http://lod.bco-dmo.org/id/dataset/649728
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.
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2016-06-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project)
2016-06-17
publication
2016-06-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-07-02
publication
https://doi.org/10.1575/1912/bco-dmo.649728.1
Mark E. Warner
University of Delaware
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: Warner, M. (2016) Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-06-17 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.649728.1 [access date]
Symbiont removed and anemone reinfected with one of two strains of Symbiodinium Dataset Description: <p>Results of laboratory experiments examining the respiratory capacity of the sea anemone<em> Exaiptasia pallid</em>a, infected with either homologous ITS2-type A4 Symbiodinium or a heterologous isolate of Symbiodinium minutum (ITS2-type B1).&nbsp; This dataset&nbsp; details the differences between host-symbiont combinations. Respiratory demand was assessed by both whole organismal oxygen consumption as well as in vitro mitochondrial activity via the enzyme citrate synthase.</p> Methods and Sampling: <p>Full details of the experimental design are provided in Hawkins <em>et al., </em>2016</p>
Funding provided by NSF Emerging Frontiers Division (NSF EF) Award Number: EF-1316055 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1316055
onGoing
Mark E. Warner
University of Delaware
302-645-4365
School of Marine Science and Policy 700 Pilottown Rd.
Lewes
DE
19958
USA
mwarner@udel.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample
symbiont_id
anemone_resp_rate
host_CS_act
symbiont_CS_act
photo_output_symb
symbio_density
symbio_biomass_fraction
symbio_resp_fraction
resp_biom_quotient
Fluorescence Microscope
oxygen sensitive optode
ThermoFisher QPCR system
theme
None, User defined
sample identification
taxon
O2 consumption
metabolic_enzyme
photosynthetic rate
abundance
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Optode
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.
Ocean Acidification: Understanding the Impact of CO2 and Temperature on the Physiological, Genetic, and Epigenetic Response of a Model Sea Anemone System with Different Symbionts
https://osprey.bco-dmo.org/project/628967
Ocean Acidification: Understanding the Impact of CO2 and Temperature on the Physiological, Genetic, and Epigenetic Response of a Model Sea Anemone System with Different Symbionts
<p>The projected rise in carbon dioxide (CO2) in the atmosphere is considered a primary threat to marine systems throughout the world due to both ocean acidification and rising ocean temperatures. Coral reefs are very sensitive to these projected changes in the earth's climate, with continued losses in growth as well as disruption (also known as bleaching) in the symbiotic relationship between the algae (Symbiodinium) living within a diversity of host animals, including stony corals, soft corals and sea anemones. While much information has been gleaned as to how acidification may affect stony corals, considerably less is known about the interactive effects of acidification and temperature to other symbiotic anthozoans.</p>
<p>To this end, this proposal will investigate the long-term impacts of elevated CO2 and temperature on the model sea anemone, <em>Aiptasia pallida</em>, while harboring four different genotypes of Symbiodinium. The primary goals of this project are (1) to determine the sensitivity and capacity for acclimation in molecular and physiological processes while exposed to elevated CO2 and temperature, and (2) to assess the degree to which acclimated adult animals may confer (or transfer) an imprinted physiological characteristic to the next generation of asexual offspring. A series of long-term