http://lod.bco-dmo.org/id/dataset/853900 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 2021-06-16 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey 2021-06-16 publication 2021-06-16 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2021-06-17 publication https://doi.org/10.26008/1912/bco-dmo.853900.1 Hans G. Dam University of Connecticut 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: Dam, H. G. (2021) Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.853900.1 [access date] Chemical Defenses-5: Park and Dam 2021 Dataset Description: Methods and Sampling: &lt;p&gt;Refer to the Methods section of Park &amp;amp; Dam (2021).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Sample collection and culture:&lt;/strong&gt;&lt;br /&gt; The toxigenic dinoflagellate, &lt;em&gt;Alexandrium catenella&lt;/em&gt; (strain BF-5, isolated from the Bay of Fundy, Canada) was grown in F/2 medium without silicate. Cultures were maintained in the exponential growth phase and all experiments were conducted in an environmental chamber kept at 18°C and illuminated with fluorescent lighting (~100 µM m⁻² s⁻¹) set to a 12 h:12 h light:dark photoperiod. The calanoid copepod &lt;em&gt;Acartia hudsonica,&lt;/em&gt; historically co-occurring with toxic &lt;em&gt;A. catenella,&lt;/em&gt; was collected from Casco Bay, Maine, U.S.A. (43°39′N, 74°47′W), a location in which blooms of &lt;em&gt;A. catenella&lt;/em&gt; are common. Triplicate copepod cultures were maintained with a mixed diet of &lt;em&gt;Rhodomonas &lt;/em&gt;sp., &lt;em&gt;Tetraselmis&lt;/em&gt; sp., and &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt;.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Grazer-induced toxin production assay:&lt;/strong&gt;&lt;br /&gt; &lt;em&gt;Alexandrium catenella&lt;/em&gt; cells were placed in 500 ml bottles (300 cells ml⁻¹) either without copepods (controls: constitutive toxin production) or with 20 adult female &lt;em&gt;A. hudsonica&lt;/em&gt; (treatments) for a period of 96 h. Experiments were done in quadruplicate sets for both control and treatment, and carried out at 18 °C in a walk-in environmental chamber as described above. For the time series analysis, &lt;em&gt;A. catenella&lt;/em&gt; cells were harvested at the conclusion of each exposure time (0, 4, 8, 24, 48, 72, and 96 h) after which cells were gently separated by wet-sieving onto a 63 μm mesh to remove copepods, nauplii, eggs, and fecal pellets. Two aliquots from each bottle were filtered onto 5 μm pore size polycarbonate membranes; one for toxin analysis and another for RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Toxin and gene expression analysis:&lt;/strong&gt;&lt;br /&gt; PST concentrations were determined by reverse-phase ion-pairing high performance liquid chromatography (HPLC) using the post-column oxidative fluorescence method. Gene expression analyses were conducted using reverse transcription quantitative PCR (RT-qPCR). From previous studies several pairs of primers were designed and tested for specificity and PCR efficiency by RT-qPCR. All quantitative PCRs (qPCRs) were performed on a StepOnePlus™ real-time PCR system (Applied Biosystems) and run in 10 μL reactions with Fast SYBR® Green Master Mix (Applied Biosystems).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130284 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130284 completed Hans G. Dam University of Connecticut 860-405-9098 Dept. of Marine Sciences 1080 Shennecossett Road Groton CT 06340-6048 USA hans.dam@uconn.edu pointOfContact asNeeded Dataset Version: 1 Unknown Name Day Hour Cell_Number Growth_Rate Toxin_Content utox Rtox GTX3 GTX4 NEO STX C2 RGE_stxA4 RGE_stxG RGE_cyc g g_modified Cm Cm_modified I I_modified HPLC system (Waters, Milford, MA) Fastprep-24 Tissue and Cell Homogenizer (MP Biomedicals, Solon, OH) Olympus IX70 inverted system microscope StepOnePlus™ real-time PCR system (Applied BiosystemsTM) theme None, User defined sample identification time_elapsed