supplied Instrument Name: Scale PI Supplied Instrument Description:Specimens were immediately weighed, photographed, and placed into individual mesh containers within 7 x 1200 L outdoor mesocosms (6 specimens per mesocosm) filled with seawater from the nearby Sitka Channel. Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Forty-two specimens of Apostichopus californicus were collected by SCUBA divers in Thimbleberry Bay (57.031861N, 135.250972W), 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
Shaking incubator
Shaking incubator
PI Supplied Instrument Name: Shaking incubator PI Supplied Instrument Description:RIPA buffer (2 mL; 150mM NaCl, 10 mM Tris, 1 mM EDTA, 1% Triton X-100, 0.01% sodium doecyl sulfate, and 0.01% sodium deoxycholate) was added to each sample, and samples were homogenized in a mortar and pestle for 2 min or until the tissue was completely homogenized. Samples were incubated at room temperature in a shaking incubator for 2 h. Instrument Name: Shaker Instrument Short Name: Instrument Description: A Shaker is a piece of lab equipment used to mix, blend, or to agitate substances in tube(s) or flask(s) by shaking them, which is mainly used in the fields of chemistry and biology. A shaker contains an oscillating board which is used to place the flasks, beakers, test tubes, etc.
Spectrophotometer
Spectrophotometer
PI Supplied Instrument Name: Spectrophotometer PI Supplied Instrument Description:Bradford reagent (1500 µL) was added to 30 µL sample, allowed to incubate at room temperature for 15 min, then absorbance at 595 nm measured on a spectrophotometer. Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/