http://lod.bco-dmo.org/id/dataset/887553
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
2023-01-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phenotypic responses of Eastern oyster in response to variable length OA exposure conducted in summer 2017 with oysters sampled in Plum Island.
2023-01-20
publication
2023-01-20
revision
BCO-DMO Linked Data URI
2023-01-20
creation
http://lod.bco-dmo.org/id/dataset/887553
Katie Lotterhos
Northeastern University
principalInvestigator
Justin B. Ries
Northeastern University
principalInvestigator
Louise Cameron
Northeastern University
principalInvestigator
Alan Downey-Wall
Northeastern University
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: Downey-Wall, A., Lotterhos, K., Ries, J. B., Cameron, L. (2023) Phenotypic responses of Eastern oyster in response to variable length OA exposure conducted in summer 2017 with oysters sampled in Plum Island. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-01-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/887553 [access date]
Ocean Acidification Experiment: Phenotypic Measurements Dataset Description: <div class="fieldset-wrapper">
<div class="field field-name-field-dataset-description field-type-text-long field-label-hidden">
<div class="field-items">
<div class="field-item even">
<p><strong>Data have not been made public due to unanswered questions and data quality issues. Final review by the data submitter was not received after it was imported into the BCO-DMO data system. </strong></p>
<p><strong>Reason: the submitter did&nbsp; not provide enough metadata descriptions, context and details about data relations. </strong></p>
<p>&nbsp;</p>
<p>The data was collected as part of a larger study aimed at assessing the molecular response of adult Eastern oyster (<em>C. virginica</em>) to OA exposure over time. Specifically, the aim of this work was to investigate the association of these molecular responses with oysters' capacity to regulate internal chemistry and calcification. Please see the linked Dryad and Github respository for additional information about associated molecular data.</p>
<p>This data was collected by Alan Downey-Wall and other members of the Lotterhos and Ries Lab at Northeastern University.</p>
</div>
</div>
</div>
</div> Methods and Sampling: <p>These data water quality readings for oysters exposed to ocean acidification at multiple timepoints over an 80 day period. The experiment was conducted in the summer of 2017 at the Northeastern University's Marine Science Center with a flow-through seawater system that draws water from Broad Sound in Nahant, Massachusetts (42.416884, −70.907564) using oysters collected from Plum Island Sound, Massachusetts, USA (Site 1, 42.751636, −70.837023; Site 2, 42.725186, −70.855022; Site 3, 42.681764, −70.813498) in late April.</p>
<p><strong>Calcification Rate: </strong>Net calcification rate was calculated for oysters surviving to either 50 or 80 days (n = 35) by buoyantly weighing oysters prior to exposure (BW<sub>1</sub>) and on day 33 or 34 of the exposure (BW<sub>2</sub>) following the methods of Ries et al. (2009). Buoyant weight was measured in a 27.65 liter tank (48 cm long, 24 cm wide and 24 cm deep) filled with seawater from the flow-through system and was maintained at treatment temperature by an Aqua Euro USA Model MC-1/4HP aquarium chiller. Buoyant weight was measured by completely submerging the oyster on a flat platform suspended from a bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g). Care was taken to ensure no bubbles were trapped inside oyster shells. Oysters were weighed three times in the weighing basket, removing the oyster from the basket between each measurement. If replicate measurements varied by more than 0.01 g, oysters were re-weighed. A standard of known weight was weighed every 20 oysters to ensure that no drift was occurring in the scale. To establish a relationship between buoyant weight and dry weight for the purpose of estimating net calcification rate, shells of oysters sampled for tissue within four days of a buoyant weight measurement were soaked in 10% ethanol to remove salts, dried, and weighed. The dry weight was then regressed against the buoyant weight measurement to establish an empirical dry-buoyant weight relationship:</p>
<p>DryWgt<sub>BWi</sub>(mg)&nbsp; = 1.87*BWi −2.74</p>
<p>This empirical relationship was then used to calculate dry shell weight at each buoyant weight time point via linear regression. Calculated dry weights were then used to calculate daily calcification rate:</p>
<p>calcification rate (%) = (DryWgt<sub>BW2</sub> −DryWgt<sub>BW1</sub> )/n * 100/DryWgt<sub>BW1</sub></p>
<p>where dry weight (DryWgt<sub>BWi</sub>) was calculated for each individual using the buoyant weight pre-exposure (BW1) and 33-34 days into the exposure (BW2) and n was the number of days between the two measurements. Lastly, the average daily change in dry weight was divided by initial dry weight to standardize calcification rate for allometric effects, and multiplied by 100 to convert that fraction into a percent.</p>
<p>&nbsp;</p>
<p><strong>Extrapallial Fluid: </strong>Oyster pH<sub>EPF</sub> was measured by removing each oyster from its tank, inserting a 5 mL syringe with a flexible 18-gauge polypropylene tip through the luer-lock port into the oyster's extrapallial cavity, and extracting ~0.5–2 mL of extrapallial fluid. Care was taken to avoid puncturing the mantle tissue and inadvertently sampling either the hemolymph or stomach fluid. The pH<sub>EPF</sub> was measured immediately after extraction with an Orion 91'10DJWP Double Junction micro-pH probe calibrated with pH 7.01 and 10.01 NBS buffers (for slope) and Dickson seawater Certified Reference Material (for intercept).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635423 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635423
onGoing
Katie Lotterhos
Northeastern University
781-581-7370 X304
Northeastern University Marine Sciences Center 430 Nahant Rd.
