http://lod.bco-dmo.org/id/dataset/649873
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
2016-06-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project)
2018-03-15
publication
2018-03-15
revision
BCO-DMO Linked Data URI
2018-03-15
creation
http://lod.bco-dmo.org/id/dataset/649873
David A. Hutchins
University of Southern California
principalInvestigator
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Eric A. Webb
University of Southern California
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: Hutchins, D. A., Webb, E. A., Saito, M. A. (2018) Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2018-03-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/649873 [access date]
Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 Dataset Description: <p><em>Trichodesmium erythraeum</em> was grown in biological triplicate under two CO2 regimes (380 and 750 uatm pCO2) and four different nutrient regimes (replete, phosphorus-limited,iron-limited, iron/phosphorus colimited).&nbsp;&nbsp;</p>
<p>Raw sequence reads from the <em>Trichodesmium </em><em>erythraeum</em><em> </em>used in this experiment can be accessed at The National Center for Biotechnology Information (NCBI) under the BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA312342" target="_blank">PRJNA312342</a>.&nbsp;</p>
<p>Protein sequences can be accessed through NCBI BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA318/" target="_blank">PRJNA318</a>.<br />
<br />
The&nbsp;fasta&nbsp;file&nbsp;<a href="https://datadocs.bco-dmo.org/docs/302/HiCO2_AdaptCyano/data_docs/IMG_Trichodesmium_IMS101_genes.fasta">IMG_Trichodesmium_IMS101_genes.fasta</a>&nbsp;(5.4 MB) contains all of the Integrated Microbial Genomes (IMG)-annotated genes in the Trichodesmium&nbsp;erythraeum&nbsp;IMS101 genome.&nbsp; More information can be found at the IMG Trichodesmium genome portal, "<a href="https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&amp;page=proteinCodingGenes&amp;taxon_oid=637000329" target="_blank">genes page</a>" and <a href="https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&amp;page=taxonDetail&amp;taxon_oid=637000329" target="_blank">IMG Genome ID&nbsp;637000329</a>&nbsp;page.</p>
Raw spectra are available as dataset PXD010515 in the PRIDE proteome-exchange repository (doi: 10.6019/PXD010515).
These results were published in:
* Walworth et al., 2016a
* Walworth et al., 2016b
* Walworth et al., 2018
<p><strong>Related dataset:&nbsp;</strong><a href="https://www.bco-dmo.org/dataset/649904" target="_blank">Trichodesmium physiology and cell growth</a></p> Methods and Sampling: <p>The following are excerpts from Walworth et al. 2016a.&nbsp;Please refer to this reference for more details of the methodology used to generate these data.</p>
<p>"Protein spectral counts are generated by extracting proteins from cells, digesting into smaller peptides, separating them on HPLC (high-performance liquid chromatography), and measuring peptide masses on a mass spectrometer to ascertain mass-to-charge ratio. Peptide fragment ratios are then compared to a reference genome and spectral counts per protein are enumerated."</p>
<p>"Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean."</p>
<p>"Spectral counts compare a specific protein’s abundance between treatments, rather than against other&nbsp;proteins,&nbsp;because the sensitivity of spectral counts can vary between proteins depending on the number of tryptic peptides within the sequence and their chemical characteristics."&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260490 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260490
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260233 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260233
completed
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
266 Woods Hole Rd. MS #51 Watson Lab
Woods Hole
MA
02543
USA
msaito@whoi.edu
pointOfContact
Eric A. Webb
University of Southern California
213-740-7954
Department of Biological Sciences, Marine and Environmental Biology Section; Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway AHF 331
Los Angeles
CA
90089-0371
USA
eawebb@usc.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Locus_Tag
COG_category
gene_product
pCO2_380_1
pCO2_380_2
pCO2_380_3
pCO2_750_1
pCO2_750_2
pCO2_750_3
pCO2_380plusPlim_1
pCO2_380plusPlim_2
pCO2_380plusPlim_3
pCO2_750plusPlim_1
pCO2_750plusPlim_2
pCO2_750plusPlim_3
pCO2_380plusFelim_1
pCO2_380plusFelim_2
pCO2_380plusFelim_3
pCO2_750plusFelim_1
pCO2_750plusFelim_2
pCO2_750plusFelim_3
pCO2_380plusFePlim_1
pCO2_380plusFePlim_2
pCO2_380plusFePlim_3
pCO2_750plusFePlim_1
pCO2_750plusFePlim_2
pCO2_750plusFePlim_3
CM140 Total Inorganic Carbon Analyzer
Shimadzu gas chromatograph GC-8a
Michrom Advance nanoflow LC and autosampler
Thermo Fusion mass spectrometer
Orion 5 STAR pH meter
Turner 10 AU fluorometer
theme
None, User defined
sample description
Clusters of Orthologous Groups (COG) categories
No BCO-DMO term
spectral counts
featureType
BCO-DMO Standard Parameters
CO2 Coulometer
Gas Chromatograph
High-Performance Liquid Chromatograph
Mass Spectrometer
pH Sensor
Turner Designs Fluorometer 10-AU
instrument
BCO-DMO Standard Instruments
lab_Webb_Hutchins_Fu
service
Deployment Activity
Southern California
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.
