http://lod.bco-dmo.org/id/dataset/546152
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
2015-01-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Laboratory results on symbiont type in recovering Porites divaricata corals collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project)
2015-01-29
publication
2015-01-29
revision
BCO-DMO Linked Data URI
2015-01-29
creation
http://lod.bco-dmo.org/id/dataset/546152
Mary Alice Coffroth
State University of New York at Buffalo
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: Coffroth, M. A. (2015) Laboratory results on symbiont type in recovering Porites divaricata corals collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-01-29) Version Date 2015-01-29 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546152 [access date]
symbiont type in recovering Porites divaricata corals Dataset Description: <p>Data on symbiont type in recovering corals (<em>Porites divaracata</em>) by treatment following inoculation with a specific symbiont type following heat-induced bleaching.</p>
<p><strong>Related Reference:</strong></p>
<p>Coffroth MA, Poland DM, Petrou EL, Brazeau DA, Holmberg JC (2010) Environmental Symbiont Acquisition May Not Be the Solution to Warming Seas for Reef-Building Corals. PLoS ONE 5(10): e13258. doi:10.1371/journal.pone.0013258.<a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013258" target="_blank"> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013258</a></p> Methods and Sampling: <p>All cultures were obtained from the BURR Culture Collection and used to inoculate bleached colonies of <em>Porites divaricata</em>.&nbsp;Collections were made in the vicinity of Long Key, FL, oceanside (N24<sup>o</sup> 49.791’ W80<sup>o</sup> 45.743’) and experimentation was performed at the Keys Marine Laboratory, Long Key, FL</p>
<p>Coral colonies were sampled a total of 4 times throughout the experiment. Symbionts present in the tissue samples were characterized based on sequence variation in the symbiont chloroplast 23S rDNA following the protocols of Santos et al. 2003, Mar.Biotech. 5:130-140</p>
<p><strong>Reference:</strong><br />
- Santos SR, Gutiérrez-Rodríguez C, Coffroth MA (2003) Phylogenetic identification of symbiotic dinoflagellates via length heteroplasmy in domain V of chloroplast large subunit (cp23S)-rDNA sequences. Mar Biotech 5: 130-140 for technique to characterize symbionts based on of chloroplast large subunit (cp23S)-rDNA</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0926822 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0926822
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0424996 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0424996
completed
Mary Alice Coffroth
State University of New York at Buffalo
716-645-4871
Department of Geology 126 Cooke Hall
Buffalo
NY
14260
USA
Coffroth@buffalo.edu
pointOfContact
asNeeded
Dataset Version: 2015-01-29
Unknown
lab
lat
lon
genotype
treatment_inoculant
sample_id
date
description
strong_base_pairs
weak_base_pairs
comments
Automated Sequencer
Spectrophotometer
Thermal Cycler
theme
None, User defined
laboratory
latitude
longitude
No BCO-DMO term
treatment
sample identification
date
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Spectrophotometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Coffroth_2010
service
Deployment Activity
State University of New York at Buffalo
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.
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
https://osprey.bco-dmo.org/project/472478
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
<p>PROJECT SUMMARY:<br />
The symbiosis between corals (Cnidaria:Hexacorallia:Scleractinia) and photosynthetic dinoflagellate symbionts (Alveolata: Dinophycea: Symbiodinium) provides the foundation and structure of the coral reef ecosystem, as well as significant contributions to global carbon and biogeochemical cycles. Given the importance of this symbiosis to the coral-algal holobiont and the reef ecosystem, understanding the mechanisms governing the establishment and long term maintenance of this symbiosis is essential. The overall aim of this project is to identify the mechanisms and selective processes that lead to the final assemblage of symbionts harbored by adult hosts. This question will be approached from two perspectives, ecologic and genomic, with the specific aims of determining (1) if different Symbiodinium strains differentially affect fitness of corals as the adult settles into a mature symbiosis (2) if competition among symbionts or environmental conditions contribute to the final host-symbiont pairing and (3) how host/symbiont transcriptomes varying as the symbiont community within a host is winnowed to the final assemblage found in the adult host. Traits that directly affect coral fitness (i.e. growth, survivorship, energy production) will be measured under different environmental conditions over the ontogeny of coral recruits that are experimentally infected with different types of Symbiodinium. Concurrently, high throughput gene expression profiling will be used to follow changes in gene expression between host and symbiont. Together, these data will be used to validate or falsify the hypotheses that the final symbiont assemblage found in the adult host is determined by (a) host selection (b) competition among symbionts and/or (c) environmental condition.</p>
<p>This study pools the expertise of two labs that have focused on these aspects of the symbiosis. The Coffroth lab pioneered the studies on early ontogeny of the symbiosis and symbiont diversity and will continue to take the lead in the ecological studies. The Medina lab is at the forefront in the development and utilization of genomic technology to study transcriptomic changes during the establishment and breakdown of the symbiosis. Furthermore, the Medina lab has the coral microarrays to be used in this study and in 2009 will also have oligo arrays for two Symbiodinium species based on 454 EST data. Although several groups have initial studies of the host transcriptome, none have combined an approach that examines the host and the symbiont in a single experiment. This will be a powerful approach as it will allow the investigators to track complementary changes in gene expression between host and symbiont and relate those to turnover in the symbiont community as the final symbiont complement is established.</p>
