http://lod.bco-dmo.org/id/dataset/887456
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
2023-01-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Water quality of experiment measuring phenotypic responses of Eastern oyster in response to variable length OA exposure conducted in summer 2017 with oysters sampled in Plum Island.
2023-01-19
publication
2023-01-19
revision
BCO-DMO Linked Data URI
2023-01-19
creation
http://lod.bco-dmo.org/id/dataset/887456
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) Water quality of experiment measuring 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 2023-01-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/887456 [access date]
Ocean Acidification Experiment: Water Quality Dataset Description: <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> 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>Water Chemistry: </strong>Temperature, pH, and salinity of all tanks were measured three times per week (M,W, and F) for the duration of the experiment. Seawater pH was measured with an Accumet solid state pH electrode (precision = 1 mV) calibrated with pH 7.01 and pH 10.01 NBS buffers (for calibration slope) and Dickson seawater Certified Reference Material (for calibration intercept). Complete carbonate chemistry was determined for each tank every 2 weeks. In brief, seawater samples were collected every 2 weeks in 250 ml borosilicate ground-glass stoppered bottles sealed with vacuum grease from each tank and immediately poisoned with 100 μl saturated HgCl<sub>2</sub> solution, then refrigerated until analysis of dissolved inorganic carbon (DIC) and total alkalinity (TA) was performed. DIC, TA, salinity, and temperature were used to calculate calcite saturation state, pH, CO<sup>2−</sup><sub>3,</sub> HCO<sup>−</sup><sub>3,</sub> aqueous CO<sub>2</sub>, and pCO<sub>2</sub> of each sample using CO<sub>2</sub>SYS version 2.1 (Pierrot et al., 2011).</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
Timepoint
date
PCO2
Shelf
Tank
TankID
Experimental_Cat
Exp_Temp
Sal_Corr
Temperature
pH_scaleFree
pH_NBS
pH_SW
pH_Total
CarbChem_date
Calc_corr_CT
Calc_corr_AT
Calc_pH_out
Calc_fCO2_out
Calc_pCO2_out
Calc_HCO3_out
Calc_CO3_out
Calc_CO2_out
Calc_B_Alk_out
Calc_OH_out
Calc_P_Alk_out
Calc_Si_Alk_out
Calc_Revelle_out
Calc_Ca_out
Calc_Ar_out
Calc_CO2_dry_out
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 time
date
Partial pressure of CO2
sample description
tank
salinity
water temperature at measurement depth
pH
carbon dioxide
dissolved inorganic Carbon
total alkalinity (TA)
fugacity of CO2
bicarbonate concentration [HCO3]-
Carbonate concentration [CO3]2-
No BCO-DMO term
Calcium
Ar
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 Water quality of experiment measuring 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/887595.rdf
Name: Timepoint
Units: unitless
Description: <p>Unique timepoint category</p>
http://lod.bco-dmo.org/id/dataset-parameter/887596.rdf
Name: date
Units: unitless
Description: <p>Triweekly water chemistry sample date in ISO format (YYY-MM-DD), UTC time</p>
http://lod.bco-dmo.org/id/dataset-parameter/887597.rdf
Name: PCO2
Units: uatm
Description: <p>pCO2 treatment (categorical)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887598.rdf
Name: Shelf
Units: unitless
Description: <p>Shelf in experimental array (1-6)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887599.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/887600.rdf
Name: TankID
Units: unitless
Description: <p>Unique tank ID across experiment (1-18)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887601.rdf
Name: Experimental_Cat
Units: unitless
Description: <p>Experimental window (day 9 or day 80)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887602.rdf
Name: Exp_Temp
Units: unitless
Description: <p>Experimental target temperature (catergorical)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887603.rdf
Name: Sal_Corr
Units: psu
Description: <p>Tank salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/887604.rdf
Name: Temperature