cell_concentration growth No BCO-DMO term featureType BCO-DMO Standard Parameters High-Performance Liquid Chromatograph Homogenizer Inverted Microscope qPCR 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. Chemical Defenses in a Toxic Dinoflagellate: Mechanisms and Constraints https://osprey.bco-dmo.org/project/561498 Chemical Defenses in a Toxic Dinoflagellate: Mechanisms and Constraints <p><em>Description from NSF award abstract:</em><br /> Species of the dinoflagellate genus Alexandrium occur around the globe, and some species, because of their toxin production, have been hypothesized to be keystone species. Alexandrium produces chemical compounds that appear to target different consumers. Neurotoxins such as PST target metazoan grazers. In preliminary experiments in their laboratory, the investigators also verified the presence of reactive oxygen species that target, at a minimum, protistan grazers. Such compounds reduce grazer fitness, and, at least in the case of PST, have been shown to have profound evolutionary effects on grazers. Grazer adaptation, in turn, can affect Alexandrium population dynamics. A common assumption is that production of toxic compounds in phytoplankton represents an adaptive defense. However, unequivocal experimental evidence in support of this hypothesis is scarce. This project will be a rigorous experimental test of the chemical defense hypothesis. The project's investigators will investigate a series of experimentally falsifiable hypotheses with both metazoan and protistan grazers challenged with Alexandrium. This project will provide novel understanding of, and insight into, the factors that determine grazer-induced toxin production, the relationship between degree of chemical defense and susceptibility to grazing, and the costs and tradeoffs of the purported mechanisms of chemical defense in Alexandrium. Verification or refutation of the chemical defense hypothesis is essential to conceptual models of the formation, control and persistence of toxic algal blooms, and chemically-mediated predator-prey interactions.</p> Chemical Defenses largerWorkCitation project eng; USA oceans -72.06196 -72.06196 41.320717 41.320717 2011-09-01 2018-05-31 New England waters from Connecticut to Maine 0 BCO-DMO catalogue of parameters from Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey 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/853914.rdf Name: Name Units: unitless Description: <p>Alexandrium catenella cells, either without grazers (control) or with grazers (treatment)</p> http://lod.bco-dmo.org/id/dataset-parameter/853915.rdf Name: Day Units: days Description: <p>Experimental time for a period of 4 days</p> http://lod.bco-dmo.org/id/dataset-parameter/853916.rdf Name: Hour Units: hours Description: <p>Harvested time at the conclusion of each exposure hr (0, 4, 8, 24, 48, 72, and 96 hr)</p> http://lod.bco-dmo.org/id/dataset-parameter/853917.rdf Name: Cell_Number Units: cells per milliliter (cells ml-1) Description: <p>Cell concentration</p> http://lod.bco-dmo.org/id/dataset-parameter/853918.rdf Name: Growth_Rate Units: per day (d-1) Description: <p>Net growth rate</p> http://lod.bco-dmo.org/id/dataset-parameter/853919.rdf Name: Toxin_Content Units: femtomoles per cell (fmol cell-1) Description: <p>Total cellular toxin content</p> http://lod.bco-dmo.org/id/dataset-parameter/853920.rdf Name: utox Units: per day (d-1) Description: <p>Toxin production rate</p> http://lod.bco-dmo.org/id/dataset-parameter/853921.rdf Name: Rtox Units: femtomoles per cell per day (fmol cell-1 d-1) Description: <p>Net toxin production rate</p> http://lod.bco-dmo.org/id/dataset-parameter/853922.rdf Name: GTX3 Units: femtomoles per cell (fmol cell-1) Description: <p>gonyautoxin 3</p> http://lod.bco-dmo.org/id/dataset-parameter/853923.rdf Name: GTX4 Units: femtomoles per cell (fmol cell-1) Description: <p>gonyautoxin 4</p> http://lod.bco-dmo.org/id/dataset-parameter/853924.rdf Name: NEO Units: femtomoles per cell (fmol cell-1) Description: <p>neosaxitoxin</p> http://lod.bco-dmo.org/id/dataset-parameter/853925.rdf Name: STX Units: femtomoles per cell (fmol cell-1) Description: <p>saxitoxin</p> http://lod.bco-dmo.org/id/dataset-parameter/853926.rdf Name: C2 Units: femtomoles per cell (fmol cell-1) Description: <p>C-2 toxin</p> http://lod.bco-dmo.org/id/dataset-parameter/853927.rdf Name: RGE_stxA4 Units: unitless Description: <p>Relative gene expression level of the stxA4 gene compared to the reference gene (lbpn)</p> http://lod.bco-dmo.org/id/dataset-parameter/853928.rdf Name: RGE_stxG Units: unitless Description: <p>Relative gene expression level of the stxG gene compared to the reference gene (lbpn)</p> http://lod.bco-dmo.org/id/dataset-parameter/853929.rdf Name: RGE_cyc Units: unitless Description: <p>Relative gene expression level of the cyc gene compared to the reference gene (lbpn)</p> http://lod.bco-dmo.org/id/dataset-parameter/853930.rdf Name: g Units: per day (d-1) Description: <p>Grazing rate</p> http://lod.bco-dmo.org/id/dataset-parameter/853931.rdf Name: g_modified Units: per day (d-1) Description: <p>Modified grazing rate (this study)</p> http://lod.bco-dmo.org/id/dataset-parameter/853932.rdf Name: Cm Units: cells per milliliter (cells ml-1) Description: <p>Average cell concentration</p> http://lod.bco-dmo.org/id/dataset-parameter/853933.rdf Name: Cm_modified Units: cells per milliliter (cells ml-1) Description: <p>Modified average cell concentration (this study)</p> http://lod.bco-dmo.org/id/dataset-parameter/853934.rdf Name: I Units: cells per copepod per day (cells cop-1 d-1) Description: <p>Ingestion rate</p> http://lod.bco-dmo.org/id/dataset-parameter/853935.rdf Name: I_modified Units: cells per copepod per day (cells cop-1 d-1) Description: <p>Modified ingestion rate (this study)</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 4844 https://darchive.mblwhoilibrary.org/bitstream/1912/27251/1/dataset-853900_chemical-defenses-5-park-and-dam-2021__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.853900.1 download onLine dataset &lt;p&gt;Refer to the Methods section of Park &amp;amp; Dam (2021).&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Sample collection and culture:&lt;/strong&gt;&lt;br /&gt; The toxigenic dinoflagellate, &lt;em&gt;Alexandrium catenella&lt;/em&gt; (strain BF-5, isolated from the Bay of Fundy, Canada) was grown in F/2 medium without silicate. Cultures were maintained in the exponential growth phase and all experiments were conducted in an environmental chamber kept at 18°C and illuminated with fluorescent lighting (~100 µM m⁻² s⁻¹) set to a 12 h:12 h light:dark photoperiod. The calanoid copepod &lt;em&gt;Acartia hudsonica,&lt;/em&gt; historically co-occurring with toxic &lt;em&gt;A. catenella,&lt;/em&gt; was collected from Casco Bay, Maine, U.S.A. (43°39′N, 74°47′W), a location in which blooms of &lt;em&gt;A. catenella&lt;/em&gt; are common. Triplicate copepod cultures were maintained with a mixed diet of &lt;em&gt;Rhodomonas &lt;/em&gt;sp., &lt;em&gt;Tetraselmis&lt;/em&gt; sp., and &lt;em&gt;Thalassiosira weissflogii&lt;/em&gt;.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Grazer-induced toxin production assay:&lt;/strong&gt;&lt;br /&gt; &lt;em&gt;Alexandrium catenella&lt;/em&gt; cells were placed in 500 ml bottles (300 cells ml⁻¹) either without copepods (controls: constitutive toxin production) or with 20 adult female &lt;em&gt;A. hudsonica&lt;/em&gt; (treatments) for a period of 96 h. Experiments were done in quadruplicate sets for both control and treatment, and carried out at 18 °C in a walk-in environmental chamber as described above. For the time series analysis, &lt;em&gt;A. catenella&lt;/em&gt; cells were harvested at the conclusion of each exposure time (0, 4, 8, 24, 48, 72, and 96 h) after which cells were gently separated by wet-sieving onto a 63 μm mesh to remove copepods, nauplii, eggs, and fecal pellets. Two aliquots from each bottle were filtered onto 5 μm pore size polycarbonate membranes; one for toxin analysis and another for RNA extraction.