http://lod.bco-dmo.org/id/dataset/869011
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
2022-02-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Data resulting from testing dilution experiments conducted in the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii
2022-02-01
publication
2022-02-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-02-09
publication
https://doi.org/10.26008/1912/bco-dmo.869011.1
Erica Goetze
University of Hawaiʻi at Mānoa
principalInvestigator
Petra H. Lenz
University of Hawaiʻi at Mānoa
principalInvestigator
Karen E. Selph
University of Hawaiʻi at Mānoa
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: Goetze, E., Lenz, P., Selph, K. E. (2022) Data resulting from testing dilution experiments conducted in the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-02-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.869011.1 [access date]
Quantitative PCR: Dilution test Dataset Description: Methods and Sampling: <p><strong>Methodology:</strong><br />
Complete methodology is detailed in Jungbluth et al. (accepted 2022, Limnology and Oceanography Methods). Briefly, qPCR assays were developed for four copepod species: <em>Parvocalanus crassirostris</em>, <em>Bestiolina similis, Oithona simplex, </em>and<em> Oithona attenuata. </em>The assays were optimized and applied to mixed field samples to estimate biomass of nauplii of each species, over 5 orders of magnitude in length-based biomass and DNA copy number measured with qPCR.</p>
<p><strong>Sampling and Analytical Procedures:</strong><br />
Zooplankton samples were either collected from the field with a Niskin bottle or 150 µm mesh plankton net with filtering cod end, or cultured in the laboratory, then preserved in 95% molecular ethyl alcohol and stored in the freezer until processing. Field samples were collected from southern Kāne‘ohe Bay on the island of Oahu, Hawai‘i. DNA was extracted from individual copepods of all focal and non-focal species from the area and used to assess whether our qPCR assays were working as expected. Dilutions of the various focal and non-focal species were tested to look at the range of focal species DNA that was detectible with the assays. Finally, the DNA copy number measurements were compared with length-based and laboratory-measured carbon biomass of each species to assess the accuracy of using qPCR to estimate copepod naupliar biomass from mixed field samples.&nbsp;&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1255697
completed
Erica Goetze
University of Hawaiʻi at Mānoa
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
Petra H. Lenz
University of Hawaiʻi at Mānoa
808-956-8003
Pacific Biosciences Research Center (PBRC), Bekesy Laboratory of Neurobiology 1993 East-West Road
Honolulu
HI
96822
United States
petra@hawaii.edu
pointOfContact
Karen E. Selph
University of Hawaiʻi at Mānoa
808-956-7941
Department of Oceanography 1000 Pope Road, MSB 205
Honolulu
HI
96822
USA
selph@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
FocalSpecies
Experiment
Sample_Name
TotalFocal_DNA
Cq_Mean
SD_Cq
Concentration_Mean
SD_Concentration
Applied Biosystems 3730XL
Exeter Analytical CE 440
Qubit Fluorometer (Invitrogen)
Olympus dissection microscope (model SZX16)
Light Cycler 96 Quantitative PCR Thermalcycler (Roche)
theme
None, User defined
species scientific name (binomial)
experiment id
sample identification
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Elemental Analyzer
Fluorometer
Microscope - Optical
qPCR Thermal Cycler
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.
EAGER: New molecular methods for studying copepod nauplii in the field
https://osprey.bco-dmo.org/project/473049
EAGER: New molecular methods for studying copepod nauplii in the field
<p><em>Description from NSF Award Abstract:</em><br />
The most abundant metazoans in the open sea are often the earliest developmental stages of copepods, their nauplii. Nauplii remain under-studied due to the limitations of conventional techniques and an historical emphasis on studying the larger mesozooplankton. However, there is increasing recognition that nauplii play important roles in food web dynamics, and considerable evidence that nauplii may be important trophic intermediaries between microbial and classical food webs due to their high abundance, high weight-specific ingestion rates, and ability to feed on relatively small particles. This team of investigators is developing a novel molecular approach to studying diverse populations of nauplii in mixed field samples based on quantitative Polymerase Chain Reaction (qPCR). They propose to complete development and validation of this qPCR-based technique for enumeration of nauplii, and evaluate its utility in the field. The specific objectives of this research are to identify and reduce technical and biological sources of error in the methodology, determine the accuracy of the method across a range of environmental conditions, and complete one paired field experiment that compares the grazing impact of naupliar and protozoan micro-grazers in a model subtropical coastal ecosystem.</p>
<p><strong>Note:</strong> This project is funded by an NSF EAGER award.</p>
<p><em>Related publications:</em><br />
Jungbluth, M.J., Goetze, E., and Lenz, P.H. 2013. Measuring copepod naupliar abundance in a subtropical bay using quantitative PCR. Marine Biology, 160: 3125-3141. doi: <a href="http://dx.doi.org/10.1007/s00227-013-2300-y" target="_blank">10.1007/s00227-013-2300-y</a></p>
