http://lod.bco-dmo.org/id/dataset/719932
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
2017-11-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sea star specimen voucher data from the California Academy of Sciences (Sea Star Microbiology project)
publication
revision
BCO-DMO Linked Data URI
creation
http://lod.bco-dmo.org/id/dataset/719932
Ian Hewson
Cornell University
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: Hewson, I. (1969) Sea star specimen voucher data from the California Academy of Sciences (Sea Star Microbiology project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/719932 [access date]
Sea star specimen information from the California Academy of Sciences Dataset Description: <p>Note: This dataset was submitted to BCO-DMO and is in the process of being served.</p>
<p>This dataset includes sea star specimen&nbsp;information from the&nbsp;California Academy of Sciences.&nbsp;The specimens described in this dataset were used in a&nbsp;survey of historical sea star-associated densovirus (SSaDV)&nbsp;presence and genome variation.&nbsp;</p> Methods and Sampling: <p><strong>Methodology: </strong>A survey of historical SSaDV presence and genome variation was performed on specimens donated by the LA County Museum of Natural History and the California Academy of Sciences.&nbsp;</p>
<p><strong>Sampling and analytical procedures:</strong> SSaDV was detected using primers/probes targeting two genes on its genome in historical samples from 1942 to present (Hewson et al., 2014). We sought to extend this survey with additional specimens donated from the California Academy of Sciences (SF) and the LA County of Natural History, and to study genome variation in SSaDV by full-length genome sequencing. Donated samples were sampled at the museums by clipping 5 tube feet from each ethanol-preserved sample and placing these into sterile 1.5 ml cryovials. The samples were then returned to the lab at Cornell University for processing.&nbsp;</p>
<p>SSaDV abundance/load will be determined by qPCR following the approach of Hewson et al., 2014 (PNAS). Genome variation will be studied by applying PCR to qPCR positive samples to amplify overlapping parts of the SSaDV genome and then studying their direct sequence-sequence variation.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1537111 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1537111
onGoing
Ian Hewson
Cornell University
1-607-255-0151
Department of Microbiology Wing Hall 403
Ithaca
NY
14853
USA
hewson@cornell.edu
pointOfContact
asNeeded
Unknown
CatNum
Hewson_Lab_Z_Num
Size
AccNum
AccAcro
Phylum
Family
HigherClassif
Genus
Species
Author
Locality
BegDepth
EndDepth
DepthUnits
Intertidal
Substratum
CollName
CollDate
Identifier
IdDate
OrigFix
Preservative
Photos
FieldNum
NumSpecimens
ExpeditionName
GenBankNum
CollectMethod
Collector
CollDateText
IdDateText
BegDepthMeters
EndDepthMeters
BLatDeg
BLatMin
BLatSec
LatHemi
ELatDeg
ELatMin
ELatSec
BLongDeg
BLongMin
BLongSec
LongHemi
ELongDeg
ELongMin
ELongSec
BegLat
EndLat
BegLong
EndLong
theme
None, User defined
sample description
sample identification
length
taxon
site
depth
site description
Cruise identfier
accession number
date
latitude
longitude
featureType
BCO-DMO Standard Parameters
SeaStarMicrobiology_Hewson
service
Deployment Activity
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.
Microbial ecology of sea star wasting disease
http://seastarwastingdisease.wordpress.com
Microbial ecology of sea star wasting disease
<p>Beginning in June 2013 and continuing to present (May 2015), over 20 species of sea stars (Asteroidea, Echinodermata) have been affected by sea star wasting disease (SSWD), affecting populations from central Alaska to Baja California. The disease has lead to greatly reduced abundance or disappearance of these keystone predators, which may result in profound alteration to benthic community structure. Recent work has identified the sea star associated densovirus (SSaDV) as the most likely causative agent of the disease. SSaDV is related to densoviruses inhabiting other echinoderms worldwide, and has been present in West Coast asteroid populations for at least 72 years. Hence, there remain significant knowledge gaps in our understanding of how SSaDV actually elicits SSWD symptoms, especially how the echinoderm host, densovirus and microbiome constituents interact. This project will address three major questions: 1) does viral infection change the composition of the sea star microbiome?, 2) what is the variation of viral genomes and their associated virulence?, and 3) does larval dispersal spread the disease between habitats? This project will address these hypotheses through time-course measurements of host, pathogen and associated microorganisms, genome-genome comparisons between historical and contemporary viral strains, and through experiments targeting larvae and juvenile asteroids in aquaria and in nature. </p>
