|Allen, Andrew E||J. Craig Venter Institute (JCVI)||Principal Investigator|
|Kustka, Adam||Rutgers University||Contact|
|Rauch, Shannon||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
Ten diel microarray experiments were completed (seven for P. tricornutum encompassing three Fe concentrations, and three for T. pseudonana encompassing two Fe concentrations).
The following description is from a final report for an NSF OCE award provided by the dataset contact.
As biomass increases, steady state Fe prime invariably changes; this was minimized to less than 5% under all Fe conditions by making modifications to the Aquil recipe. In addition, excursions in media pH (which also change Fe' prime) were minimized by acclimating cells to pH buffer (EPPS) treated with chelex-100 resin.
A maximum of 750 pmol/L Fe prime is assumed because of Fe hydroxide precipitation, but for simplicity, the investigators report the results as Fe prime even at concentrations exceeding this maximum. Steady-state uptake rates for several diatoms continue to increase with increasing total Fe within the region of Fe hydroxide precipitation (Sunda and Huntsman 1995; Mar Chem 50:189).
In T. pseudonana experiment E, addition of Fe to remaining low Fe cultures after diel sampling resulted in an increase in growth rate after 24 h, confirming growth rate limitation by Fe. The similar Fv/Fm values under low and high Fe are consistent with the data of Price 2005 (Limnol. Oceanogr. 50:1159).
In P. tricornutum experiment C, the pH buffer stock solution was not properly buffered before use in cultures. While these particular experiments will need to be repeated, these samples may be useful for comparing the diatom transcriptomes during holocene and anthropocene conditions, as these pH values are consistent with predicted values for 2100 (Gruber et al. 1996 Global Biogeochemical Cycles).
PI-provided parameter names were modified to conform with BCO-DMO conventions.
|species||Name of the diatom species.||dimensionless|
|exp_id||Identifier for the experiment; originally named 'cluster'.||dimensionless|
|fe_prime||Fe prime is the sum of all concentrations of Fe not bound to EDTA species. It is calculated according to thermodynamic equilibrium constants and photochemical reduction rate constants for FeEDTA species.||pMol|
|growth_rate||Cell specific growth rate (per day), calculated as the slope of the linear regression between ln (cell density) versus time. Originally named 'mu'.||ln(cell density)/day|
|growth_rate_se||Standard error of growth_rate.||dimensionless|
|Fv_to_Fm||Also referred to as (delta F)/Fm; Fv_to_Fm is the variable to maximum chlorophyll fluorescence, explicitly calculated as [F(knot)-F(maximum)]/F(maximum) and measured using the DCMU method.||dimensionless|
|Fv_to_Fm_sd||Standard deviation of Fv_to_Fm.||dimensionless|
|pH||pH of buffer solution.||pH scale|
|pH_sd||Standard deviation of the pH.||dimensionless|
|Start Date|| |
|End Date|| |
Research for the project 'Expression profiling and functional genomics of a pennate diatom: Mechanisms of iron acquisition, stress acclimation, and recovery' was conducted at Dr. Kustka's lab at the Rutgers-Newark campus: 101 Warren Street, Smith Hall Room 140 Newark, New Jersey, 07102
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-02-20 10:45:54