ERDDAP > info > bcodmo_dataset_3668

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
	set	data	graph		files	public	[T_pseudonana_growth] - Results from metal limitation experiments (Cu, Zn, Fe, Mn) conducted in the diatom T. pseudonana carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011 (Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery)		I   M	background			BCO-DMO	bcodmo_dataset_3668

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	""
attribute	NC_GLOBAL	awards_0_award_nid	String	54979
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-0727997
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0727997
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	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Summary of steady state <i>T. pseudonana</i> growth rate experiments sampled for transcriptomic microarray analysis under varied conditions of divalent metal availability. PI: Andrew Allen (J. Craig Venter Institue, Inc.) Contact: Adam Kustka (Rutgers University) Version: 27 June 2012
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	2012-06-27T19:56:23Z
attribute	NC_GLOBAL	date_modified	String	2019-02-22T20:59:04Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.3668.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/3668
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, condition, data, dataset, dmo, erddap, growth, growth_rate, growth_rate_se, management, metal, oceanography, office, p_cu_prime, p_fe_prime, p_mn_prime, p_zn_prime, preliminary, prime, rate, sample
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/3668/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/3668
attribute	NC_GLOBAL	param_mapping	String	{'3668': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/3668/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	J. Craig Venter Institute
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	JCVI
attribute	NC_GLOBAL	people_0_person_name	String	Andrew E Allen
attribute	NC_GLOBAL	people_0_person_nid	String	51525
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	Rutgers University
attribute	NC_GLOBAL	people_1_person_name	String	Adam Kustka
attribute	NC_GLOBAL	people_1_person_nid	String	51526
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	Shannon Rauch
attribute	NC_GLOBAL	people_2_person_nid	String	51498
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	Pennate Diatom Genomics
attribute	NC_GLOBAL	projects_0_acronym	String	Pennate Diatom Genomics
attribute	NC_GLOBAL	projects_0_description	String	Abstract: Iron (Fe) availability plays an increasingly well known role regulating the fate of upwelled nitrate and determining the size structure and community composition of phytoplankton assemblages in the ocean. All Fe enrichment experiments conducted to date have reported increases in the biomass and photosynthetic capacity of diatoms. Mounting evidence from field experiments, detailed physiological investigation, and genomic sequence data suggest fundamental differences in Fe bioavailability and uptake mechanisms, storage capacity, and stress recovery between pennate and centric diatoms. Pennate diatoms often dominate the phytoplankton assemblage after mesoscale Fe addition experiments because, in part, they are able to maintain cell viability during long periods of chronic Fe stress. The underlying molecular bases for these adaptations are virtually unknown. Preliminary primary metabolite data of Fe-limited P. tricornutum suggest that metabolic reconfigurations are necessary to meet increased demand for Fe-stress metabolites such as those involved in defense from reactive oxygen species (ROS) and intracellular metal chelation. Cellular nitrogen (N) status, and the accumulation of glutamate in particular, appears likely to play a primary role in recovery from Fe stress. This project capitalizes on the extremely well annotated Phaeodactylum tricornutum genome sequence to characterize global patterns of gene expression in response to shifts into and out of Fe and N stress and over the course of the diel cycle. The primary goal is to determine the molecular and physiological processes that constrain and define different phases and levels of Fe-stress acclimation. Oceanic physiological regimes have recently been defined according to different combinations of Fe and N availability and physiological indicators of the resident phytoplankton. This research will provide molecular-level insights into defense, acclimation, and regulatory mechanisms and pathways that govern survival strategies in situations of oceanographically-relevant stress and thus are of major ecological and biogeochemical consequence. Preliminary EST and partial genome microarray data, for example, indicate that chaperones and proteases play a significant role in monitoring cellular health and balancing the difference between investment in defense or activation of programmed cell death (PCD). The proposed research will provide insights into the regulation of this fascinating and delicate balance. Such basic cellular processes play an important biogeochemical role in controlling bloom dynamics and regulating particle flux. Analysis of global gene expression will be compared with state of the art monitoring of intracellular metal levels and primary metabolite profiles using ICP-MS and gas chromatograph-mass spectroscopy (GC-MS) to determine the factors that determine cell survivability. The combination of global gene expression profiling and analysis of intracellular metal and metabolite pools will supply, for the first time, a holistic picture of the global cellular response of a marine pennate diatom to Fe-stress. P. tricornutum transcriptome profiles resulting from exposure to Fe - hydroxamate siderophores and heme-bound Fe (two classes of Fe binding ligands that are believed to comprise two major components of Fe in seawater) will be evaluated to understand the network of genes involved in recognizing and assimilating these compounds. An advanced reverse-genetics system for manipulating levels of gene expression in P. tricornutum will be used to evaluate the specific role of particular genes and pathways in facilitating Fe stress acclimation.  