1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:Ta12,

Environmental Sample Collection

Transfer 1 ml of whole seawater to a 2 ml cryovial.
Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%.
Incubate at 4 degrees celsius for 30 min.
Flash freeze in liquid N2 and store at -80 degrees celsius.

Fluorescent DNA staining (for bacterial and viral abundances)

Thaw samples.
To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)
Heat to 80 degrees celsius for 10 min in the dark
Cool at RT for 5 min
Analyze via flow cytometry

Analysis (for bacterial and viral abundances)

Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences).

An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads.
A gating hierarchy is established using both beads and previously determined virus and bacteria populations as reference (Sybr Gold Fluorescence versus SSC cytogram).
Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission.

Analysis (for chlorophyll containing cells)

Samples are analyzed on a BD Accuri C6. Fixed, frozen samples are thawed and analyzed immediately.

An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using various sized fluorescent beads as reference points (1.0, 2.0, 3.0, 6.0 and 10 um).
Gating is established using both beads and previously determined phytoplankton populations as reference (Chlorophyll Fluorescence versus FSC cytogram).
Samples are analyzed using 488nm laser for excitation and the default BD Accuri threshold (80,000 RFU) on FSC is used.

TE buffer with SYBR Gold recipe

1X TE (for 100 mls)

1 ml of 1M Tris, pH 8.0
1 ml of 0.5 mM EDTA
98 mls MQ water
Store 4 degrees celsius

1X TE + SYBR Gold (for 10 mls)

Filter 10 mls 1 TE buffer, 0.22 um filter
1:20,0000 dilution of SYBR Gold (Molecular Probes) stock (0.5 ul stock to 10 mls TE buffer)

1d:T90d,Description from NSF award abstract: Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression. It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.6:["$","$L1b",null,{"dataset":{"_id":"652223","description":"

Enumeration of Bacteria, viruses, and chlorophyll containing particles using flow cytometry.

For related datasets, click on the project link at the top of the page.

\n","problem":"","acquisition":"$1c","processing":"

DMO notes:

-Changed parameter names to meet BCO-DMO naming conventions
\n-Added ISO_DateTime column
\n-Removed 4 unnecessary lat/lon columns (2 remain).

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Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-07-20 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.652223.1 [access date]","citationParts":{"identifier":"doi:10.1575/1912/bco-dmo.652223.1","versionDate":"2016-07-20","versionId":"1","year":"2016","title":"Abundance of bacteria viruses and chlorophyll containing cells collected from the R/V Oceanus OC1504A in the Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W during 2015","authors":"Thamatrakoln, K., Brzezinski, M.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.1575/1912/bco-dmo.652223.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2015-04-20T04:00:00.000Z","end":"2015-05-01T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1429502400","label":"2015-04-20"},"end":{"value":"1430452800","label":"2015-05-01"}},"spatial_extent":{"shape":"polygon","center":{"latitude":39.104505,"longitude":-122.64593},"wkt":"POLYGON ((-124.48169 34.55467, -120.81017 34.55467, -120.81017 43.65434, -124.48169 43.65434, -124.48169 34.55467))","north":43.65434,"east":-120.81017,"south":34.55467,"west":-124.48169},"dataset_type":["Cruise Results"],"keywords":["oceans"],"data_files":[{"id":"901066","title":"chl_bact_virus.csv","url":"https://datadocs.bco-dmo.org/dataset/652223/file/YVVZJoDizlk87/chl_bact_virus.csv","showTableUrl":"https://www.bco-dmo.org/dataset/652223/data/view/901066","description":"Primary data file for dataset ID 652223","filename":"chl_bact_virus.csv","bytesize":6059,"checksum":{"value":"61526d1904349c31a8b8172467c4b0f4","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"bcodmo_dataset_652223","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"558200","name":"Kimberlee Thamatrakoln"},"performedAtOrganization":{"_id":"236","name":"Rutgers University"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"50663","name":"Mark A. Brzezinski"},"performedAtOrganization":{"_id":"253","name":"University of California-Santa Barbara"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"558200","name":"Kimberlee Thamatrakoln"},"performedAtOrganization":{"_id":"236","name":"Rutgers University"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"650173","name":"Hannah Ake"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"560135","name":"OC1504A","synonyms":["MUSiCC"],"dates":{"start":"2015-04-19T00:00:00.000Z","end":"2015-05-02T00:00:00.000Z"},"platform":{"_id":"53997","name":"R/V Oceanus"},"chiefScientists":[{"id":"558200","name":"Kimberlee Thamatrakoln","role":"Chief Scientist"},{"id":"50663","name":"Mark A. 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They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. Description from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm","type_acronym":"Flow Cytometer"},{"_id":"652273","name":"BD Accuri C6","description":"Chlorophyll containing cells analyzed on this flow cytometer.","type_id":"660","type_name":"Flow Cytometer","type_desc":"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. Description from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm","type_acronym":"Flow Cytometer"}],"parameters":[{"_id":"652236","name":"cast","format":"","frictionlessType":"","description":"