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Toxin and gene expression analysis:&lt;/strong&gt;&lt;br /&gt; PST concentrations were determined by reverse-phase ion-pairing high performance liquid chromatography (HPLC) using the post-column oxidative fluorescence method. Gene expression analyses were conducted using reverse transcription quantitative PCR (RT-qPCR). From previous studies several pairs of primers were designed and tested for specificity and PCR efficiency by RT-qPCR. All quantitative PCRs (qPCRs) were performed on a StepOnePlus™ real-time PCR system (Applied Biosystems) and run in 10 μL reactions with Fast SYBR® Green Master Mix (Applied Biosystems).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Data Processing:&lt;/strong&gt;&lt;br /&gt; A Kruskal-Wallis one-way ANOVA on ranks was used and all pairwise comparisons among controls/treatments were assessed with the Student-Newman-Keul’s (SNK) post-hoc procedure. The effects of day, presence of grazer, and their interaction on cell concentration, toxin content, toxin profile, growth rate, and relative gene expression (four independent replicates per test and two samples for PST analysis) were tested by two-way ANOVA. Time-dependent changes in these variables were also tested separately by regression analysis for the control and treatments. Ingestion rates were tested with a Mann-Whitney U Test to compare the Frost equation to our modified equation. All statistical analyses were performed using SigmaPlot version 11.0 and SPSS version 26 software.&lt;/p&gt; 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 HPLC system (Waters, Milford, MA) HPLC system (Waters, Milford, MA) PI Supplied Instrument Name: HPLC system (Waters, Milford, MA) PI Supplied Instrument Description:High Performance Liquid Chromatography (HPLC) is a form of column chromatography that pumps a sample mixture or analyte in a solvent (known as the mobile phase) at high pressure through a column with chromatographic packing material (stationary phase). Scanning Fluorescence Detector (Waters 474, Waters, Milford, MA) was used for in-vitro diagnostic testing to analyze compounds of STX and its derivatives. Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/ Fastprep-24 Tissue and Cell Homogenizer (MP Biomedicals, Solon, OH) Fastprep-24 Tissue and Cell Homogenizer (MP Biomedicals, Solon, OH) PI Supplied Instrument Name: Fastprep-24 Tissue and Cell Homogenizer (MP Biomedicals, Solon, OH) PI Supplied Instrument Description:The FastPrep of benchtop instrument utilizes bead-beating technology to lyse, homogenize and grind routine and difficult samples in 40 seconds or less. A completely self-contained system, FastPrep instrument eliminates the risk of cross-contamination and time-consuming clean up. The use of interchangeable adapters offers exceptional versatility in sample size and temperature with ambient, cryogenic and all-metal options. Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Olympus IX70 inverted system microscope Olympus IX70 inverted system microscope PI Supplied Instrument Name: Olympus IX70 inverted system microscope PI Supplied Instrument Description:The IX70 inverted tissue culture microscope is a research-level instrument capable of imaging specimens in a variety of illumination modes including brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana). Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives. The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/ StepOnePlus™ real-time PCR system (Applied BiosystemsTM) StepOnePlus™ real-time PCR system (Applied BiosystemsTM) PI Supplied Instrument Name: StepOnePlus™ real-time PCR system (Applied BiosystemsTM) PI Supplied Instrument Description:The system can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 4-color optical recording, the StepOnePlus™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications. Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).