http://lod.bco-dmo.org/id/dataset/829113
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
2020-11-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phenotypic information collected from white plague disease exposure in a controlled environment at The University of the Virgin Islands Center for Marine and Environmental Studies in June of 2017
2020-11-17
publication
2020-11-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-11-18
publication
https://doi.org/10.26008/1912/bco-dmo.829113.1
Dr Laura Mydlarz
University of Texas at Arlington
principalInvestigator
Marilyn Brandt
University of the Virgin Islands Center for Marine and Environmental Studies
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
documentDigital
Cite this dataset as: Mydlarz, L., Brandt, M., MacKnight, N. (2020) Phenotypic information collected from white plague disease exposure in a controlled environment at The University of the Virgin Islands Center for Marine and Environmental Studies in June of 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-11-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.829113.1 [access date]
Acquisition Description: <p>Location:&nbsp;Brewer’s Bay (18.34403, -64.98435), St. Thomas, The U.S. Virgin Islands</p>
<p>Disease prevalence was recorded as the percentage of individuals infected by the end of the seven-day study. Disease prevalence among species was compared using a Fisher’s Exact Test in R. A photograph and timestamp was captured upon appearance of lesions and then immediately before each fragment was culled around 30% tissue loss. Disease severity was measured by calculating the rate of lesion progression across the coral fragment as the amount of tissue lost between the appearance of the lesion to the time it was culled divided by that time period. Time to infection was measured by the number of days it took for each coral fragment to show lesions throughout the seven-day study and visualized with a survival plot through a Kaplan-Meier estimate of the survivorship by using the <em>survfit</em> function in the R package <em>survival </em>(Therneau, 2020). The relative risk of each species was also calculated as: “Relative risk (RR) = Risk in exposed / Risk in non-exposed” where the <em>risk in exposed </em>individuals was calculated as the prevalence (diseased/total population) of those exposed to disease and <em>risk in non-exposed</em> individuals was calculated as the prevalence (diseased/total population) of those not exposed to disease.</p>
<p>Disease transmission and phenotypic sampling matched the methods from this published study “Species-specific susceptibility to white plague disease in three common Caribbean corals” Williams et al. (2020). Dr. Marilyn Brandt was the lead PI in that investigation and a CO-PI in the investigation being submitted.<br />
<br />
Instruments:&nbsp;<br />
Band Saw to fragment colonies. Camera and ruler to take photographs. Hammer and chisel to take samples of culled coral. Samples flash frozen in liquid nitrogen, stored in -80˚C until shipped via dry shipper to The University of Texas at Arlington for molecular work.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1712134 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1712134
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1712240 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1712240
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1712540 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1712540
completed
Dr Laura Mydlarz
University of Texas at Arlington
817-272-0397
501 S. Nedderman Dr. 337 Life Sciences Building
Arlington
TX
76013
United States
mydlarz@uta.edu
pointOfContact
Marilyn Brandt
University of the Virgin Islands Center for Marine and Environmental Studies
340-693-1379
2 John Brewers Bay
St. Thomas, USVI
00802
mbrandt@uvi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Species
Treatment
Colony
Bucket
Parent_ID
ID
Rate_type
Days_to_infection
cm2_lost
Time_frame_min
Time_frame_hours
Time_frame_days
cm2_per_min
cm2_per_day
percent_lost
percent_lost_per_min
percent_lost_per_hour
percent_lost_per_day
theme
None, User defined
species
treatment
sample description
tank
time_elapsed
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.
Immunity to Community: Can Quantifying Immune Traits Inform Reef Community Structure?
https://www.bco-dmo.org/project/727496
Immunity to Community: Can Quantifying Immune Traits Inform Reef Community Structure?