Nahant
MA
01908
USA
k.lotterhos@northeastern.edu
pointOfContact
Justin B. Ries
Northeastern University
781-581-7370
Northeastern University Marine Science Center 430 Nahant Rd.
Nahant
MA
01908
USA
j.ries@northeastern.edu
pointOfContact
Louise Cameron
Northeastern University
857-308-6256
Northeastern University Marine Science Center 430 Nahant Rd.
Nahant
MA
01908
USA
louise.cameron93@gmail.com
pointOfContact
Alan Downey-Wall
Northeastern University
adw@bu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
ID
Exposure_Extra
shelf
tank
tankID
pCO2
length
width
pop
sample_date
Timepoint
pHMeasured
pHNBS
pHSW
pHTotal
PercentChangePerDayStandardized_Exposure
Aqua Euro USA Model MC-1/4HP aquarium chiller
YSI 3200 conductivity probe (precision = 0.1 ppt)
Orion 91'10DJWP Double Junction micro-pH probe+
Accumet solid state pH electrode (precision = 1mV)
Bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g)
NIST-standardized glass thermometer (precision = 0.1 °C)
VINDTA 3C coupled alkalinity gram titration and coulometric DIC analyzer system
theme
None, User defined
sample description
tank
Partial pressure of CO2
length
width
date
sample time
pH
weight
featureType
BCO-DMO Standard Parameters
Aquarium chiller
Conductivity Meter
pH Sensor
pH Sensor
scale or balance
Thermometer
Titrator
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.
Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?
https://osprey.bco-dmo.org/project/666496
Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?
<p><em>NSF Award Abstract:</em><br />
Marine ecosystems worldwide are threatened by ocean acidification, a process caused by the unprecedented rate at which carbon dioxide is increasing in the atmosphere. Since ocean change is predicted to be rapid, extreme, and widespread, marine species may face an "adapt-or-die" scenario. However, modifications to the DNA sequence may be induced in response to a stress like ocean acidification and then inherited. Such "epigenetic" modifications may hold the key to population viability under global climate change, but they have been understudied. The aim of this research is to characterize the role of DNA methylation, a heritable epigenetic system, in the response of Eastern oysters (Crassostrea virginica) to ocean acidification. The intellectual merit lies in the integrative approach, which will characterize the role of DNA methylation in the intergenerational response of oysters to ocean acidification. These interdisciplinary data, spanning from molecular to organismal levels, will provide insight into mechanisms that underlie the capacity of marine invertebrates to respond to ocean acidification and lay the foundation for future transgenerational studies. Ocean acidification currently threatens marine species worldwide and has already caused significant losses in aquaculture, especially in Crassostrea species. This research has broader impacts for breeding, aquaculture, and the economy. Under the investigators' "Epigenetics to Ocean" (E2O) training program, the investigators will build STEM talent in bioinformatics and biogeochemistry, expose girls in low-income school districts to careers in genomics, and advance the field through open science and reproducibility.</p>
<p>This research will specifically test if intermittent exposure to low pH induces a methylation response with downstream beneficial effects for biomineralization. These methylation states could be inherited and confer a fitness advantage to larvae that possess them. Phase 1 of the project will use an exposure experiment to determine the degree to which DNA methylation is altered and regulates the response to OA. Data from this experiment will be used to test the hypotheses that (i) DNA methylation, induced in the tissue of shell formation (i.e., mantle tissue), is correlated with changes in transcription and regulation of pallial fluid pH (calcifying fluid pH, measured by microelectrode), and (ii) that methylation changes induced in the mantle tissue are also induced in the germline --indicating that such changes are potentially heritable. Phase 2 of the project will use a pair-mated cross experiment to test the hypothesis that parental exposure to OA alters larval traits (calcification rate, shell structure, and polymorph mineralogy). Larvae will be generated from parents exposed to OA or control seawater, and then raised under control or OA conditions. Results will be used to (i) characterize inheritance of induced methylation states, (ii) estimate the variance in larval traits explained by genotype, non-genetic maternal/paternal effects, adult OA exposure, larval OA exposure, and parental methylome, and (iii) test the hypothesis that adult exposure alters the heritability (a quantity that predicts evolutionary response) of larval traits. Since the effects of epigenetic phenomena on estimates of heritability are highly debated, the results would advance understanding of this important issue. Because the investigators could discover that DNA methylation is a mechanism for heritable plastic responses to OA, knowledge of this mechanism would significantly improve and potentially transform predictive models for how organisms respond to global change.</p>
Epigenetics to Ocean
largerWorkCitation
project
eng; USA
oceans
-70.855022
-70.813498
42.681764
42.751636
2017-01-01
2017-12-31
Coastal Massachusetts near Nahant: 42°25'06"N 70°54'14"W
0
BCO-DMO catalogue of parameters from Phenotypic responses of Eastern oyster in response to variable length OA exposure conducted in summer 2017 with oysters sampled in Plum Island.