<p>This project will address three fundamental questions relating to Sea Star Wasting Disease (SSWD): 1) How does SSaDV causes SSWD symptoms and how does the disease progress from primary infection through animal mortality; 2) How do current genotypes of SSaDV vary from those present historically, and is virulence related to genome polymorphisms; and 3) Are larvae and juvenile asteroids differentially affected by SSaDV, and are broadcast-spawned bipinarria a viable mechanism for SSaDV dispersal between distant habitats. The first question will be addressed by experimental inoculation of naïve sea stars with SSaDV, then time-course monitoring of host transcription (i.e. transcriptomics via RNAseq), microbiome composition via 16S rRNA sequencing and quantitative PCR, and viral load and prevalence using quantitatice PCR. The second question will be addressed by amplifying the entire genome of SSaDV and related densoviruses, then perform genome-genome comparisons to identify polymorphic DNA in key protein-encoding regions. The third question will be addressed by collecting bipinarria from plankton at field locations adjacent to spawning asteroid populations, and by performing time-course observations of captive juvenile sea stars and monitoring their bacterial and viral loads using quantitative PCR. This work will be performed primarily in the Salish Sea region, with SSaDV - naïve asteroids collected from Alaskan waters.</p>
Sea Star Microbiology
largerWorkCitation
project
eng; USA
oceans
Salish Sea and Alaskan Waters
0
BCO-DMO catalogue of parameters from Sea star specimen voucher data from the California Academy of Sciences (Sea Star Microbiology 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/721251.rdf
Name: CatNum
Units: unitless
Description: <p>Identifier for the specimen in the catalog</p>
http://lod.bco-dmo.org/id/dataset-parameter/721252.rdf
Name: Hewson_Lab_Z_Num
Units: unitless
Description: <p>Identifier for the sample taken from the specimen used in the Hewson lab</p>
http://lod.bco-dmo.org/id/dataset-parameter/721253.rdf
Name: Size
Units: various
Description: <p>Size of the specimen (both numeric and descriptive). Numeric values are in cm.</p>
http://lod.bco-dmo.org/id/dataset-parameter/721254.rdf
Name: AccNum
Units: unitless
Description: <p>California Academy of Sciences Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/721255.rdf
Name: AccAcro
Units: unitless
Description: <p>California Academy of Sciences Accession Acronym</p>
http://lod.bco-dmo.org/id/dataset-parameter/721256.rdf
Name: Phylum
Units: unitless
Description: <p>Specimen phylum</p>
http://lod.bco-dmo.org/id/dataset-parameter/721257.rdf
Name: Family
Units: unitless
Description: <p>Specimen family</p>
http://lod.bco-dmo.org/id/dataset-parameter/721258.rdf
Name: HigherClassif
Units: unitless
Description: <p>Specimen taxanomic information</p>
http://lod.bco-dmo.org/id/dataset-parameter/721259.rdf
Name: Genus
Units: unitless
Description: <p>Specimen genus</p>
http://lod.bco-dmo.org/id/dataset-parameter/721260.rdf
Name: Species
Units: unitless
Description: <p>Specimen species</p>
http://lod.bco-dmo.org/id/dataset-parameter/721261.rdf
Name: Author
Units: unitless
Description: <p>Author of the species description</p>
http://lod.bco-dmo.org/id/dataset-parameter/721262.rdf
Name: Locality
Units: unitless
Description: <p>Specimen collection location</p>
http://lod.bco-dmo.org/id/dataset-parameter/721263.rdf
Name: BegDepth
Units: various
Description: <p>Start of specimen collection depth range</p>
http://lod.bco-dmo.org/id/dataset-parameter/721264.rdf
Name: EndDepth
Units: various
Description: <p>End of specimen collection depth range</p>
http://lod.bco-dmo.org/id/dataset-parameter/721265.rdf
Name: DepthUnits
Units: various
Description: <p>Units of beginning and end depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/721266.rdf
Name: Intertidal
Units: unitless
Description: <p>Location description indicating whether the collection site was intertidal (TRUE or FALSE)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721267.rdf
Name: Substratum
Units: unitless
Description: <p>Description of sample location substratum</p>
http://lod.bco-dmo.org/id/dataset-parameter/721268.rdf
Name: CollName
Units: unitless
Description: <p>Collection the specimen belongs to</p>
http://lod.bco-dmo.org/id/dataset-parameter/721269.rdf
Name: CollDate
Units: date
Description: <p>Date of organism accession to collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721270.rdf
Name: Identifier
Units: unitless
Description: <p>Person who made the identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/721271.rdf
Name: IdDate
Units: date
Description: <p>Date of the identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/721272.rdf
Name: OrigFix
Units: unitless
Description: <p>Original preservative used to fix the specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/721273.rdf
Name: Preservative
Units: unitless
Description: <p>Preservative used for long-term preservation</p>
http://lod.bco-dmo.org/id/dataset-parameter/721274.rdf
Name: Photos
Units: unitless
Description: <p>Denotes whether photos are available</p>
http://lod.bco-dmo.org/id/dataset-parameter/721275.rdf
Name: FieldNum
Units: unitless
Description: <p>Specimen number designated by field collector</p>
http://lod.bco-dmo.org/id/dataset-parameter/721276.rdf
Name: NumSpecimens
Units: unitless
Description: <p>Number of specimens in collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721277.rdf
Name: ExpeditionName
Units: unitless
Description: <p>Expedition name that collected the specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/721278.rdf
Name: GenBankNum