Broader Impacts: This research integrates important current themes in biogeochemistry, microbial ecology, marine sciences, and genome biology and will provide insight into factors that control the distribution and nutrient biogeochemistry of diatoms. By partnering with Affymetrix, through their Microbiology Program, a diatom microarray resource will be made available for the first time for open purchase and use. As part of the proposed research, a high school teacher from one of the local school systems with large underrepresented student populations will be recruited to work on a related topic. Upon completion of his/her paid internship, the teacher will design a classroom activity for use the following school year. As a further point of dissemination, the activity will be incorporated into a curriculum installment focused on marine and phytoplankton genomics for an existing mobile laboratory program called DISCOVER GENOMICS!, which interacts with middle school students in the Washington, D.C. Metropolitan area.
attribute	NC_GLOBAL	projects_0_end_date	String	2011-08
attribute	NC_GLOBAL	projects_0_name	String	Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery
attribute	NC_GLOBAL	projects_0_project_nid	String	2217
attribute	NC_GLOBAL	projects_0_start_date	String	2007-09
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	subsetVariables	String	p_fe_prime
attribute	NC_GLOBAL	summary	String	Results from metal limitation experiments (Cu, Zn, Fe, Mn) conducted in the diatom T. pseudonana carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011
attribute	NC_GLOBAL	title	String	[T_pseudonana_growth] - Results from metal limitation experiments (Cu, Zn, Fe, Mn) conducted in the diatom T. pseudonana carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011 (Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	sample		String
attribute	sample	bcodmo_name	String	sample
attribute	sample	description	String	Vial sample numbers (unique ID's).
attribute	sample	long_name	String	Sample
attribute	sample	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	sample	units	String	dimensionless
variable	metal		String
attribute	metal	bcodmo_name	String	unknown
attribute	metal	description	String	Metal of interest.
attribute	metal	long_name	String	Metal
attribute	metal	units	String	dimensionless
variable	condition		String
attribute	condition	bcodmo_name	String	unknown
attribute	condition	description	String	Condition of the metal of interest under which the experiment was carried out.
attribute	condition	long_name	String	Condition
attribute	condition	units	String	dimensionless
variable	growth_rate		float
attribute	growth_rate	_FillValue	float	NaN
attribute	growth_rate	actual_range	float	0.89, 1.92
attribute	growth_rate	bcodmo_name	String	unknown
attribute	growth_rate	description	String	Cell specific growth rate (per day), calculated as the slope of the linear regression between ln (cell density) versus time.
attribute	growth_rate	long_name	String	Growth Rate
attribute	growth_rate	units	String	ln(cell density)/day
variable	growth_rate_se		float
attribute	growth_rate_se	_FillValue	float	NaN
attribute	growth_rate_se	actual_range	float	0.07, 0.1
attribute	growth_rate_se	bcodmo_name	String	unknown
attribute	growth_rate_se	description	String	Standard error of growth_rate.
attribute	growth_rate_se	long_name	String	Growth Rate Se
attribute	growth_rate_se	units	String	dimensionless
variable	p_fe_prime		float
attribute	p_fe_prime	_FillValue	float	NaN
attribute	p_fe_prime	actual_range	float	10.92, 10.92
attribute	p_fe_prime	bcodmo_name	String	unknown
attribute	p_fe_prime	description	String	The negative log of fe_prime concentration (which is the summed concentration of all Fe species not complexed to EDTA). The additional effect of photochemistry of FeEDTA complexes on calculating fe_prime_log was considered. Originally notated as pFe'.
attribute	p_fe_prime	long_name	String	P Fe Prime
attribute	p_fe_prime	units	String	dimensionless
variable	p_cu_prime		float
attribute	p_cu_prime	_FillValue	float	NaN
attribute	p_cu_prime	actual_range	float	12.62, 15.14
attribute	p_cu_prime	bcodmo_name	String	unknown
attribute	p_cu_prime	description	String	The negative log of Cu prime concentration (which is the summed concentration of all Cu species not complexed to either EDTA or TETA). Originally notated as pCu'.
attribute	p_cu_prime	long_name	String	P Cu Prime
attribute	p_cu_prime	units	String	dimensionless
variable	p_mn_prime		float
attribute	p_mn_prime	_FillValue	float	NaN
attribute	p_mn_prime	actual_range	float	8.01, 9.39
attribute	p_mn_prime	bcodmo_name	String	unknown
attribute	p_mn_prime	description	String	The negative log of the Mn prime concentration (which is the summed concentration of all Mn species not complexed to EDTA). Originally notated as pMn'.
attribute	p_mn_prime	long_name	String	P Mn Prime
attribute	p_mn_prime	units	String	dimensionless
variable	p_zn_prime		float
attribute	p_zn_prime	_FillValue	float	NaN
attribute	p_zn_prime	actual_range	float	10.92, 11.82
attribute	p_zn_prime	bcodmo_name	String	unknown
attribute	p_zn_prime	description	String	The negative log of the Zn prime concentration (which is the summed concentration of all Zn species not complexed to EDTA). Originally notated as pZn'.
attribute	p_zn_prime	long_name	String	P Zn Prime
attribute	p_zn_prime	units	String	dimensionless

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.