Adaptation of key N2-fixing cyanobacteria to changing CO2
https://osprey.bco-dmo.org/project/551230
Adaptation of key N2-fixing cyanobacteria to changing CO2
<p><em>Description from NSF award abstract:</em><br />
This study will employ a novel combination of experimental evolution techniques and state-of-the-art molecular methods to yield unique insights into adaptive changes in the keystone marine cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> in response to selection by high CO2. Several studies have suggested that N2-fixation rates of the biogeochemically-critical cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> may increase dramatically in the future high CO2 ocean, but these have all used the same limited set of cultured isolates and considered cells only briefly acclimated to elevated CO2. The investigator's new results, however, demonstrate that a broad diversity of high- and low-CO2 adapted ecotypes exists within each diazotroph genus. Furthermore, in a preliminary four year experimental evolution study with <em>Trichodesmium</em>, the PIs observed large adaptive responses following 500-700 generations of selection by high CO2- but in a completely unexpected way. All of the six replicate high CO2-adapted cell lines exhibited strong constitutive up-regulation of N2 fixation rates. These very elevated N2 fixation rates continued, even though the cultures have were switched back to low-CO2 conditions for many months. Expression of the nif operon and N assimilatory genes was also up-regulated in these cell lines, as is expression of many intergenic regions of the genome.</p>
<p><strong>The investigators hypothesize that constitutive up-regulation of cellular N2 fixation systems may be a common adaptive response of both <em>Trichodesmium</em> and <em>Crocosphaera</em> under extended selection by elevated CO2. This project will test this hypothesis in a four-year experimental evolution study to determine the adaptive responses of both high- and low-CO2 specialized ecotypes of these two diazotrophs to increased CO2.</strong></p>
<p>The investigators will grow representative high- and low-CO2 adapted ecotypes from each genus in well-replicated cell lines at 380 ppm and 750 ppm CO2 for up to 1000 generations. Periodically, they will perform "switch" experiments to measure N2 and CO2 fixation rates and growth rates of high CO2-selected cell lines grown briefly (one week) at low CO2, and vice versa. These switch experiments will allow screening for cell lines which exhibit adaptive changes in phenotypically-expressed rate parameters, such as those observed in the preliminary <em>Trichodesmium</em> study. Evolutionary mechanisms in the CO2-selected cell lines will be examined by comparison of changes in their genomes, transcriptomes, and proteomes over time relative to reference genomes, using frozen samples archived monthly during the preceding selection period. Examination of these molecular and biochemical changes will be coordinated with an in-depth array of physiological and biogeochemical analyses. This combined approach will allow an evaluation of potential adaptive mechanisms in diazotrophic cyanobacteria ranging from indel, duplication, single nucleotide polymorphism, and transposition mutations to altered putative non-coding RNA expression, protein expression, and post-translational protein modifications, and then allow the investigators to link these mechanisms directly with their potential impacts on ecosystem-level biogeochemical processes like N2 and CO2 fixation. Finally, the research team will determine how long term selection by high CO2 affects the iron and phosphorus requirements of <em>Trichodesmium </em>and <em>Crocosphaera</em>, since constitutive up-regulation of N2 fixation would also have major implications for limitation of diazotrophs by these two critical nutrients in the future high CO2 ocean.</p>
HiCO2_AdaptCyano
largerWorkCitation
project
eng; USA
biota
oceans
Southern California
2018-03-15
Culture study at the University of Southern California, Los Angeles
0
BCO-DMO catalogue of parameters from Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano 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/685525.rdf
Name: Locus_Tag
Units: text
Description: <p>Locus identfier</p>
http://lod.bco-dmo.org/id/dataset-parameter/685527.rdf
Name: COG_category
Units: text
