http://lod.bco-dmo.org/id/dataset/756404
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
2019-02-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C
2019-03-04
publication
2019-03-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-10-02
publication
https://doi.org/10.1575/1912/bco-dmo.756404.1
Mary Alice Coffroth
State University of New York at Buffalo
principalInvestigator
Casey terHorst
California State University Northridge
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., terHorst, C. (2019) Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-03-04 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.756404.1 [access date]
Microsatellite loci for B. antillogorgium cultures Dataset Description: <p>This dataset includes the microsatellite locus allele size for <em>Breviolum </em><em>antillogorgium</em> cultures isolated from the octocoral <em>Antillogorgia </em><em>bipinnata</em> and used in 2018 growth experiments to compare growth at 26 and 30 degrees C.;</p> Methods and Sampling: <p><em>Breviolum antillogorgium</em> cultures were initially isolated from <em>Antillogorgia bipinnata </em>colonies collected at in the upper Florida Reef tract at Elbow Reef (N 25 07.956 W 80 15.810) in September 2016. Culture isolations and cell growth experimentation occurred in the Coffroth lab, University at Buffalo.</p>
<p>DNA was extracted from symbiont cells following Coffroth et al. (1992) and re-suspended in TE buffer (5-15µl, diluted to a concentration of 5ng/µl). Symbionts were characterized using six polymorphic microsatellite loci, B7SYM4, B7SYM8, B7Sym34, B7Sym36, CA6.38 and GV-1C following the protocols of Pettay and LaJeunesse (2007), Andras et al (2009) and Santos et al (2003b).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559286 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559286
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
Casey terHorst
California State University Northridge
818-677-3352
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
casey.terhorst@csun.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Culture_ID
Incubation_Temperature
Host
Putative_Species
Location
Latitude
Longitude
State_Country
Ocean
Host_stage
Axenic
Isolated_by
Year_isolated
ITS2_type
cp_type
GV_1C
B7SYM34
BYSYM36
CA6_38
B7SYM4
B7SYM8
I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences)
a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler
theme
None, User defined
sample identification
incubation temperature
species scientific name (binomial)
region
latitude
longitude
stage
sample description
person name
year
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
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.
RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs
https://osprey.bco-dmo.org/project/632538
RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs
<p><em>Description from NSF award abstract:</em><br />
On coral reefs, mutualisms with single celled algae (Symbiodinium) and reef species literally and figuratively form the foundation of reef ecosystems. Coral reefs are among the most threatened ecosystems under a changing climate and are rapidly declining due to increasing levels of environmental stress, namely increased temperatures. Climate change is resulting in even warmer ocean temperatures that threaten associations between Symbiodinium and their hosts. In this project the investigators examine the genetic diversity of Symbiodinium and the potential for this important species to evolve in response to temperature. The project will also address whether the ecological and evolutionary dynamics of the Symbiodinium population affect the performance of their host. If so, this suggests that the evolution of microscopic organisms with short generation times could confer adaptation to longer-lived host species on ecologically and economically vital coral reefs. Given that diversity is already being lost on many reefs, considering how evolutionary changes in Symbiodinium will affect reef species is crucial for predicting the responses of reefs to future climate change. This project provides training for two graduate students and several undergraduates at a Hispanic-serving institution. This work includes outreach to the students and the general public through the Aquarium of Niagara, local K-12 schools, and web-based education modules.</p>
<p>The effects of evolution on contemporary ecological processes are at the forefront of research in evolutionary ecology. This project will answer the call for experiments elucidating the effects of genetic variation in Symbiodinium performance and the effect on the response of the holobiont (host and symbiont) to increased temperature. These experiments examine the effects of temperature through both ecological and evolutionary mechanisms and will determine the relative importance of adaptation and acclimatization in replicated experimental populations. The investigators will examine how genetic variation within a species (Symbiodinium antillogorgium) affects symbiont performance in culture and in the host and how this affects the response of the holobiont to increased temperature. Further, the project examines whether holobiont response to increased temperature associated with climate change depends on particular GxG host-symbiont combinations. Moreover, the investigators will examine the effects of symbiont history on mutualist hosts, which have been largely ignored in eco-evolutionary studies. These experiments provide a first step in predicting whether invertebrate hosts on coral reefs will respond to global change via adaptation of their symbionts.</p>
