BCO-DMO | ERDDAP - bcodmo_dataset_666234

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\nalong the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed\nusing an Olympus CKX41 inverted microscope by single cell isolation with a\nmicropipette (Anderson 2005). Diatom species were identified by morphological\ncharacterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with\nthe DNeasy Plant Mini Kit according to the manufacturer\\u2019s protocols\n(Qiagen). Amplification of the nuclear 18S rDNA region was achieved with\nstandard PCR protocols using eukaryotic-specific, universal 18S forward and\nreverse primers. Primer sequences were obtained from Medlin et al. (1982). The\nlength of the region amplified is approximately 1800 base pairs (bp\n).\\u00a0Pseudo-nitzschia\\u00a0species are often difficult to identify by their\n18S rDNA sequence, therefore, additional support of the taxonomic\nidentification of\\u00a0P.\\u00a0subcurvata\\u00a0was provided through sequencing\nof the 18S-ITS1-5.8S regions. Amplification of this region was performed with\nthe 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were\npurified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT\n(Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were\nedited using Geneious Pro software\n([http://www.geneious.com](\\\\\"http://www.geneious.com\\\\\"), Kearse et al.,\n2012) and BLASTn sequence homology searches were performed against the NCBI\nnucleotide non-redundant (nr) database to determine species with a cutoff\nidentity of 98%.\n \nDiatom phylogenetic analysis was performed with Geneious Pro and included 71\nadditional diatom 18S rDNA sequences from publically available genomes and\ntranscriptomes, including those in the MMETSP database. Diatom sequences were\ntrimmed to the same length and aligned with MUSCLE (Edgar 2004). A\nphylogenetic tree was created in Mega with the Maximum-likelihood method of\ntree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor\n1969), and 100 bootstrap replicates.\n \nIsolates were maintained at 4 deg C in constant irradiance at intensities of\neither 10\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(low light) or\n90\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(growth saturating light) and with\nmedia containing high and low iron concentrations. Cultures were grown in the\nsynthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and\ntrace metal ion buffer containing 100\\u00a0umol\\u00a0L-1\\u00a0EDTA. The growth\nmedia also contained 300 \\u03bcmol L-1\\u00a0nitrate,\n200\\u00a0umol\\u00a0L-1\\u00a0silicic acid and\n20\\u00a0umol\\u00a0L-1\\u00a0phosphate. Premixed Fe-EDTA (1:1) was added\nseparately for total iron concentrations of either 1370 nmol L-1\\u00a0or 3.1\nnmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge\ntubes (Nalgene) and maintained in exponential phase by dilution. Specific\ngrowth rates of successive transfers were calculated from the linear\nregression of the natural\\u00a0log of\\u00a0in\nvivo\\u00a0chlorophyll\\u00a0a\\u00a0fluorescence using a Turner 10-AU\nfluorometer (Brand et al. 1981).\\u00a0\n \nTo estimate biovolumes of each diatom species, frustules were viewed using an\nOlympus BX61 Upright Wide Field Microscope with the differential interference\ncontrast (DIC) imaging mode and a 60X/1.42 Oil PlanApo N objective lens. Valve\napical length (AL), transapical width (TW), and\\u00a0pervalvar\\u00a0height\n(PH) dimensions were estimated with Scion Image software ([http://scion-\nimage.software.informer.com/](\\\\\"http://scion-image.software.informer.com/\\\\\")\nJune 2015).\n \n\\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
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 \n Adrian Marchetti, PI \n 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/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 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<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.666234.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/666234
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).\n\nInverted 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.\n\nThe 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/
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/
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
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/666234/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/666234
attribute	NC_GLOBAL	param_mapping	String	{'666234': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/666234/parameters
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	Polar_Transcriptomes
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.\nAlthough 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
attribute	NC_GLOBAL	projects_0_start_date	String	2014-08
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
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	[Cell biovolumes] - Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica Peninsula during 2014 (Polar Transcriptome project). (Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	species		String
attribute	species	bcodmo_name	String	species
attribute	species	description	String	Species sampled
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	bcodmo_name	String	unknown
attribute	biovolume_cell	description	String	Volume per cell
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	bcodmo_name	String	number
attribute	sample_size	description	String	Sample size of cells
attribute	sample_size	long_name	String	Sample Size
attribute	sample_size	units	String	number