Description: <p>Clusters of Orthologous Groups; generated by comparing the protein sequences of complete genomes; classified into functional <a href="http://dmoserv3.bco-dmo.org/data_docs/HiCO2_AdaptCyano/COGcategories.png" target="_blank">categories</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/685528.rdf
Name: gene_product
Units: text
Description: <p>protein identified by the gene in the first column</p>
http://lod.bco-dmo.org/id/dataset-parameter/685529.rdf
Name: pCO2_380_1
Units: counts
Description: <p>these columns are spectral counts defined as the total number of spectra identified for a protein; a semiquantitative measure of protein abundance; 380 uatm CO2-replete nutrients (unlimited Fe and P); first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685530.rdf
Name: pCO2_380_2
Units: counts
Description: <p>380 uatm CO2-replete nutrients (unlimited Fe and P); second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685531.rdf
Name: pCO2_380_3
Units: counts
Description: <p>380 uatm CO2-replete nutrients (unlimited Fe and P); third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685532.rdf
Name: pCO2_750_1
Units: counts
Description: <p>750 uatm CO2-replete nutrients (unlimited Fe and P); first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685533.rdf
Name: pCO2_750_2
Units: counts
Description: <p>750 uatm CO2-replete nutrients (unlimited Fe and P); second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685534.rdf
Name: pCO2_750_3
Units: counts
Description: <p>750 uatm CO2-replete nutrients (unlimited Fe and P); third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685535.rdf
Name: pCO2_380plusPlim_1
Units: counts
Description: <p>380 uatm CO2 P limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685536.rdf
Name: pCO2_380plusPlim_2
Units: counts
Description: <p>380 uatm CO2 P limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685537.rdf
Name: pCO2_380plusPlim_3
Units: counts
Description: <p>380 uatm CO2 P limited; third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685538.rdf
Name: pCO2_750plusPlim_1
Units: counts
Description: <p>750 uatm CO2 P limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685539.rdf
Name: pCO2_750plusPlim_2
Units: counts
Description: <p>750 uatm CO2 P limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685540.rdf
Name: pCO2_750plusPlim_3
Units: counts
Description: <p>750 uatm CO2 P limited; third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685541.rdf
Name: pCO2_380plusFelim_1
Units: counts
Description: <p>380 uatm CO2 Fe limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685542.rdf
Name: pCO2_380plusFelim_2
Units: counts
Description: <p>380 uatm CO2 Fe limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685543.rdf
Name: pCO2_380plusFelim_3
Units: counts
Description: <p>380 uatm CO2 Fe limited; third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685544.rdf
Name: pCO2_750plusFelim_1
Units: counts
Description: <p>750 uatm CO2 Fe limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685545.rdf
Name: pCO2_750plusFelim_2
Units: counts
Description: <p>750 uatm CO2 Fe limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685546.rdf
Name: pCO2_750plusFelim_3
Units: counts
Description: <p>750 uatm CO2 Fe limited; third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685547.rdf
Name: pCO2_380plusFePlim_1
Units: counts
Description: <p>380 uatm CO2 iron/phosphorus co-limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685548.rdf
Name: pCO2_380plusFePlim_2
Units: counts
Description: <p>380 uatm CO2 iron/phosphorus co-limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685549.rdf
Name: pCO2_380plusFePlim_3
Units: counts
Description: <p>380 uatm CO2 iron/phosphorus co-limited; third replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685550.rdf
Name: pCO2_750plusFePlim_1
Units: counts
Description: <p>750 uatm CO2 iron/phosphorus co-limited; first replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685551.rdf
Name: pCO2_750plusFePlim_2
Units: counts
Description: <p>750 uatm CO2 iron/phosphorus co-limited; second replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/685552.rdf
Name: pCO2_750plusFePlim_3
Units: counts
Description: <p>750 uatm CO2 iron/phosphorus co-limited; third replicate</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
481164
https://datadocs.bco-dmo.org/file/rggpGyphAWmzz/trichodesmium380_750_v2.csv
trichodesmium380_750_v2.csv
Primary data file for dataset ID 649873
download
https://osprey.bco-dmo.org/dataset/649873/data/download
download
onLine
