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Title Sum-
Institution Dataset ID
   set  data   graph     files  public 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
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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 (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 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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2012-06-27T19:56:23Z
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 (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/3668 (external link)
attribute NC_GLOBAL param_mapping String {'3668': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/3668/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:
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 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 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/ (external link)
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.

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