experiments will be conducted with each animal/algal combination (holobiont) in order to collect initial (3 month) stress markers and genomic data and then follow animal response and asexual reproduction through several generations for one year. The possibility for enhanced resilience or acclimation will be measured by tracking the recovery of each holobiont, followed by repeated exposure to elevated temperature while held in high CO2. This project will tease apart fine scale mechanisms of stress, acclimation, or amelioration that may vary as a function of algal genotype and host animal response, and the degree to which environmental imprinting may pre-acclimate propagules. Project results will provide information regarding how future acidification and warming will affect cnidarian-algal symbioses, and the fundamental profile of their flexibility in stress response processes across organismal, metabolic, genomic and epigenetic scales.</p>
AnemoneOA
largerWorkCitation
project
eng; USA
biota
oceans
2016-06-17
Lewes, Delaware
0
BCO-DMO catalogue of parameters from Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA 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
http://lod.bco-dmo.org/id/dataset-parameter/649733.rdf
Name: sample
Units: unitless
Description: <p>Sample ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/649734.rdf
Name: symbiont_id
Units: text
Description: <p>Symbiont identity; i.e. Homologous ITS2-type A4 Symbiodinium or Symbiodinium minutum ITS2-type B1</p>
http://lod.bco-dmo.org/id/dataset-parameter/649735.rdf
Name: anemone_resp_rate
Units: micromoles of oxygen per hour per milligram protein
Description: <p>Host protein-normalised holobiont respiration rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/649736.rdf
Name: host_CS_act
Units: Units per milligram protein
Description: <p>Host (anemone) citrate synthase specific activity</p>
http://lod.bco-dmo.org/id/dataset-parameter/649737.rdf
Name: symbiont_CS_act
Units: Units per milligram protein
Description: <p>Symbiont (Symbiodinium) citrate synthase specific activity</p>
http://lod.bco-dmo.org/id/dataset-parameter/649738.rdf
Name: photo_output_symb
Units: picomoles oxygen per hour per cell
Description: <p>Net photosynthesis per symbiont cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/649739.rdf
Name: symbio_density
Units: million cells per mg protein
Description: <p>Host protein-normalised symbiont density</p>
http://lod.bco-dmo.org/id/dataset-parameter/649740.rdf
Name: symbio_biomass_fraction
Units: milligrams per milligrams(dimensionless)
Description: <p>Symbiont biomass fraction (calculated as total symbiont protein [mg]/total host+symbiont protein [mg])</p>
http://lod.bco-dmo.org/id/dataset-parameter/649741.rdf
Name: symbio_resp_fraction
Units: dimensionless
Description: <p>Symbiont respiration fraction (calculated as total symbiont citrate synthase activity [U]/total host+symbiont citrate synthase activity [U])</p>
http://lod.bco-dmo.org/id/dataset-parameter/649742.rdf
Name: resp_biom_quotient
Units: dimensionless
Description: <p>Symbiont respiration fraction/Symbiont biomass fraction</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
4507
https://darchive.mblwhoilibrary.org/bitstream/1912/24305/1/dataset-649728_host-symbiont-reinfections__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.649728.1
download
onLine
dataset
<p>Full details of the experimental design are provided in Hawkins <em>et al., </em>2016</p>
Specified by the Principal Investigator(s)
<p><strong>Anemone Husbandry, Symbiodinium Removal, and Re-infection:</strong></p>
