http://lod.bco-dmo.org/id/dataset/546671
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)
GenBank BLAST results of copepod nauplii gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project)
2015-01-15
publication
2015-01-15
revision
BCO-DMO Linked Data URI
2015-01-15
creation
http://lod.bco-dmo.org/id/dataset/546671
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) GenBank BLAST results of copepod nauplii gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project). 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/546671 [access date]
GenBank BLAST results of copepod nauplii gut contents Dataset Description: <p>Field collected copepod nauplii gut content sequences were identified using the BLASTN algorithm on GenBank or by comparison to a sequence library of local copepod species constructed for this project. Blast searches of the GenBank database were conducted on May 16, 2013. BLASTed sequences were identified to the taxonomic level at which there was consensus among matches within 10% of the best score.</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>See <a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Kimmerer_genetics_methodology.pdf" target="_blank">Methodology</a> (pdf).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0929075 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0929075
completed
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
GenBank_id
BLAST_score
domain
tax_rank_1
tax_rank_2
tax_rank_3
tax_rank_4
tax_rank_5
tax_rank_6
tax_rank_7
tax_rank_8
tax_rank_9
tax_rank_10
tax_rank_11
tax_rank_12
tax_rank_13
tax_rank_14
tax_rank_15
tax_rank_16
Automated Sequencer
HPLC
Plankton Net
Thermal Cycler
theme
None, User defined
sample identification
accession number
No BCO-DMO term
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
High-Performance Liquid Chromatograph
Plankton Net
Thermal Cycler
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://osprey.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 GenBank BLAST results of copepod nauplii gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii 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
http://lod.bco-dmo.org/id/dataset-parameter/546703.rdf
Name: sequence_id
Units: unitless
Description: <p>squence identification: sample name followed by sequence number. TDF=adult; TDN = nauplii</p>
http://lod.bco-dmo.org/id/dataset-parameter/546704.rdf
Name: GenBank_id
Units: unitless
Description: <p>GenBank accession number of BLAST hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/546705.rdf
Name: BLAST_score
Units: unitless
Description: <p>BLAST score: statistical significance of sequence matches to GenBank database</p>
http://lod.bco-dmo.org/id/dataset-parameter/546706.rdf
Name: domain
Units: unitless
Description: <p>taxonomic domain: Bacteria or Eukaryota</p>
http://lod.bco-dmo.org/id/dataset-parameter/546707.rdf
Name: tax_rank_1
Units: unitless
Description: <p>highest taxonomic name</p>
http://lod.bco-dmo.org/id/dataset-parameter/546708.rdf
Name: tax_rank_2
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546709.rdf
Name: tax_rank_3
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546710.rdf
Name: tax_rank_4
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546711.rdf
Name: tax_rank_5
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546712.rdf
Name: tax_rank_6
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546713.rdf
Name: tax_rank_7
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546714.rdf
Name: tax_rank_8
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546715.rdf
Name: tax_rank_9
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546716.rdf
Name: tax_rank_10
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546717.rdf
Name: tax_rank_11
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546718.rdf
Name: tax_rank_12
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546719.rdf
Name: tax_rank_13
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546720.rdf
Name: tax_rank_14
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546721.rdf
Name: tax_rank_15
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</p>
http://lod.bco-dmo.org/id/dataset-parameter/546722.rdf
Name: tax_rank_16
Units: unitless
Description: <p>taxonomic name; more specific than preceeding</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
2224451
https://datadocs.bco-dmo.org/file/0AAMn5rFJP1y5o/naup_blast.csv
naup_blast.csv
Primary data file for dataset ID 546671
download
https://osprey.bco-dmo.org/dataset/546671/data/download
download
onLine
dataset
<p>See <a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Kimmerer_genetics_methodology.pdf" target="_blank">Methodology</a> (pdf).</p>
Specified by the Principal Investigator(s)
<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 />
- replaced blanks with underscores<br />
- moved sequence id's to separate column<br />
- replaced '?' with '_maybe'<br />
- changed Pseudodioptamus to Pseudodiaptomus</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
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:ABI 3130 Genetic Analyzer 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.
HPLC
HPLC
PI Supplied Instrument Name: HPLC Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
Plankton Net
Plankton Net
PI Supplied Instrument Name: Plankton Net PI Supplied Instrument Description:Mesh size 100 microns or 150 microns Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: Kimmerer_2013
Kimmerer_2013
SFSU RTC
laboratory
Kimmerer_2013
William Kimmerer
San Francisco State University
SFSU RTC
laboratory