Dataset: White Plague Disease Transmission Phenotypic Response

Name: 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
Published: 2020-11-17
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.829113.1

Spatial Extent: N:18.34403 E:-64.98435 S:18.34403 W:-64.98435

Temporal Extent: 2017-06

Project:

Immunity to Community: Can Quantifying Immune Traits Inform Reef Community Structure? (Coral Immune Traits)

Principal Investigator:

Laura Mydlarz (University of Texas at Arlington, UT Arlington)

Co-Principal Investigator:

Marilyn Brandt (University of the Virgin Islands Center for Marine and Environmental Studies)

Student:

Nicholas MacKnight (University of Texas at Arlington, UT Arlington)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-11-17

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-11-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.829113.1	2020-11-18

Methods & Sampling

Location: Brewer’s Bay (18.34403, -64.98435), St. Thomas, The U.S. Virgin Islands

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 survfit function in the R package survival (Therneau, 2020). The relative risk of each species was also calculated as: “Relative risk (RR) = Risk in exposed / Risk in non-exposed” where the risk in exposed individuals was calculated as the prevalence (diseased/total population) of those exposed to disease and risk in non-exposed individuals was calculated as the prevalence (diseased/total population) of those not exposed to disease.

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.

Instruments:
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.

Data Processing Description

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).

BCO-DMO Data Manager Processing Notes:
* Extracted data submitted in Excel file "EAGER_PhenotypeDATA_BCODMO_Submission.xlsx" to csv
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions: only A-Za-z0-9 and underscore allowed. Can not start with a number. (spaces, +, and - changed to underscores).
* Rounded Time frame (hours) and (days) to three decimal places.
* 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. Units provided in parameter information.
* Provided species names checked using the World Register of Marine Species taxa match tool. Corrected species name in the dataset Sidereastrea siderea -> Siderastrea siderea http://www.marinespecies.org/aphia.php?p=taxdetails&id=207516
* Species list with exact match to AphiaID taxonomic identifiers added to supplemental documents.

Data Files

File
coral_pheno.csv (Comma Separated Values (.csv), 6.18 KB) MD5:a02cf87b6126443f6b49094f980124cb Primary data file for dataset ID 829113

Supplemental Files

File
Species list and identifiers filename: species_list.csv (Comma Separated Values (.csv), 219 bytes) MD5:a9685f29c346ef03a257404657578731 Coral scientific name (Genus species) and AphiaID (taxonomic identifier).

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1712134
NSF Division of Ocean Sciences	OCE-1712240
NSF Division of Ocean Sciences	OCE-1712540

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Species	Species (scientific name in format Genus species).	unitless	species
Treatment	Treatment type (Disease or Control).	unitless	treatment
Colony	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.	unitless	sample_descrip
Bucket	Aquaria identifier. "C" for controls, "D" for disease-exposed. Numbers are identifiers that do not have a broader meaning.	unitless	tank
Parent_ID	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.	unitless	sample_descrip
ID	Colony identifier, pairing coral fragments to their origin parent ID.	unitless	sample_descrip
Rate_type	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.	unitless	treatment
Days_to_infection	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.	days	sample_descrip
cm2_lost	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.	square centimeters (cm^2)	sample_descrip
Time_frame_min	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.	minutes	time_elapsed
Time_frame_hours	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.	hours	time_elapsed
Time_frame_days	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.	days	time_elapsed
cm2_per_min	lesion progression rate in centimeters squared per minute	cm^2/min	sample_descrip
cm2_per_day	lesion progression rate in centimeters squared per day	cm^2/day	sample_descrip
percent_lost	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.	percent (%)	sample_descrip
percent_lost_per_min	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.	percent per minute (%/min)	sample_descrip
percent_lost_per_hour	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.	percent per hour (%/hr)	sample_descrip
percent_lost_per_day	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.	percent per day (%/d)	sample_descrip

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Dataset: White Plague Disease Transmission Phenotypic Response