<p>Anemones were maintained in 15-L tanks supplied with constantly running natural seawater (1-micron-filtered and UV-sterilized, 26<sup>◦</sup>C, 1 L min<sup>−1 </sup>flow rate). Irradiance (100 μmol photons m<sup>−2 </sup>s<sup>−1 </sup>) was provided on a 12 h:12h light:dark cycle (lights on at 06:00) provided by cool white LEDs (Cree XP-G2; LED Supply, Randolph, VT, USA). Aposymbiotic <em>E. pallida </em>were obtained by subjecting a subset of anemones to a menthol treatment (Wang et al., 2012; Matthews et al., 2015), with dark-incubation. Aposymbiosis was confirmed by the complete absence of <em>Symbiodinium </em>using a fluorescence microscope [EVOS system, ThermoFisher (Life Technologies), Waltham, MA, USA; excitation: 628 ± 20 nm, emission: 692 ± 20 nm]. Aposymbiotic animals were maintained in a 30-L aquarium in the dark, and checked monthly for the presence of algal symbionts. Novel <em>E. pallida-Symbiodinium </em>associations were established by exposing aposymbiotic anemones to one of two different <em>Symbiodinium </em>species (∼1000 cells mL<sup>−1 </sup>in 500 mL seawater) according to the methods of Hoadley et al. (2015). One group (<em>n </em>&gt; 30 animals) was incubated with a homologous, monoclonal <em>Symbiodinium </em>culture established from <em>Symbiodinium </em>originally isolated from the same <em>E. pallida </em>population and maintained in semi-continuous growth in f/2-Si culture media (Guillard, 1973) for period of at least 1 year. Another set of anemones (<em>n </em>&gt; 30) was exposed to a heterologous culture of <em>Symbiodinium minutum </em>(ID: Pk702) originally isolated from the octocoral <em>Plexaura kuna</em>. Algae were noted as ITS2-types A4 and B1 for the homologous symbiont and <em>S. minutum </em>isolates, respectively. Newly symbiotic animals were maintained in separate flow-through tanks for at least 3 months before any physiological analysis was undertaken. A third group of aposymbiotic anemones (<em>n </em>= 24) were placed under lights for 8 weeks without being exposed to any <em>Symbiodinium </em>cells. These anemones remained aposymbiotic (as confirmed by fluorescence microscopy). To confirm symbiont genetic identity in re-infected animals, <em>Symbiodinium </em>DNA was extracted from 5 to 10 anemones per group, and the ITS2 region was amplified as described by LaJeunesse (2002). In all instances, anemones contained the appropriate ITS2-type.</p>
<p><strong>Measurements of Respiration and Photosynthesis as In-vivo Oxygen Flux:</strong></p>
<p>Respiration and photosynthesis of individual anemones [oral disk diameter &gt;4mm for natural <em>E. pallida </em>(<em>n </em>= 53), 4–6mm for re-infected animals (<em>n </em>= 19 per <em>Symbiodinium </em>species)] was measured in sealed glass scintillation vials fitted with an internal stir bar and an oxygen sensitive optode (Fibox 4, PreSens Gmbh, Regensburg, Germany). Vials were immersed in a constant 26<sup>◦</sup>C water bath and maintained in darkness for 15min. Illumination was provided for 20 min at an irradiance of 200 μmol photons m<sup>−2 </sup>s<sup>−1 </sup>after which, the LEDs were turned off for a final 30-min period to allow measurement of steady-state dark respiration. Background O<sub>2 </sub>flux was determined using vials containing 1-μm-filtered, UV-sterilized seawater, and was found to be negligible. After respirometry assays, each anemone was snap-frozen in liquid nitrogen, and stored at −80<sup>◦</sup>C. Rates of holobiont dark respiration were calculated as moles O<sub>2 </sub>consumed hour<sup>−1</sup>. Dark respiration rates were then subtracted from net photosynthetic rates (moles O<sub>2 </sub>produced hour<sup>−1 </sup>during the light-phase) to generate values for gross photosynthesis. Respiration- and gross photosynthesis rates were normalized to soluble animal protein and symbiont cell number, respectively.</p>
<p><strong>Anemone Processing and Symbiodinium Density Analysis:</strong></p>