Host Symbiont Temp Response
largerWorkCitation
project
eng; USA
biota
oceans
-80.2635
-80.2635
25.1326
25.1326
2016-01-01
2016-12-30
Florida Keys, Caribbean
0
BCO-DMO catalogue of parameters from Microsatellite loci for Breviolum antillogorgium cultures isolated from the octocoral Antillogorgia bipinnata and used in 2018 growth experiments to compare growth at 26 and 30 degrees C
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/756424.rdf
Name: Culture_ID
Units: Unitless
Description: <p>Identification of sample given as culture name (16-0587)</p>
http://lod.bco-dmo.org/id/dataset-parameter/756425.rdf
Name: Incubation_Temperature
Units: Degree Celsius
Description: <p>Temperature at which the culture is maintained</p>
http://lod.bco-dmo.org/id/dataset-parameter/756426.rdf
Name: Host
Units: Unitless
Description: <p>Octocoral from which the symbiont was isolated. Note - In the vast majority of cases the culture is NOT representative of the host symbiont population (Santos et al 2001)</p>
http://lod.bco-dmo.org/id/dataset-parameter/756427.rdf
Name: Putative_Species
Units: Unitless
Description: <p>Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/756428.rdf
Name: Location
Units: Unitless
Description: <p>collection location</p>
http://lod.bco-dmo.org/id/dataset-parameter/756429.rdf
Name: Latitude
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/756430.rdf
Name: Longitude
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/756431.rdf
Name: State_Country
Units: unitless
Description: <p>collection state and country</p>
http://lod.bco-dmo.org/id/dataset-parameter/756432.rdf
Name: Ocean
Units: unitless
Description: <p>ocean or sea of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/756433.rdf
Name: Host_stage
Units: unitless
Description: <p>growth stage of host</p>
http://lod.bco-dmo.org/id/dataset-parameter/756434.rdf
Name: Axenic
Units: unitless
Description: <p>culture is free from other living organisms</p>
http://lod.bco-dmo.org/id/dataset-parameter/756435.rdf
Name: Isolated_by
Units: unitless
Description: <p>person who isolated sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/756436.rdf
Name: Year_isolated
Units: unitless
Description: <p>the year the culture was isolated</p>
http://lod.bco-dmo.org/id/dataset-parameter/756437.rdf
Name: ITS2_type
Units: Unitless
Description: <p>Classification based on sequence of ITS2 following LaJeunesse et al (2012) and Parkinson et al (2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/756438.rdf
Name: cp_type
Units: base pairs (bp)
Description: <p>Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003a)</p>
http://lod.bco-dmo.org/id/dataset-parameter/756439.rdf
Name: GV_1C
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</p>
http://lod.bco-dmo.org/id/dataset-parameter/756440.rdf
Name: B7SYM34
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</p>
http://lod.bco-dmo.org/id/dataset-parameter/756441.rdf
Name: BYSYM36
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</p>
http://lod.bco-dmo.org/id/dataset-parameter/756442.rdf
Name: CA6_38
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</p>
http://lod.bco-dmo.org/id/dataset-parameter/756443.rdf
Name: B7SYM4
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</p>
http://lod.bco-dmo.org/id/dataset-parameter/756444.rdf
Name: B7SYM8
Units: base pairs (bp)
Description: <p>Microsatellite locus allele size</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
1223
https://darchive.mblwhoilibrary.org/bitstream/1912/24645/1/dataset-756404_breviolum-antillogorgium-microsatellite-loci__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.756404.1
download
onLine
dataset
<p><em>Breviolum antillogorgium</em> cultures were initially isolated from <em>Antillogorgia bipinnata </em>colonies collected at in the upper Florida Reef tract at Elbow Reef (N 25 07.956 W 80 15.810) in September 2016. Culture isolations and cell growth experimentation occurred in the Coffroth lab, University at Buffalo.</p>
<p>DNA was extracted from symbiont cells following Coffroth et al. (1992) and re-suspended in TE buffer (5-15µl, diluted to a concentration of 5ng/µl). Symbionts were characterized using six polymorphic microsatellite loci, B7SYM4, B7SYM8, B7Sym34, B7Sym36, CA6.38 and GV-1C following the protocols of Pettay and LaJeunesse (2007), Andras et al (2009) and Santos et al (2003b).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- converted latitude and longitude to decimal degrees</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
I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences)
I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences)
PI Supplied Instrument Name: I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences) PI Supplied Instrument Description:Fragment analysis of the PCR product of the microsatellite loci were run a on a 25 cm long, 0.25 mm thick, 6.5% non-denaturing polyacrylamide gel on an automated LI-COR 4200 NEN Global IR2 DNA sequencing system (LI-COR Biosciences). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler
a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler
PI Supplied Instrument Name: a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler PI Supplied Instrument Description:Used to amplify microsatellite loci. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)