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Dataset Title:  Experimental results of turbulence-exposed sand dollar Dendraster excentricus
larvae and their response to a variety of settlement cues
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_740414)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Data Access Form | Files
 
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Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  figure {
    Byte _FillValue 127;
    Byte actual_range 1, 3;
    String bcodmo_name "unknown";
    String description "figure number from BMC Zoology publication";
    String long_name "Figure";
    String units "unitless";
  }
  competence {
    String bcodmo_name "unknown";
    String description "readiness of the larvae to settle";
    String long_name "Competence";
    String units "unitless";
  }
  date_expt {
    String bcodmo_name "date";
    String description "date of experiment formatted as yyyy-mm-dd";
    String long_name "Date Expt";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String source_name "date_expt";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  species {
    String bcodmo_name "species";
    String description "species name";
    String long_name "Species";
    String units "unitless";
  }
  rpm {
    String bcodmo_name "unknown";
    String description "rotations per minute of the Taylor-Couette cell; unmanip = no rotation applied";
    String long_name "RPM";
    String units "rotations per minute";
  }
  replicate {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "replicate";
    String description "replicate number";
    String long_name "Replicate";
    String units "unitless";
  }
  dpf {
    Byte _FillValue 127;
    Byte actual_range 10, 18;
    String bcodmo_name "days";
    String description "days post fertilization";
    String long_name "DPF";
    String units "days";
  }
  cue {
    String bcodmo_name "treatment";
    String description "settlement inducing media; MFSW = Millipore-filtered seawater; KCl = potassium chloride in seawater";
    String long_name "Cue";
    String units "unitless";
  }
  number_larvae {
    Byte _FillValue 127;
    Byte actual_range 12, 27;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of larvae in experiment";
    String long_name "Number Larvae";
    String units "larvae";
  }
  number_settled {
    Byte _FillValue 127;
    Byte actual_range 0, 11;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae";
    String long_name "Number Settled";
    String units "larvae";
  }
  number_settled_0hr {
    Byte _FillValue 127;
    Byte actual_range 0, 17;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at time 0";
    String long_name "Number Settled 0hr";
    String units "larvae";
  }
  number_settled_1hr {
    Byte _FillValue 127;
    Byte actual_range 0, 22;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at 1 hour";
    String long_name "Number Settled 1hr";
    String units "larvae";
  }
  number_settled_16hr {
    Byte _FillValue 127;
    Byte actual_range 0, 27;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at 16 hours";
    String long_name "Number Settled 16hr";
    String units "larvae";
  }
  number_on_bottom {
    Byte _FillValue 127;
    Byte actual_range 0, 14;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae";
    String long_name "Number On Bottom";
    String units "larvae";
  }
  number_settled_1_5hr {
    Byte _FillValue 127;
    Byte actual_range 0, 13;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at 1.5 hours";
    String long_name "Number Settled 1 5hr";
    String units "larvae";
  }
  number_settled_8hr {
    Byte _FillValue 127;
    Byte actual_range 0, 17;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at 8 hours";
    String long_name "Number Settled 8hr";
    String units "larvae";
  }
  number_settled_18hr {
    Byte _FillValue 127;
    Byte actual_range 0, 17;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of settled larvae at 18 hours";
    String long_name "Number Settled 18hr";
    String units "larvae";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Figure 1: Early competent sand dollar larvae do not display 'desperate'
behaviors at settlement, with or without turbulence exposure. We either
exposed D. excentricus larvae 10 day post fertilization (dpf) (reared at
~20\\u00b0C) to 3 min of 6 W/kg turbulent shear or did not. Then, we
transferred exposed and control larvae into one of two settlement conditions:
24 hrs in MFSW alone (left side of graph) or a 1 hr exposure to 40mM excess
KCl in MFSW \\u2013to assess competence\\u2013 followed by a 24 hr recovery in
MFSW. We detected an effect both of turbulence exposure (F1,12=5.36, p<0.02)
and settlement medium (F1,12=228.93, p<0.001) on proportion of larvae settled,
but no clear interaction (F1,12=3.41, p=0.09).
 
Figure 2: Fully competent sand dollar larvae exposed to turbulence are less
choosy about settlement substrate, and thus behave like 'desperate' larvae. We
either exposed D.\\u00a0excentricus larvae 11\\u00a0dpf\\u00a0(reared at
~20\\u00b0C) to 3 min of 6 W/kg turbulent shear or did not (\\\"no turbulence\\\").
Then, we transferred exposed and control larvae into one of two settlement
conditions: 0% extract of sand from sand dollar aquaria (MFSW; no inducer) or
40% extract of sand from sand dollar aquaria (strong natural inducer), and
counted the numbers settled at 1 and 16 hrs. We also exposed a separate set of
control (no turbulence) larvae for 1 hr to 40mM excess KCl in MFSW, followed
by recovery in MFSW. More than 95% of these latter larvae settled, confirming
that the larvae in this experiment were indeed fully competent.