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/887579.rdf
Name: ID
Units: unitless
Description: <p>Oyster ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/887580.rdf
Name: Exposure_Extra
Units: unitless
Description: <p>Oysters part of planned exposure (Exposure) compare to extra oysters at the end of exposure (Exposure-Extra)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887581.rdf
Name: shelf
Units: unitless
Description: <p>Shelf in experimental array (1-6)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887582.rdf
Name: tank
Units: unitless
Description: <p>Tank ID for each shelf in experimental array (1-3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887583.rdf
Name: tankID
Units: unitless
Description: <p>Unique tank ID across experiment (1-18)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887584.rdf
Name: pCO2
Units: uatm
Description: <p>pCO2 treatment (categorical)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887585.rdf
Name: length
Units: centimeter (cm)
Description: <p>Length of oyster at collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/887586.rdf
Name: width
Units: centimeter (cm)
Description: <p>Width of oyster at collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/887587.rdf
Name: pop
Units: unitless
Description: <p>Population collected from (Ipswich, Rowley, Rowley2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887588.rdf
Name: sample_date
Units: unitless
Description: <p>Sample date in ISO format (YYY-MM-DD), UTC time</p>
http://lod.bco-dmo.org/id/dataset-parameter/887589.rdf
Name: Timepoint
Units: unitless
Description: <p>Day collected (from start of exposure) in ISO format (YYY-MM-DD), UTC time</p>
http://lod.bco-dmo.org/id/dataset-parameter/887590.rdf
Name: pHMeasured
Units: pH
Description: <p>EPF pH (Uncorrected value)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887591.rdf
Name: pHNBS
Units: pH
Description: <p>EPF pH NBS Scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/887592.rdf
Name: pHSW
Units: pH
Description: <p>EPF pH Seawater Scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/887593.rdf
Name: pHTotal
Units: pH
Description: <p>EPF pH Total Scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/887594.rdf
Name: PercentChangePerDayStandardized_Exposure
Units: percentage (%)
Description: <p>The percent change in buoyant weight over the first 34 days of experimental exposure to OA (see methods for details on this calculation). Percent delta dry weight per day divided by starting dry weight (Calcification Rate %)</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
https://osprey.bco-dmo.org/dataset/887553/data/download
download
onLine
dataset
<p>These data water quality readings for oysters exposed to ocean acidification at multiple timepoints over an 80 day period. The experiment was conducted in the summer of 2017 at the Northeastern University's Marine Science Center with a flow-through seawater system that draws water from Broad Sound in Nahant, Massachusetts (42.416884, −70.907564) using oysters collected from Plum Island Sound, Massachusetts, USA (Site 1, 42.751636, −70.837023; Site 2, 42.725186, −70.855022; Site 3, 42.681764, −70.813498) in late April.</p>
<p><strong>Calcification Rate: </strong>Net calcification rate was calculated for oysters surviving to either 50 or 80 days (n = 35) by buoyantly weighing oysters prior to exposure (BW<sub>1</sub>) and on day 33 or 34 of the exposure (BW<sub>2</sub>) following the methods of Ries et al. (2009). Buoyant weight was measured in a 27.65 liter tank (48 cm long, 24 cm wide and 24 cm deep) filled with seawater from the flow-through system and was maintained at treatment temperature by an Aqua Euro USA Model MC-1/4HP aquarium chiller. Buoyant weight was measured by completely submerging the oyster on a flat platform suspended from a bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g). Care was taken to ensure no bubbles were trapped inside oyster shells. Oysters were weighed three times in the weighing basket, removing the oyster from the basket between each measurement. If replicate measurements varied by more than 0.01 g, oysters were re-weighed. A standard of known weight was weighed every 20 oysters to ensure that no drift was occurring in the scale. To establish a relationship between buoyant weight and dry weight for the purpose of estimating net calcification rate, shells of oysters sampled for tissue within four days of a buoyant weight measurement were soaked in 10% ethanol to remove salts, dried, and weighed. The dry weight was then regressed against the buoyant weight measurement to establish an empirical dry-buoyant weight relationship:</p>
