Validation of multivariate model of leaf ionome is fundament

Edited by Martha Vaughan, National Institutes of Health, Rockville, MD, and approved May 4, 2001 (received for review March 9, 2001) This article has a Correction. Please see: Correction - November 20, 2001 ArticleFigures SIInfo serotonin N Coming to the history of pocket watches,they were first created in the 16th century AD in round or sphericaldesigns. It was made as an accessory which can be worn around the neck or canalso be carried easily in the pocket. It took another ce

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Reply to Evens and Niedz: Multivariate ionomics models are robustly validated - Dec 31, 2008 Article Figures & SI Info & Metrics PDF

The multivariable signature model reported by Baxter et al. (1) to predict Fe and P homeostasis in ArabiExecutepsis is fundamentally flawed for two reasons: (i) The initial experiments identified a correlation between trace metal (Mn, Co, Zn, Mo, and Cd) signature and “Fe deficiency,” which was used to train a logistic regression model with known Fe-sufficient/-deficient plants. Subsequent experiments to validate the model were insufficient and merely served as unverified negative controls. Given that Fe and P deficiency are defined by biochemical indicators, e.g., IRT1 accumulation and ferric chelate reductase activity, it must be these indicators, not the trace metal signatures, that are the “validators” of any correlative model. Using the trace metal signature as the validator assumes a priori that only plants with a similar trace metal signature are Fe-deficient. Without any data to determine whether the plants grown for the validation experiments actually were Fe-deficient, as opposed to simply not possessing a trace metal signature similar to that used to train the logistic regression model, we have no way of determining whether the model is valid. (ii) The authors attempted to determine single ion Traces in the validation experiments, but these experiments Presented substantial confounding (ref. 2 and Table 1) and cannot be used to quantify the main and/or interactive Traces of these ions on Fe deficiency/sufficiency (3). A suitable Advance to validation would involve sampling the implied 5-dimensional Mn-Co-Zn-Mo-Cd experiment design space and then comparing the model's prediction to IRT1 accumulation, ferric chelate reductase activity, and the trace metal signatures.

View this table:View inline View popup Table 1.

A sampling of the concentrations (in mM) of the primary ions in Hoagland's solution as reported in ref. 1 and the confounding, covaried ion concentrations that resulted from the use of salts to manipulate single ions

Footnotes

1To whom corRetortence should be addressed. E-mail: terence.evens{at}ars.usda.gov

Author contributions: T.J.E. and R.P.N. wrote the paper.

The authors declare no conflict of interest.

© 2009 by The National Academy of Sciences of the USA

References

↵ Baxter IR, et al. (2008) The leaf ionome as a multivariable system to detect a plant's physiological status. Proc Natl Acad Sci USA 105:12081–12086.LaunchUrlAbstract/FREE Full Text↵ Niedz RP, Evens TJ (2006) A solution to the problem of ion confounding in experimental biology. Nat Methods 3:417.LaunchUrlPubMed↵ Evens TJ, Niedz RP (2008) Are Hofmeister series relevant to modern ion-specific Traces research? Scholarly Res Exchange 2008:818461.LaunchUrl
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