http://lod.bco-dmo.org/id/dataset/3667
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2012-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2012-06-27
publication
2012-06-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-02-22
publication
https://doi.org/10.1575/1912/bco-dmo.3667.1
Andrew E. Allen
J. Craig Venter Institute
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Allen, A. (2012) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2012-06-27 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.3667.1 [access date]
Trace metal controlled diel microarray experiments with diatoms. Dataset Description: <p>Ten diel microarray experiments were completed (seven for <em>P. tricornutum</em> encompassing three Fe concentrations, and three for <em>T. pseudonana</em> encompassing two Fe concentrations).</p> Methods and Sampling: <p>The following description is from a final report for an NSF OCE award provided by the dataset contact.</p>
<p>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.</p>
<p>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).</p>
<p>In <em>T. pseudonana</em> 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).</p>
<p>In <em>P. tricornutum</em> 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).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0727997 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0727997
completed
Andrew E. Allen
J. Craig Venter Institute
858-200-1826
4120 Capricorn Lane
La Jolla
CA
92037
USA
aallen@jcvi.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
exp_id
fe_prime
growth_rate
growth_rate_se
Fv_to_Fm
Fv_to_Fm_sd
pH
pH_sd
theme
None, User defined
species scientific name (binomial)
experiment id
No BCO-DMO term
pH
featureType
BCO-DMO Standard Parameters
lab_Kustka_Allen
service
Deployment Activity
Newark, NJ
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery
https://osprey.bco-dmo.org/project/2217
Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery
<p>Abstract:<br />
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 <i>P. tricornutum</i> 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 <i>Phaeodactylum tricornutum</i> 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).</p>
<p>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. <i>P. tricornutum</i> 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 <i>P. tricornutum</i> will be used to evaluate the specific role of particular genes and pathways in facilitating Fe stress acclimation. </p>
<p>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.</p>
Pennate Diatom Genomics
largerWorkCitation
project
eng; USA
oceans
Newark, NJ
2012-06-27
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/28077.rdf
Name: species
Units: dimensionless
Description: <p>Name of the diatom species.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28078.rdf
Name: exp_id
Units: dimensionless
Description: <p>Identifier for the experiment; originally named 'cluster'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28079.rdf
Name: fe_prime
Units: pMol
Description: <p>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.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28080.rdf
Name: growth_rate
Units: ln(cell density)/day
Description: <p>Cell specific growth rate (per day), calculated as the slope of the linear regression between ln (cell density) versus time. Originally named 'mu'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28081.rdf
Name: growth_rate_se
Units: dimensionless
Description: <p>Standard error of growth_rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28082.rdf
Name: Fv_to_Fm
Units: dimensionless
Description: <p>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.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28083.rdf
Name: Fv_to_Fm_sd
Units: dimensionless
Description: <p>Standard deviation of Fv_to_Fm.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28084.rdf
Name: pH
Units: pH scale
Description: <p>pH of buffer solution.</p>
http://lod.bco-dmo.org/id/dataset-parameter/28085.rdf
Name: pH_sd
Units: dimensionless
Description: <p>Standard deviation of the pH.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
593
https://darchive.mblwhoilibrary.org/bitstream/1912/23715/1/dataset-3667_tracemetalmicroarray__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.3667.1
download
onLine
dataset
<p>The following description is from a final report for an NSF OCE award provided by the dataset contact.</p>
<p>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.</p>
<p>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).</p>
<p>In <em>T. pseudonana</em> 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).</p>
<p>In <em>P. tricornutum</em> 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).</p>
Specified by the Principal Investigator(s)
<p>PI-provided parameter names were modified to conform with BCO-DMO conventions.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Deployment: lab_Kustka_Allen
lab_Kustka_Allen
Rutgers_Newark
laboratory
lab_Kustka_Allen
Andrew E. Allen
J. Craig Venter Institute
Rutgers_Newark
laboratory