http://lod.bco-dmo.org/id/dataset/546536
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
2015-02-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental results describing Copepod fed phytoplankton mixtures that were analyzed at San Francisco State University in 2013
2015-01-15
publication
2015-01-15
revision
BCO-DMO Linked Data URI
2015-01-15
creation
http://lod.bco-dmo.org/id/dataset/546536
William Kimmerer
San Francisco State University
principalInvestigator
Sarah Cohen
San Francisco State 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: Kimmerer, W., Cohen, S. (2015) Experimental results describing Copepod fed phytoplankton mixtures that were analyzed at San Francisco State University in 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-01-15) Version Date 2015-01-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546536 [access date]
Copepod fed phytoplankton mixtures Dataset Description: <p>An approach was developed to recover prey DNA from gut contents of nauplii of a&nbsp;predatory copepod by blocking the detection of predator, <em>Tortanus dextrilobatus,</em>&nbsp;with ligase and a blocking&nbsp;oligonucleotide and amplifying prey DNA with universal primers. Adding 25 U of&nbsp;ligase improved predator clamping, while 100 and 200 U reduced efficiency. Field collected&nbsp;nauplii consumed a broad range of prey.This dataset measures the performance of the blocking oligonucleotide&nbsp;with increasing amounts of ligase and at two ratios of prey to predator DNA concentration. Data are also shown for wild nauplii at 25 and 100 U of ligase.</p>
<p>This dataset is published in Figure 2, Craig et al (2014).</p>
<p><strong>Related Reference:</strong></p>
<p>* Craig, Carrie, Wim J. Kimmerer, and C. Sarah Cohen. 2014. A DNA-based method for investigating feeding by copepod nauplii. Journal of Plankton Research 36 (1): 271-275</p>
<p>Vogt, R.A., T.R. Ignoffo, L.J. Sullivan, J. Herndon, J.H. Stillman, and W. Kimmerer. 2013. Feeding capabilities and limitations in the nauplii of two pelagic estuarine copepods, <em>Pseudodiaptomus marinus</em> and <em>Oithona davisae</em>.&nbsp; Limnology and Oceanography 58: 2145-2157.</p> Methods and Sampling: <p>mix1=Artificial mixture of 1 part prey to 100,000 parts predator<br />
mix2=Artificial mixture of 1 part prey to 10,000 parts predator</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0929075 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0929075
onGoing
William Kimmerer
San Francisco State University
(415) 338-3515
San Francisco State University / Romberg Tiburon Center 3152 Paradise Drive
Tiburon
CA
94920
kimmerer@sfsu.edu
pointOfContact
Sarah Cohen
San Francisco State University
415-338-3750
Romberg Tiburon Center 3152 Paradise Drive
Tiburon
CA
94920
USA
sarahcoh@sfsu.edu
pointOfContact
asNeeded
Dataset Version: 2015-01-15
Unknown
sequence_id
ligase
prey_pred_mix1
prey_pred_mix2
wild_gut
Fluorometer
Spectrophotometer
theme
None, User defined
sample identification
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Fluorometer
Spectrophotometer
plate reader
instrument
BCO-DMO Standard Instruments
Kimmerer_2013
service
Deployment Activity
San Francisco State University lab
place
Locations
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.