<p>DryWgt<sub>BWi</sub>(mg)&nbsp; = 1.87*BWi −2.74</p>
<p>This empirical relationship was then used to calculate dry shell weight at each buoyant weight time point via linear regression. Calculated dry weights were then used to calculate daily calcification rate:</p>
<p>calcification rate (%) = (DryWgt<sub>BW2</sub> −DryWgt<sub>BW1</sub> )/n * 100/DryWgt<sub>BW1</sub></p>
<p>where dry weight (DryWgt<sub>BWi</sub>) was calculated for each individual using the buoyant weight pre-exposure (BW1) and 33-34 days into the exposure (BW2) and n was the number of days between the two measurements. Lastly, the average daily change in dry weight was divided by initial dry weight to standardize calcification rate for allometric effects, and multiplied by 100 to convert that fraction into a percent.</p>
<p>&nbsp;</p>
<p><strong>Extrapallial Fluid: </strong>Oyster pH<sub>EPF</sub> was measured by removing each oyster from its tank, inserting a 5 mL syringe with a flexible 18-gauge polypropylene tip through the luer-lock port into the oyster's extrapallial cavity, and extracting ~0.5–2 mL of extrapallial fluid. Care was taken to avoid puncturing the mantle tissue and inadvertently sampling either the hemolymph or stomach fluid. The pH<sub>EPF</sub> was measured immediately after extraction with an Orion 91'10DJWP Double Junction micro-pH probe calibrated with pH 7.01 and 10.01 NBS buffers (for slope) and Dickson seawater Certified Reference Material (for intercept).</p>
Specified by the Principal Investigator(s)
<p>Link to data processing: https://github.com/epigeneticstoocean/AE17_Cvirginica_MolecularResponse</p>
Specified by the Principal Investigator(s)
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
Aqua Euro USA Model MC-1/4HP aquarium chiller
Aqua Euro USA Model MC-1/4HP aquarium chiller
PI Supplied Instrument Name: Aqua Euro USA Model MC-1/4HP aquarium chiller Instrument Name: Aquarium chiller Instrument Short Name:Aquarium chiller Instrument Description: Immersible or in-line liquid cooling device, usually with temperature control.
YSI 3200 conductivity probe (precision = 0.1 ppt)
YSI 3200 conductivity probe (precision = 0.1 ppt)
PI Supplied Instrument Name: YSI 3200 conductivity probe (precision = 0.1 ppt) Instrument Name: Conductivity Meter Instrument Short Name:Conductivity Meter Instrument Description: Conductivity Meter - An electrical conductivity meter (EC meter) measures the electrical conductivity in a solution. Commonly used in hydroponics, aquaculture and freshwater systems to monitor the amount of nutrients, salts or impurities in the water.
Orion 91'10DJWP Double Junction micro-pH probe+
Orion 91'10DJWP Double Junction micro-pH probe+
PI Supplied Instrument Name: Orion 91'10DJWP Double Junction micro-pH probe+ Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
Accumet solid state pH electrode (precision = 1mV)
Accumet solid state pH electrode (precision = 1mV)
PI Supplied Instrument Name: Accumet solid state pH electrode (precision = 1mV) Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
Bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g)
Bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g)
PI Supplied Instrument Name: Bottom-loading scale (Cole Parmer Symmetry S-PT 413E, precision = 0.001 g) 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/
NIST-standardized glass thermometer (precision = 0.1 °C)
NIST-standardized glass thermometer (precision = 0.1 °C)
PI Supplied Instrument Name: NIST-standardized glass thermometer (precision = 0.1 °C) Instrument Name: Thermometer Instrument Short Name: Instrument Description: A device designed to measure temperature.
VINDTA 3C coupled alkalinity gram titration and coulometric DIC analyzer system
VINDTA 3C coupled alkalinity gram titration and coulometric DIC analyzer system
PI Supplied Instrument Name: VINDTA 3C coupled alkalinity gram titration and coulometric DIC analyzer system Instrument Name: Titrator Instrument Short Name:Titrator Instrument Description: Titrators are instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB12/