<p>Anemones were thawed in their 2-mL screw cap vials and 0.6–1mL ice-cold lysis buffer (25mM Tris, pH 7.8, 1mM EDTA, 10% glycerol [v/v]) was added to each vial. Anemones were then homogenized in a chilled bead-beater (FastPrep<sup> </sup>-24, MP Bio, Santa Ana, CA, USA) for 60s at a speed of 6m s<sup>−1 </sup>with a 5-mm-diameter stainless steel bead. The homogenate was inspected visually (100× magnification) to confirm anemone tissue disruption and <em>Symbiodinium </em>cell integrity. A 100-μL sample was removed, fixed with 5μL glutaraldehyde (8% [w/v] stock solution in water), and stored at 4<sup>◦</sup>C in the dark for later quantification of <em>Symbiodinium </em>cell densities. The remaining homogenate was centrifuged at 3000 × g for 30 s. Two hundred microliters of the supernatant were removed for animal DNA extraction (see below) and the pellet was re-suspended. The sample was then centrifuged for 5min at 700 × g to separate the <em>Symbiodinium </em>cells from the remaining anemone material. The <em>Symbiodinium </em>pellet was immediately snap-frozen in liquid nitrogen and transferred to a −80<sup>◦</sup>C freezer. The supernatant (“anemone fraction”) was centrifuged at high speed (16,100 × g, 20min) to remove particulates, and aliquots of the clear supernatant were snap- frozen and stored at −80<sup>◦</sup>C.</p>
<p>In order to remove residual animal protein, <em>Symbiodinium </em>pellets were thawed, re-suspended in 1 mL ice-cold wash buffer (as lysis buffer above, but with the addition of 0.01% [v/v] Triton X-100), and centrifuged for 5 min at 700 × g. The supernatant was discarded and the pellet re-suspended in fresh ice-cold wash buffer. This procedure was repeated four times, after which the supernatant was clear and the pellet dark brown, with little evidence of contaminating anemone material. <em>Symbiodinium </em>cells were finally re-suspended in 300μL ice-cold lysis buffer in a clean 1.5-mL tube containing a 200-μL-volume of 0.5- mm-diameter acid-washed glass beads. Cells were lysed in a chilled bead-beater (see above) for 3 min at a speed of 6.5 m s<sup>−1</sup>. The lysate was inspected visually (100× magnification), before centrifugation to remove particulates (16,100 × g, 20 min). Aliquots of the supernatant were then snap-frozen in liquid nitrogen and stored at −80<sup>◦</sup>C.</p>
<p>Total soluble anemone and <em>Symbiodinium </em>protein were determined using a linearized Bradford assay (Ernst and Zor, 2010). To test the effectiveness of the algal washing steps described above, a standard curve was constructed by spiking 12 <em>Symbiodinium </em>pellets from similar-sized anemones (in triplicate) with 24–1200 μg anemone protein “contamination” originating from crude homogenates that had been gently centrifuged (500 × g for 5 min) to remove algal cells. Algal pellets were then washed and a 50-μL sample was removed and fixed for cell counts. The remaining cells were lysed as described above. <em>Symbiodinium </em>protein content was then measured for each pellet, normalized to cell number (see below), and plotted against the respective amount of anemone material added.</p>
<p><em>Symbiodinium </em>densities were quantified using an Improved Neubauer hemocytometer and a fluorescence microscope to visualize cells’ chlorophyll <em>a </em>fluorescence (see above). Field of view was determined using the EVOS operating software (4× objective), and cells were counted using the “Analyze Particles” tool in ImageJ (NIH, Bethesda, MD, USA). At least 6 independent images were analyzed for each sample, and cell numbers were normalized to anemone protein content.</p>
<p><strong>Biochemical Analysis of Mitochondrial Function:</strong></p>