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\nalong the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed\nusing an Olympus CKX41 inverted microscope by single cell isolation with a\nmicropipette (Anderson 2005). Diatom species were identified by morphological\ncharacterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with\nthe DNeasy Plant Mini Kit according to the manufacturer\\u2019s protocols\n(Qiagen). Amplification of the nuclear 18S rDNA region was achieved with\nstandard PCR protocols using eukaryotic-specific, universal 18S forward and\nreverse primers. Primer sequences were obtained from Medlin et al. (1982). The\nlength of the region amplified is approximately 1800 base pairs (bp\n).\\u00a0Pseudo-nitzschia\\u00a0species are often difficult to identify by their\n18S rDNA sequence, therefore, additional support of the taxonomic\nidentification of\\u00a0P.\\u00a0subcurvata\\u00a0was provided through sequencing\nof the 18S-ITS1-5.8S regions. Amplification of this region was performed with\nthe 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were\npurified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT\n(Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were\nedited using Geneious Pro software\n([http://www.geneious.com](\\\\\"http://www.geneious.com\\\\\"), Kearse et al.,\n2012) and BLASTn sequence homology searches were performed against the NCBI\nnucleotide non-redundant (nr) database to determine species with a cutoff\nidentity of 98%.\n \nDiatom phylogenetic analysis was performed with Geneious Pro and included 71\nadditional diatom 18S rDNA sequences from publically available genomes and\ntranscriptomes, including those in the MMETSP database. Diatom sequences were\ntrimmed to the same length and aligned with MUSCLE (Edgar 2004). A\nphylogenetic tree was created in Mega with the Maximum-likelihood method of\ntree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor\n1969), and 100 bootstrap replicates.\n \nIsolates were maintained at 4 deg C in constant irradiance at intensities of\neither 10\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(low light) or\n90\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(growth saturating light) and with\nmedia containing high and low iron concentrations. Cultures were grown in the\nsynthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and\ntrace metal ion buffer containing 100\\u00a0umol\\u00a0L-1\\u00a0EDTA. The growth\nmedia also contained 300 \\u03bcmol L-1\\u00a0nitrate,\n200\\u00a0umol\\u00a0L-1\\u00a0silicic acid and\n20\\u00a0umol\\u00a0L-1\\u00a0phosphate. Premixed Fe-EDTA (1:1) was added\nseparately for total iron concentrations of either 1370 nmol L-1\\u00a0or 3.1\nnmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge\ntubes (Nalgene) and maintained in exponential phase by dilution. Specific\ngrowth rates of successive transfers were calculated from the linear\nregression of the natural\\u00a0log of\\u00a0in\nvivo\\u00a0chlorophyll\\u00a0a\\u00a0fluorescence using a Turner 10-AU\nfluorometer (Brand et al. 1981).\\u00a0\n \nTo estimate biovolumes of each diatom species, frustules were viewed using an\nOlympus BX61 Upright Wide Field Microscope with the differential interference\ncontrast (DIC) imaging mode and a 60X/1.42 Oil PlanApo N objective lens. Valve\napical length (AL), transapical width (TW), and\\u00a0pervalvar\\u00a0height\n(PH) dimensions were estimated with Scion Image software ([http://scion-\nimage.software.informer.com/](\\\\\"http://scion-image.software.informer.com/\\\\\")\nJune 2015).\n \n\\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 \n Adrian Marchetti, PI \n 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 2.3 19 Dec 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<now

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).\n\nInverted 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.\n\nThe 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

attribute

NC_GLOBAL

license

String

https://www.bco-dmo.org/dataset/666234/license (external link)

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

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

attribute

NC_GLOBAL

project

String

Polar_Transcriptomes

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.\nAlthough 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

Biological and Chemical Oceanographic Data Management Office (BCO-DMO)

attribute

NC_GLOBAL

publisher_type

String

institution

attribute

NC_GLOBAL

sourceUrl

String

(local files)

attribute

NC_GLOBAL

standard_name_vocabulary

String

CF Standard Name Table v55

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

[Cell biovolumes] - Biovolume data from samples obtained on Gould cruise LMG1411 in the Western Antarctica Peninsula during 2014 (Polar Transcriptome project). (Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators)

attribute

NC_GLOBAL

version

String

attribute

NC_GLOBAL

xml_source

String

osprey2erddap.update_xml() v1.3

variable

species

String

attribute

species

bcodmo_name

String

species

attribute

species

description

String

Species sampled

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

bcodmo_name

String

unknown

attribute

biovolume_cell

description

String

Volume per cell

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

bcodmo_name

String

number

attribute

sample_size

description

String

Sample size of cells

attribute

sample_size

long_name

String

Sample Size

attribute

sample_size

units

String

number

ERDDAP, Version 2.22
Disclaimers | Privacy Policy | Contact