<p>The data resulting form the study will bridge an important gap in our understanding of the establishment and maintenance of coral-Symbiodinium symbiosis. Understanding the mechanism(s) regulating the establishment of the symbiosis will broaden our knowledge and help to predict the response of this symbiosis to future climate conditions. As in the past, the genomic tools (arrays, ESTs) will be made readily available to researchers via array distribution at cost, microarray analysis training, or sequence data, providing valuable resources to continue exploring these systems.</p>
<p>In conjunction the Aquarium of Niagara, Coffroth will develop educational and outreach programs to train and disseminate information on coral reefs to local area teachers and the general public. The Medina lab will continue to produce science and environment podcasts in multiple languages (English, Spanish and Hmong) with undergraduate students at UC Merced and will continue to collaborate with the California Academy of Sciences (CAS) in their coral reef outreach efforts. Additionally, this work will result in the training and mentoring of a postdoctoral fellow, at least one graduate student and at least 2 undergraduates. Through this project these students will have the opportunity to participate in research in both a lab and field setting, learning a range of ecological, molecular and algal culturing techniques. The extensive culture collection housed at the University at Buffalo is an important resource that is available to researchers worldwide which the proposed funding will help to maintain. Our EST annotations are publicly available through our EST database (<a href="http://montastraea.psu.edu/SymBioSys/" target="_blank">http://montastraea.psu.edu/SymBioSys/</a>).</p>
SymBioSys
largerWorkCitation
project
eng; USA
biota
oceans
State University of New York at Buffalo
2015-01-29
Florida Keys, Bahamas, Panama, Mexico
0
BCO-DMO catalogue of parameters from Laboratory results on symbiont type in recovering Porites divaricata corals collected from the Florida Keys, Bahamas, Panama, and Mexico during 2010 (SymBioSys 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/546164.rdf
Name: lab
Units: unitless
Description: <p>laboratory identification; for mapping puposes</p>
http://lod.bco-dmo.org/id/dataset-parameter/546165.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude of lab; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/546166.rdf
Name: lon
Units: decimal degrees
Description: <p>londitude of lab; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/546167.rdf
Name: genotype
Units: unitless
Description: <p>23S chloroplast genotype</p>
http://lod.bco-dmo.org/id/dataset-parameter/546168.rdf
Name: treatment_inoculant
Units: unitless
Description: <p>infection treatment of Porites: Symbiodinium types A188; B211; B224 and D206 (letter=clade code; number=base pair size of the particular cp23S-rDNA domain V allele)</p>
http://lod.bco-dmo.org/id/dataset-parameter/546169.rdf
Name: sample_id
Units: unitless
Description: <p>specimen identification: Pd=Porites divaricata</p>
http://lod.bco-dmo.org/id/dataset-parameter/546170.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/546171.rdf
Name: description
Units: unitless
Description: <p>whether sampling was pre- or post-bleaching</p>
http://lod.bco-dmo.org/id/dataset-parameter/546172.rdf
Name: strong_base_pairs
Units: unitless
Description: <p>sequence variation of strong base pairs of symbiont chloroplast 23S rDNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/546173.rdf
Name: weak_base_pairs
Units: unitless
Description: <p>sequence variation of weak base pairs of symbiont chloroplast 23S rDNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/546174.rdf
Name: comments
Units: unitless
Description: <p>comments</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
58679
https://datadocs.bco-dmo.org/file/N77GrVntPW6QM0/symb_type.csv
symb_type.csv
Primary data file for dataset ID 546152
download
https://osprey.bco-dmo.org/dataset/546152/data/download
download
onLine
dataset
<p>All cultures were obtained from the BURR Culture Collection and used to inoculate bleached colonies of <em>Porites divaricata</em>.&nbsp;Collections were made in the vicinity of Long Key, FL, oceanside (N24<sup>o</sup> 49.791’ W80<sup>o</sup> 45.743’) and experimentation was performed at the Keys Marine Laboratory, Long Key, FL</p>
<p>Coral colonies were sampled a total of 4 times throughout the experiment. Symbionts present in the tissue samples were characterized based on sequence variation in the symbiont chloroplast 23S rDNA following the protocols of Santos et al. 2003, Mar.Biotech. 5:130-140</p>
<p><strong>Reference:</strong><br />
- Santos SR, Gutiérrez-Rodríguez C, Coffroth MA (2003) Phylogenetic identification of symbiotic dinoflagellates via length heteroplasmy in domain V of chloroplast large subunit (cp23S)-rDNA sequences. Mar Biotech 5: 130-140 for technique to characterize symbionts based on of chloroplast large subunit (cp23S)-rDNA</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- original file: Coffroth et al 2010_ Data Summary_cp-type.xlsx<br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- changed parameter names to be BCO-DMO compatible<br />
- combined 7 tables and reformated data to flat file<br />
- removed or replaced spaces with underscores<br />
- replaced &gt; with gt_ and &lt; with lt_<br />
- changed 'no amp' to 'no_amplification'</p>
<p><strong>Revisions:&nbsp;</strong><br />
2015-01-29: small formatting changes to strong and weak bp columns<br />
2015-01-15: originally submitted data</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
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA) Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Spectrophotometer
Spectrophotometer
PI Supplied Instrument Name: Spectrophotometer PI Supplied Instrument Description:Nano-Drop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler PI Supplied Instrument Description:Stratagene Mx3005P QPCR System (Stratagene, La Jolla, CA.) Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: Coffroth_2010
Coffroth_2010
SUNY-Buffalo
laboratory
Coffroth_2010
Mary Alice Coffroth
State University of New York at Buffalo
SUNY-Buffalo
laboratory