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Grid DAP Data | Sub- set | Table DAP Data | Make A Graph | W M S | Source Data Files | Acces- sible | Title | Sum- mary | FGDC, ISO, Metadata | Back- ground Info | RSS | E | Institution | Dataset ID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
set | data | graph | files | public | [Breviolum antillogorgium microsatellite loci] - 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 (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs) | F I M | background | BCO-DMO | bcodmo_dataset_756404 |
Row Type | Variable Name | Attribute Name | Data Type | Value |
---|---|---|---|---|
attribute | NC_GLOBAL | access_formats | String | .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson |
attribute | NC_GLOBAL | acquisition_description | String | Breviolum antillogorgium cultures were initially isolated from Antillogorgia bipinnata 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. DNA was extracted from symbiont cells following Coffroth et al. (1992) and re- suspended in TE buffer (5-15\u00b5l, diluted to a concentration of 5ng/\u00b5l). 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). |
attribute | NC_GLOBAL | awards_0_award_nid | String | 658940 |
attribute | NC_GLOBAL | awards_0_award_number | String | OCE-1559286 |
attribute | NC_GLOBAL | awards_0_data_url | String | https://www.nsf.gov/awardsearch/showAward?AWD_ID=1559286 |
attribute | NC_GLOBAL | awards_0_funder_name | String | NSF Division of Ocean Sciences |
attribute | NC_GLOBAL | awards_0_funding_acronym | String | NSF OCE |
attribute | NC_GLOBAL | awards_0_funding_source_nid | String | 355 |
attribute | NC_GLOBAL | awards_0_program_manager | String | David L. Garrison |
attribute | NC_GLOBAL | awards_0_program_manager_nid | String | 50534 |
attribute | NC_GLOBAL | cdm_data_type | String | Other |
attribute | NC_GLOBAL | comment | String | Microsatellite loci for B. antillogorgium cultures PIs: C. terHorst (CSU), M.A. Coffroth (UBuffalo) version: 2019-03-04 |
attribute | NC_GLOBAL | Conventions | String | COARDS, CF-1.6, ACDD-1.3 |
attribute | NC_GLOBAL | creator_email | String | info at bco-dmo.org |
attribute | NC_GLOBAL | creator_name | String | BCO-DMO |
attribute | NC_GLOBAL | creator_type | String | institution |
attribute | NC_GLOBAL | creator_url | String | https://www.bco-dmo.org/ |
attribute | NC_GLOBAL | data_source | String | extract_data_as_tsv version 2.3 19 Dec 2019 |
attribute | NC_GLOBAL | date_created | String | 2019-02-20T20:43:26Z |
attribute | NC_GLOBAL | date_modified | String | 2019-03-04T20:41:41Z |
attribute | NC_GLOBAL | defaultDataQuery | String | &time<now |
attribute | NC_GLOBAL | doi | String | 10.1575/1912/bco-dmo.756404.1 |
attribute | NC_GLOBAL | Easternmost_Easting | double | -80.2635 |
attribute | NC_GLOBAL | geospatial_lat_max | double | 25.1326 |
attribute | NC_GLOBAL | geospatial_lat_min | double | 25.1326 |
attribute | NC_GLOBAL | geospatial_lat_units | String | degrees_north |
attribute | NC_GLOBAL | geospatial_lon_max | double | -80.2635 |
attribute | NC_GLOBAL | geospatial_lon_min | double | -80.2635 |
attribute | NC_GLOBAL | geospatial_lon_units | String | degrees_east |
attribute | NC_GLOBAL | infoUrl | String | https://www.bco-dmo.org/dataset/756404 |
attribute | NC_GLOBAL | institution | String | BCO-DMO |
attribute | NC_GLOBAL | instruments_0_acronym | String | Automated Sequencer |
attribute | NC_GLOBAL | instruments_0_dataset_instrument_description | String | 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). |
attribute | NC_GLOBAL | instruments_0_dataset_instrument_nid | String | 756412 |
attribute | NC_GLOBAL | instruments_0_description | String | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
attribute | NC_GLOBAL | instruments_0_instrument_name | String | Automated DNA Sequencer |
attribute | NC_GLOBAL | instruments_0_instrument_nid | String | 649 |
attribute | NC_GLOBAL | instruments_0_supplied_name | String | I-COR 4200 NEN® Global IR2 DNA sequencing system (LI-COR Biosciences) |
attribute | NC_GLOBAL | instruments_1_acronym | String | Thermal Cycler |
attribute | NC_GLOBAL | instruments_1_dataset_instrument_description | String | Used to amplify microsatellite loci. |
attribute | NC_GLOBAL | instruments_1_dataset_instrument_nid | String | 756422 |
attribute | NC_GLOBAL | instruments_1_description | String | General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) |