Units: unitless
Description: <p>Genbank accession number for genetic work</p>
http://lod.bco-dmo.org/id/dataset-parameter/721279.rdf
Name: CollectMethod
Units: unitless
Description: <p>Method of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721280.rdf
Name: Collector
Units: unitless
Description: <p>Name of collector or vessel</p>
http://lod.bco-dmo.org/id/dataset-parameter/721281.rdf
Name: CollDateText
Units: date
Description: <p>Date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721282.rdf
Name: IdDateText
Units: date
Description: <p>Date of identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/721283.rdf
Name: BegDepthMeters
Units: meters
Description: <p>Beginning depth of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721284.rdf
Name: EndDepthMeters
Units: meters
Description: <p>Ending depth of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/721285.rdf
Name: BLatDeg
Units: degrees
Description: <p>Beginning latitude degrees</p>
http://lod.bco-dmo.org/id/dataset-parameter/721286.rdf
Name: BLatMin
Units: minutes
Description: <p>Beginning latitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/721287.rdf
Name: BLatSec
Units: seconds
Description: <p>Beginning latitude seconds</p>
http://lod.bco-dmo.org/id/dataset-parameter/721288.rdf
Name: LatHemi
Units: unitless
Description: <p>Latitude hemisphere (N = north or S = south)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721289.rdf
Name: ELatDeg
Units: degrees
Description: <p>Ending latitude degrees</p>
http://lod.bco-dmo.org/id/dataset-parameter/721290.rdf
Name: ELatMin
Units: minutes
Description: <p>Ending latitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/721291.rdf
Name: ELatSec
Units: seconds
Description: <p>Ending latitude seconds</p>
http://lod.bco-dmo.org/id/dataset-parameter/721292.rdf
Name: BLongDeg
Units: degrees
Description: <p>Beginning longitude degrees</p>
http://lod.bco-dmo.org/id/dataset-parameter/721293.rdf
Name: BLongMin
Units: minutes
Description: <p>Beginning longitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/721294.rdf
Name: BLongSec
Units: seconds
Description: <p>Beginning longitude seconds</p>
http://lod.bco-dmo.org/id/dataset-parameter/721295.rdf
Name: LongHemi
Units: unitless
Description: <p>Longitude hemisphere (W = west or E = east)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721296.rdf
Name: ELongDeg
Units: degrees
Description: <p>Ending longitude degrees</p>
http://lod.bco-dmo.org/id/dataset-parameter/721297.rdf
Name: ELongMin
Units: minutes
Description: <p>Ending longitude minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/721298.rdf
Name: ELongSec
Units: seconds
Description: <p>Ending longitude seconds</p>
http://lod.bco-dmo.org/id/dataset-parameter/721299.rdf
Name: BegLat
Units: decimal degrees
Description: <p>Start of specimen collection latitude range</p>
http://lod.bco-dmo.org/id/dataset-parameter/721300.rdf
Name: EndLat
Units: decimal degrees
Description: <p>End of specimen collection latitude range</p>
http://lod.bco-dmo.org/id/dataset-parameter/721301.rdf
Name: BegLong
Units: decimal degrees
Description: <p>Start of specimen collection longitude range</p>
http://lod.bco-dmo.org/id/dataset-parameter/721302.rdf
Name: EndLong
Units: decimal degrees
Description: <p>End of specimen collection longitude range</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
14811
https://datadocs.bco-dmo.org/file/B11vAN3SYLE7Z/CAS.csv
CAS.csv
Primary data file for dataset ID 719932
download
https://osprey.bco-dmo.org/dataset/719932/data/download
download
onLine
dataset
<p><strong>Methodology: </strong>A survey of historical SSaDV presence and genome variation was performed on specimens donated by the LA County Museum of Natural History and the California Academy of Sciences.&nbsp;</p>
<p><strong>Sampling and analytical procedures:</strong> SSaDV was detected using primers/probes targeting two genes on its genome in historical samples from 1942 to present (Hewson et al., 2014). We sought to extend this survey with additional specimens donated from the California Academy of Sciences (SF) and the LA County of Natural History, and to study genome variation in SSaDV by full-length genome sequencing. Donated samples were sampled at the museums by clipping 5 tube feet from each ethanol-preserved sample and placing these into sterile 1.5 ml cryovials. The samples were then returned to the lab at Cornell University for processing.&nbsp;</p>
<p>SSaDV abundance/load will be determined by qPCR following the approach of Hewson et al., 2014 (PNAS). Genome variation will be studied by applying PCR to qPCR positive samples to amplify overlapping parts of the SSaDV genome and then studying their direct sequence-sequence variation.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* removed quotation marks around ship names due to character restrictions<br />
* commas changed to semicolons in text fields of data to support&nbsp;csv&nbsp;versions of the data.<br />
* version 2018-02-21 replaces version&nbsp;2017-10-06 with the only change being that a blank column with parameter "Coord" was removed.</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
Deployment: SeaStarMicrobiology_Hewson
SeaStarMicrobiology_Hewson
shoreside Alaska
shoreside
SeaStarMicrobiology_Hewson
Ian Hewson
shoreside Alaska
shoreside