cast number

","units":{"_id":"","name":"unitless"},"type":{"_id":"761","name":"cast","description":"

cast or profile number

"}},{"_id":"652237","name":"depth","format":"","frictionlessType":"","description":"

depth of sample collection

","units":{"_id":"","name":"meters"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"652238","name":"date_local","format":"","frictionlessType":"","description":"

local date of cast; mm-bbb-yy

","units":{"_id":"","name":"unitless"},"type":{"_id":"799","name":"date_local","description":"

local month, day and year, usually as a text string, e.g. feb10_1995. It is better to use one of the other forms of presenting date and time data so that the data can be used in computations and for comparisons. Note, if the string begins with numbers but also includes letters, there may be problems using the field name for retrieval.

"}},{"_id":"652239","name":"time_local","format":"","frictionlessType":"","description":"

local time of cast; HH:MM

","units":{"_id":"","name":"unitless"},"type":{"_id":"1007","name":"time_local","description":"

time of day, local time, using 2400 clock format

"}},{"_id":"652240","name":"time_utc","format":"","frictionlessType":"","description":"

UTC time of cast; HH:MM

","units":{"_id":"","name":"unitless"},"type":{"_id":"1011","name":"time_utc","description":"

UTC time, using 2400 clock format

"}},{"_id":"652241","name":"date_utc","format":"","frictionlessType":"","description":"

UTC date of cast; mm-bbb-yy

","units":{"_id":"","name":"unitless"},"type":{"_id":"798","name":"date_utc","description":"

UTC month, day and year, usually as a text string, e.g. feb10_1995. It is better to use one of the other forms of presenting date and time data so that the data can be used in computations and for comparisons. Note, if the string begins with numbers but also includes letters, there may be problems using the field name for retrieval. Use date_gmt for future data sets.

"}},{"_id":"652242","name":"station","format":"","frictionlessType":"","description":"

consecutive station number

","units":{"_id":"","name":"unitless"},"type":{"_id":"987","name":"station","description":"

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

"}},{"_id":"652243","name":"lat","format":"","frictionlessType":"","description":"

latitude

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"652244","name":"lon","format":"","frictionlessType":"","description":"

longitude

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"652245","name":"bacteria","format":"","frictionlessType":"","description":"

bacteria-like particle abundance

","units":{"_id":"","name":"bacteria per milliliter"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}},{"_id":"652246","name":"virus","format":"","frictionlessType":"","description":"

virus-like particle abundance (VLP)

","units":{"_id":"","name":"VLP per milliliter"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}},{"_id":"652247","name":"chl_total","format":"","frictionlessType":"","description":"

chlorophyll containing cells

","units":{"_id":"","name":"cells per milliliter"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}},{"_id":"652248","name":"ISO_DateTime_UTC","format":"","frictionlessType":"","description":"

DateTime (UTC) ISO formatted

","units":{"_id":"","name":"unitless"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Date/Time (UTC) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}},{"_id":"652249","name":"cruise_id","format":"","frictionlessType":"","description":"

The name of the cruise that collected these data.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1102","name":"cruise_id","description":"

cruise designation; name

"}}],"related_publications":[],"related_datasets":[],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/652223/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"ERDDAP","items":[{"name":"SUBSET DATA","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.html","contentType":"text/html","actionType":"tool"},{"name":"VIEW TABLE","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.htmlTable","contentType":"text/html","actionType":"view"},{"name":"CSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.csv","contentType":"text/csv","actionType":"download"},{"name":"TSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.tsv","contentType":"text/tsv","actionType":"download"},{"name":"GeoJSON","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.geoJson","contentType":"application/geo+json","actionType":"download"},{"name":"MATLAB","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.mat","contentType":"text/x-matlab","actionType":"download"},{"name":"netCDF","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.nc","contentType":"application/x-netcdf","actionType":"download"},{"name":"ODV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652223.odvTxt","contentType":"text/plain","actionType":"download"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/652223/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/652223/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/652223/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"558198","name":"Linking physiological and molecular aspects of diatom silicification in field populations","acronym":"Diatom Silicification","description":"$1d"}],"archives":[{"id_value":"10.1575/1912/bco-dmo.652223.1","url":"https://doi.org/10.1575/1912/bco-dmo.652223.1","date_assigned":"2019-06-06","version_date":"2016-07-20","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":115},"downloads":{"count":376}}},"fileId":"901066"}]