<p>Anemone and <em>Symbiodinium </em>aerobic capacity was quantified as the activity of the TCA cycle rate-limiting enzyme citrate synthase (CS), measured according the methods of Srere (1969) modified for use with small marine invertebrates. All samples were analyzed within 1 month of freezing. Representative results of assay optimization and validation procedures are provided in ESM Figure S1. Briefly, 20μL of thawed anemone or <em>Symbiodinium </em>supernatant (diluted to yield 2–6μg of protein) was added in triplicate to wells in a 96-well plate (Greiner Bio- One, Monroe, NC, USA) alongside triplicate blanks (20 μL lysis buffer) and positive controls [20 μL citrate synthase (1 U mL<sup>−1 </sup>in lysis buffer; Sigma-Aldrich, St. Louis, MO, USA)]. One hundred and seventy microliters of assay buffer (111mM Tris, pH 7.8, 0.11% [v/v] Triton X-100) containing 294μM 5,5<sup>′</sup>-dithiobis- (2-nitrobenzoic acid) (DTNB; Sigma-Aldrich, see above) and 588 μM acetyl-coenzyme A (Sigma-Aldrich, see above) were then added to all wells. DTNB stock solutions (5 mM) were made fresh in 0.1 mM Tris buffer, pH 8.0. Acetyl-coenzyme A solutions were prepared at a concentration of 12.35 mM in distilled water, stored in aliquots at −80<sup>◦</sup>C, and used within 6 months.</p>
<p>To control for non-CS-specific reaction products following the addition of assay buffer, baseline absorbance (λ = 412 nm) was recorded for 3min using a microplate reader (Fluostar Omega, BMG, Cary, NC, USA) maintained at a temperature of 26<sup>◦ </sup>C. The CS-catalyzed reaction was initiated by adding 10 μL oxaloacetate to each well (OA; Sigma-Aldrich, see above; 12 mM stock solution prepared fresh in distilled water and stored on ice), giving a final concentration of 600 μM OA. Sample absorbance was monitored at 412 nm for a further 3 min, and CS enzyme activity was derived using the following equation:</p>
<p><em>CS Specific Activity </em><sup> </sup><em>U mg</em><sup>−1</sup><sup> </sup></p>
<p><sub>= </sub><sup> </sup><sup>△</sup><sup>412</sup><sub><em>OA </em></sub><sup>− </sup><sup>△</sup><sup>412</sup><sub><em>blank</em></sub><sup> </sup><sup>× </sup><sup><em>V</em></sup><em>reaction </em><sup>× </sup><sup><em>D / </em></sup>13.6 ×<em>L </em>× <em>V</em><sub><em>sample </em></sub>×<em>P</em></p>
<p>Where 412 is the linear rate of change in 412-nm absorbance prior to and after the addition of OA, V is the volume (mL), D is the sample dilution factor, 13.6 (mM<sup>−1 </sup>cm<sup>−1</sup>) is the 412-nm extinction coefficient for the reaction product, L is the optical path-length (cm) and P is the sample protein concentration (mg mL<sup>−1</sup>). Total <em>Symbiodinium </em>and animal CS activities were calculated as the product of the respective specific activity and total protein contents.</p>
<p><strong>Quantification of Anemone Mitochondrial Copy Number:</strong></p>
<p>Anemone genomic DNA was extracted using two independent methods. For some animals (<em>n </em>= 33), DNA was extracted using a Wizard<sup> </sup>Genomic DNA Extraction kit (Promega Corporation, Madison, WI, USA). The DNA pellet was washed with ethanol, air-dried under sterile conditions at 30<sup>◦ </sup>C, and finally dissolved in 50 μL nuclease- free water (BioExpress, Kaysville, UT, USA). DNA from a second group (<em>n </em>= 20) was extracted and purified using a QiaAmp DNA Mini kit (Qiagen, Germantown, MD, USA). DNA concentration was measured using a Quant-iT PicoGreen<sup> </sup>assay (ThermoFisher [Invitrogen], Waltham, MA, USA) and purity was determined spectrophotometrically as the 260/230 nm and 260/280 nm absorbance ratios (NanoDrop<sup> </sup>, ThermoFisher, Waltham, MA, USA). The 260/280nm ratio was consistently &gt;1.8, but the 260/230 nm ratio was variable, particularly in samples purified using the Wizard<sup> </sup>Promega kit (range = 1.4–2.2), however, this had a negligible effect on the efficiency of subsequent QPCR reactions.</p>
<p><strong>Primer Design and Standard Curve Construction:</strong></p>
