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     data   graph     files  public Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica
Peninsula during 2014 (Polar Transcriptome project).
   ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_666234

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Nine species of diatoms were isolated from the Western Antarctic Peninsula
along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed
using an Olympus CKX41 inverted microscope by single cell isolation with a
micropipette (Anderson 2005). Diatom species were identified by morphological
characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with
the DNeasy Plant Mini Kit according to the manufacturer\u2019s protocols
(Qiagen). Amplification of the nuclear 18S rDNA region was achieved with
standard PCR protocols using eukaryotic-specific, universal 18S forward and
reverse primers. Primer sequences were obtained from Medlin et al. (1982). The
length of the region amplified is approximately 1800 base pairs (bp
).\u00a0Pseudo-nitzschia\u00a0species are often difficult to identify by their
18S rDNA sequence, therefore, additional support of the taxonomic
identification of\u00a0P.\u00a0subcurvata\u00a0was provided through sequencing
of the 18S-ITS1-5.8S regions. Amplification of this region was performed with
the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were
purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT
(Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were
edited using Geneious Pro software
([http://www.geneious.com](\\"http://www.geneious.com\\"), Kearse et al.,
2012) and BLASTn sequence homology searches were performed against the NCBI
nucleotide non-redundant (nr) database to determine species with a cutoff
identity of 98%.

Diatom phylogenetic analysis was performed with Geneious Pro and included 71
additional diatom 18S rDNA sequences from publically available genomes and
transcriptomes, including those in the MMETSP database. Diatom sequences were
trimmed to the same length and aligned with MUSCLE (Edgar 2004). A
phylogenetic tree was created in Mega with the Maximum-likelihood method of
tree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor
1969), and 100 bootstrap replicates.

Isolates were maintained at 4 deg C in constant irradiance at intensities of
either 10\u00a0umol\u00a0photons m-2\u00a0s-1\u00a0(low light) or
90\u00a0umol\u00a0photons m-2\u00a0s-1\u00a0(growth saturating light) and with
media containing high and low iron concentrations. Cultures were grown in the
synthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and
trace metal ion buffer containing 100\u00a0umol\u00a0L-1\u00a0EDTA. The growth
media also contained 300 \u03bcmol L-1\u00a0nitrate,
200\u00a0umol\u00a0L-1\u00a0silicic acid and
20\u00a0umol\u00a0L-1\u00a0phosphate. Premixed Fe-EDTA (1:1) was added
separately for total iron concentrations of either 1370 nmol L-1\u00a0or 3.1
nmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge
tubes (Nalgene) and maintained in exponential phase by dilution. Specific
growth rates of successive transfers were calculated from the linear
regression of the natural\u00a0log of\u00a0in
vivo\u00a0chlorophyll\u00a0a\u00a0fluorescence using a Turner 10-AU
fluorometer (Brand et al. 1981).\u00a0

To estimate biovolumes of each diatom species, frustules were viewed using an
Olympus BX61 Upright Wide Field Microscope with the differential interference
contrast (DIC) imaging mode and a 60X/1.42 Oil PlanApo N objective lens. Valve
apical length (AL), transapical width (TW), and\u00a0pervalvar\u00a0height
(PH) dimensions were estimated with Scion Image software ([http://scion-
image.software.informer.com/](\\"http://scion-image.software.informer.com/\\")
June 2015).

\u00a0
attribute NC_GLOBAL awards_0_award_nid String 653228
attribute NC_GLOBAL awards_0_award_number String PLR-1341479
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1341479 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Dr Chris H. Fritsen
attribute NC_GLOBAL awards_0_program_manager_nid String 50502
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Biovolume Data
Adrian Marchetti, PI
Version 11 October 2016
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.2d 13 Jun 2019
attribute NC_GLOBAL date_created String 2016-11-28T18:00:14Z
attribute NC_GLOBAL date_modified String 2019-04-17T19:45:36Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.666234.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/666234 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Inverted Microscope
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to perform isolations
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 666241
attribute NC_GLOBAL instruments_0_description String An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).

Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.

