http://lod.bco-dmo.org/id/dataset/913620
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
2023-10-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Chemotaxis of Pseudoalteromonas haloplanktis towards exudates of phage-infected and control Synechoccocus (VIC project)
2023-10-18
publication
2023-10-18
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2025-12-23
publication
https://doi.org/10.26008/1912/bco-dmo.913620.1
Sheri Floge
Wake Forest University
principalInvestigator
Jeffrey Guasto
Tufts University
principalInvestigator
Richard J. Henshaw
ETH-Zurich
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: Floge, S., Guasto, J., Henshaw, R. J. (2025) Chemotaxis of Pseudoalteromonas haloplanktis towards exudates of phage-infected and control Synechoccocus (VIC project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-10-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.913620.1 [access date]
Dataset Description: <p>This data set summarises the chemotactic response of the&nbsp;model heterotrophic bacteria <em>Psuedoalteromonas haloplanktis</em>&nbsp;towards phage-infected cyanobacteria&nbsp;Synechococcus&nbsp;cells/exudates respectively. Phage treatments are fully described in:&nbsp;https://doi.org/10.1038/s43705-022-00169-6.</p> Methods and Sampling: <p><strong>Experimental Culture Details:</strong></p>
<p>Pseudoalteromonas haloplanktis (ATCC 700530) from −80°C stock were grown in 2216 media for 24 hours at room temperature without agitation. The overnight culture was then centrifuged (1500 RCF for 5 min), and 4 ml of culture was washed twice and resuspended in 0.5 ml of ASW.</p>
<p>Artificial seawater (ASW) was prepared following the NCMA ESAW Medium recipe, which was adapted from Harrison et al.and modified by Berges, and filtered through a 0.2um filter immediately prior to use.</p>
<p>Axenic Synechococcus WH8102 (CCMP 490 2370) were grown in SN media, prepared with ASW, in sterile 40 ml polystyrene culture flasks at 22°C on a 14 h : 10 h light-dark cycle at 50 µmol photons m−2 s −1 . Culture growth was tracked using a SpectraMax ID3 plate reader (Molecular Devices) and cell counts were measured using a CytoFLEX flow cytometer (Beckman Coulter).</p>
<p><strong>Microfluidic Device Details:&nbsp;</strong></p>
<p>A simple three-inlet gradient generation microfluidic device was used to produce the chemical gradients.&nbsp; Microfluidic devices were made using standard soft lithography techniques. Polydimethylsiloxane (Dow Corning SYLGARD 184) channels were cast on photoresist (Microchem) moulds fabricated via photolithography and plasma bonded to standard glass slides. Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump (Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. A chemostimulus gradient develops in the channel via diffusion, and the chemotactic response of the cell population was observed over time. Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). An example of the gradient generator used can be found in:&nbsp; https://doi.org/10.7554/eLife.85348</p>
<p><strong>Experiment Details:</strong></p>
<p>Six microfluidic experiments were conducted each on different days: three with phage infection and three control, uninfected experiments.&nbsp;Both uninfected and phage-infected experiments were performed identically, with the substitution of phage addition for an equivalent volume of SN media in the uninfected experiments.&nbsp;All infection experiments were performed within a week using the same phage stock, with the infectious phage titer of the stock determined to be 1.4x10^8 pfu/ml via plaque assay method with&nbsp;Synechococcus&nbsp;WH8102 as the host.&nbsp;One day prior to experiments, exponential phase&nbsp;Synechococcus&nbsp;cultures were diluted with fresh SN media to a cell concentration of 7-9x10^5 cells/ml.&nbsp;</p>
<p>This data set summarises the chemotactic response of a model marine bacteria (Pseudoalteromonas haloplanktis&nbsp; ATCC 700530) to filtered exudates of the cyanobacteria&nbsp;Synechococcus&nbsp;sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -&gt; T6), with the initial assays split into 4 biological replicates (named A, B, C, and D). The two treatments were:</p>
<p>1)&nbsp;A control treatment (named "Control", or shortened to "C")</p>
<p>2)&nbsp;A phage-infected treatment (named "Phage", or shortened to "P"), where host Synechococcus were infected with the T-4 like Myovirus S-SSM5, with data collected over the pre-lysis cycle.</p>
