Accessing BCO-DMO data
Brought to you by BCO-DMO
|
|
BCO-DMO ERDDAP
Accessing BCO-DMO data |
log in
Brought to you by BCO-DMO |
| Dataset Title: | [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) 
|
| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_3667) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
| Make a graph
|
Attributes {
s {
species {
String bcodmo_name "species";
String description "Name of the diatom species.";
String long_name "Species";
String units "dimensionless";
}
exp_id {
String bcodmo_name "exp_id";
String description "Identifier for the experiment; originally named 'cluster'.";
String long_name "Exp Id";
String units "dimensionless";
}
fe_prime {
Int16 _FillValue 32767;
Int16 actual_range 27, 3240;
String bcodmo_name "unknown";
String description "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.";
String long_name "Fe Prime";
String units "pMol";
}
growth_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.47, 1.64;
String bcodmo_name "unknown";
String description "Cell specific growth rate (per day), calculated as the slope of the linear regression between ln (cell density) versus time. Originally named 'mu'.";
String long_name "Growth Rate";
String units "ln(cell density)/day";
}
growth_rate_se {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 0.05;
String bcodmo_name "unknown";
String description "Standard error of growth_rate.";
String long_name "Growth Rate Se";
String units "dimensionless";
}
Fv_to_Fm {
Float32 _FillValue NaN;
Float32 actual_range 0.362, 0.692;
String bcodmo_name "unknown";
String description "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.";
String long_name "Fv To Fm";
String units "dimensionless";
}
Fv_to_Fm_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.017, 0.065;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of Fv_to_Fm.";
String long_name "Fv To Fm Sd";
String units "dimensionless";
}
pH {
Float32 _FillValue NaN;
Float32 actual_range 7.8, 8.19;
String bcodmo_name "pH";
Float64 colorBarMaximum 9.0;
Float64 colorBarMinimum 7.0;
String description "pH of buffer solution.";
String long_name "Sea Water Ph Reported On Total Scale";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "pH scale";
}
pH_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.05, 0.14;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of the pH.";
String long_name "P H SD";
String units "dimensionless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"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).";
String awards_0_award_nid "54979";
String awards_0_award_number "OCE-0727997";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0727997";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"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";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2012-06-27T18:50:36Z";
String date_modified "2019-02-22T20:51:54Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.3667.1";
String history
"2024-11-23T17:32:25Z (local files)
2024-11-23T17:32:25Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_3667.html";
String infoUrl "https://www.bco-dmo.org/dataset/3667";
String institution "BCO-DMO";
String keywords "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";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/3667/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/3667";
String param_mapping "{'3667': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3667/parameters";
String people_0_affiliation "J. Craig Venter Institute";
String people_0_affiliation_acronym "JCVI";
String people_0_person_name "Andrew E Allen";
String people_0_person_nid "51525";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Rutgers University";
String people_1_person_name "Adam Kustka";
String people_1_person_nid "51526";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Shannon Rauch";
String people_2_person_nid "51498";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Pennate Diatom Genomics";
String projects_0_acronym "Pennate Diatom Genomics";
String projects_0_description
"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.";
String projects_0_end_date "2011-08";
String projects_0_name "Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery";
String projects_0_project_nid "2217";
String projects_0_start_date "2007-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "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).";
String title "[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)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.