http://lod.bco-dmo.org/id/dataset/718580
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
2017-11-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Retinoid data from SPOT cruises during different months (2016-2017)
2017-11-03
publication
2017-11-03
revision
BCO-DMO Linked Data URI
2017-11-03
creation
http://lod.bco-dmo.org/id/dataset/718580
Sergio A. Sanudo-Wilhelmy
University of Southern California
principalInvestigator
Jed A. Fuhrman
University of Southern California
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: Sanudo-Wilhelmy, S. A., Fuhrman, J. A. (2017) Retinoid data from SPOT cruises during different months (2016-2017). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-11-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/718580 [access date]
Dataset Description: <p>Location: San Pedro Ocean Time Series (SPOT) station (33°33′N, 118°24′W)</p>
<p>Samples for quantification of retinal oxime were collected at a six of depths within the euphotic zone (5-250m). Seawater was collected from each CTD depth using Niskin bottles and immediately filtered. Particulate samples were collected using in-line 0.2µm, 3µm and 10µm pore-size filters and a peristaltic pump (flow rate &lt; 50 ml per minute), transferred into sterile cryovials and were immediately stored at -80 degrees C until analysis.</p>
<p>Pigments were extracted from the filters in 3 mL of methanol, BHT (butylated hydroxytoluene) was added and placed in a -20 degrees C freezer overnight. The retinal oxime was formed by the addition of hydroxylamine hydrochloride and irradiated under yellow light for 2 hours before analysis. Retinal oxime samples were analyzed by liquid chromatography/triple mass spectrometry (LC/MS/MS/MS). The LCMS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system.</p>
<p>For chlorophyll-a measurements, 100 microliters of the pigment extraction were diluted in acetone (50x dilution) and analyzed using a Turner 10AU fluorometer.</p>
<p>Bacterial production was estimated by incorporation of [3H] thymidine and [3H] leucine into DNA and protein, respectively, as earlier described (Simon &amp; Azam, 1989, Fuhrman and Azam 1982).</p> Methods and Sampling: <p>Deployment:&nbsp;SPOT<br />
Platform: RV Yellowfin and RV Nerissa<br />
Platform Type: &nbsp;vessel<br />
Start Date:&nbsp;09/14/2016<br />
End Date:&nbsp;07/11/2017</p>
<p>The SPOT sampling for the months of May and July were carried out on the research vessel Nerissa of the Orange County Sanitation District. This was because the RV Yellowfin was in the dry dock for maintenance and repairs. Unfortunately, the light intensity for those two months is missing due to problems with the sensor.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335269 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1335269
completed
Sergio A. Sanudo-Wilhelmy
University of Southern California
213-821-1302
3616 Trousdale Pkwy Dept. of Biological Sciences, AHF 206, Mail Code: 0371
Los Angeles
CA
90089
USA
sanudo@usc.edu
pointOfContact
Jed A. Fuhrman
University of Southern California
213-740-5757
Dept. Biological Sciences, Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089-0371
USA
fuhrman@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Date
Time
Longitude
Latitude
Depth
Microbial_Size_fraction
PR_retinal_Oxime_sw
STDEV_retinal_oxime_sw
Chl_a_sw_avg
STDEV_Chl_a_sw
Leucine_BP
Thymidine_BP
PAR
ISO_DateTime_start
Turner 10AU fluorometer
ThermoTSQ Quantum Access electro-spray ionization triple quadupole mass spectrometer
theme
None, User defined
Cruise identfier
date
time of day
longitude
latitude
depth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Fluorometer
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
SPOT_20160914
SPOT_20161130
SPOT_20170131
SPOT_20170315
SPOT_20170524
SPOT_20170711
service
Deployment Activity
San Pedro Basin
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.
Environmental regulation of retinal and bacteriochlorophyll biosynthesis
https://osprey.bco-dmo.org/project/564190
Environmental regulation of retinal and bacteriochlorophyll biosynthesis
<p><em>Description from NSF award abstract:</em><br />
Rhodopsins are the simplest energy-harvesting photoproteins and community metagenomics have revealed that their synthesis genes are ubiquitous throughout the world oceans. These include microbial rhodopsin (proteorhodopsin (PR)), which occur in an estimated 75% of marine bacteria and archaea in oceanic surface waters. The discovery of this abundant and widespread photoprotein in the surface ocean has challenged the notion that solar energy can only be converted into chemical energy for growth in marine ecosystems through chlorophyll-based photosynthesis. Although the potential of light-driven energy flux in ocean ecosystems through PR could be significant, the physiological and ecological functions of this type of rhodopsin remains undetermined, mainly due to the lack of a technique for a direct measurement of this photoprotein. To evaluate the ecological relevance of PR in the marine environment, the investigators have developed a new analytical technique to measure the concentrations of the light-sensitive pigment in the PR, the chromophore retinal. Because rhodopsins have a single retinal chromophore associated with the polypeptide opsin, the total number of retinal molecules is equivalent to the total number of PR.</p>