dataset
<p>The following are excerpts from Walworth et al. 2016a.&nbsp;Please refer to this reference for more details of the methodology used to generate these data.</p>
<p>"Protein spectral counts are generated by extracting proteins from cells, digesting into smaller peptides, separating them on HPLC (high-performance liquid chromatography), and measuring peptide masses on a mass spectrometer to ascertain mass-to-charge ratio. Peptide fragment ratios are then compared to a reference genome and spectral counts per protein are enumerated."</p>
<p>"Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean."</p>
<p>"Spectral counts compare a specific protein’s abundance between treatments, rather than against other&nbsp;proteins,&nbsp;because the sensitivity of spectral counts can vary between proteins depending on the number of tryptic peptides within the sequence and their chemical characteristics."&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO data manager notes:<br />
* Data version 2: 2018-03-15 replaces version 1: 2016-06-22. Data version 2 removed column "accession_numbers" containing protein sequence accession numbers at NCBI which were no loger valid due to an annotation remapping effort.&nbsp; The appropriate protein accessions can instead be found through the NCBI BioProject page:&nbsp;&nbsp;<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA318/" target="_blank">PRJNA318</a>.&nbsp; The data parameter "Gene ID" was changed to name "Locus Tag" to be consistent&nbsp;with&nbsp;terminology at IMG and NCBI.</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
CM140 Total Inorganic Carbon Analyzer
CM140 Total Inorganic Carbon Analyzer
PI Supplied Instrument Name: CM140 Total Inorganic Carbon Analyzer PI Supplied Instrument Description:Dissolved inorganic carbon was measured with CO2 coulometry (model CM 140, UIC). Instrument Name: CO2 Coulometer Instrument Short Name:CO2 coulometer Instrument Description: A CO2 coulometer semi-automatically controls the sample handling and extraction of CO2 from seawater samples. Samples are acidified and the CO2 gas is bubbled into a titration cell where CO2 is converted to hydroxyethylcarbonic acid which is then automatically titrated with a coulometrically-generated base to a colorimetric endpoint. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB12
Shimadzu gas chromatograph GC-8a
Shimadzu gas chromatograph GC-8a
PI Supplied Instrument Name: Shimadzu gas chromatograph GC-8a PI Supplied Instrument Description:Shimadzu Scientific Instruments, Columbia, Maryland. Equipped with a flame ionization detector. Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
Michrom Advance nanoflow LC and autosampler
Michrom Advance nanoflow LC and autosampler
PI Supplied Instrument Name: Michrom Advance nanoflow LC and autosampler PI Supplied Instrument Description:Michrom Bioresources. And a 100 μm inner diameter 15 cm long capillary column with a pulled tip (packed in-lab with MAGIC C18AQ 200 Å pore size 3 μm particle size from Michrom Bioresources). 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/
Thermo Fusion mass spectrometer
Thermo Fusion mass spectrometer
PI Supplied Instrument Name: Thermo Fusion mass spectrometer PI Supplied Instrument Description:With MS1 scans at an Orbitrap resolution of 60 K, 350–1,800 m/z scan range, 2.0e5 automatic gain control target, and a maximum injection time of 35 ms. MS2 scans were analysed on the linear ion trap in topN data dependent mode at a cycle time of 3 s using normal scan rate and range with a maximum injection time of 75 ms and a 0.7 m/z isolation window. Charge states of 2–7 were analysed with a dynamic exclusion of 15 s with a mass tolerance of 10 p.p.m. Monoisotopic precursor selection was used, and a user-defined lock mass of 445.12003 m/z. 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/
Orion 5 STAR pH meter
Orion 5 STAR pH meter
PI Supplied Instrument Name: Orion 5 STAR pH meter PI Supplied Instrument Description:Thermo Fisher Scientific. With a combined glass electrode. The metre was calibrated with National Bureau of Standards buffer solutions of pH 4, 7 and 10. Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
Turner 10 AU fluorometer
Turner 10 AU fluorometer
PI Supplied Instrument Name: Turner 10 AU fluorometer Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/
Deployment: lab_Webb_Hutchins_Fu
lab_Webb_Hutchins_Fu
Webb-Hutchins-Fu USC
laboratory
Webb-Hutchins-Fu USC
laboratory