ERDDAP > info > bcodmo_dataset_665407

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[Presence and absence of iron and light-related functional genes] - Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) (Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators)		I   M	background			BCO-DMO	bcodmo_dataset_665407

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 Photophysiological parameters were measured with a Fluorescence Induction Relaxation System (FIRe) (Satatlantic). Samples were dark acclimated for at least 10 minutes and measurements were taken of each culture for photosynthetic efficiency (Fv:Fm), and functional absorption cross-section of PSII (oPSII\u00a0[A2\u00a0quanta-1]). FIRe parameters were set to measure single turnover flash of PSII reaction centers (single closure event) with a sample delay of 100, and a total of 50 samples (Gorbunov and Falkowski 2004). \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	Presence and Absence 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/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2016-11-21T20:13:31Z
attribute	NC_GLOBAL	date_modified	String	2019-04-17T20:51:30Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.665407.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/665407
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	665414
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/
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_acronym	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Used to determine RNA integrity
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	665417
attribute	NC_GLOBAL	instruments_1_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_1_instrument_name	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	626182
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Agilent Bioanalyzer 2100
attribute	NC_GLOBAL	keywords	String	accession, accession_link, bco, bco-dmo, biological, chemical, data, dataset, description, dmo, erddap, evalue, KO_num, link, management, num, oceanography, office, preliminary, protein, rpkm, species
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/665407/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/665407
attribute	NC_GLOBAL	param_mapping	String	{'665407': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/665407/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. 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
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	Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project)
attribute	NC_GLOBAL	title	String	[Presence and absence of iron and light-related functional genes] - Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes 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 analyzed
attribute	species	long_name	String	Species
attribute	species	units	String	unitless
variable	description		String
attribute	description	bcodmo_name	String	sample_descrip
attribute	description	description	String	Category of genes of interest
attribute	description	long_name	String	Description
attribute	description	units	String	unitless
variable	protein		String
attribute	protein	bcodmo_name	String	sample
attribute	protein	description	String	Gene name
attribute	protein	long_name	String	Protein
attribute	protein	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	protein	units	String	unitless
variable	RPKM		int
attribute	RPKM	_FillValue	int	2147483647
attribute	RPKM	actual_range	int	2, 45293
attribute	RPKM	bcodmo_name	String	unknown
attribute	RPKM	description	String	Presence of a gene is denoted with semi-qualitative RPKM (Reads Per Kilobase of transcript per Million) values
attribute	RPKM	long_name	String	RPKM
attribute	RPKM	units	String	unitless
variable	evalue		double
attribute	evalue	_FillValue	double	NaN
attribute	evalue	actual_range	double	-3.0E-6, 0.0
attribute	evalue	bcodmo_name	String	unknown
attribute	evalue	description	String	E-values
attribute	evalue	long_name	String	Evalue
attribute	evalue	units	String	unitless
variable	KO_num		String
attribute	KO_num	bcodmo_name	String	accession number
attribute	KO_num	description	String	Listed for genes that had a homolog in the KEGG database
attribute	KO_num	long_name	String	KO Num
attribute	KO_num	units	String	unitless
variable	accession_link		String
attribute	accession_link	bcodmo_name	String	accession number
attribute	accession_link	description	String	Accession link for K0 number
attribute	accession_link	long_name	String	Accession Link
attribute	accession_link	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.