http://lod.bco-dmo.org/id/dataset/719924
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 LA County Museum of Natural History (Sea Star Microbiology project)
2017-10-13
publication
2017-10-13
revision
BCO-DMO Linked Data URI
2017-10-13
creation
http://lod.bco-dmo.org/id/dataset/719924
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. (2017) Sea star specimen voucher data from the LA County Museum of Natural History (Sea Star Microbiology project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-10-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/719924 [access date]
Sea star specimen information from the LA County Museum of Natural History Dataset Description: <p>This dataset includes sea star specimen&nbsp;information from the&nbsp;LA County Museum of Natural History.</p>
<p>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 1947 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>
<p>Note that species identifications in this dataset with a question mark&nbsp;indicate a questionable identification.</p>
<p>References:</p>
<p>Hewson, I., Button, J. B., Gudenkauf, B. M., Miner, B., Newton, A. L., Gaydos, J. K., ... &amp; Fradkin, S. (2014). Densovirus associated with sea-star wasting disease and mass mortality.&nbsp;<em>Proceedings of the National Academy of Sciences</em>,&nbsp;<em>111</em>(48), 17278-17283.&nbsp;doi:&nbsp;<a href="http://doi.org/10.1073/pnas.1416625111" target="_blank">10.1073/pnas.1416625111</a></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
completed
Ian Hewson
Cornell University
1-607-255-0151
Department of Microbiology Wing Hall 403
Ithaca
NY
14853
USA
hewson@cornell.edu
pointOfContact
asNeeded
Unknown
date_sampled
HEWSON_Z_num
LACM_num
id
count
Field_num
locality
date_descriptive
year
collection
location_in_collection
Comments
theme
None, User defined
date
sample identification
sample description
taxon
No BCO-DMO term
site description
site
year
comments
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.
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
2017-10-13
Salish Sea and Alaskan Waters
0
BCO-DMO catalogue of parameters from Sea star specimen voucher data from the LA County Museum of Natural History (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/720717.rdf
Name: date_sampled
Units: unitless
Description: <p>Date a sample was taken from the specimen in forat dd-mmm-yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/720718.rdf
Name: HEWSON_Z_num
Units: unitless
Description: <p>Sample identifier used internally in the Hewson lab</p>
http://lod.bco-dmo.org/id/dataset-parameter/720719.rdf
Name: LACM_num
Units: unitless
Description: <p>The specimen identifier used in the collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/720720.rdf
Name: id
Units: unitless
Description: <p>Taxanomic identification of the specimen to the Genus or Genus species level. A question mark at the end indicates the identification was questionable.</p>
http://lod.bco-dmo.org/id/dataset-parameter/720721.rdf
Name: count
Units: unknown
Description: <p>unknown</p>
http://lod.bco-dmo.org/id/dataset-parameter/720722.rdf
Name: Field_num
Units: unitless
Description: <p>Field location identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/720723.rdf
Name: locality
Units: unitless
Description: <p>Field location descriptive name</p>
http://lod.bco-dmo.org/id/dataset-parameter/720724.rdf
Name: date_descriptive
Units: unitless
Description: <p>Date the specimen was collected in various formats and time resolutions.</p>
http://lod.bco-dmo.org/id/dataset-parameter/720725.rdf
Name: year
Units: unitless
Description: <p>Year specimen was collected in format yyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/720726.rdf
Name: collection
Units: unitless
Description: <p>Collection the specimen was part of</p>
http://lod.bco-dmo.org/id/dataset-parameter/720727.rdf
Name: location_in_collection
Units: unitless
Description: <p>Location of specimen within the collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/720728.rdf
Name: Comments
Units: untiless
Description: <p>Comments</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
5989
https://datadocs.bco-dmo.org/file/qAAoq7zh7rZBLl/LACM.csv
LACM.csv
Primary data file for dataset ID 719924
download
https://osprey.bco-dmo.org/dataset/719924/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 1947 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>
<p>Note that species identifications in this dataset with a question mark&nbsp;indicate a questionable identification.</p>
<p>References:</p>
<p>Hewson, I., Button, J. B., Gudenkauf, B. M., Miner, B., Newton, A. L., Gaydos, J. K., ... &amp; Fradkin, S. (2014). Densovirus associated with sea-star wasting disease and mass mortality.&nbsp;<em>Proceedings of the National Academy of Sciences</em>,&nbsp;<em>111</em>(48), 17278-17283.&nbsp;doi:&nbsp;<a href="http://doi.org/10.1073/pnas.1416625111" target="_blank">10.1073/pnas.1416625111</a></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 />
* added data column "year" since the date had mixed formats (date ranges, partial dates)<br />
* commas changed to semicolons in text fields of data to support csv&nbsp;versions of the data.<br />
* split collection/location in collection into two separate&nbsp;columns "collection" and "location_in_collection."</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