http://lod.bco-dmo.org/id/dataset/3784
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
2012-11-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Links to published DMSP-dependent protein structures for the apoenzyme DmdA from Pelagibacter ubique at NCBI's MMDB (En-Gen DMSP Cycling project)
2012-11-19
publication
2012-11-19
revision
BCO-DMO Linked Data URI
2012-11-19
creation
http://lod.bco-dmo.org/id/dataset/3784
Mary Ann Moran
University of Georgia
principalInvestigator
Ronald P. Kiene
Dauphin Island Sea Lab
principalInvestigator
William Whitman
University of Georgia
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: Moran, M., Whitman, W., Kiene, R. P. (2012) Links to published DMSP-dependent protein structures for the apoenzyme DmdA from Pelagibacter ubique at NCBI's MMDB (En-Gen DMSP Cycling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 19 Nov 2012) Version Date 2012-11-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3784 [access date]
Links to published DMSP-dependent protein structures at NCBI's MMDB. Dataset Description: <p>Links are provided to published protein structures for the apoenzyme DmdA from <em>Pelagibacter ubique</em>, as well as for DmdA co-crystals soaked with substrate DMSP or the cofactor tetrahydrofolate (THF) accessible via NCBI's Molecular Modeling Database (MMDB).</p>
<p><strong>Experimental design, methods, and results are further described in:</strong><br />
<strong>D. J. Schuller</strong>, C. R. Reisch, M. A. Moran, W. B. Whitman, and W. N. Lanzilotta (2012). Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelegabacter ubique. Protein Science, vol. 21, p. 289. doi: <a href="http://dx.doi.org/10.1002/pro.2015" target="_blank">10.1002/pro.2015</a></p> Methods and Sampling: <p>See Schuller et al. 2012 for detailed methods, which are paraphrased below:<br />
"Expression and isolation of the dimethylsulfoniopropionate-dependent demethylase (DmdA) from recombinant E. coli that expressed the <em>P. ubique</em> DmdA (SAR11_0246) gene was performed as previously described in Reisch et al. (2008). Crystal screening of DmdA was performed in an anaerobic chamber consisting of an atmosphere of 95% nitrogen and 5% hydrogen using the microbatch diffusion technique and an IMPAX I-5 (Douglas Instruments, East Garston, United Kingdom) crystallization robot.</p>
<p>In addition to the native crystals, data was also collected on crystals that had been treated with either the substrate (2 mM DMSP) or the cofactor, tetrahydrofolate (2 mM THF). In both cases a solution of mother liquor was prepared, under anaerobic conditions,containing either DMSP or THF.</p>
<p>All data sets were collected at the Advanced Photon SER-CAT on beamline 22-ID (<a href="http://www.ser.aps.anl.gov/" target="_blank">http://www.ser.aps.anl.gov/</a>). Several programs from the CCP4 program suite (<a href="http://www.ccp4.ac.uk/" target="_blank">CCP4 website</a>) were employed during structure determination and refinement. Various molecular replacement attempts were made using the program PHASER."</p>
<p><strong>References:</strong><br />
Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB (2011). Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473:208–211.<strong> </strong>doi:<a href="http://dx.doi.org/10.1038/nature10078" target="_blank">10.1038/nature10078</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0724017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0724017
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Ronald P. Kiene
Dauphin Island Sea Lab
pointOfContact
William Whitman
University of Georgia
706-542-4219
Depmartment of Microbiogy 541 Biological Sciences
Athens
GA
30602
USA
whitman@uga.edu
pointOfContact
asNeeded
Dataset Version: 19 Nov 2012
Unknown
protein_name
taxon
strain
PDB_ID
MMDB_ID
theme
None, User defined
No BCO-DMO term
taxon
featureType
BCO-DMO Standard Parameters
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.