 
Figure 3: Fully competent sand dollar larvae exposed to turbulence are less
choosy about settlement substrate, and thus behave like 'desperate' larvae. We
either exposed D. excentricus larvae 40 dpf (reared at ~14\\u00b0C) to 3 min of
6 W/kg turbulent shear or did not (\\\"no turbulence\\\"). Then, we transferred
exposed and control larvae into one of two settlement conditions: 0% extract
of sand from sand dollar aquaria (MFSW; no inducer) or 200% extract of sand
from a beach without sand dollars (poor quality natural inducer), and counted
the numbers settled at 1.5, 3, 7.5 and 19 hrs. We also exposed a separate set
of control (no turbulence) larvae to a strong natural inducer (30% extract of
sand from sand dollar aquaria; right side of graph). This treatment not only
confirms that the larvae were fully competent (100% of larvae settled by 8
hrs), but indicates the expected rate of settlement response in a strong cue
as a basis of comparison to the sub-optimal cues described above.
 
We performed all statistical analyses using R (version 3.4.2) and the lme4
package.";
    String awards_0_award_nid "505515";
    String awards_0_award_number "OCE-1356966";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1356966";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String awards_1_award_nid "505516";
    String awards_1_award_number "OCE-1357033";
    String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1357033";
    String awards_1_funder_name "NSF Division of Ocean Sciences";
    String awards_1_funding_acronym "NSF OCE";
    String awards_1_funding_source_nid "355";
    String awards_1_program_manager "Michael E. Sieracki";
    String awards_1_program_manager_nid "50446";
    String awards_2_award_nid "505517";
    String awards_2_award_number "OCE-1357077";
    String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1357077";
    String awards_2_funder_name "NSF Division of Ocean Sciences";
    String awards_2_funding_acronym "NSF OCE";
    String awards_2_funding_source_nid "355";
    String awards_2_program_manager "Michael E. Sieracki";
    String awards_2_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"Settling response of sand dollar D.excentricus to turbulence 
   P.I.: M. Ferner (SFSU) 
   version: 2018-07-19 
   NOTE: to be published in Hodin et al, BMC Zoology, Figs. 1, 2, 3";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2018-07-19T13:39:23Z";
    String date_modified "2019-12-04T14:36:48Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.740414.1";
    String history 
"2022-08-09T14:09:44Z (local files)
2022-08-09T14:09:44Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_740414.das";
    String infoUrl "https://www.bco-dmo.org/dataset/740414";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_description 
"To generate turbulence intensities (quantified in terms of the energy dissipation rate, in units ofWkg−1) ranging from those found in open ocean waters to those arising on wave-battered coasts, we employed a Taylor–Couette cell [29], an apparatus composed of two vertically oriented, coaxial cylinders separated by a 3.5mm gap that contains seawater (described in greater detail in [1]). We held the stationary inner cylinder, and thus the water in the gap, at 19–21◦C by means of a circulating water stream from a temperature-controlled water bath passing through the cylinder’s interior. During operation, the outer cylinder rotated at a prescribed speed causing relative motion between the cylinders and thereby shearing the seawater between them. At rotation speeds employed for testing sand dollar larvae, the
sheared flow was turbulent [1].
[1]Gaylord B, Hodin J, Ferner MC. 2013 Turbulent shear spurs settlement in larval sea urchins. Proc. Natl Acad. Sci. USA 110, 6901–6906. (doi:10.1073/pnas.
