http://lod.bco-dmo.org/id/dataset/516730
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
2014-06-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental results: Fe limited diatoms were supplied with excess 57Fe and the new Fe was tracked to better understand storage mechanisms; conducted in the Kustka lab at Rutgers
2014-06-13
publication
2014-06-13
revision
BCO-DMO Linked Data URI
2014-06-13
creation
http://lod.bco-dmo.org/id/dataset/516730
Adam Kustka
Rutgers University
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: Kustka, A. (2014) Experimental results: Fe limited diatoms were supplied with excess 57Fe and the new Fe was tracked to better understand storage mechanisms; conducted in the Kustka lab at Rutgers. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 13 June 2014) Version Date 2014-06-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/516730 [access date]
Fe limited diatoms were supplied with excess 57Fe and the new Fe was tracked to better understand storage mechanisms. Dataset Description: <p><strong>Status (June 2014): Data and metadata have been contributed to BCO-DMO. Data are restricted until April 2015.</strong> Manuscript submission is expected during the fall 2014.</p>
<p>Data contributed include 3 Excel files of ion intensities of 12C, 28Si, 31P, 56Fe, 40Ca and 57Fe within each region of interest as well as the Mathematica script written by A. Kustka used to conduct the Monte Carlo permutation.</p> Methods and Sampling: <p>Experiments were conducted to probe the intracellular iron (Fe) distribution in <em>Thalassiosira pseudonana</em>. These experiments can be summarized as follows:</p>
<p>Three cells of <em>T. pseudonana</em> were analyzed for relative elemental contents at nanometer scale resolution using NanoSIMS mass spectrometry. These diatoms were first grown under low Fe reflecting natural abundance iron isotopic ratios and then spiked with excessive concentrations of Fe heavily enriched in 57Fe, in order to track the fate of newly incorporated 57Fe relative to pre-existing pools of 56Fe. The spatial distribution of this newly incorporated iron was evaluated using Geary's C statistic of spatial correlation, and significant deviations from random were established by a Monte Carlo permutation experiment.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0727889 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0727889
onGoing
Adam Kustka
Rutgers University
973-353-5509
Department of Earth & Environmental Sciences 101 Warren St., Smith Hall Room 135
Newark
NJ
07102
United States
kustka@andromeda.rutgers.edu
pointOfContact
asNeeded
Dataset Version: 13 June 2014
Unknown
diatom
ROI_num
C12
Si28
P31
Fe56
Ca40
Fe57
ROI_area
ROI_diam
ROI_X
ROI_Y
ROI_XSTG
ROI_YSTG
NanoSIMS mass spectrometry
theme
None, User defined
individual
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
lab_Kustka
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.
Iron storage in diatoms and N2 fixing cyanobacteria: mechanisms, regulation and biogeochemical significance
https://osprey.bco-dmo.org/project/505450
Iron storage in diatoms and N2 fixing cyanobacteria: mechanisms, regulation and biogeochemical significance
<p><em>From NSF Award Abstract:</em><br />
Most studies on the Fe physiology of phytoplankton have focused on the induction of high affinity uptake pathways or the rearrangement of photosynthetic machinery to decrease cellular demand. By contrast, little attention has been given to the mechanisms of intracellular Fe storage. Proper handling and storage of Fe on timescales of generations can ensure adequate Fe nutrition in episodic environments. Furthermore short term storage of Fe is essential to "buffer" the intracellular redox-labile Fe concentration and prevent Fenton production of reactive oxygen species. Even though sufficient Fe can be stored for at least 4 cell divisions, much more than in the cases of P, N and (especially) C, our understanding of Fe storage lags far behind what is known for those elements. Since the biogeochemical cycles of Fe and C, N and P are linked via the Fe quotas of phytoplankton, it is critical that we understand the environmental and physiological controls of Fe storage. Fe can be stored in proteins such as those of the ferritin superfamily or sequestered into intracellular vacuoles. Some marine diatoms, such as Phaeodactylum tricornutum have ferritin genes. However ferritin has not been detected bioinformatically or by evolutionary PCR methods in other diatoms such as Thalassiosira pseudonana. The investigators have measured the Fe-dependent regulation of transcript and protein abundance of NRAMP, a protein likely involved in vacuolar Fe metabolism, an alternative method of Fe storage found in Arabidopsis thaliana and yeast. It is proposed that the regulation and biogeochemical significance of ferritin and vacuole-mediated Fe storage may differ for different diatom groups. The filamentous N2 fixing cyanobacterium, Trichodesmium erythraeum, possesses three ferritin/ bacterioferritin genes, suggesting specialization of these proteins. Both Fe storage and Fe buffering are likely critical functions in Trichodesmium, yet nothing is known of either aspect of Fe homeostasis. This project aims to elucidate intracellular cycling and storage of Fe in marine diatoms and N2 fixing cyanobacteria and the relationship between Fe storage and cell quota. Specific objectives are to:</p>
