ERDDAP > info > bcodmo_dataset_3667

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	Results from trace metal controlled diel microarray experiments with diatoms carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011		I   M	background			BCO-DMO	bcodmo_dataset_3667

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	The following description is from a final report for an NSF OCE award provided by the dataset contact. As biomass increases, steady state Fe prime invariably changes; this was minimized to less than 5% under all Fe conditions by making modifications to the Aquil recipe. In addition, excursions in media pH (which also change Fe' prime) were minimized by acclimating cells to pH buffer (EPPS) treated with chelex-100 resin. A maximum of 750 pmol/L Fe prime is assumed because of Fe hydroxide precipitation, but for simplicity, the investigators report the results as Fe prime even at concentrations exceeding this maximum. Steady-state uptake rates for several diatoms continue to increase with increasing total Fe within the region of Fe hydroxide precipitation (Sunda and Huntsman 1995; Mar Chem 50:189). In T. pseudonana experiment E, addition of Fe to remaining low Fe cultures after diel sampling resulted in an increase in growth rate after 24 h, confirming growth rate limitation by Fe. The similar Fv/Fm values under low and high Fe are consistent with the data of Price 2005 (Limnol. Oceanogr. 50:1159). In P. tricornutum experiment C, the pH buffer stock solution was not properly buffered before use in cultures. While these particular experiments will need to be repeated, these samples may be useful for comparing the diatom transcriptomes during holocene and anthropocene conditions, as these pH values are consistent with predicted values for 2100 (Gruber et al. 1996 Global Biogeochemical Cycles).
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 trace metal controlled diel microarray experiments with diatoms. 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	2012-06-27T18:50:36Z
attribute	NC_GLOBAL	date_modified	String	2019-02-22T20:51:54Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.3667.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/3667
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, chemistry, data, dataset, dmo, earth, Earth Science > Oceans > Ocean Chemistry > pH, erddap, exp, exp_id, fe_prime, Fv_to_Fm, Fv_to_Fm_sd, growth, growth_rate, growth_rate_se, management, ocean, oceanography, oceans, office, pH_sd, preliminary, prime, rate, reported, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, species, total, water
attribute	NC_GLOBAL	keywords_vocabulary	String	GCMD Science Keywords
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/3667/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/3667
attribute	NC_GLOBAL	param_mapping	String	{'3667': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/3667/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	summary	String	Results from trace metal controlled diel microarray experiments with diatoms carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011. Ten diel microarray experiments were completed (seven for P. tricornutum encompassing three Fe concentrations, and three for T. pseudonana encompassing two Fe concentrations).
attribute	NC_GLOBAL	title	String	Results from trace metal controlled diel microarray experiments with diatoms carried out in the Kustka and Allen labs at Rutgers in Newark, NJ from 2007-2011
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	Name of the diatom species.
attribute	species	long_name	String	Species
attribute	species	units	String	dimensionless
variable	exp_id		String
attribute	exp_id	bcodmo_name	String	exp_id
attribute	exp_id	description	String	Identifier for the experiment; originally named 'cluster'.
attribute	exp_id	long_name	String	Exp Id
attribute	exp_id	units	String	dimensionless
variable	fe_prime		short
attribute	fe_prime	_FillValue	short	32767
attribute	fe_prime	actual_range	short	27, 3240
attribute	fe_prime	bcodmo_name	String	unknown
attribute	fe_prime	description	String	Fe prime is the sum of all concentrations of Fe not bound to EDTA species. It is calculated according to thermodynamic equilibrium constants and photochemical reduction rate constants for FeEDTA species.
attribute	fe_prime	long_name	String	Fe Prime
attribute	fe_prime	units	String	pMol
variable	growth_rate		float
attribute	growth_rate	_FillValue	float	NaN
attribute	growth_rate	actual_range	float	0.47, 1.64
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. Originally named 'mu'.
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	0.01, 0.05
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	Fv_to_Fm		float
attribute	Fv_to_Fm	_FillValue	float	NaN
attribute	Fv_to_Fm	actual_range	float	0.362, 0.692
attribute	Fv_to_Fm	bcodmo_name	String	unknown
attribute	Fv_to_Fm	description	String	Also referred to as (delta F)/Fm; Fv_to_Fm is the variable to maximum chlorophyll fluorescence, explicitly calculated as [F(knot)-F(maximum)]/F(maximum) and measured using the DCMU method.
attribute	Fv_to_Fm	long_name	String	Fv To Fm
attribute	Fv_to_Fm	units	String	dimensionless
variable	Fv_to_Fm_sd		float
attribute	Fv_to_Fm_sd	_FillValue	float	NaN
attribute	Fv_to_Fm_sd	actual_range	float	0.017, 0.065
attribute	Fv_to_Fm_sd	bcodmo_name	String	unknown
attribute	Fv_to_Fm_sd	colorBarMaximum	double	50.0
attribute	Fv_to_Fm_sd	colorBarMinimum	double	0.0
attribute	Fv_to_Fm_sd	description	String	Standard deviation of Fv_to_Fm.
attribute	Fv_to_Fm_sd	long_name	String	Fv To Fm Sd
attribute	Fv_to_Fm_sd	units	String	dimensionless
variable	pH		float
attribute	pH	_FillValue	float	NaN
attribute	pH	actual_range	float	7.8, 8.19
attribute	pH	bcodmo_name	String	pH
attribute	pH	colorBarMaximum	double	9.0
attribute	pH	colorBarMinimum	double	7.0
attribute	pH	description	String	pH of buffer solution.
attribute	pH	long_name	String	Sea Water Ph Reported On Total Scale
attribute	pH	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/
attribute	pH	units	String	pH scale
variable	pH_sd		float
attribute	pH_sd	_FillValue	float	NaN
attribute	pH_sd	actual_range	float	0.05, 0.14
attribute	pH_sd	bcodmo_name	String	unknown
attribute	pH_sd	colorBarMaximum	double	50.0
attribute	pH_sd	colorBarMinimum	double	0.0
attribute	pH_sd	description	String	Standard deviation of the pH.
attribute	pH_sd	long_name	String	P H SD
attribute	pH_sd	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.