http://lod.bco-dmo.org/id/dataset/546558 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 Pseudodiaptomus marinus gut minimum fluorescence thresholds 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/546558 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 Pseudodiaptomus marinus gut minimum fluorescence thresholds 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/546558 [access date] Pseudodiaptomus marinus gut minimum fluorescence thresholds Dataset Description: &lt;p&gt;Minimum fluorescence thresholds were measured for adult and nauplius&amp;nbsp;&lt;em&gt;Pseudodiaptomus marinus&lt;/em&gt; guts.&lt;/p&gt; Methods and Sampling: &lt;p&gt;The copepod &lt;em&gt;Pseudodiaptomus marinus&lt;/em&gt; was cultured at RTC and used in the experiments. The evening before an experiment the copepods were size fractioned to separate the adults from the nauplii (larval stage) and were placed in 0.45 µm filtered San Francisco Bay water with the alga &lt;em&gt;Rhodomonas salina, &lt;/em&gt;to allow for feeding&lt;em&gt;.&lt;/em&gt; We handpicked 25 adults and 50 nauplii (Naupliar stage 3 and 4) which were maintained in 3 L of previously described water. The following morning (0900) the copepods were rinsed into freshly filtered 0.45 µm San Francisco Bay water and held for three hours to allow the individuals to clear the contents of their guts. While the copepods cleared their guts, the ciliates (&lt;em&gt;Codonellopsis sp. &lt;/em&gt;or &lt;em&gt;Favella sp.&lt;/em&gt;) were stained with the fluorescent stain, CellTracker™ Green CMFDA (5-chloromethylfluorescein diacetate) (Li et al. 1996) for one hour at 1 µmolar solution. After staining was complete, the ciliates were rinsed from the stain by being rinsed over a 35µm mesh and gently dunked into clean 0.45 µm filtered San Francisco Bay water. The ciliates were then resuspended and introduced to the copepods, which were allowed to feed for 1 hour.&lt;/p&gt; &lt;p&gt;To obtain the best images of the copepod digestive track the individuals needed to be alive. After 1 hour of feeding the copepods were rinsed over a 100 µm mesh which allowed for the separation of the ciliates and copepods. Using a dissecting microscope, individuals were transferred to a microscope slide in a small amount of water, which held each individual on its side for the best image of the gut. Once in place the microscope slide was transferred to the Olympus IX83 Epifluorescence microscope, and each individual was imaged under two settings. The first setting was bright-field and the second setting was the GFP filter (395 nm excitation, 500 nm emission) which allowed for the detection of the stained ciliate in the digestive track. This experiment was repeated twice.&lt;/p&gt; &lt;p&gt;Our next approach to identify the grazing of copepods on ciliates focused on offering the copepods a natural assemblage of food that was spiked with a known amount of stained ciliates. Three liters of surface seawater was collected from the seawall at RTC, size fractioned by reverse filtration into a 20-50 µm cohort, which removed other large grazers yet maintained other species of ciliates and phytoplankton. Cultured &lt;em&gt;Favella sp.&lt;/em&gt; was stained as previously described and then introduced to the natural assemblage. Two containers (1500 ml each) were made and the copepods were allowed to feed for 1 hour. At the end of the grazing period 3 replicate samples of 50 ml each were preserved with 0.1% Acid Lugol and 3 replicate samples of 50 ml each were preserved in 50% Glutaraldehyde.&lt;/p&gt; 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 date species stage file_rep_num threshold Fluorometer Spectrophotometer theme None, User defined date species scientific name (binomial) stage No BCO-DMO term featureType BCO-DMO Standard Parameters Fluorometer plate reader Spectrophotometer 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 Experimental results describing Pseudodiaptomus marinus gut minimum fluorescence thresholds 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/546568.rdf Name: date Units: yyyy-mm-dd Description: <p>experiment data</p> http://lod.bco-dmo.org/id/dataset-parameter/546569.rdf Name: species Units: unitless Description: <p>copepod species</p> http://lod.bco-dmo.org/id/dataset-parameter/546570.rdf Name: stage Units: unitless Description: <p>copepod life stage: N=nauplius</p> http://lod.bco-dmo.org/id/dataset-parameter/546571.rdf Name: file_rep_num Units: unitless Description: <p>file replicate number</p> http://lod.bco-dmo.org/id/dataset-parameter/546572.rdf Name: threshold Units: relative fluorescence units in the plate reader Description: <p>the threshold for deciding if a pixel is or is not showing fluorescence beyond the background; determined by observations on copepods without food in their guts.