6 research outputs found
Figure 5
Observed and predicted profiles of PHO2 and IPS1
under Pi-depletion and repletion conditions. Panels A and B correspond to PHO2,
and C and D to IPS1. Panels A and C show predicted profiles of PiOM and PsTR
models, while panels B and D depict models incorporating RNA-protection. The blue dashed lines show the fold change in RNA-SEQ values from [20]. The red and black
lines denote PsTR and PiOM models,
respectively. The grey zones denote the
period of Pi-resupply
Figure 4
<p>Fitting of
different hypothesis models to PHO2 data. Panel A represents the fits of PiOM
model. Panel B-F depicts the fit offered by individual hypothesis, labelled in
the respective panel. Red dashed lines represent the 80% prediction interval of
the respective hypothesis model. These simulations have been carried out by
sampling parameter values from normal (Gaussian) distributions with means and
standard deviations given from the parameter fitting in Monolix. Circle
represents the qRT-PCR data. Square and triangles denotes fold change mRNA-seq data, respectively.</p
Table 1
List of AIC, -2 log-likelihood and P-value for
the hypothesis models. The AIC and log-likelihood values were generated for
each model while estimating parameters using MONOLIX. The relationship between
the P-value and â–³AIC is following: P-value
= Probability (χ2 k > △AIC + 2k). Here, k is the
degree of freedom (i.e. the difference in T - the total number of model
parameters, including both structural and statistical model). Using this
relationship, P-value was calculated using Chi-squared distribution (CHIDIST)
function in Microsoft Excel, while comparing the AIC value and number of
parameters for each hypothesis model with the original model (PiOM)
Figure 2
Schematic representation of the molecular
regulation of Pi uptake. (A) A simplified
depiction of the molecular network
regulating Pi acquisition. (B-F) five hypotheses to explain the observed PHO2
dynamics under Pi-deficient conditions.
Panel (B-F) depicts individual hypotheses (model) in a single root cell (thick
black box). Red lines and letters denote the assumed reactions and species,
respectively. Each hypothesis assumed the presence of an unknown regulator Z
(B-E) or R (F) acting in different manners. Protein, ligand, mRNA, complexes
and Pi ions are denoted by rectangles (pink), red ellipse, parallelogram
(green), squares (transparent) and blue ellipse, respectively. Pointed solid
arrows denote direct interactions and fluxes, barred arrows denote inhibition
or repression, and dashed lines represent indirect interactions. ø denotes
endogenous production and degradation of the molecules
Figure 1
<p>Expression
profiles of (A) PHO2, (B) IPS1 and (C) miR399 in Pi-starved rice seedling (cv. Nippobare)
roots. The expression levels are relative to the +P condition at time point
zero. Errors bars are SE and n = 3. Relative expression levels were normalized
to that of an internal control, Os-ACTIN.</p