attribute | NC_GLOBAL | instruments_1_instrument_name | String | PCR Thermal Cycler |
attribute | NC_GLOBAL | instruments_1_instrument_nid | String | 471582 |
attribute | NC_GLOBAL | instruments_1_supplied_name | String | a PTC-100 MJ Research Inc. thermal cycler or a BioRad T100-Thermal Cycler |
attribute | NC_GLOBAL | keywords | String | axenic, B7SYM34, B7SYM4, B7SYM8, bco, bco-dmo, biological, bysym36, ca6, CA6_38, chemical, country, cp_type, culture, Culture_ID, data, dataset, dmo, erddap, GV_1C, host, Host_stage, incubation, Incubation_Temperature, isolated, Isolated_by, its2, ITS2_type, latitude, Location, longitude, management, ocean, oceanography, office, preliminary, putative, Putative_Species, species, stage, state, State_Country, sym34, sym4, sym8, temperature, type, year, Year_isolated |
attribute | NC_GLOBAL | license | String | https://www.bco-dmo.org/dataset/756404/license |
attribute | NC_GLOBAL | metadata_source | String | https://www.bco-dmo.org/api/dataset/756404 |
attribute | NC_GLOBAL | Northernmost_Northing | double | 25.1326 |
attribute | NC_GLOBAL | param_mapping | String | {'756404': {'Latitude': 'flag - latitude', 'Longitude': 'flag - longitude'}} |
attribute | NC_GLOBAL | parameter_source | String | https://www.bco-dmo.org/mapserver/dataset/756404/parameters |
attribute | NC_GLOBAL | people_0_affiliation | String | State University of New York at Buffalo |
attribute | NC_GLOBAL | people_0_affiliation_acronym | String | SUNY Buffalo |
attribute | NC_GLOBAL | people_0_person_name | String | Mary Alice Coffroth |
attribute | NC_GLOBAL | people_0_person_nid | String | 472488 |
attribute | NC_GLOBAL | people_0_role | String | Principal Investigator |
attribute | NC_GLOBAL | people_0_role_type | String | originator |
attribute | NC_GLOBAL | people_1_affiliation | String | California State University Northridge |
attribute | NC_GLOBAL | people_1_affiliation_acronym | String | CSU-Northridge |
attribute | NC_GLOBAL | people_1_person_name | String | Casey terHorst |
attribute | NC_GLOBAL | people_1_person_nid | String | 632541 |
attribute | NC_GLOBAL | people_1_role | String | Co-Principal Investigator |
attribute | NC_GLOBAL | people_1_role_type | String | originator |
attribute | NC_GLOBAL | people_2_affiliation | String | Woods Hole Oceanographic Institution |
attribute | NC_GLOBAL | people_2_affiliation_acronym | String | WHOI BCO-DMO |
attribute | NC_GLOBAL | people_2_person_name | String | Nancy Copley |
attribute | NC_GLOBAL | people_2_person_nid | String | 50396 |
attribute | NC_GLOBAL | people_2_role | String | BCO-DMO Data Manager |
attribute | NC_GLOBAL | people_2_role_type | String | related |
attribute | NC_GLOBAL | project | String | Host Symbiont Temp Response |
attribute | NC_GLOBAL | projects_0_acronym | String | Host Symbiont Temp Response |
attribute | NC_GLOBAL | projects_0_description | String | Description from NSF award abstract: 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. 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. |
attribute | NC_GLOBAL | projects_0_end_date | String | 2020-03 |
attribute | NC_GLOBAL | projects_0_geolocation | String | Florida Keys, Caribbean |
attribute | NC_GLOBAL | projects_0_name | String | RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs |
attribute | NC_GLOBAL | projects_0_project_nid | String | 632538 |
attribute | NC_GLOBAL | projects_0_start_date | String | 2016-04 |
attribute | NC_GLOBAL | publisher_name | String | Biological and Chemical Oceanographic Data Management Office (BCO-DMO) |
attribute | NC_GLOBAL | publisher_type | String | institution |
attribute | NC_GLOBAL | sourceUrl | String | (local files) |
attribute | NC_GLOBAL | Southernmost_Northing | double | 25.1326 |
attribute | NC_GLOBAL | standard_name_vocabulary | String | CF Standard Name Table v55 |
attribute | NC_GLOBAL | subsetVariables | String | Host,Putative_Species,Location,latitude,longitude,State_Country,Ocean,Host_stage,Axenic,Isolated_by,Year_isolated,ITS2_type,B7SYM4 |
attribute | NC_GLOBAL | summary | String | 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 |
attribute | NC_GLOBAL | title | String | [Breviolum antillogorgium microsatellite loci] - 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 (RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs) |
attribute | NC_GLOBAL | version | String | 1 |