<p>This project will employ the PI's newly developed protocol to examine the effects of light, organic carbon and trace metals availability on PR and bacteriochlorophyll synthesis using field and laboratory manipulations. Such experiments will establish the impact of abiotic factors on the two known bacterial photoheterotrophic metabolisms. The laboratory studies will be complemented with the analyses of those pigments in field samples collected along spatial and temporal gradients in light intensity, organic carbon and trace metals in different oceanographic regimes. Gene expression patterns will be determined in concert with changes in retinal and bacteriochlorophyll concentrations and microbial growth responses in the field and in the laboratory. Therefore, the combination of observational and manipulative approaches, will address fundamental questions in regard to the impact of retinal-based photochemical energy transformation in the ocean, a process that still is not well understood.</p>
Marine Retinoids
largerWorkCitation
project
eng; USA
oceans
San Pedro Basin
-118.4
-118.4
33.55
33.55
2016-09-14
2017-07-11
Mediterrean Sea and the North Pacific Ocean
0
BCO-DMO catalogue of parameters from Retinoid data from SPOT cruises during different months (2016-2017)
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/723401.rdf
Name: Cruise
Units: SPOT month and year
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/723402.rdf
Name: Date
Units: mm/dd/yy
Description: <p>Sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/723403.rdf
Name: Time
Units: hh:mm-hh:mm
Description: <p>Start and end times of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/723404.rdf
Name: Longitude
Units: decimal degrees
Description: <p>SPOT longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/723405.rdf
Name: Latitude
Units: decimal degrees
Description: <p>SPOT latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/723406.rdf
Name: Depth
Units: meters
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/723407.rdf
Name: Microbial_Size_fraction
Units: micrometers(µm)
Description: <p>Size range of particles collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/723408.rdf
Name: PR_retinal_Oxime_sw
Units: picomolar (pico mol L-1)
Description: <p>Average Proteorhodopsin concentrations of triplicate analytical replicates of retinal oxime using HPLC-MS</p>
http://lod.bco-dmo.org/id/dataset-parameter/723409.rdf
Name: STDEV_retinal_oxime_sw
Units: picomolar (pico mol L-1)
Description: <p>Standard deviation of Proteorhodopsin concentrations of triplicate analytical replicates of retinal oxime using HPLC-MS</p>
http://lod.bco-dmo.org/id/dataset-parameter/723410.rdf
Name: Chl_a_sw_avg
Units: picomolar (pico mol L-1)
Description: <p>Average Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/723411.rdf
Name: STDEV_Chl_a_sw
Units: picomolar (pico mol -L)
Description: <p>Standard deviation of Chlorophyll-a concentrations of triplicate analytical replicates using a 10-AU fluorometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/723412.rdf
Name: Leucine_BP
Units: lls ml-1 day-1
Description: <p>Bacterial production calculated from Leucine uptake</p>
http://lod.bco-dmo.org/id/dataset-parameter/723413.rdf
Name: Thymidine_BP
Units: cells ml-1 day-1
Description: <p>Bacterial production calculated from Thymidine uptake</p>
http://lod.bco-dmo.org/id/dataset-parameter/723414.rdf
Name: PAR
Units: micro Einsteins per square meter per second
Description: <p>Photosynthetically active radiation (400-700nm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/723415.rdf
Name: ISO_DateTime_start
Units: yyyy-mm-ddThh:mm:ss
Description: <p>Time at sampling start</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
12490
https://datadocs.bco-dmo.org/file/nGGl0xWsxZ4yq6/SPOT_cruise.csv
SPOT_cruise.csv
Primary data file for dataset ID 718580
download
https://osprey.bco-dmo.org/dataset/718580/data/download
download
onLine
dataset
<p>Deployment:&nbsp;SPOT<br />
Platform: RV Yellowfin and RV Nerissa<br />
Platform Type: &nbsp;vessel<br />
Start Date:&nbsp;09/14/2016<br />
End Date:&nbsp;07/11/2017</p>
<p>The SPOT sampling for the months of May and July were carried out on the research vessel Nerissa of the Orange County Sanitation District. This was because the RV Yellowfin was in the dry dock for maintenance and repairs. Unfortunately, the light intensity for those two months is missing due to problems with the sensor.</p>
Specified by the Principal Investigator(s)
<p>The LC-MS data was processed using LCQUAN quantitative software from Thermo Scientific.</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
Turner 10AU fluorometer
Turner 10AU fluorometer
PI Supplied Instrument Name: Turner 10AU fluorometer 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/
ThermoTSQ Quantum Access electro-spray ionization triple quadupole mass spectrometer
ThermoTSQ Quantum Access electro-spray ionization triple quadupole mass spectrometer
PI Supplied Instrument Name: ThermoTSQ Quantum Access electro-spray ionization triple quadupole mass spectrometer PI Supplied Instrument Description:The LC-MS system used for the pigment quantification consists of a Thermo TSQ Quantum Access electro-spray ionization triple quadruple mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography pump and auto-sampler. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Cruise: SPOT_20160914
SPOT_20160914
R/V Yellowfin
R/V Yellowfin
vessel
SPOT_20160914
Sergio A. Sanudo-Wilhelmy
University of Southern California
Cruise: SPOT_20161130
SPOT_20161130
R/V Yellowfin
R/V Yellowfin
vessel
SPOT_20161130
Sergio A. Sanudo-Wilhelmy
University of Southern California
Cruise: SPOT_20170131
SPOT_20170131
R/V Yellowfin
R/V Yellowfin
vessel
SPOT_20170131
Sergio A. Sanudo-Wilhelmy
University of Southern California
Cruise: SPOT_20170315
SPOT_20170315
R/V Yellowfin
R/V Yellowfin
vessel
SPOT_20170315
Sergio A. Sanudo-Wilhelmy
University of Southern California
Cruise: SPOT_20170524
SPOT_20170524
R/V Nerissa
vessel
SPOT_20170524
Sergio A. Sanudo-Wilhelmy
University of Southern California
Cruise: SPOT_20170711
SPOT_20170711
R/V Nerissa
vessel
SPOT_20170711
Sergio A. Sanudo-Wilhelmy
University of Southern California
R/V Yellowfin
R/V Yellowfin
vessel
R/V Nerissa
vessel