Researchers are exploring whether these ubiquitous fluorinated molecules might worsen infections or hamper vaccine effectiveness.
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Edited by Julia Bailey-Serres, University of California, Riverside, CA, and approved July 31, 2017 (received for review May 7, 2017)
Article Figures & SI
Figures
- Fig. 1.
Markers and genes differentially expressed in the root stem cell niche. (A–D) Marker lines for the SCN (A), QC (B), xylem (C), and CEI (D) cells. The SCN encompasses several stem cell populations, which include, among others, xylem, CEI, and QC cells. (E) PCA of the genes enriched in each stem cell or developmental zone. Genes for the PCA are represented by their expression patterns across stem cell type and root zone. Elements in the graph represent genes; shapes and colors indicate the cell or zone of enrichment of a particular gene. (F) Venn diagram of the number of genes and TFs identified in each stem cell type. Of the 1,625 genes enriched in the stem cells, 402 were found to be enriched in the SCN and in one or more of the cell types (not shown in the diagram for clarity, see Dataset S2).
- Fig. 2.
Network of QC-enriched TFs. (A) Network among the QC-enriched TFs inferred with the 12 developmental time points of the Arabidopsis root. Node sizes indicate importance of the nodes in terms of the number of TFs that they regulate. Color-coded nodes represent genes downstream of PAN that were used for the mathematical model and experimental confirmations. (B–I) Confocal images of 5-d-old Arabidopsis roots. (Scale bar: 20 μm.) (B) Col-0 wild-type root. (C) pan057190 root showing a disorganized SCN. (D) pWOX5:erGFP root. (E) pWOX5:erGFP;pan057190 root showing changes in QC marker expression. (F–I) Confocal images with mPSPI staining for starch granules. (F) pWOX5:erGFP root. (G) pWOX5:erGFP;pan057190 root showing differentiated columella stem cells. (H) 35S:PAN root showing extra columella stem cell layers. (I) XVE:PAN root showing QC divisions and extra columella stem cell layers. (J) Quantification of the number of columella stem cell layers in the different lines. (K) Quantification of the number of roots showing QC divisions. Significant statistical difference, *P < 0.05, Wilcoxon rank sum test between XVE:PAN upon β-estradiol treatment (BE) and Col-0 WT control. Significant statistical difference, **P < 0.05, Wilcoxon rank sum test) between XVE:PAN upon β-estradiol treatment (BE) and XVE:PAN control treatment (MS). (J and K) Number of roots examined: WT Col-0, n = 41; XVE:PAN MS, n = 47; and XVE:PAN BE, n = 55. White arrows indicate QC cells and black arrows indicate columella stem cells.
- Fig. 3.
PAN subnetwork in the QC inferred with the 12 developmental time points of the Arabidopsis root. (A) Optimal configuration (combination of signs—activation or repression—of the regulations that were inferred with undefined signs, which best fits the data in the simulations of the equations) of the subnetwork of PAN and its downstream targets. (B and C) Resulting expression values of PAN and its downstream targets, over time, after simulating the optimal configuration of the model. Simulations were run for 5 d and plots are shown until all factors reached steady states in the WT and pan mutant simulations. (B) Model simulated with the fitted equation parameters. (C) Model simulated with the PAN-associated parameters set to zero to simulate a pan mutant situation. (D) Normalized expression values of PAN and its predicted downstream targets in Col-0 wild type and in pan mutant. Statistically significant changes of expression between the mutant and the wild type, *q < 0.05.
- Fig. 4.
Network of the 201 TFs enriched in the SCN, inferred with the 12 developmental time points of the Arabidopsis root. Clusters of nodes indicate groups of TFs functionally related or functioning in the same cell type. Node sizes indicate importance of the nodes in terms of the number of TFs that they regulate. The highly connected groups of genes or subnetworks correspond to the DBN inferred for each cluster. Green (orange) nodes represent factors that are differentially down-regulated (up-regulated) in the pan mutant with respect to Col-0 wild type. Blue represents the PAN node.
Data supplements
Predicting GRNs in Arabidopsis root stem cells
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- Biological Sciences
- Plant Biology
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