http://lod.bco-dmo.org/id/dataset/683783
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
2017-03-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Number of Briareum asbestinum juveniles at 4 sites with a given Symbiodinium type over time (months) during 1999-2002 (Fig. 2, Poland et al 2013) (SymBioSys project)
2017-03-10
publication
2017-03-10
revision
BCO-DMO Linked Data URI
2017-03-10
creation
http://lod.bco-dmo.org/id/dataset/683783
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. (2017) Number of Briareum asbestinum juveniles at 4 sites with a given Symbiodinium type over time (months) during 1999-2002 (Fig. 2, Poland et al 2013) (SymBioSys project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-03-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/683783 [access date]
Symbiont types by site and month Dataset Description: <p>Data on symbiont <em>Symbiodinium</em>&nbsp;type in&nbsp;<em>Briareum </em><em>asbestinum</em> juveniles, 1999-2002. These data were used for Figure 2 in Poland et al (2013) MEPS.</p> Methods and Sampling: <p>For details, see Poland et al 2013. <em>Briareum </em><em>asbestinum</em> larvae, collected directly from the surface of the maternal colonies at the Florida Bay, reared for three days in filtered seawater and then divided into 3 replicate groups and transferred to 1 of the 3 study sites (Florida Bay, Grassbed or Outer Reef tract) where they were placed in 2 l jugs (500−2000 larvae jug−1) and allowed to settle on dead gorgonian branches (the preferred settlement site). After 3 to 7 d, the branches with newly settled juveniles were removed from the jugs and suspended off the substrate at each site. Deployment techniques varied along the Outer Reef tract site. In 1999, <em>Briareum </em><em>asbestinum</em> juveniles were settled onto plexi-glass plates and were floated 0.5 m above the substrate on a shallow (5 m) part of the Tennessee reef tract, while in 2000 to 2002 juveniles were settled on branches and maintained within the jugs to avoid fish predation. In 2000 and 2001 these jugs were suspended at 5 m below the surface above the deeper (23 m) part of the reef tract and in 2002, the jugs containing juveniles were floated 0.5 to 1.0 m above the substrate at 23 m depth at this same site. Data from the outer reef tract provided a comparison of symbiont types infecting juvenile hosts in the same area over depth and time.</p>
<p>Symbiont identification/typing followed that of Santos et al. 2003, Mar.Biotech. 5:130-140</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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-9907319 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=9907319
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
Unknown
site
lat
lon
year
cptype
Jun
Jul
Aug
Sep
Oct
Nov
Dec
Jan
Feb
Mar
Apr
May
Automated Sequencer
Thermal Cycler
theme
None, User defined
site
latitude
longitude
year
sample description
month of year
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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
2017-03-10
Florida Keys, Bahamas, Panama, Mexico
0
BCO-DMO catalogue of parameters from Number of Briareum asbestinum juveniles at 4 sites with a given Symbiodinium type over time (months) during 1999-2002 (Fig. 2, Poland et al 2013) (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/683795.rdf
Name: site
Units: unitless
Description: <p>location of sample collections</p>
http://lod.bco-dmo.org/id/dataset-parameter/683796.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/683797.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/683798.rdf
Name: year
Units: unitless
Description: <p>year of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/683799.rdf
Name: cptype
Units: unitless
Description: <p>symbiont genetic type identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/683800.rdf
Name: Jun
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in June</p>
http://lod.bco-dmo.org/id/dataset-parameter/683801.rdf
Name: Jul
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in July</p>
http://lod.bco-dmo.org/id/dataset-parameter/683802.rdf
Name: Aug
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in August</p>
http://lod.bco-dmo.org/id/dataset-parameter/683803.rdf
Name: Sep
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in September</p>
http://lod.bco-dmo.org/id/dataset-parameter/683804.rdf
Name: Oct
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in October</p>
http://lod.bco-dmo.org/id/dataset-parameter/683805.rdf
Name: Nov
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in November</p>
http://lod.bco-dmo.org/id/dataset-parameter/683806.rdf
Name: Dec
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in December</p>
http://lod.bco-dmo.org/id/dataset-parameter/683807.rdf
Name: Jan
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in January</p>
http://lod.bco-dmo.org/id/dataset-parameter/683808.rdf
Name: Feb
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in February</p>
http://lod.bco-dmo.org/id/dataset-parameter/683809.rdf
Name: Mar
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in March</p>
http://lod.bco-dmo.org/id/dataset-parameter/683810.rdf
Name: Apr
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in April</p>
http://lod.bco-dmo.org/id/dataset-parameter/683811.rdf
Name: May
Units: unitless
Description: <p>number of Briareum asbestinum juveniles with symbiont type in May</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
8876
https://datadocs.bco-dmo.org/file/VJJWqmzHxrR9ox/Poland_2013_symb_type.csv
Poland_2013_symb_type.csv
Primary data file for dataset ID 683783
download
https://osprey.bco-dmo.org/dataset/683783/data/download
download
onLine
dataset
<p>For details, see Poland et al 2013. <em>Briareum </em><em>asbestinum</em> larvae, collected directly from the surface of the maternal colonies at the Florida Bay, reared for three days in filtered seawater and then divided into 3 replicate groups and transferred to 1 of the 3 study sites (Florida Bay, Grassbed or Outer Reef tract) where they were placed in 2 l jugs (500−2000 larvae jug−1) and allowed to settle on dead gorgonian branches (the preferred settlement site). After 3 to 7 d, the branches with newly settled juveniles were removed from the jugs and suspended off the substrate at each site. Deployment techniques varied along the Outer Reef tract site. In 1999, <em>Briareum </em><em>asbestinum</em> juveniles were settled onto plexi-glass plates and were floated 0.5 m above the substrate on a shallow (5 m) part of the Tennessee reef tract, while in 2000 to 2002 juveniles were settled on branches and maintained within the jugs to avoid fish predation. In 2000 and 2001 these jugs were suspended at 5 m below the surface above the deeper (23 m) part of the reef tract and in 2002, the jugs containing juveniles were floated 0.5 to 1.0 m above the substrate at 23 m depth at this same site. Data from the outer reef tract provided a comparison of symbiont types infecting juvenile hosts in the same area over depth and time.</p>
<p>Symbiont identification/typing followed that of Santos et al. 2003, Mar.Biotech. 5:130-140</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- original file: Poland et al 2013_symbiont type by site &amp; month.xlsx<br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- changed parameter names to be BCO-DMO compatible<br />
- replaced spaces with underscores<br />
- blank values replaced with no data value 'nd'</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.
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler PI Supplied Instrument Description:MJ Research PTC-100 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