BCO-DMO ERDDAP
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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\nby the dataset contact.\n \nAs biomass increases, steady state Fe prime invariably changes; this was\nminimized to less than 5% under all Fe conditions by making modifications to\nthe Aquil recipe. In addition, excursions in media pH (which also change Fe'\nprime) were minimized by acclimating cells to pH buffer (EPPS) treated with\nchelex-100 resin.\n \nA maximum of 750 pmol/L Fe prime is assumed because of Fe hydroxide\nprecipitation, but for simplicity, the investigators report the results as Fe\nprime even at concentrations exceeding this maximum. Steady-state uptake rates\nfor several diatoms continue to increase with increasing total Fe within the\nregion of Fe hydroxide precipitation (Sunda and Huntsman 1995; Mar Chem\n50:189).\n \nIn T. pseudonana experiment E, addition of Fe to remaining low Fe cultures\nafter diel sampling resulted in an increase in growth rate after 24 h,\nconfirming growth rate limitation by Fe. The similar Fv/Fm values under low\nand high Fe are consistent with the data of Price 2005 (Limnol. Oceanogr.\n50:1159).\n \nIn P. tricornutum experiment C, the pH buffer stock solution was not properly\nbuffered before use in cultures. While these particular experiments will need\nto be repeated, these samples may be useful for comparing the diatom\ntranscriptomes during holocene and anthropocene conditions, as these pH values\nare consistent with predicted values for 2100 (Gruber et al. 1996 Global\nBiogeochemical 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 (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 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. \n PI: Andrew Allen (J. Craig Venter Institue, Inc.) \n Contact: Adam Kustka (Rutgers University) \n 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/ (external link)
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 (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/3667 (external link)
attribute NC_GLOBAL param_mapping String {'3667': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/3667/parameters (external link)
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:\nIron (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).\nThe 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. \nBroader 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 [trace_metal_microarray] - 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 (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 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/ (external link)
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

 
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