http://lod.bco-dmo.org/id/dataset/3225
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
2010-06-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Gene expression data from Trichodesmium culture experiments on phosphorus (P) uptake and dissolved organic phosphorus (DOP) hydrolysis, 2007-2008 (C-MORE project)
2009-09-14
publication
2009-09-14
revision
BCO-DMO Linked Data URI
2009-09-14
creation
http://lod.bco-dmo.org/id/dataset/3225
Sonya T. Dyhrman
Woods Hole Oceanographic Institution
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: Dyhrman, S. T. (2009) Gene expression data from Trichodesmium culture experiments on phosphorus (P) uptake and dissolved organic phosphorus (DOP) hydrolysis, 2007-2008 (C-MORE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 14 September 2009) Version Date 2009-09-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3225 [access date]
Gene expression data Dataset Description: <p>C-MORE Gene Expression<br />
Gene expression data from Trichodesmium culture experiments<br />
<br />
&nbsp;</p> Methods and Sampling: <h4>Reference:</h4>
<p>Orchard et al. (2009) <br />
Elizabeth D. Orchard, Eric A. Webb, Sonya T. Dyhrman. 2009. &quot;Molecular analysis of the phosphorus starvation response in Trichodesmium spp.&quot;. Environmental Microbiology 11:2400-2411. <br />
DOI: 10.1111/j.1462-2920.2009.01968.x <br />
US: http://dx.doi.org/10.1111/j.1462-2920.2009.01968.x</p>
<p>This dataset includes some acronyms, defined as follows:</p>
<pre>
Pphosphorus
phoAalkaline phosphatase
sphXsphX gene
pstSpstS gene
nifHnitrogenase iron protein
APAalkaline phosphatase activity
</pre>
<p>&nbsp;</p>
<p>Experiments were conducted to study the expression of genes involved in Phosphorus (P) uptake and (Dissolved Organic Phosphorus) DOP hydrolysis. There were two different types of experimental design: (i) 'transfer experiment' wherein exponentially growing cells were transferred to replete (+P) and no P (-P) media, and (ii) 're-feed experiment' in which cells were starved for P and then P was added back in. Each of these experiments was replicated with similar results.</p>
onGoing
Sonya T. Dyhrman
Woods Hole Oceanographic Institution
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
asNeeded
Dataset Version: 14 September 2009
Unknown
gene_name
experiment_type
hours_from_start
gene_expression_P_limited
stderr_gene_expression_P_limited
gene_expression_P_replete
stderr_gene_expression_P_replete
statistically_different
theme
None, User defined
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
lab_WHOI_sd_C-MORE
service
Deployment Activity
Sonya Dyhrman's Lab, Redfield Bldg, Woods Hole MA
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.
Center for Microbial Oceanography: Research and Education
http://cmore.soest.hawaii.edu/
Center for Microbial Oceanography: Research and Education
<h3>Project summary</h3>
<p>The <strong>Center for Microbial Oceanography: Research and Education</strong> (C-MORE) is a recently established (August 2006; NSF award: EF-0424599) NSF-sponsored Science and Technology Center designed to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements and energy in the marine environment. Stated holistically, C-MORE's primary mission is: <em>Linking Genomes to Biomes</em>.</p>
<p>We believe that the time is right to address several major, long-standing questions in microbial oceanography. Recent advances in the application of molecular techniques have provided an unprecedented view of the structure, diversity and possible function of sea microbes. By combining these and other novel approaches with more well-established techniques in microbiology, oceanography and ecology, it may be possible to develop a meaningful predictive understanding of the ocean with respect to energy transduction, carbon sequestration, bioelement cycling and the probable response of marine ecosystems to global environmental variability and climate change. The strength of C-MORE resides in the synergy created by bringing together experts who traditionally have not worked together and this, in turn, will facilitate the creation and dissemination of new knowledge on the role of marine microbes in global habitability.</p>
<p>The new Center will design and conduct novel research, broker partnerships, increase diversity of human resources, implement education and outreach programs, and utilize comprehensive information about microbial life in the sea. The Center will bring together teams of scientists, educators and community members who otherwise do not have an opportunity to communicate, collaborate or design creative solutions to long-term ecosystem scale problems. The Center's research will be organized around four interconnected themes:</p>