Units: Degrees Celsius (°C)
Description: <p>Tank temperatue</p>
http://lod.bco-dmo.org/id/dataset-parameter/887605.rdf
Name: pH_scaleFree
Units: pH
Description: <p>Tank pH (scale free)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887606.rdf
Name: pH_NBS
Units: pH
Description: <p>Tank pH (NBS)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887607.rdf
Name: pH_SW
Units: pH
Description: <p>Tank pH (Seawater)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887608.rdf
Name: pH_Total
Units: pH
Description: <p>Tank pH (Total)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887609.rdf
Name: CarbChem_date
Units: Date
Description: <p>Biweekly carbonate chemistry sample date in ISO format (YYY-MM-DD), UTC time</p>
http://lod.bco-dmo.org/id/dataset-parameter/887610.rdf
Name: Calc_corr_CT
Units: uM
Description: <p>Total DIC</p>
http://lod.bco-dmo.org/id/dataset-parameter/887611.rdf
Name: Calc_corr_AT
Units: μmol/kg-SW
Description: <p>Alkalinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/887612.rdf
Name: Calc_pH_out
Units: mol/kg
Description: <p>Calculated pH (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887613.rdf
Name: Calc_fCO2_out
Units: uatm
Description: <p>Calculated fCO2 (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887614.rdf
Name: Calc_pCO2_out
Units: uatm
Description: <p>Calculated pCO2 (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887615.rdf
Name: Calc_HCO3_out
Units: μmol/kg-SW
Description: <p>Calculated HCO3 (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887616.rdf
Name: Calc_CO3_out
Units: μmol/kg-SW
Description: <p>Calculated CO3 (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887617.rdf
Name: Calc_CO2_out
Units: μmol/kg-SW
Description: <p>Calculated CO2 (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887618.rdf
Name: Calc_B_Alk_out
Units: μmol/kg-SW
Description: <p>Calculated B_Alk (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887619.rdf
Name: Calc_OH_out
Units: μmol/kg-SW
Description: <p>Calculated OH (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887620.rdf
Name: Calc_P_Alk_out
Units: μmol/kg-SW
Description: <p>Calculated P_Alk (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887621.rdf
Name: Calc_Si_Alk_out
Units: μmol/kg-SW
Description: <p>Calculated Si_Alk (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887622.rdf
Name: Calc_Revelle_out
Units: μmol/kg-SW
Description: <p>Calculated Revelle (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887623.rdf
Name: Calc_Ca_out
Units: μmol/kg-SW
Description: <p>Calculated Ca (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887624.rdf
Name: Calc_Ar_out
Units: μmol/kg-SW
Description: <p>Calculated Ar (Generated by CO2Sys)</p>
http://lod.bco-dmo.org/id/dataset-parameter/887625.rdf
Name: Calc_CO2_dry_out
Units: ppm
Description: <p>Calculated CO2_dry (Generated by CO2Sys)</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/887456/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>Water Chemistry: </strong>Temperature, pH, and salinity of all tanks were measured three times per week (M,W, and F) for the duration of the experiment. Seawater pH was measured with an Accumet solid state pH electrode (precision = 1 mV) calibrated with pH 7.01 and pH 10.01 NBS buffers (for calibration slope) and Dickson seawater Certified Reference Material (for calibration intercept). Complete carbonate chemistry was determined for each tank every 2 weeks. In brief, seawater samples were collected every 2 weeks in 250 ml borosilicate ground-glass stoppered bottles sealed with vacuum grease from each tank and immediately poisoned with 100 μl saturated HgCl<sub>2</sub> solution, then refrigerated until analysis of dissolved inorganic carbon (DIC) and total alkalinity (TA) was performed. DIC, TA, salinity, and temperature were used to calculate calcite saturation state, pH, CO<sup>2−</sup><sub>3,</sub> HCO<sup>−</sup><sub>3,</sub> aqueous CO<sub>2</sub>, and pCO<sub>2</sub> of each sample using CO<sub>2</sub>SYS version 2.1 (Pierrot et al., 2011).</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/