<p>Jungbluth, M.J., and Lenz, P.H. 2013. Copepod diversity in a subtropical bay based on a fragment of the mitochondrial COI gene. Journal of Plankton Research, 35(3): 630-643. doi: <a href="http://dx.doi.org/10.1093/plankt/fbt015" target="_blank">10.1093/plankt/fbt015</a></p>
EAGER: Copepod nauplii
largerWorkCitation
project
eng; USA
oceans
-157.8
-157.8
21.45
21.45
2014-06-01
2014-06-30
Kaneohe Bay, Oahu, Hawaii
0
BCO-DMO catalogue of parameters from Data resulting from testing dilution experiments conducted in the development of four assays to quantify copeod naupliar biomass in Kaneohe Bay, Hawaii
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/869069.rdf
Name: FocalSpecies
Units: unitless
Description: <p>Species that is the target of the assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/869070.rdf
Name: Experiment
Units: unitless
Description: <p>Corresponding experiment ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/869071.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name and dilution level</p>
http://lod.bco-dmo.org/id/dataset-parameter/869072.rdf
Name: TotalFocal_DNA
Units: nanograms per microliter (ng/uL)
Description: <p>Amount of focal species DNA diluted into non-focal species DNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/869073.rdf
Name: Cq_Mean
Units: unitless
Description: <p>Cycle threshold measured in qPCR, mean</p>
http://lod.bco-dmo.org/id/dataset-parameter/869074.rdf
Name: SD_Cq
Units: unitless
Description: <p>Cycle threshold measured in qPCR, standard deviation</p>
http://lod.bco-dmo.org/id/dataset-parameter/869075.rdf
Name: Concentration_Mean
Units: nanograms per microliter (ng/uL)
Description: <p>Mean concentration of DNA measured in qPCR, ng/ul</p>
http://lod.bco-dmo.org/id/dataset-parameter/869076.rdf
Name: SD_Concentration
Units: nanograms per microliter (ng/uL)
Description: <p>Standard deviation of concentration measured in qPCR</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://doi.org/10.26008/1912/bco-dmo.869011.1
download
onLine
dataset
<p><strong>Methodology:</strong><br />
Complete methodology is detailed in Jungbluth et al. (accepted 2022, Limnology and Oceanography Methods). Briefly, qPCR assays were developed for four copepod species: <em>Parvocalanus crassirostris</em>, <em>Bestiolina similis, Oithona simplex, </em>and<em> Oithona attenuata. </em>The assays were optimized and applied to mixed field samples to estimate biomass of nauplii of each species, over 5 orders of magnitude in length-based biomass and DNA copy number measured with qPCR.</p>
<p><strong>Sampling and Analytical Procedures:</strong><br />
Zooplankton samples were either collected from the field with a Niskin bottle or 150 µm mesh plankton net with filtering cod end, or cultured in the laboratory, then preserved in 95% molecular ethyl alcohol and stored in the freezer until processing. Field samples were collected from southern Kāne‘ohe Bay on the island of Oahu, Hawai‘i. DNA was extracted from individual copepods of all focal and non-focal species from the area and used to assess whether our qPCR assays were working as expected. Dilutions of the various focal and non-focal species were tested to look at the range of focal species DNA that was detectible with the assays. Finally, the DNA copy number measurements were compared with length-based and laboratory-measured carbon biomass of each species to assess the accuracy of using qPCR to estimate copepod naupliar biomass from mixed field samples.&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Light Cycler 96 software (Roche, v. 1.1.0.1320)<br />
<em>R</em> (R core team, 2017), packages <em>stats</em> (base R) and <em>car</em> (Fox and Weisberg 2019)</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to comply with BCO-DMO naming conventions.</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
Applied Biosystems 3730XL
Applied Biosystems 3730XL
PI Supplied Instrument Name: Applied Biosystems 3730XL PI Supplied Instrument Description:Applied Biosystems 3730XL, with BigDye terminator chemistry v3.1, was used for sequencing species and qPCR products. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Exeter Analytical CE 440
Exeter Analytical CE 440
PI Supplied Instrument Name: Exeter Analytical CE 440 PI Supplied Instrument Description:Exeter Analytical CE 440 was used for CHN analysis of copepods. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Qubit Fluorometer (Invitrogen)
Qubit Fluorometer (Invitrogen)
PI Supplied Instrument Name: Qubit Fluorometer (Invitrogen) PI Supplied Instrument Description:A Qubit Fluorometer (Invitrogen) with the HS Assay was used for measurement of total DNA. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Olympus dissection microscope (model SZX16)
Olympus dissection microscope (model SZX16)
PI Supplied Instrument Name: Olympus dissection microscope (model SZX16) PI Supplied Instrument Description:An Olympus dissection microscope (model SZX16) fitted with Luminera Infinity-3 was used for sorting and sizing copepod nauplii. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Light Cycler 96 Quantitative PCR Thermalcycler (Roche)
Light Cycler 96 Quantitative PCR Thermalcycler (Roche)
PI Supplied Instrument Name: Light Cycler 96 Quantitative PCR Thermalcycler (Roche) PI Supplied Instrument Description:A light Cycler 96 Quantitative PCR Thermalcycler (Roche) was used for qPCR measurements. 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).