http://lod.bco-dmo.org/id/dataset/661577
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
2016-10-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Buoyant single cell densities of marine bacterial isolates in pure water, deuterated water and artificial seawater (Bacterioplankton single-cell growth project)
2016-10-19
publication
2016-10-19
revision
BCO-DMO Linked Data URI
2016-10-19
creation
http://lod.bco-dmo.org/id/dataset/661577
Dr Martin Polz
Massachusetts Institute of Technology
principalInvestigator
Scott Manalis
Massachusetts Institute of Technology
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: Polz, M., Manalis, S. (2016) Buoyant single cell densities of marine bacterial isolates in pure water, deuterated water and artificial seawater (Bacterioplankton single-cell growth project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/661577 [access date]
Data for measurement of single cell buoyant density of bacterial isolates Dataset Description: <p>Mass and density measurements of single cells from 8 microbial strains measured in pure water, deuterated water and artificial seawater.</p>
<p>These data are to appear in a paper entitled "Direct single-cell biomass estimates for marine bacteria via Archimedes' principle" by Nathan Cermak, Jamie W. Becker, Scott M. Knudsen, Sallie W. Chisholm, Scott R. Manalis, and Martin F. Polz. ISME Journal (In Press)</p> Methods and Sampling: <p>We measured single cell buoyant mass (cell mass minus the mass of the fluid it displaces) using a suspended microchannel resonator. This is a custom-fabricated silicon microfluidic chip with a fluid-filled resonator. When a cell flows through the resonator in a fraction of a second, it briefly changes the resonator's total mass, which changes its resonant frequency. By tracking the resonator's resonant frequency, we can weigh single cells. The baseline frequency of the resonator is also proportional to the fluid density, and we quantify this relationship in advance using sodium-chloride solutions as density standards.</p>
<p>In this measurement, cells were grown in either 2216 marine broth (13B01) or&nbsp;dilute seawater-based media (all others). Cells were taken from exponential growth phase (except for 13B01 which was measured in both stationary and exponential phases) and fixed with either formaldehyde or glutaraldehyde.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1129359 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1129359
completed
Dr Martin Polz
Massachusetts Institute of Technology
Room 48-415/417 15 Vassar Street
Cambridge
MA
02139
USA
mpolz@mit.edu
pointOfContact
Scott Manalis
Massachusetts Institute of Technology
617-253-5039
77 Massachusetts Avenue
Cambridge
MA
02139
USA
srm@mit.edu
pointOfContact
asNeeded
Unknown
strain
fluid
cell_id
buoyantMass_fg
time_hr
baselineFrequency_hz
fluidDensity_gpermL
theme
None, User defined
taxon
treatment
sample identification
mass
time_elapsed
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Suspended Microchannel Resonator
instrument
BCO-DMO Standard Instruments
Polz_lab
service
Deployment Activity
Cambridge, MA
place
Locations
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.
Linking Single-Cell Growth Rates and Genomics
https://osprey.bco-dmo.org/project/564848
Linking Single-Cell Growth Rates and Genomics
<p><em>Description from NSF award abstract:</em><br />
Marine ecosystems are primarily microbial in nature. Microscopic organisms represent over 90% of biomass, including the major primary producers, and drive biogeochemical processes. Although this insight is merely 30 years old, it has led to concerted efforts in studying the structure and functioning of microbial communities in the ocean. Techniques are now available to estimate many key ecological parameters of microbial life; however, one fundamental gap is that estimates of microbial growth rates in the wild remain poorly constrained. Questions, which have largely remained unsolved, are:</p>
<p>What does the growth rate distribution look like for free-living microbes?<br />
Which species grow at what rates?<br />
How do environmental changes (e.g., nutrients, light) affect growth rates of different microbes?</p>
<p>To begin to address these questions, this project will develop a single-cell based system that allows coupled measurement of in situ growth rates and genomic characteristics. The suspended microchannel resonator (SMR) is a well-developed microfluidics-based mass-sensor that has sufficient resolution for measuring the natural range in size and growth rate of ocean microbes; here, this system will be adapted to enable: (i) capture and growth measurement of individual microbial cells in their native seawater microenvironment, (ii) genomic analysis of the same cells for which growth rates have been determined, and (iii) direct analysis of bacterioplankton communities obtained from mesocosm and natural ocean samples. This system is unique in that it couples quantitative growth rate determination and genomic identification of individual microbial cells in their natural microenvironment, and therefore promises to be applicable to the above questions.</p>
<p>Understanding what regulates bacterial growth on the single cell and population level is of fundamental importance in linking microbial diversity to function, and to model and predict carbon fluxes in the ocean. This project establishes a prototype system to couple determination of growth and genomics on the single cell level, for which no data currently exist. Future directions will include design of a system with increased throughput and capability of running onboard ship or autonomous sampling devices.</p>
Bacterioplankton single-cell growth
largerWorkCitation
project
eng; USA
biota
oceans
Cambridge, MA
2016-10-19
Lab-based
0
BCO-DMO catalogue of parameters from Buoyant single cell densities of marine bacterial isolates in pure water, deuterated water and artificial seawater (Bacterioplankton single-cell growth 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/661586.rdf
Name: strain
Units: unitless
Description: <p>Bacterial strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/661587.rdf
Name: fluid
Units: unitless
Description: <p>Type of fluid the cells were measured in: H2O is pure water; D2O is pure deuterated water; and ASW is artificial seawater (made from sea salts from sigma aldrich).</p>
http://lod.bco-dmo.org/id/dataset-parameter/661588.rdf
Name: cell_id
Units: unitless
Description: <p>Cell identification number</p>
http://lod.bco-dmo.org/id/dataset-parameter/661589.rdf
Name: buoyantMass_fg
Units: femtograms (fg)
Description: <p>The cell's buoyant mass</p>
http://lod.bco-dmo.org/id/dataset-parameter/661590.rdf
Name: time_hr
Units: hours
Description: <p>The time elative to the start of the experiment at which the cell was measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/661591.rdf
Name: baselineFrequency_hz
Units: hertz
Description: <p>The resonator's baseline frequency at the time of measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/661592.rdf
Name: fluidDensity_gpermL
Units: grams/milliliter (g/ml)
Description: <p>The density of the fluid in which the cell was immersed; calculated based on the resonator's baseline frequency</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
776062
https://datadocs.bco-dmo.org/file/l880lQlH6kl0KO/cell_densities.csv
cell_densities.csv
Primary data file for dataset ID 661577
download
https://osprey.bco-dmo.org/dataset/661577/data/download
download
onLine
dataset
<p>We measured single cell buoyant mass (cell mass minus the mass of the fluid it displaces) using a suspended microchannel resonator. This is a custom-fabricated silicon microfluidic chip with a fluid-filled resonator. When a cell flows through the resonator in a fraction of a second, it briefly changes the resonator's total mass, which changes its resonant frequency. By tracking the resonator's resonant frequency, we can weigh single cells. The baseline frequency of the resonator is also proportional to the fluid density, and we quantify this relationship in advance using sodium-chloride solutions as density standards.</p>
<p>In this measurement, cells were grown in either 2216 marine broth (13B01) or&nbsp;dilute seawater-based media (all others). Cells were taken from exponential growth phase (except for 13B01 which was measured in both stationary and exponential phases) and fixed with either formaldehyde or glutaraldehyde.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added 'cell_id' parameter name</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
PI Supplied Instrument Name: PI Supplied Instrument Description:A custom-fabricated silicon microfluidic chip with a fluid-filled resonator to measure mass and density of single cells. Instrument Name: Suspended Microchannel Resonator Instrument Short Name:SMR Instrument Description: A high-precision instrument for measuring single-cell mass, volume, and density using one or two resonators connected by a serpentine fluidic channel. During operation of the dual SMR, a dilute cell population suspended in cell media, Fluid 1, is delivered to the sample bypass via pressure-driven flow (Figure 2A, Supplementary Figure 1), and single cells flow into the first SMR (SMR1) for the first buoyant mass measurement. The cells then travel through a microchannel to a cross-junction, where a second fluid of different density is introduced. After the cross-junction, cells continue through a long serpentine channel, which facilitates mixing of the two fluids. The cells next enter a second cantilever (SMR2) for a buoyant mass measurement in the mixed fluid, Fluid 2. As cells flow through each cantilever, a change in resonance frequency is recorded (Figure 2B), which is determined by each cell's buoyant mass in each cantilever's corresponding fluid.
Reference: Bryan, A.K. et al. (2015) Measuring single cell mass, volume, and density with dual suspended microchannel resonators. Proc Natl Acad Sci USA 108: 10992–10996 doi:10.1073/pnas.1104651108. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895367/
Deployment: Polz_lab
Polz_lab
MIT
laboratory
Polz_lab
Dr Martin Polz
Massachusetts Institute of Technology
MIT
laboratory