<p>Oligonucleotide primers are provided in the referenced publication (Hawkins et al. 2016). Primer validation was undertaken using end-point PCR, with each reaction containing 20 ng anemone DNA in a 20-μL mix of 1× Standard Mg-free PCR buffer, 0.25 U Taq DNA polymerase, 0.25 μM (<em>CO1 </em>and <em>ATP6</em>) or 0.5 μM primers (<em>EF- 1-</em>α), 2.5 mM MgCl2, and 0.25 mM dNTPs. Cycling conditions were 94<sup>◦</sup>C for 2 min, followed by thirty cycles of 94<sup>◦</sup>C for 15 s, 60<sup>◦</sup>C for 30 s, and 72<sup>◦ </sup>C for 30 s, with a final elongation at 72<sup>◦ </sup>C for 10 min. Agarose gel electrophoresis confirmed a single PCR product for each primer set and, after product purification, amplicons were sequenced in both directions using the respective PCR primers. Electropherograms were inspected visually to confirm the reliability of base-calling and sequences were compared to NCBI Genbank or <em>Aiptasia </em>genome databases. In all cases the sequences aligned most strongly with those used for primer design. Longer sequences of each of the three target genes was amplified and subsequently cloned in order to create material for QPCR standard curves.</p>
<p><strong>QPCR Analysis:</strong></p>
<p>Duplicate 2-μL aliquots of extracted DNA (5–10 ng μL<sup>−1</sup>) were added to a 18-μL reaction mix (SensiMix<sup>TM </sup>SYBR Hi-ROX; Bioline, Taunton, MA, USA) such that the final mix contained 0.25 μM <em>CO1 </em>or <em>ATP6 </em>primers, or 0.5 μM <em>EF-1-</em>α primer. Gene- fragments were amplified using an AB-7500 real-time QPCR system [ThermoFisher (Applied Biosystems), Waltham, MA, USA], with the following cycling conditions: 94<sup>◦ </sup>C for 10 min, followed by 40 cycles of 94<sup>◦</sup>C for 15 s, 60<sup>◦</sup>C for 1 min, and 72<sup>◦</sup>C for 15 s. A melt-curve analysis (60–94<sup>◦</sup>C in 0.3<sup>◦</sup>C increments, 30s per step) was carried out in order to detect non-specific amplification products. A single PCR product was detected in all cases, with a melting temperature within 1<sup>◦</sup>C of the theoretical melting temperature of the sequenced amplicon as determined by a web-based tool (OligoCalc; Kibbe, 2007). Baseline values were determined automatically and threshold value was set manually at 0.04 (maintained across all samples and standards). Amplification efficiencies were 93–96% in all instances. The number of <em>CO1, ATP6, </em>and <em>EF-1-</em>α sequences per 20-μL reaction was determined by comparing mean C<sub>t </sub>values for each sample to the respective log-dilution standard curve, and <em>CO1</em>/<em>EF-1-</em>α and <em>ATP6</em>/<em>EF-1-</em>α ratios were then calculated.</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
Fluorescence Microscope
Fluorescence Microscope
PI Supplied Instrument Name: Fluorescence Microscope PI Supplied Instrument Description:[EVOS system, ThermoFisher (Life Technologies), Waltham, MA, USA; excitation: 628 ± 20 nm, emission: 692 ± 20 nm].
Field of view was determined using the EVOS operating software (4× objective), and cells were counted using the “Analyze Particles” tool in ImageJ (NIH, Bethesda, MD, USA). Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
oxygen sensitive optode
oxygen sensitive optode
PI Supplied Instrument Name: oxygen sensitive optode PI Supplied Instrument Description:an oxygen sensitive optode (Fibox 4, PreSens Gmbh, Regensburg, Germany). Instrument Name: Optode Instrument Short Name: Instrument Description: An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.
ThermoFisher QPCR system
ThermoFisher QPCR system
PI Supplied Instrument Name: ThermoFisher QPCR system PI Supplied Instrument Description:AB-7500 real-time QPCR system [ThermoFisher (Applied Biosystems), Waltham, MA, USA], with the following cycling conditions: 94◦ C for 10 min, followed by 40 cycles of 94◦C for 15 s, 60◦C for 1 min, and 72◦C for 15 s. 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)