attribute | NC_GLOBAL | Westernmost_Easting | double | -80.2635 |
attribute | NC_GLOBAL | xml_source | String | osprey2erddap.update_xml() v1.3 |
variable | Culture_ID | String | ||
attribute | Culture_ID | bcodmo_name | String | sample |
attribute | Culture_ID | description | String | Identification of sample given as culture name (16-0587) |
attribute | Culture_ID | long_name | String | Culture ID |
attribute | Culture_ID | nerc_identifier | String | https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ |
attribute | Culture_ID | units | String | Unitless |
variable | Incubation_Temperature | byte | ||
attribute | Incubation_Temperature | _FillValue | byte | 127 |
attribute | Incubation_Temperature | actual_range | byte | 26, 30 |
attribute | Incubation_Temperature | bcodmo_name | String | temp_inc |
attribute | Incubation_Temperature | description | String | Temperature at which the culture is maintained |
attribute | Incubation_Temperature | long_name | String | Incubation Temperature |
attribute | Incubation_Temperature | nerc_identifier | String | https://vocab.nerc.ac.uk/collection/P01/current/TINCDTNX/ |
attribute | Incubation_Temperature | units | String | Degree Celsius |
variable | Host | String | ||
attribute | Host | bcodmo_name | String | species |
attribute | Host | description | String | 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) |
attribute | Host | long_name | String | Host |
attribute | Host | units | String | Unitless |
variable | Putative_Species | String | ||
attribute | Putative_Species | bcodmo_name | String | species |
attribute | Putative_Species | description | String | Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015) |
attribute | Putative_Species | long_name | String | Putative Species |
attribute | Putative_Species | units | String | Unitless |
variable | Location | String | ||
attribute | Location | bcodmo_name | String | region |
attribute | Location | description | String | collection location |
attribute | Location | long_name | String | Location |
attribute | Location | units | String | Unitless |
variable | latitude | double | ||
attribute | latitude | _CoordinateAxisType | String | Lat |
attribute | latitude | _FillValue | double | NaN |
attribute | latitude | actual_range | double | 25.1326, 25.1326 |
attribute | latitude | axis | String | Y |
attribute | latitude | bcodmo_name | String | latitude |
attribute | latitude | colorBarMaximum | double | 90.0 |
attribute | latitude | colorBarMinimum | double | -90.0 |
attribute | latitude | description | String | latitude; north is positive |
attribute | latitude | ioos_category | String | Location |
attribute | latitude | long_name | String | Latitude |
attribute | latitude | nerc_identifier | String | https://vocab.nerc.ac.uk/collection/P09/current/LATX/ |
attribute | latitude | standard_name | String | latitude |
attribute | latitude | units | String | degrees_north |
variable | longitude | double | ||
attribute | longitude | _CoordinateAxisType | String | Lon |
attribute | longitude | _FillValue | double | NaN |
attribute | longitude | actual_range | double | -80.2635, -80.2635 |
attribute | longitude | axis | String | X |
attribute | longitude | bcodmo_name | String | longitude |
attribute | longitude | colorBarMaximum | double | 180.0 |
attribute | longitude | colorBarMinimum | double | -180.0 |
attribute | longitude | description | String | longitude; east is positive |
attribute | longitude | ioos_category | String | Location |
attribute | longitude | long_name | String | Longitude |
attribute | longitude | nerc_identifier | String | https://vocab.nerc.ac.uk/collection/P09/current/LONX/ |
attribute | longitude | standard_name | String | longitude |
attribute | longitude | units | String | degrees_east |
variable | State_Country | String | ||
attribute | State_Country | bcodmo_name | String | region |
attribute | State_Country | description | String | collection state and country |
attribute | State_Country | long_name | String | State Country |
attribute | State_Country | units | String | unitless |
variable | Ocean | String | ||
attribute | Ocean | bcodmo_name | String | region |
attribute | Ocean | description | String | ocean or sea of collection |
attribute | Ocean | long_name | String | Ocean |
attribute | Ocean | units | String | unitless |
variable | Host_stage | String | ||