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
https://osprey.bco-dmo.org/project/2244
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
<p>The recent discovery of key genes that mediate competing pathways at a critical juncture in the marine sulfur cycle has allowed biogeochemists to make rapid advances in understanding where and when sulfur transformations occur in the ocean, and most importantly, what factors regulate them. This project describes an environmental functional genomics project that will rapidly increase our knowledge of the role that bacterioplankton play in dimethylsulfoniopropionate (DMSP) cycling in ocean surface waters, focusing particularly on biological controls of volatile sulfur exchange across the ocean/atmosphere boundary.</p>
<p>The investigators have asked three critical hypotheses to explain the regulation of bacterial DMSP degradation: that involve investigations on the energy constraints of DMSP cycling, the role that DMSP concentration in the oceans plays, and the sulfur requirements for bacterial growth. These research areas serve as the focus for hypothesis-driven laboratory and field studies using functional genomics approaches that will track patterns in gene expression in relation to sulfur metabolism. The hypotheses will be tested with:<br />
1) chemostat systems with a model marine bacterium Silicibacter pomeroyi;<br />
2) microcosm experiments with Gulf of Mexico seawater; and<br />
3) field studies at various sites in the Gulf of Mexico. Marine bacterioplankton play a key role in regulating the flux of DMSP-derived sulfur to the atmosphere, a process of great importance for global climate regulation and marine productivity.</p>
<p>The investigators will also be involved in graduate and undergraduate student education, and two post-doctoral associates will be trained to address multidisciplinary challenges in environmental microbiology. High school biology students in Athens, GA will participate in marine microbial biology research that includes bacterial diversity and discovery studies in coastal Georgia, follow-up training in molecular tools and bioinformatics in their own classroom, and summer internships at the University of Georgia and Dauphin Island Sea Laboratory.</p>
<p>(The description above is from the NSF Award Abstract).</p>
En-Gen DMSP Cycling
largerWorkCitation
project
eng; USA
oceans
2012-11-19
Sapelo Island, GA, USA, 31.4° N Lat, 81.3° W Lon / Dauphin Island, AL, USA, 30.3 ° N Lat, 88.1° W Lon
0
BCO-DMO catalogue of parameters from Links to published DMSP-dependent protein structures for the apoenzyme DmdA from Pelagibacter ubique at NCBI's MMDB (En-Gen DMSP Cycling 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/30841.rdf
Name: protein_name
Units: text
Description: <p>Name/description of the protein structure.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30842.rdf
Name: taxon
Units: text
Description: <p>Scientific name of the organism of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30843.rdf
Name: strain
Units: text
Description: <p>Name of the bacterial strain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30844.rdf
Name: PDB_ID
Units: unitless
Description: <p>Protein structure ID number at the Protein Data Bank (<a href="http://www.rcsb.org/pdb/home/home.do" target="_blank">http://www.rcsb.org/pdb/home/home.do</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/30845.rdf
Name: MMDB_ID
Units: unitless
Description: <p>Protein structure ID number at NCBI's Molecular Modeling Database (MMDB).</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
542
https://datadocs.bco-dmo.org/file/JEE1n53cKg9J2y/DMSP_dependent_proteins.csv
DMSP_dependent_proteins.csv
Primary data file for dataset ID 3784
download
https://osprey.bco-dmo.org/dataset/3784/data/download
download
onLine
dataset
<p>See Schuller et al. 2012 for detailed methods, which are paraphrased below:<br />
"Expression and isolation of the dimethylsulfoniopropionate-dependent demethylase (DmdA) from recombinant E. coli that expressed the <em>P. ubique</em> DmdA (SAR11_0246) gene was performed as previously described in Reisch et al. (2008). Crystal screening of DmdA was performed in an anaerobic chamber consisting of an atmosphere of 95% nitrogen and 5% hydrogen using the microbatch diffusion technique and an IMPAX I-5 (Douglas Instruments, East Garston, United Kingdom) crystallization robot.</p>
<p>In addition to the native crystals, data was also collected on crystals that had been treated with either the substrate (2 mM DMSP) or the cofactor, tetrahydrofolate (2 mM THF). In both cases a solution of mother liquor was prepared, under anaerobic conditions,containing either DMSP or THF.</p>
<p>All data sets were collected at the Advanced Photon SER-CAT on beamline 22-ID (<a href="http://www.ser.aps.anl.gov/" target="_blank">http://www.ser.aps.anl.gov/</a>). Several programs from the CCP4 program suite (<a href="http://www.ccp4.ac.uk/" target="_blank">CCP4 website</a>) were employed during structure determination and refinement. Various molecular replacement attempts were made using the program PHASER."</p>
<p><strong>References:</strong><br />
Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB (2011). Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473:208–211.<strong> </strong>doi:<a href="http://dx.doi.org/10.1038/nature10078" target="_blank">10.1038/nature10078</a></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