<ul>
<li>(Theme I) microbial biodiversity,</li>
<li>(Theme II) metabolism and C-N-P-energy flow,</li>
<li>(Theme III) remote and continuous sensing and links to climate variability, and</li>
<li>(Theme IV) ecosystem modeling, simulation and prediction.</li>
</ul>
<p> Each theme will have a leader to help coordinate the research programs and to facilitate interactions among the other related themes. The education programs will focus on pre-college curriculum enhancements, in service teacher training and formal undergraduate/graduate and post-doctoral programs to prepare the next generation of microbial oceanographers. The Center will establish and maintain creative outreach programs to help diffuse the new knowledge gained into society at large including policymakers. The Center's activities will be dispersed among five partner institutions:</p>
<ul>
<li>Massachusetts Institute of Technology,</li>
<li>Woods Hole Oceanographic Institution,</li>
<li>Monterey Bay Aquarium Research Institute,</li>
<li>University of California at Santa Cruz and</li>
<li>Oregon State University</li>
</ul>
<p>and will be coordinated at the University of Hawaii at Manoa.</p>
<h4>Related Files:</h4>
<p><a href="http://bcodata.whoi.edu/C-MORE/C-MORE_SIP_ver_09-01-2008.pdf">Strategic plan (PDF file)</a></p>
C-MORE
largerWorkCitation
project
eng; USA
oceans
Sonya Dyhrman's Lab, Redfield Bldg, Woods Hole MA
2009-09-14
North Pacific Subtropical Gyre (large region around 22 45 N, 158 W)
0
BCO-DMO catalogue of parameters from Gene expression data from Trichodesmium culture experiments on phosphorus (P) uptake and dissolved organic phosphorus (DOP) hydrolysis, 2007-2008 (C-MORE 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
http://lod.bco-dmo.org/id/dataset-parameter/20235.rdf
Name: gene_name
Units: text
Description: <p>gene name</p>
http://lod.bco-dmo.org/id/dataset-parameter/20236.rdf
Name: experiment_type
Units: text
Description: <p>experiment type</p>
http://lod.bco-dmo.org/id/dataset-parameter/20237.rdf
Name: hours_from_start
Units: hours
Description: <p>hours from experiment start</p>
http://lod.bco-dmo.org/id/dataset-parameter/20238.rdf
Name: gene_expression_P_limited
Units: phophorus limited
Description: <p>gene expression ratio relative to time 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/20239.rdf
Name: stderr_gene_expression_P_limited
Units: dimensionless
Description: <p>standard error for the gene_expression_P_limited data</p>
http://lod.bco-dmo.org/id/dataset-parameter/20240.rdf
Name: gene_expression_P_replete
Units: phophorus replete
Description: <p>gene expression ratio relative to time 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/20241.rdf
Name: stderr_gene_expression_P_replete
Units: dimensionless
Description: <p>standard error for the gene_expression_P_replete data</p>
http://lod.bco-dmo.org/id/dataset-parameter/20242.rdf
Name: statistically_different
Units: text
Description: <p>indicates statistical differences between the P_limited and P_replete gene expression data (y or n)</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
1717
https://datadocs.bco-dmo.org/file/ZZZgK19hoKEBJ4/gene_expression.csv
gene_expression.csv
Primary data file for dataset ID 3225
download
https://osprey.bco-dmo.org/dataset/3225/data/download
download
onLine
dataset
<h4>Reference:</h4>
<p>Orchard et al. (2009) <br />
Elizabeth D. Orchard, Eric A. Webb, Sonya T. Dyhrman. 2009. &quot;Molecular analysis of the phosphorus starvation response in Trichodesmium spp.&quot;. Environmental Microbiology 11:2400-2411. <br />
DOI: 10.1111/j.1462-2920.2009.01968.x <br />
US: http://dx.doi.org/10.1111/j.1462-2920.2009.01968.x</p>
<p>This dataset includes some acronyms, defined as follows:</p>
<pre>
Pphosphorus
phoAalkaline phosphatase
sphXsphX gene
pstSpstS gene
nifHnitrogenase iron protein
APAalkaline phosphatase activity
</pre>
<p>&nbsp;</p>
<p>Experiments were conducted to study the expression of genes involved in Phosphorus (P) uptake and (Dissolved Organic Phosphorus) DOP hydrolysis. There were two different types of experimental design: (i) 'transfer experiment' wherein exponentially growing cells were transferred to replete (+P) and no P (-P) media, and (ii) 're-feed experiment' in which cells were starved for P and then P was added back in. Each of these experiments was replicated with similar results.</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_WHOI_sd_C-MORE
lab_WHOI_sd_C-MORE
WHOI
laboratory
lab_WHOI_sd_C-MORE
Sonya T. Dyhrman
Woods Hole Oceanographic Institution
WHOI
laboratory