Dataset: Fig2_copepod feeding on prey mixtures
Deployment: Kimmerer_2013

Copepod fed phytoplankton mixtures

Principal Investigator:

William Kimmerer (San Francisco State University, SFSU)

Co-Principal Investigator:

Sarah Cohen (San Francisco State University, SFSU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Feeding and food limitation in copepod nauplii, the neglected life stage (food limitation in copepod nauplii)

Current State:

Final no updates expected

Version:

2015-01-15

Version Date:

2015-01-15

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/546542/data

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Description

An approach was developed to recover prey DNA from gut contents of nauplii of a predatory copepod by blocking the detection of predator, Tortanus dextrilobatus, with ligase and a blocking oligonucleotide and amplifying prey DNA with universal primers. Adding 25 U of ligase improved predator clamping, while 100 and 200 U reduced efficiency. Field collected nauplii consumed a broad range of prey.This dataset measures the performance of the blocking oligonucleotide 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.

This dataset is published in Figure 2, Craig et al (2014).

Related Reference:

* 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

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, Pseudodiaptomus marinus and Oithona davisae. Limnology and Oceanography 58: 2145-2157.

Methods & Sampling

Dataset acquisition description

mix1=Artificial mixture of 1 part prey to 100,000 parts predator
mix2=Artificial mixture of 1 part prey to 10,000 parts predator

Data Processing Description

Dataset Processing Description

Raw data was plotted to determine gut fluorescence in raw units, subtracting background fluorescence from copepods with empty guts (background).

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- reordered columns

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0929075	NSF Division of Ocean Sciences

Instruments

Fluorometer

Supplied Description:

Turner 10AU

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic 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.

plate reader

Supplied Name:

Supplied 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 Type

Generic Name: plate reader

Generic 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.

Spectrophotometer

Supplied Description:

Agilent 8453 spectrophotometer (Agilent Technologies)

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sequence_id	sequence identification or sample name: TDF=adult; TDN = nauplii	unitless	sample
ligase	amount of ligase in PCR	enzyme units	no_bcodmo_term
prey_pred_mix1	Artificial mixture of 1 part prey to 100,000 parts predator	percent	no_bcodmo_term
prey_pred_mix2	Artificial mixture of 1 part prey to 10,000 parts predator	percent	no_bcodmo_term
wild_gut	Natural mixture found in field-caught animals	percent	no_bcodmo_term

Database

Contribute Data

Dataset: Fig2_copepod feeding on prey mixtures
Deployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Fig2_copepod feeding on prey mixturesDeployment: Kimmerer_2013

Dataset acquisition description

Dataset Processing Description

Dataset: Fig2_copepod feeding on prey mixtures
Deployment: Kimmerer_2013