<p>NSF abstract:</p>
<p>Coral diseases have increased significantly throughout the past 30 years. Climate change and other detrimental environment factors are likely to blame. Unhealthy coral reefs cannot support the fish and other life that make the reef a vibrant and diverse ecosystem. Corals reefs in the Caribbean Sea are disease hotspots and many reefs have experienced population collapses due to outbreaks of disease. Importantly, coral species vary in their susceptible to disease, but the reasons behind this variation are unknown. This project will quantify coral susceptibility to disease by examining coral immunity using several novel approaches and experiments. Seven species of coral that differ in disease susceptibility, growth rates, growth form and reproductive strategies will be used. Immune responses of each species of coral will be measured by exposing the corals to bacterial immune stimulators. Susceptibility to white plague disease, a prevalent disease affecting many species of corals, will also be measured by exposing the corals to active white plague disease and calculating disease transmission rates. The immune response and disease transmission data for each coral species will be used to develop a predictive model to determine how different coral communities will respond to disease threats under climate change scenarios. This project will support graduate students at University of Texas, Arlington (Hispanic-serving Institution) and University of Virgin Islands (Historically Black University) and many undergraduate students at all three institutions (Mote Marine Laboratory). This research will be highlighted at outreach events at all three institutions which take place regularly and include Earth Day Texas in Dallas, TX, Mote's Living Reef Exhibit and Aquarium in Sarasota, FL and "Reef Fest" and Agricultural fairs in the U.S. Virgin Islands.</p>
<p>Environmental changes, such as ocean warming, have led to an increase in the prevalence of coral diseases, causing region-wide population collapses in some locations. However, not all coral species, or even populations within species, are affected by disease equally. Some species are host to many different types of diseases, but have limited mortality. Other species suffer significant disease-related mortality. How and why disease susceptibility differs among species and the effects of this differential susceptibility on reef community structure and composition are currently unknown. This project will use immune-challenge experiments that will quantify novel components of the innate immune system of corals, coupled with the application of a trait-based model, to fulfill three goals: 1) Determine variability of coral immune traits in seven common coral species found on Caribbean reefs, 2) Determine the variability in resistance to white plague disease transmission in the same coral species 3) Develop a predictive model of coral community assemblage that incorporates immune traits. Quantification of coral immunity will also incorporate unique approaches, such as combining full transcriptome sequencing with protein activity assays for a gene-to-phenotype analysis. Data will be mapped onto immune pathways for comprehensive pathway evaluation between coral species and these will serve as trait inputs into a "traitspace" model. These traits will provide continuous data within the model, which will create a probability density function (PDF) for the trait distributions of each species. These PDFs will then be used to determine the probability of species under different disease exposure scenarios. Model analyses will determine which traits influence community structure and characterize how disease exposure and the immune response will predict community assemblages through space and time. The completion and application of a trait-base model that incorporates extensive immunity parameters (none of which have been applied to trait models within coral ecosystems) is a distinct product from this project.</p>
Coral Immune Traits
largerWorkCitation
project
eng; USA
oceans
-64.98435
-64.98435
18.34403
18.34403
2017-06-01
2017-06-01
US Virgin Islands
0
BCO-DMO catalogue of parameters from Phenotypic information collected from white plague disease exposure in a controlled environment at The University of the Virgin Islands Center for Marine and Environmental Studies in June of 2017
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/829221.rdf
Name: Species
Units: unitless
Description: Species (scientific name in format Genus species).
http://lod.bco-dmo.org/id/dataset-parameter/829222.rdf
Name: Treatment
Units: unitless
Description: Treatment type (Disease or Control).
http://lod.bco-dmo.org/id/dataset-parameter/829223.rdf
Name: Colony
Units: unitless
Description: Originating colony that fragment came from. Each colony was fragmented in two to have one fragment exposed to a white plague infected O.franksi and the other to remain as a paired control and exposed to a healthy O. franksi.
http://lod.bco-dmo.org/id/dataset-parameter/829224.rdf
Name: Bucket
Units: unitless
Description: Aquaria identifier. "C" for controls, "D" for disease-exposed. Numbers are identifiers that do not have a broader meaning.
http://lod.bco-dmo.org/id/dataset-parameter/829225.rdf
Name: Parent_ID
Units: unitless
Description: Coral colony genotype identifier. Two coral fragments came from the same parent colony. One fragment went to a control bucket, another to the disease-exposed bucket.
http://lod.bco-dmo.org/id/dataset-parameter/829226.rdf
Name: ID
Units: unitless
Description: Colony identifier, pairing coral fragments to their origin parent ID.
