ERDDAP > info > bcodmo_dataset_756404

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	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		I   M	background			BCO-DMO	bcodmo_dataset_756404

The Dataset's Variables and Attributes

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	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	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.