<p>These treatments are fully described in:&nbsp;https://doi.org/10.1038/s43705-022-00169-6. The filtrates were kept frozen at -80C in 1ml aliquots, and only thawed to room temperature immediately prior to experimental use.</p>
<p>For two time points (T1 = 2 hpi, T6 = 12 hpi; hpi: hours post-infection), two sets of chemotaxis assays were collected: Phage vs ASW, Control vs ASW.&nbsp; Each set comprised of three physical replicates, repeated with two biological replicates corresponding to filtrate samples A and B.&nbsp;The chemotactic preference of&nbsp;P. haloplanktis&nbsp;was measured by analyzing the cell distribution over time and comparing the cell populations on opposite sides of the channel.</p>
<p><strong>Flow Cytometry Data Details</strong></p>
<p>This data is captured in Supplemental File&nbsp;fcm.countdata_synwh8102_s-ssm5.csv.</p>
<p>Flow cytometry data quantifying&nbsp;<em>Synechococcus&nbsp;</em>cell concentrations and S-SSM5 cyanophage particle concentrations in each biological replicate culture. Samples were collected from cultures, fixed in 0.5% glutaraldehyde, and flash frozen in LN2 before being stored at -80°C. Samples were thawed on ice prior to being quantified.</p>
<p>The Sample Name column indicates the time at which samples were collected (e.g., 1hpi = 1-hour post-infection). Samples named ‘SN’, ‘SW’, or ‘TE Blank’ correspond to blanks (negative controls) performed with SN media, 0.2μm filtered natural seawater, and TE buffer. The Sample Type column indicates whether&nbsp;<em>Synechococcus</em>&nbsp;cells or S-SSM5 cyanophage were quantified.&nbsp;<em>Synechococcus&nbsp;</em>were detected by chlorophyll-a autofluorescence using a 488nm laser with emission detected using a 690/50nm filter. A violet laser (405nm) was used to detect side scatter of particles (405/10nm emission filter). Cyanophages were stained with SYBR Green I which was also excited using a 488nm laser with emission detected using a 525/40nm filter. Size of particles was determined using the same violet side scatter parameters as above. The condition and replicate number are both indicated in the Treatment column.</p>
<p>Raw counts are given in the Count column with blank subtracted counts shown in the Blank Adjusted Count column. The acquisition time, volume of sample run, and the calculated concentration of either Synechococcus or cyanophage are given in the following columns, respectively. ‘NA’ indicates that data were not acquired for those specific samples. Particle concentrations were determined by calculating the number of gated particles per volume of sample analyzed, then accounting for the sample dilution.</p>
<p>The flow cytometry data support the chemotaxis experiments by providing data to show that uninfected&nbsp;<em>Synechococcus&nbsp;</em>cultures maintained their cell concentrations over the course of each experiment and that no cyanophage were detected in these cultures. Similarly, cyanophage-infected&nbsp;<em>Synechococcus&nbsp;</em>cultures displayed cell loss characteristic of viral lysis and increases in cyanophage concentration which combined are indicative of a productive infection. These data support that the observed directional motility biases (or lack thereof) in chemotaxis of&nbsp;<em>V. alginolyticus&nbsp;</em>were indeed in response to either uninfected and cyanophage-infected&nbsp;<em>Synechococcus</em>.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829905 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829905
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829827 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829827
completed
Sheri Floge
Wake Forest University
207-841-0457
1834 Wake Forest Rd. Winston Hall, Rm 226
Winston-Salem
NC
27109
US
floges@wfu.edu
pointOfContact
Jeffrey Guasto
Tufts University
617-627-6838
Department of Mechanical Engineering Robinson Hall, Rm 173, 200 College Avenue
Medford
MA
02155
US
Jeffrey.Guasto@tufts.edu
pointOfContact
Richard J. Henshaw
ETH-Zurich
rhenshaw@ethz.ch
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment_ID
Experiment_type
Bioreplicate_ID
Time_point_ID
Treatment
Time_t
beta_Repeat_1
beta_Repeat_2
beta_Repeat_3
Average
Standard_Error
CMOS camera (Grasshopper, Teledyne FLIR)
CytoFLEX flow cytometer (Beckman Coulter)
Zeiss AxioObserver Inverted microscope
SpectraMax ID3 plate reader (Molecular Devices)
Harvard Apparatus syringe pump
theme
None, User defined
experiment id
experiment type
replicate
time_point
treatment
sample time
count
featureType
BCO-DMO Standard Parameters
Camera
Flow Cytometer
Inverted Microscope
plate reader
Pump
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.
Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux
https://osprey.bco-dmo.org/project/783777
Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux
<p><em>NSF Award Abstract:</em><br />
Drifting photosynthetic microbes in surface ocean waters carry out nearly half of global carbon (C) fixation, both supporting the marine food web and reducing atmospheric carbon dioxide (CO2) levels. The fate of C in ocean ecosystems is controlled by myriad individual interactions within a highly interconnected planktonic food web, the sheer complexity of which has hindered predictive understanding of global C cycling. Chemical cues govern microbial interactions, and during infection, marine viruses manipulate the metabolism of phytoplankton and bacteria, facilitating the release of dissolved organic matter from infected cells. This research aims to determine how viral metabolic reprogramming of and organic matter release from intact, infected phytoplankton influences microbial interactions and C cycling. The interdisciplinary, collaborative nature of the project will enable direct training of two postdoctoral researchers, one graduate student, and undergraduate students in viral ecology, microfluidics, and metabolomics. An educational outreach program that engages middle school students in hands-on, high speed imaging of microbes will be expanded, and the project will culminate in a three-day workshop to advance the application of microfluidic devices and mass spectrometry analyses in microbial ecology.</p>
<p>The overarching hypothesis behind this research is that viral infection alters the chemical landscape of intact, infected picophytoplankton cells, attracting neighboring chemotactic bacteria and protistan zooplankton, and altering C flux pathways. To test this idea, a series of linked multi-scale laboratory-based experiments will be run to 1) Characterize the response of diverse model marine microbes to dissolved organic matter (DOM) released from intact, virus-infected picophytoplankton using microfluidics-based chemotaxis assays, 2) Identify key viral-derived DOM compounds eliciting chemotactic responses using stable isotope labeling, metabolomics analyses, and chemotaxis assays, and 3) Quantify micron-scale cross-trophic encounter dynamics and evaluate their impact on bulk-scale C cycling using liter-scale measurements of C dynamics linked to high spatiotemporal resolution live imaging of microbial food webs. The ultimate goal of the project is to develop a mechanistic understanding of the role of intact, virus-infected cells in oceanic C cycling.</p>
VIC
largerWorkCitation
project
eng; USA
oceans
2021-10-01
2023-04-01
Culture-based work
0
BCO-DMO catalogue of parameters from Chemotaxis of Pseudoalteromonas haloplanktis towards exudates of phage-infected and control Synechoccocus (VIC 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/916926.rdf
Name: Experiment_ID
Units: unitless
Description: <p>Experiment ID based on experiment type, bioreplicate ID, time point, and treatment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916927.rdf
Name: Experiment_type
Units: unitless
Description: <p>Experiment type: control vs artificial seawater (ASW) (CvsASW) or phage vs artificial seawater (PvsASW).</p>
http://lod.bco-dmo.org/id/dataset-parameter/916928.rdf
Name: Bioreplicate_ID
Units: unitless
Description: <p>Biological replicates corresponding to filtrate samples A and B.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916929.rdf
Name: Time_point_ID
Units: unitless
Description: <p>Time point when measurement was taken during experiment: T1 or T6 (first and last timepoints in time series). T1 indicates 2 hours post-infection, T6 indicates 12 hours post-infection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916930.rdf
Name: Treatment
Units: unitless
Description: <p>Experimental treatment: control experiment or control (CvsASW) + phage experiment (PvsASW).</p>
http://lod.bco-dmo.org/id/dataset-parameter/916931.rdf
Name: Time_t
Units: minutes
Description: <p>Time when distribution value of P. haloplanktis cells at a given location was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916932.rdf
Name: beta_Repeat_1
Units: unitless
Description: <p>P. haloplanktis cell distribution value during repeat 1.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916933.rdf
Name: beta_Repeat_2
Units: unitless
Description: <p>P. haloplanktis cell distribution value during repeat 2.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916934.rdf
Name: beta_Repeat_3
Units: unitless
Description: <p>P. haloplanktis cell distribution value during repeat 3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916935.rdf
Name: Average
Units: unitless