</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 1938 https://datadocs.bco-dmo.org/file/wnnxNXwHv8VYDy/fluor_thresholds.csv fluor_thresholds.csv Primary data file for dataset ID 546558 download https://osprey.bco-dmo.org/dataset/546558/data/download download onLine dataset &lt;p&gt;The copepod &lt;em&gt;Pseudodiaptomus marinus&lt;/em&gt; was cultured at RTC and used in the experiments. The evening before an experiment the copepods were size fractioned to separate the adults from the nauplii (larval stage) and were placed in 0.45 µm filtered San Francisco Bay water with the alga &lt;em&gt;Rhodomonas salina, &lt;/em&gt;to allow for feeding&lt;em&gt;.&lt;/em&gt; We handpicked 25 adults and 50 nauplii (Naupliar stage 3 and 4) which were maintained in 3 L of previously described water. The following morning (0900) the copepods were rinsed into freshly filtered 0.45 µm San Francisco Bay water and held for three hours to allow the individuals to clear the contents of their guts. While the copepods cleared their guts, the ciliates (&lt;em&gt;Codonellopsis sp. &lt;/em&gt;or &lt;em&gt;Favella sp.&lt;/em&gt;) were stained with the fluorescent stain, CellTracker™ Green CMFDA (5-chloromethylfluorescein diacetate) (Li et al. 1996) for one hour at 1 µmolar solution. After staining was complete, the ciliates were rinsed from the stain by being rinsed over a 35µm mesh and gently dunked into clean 0.45 µm filtered San Francisco Bay water. The ciliates were then resuspended and introduced to the copepods, which were allowed to feed for 1 hour.&lt;/p&gt; &lt;p&gt;To obtain the best images of the copepod digestive track the individuals needed to be alive. After 1 hour of feeding the copepods were rinsed over a 100 µm mesh which allowed for the separation of the ciliates and copepods. Using a dissecting microscope, individuals were transferred to a microscope slide in a small amount of water, which held each individual on its side for the best image of the gut. Once in place the microscope slide was transferred to the Olympus IX83 Epifluorescence microscope, and each individual was imaged under two settings. The first setting was bright-field and the second setting was the GFP filter (395 nm excitation, 500 nm emission) which allowed for the detection of the stained ciliate in the digestive track. This experiment was repeated twice.&lt;/p&gt; &lt;p&gt;Our next approach to identify the grazing of copepods on ciliates focused on offering the copepods a natural assemblage of food that was spiked with a known amount of stained ciliates. Three liters of surface seawater was collected from the seawall at RTC, size fractioned by reverse filtration into a 20-50 µm cohort, which removed other large grazers yet maintained other species of ciliates and phytoplankton. Cultured &lt;em&gt;Favella sp.&lt;/em&gt; was stained as previously described and then introduced to the natural assemblage. Two containers (1500 ml each) were made and the copepods were allowed to feed for 1 hour. At the end of the grazing period 3 replicate samples of 50 ml each were preserved with 0.1% Acid Lugol and 3 replicate samples of 50 ml each were preserved in 50% Glutaraldehyde.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;The images were analyzed using Photoshop and Image J to calculate a Gut Fullness Index which was calculated as a percent. All images were processed identically including, calculation of total gut volume, a threshold correction to account for autofluorescence, and amount of gut full of the food item.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - added conventional header with dataset name, PI name, version date, reference information&lt;br /&gt; - renamed parameters to BCO-DMO standard&lt;br /&gt; - replaced space with underscore&lt;br /&gt; - reformated date from mmm/dd/yyyy to yyyy-mm-dd&lt;/p&gt; 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/ 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. 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/ Deployment: Kimmerer_2013 Kimmerer_2013 SFSU RTC laboratory Kimmerer_2013 William Kimmerer San Francisco State University SFSU RTC laboratory