Feeding and food limitation in copepod nauplii, the neglected life stage
https://www.bco-dmo.org/project/546027
Feeding and food limitation in copepod nauplii, the neglected life stage
<p>This project will investigate feeding by copepod nauplius larvae, the most abundant metazoans in the sea. It will answer three questions: 1) How does food selection by adults and nauplii differ when they are fed multiple prey species in the laboratory? 2) How does food selection by adults and nauplii differ when they are feeding on natural prey assemblages? and, 3) How do growth, development, and survival differ between copepodites and nauplii when their growth is food limited? Comparative experiments and field-based measurements will contrast the food consumed, and the effects of food limitation, between nauplii and later life stages. This contrast will include attributes of food such as size, taxon, and motility, and will include experiments with cultured prey offered singly or in a mixture, and natural prey, and apply genetic techniques to determine prey consumption by a predatory copepod. Copepods will be collected from the San Francisco Estuary, with four species selected for experiments to span taxonomic groups, sizes, salinity ranges, and general feeding behavior. A variety of techniques will be applied to account for the inevitable biases and limitations of each; all but one have previously been applied in our laboratories. These will include laboratory feeding experiments using cultured prey individually and in mixtures, and experiments using natural prey. Consumption of prey in experimental bottles will be measured as chlorophyll concentration and through particle counts by microscopy and flow cytometry. Radioactively labeled prey will be used in short incubations to determine feeding on particular prey types. Samples from the field will be examined for gut fluorescence. Separate experiments will determine how nauplii and copepodites survive and grow at different concentrations of food. Investigations of feeding by a predatory copepod (Tortanus dextrilobatus) will use molecular techniques to identify mitochondrial and nuclear DNA from diverse suspected prey species. Specific primers will be developed for common zooplankton species consumed by T. dextrilobatus in the laboratory. General primers and screening protocols developed here will be useful for identifying food web interactions in other estuarine communities.</p>
<p>Copepod nauplii are important both in their diverse trophic roles in ocean foodwebs and in the population dynamics of copepods. Nauplii have a completely different feeding apparatus from later stages, and the first feeding stage can be very sensitive to starvation, making these life stages critical to population dynamics. Yet extant copepod population models treat nauplii as miniature adults. This work will provide valuable input to the growing efforts at modeling ocean ecosystems. </p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Project_further_details_Kimmerer_copepod_naup_feeding.pdf" target="_blank">Further details from final report (pdf)</a></p>
food limitation in copepod nauplii
largerWorkCitation
project
eng; USA
biota
oceans
San Francisco State University lab
2015-01-15
San Francisco Estuary
0
BCO-DMO catalogue of parameters from Experimental results describing Copepod fed phytoplankton mixtures that were analyzed at San Francisco State University in 2013
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/546553.rdf
Name: sequence_id
Units: unitless
Description: sequence identification or sample name: TDF=adult; TDN = nauplii
http://lod.bco-dmo.org/id/dataset-parameter/546554.rdf
Name: ligase
Units: enzyme units
Description: amount of ligase in PCR
http://lod.bco-dmo.org/id/dataset-parameter/546555.rdf
Name: prey_pred_mix1
Units: percent
Description: Artificial mixture of 1 part prey to 100,000 parts predator
http://lod.bco-dmo.org/id/dataset-parameter/546556.rdf
Name: prey_pred_mix2
Units: percent
Description: Artificial mixture of 1 part prey to 10,000 parts predator
http://lod.bco-dmo.org/id/dataset-parameter/546557.rdf
Name: wild_gut
Units: percent
Description: Natural mixture found in field-caught animals
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
243
https://datadocs.bco-dmo.org/file/B11vMDjF8l8XXj/fig2_food_mix.csv
fig2_food_mix.csv
Primary data file for dataset ID 546536
download
https://www.bco-dmo.org/dataset/546536/data/download
download
onLine
dataset
<p>mix1=Artificial mixture of 1 part prey to 100,000 parts predator<br />
mix2=Artificial mixture of 1 part prey to 10,000 parts predator</p>
Specified by the Principal Investigator(s)
<p>Raw data was plotted to determine gut fluorescence in raw units, subtracting background fluorescence from copepods with empty guts (background).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
- reordered columns</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
Fluorometer
Fluorometer
PI Supplied Instrument Name: Fluorometer PI Supplied Instrument Description:Turner 10AU 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/
Spectrophotometer
Spectrophotometer
PI Supplied Instrument Name: Spectrophotometer PI Supplied Instrument Description:Agilent 8453 spectrophotometer (Agilent Technologies) Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
PI Supplied Instrument Name: PI Supplied Instrument Description:Tecan Infinite F200 or Biotek Synergy 2 microplate reader was used for each analysis. Each microplate reader contained a 430/20 EX, 680/20 EMfilter pair for Chl a. Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
Deployment: Kimmerer_2013
Kimmerer_2013
SFSU RTC
laboratory
Kimmerer_2013
William Kimmerer
San Francisco State University
SFSU RTC
laboratory