Description: <p>Average cell distribution value from repeats 1, 2, and 3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/916936.rdf
Name: Standard_Error
Units: unitless
Description: <p>Standard error of distribution value from repeats 1, 2, and 3.</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
https://doi.org/10.26008/1912/bco-dmo.913620.1
download
onLine
dataset
<p><strong>Experimental Culture Details:</strong></p>
<p>Pseudoalteromonas haloplanktis (ATCC 700530) from −80°C stock were grown in 2216 media for 24 hours at room temperature without agitation. The overnight culture was then centrifuged (1500 RCF for 5 min), and 4 ml of culture was washed twice and resuspended in 0.5 ml of ASW.</p>
<p>Artificial seawater (ASW) was prepared following the NCMA ESAW Medium recipe, which was adapted from Harrison et al.and modified by Berges, and filtered through a 0.2um filter immediately prior to use.</p>
<p>Axenic Synechococcus WH8102 (CCMP 490 2370) were grown in SN media, prepared with ASW, in sterile 40 ml polystyrene culture flasks at 22°C on a 14 h : 10 h light-dark cycle at 50 µmol photons m−2 s −1 . Culture growth was tracked using a SpectraMax ID3 plate reader (Molecular Devices) and cell counts were measured using a CytoFLEX flow cytometer (Beckman Coulter).</p>
<p><strong>Microfluidic Device Details:&nbsp;</strong></p>
<p>A simple three-inlet gradient generation microfluidic device was used to produce the chemical gradients.&nbsp; Microfluidic devices were made using standard soft lithography techniques. Polydimethylsiloxane (Dow Corning SYLGARD 184) channels were cast on photoresist (Microchem) moulds fabricated via photolithography and plasma bonded to standard glass slides. Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump (Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. A chemostimulus gradient develops in the channel via diffusion, and the chemotactic response of the cell population was observed over time. Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). An example of the gradient generator used can be found in:&nbsp; https://doi.org/10.7554/eLife.85348</p>
<p><strong>Experiment Details:</strong></p>
<p>Six microfluidic experiments were conducted each on different days: three with phage infection and three control, uninfected experiments.&nbsp;Both uninfected and phage-infected experiments were performed identically, with the substitution of phage addition for an equivalent volume of SN media in the uninfected experiments.&nbsp;All infection experiments were performed within a week using the same phage stock, with the infectious phage titer of the stock determined to be 1.4x10^8 pfu/ml via plaque assay method with&nbsp;Synechococcus&nbsp;WH8102 as the host.&nbsp;One day prior to experiments, exponential phase&nbsp;Synechococcus&nbsp;cultures were diluted with fresh SN media to a cell concentration of 7-9x10^5 cells/ml.&nbsp;</p>
<p>This data set summarises the chemotactic response of a model marine bacteria (Pseudoalteromonas haloplanktis&nbsp; ATCC 700530) to filtered exudates of the cyanobacteria&nbsp;Synechococcus&nbsp;sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -&gt; T6), with the initial assays split into 4 biological replicates (named A, B, C, and D). The two treatments were:</p>
<p>1)&nbsp;A control treatment (named "Control", or shortened to "C")</p>
<p>2)&nbsp;A phage-infected treatment (named "Phage", or shortened to "P"), where host Synechococcus were infected with the T-4 like Myovirus S-SSM5, with data collected over the pre-lysis cycle.</p>
<p>These treatments are fully described in:&nbsp;https://doi.org/10.1038/s43705-022-00169-6. The filtrates were kept frozen at -80C in 1ml aliquots, and only thawed to room temperature immediately prior to experimental use.</p>
<p>For two time points (T1 = 2 hpi, T6 = 12 hpi; hpi: hours post-infection), two sets of chemotaxis assays were collected: Phage vs ASW, Control vs ASW.&nbsp; Each set comprised of three physical replicates, repeated with two biological replicates corresponding to filtrate samples A and B.&nbsp;The chemotactic preference of&nbsp;P. haloplanktis&nbsp;was measured by analyzing the cell distribution over time and comparing the cell populations on opposite sides of the channel.</p>
<p><strong>Flow Cytometry Data Details</strong></p>
<p>This data is captured in Supplemental File&nbsp;fcm.countdata_synwh8102_s-ssm5.csv.</p>
<p>Flow cytometry data quantifying&nbsp;<em>Synechococcus&nbsp;</em>cell concentrations and S-SSM5 cyanophage particle concentrations in each biological replicate culture. Samples were collected from cultures, fixed in 0.5% glutaraldehyde, and flash frozen in LN2 before being stored at -80°C. Samples were thawed on ice prior to being quantified.</p>