attribute | Host_stage | bcodmo_name | String | stage |
attribute | Host_stage | description | String | growth stage of host |
attribute | Host_stage | long_name | String | Host Stage |
attribute | Host_stage | units | String | unitless |
variable | Axenic | String | ||
attribute | Axenic | bcodmo_name | String | sample_descrip |
attribute | Axenic | description | String | culture is free from other living organisms |
attribute | Axenic | long_name | String | Axenic |
attribute | Axenic | units | String | unitless |
variable | Isolated_by | String | ||
attribute | Isolated_by | bcodmo_name | String | person |
attribute | Isolated_by | description | String | person who isolated sample |
attribute | Isolated_by | long_name | String | Isolated By |
attribute | Isolated_by | units | String | unitless |
variable | Year_isolated | short | ||
attribute | Year_isolated | _FillValue | short | 32767 |
attribute | Year_isolated | actual_range | short | 2016, 2016 |
attribute | Year_isolated | bcodmo_name | String | year |
attribute | Year_isolated | description | String | the year the culture was isolated |
attribute | Year_isolated | long_name | String | Year Isolated |
attribute | Year_isolated | nerc_identifier | String | https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/ |
attribute | Year_isolated | units | String | unitless |
variable | ITS2_type | String | ||
attribute | ITS2_type | bcodmo_name | String | unknown |
attribute | ITS2_type | description | String | Classification based on sequence of ITS2 following LaJeunesse et al (2012) and Parkinson et al (2015) |
attribute | ITS2_type | long_name | String | ITS2 Type |
attribute | ITS2_type | units | String | Unitless |
variable | cp_type | short | ||
attribute | cp_type | _FillValue | short | 32767 |
attribute | cp_type | actual_range | short | 184, 185 |
attribute | cp_type | bcodmo_name | String | unknown |
attribute | cp_type | description | String | Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003a) |
attribute | cp_type | long_name | String | Cp Type |
attribute | cp_type | units | String | base pairs (bp) |
variable | GV_1C | short | ||
attribute | GV_1C | _FillValue | short | 32767 |
attribute | GV_1C | actual_range | short | 298, 330 |
attribute | GV_1C | bcodmo_name | String | unknown |
attribute | GV_1C | description | String | Microsatellite locus allele size |
attribute | GV_1C | long_name | String | GV 1 C |
attribute | GV_1C | units | String | base pairs (bp) |
variable | B7SYM34 | short | ||
attribute | B7SYM34 | _FillValue | short | 32767 |
attribute | B7SYM34 | actual_range | short | 277, 285 |
attribute | B7SYM34 | bcodmo_name | String | unknown |
attribute | B7SYM34 | description | String | Microsatellite locus allele size |
attribute | B7SYM34 | long_name | String | B7 SYM34 |
attribute | B7SYM34 | units | String | base pairs (bp) |
variable | BYSYM36 | short | ||
attribute | BYSYM36 | _FillValue | short | 32767 |
attribute | BYSYM36 | actual_range | short | 183, 185 |
attribute | BYSYM36 | bcodmo_name | String | unknown |
attribute | BYSYM36 | description | String | Microsatellite locus allele size |
attribute | BYSYM36 | long_name | String | BYSYM36 |
attribute | BYSYM36 | units | String | base pairs (bp) |
variable | CA6_38 | byte | ||
attribute | CA6_38 | _FillValue | byte | 127 |
attribute | CA6_38 | actual_range | byte | 119, 125 |
attribute | CA6_38 | bcodmo_name | String | unknown |
attribute | CA6_38 | description | String | Microsatellite locus allele size |
attribute | CA6_38 | long_name | String | CA6 38 |
attribute | CA6_38 | units | String | base pairs (bp) |
variable | B7SYM4 | short | ||
attribute | B7SYM4 | _FillValue | short | 32767 |
attribute | B7SYM4 | actual_range | short | 149, 149 |
attribute | B7SYM4 | bcodmo_name | String | unknown |
attribute | B7SYM4 | description | String | Microsatellite locus allele size |
attribute | B7SYM4 | long_name | String | B7 SYM4 |
attribute | B7SYM4 | units | String | base pairs (bp) |
variable | B7SYM8 | short | ||
attribute | B7SYM8 | _FillValue | short | 32767 |
attribute | B7SYM8 | actual_range | short | 218, 220 |
attribute | B7SYM8 | bcodmo_name | String | unknown |
attribute | B7SYM8 | description | String | Microsatellite locus allele size |
attribute | B7SYM8 | long_name | String | B7 SYM8 |
attribute | B7SYM8 | units | String | base pairs (bp) |
The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.