The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Inverted Microscope
attribute NC_GLOBAL instruments_0_instrument_nid String 675
attribute NC_GLOBAL instruments_0_supplied_name String Olympus CKX41
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to estimate biovolume of diatoms
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 666243
attribute NC_GLOBAL instruments_1_description String Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB06/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Microscope-Fluorescence
attribute NC_GLOBAL instruments_1_instrument_nid String 695
attribute NC_GLOBAL instruments_1_supplied_name String Olympus BX61 Upright Wide Field Microscope
attribute NC_GLOBAL instruments_2_acronym String Bioanalyzer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used to determine RNA integrity
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 666244
attribute NC_GLOBAL instruments_2_description String A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
attribute NC_GLOBAL instruments_2_instrument_name String Bioanalyzer
attribute NC_GLOBAL instruments_2_instrument_nid String 626182
attribute NC_GLOBAL instruments_2_supplied_name String Agilent Bioanalyzer 2100
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, biovolume, biovolume_cell, cell, chemical, data, dataset, dmo, erddap, management, oceanography, office, preliminary, sample, sample_size, size, species, taxonomy
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/666234 (external link)
attribute NC_GLOBAL param_mapping String {'666234': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/666234/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of North Carolina at Chapel Hill
attribute NC_GLOBAL people_0_affiliation_acronym String UNC-Chapel Hill
attribute NC_GLOBAL people_0_person_name String Adrian Marchetti
attribute NC_GLOBAL people_0_person_nid String 527120
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of North Carolina at Chapel Hill
attribute NC_GLOBAL people_1_affiliation_acronym String UNC-Chapel Hill
attribute NC_GLOBAL people_1_person_name String Adrian Marchetti
attribute NC_GLOBAL people_1_person_nid String 527120
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Hannah Ake
attribute NC_GLOBAL people_2_person_nid String 650173
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
attribute NC_GLOBAL projects_0_acronym String Polar_Transcriptomes
attribute NC_GLOBAL projects_0_description String The Southern Ocean surrounding Antarctica is changing rapidly in response to Earth's warming climate. These changes will undoubtedly influence communities of primary producers (the organisms at the base of the food chain, particularly plant-like organisms using sunlight for energy) by altering conditions that influence their growth and composition. Because primary producers such as phytoplankton play an important role in global biogeochemical cycling, it is essential to understand how they will respond to changes in their environment. The growth of phytoplankton in certain regions of the Southern Ocean is constrained by steep gradients in chemical and physical properties that vary in both space and time. Light and iron have been identified as key variables influencing phytoplankton abundance and distribution within Antarctic waters. Microscopic algae known as diatoms are dominant members of the phytoplankton and sea ice communities, accounting for significant proportions of primary production. The overall objective of this project is to identify the molecular bases for the physiological responses of polar diatoms to varying light and iron conditions. The project should provide a means of evaluating the extent these factors regulate diatom growth and influence net community productivity in Antarctic waters. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. It will facilitate the teaching and learning of polar-related topics by translating the research objectives into readily accessible educational materials for middle-school students. This project will also provide funding to enable a graduate student and several undergraduate students to be trained in the techniques and perspectives of modern biology.
Although numerous studies have investigated how polar diatoms are affected by varying light and iron, the cellular mechanisms leading to their distinct physiological responses remain unknown. Using comparative transcriptomics, the expression patterns of key genes and metabolic pathways in several ecologically important polar diatoms recently isolated from Antarctic waters and grown under varying iron and irradiance conditions will be examined. In addition, molecular indicators for iron and light limitation will be developed within these polar diatoms through the identification of iron- and light-responsive genes -- the expression patterns of which can be used to determine their physiological status. Upon verification in laboratory cultures, these indicators will be utilized by way of metatranscriptomic sequencing to examine iron and light limitation in natural diatom assemblages collected along environmental gradients in Western Antarctic Peninsula waters. In order to fully understand the role phytoplankton play in Southern Ocean biogeochemical cycles, dependable methods that provide a means of elucidating the physiological status of phytoplankton at any given time and location are essential.
attribute NC_GLOBAL projects_0_end_date String 2017-07
attribute NC_GLOBAL projects_0_geolocation String Antarctica
attribute NC_GLOBAL projects_0_name String Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
attribute NC_GLOBAL projects_0_project_nid String 653229
attribute NC_GLOBAL projects_0_project_website String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1341479 (external link)
attribute NC_GLOBAL projects_0_start_date String 2014-08
attribute NC_GLOBAL publisher_name String Hannah Ake
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
attribute NC_GLOBAL summary String Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica Peninsula during 2014 (Polar Transcriptome project).
attribute NC_GLOBAL title String Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica Peninsula during 2014 (Polar Transcriptome project).
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable species   String  
attribute species description String Species sampled
attribute species ioos_category String Taxonomy
attribute species long_name String Species
attribute species units String unitless
variable biovolume_cell   int  
attribute biovolume_cell _FillValue int 2147483647
attribute biovolume_cell actual_range int 55, 132532
attribute biovolume_cell description String Volume per cell
attribute biovolume_cell ioos_category String Unknown
attribute biovolume_cell long_name String Biovolume Cell
attribute biovolume_cell units String um^3
variable sample_size   byte  
attribute sample_size _FillValue byte 127
attribute sample_size actual_range byte 1, 12
attribute sample_size description String Sample size of cells
attribute sample_size ioos_category String Unknown
attribute sample_size long_name String Sample Size
attribute sample_size units String number

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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