1220680110)";
    String instruments_0_dataset_instrument_nid "740425";
    String instruments_0_description "An apparatus composed of two vertically oriented, coaxial cylinders separated by a gap that contains seawater. During operation, the outer cylinder rotates at a prescribed speed causing relative motion between the cylinders and thereby shearing the seawater between them.";
    String instruments_0_instrument_name "Taylor–Couette system";
    String instruments_0_instrument_nid "640422";
    String keywords "0hr, 16hr, 18hr, 1hr, 5hr, 8hr, bco, bco-dmo, biological, bottom, chemical, competence, cue, data, dataset, date, dmo, dpf, erddap, expt, figure, larvae, management, number, number_larvae, number_on_bottom, number_settled, number_settled_0hr, number_settled_16hr, number_settled_18hr, number_settled_1_5hr, number_settled_1hr, number_settled_8hr, oceanography, office, preliminary, replicate, rpm, settled, species, time";
    String license "https://www.bco-dmo.org/dataset/740414/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/740414";
    String param_mapping "{'740414': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/740414/parameters";
    String people_0_affiliation "San Francisco State University";
    String people_0_affiliation_acronym "SFSU-RTC";
    String people_0_person_name "Dr Matthew Ferner";
    String people_0_person_nid "472791";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of California-Davis";
    String people_1_affiliation_acronym "UC Davis-BML";
    String people_1_person_name "Dr Brian Gaylord";
    String people_1_person_nid "51061";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of Washington";
    String people_2_affiliation_acronym "FHL";
    String people_2_person_name "Dr Jason Hodin";
    String people_2_person_nid "544695";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Stanford University - Hopkins";
    String people_3_affiliation_acronym "Stanford-HMS";
    String people_3_person_name "Dr Christopher Lowe";
    String people_3_person_nid "472792";
    String people_3_role "Co-Principal Investigator";
    String people_3_role_type "originator";
    String people_4_affiliation "San Francisco State University";
    String people_4_affiliation_acronym "SFSU-RTC";
    String people_4_person_name "Dr Matthew Ferner";
    String people_4_person_nid "472791";
    String people_4_role "Contact";
    String people_4_role_type "related";
    String people_5_affiliation "Woods Hole Oceanographic Institution";
    String people_5_affiliation_acronym "WHOI BCO-DMO";
    String people_5_person_name "Nancy Copley";
    String people_5_person_nid "50396";
    String people_5_role "BCO-DMO Data Manager";
    String people_5_role_type "related";
    String project "Turbulence-spurred settlement";
    String projects_0_acronym "Turbulence-spurred settlement";
    String projects_0_description 
"Description from NSF award abstract:
With this award the investigators will explore a habitat-scale oceanographic process that has the potential to integrate studies of larval delivery with an understanding of how larvae respond to substrate-associated cues. This work will build on published and preliminary data indicating that turbulent shear characteristic of high-energy near shore environments primes larvae to initiate settlement and to transform into the juvenile stage. These prior findings suggest that: 1) Because turbulence intensity varies predictably as a function of the strength of wave breaking and other factors, turbulence could operate as an indicator for larvae of their approach to suitable habitat, providing a link between larger-scale dispersal phenomena, and near-bottom search and selection behaviors; and 2) The larval response to turbulence acts in an unprecedented fashion. In contrast to typical cues, turbulence does not induce settlement directly, but rather spurs otherwise \"pre-competent\" larvae that are refractory to chemical cues to become \"competent\", thereby causing them to acquire responsiveness to such cues and undergo settlement. The interdisciplinary team has combined expertise in larval biology, sensory ecology, and organism-flow interactions necessary to address this topic. They will employ a phylogenetically robust approach to explore the scope and adaptive significance of the turbulence response in a widespread and ecologically important class of organisms (echinoids; sea urchins and their relatives), and will determine whether the response is aligned with environmental conditions characteristic of these organisms' adult habitat. They will also test for ecologically important functional consequences of precocious, turbulence-induced settlement. This work will provide a detailed look at an entirely new class of settlement inducer, one with strong potential for changing current conceptualizations of dispersing larval stages, their ability to detect signatures of habitat across multiple scales, and the ways in which organism-level traits might influence population connectivity.
How organisms with dispersing life stages find their way back to adult habitat is a fundamental question in marine ecology. Considerable research has explored links between transport, delivery, settlement, and recruitment, with important advances in knowledge. However, a complete understanding of the larval recruitment process remains elusive. Standard tools for estimating dispersal (e.g., numerical circulation models) have limited spatial resolution, which prevents them from predicting at scales below a few hundred meters how larvae will interact with the shore. Studies investigating larval attachment have focused on chemical, tactile, or near-bottom hydrodynamic cues active across microns to centimeters. The novelty of the present project is that it will focus on processes at habitat scales -- between transport and settlement -- where there is a gap in the understanding of processes.
This project will provide a framework for integrating key concepts of propagule dispersal and settlement, two fundamental but largely disjunct themes in marine science. The understanding that will come from this study will provide key information for ecosystem based management of coastal marine resources. The investigators will develop a \"Surfing to Settlement\" virtual lab activity based on their research that will be incorporated into the VirtualUrchin web platform, a widely exploited educational resource at Stanford that gets thousands of unique users per month. Through connections to the San Francisco Bay National Estuarine Research Reserve, they will integrate the \"Surfing to Settlement\" activity into one of NERRs professional development workshops for central California educators, thus disseminating this resource to and gaining valuable feedback from dozens of teachers and thousands of students.";
    String projects_0_end_date "2017-01";
    String projects_0_geolocation "Northeast Pacific";
    String projects_0_name "Turbulence-spurred settlement: Deciphering a newly recognized class of larval response";
    String projects_0_project_nid "472793";
    String projects_0_start_date "2014-02";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "species";
    String summary "Experimental results of turbulence-exposed sand dollar Dendraster excentricus larvae and their response to a variety of settlement cues.";
    String title "Experimental results of turbulence-exposed sand dollar Dendraster excentricus larvae and their response to a variety of settlement cues";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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