http://lod.bco-dmo.org/id/dataset-parameter/829227.rdf
Name: Rate_type
Units: unitless
Description: An anecdotal categorization for the progression rate of that fragment. This metric is not applied in any calculation in the publication. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829228.rdf
Name: Days_to_infection
Units: days
Description: The days it took for a particular fragment to be exposed to white plague disease to show signs of lesion presence. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829229.rdf
Name: cm2_lost
Units: square centimeters (cm^2)
Description: Area of tissue lost as a result of lesion progression. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829230.rdf
Name: Time_frame_min
Units: minutes
Description: Time frame (minutes) from the initial observation of lesion presence to when the fragment was culled from the experiment. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829231.rdf
Name: Time_frame_hours
Units: hours
Description: Time frame (hours) from the initial observation of lesion presence to when the fragment was culled from the experiment. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829232.rdf
Name: Time_frame_days
Units: days
Description: Time frame (days) from the initial observation of lesion presence to when the fragment was culled from the experiment. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829233.rdf
Name: cm2_per_min
Units: cm^2/min
Description: lesion progression rate in centimeters squared per minute
http://lod.bco-dmo.org/id/dataset-parameter/829234.rdf
Name: cm2_per_day
Units: cm^2/day
Description: lesion progression rate in centimeters squared per day
http://lod.bco-dmo.org/id/dataset-parameter/829235.rdf
Name: percent_lost
Units: percent (%)
Description: Total percent tissue loss as a result of white plague lesion progression. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829236.rdf
Name: percent_lost_per_min
Units: percent per minute (%/min)
Description: Total percent tissue loss per minute as a result of white plague lesion progression. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829237.rdf
Name: percent_lost_per_hour
Units: percent per hour (%/hr)
Description: Total percent tissue loss per hour as a result of white plague lesion progression. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
http://lod.bco-dmo.org/id/dataset-parameter/829238.rdf
Name: percent_lost_per_day
Units: percent per day (%/d)
Description: Total percent tissue loss per day as a result of white plague lesion progression. A zero "0" indicates that sample did not have any lesion growth, even if exposed to the disese as part of its treatment.
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
https://www.bco-dmo.org/dataset/829113/data/download
download
onLine
dataset
<p>Location:&nbsp;Brewer’s Bay (18.34403, -64.98435), St. Thomas, The U.S. Virgin Islands</p>
<p>Disease prevalence was recorded as the percentage of individuals infected by the end of the seven-day study. Disease prevalence among species was compared using a Fisher’s Exact Test in R. A photograph and timestamp was captured upon appearance of lesions and then immediately before each fragment was culled around 30% tissue loss. Disease severity was measured by calculating the rate of lesion progression across the coral fragment as the amount of tissue lost between the appearance of the lesion to the time it was culled divided by that time period. Time to infection was measured by the number of days it took for each coral fragment to show lesions throughout the seven-day study and visualized with a survival plot through a Kaplan-Meier estimate of the survivorship by using the <em>survfit</em> function in the R package <em>survival </em>(Therneau, 2020). The relative risk of each species was also calculated as: “Relative risk (RR) = Risk in exposed / Risk in non-exposed” where the <em>risk in exposed </em>individuals was calculated as the prevalence (diseased/total population) of those exposed to disease and <em>risk in non-exposed</em> individuals was calculated as the prevalence (diseased/total population) of those not exposed to disease.</p>
<p>Disease transmission and phenotypic sampling matched the methods from this published study “Species-specific susceptibility to white plague disease in three common Caribbean corals” Williams et al. (2020). Dr. Marilyn Brandt was the lead PI in that investigation and a CO-PI in the investigation being submitted.<br />
<br />
Instruments:&nbsp;<br />
Band Saw to fragment colonies. Camera and ruler to take photographs. Hammer and chisel to take samples of culled coral. Samples flash frozen in liquid nitrogen, stored in -80˚C until shipped via dry shipper to The University of Texas at Arlington for molecular work.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Lesion progression rate and percent tissue loss was calculated from photographs processed through ImageJ. Relative Risk was calculated using this equation: “Relative risk (RR) = Risk in exposed / Risk in non-exposed” which uses Markov Chain Monte Carlo simulations with Gibbs Sampling in OpenBUGS (OpenBUGS (MRC Biostatistics Unit, Cambridge, UK). Days to infections was visualized with a survival plot through a Kaplan-Meier estimate of the survivorship by using the survfit function in the R package survival (Therneau, 2020). Statistical significance comparisons and visualizations were processed in R v3.5.1 (Rstudio v1.2.5033).<br />
<br />
BCO-DMO Data Manager Processing Notes:<br />
* Extracted data submitted in Excel file "EAGER_PhenotypeDATA_BCODMO_Submission.xlsx" to csv<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed.&nbsp; Can not start with a number.&nbsp; (spaces, +, and - changed to underscores).&nbsp;<br />
* Rounded Time frame (hours) and (days) to three decimal places.<br />
* removed percent symbol from values in percent_lost,percent_lost_per_min,percent_lost_per_hour,percent_lost_per_day so they could be typed correctly as numeric.&nbsp; Units provided in parameter information.<br />
* Corrected species name&nbsp;Sidereastrea siderea -&gt;&nbsp; &nbsp;Siderastrea siderea&nbsp; http://www.marinespecies.org/aphia.php?p=taxdetails&amp;id=207516<br />
* Species list with exact match to AphiaID taxonomic identifiers added to supplemental documents.</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