http://lod.bco-dmo.org/id/dataset/546131
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 pre and post bleach symbiont density in Porites divaricata 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/546131
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 pre and post bleach symbiont density in Porites divaricata 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/546131 [access date]
pre- and post-bleach symbiont density in Porites divaricata Dataset Description: <p>Cell counts of symbionts by treatment of pre-bleached, bleached and recovering corals (<em>Porites divaricata</em>).</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>Collections were made in the vicinity of Long Key, FL, oceanside (N24o 49.791’ W80o 45.743’) and experimentation at the Keys Marine Laboratory, Long Key, FL.</p>
<p>Symbiont density within coral tissues was determined three times over the course of the experiment; (1) before exposure to elevated temperature, (2) when the heat treatment was terminated and (3) 5 weeks into the recovery period. Coral tissue was scraped from the colony surface and placed in 1.0 ml of 5% formalin. The length and width of the scar were measured and these dimensions (length x width) were used to estimate the surface of tissue removed. Subsequently, each tissue sample was homogenized and 9 µL aliquots were counted using a hemacytometer. A total of four replicate counts were conducted per tissue sample and mean symbiont density per mm^2 was calculated.</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
description
date
sample
culture_inoculant
symbiont_type
count_1
count_2
count3
count_4
mean_count
mean_x10000
length
width
type
surf_area
cells_mm2
cells_x10000_mm2
std_dev
Hemocytometer
theme
None, User defined
laboratory
latitude
longitude
No BCO-DMO term
date
sample identification
treatment
count
length
width
abundance
standard deviation
featureType
BCO-DMO Standard Parameters
Hemocytometer
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 pre and post bleach symbiont density in Porites divaricata 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/546175.rdf
Name: lab
Units: unitless
Description: <p>laboratory identification; for mapping puposes</p>
http://lod.bco-dmo.org/id/dataset-parameter/546176.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude of lab; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/546177.rdf
Name: lon
Units: decimal degrees
Description: <p>londitude of lab; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/546178.rdf
Name: description
Units: unitless
Description: <p>timing of sample collection: pre- or post-bleaching</p>
http://lod.bco-dmo.org/id/dataset-parameter/546179.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/546180.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/546181.rdf
Name: culture_inoculant
Units: unitless
Description: <p>Cultures 311, 702, A001 and <em>Plexaura flexuosa</em> (Pur Pflex) were obtained from the BURR Culture Collection and used to inoculate bleached colonies of <em>Porites divaricata</em> (Pd).</p>
http://lod.bco-dmo.org/id/dataset-parameter/546182.rdf
Name: symbiont_type
Units: unitless
Description: <p>The symbiont type of the culture used to inoculate bleached colonies of Porites divaricata. Symbiont type based on sequence variation in the chloroplast 23S rDNA (cp-type). Notations based on symbiont clade (Letter) and fragment size (number in bp). For example, A188 is a symbiont within clade A where the 23S rDNA fragment is 188bp in length.</p>
http://lod.bco-dmo.org/id/dataset-parameter/546183.rdf
Name: count_1
Units: cells
Description: <p>symbiont cells in first subsample</p>
http://lod.bco-dmo.org/id/dataset-parameter/546184.rdf
Name: count_2
Units: cells
Description: <p>symbiont cells in second subsample</p>
http://lod.bco-dmo.org/id/dataset-parameter/546185.rdf
Name: count3
Units: cells
Description: <p>symbiont cells in third subsample</p>
http://lod.bco-dmo.org/id/dataset-parameter/546186.rdf
Name: count_4
Units: cells
Description: <p>symbiont cells in fourth subsample</p>
http://lod.bco-dmo.org/id/dataset-parameter/546187.rdf
Name: mean_count
Units: cells
Description: <p>average number of cells in sub samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/546188.rdf
Name: mean_x10000
Units: cells x 10^4
Description: <p>average number of cells in sub samples x 10^4</p>
http://lod.bco-dmo.org/id/dataset-parameter/546189.rdf
Name: length
Units: millimeters
Description: <p>length of scar from tissue removal</p>
http://lod.bco-dmo.org/id/dataset-parameter/546190.rdf
Name: width
Units: millimeters
Description: <p>width of scar from tissue removal</p>
http://lod.bco-dmo.org/id/dataset-parameter/546191.rdf
Name: type
Units: unitless
Description: <p>symbiont type: H=?; S=?; LIGHT=?; scar_toss=discarded??</p>
http://lod.bco-dmo.org/id/dataset-parameter/546192.rdf
Name: surf_area
Units: mm^2
Description: <p>surface area of coral tissue removed</p>
http://lod.bco-dmo.org/id/dataset-parameter/546193.rdf
Name: cells_mm2
Units: cells/mm2
Description: <p>symbiont cell density</p>
http://lod.bco-dmo.org/id/dataset-parameter/546194.rdf
Name: cells_x10000_mm2
Units: cells x 10^4/mm2
Description: <p>symbiont cell density x 10^4</p>
http://lod.bco-dmo.org/id/dataset-parameter/546195.rdf
Name: std_dev
Units: cells x 10^4/mm2
Description: <p>standard deviation of cell density</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
40671
https://datadocs.bco-dmo.org/file/N77GrVjsPDMmXj/cell_counts.csv
cell_counts.csv
Primary data file for dataset ID 546131
download
https://osprey.bco-dmo.org/dataset/546131/data/download
download
onLine
dataset
<p>Collections were made in the vicinity of Long Key, FL, oceanside (N24o 49.791’ W80o 45.743’) and experimentation at the Keys Marine Laboratory, Long Key, FL.</p>
<p>Symbiont density within coral tissues was determined three times over the course of the experiment; (1) before exposure to elevated temperature, (2) when the heat treatment was terminated and (3) 5 weeks into the recovery period. Coral tissue was scraped from the colony surface and placed in 1.0 ml of 5% formalin. The length and width of the scar were measured and these dimensions (length x width) were used to estimate the surface of tissue removed. Subsequently, each tissue sample was homogenized and 9 µL aliquots were counted using a hemacytometer. A total of four replicate counts were conducted per tissue sample and mean symbiont density per mm^2 was calculated.</p>
Specified by the Principal Investigator(s)
<p>Cell counts between times (within a treatment) were compared using (repeated measures ANOVA using Greenhouse-Geisser correction for violation of assumption of sphericity, F(1.088,88.144)=137.119, p&lt;0.001; within-subject contrasts, F(1,81)=153.654, p&lt;0.001).</p>
<p><strong>BCO-DMO Processing:</strong></p>
<p>- original file: Coffroth et al 2010_ Data Summary_cell counts.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 - replaced Pur pflex -&gt; Plexaura_flexuosa; BLcntrl -&gt; bleached_control; UBLcntrl -&gt; unbleached control<br />
- combined data from all 3 dates and reformatted to flat file.</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
Hemocytometer
Hemocytometer
PI Supplied Instrument Name: Hemocytometer Instrument Name: Hemocytometer Instrument Short Name:Hemocytometer Instrument Description: A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as "haemocytometer". Description from:
http://hlsweb.dmu.ac.uk/ahs/elearning/RITA/Haem1/Haem1.html.
Deployment: Coffroth_2010
Coffroth_2010
SUNY-Buffalo
laboratory
Coffroth_2010
Mary Alice Coffroth
State University of New York at Buffalo
SUNY-Buffalo
laboratory