<p>The Sample Name column indicates the time at which samples were collected (e.g., 1hpi = 1-hour post-infection). Samples named ‘SN’, ‘SW’, or ‘TE Blank’ correspond to blanks (negative controls) performed with SN media, 0.2μm filtered natural seawater, and TE buffer. The Sample Type column indicates whether&nbsp;<em>Synechococcus</em>&nbsp;cells or S-SSM5 cyanophage were quantified.&nbsp;<em>Synechococcus&nbsp;</em>were detected by chlorophyll-a autofluorescence using a 488nm laser with emission detected using a 690/50nm filter. A violet laser (405nm) was used to detect side scatter of particles (405/10nm emission filter). Cyanophages were stained with SYBR Green I which was also excited using a 488nm laser with emission detected using a 525/40nm filter. Size of particles was determined using the same violet side scatter parameters as above. The condition and replicate number are both indicated in the Treatment column.</p>
<p>Raw counts are given in the Count column with blank subtracted counts shown in the Blank Adjusted Count column. The acquisition time, volume of sample run, and the calculated concentration of either Synechococcus or cyanophage are given in the following columns, respectively. ‘NA’ indicates that data were not acquired for those specific samples. Particle concentrations were determined by calculating the number of gated particles per volume of sample analyzed, then accounting for the sample dilution.</p>
<p>The flow cytometry data support the chemotaxis experiments by providing data to show that uninfected&nbsp;<em>Synechococcus&nbsp;</em>cultures maintained their cell concentrations over the course of each experiment and that no cyanophage were detected in these cultures. Similarly, cyanophage-infected&nbsp;<em>Synechococcus&nbsp;</em>cultures displayed cell loss characteristic of viral lysis and increases in cyanophage concentration which combined are indicative of a productive infection. These data support that the observed directional motility biases (or lack thereof) in chemotaxis of&nbsp;<em>V. alginolyticus&nbsp;</em>were indeed in response to either uninfected and cyanophage-infected&nbsp;<em>Synechococcus</em>.</p>
Specified by the Principal Investigator(s)
<p><strong>Data processing step summary:</strong></p>
<ol>
<li>Locate particles using a bandpass filter/peak finding algorithm&nbsp;(available:&nbsp;<a href="https://site.physics.georgetown.edu/matlab/">https://site.physics.georgetown.edu/matlab/</a>)</li>
<li>Bin particles according to x-position to examine distribution across the field of view</li>
</ol>
<p>All data were processed using custom MATLAB scripts (version 2021b). These MATLAB scripts are captured in the Supplemental File, Filtrate_Chemotaxis_Analysis.zip.&nbsp;</p>
Specified by the Principal Investigator(s)
Spaces in column names have been replaced with underscores ("_").
All chemotaxis data values have been rounded to maximum precision (14).
Time values have been rounded to a precision of 4.
Specified by BCO-DMO Data Managers
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
CMOS camera (Grasshopper, Teledyne FLIR)
CMOS camera (Grasshopper, Teledyne FLIR)
PI Supplied Instrument Name: CMOS camera (Grasshopper, Teledyne FLIR) PI Supplied Instrument Description:Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
CytoFLEX flow cytometer (Beckman Coulter)
CytoFLEX flow cytometer (Beckman Coulter)
PI Supplied Instrument Name: CytoFLEX flow cytometer (Beckman Coulter) PI Supplied Instrument Description:Culture growth was tracked using a SpectraMax ID3 plate reader (Molecular Devices) and cell counts were measured using a CytoFLEX flow cytometer (Beckman Coulter). Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Zeiss AxioObserver Inverted microscope
Zeiss AxioObserver Inverted microscope
PI Supplied Instrument Name: Zeiss AxioObserver Inverted microscope PI Supplied Instrument Description:Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). 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/
SpectraMax ID3 plate reader (Molecular Devices)
SpectraMax ID3 plate reader (Molecular Devices)
PI Supplied Instrument Name: SpectraMax ID3 plate reader (Molecular Devices) PI Supplied Instrument Description:Culture growth was tracked using a SpectraMax ID3 plate reader (Molecular Devices) and cell counts were measured using a CytoFLEX flow cytometer (Beckman Coulter). Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
Harvard Apparatus syringe pump
Harvard Apparatus syringe pump
PI Supplied Instrument Name: Harvard Apparatus syringe pump PI Supplied Instrument Description:The three solutions were flow stratified for a minimum of 2min using a syringe pump (Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps