http://lod.bco-dmo.org/id/dataset/827928
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
2020-10-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Whole-cell data dependent mass spectrometry proteomic approach examining Emiliania Huxleyi exposed to 3 doses of HHQ
2020-10-29
publication
2020-10-29
revision
BCO-DMO Linked Data URI
2020-10-29
creation
http://lod.bco-dmo.org/id/dataset/827928
Kristen E. Whalen
Haverford College
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
documentDigital
Cite this dataset as: Whalen, K. E. (2020) Whole-cell data dependent mass spectrometry proteomic approach examining Emiliania Huxleyi exposed to 3 doses of HHQ. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-10-29 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/827928 [access date]
Emiliania Huxleyi exposed to 3 doses of HHQ Dataset Description: <p>Data Dependent Acquisition Proteomics: <em>Emiliania Huxleyi </em>exposed to 4 treatments of HHQ (2-heptyl-4-quinolone). All files are&nbsp;in the Proteome Exchange Data Archive and publically accessible at: <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD011559" target="_blank">https://www.ebi.ac.uk/pride/archive/projects/PXD011559</a></p> Methods and Sampling: <p><em>Emiliania huxleyi</em> cells were grown to 72 hours in each treatment and 4 biological replicates from individual culture bottles were isolated for proteomics. Cells were pelleted using centrifugation and lysed with a sonicating probe. Proteins were reduced, alkylated, and digested with trypsin after being soubilized in 6M urea (see Nunn et al. 2016). All samples were desalted using NEST group desalting columns. Mass spectrometry was completed on Thermo Lumos with NanoAquity inline. Column was 75 micorn ID, packed to 30cm with Dr. Maisch C18 packing material.</p>
<p>All DDA analyses were completed in single runs on the Lumos. 130 minute total run time, gradient 2-35% ACN in 90 minutes. OT resolution 120,000, scan range 375-1575, Rf lens 35%, AGC Target 7e5 MS2: charge state 2-5, Top 20 MS2, AGC targert 5e3, dynamic exclusion 30 s.</p>
<p>Analyses performed by Brook L. Nunn and Miranda M Mudge at the University of Washington Proteomics Resource Center (<a href="https://proteomicsresource.washington.edu/" target="_blank">https://proteomicsresource.washington.edu/</a>).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657818 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657818
onGoing
Kristen E. Whalen
Haverford College
610-795-6042
370 Lancaster Ave. KINSC S314
Haverford
PA
19041
USA
kwhalen1@haverford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
theme
None, User defined
Mass Spectrometer
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: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
https://osprey.bco-dmo.org/project/709948
Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
<p><em>NSF Award Abstract:</em><br />
Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus</p>
<p>Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus into bacteria-phytoplankton interactions. Undergraduate students participate in an intense summer learning experience where research and field-based exercises are supplemented with short-lecture based modules. Students return to their home institutions and work closely with the PIs to conduct interdisciplinary research relating to the aims and scope of the summer research. This research also provides training and career development to two graduate students and a postdoctoral scientist.</p>
<p>Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and microbial trophic structure in the ocean. The intricate relationships between these two domains of life are mediated via excreted molecules that facilitate communication and determine competitive outcomes. Despite their predicted importance, identifying these released compounds has remained a challenge. The PIs recently identified a bacterial QS molecule, HHQ, produced by globally distributed marine gamma-proteobacteria, which induces phytoplankton mortality. The PIs therefore hypothesize that bacteria QS signals are critical drivers of phytoplankton population dynamics and, ultimately, biogeochemical fluxes. This project investigates the timing and magnitude of HHQ production, and the physiological and transcriptomic responses of susceptible phytoplankton species to HHQ exposure, and quantifies the influence of HHQ on natural algal and bacterial assemblages. The work connects laboratory and field-based experiments to understand the governance of chemical signaling on marine microbial interactions, and has the potential to yield broadly applicable insights into how microbial interactions influence biogeochemical fluxes in the marine environment.</p>
HHQSignals
largerWorkCitation
project
eng; USA
oceans
2020-10-29
Bergen, Norway
0
BCO-DMO catalogue of parameters from Whole-cell data dependent mass spectrometry proteomic approach examining Emiliania Huxleyi exposed to 3 doses of HHQ
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
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://osprey.bco-dmo.org/dataset/827928/data/download
download
onLine
dataset
<p><em>Emiliania huxleyi</em> cells were grown to 72 hours in each treatment and 4 biological replicates from individual culture bottles were isolated for proteomics. Cells were pelleted using centrifugation and lysed with a sonicating probe. Proteins were reduced, alkylated, and digested with trypsin after being soubilized in 6M urea (see Nunn et al. 2016). All samples were desalted using NEST group desalting columns. Mass spectrometry was completed on Thermo Lumos with NanoAquity inline. Column was 75 micorn ID, packed to 30cm with Dr. Maisch C18 packing material.</p>
<p>All DDA analyses were completed in single runs on the Lumos. 130 minute total run time, gradient 2-35% ACN in 90 minutes. OT resolution 120,000, scan range 375-1575, Rf lens 35%, AGC Target 7e5 MS2: charge state 2-5, Top 20 MS2, AGC targert 5e3, dynamic exclusion 30 s.</p>
<p>Analyses performed by Brook L. Nunn and Miranda M Mudge at the University of Washington Proteomics Resource Center (<a href="https://proteomicsresource.washington.edu/" target="_blank">https://proteomicsresource.washington.edu/</a>).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing</strong>: The database for <em>Emiliania huxleyi</em> was downloaded 2018-10-10 from Uniprot and concatenated with contaminants. Data was searched using Comet and protein inferences were completed with the TPP to generate pep.xml and prot.xml files.</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
Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer
PI Supplied Instrument Name: Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/