<p>1) Determine the factors that regulate ferritin transcription, apo-protein synthesis and ferritin iron content in P. tricornutum lab cultures. The underlying hypothesis is that ferritins serve as Fe storage reservoirs over long generational time scales. Because they are targeted to chloroplasts, ferritins may also buffer Fe to prevent oxidative stress during degradation and synthesis of photosynthetic components.</p>
<p>2) Determine the role of storage vacuoles and NRAMP in Fe storage and mobilization in lab cultures of T. pseudonana, based on the hypothesis that vacuoles store Fe and NRAMP helps mobilize Fe in T. pseudonana, T. oceanica, and possibly other centric diatoms.</p>
<p>3) Evaluate the relationships between Fe storage proteins and cellular quota in culture and field populations of Trichodesmium; it is proposed that one or more of these proteins serve as Fe reservoir over long generational, time scales, in which case they may indicate nutritional Fe status. It is hypothesized that one or more of these proteins are co-localized in cells specifically responsible for N2 fixation in Trichodesmium colonies as a mechanism to buffer the Fe released through the diel degradation of the Fe-rich nitrogenase proteins.</p>
<p>The above objectives will be addressed using genetic, immunological, and synchrotron-based approaches applied to laboratory cultures of P. tricornutum, T. pseudonana,and Trichodesmium. Trichodesmium trichomes collected from the Sargasso Sea will also be analyzed to determine the biogeochemical importance of (bacterio)ferritins as a storage mechanism in this group.</p>
Mechanisms of Fe storage in phytoplankton
largerWorkCitation
project
eng; USA
oceans
Newark, NJ
2014-06-13
0
BCO-DMO catalogue of parameters from Experimental results: Fe limited diatoms were supplied with excess 57Fe and the new Fe was tracked to better understand storage mechanisms; conducted in the Kustka lab at Rutgers
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/516929.rdf
Name: diatom
Units: integer
Description: <p>Number identifying the diatom studied.</p>
http://lod.bco-dmo.org/id/dataset-parameter/516930.rdf
Name: ROI_num
Units: integer
Description: <p>Identification number for the region of interest (ROI).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516931.rdf
Name: C12
Units: dimensionless
Description: <p>Ion intensity of Carbon-12 (12C).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516932.rdf
Name: Si28
Units: dimensionless
Description: <p>Ion intensity of Silicon-28 (28Si).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516933.rdf
Name: P31
Units: dimensionless
Description: <p>Ion intensity of Phosphorus-31 (31P).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516934.rdf
Name: Fe56
Units: dimensionless
Description: <p>Ion intensity of Iron-56 (56Fe).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516935.rdf
Name: Ca40
Units: dimensionless
Description: <p>Ion intensity of Calcium-40 (40Ca).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516936.rdf
Name: Fe57
Units: dimensionless
Description: <p>Ion intensity of Iron-57 (57Fe).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516937.rdf
Name: ROI_area
Units: microns^2
Description: <p>Area of the region of interest (ROI).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516938.rdf
Name: ROI_diam
Units: microns
Description: <p>Diamter of the region of interest (ROI).</p>
http://lod.bco-dmo.org/id/dataset-parameter/516939.rdf
Name: ROI_X
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/516940.rdf
Name: ROI_Y
Units: ?
Description: <p>?</p>
http://lod.bco-dmo.org/id/dataset-parameter/516941.rdf
Name: ROI_XSTG
Units: dimensionless
Description: <p>X stage coordinate on the nanoSIMS microscope.</p>
http://lod.bco-dmo.org/id/dataset-parameter/516942.rdf
Name: ROI_YSTG
Units: dimensionless
Description: <p>Y stage coordinate on the nanoSIMS microscope.</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
https://osprey.bco-dmo.org/dataset/516730/data/download
download
onLine
dataset
<p>Experiments were conducted to probe the intracellular iron (Fe) distribution in <em>Thalassiosira pseudonana</em>. These experiments can be summarized as follows:</p>
<p>Three cells of <em>T. pseudonana</em> were analyzed for relative elemental contents at nanometer scale resolution using NanoSIMS mass spectrometry. These diatoms were first grown under low Fe reflecting natural abundance iron isotopic ratios and then spiked with excessive concentrations of Fe heavily enriched in 57Fe, in order to track the fate of newly incorporated 57Fe relative to pre-existing pools of 56Fe. The spatial distribution of this newly incorporated iron was evaluated using Geary's C statistic of spatial correlation, and significant deviations from random were established by a Monte Carlo permutation experiment.</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
NanoSIMS mass spectrometry
NanoSIMS mass spectrometry
PI Supplied Instrument Name: NanoSIMS mass spectrometry PI Supplied Instrument Description:Three cells of T. pseudonana were analyzed for relative elemental contents at nanometer scale resolution using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS). Secondary Ion Mass Spectrometry (SIMS) is a surface analysis technique that provides information about the lateral distribution of any element and its isotopes, and quantitative information about the isotopic composition of a sample. NanoSIMS allows for elemental and isotopic analysis down to the 50-nanomenter scale. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Deployment: lab_Kustka
lab_Kustka
Rutgers_Newark
laboratory
lab_Kustka
Adam Kustka
Rutgers University
Rutgers_Newark
laboratory