Journal: Journal of Experimental Botany

Article Title: A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii , Solanum tuberosum , and Arabidopsis thaliana

doi: 10.1093/jxb/err066

Figure Lengend Snippet: Comparison of cold- and CBF-regulated pOGs of S. tuberosum (St), S. commersonii (Sc), and A. thaliana (At). (A) A total of 8714 putative orthologous groups (pOGs) were identified between At and St. The Venn diagram shows pOGs with at least one At gene on the ATH1 chip, at least one potato clone on the potato cDNA array, or at least one gene from each species in both arrays (overlap). (B) Overlaps of cold-induced and cold-repressed pOGs in Sc, St, and At are shown from the pOGs present in both arrays in A. (C) Comparison of CBF regulon pOGs in Sc, St, and At. Overlaps of CBF-induced and CBF-repressed pOGs are shown based on the pOGs present in both arrays.

Article Snippet: A list of cold-regulated A. thaliana genes was generated from a large number of previously published microarray experiments ( Vogel et al. , 2005 ; Kilian et al. , 2007 ) and new experiments (unpublished arrays have been submitted to Array Express) that used the Affymetrix ATH1 gene chip to monitor transcript levels ( Supplementary Table S2 at JXB online).

Techniques:

Journal: bioRxiv

Article Title: Plant cell wall integrity maintenance and pattern-triggered immunity modulate jointly plant stress responses in Arabidopsis thaliana

doi: 10.1101/130013

Figure Lengend Snippet: 6 d-old Col-0, bak1-5 and ixr1-1 seedlings were treated with ( A-C ) DMSO, DMSO/Sorbitol (S), Isoxaben (ISX), ISX/S or ( D-F ) boiled Driselase (bDri), bDri/S, Driselase (Dri) and Dri/S. (A, D) Jasmonic acid (JA) and (B, E) Salicylic acid (SA) contents were quantified 7 h after treatment. Values are means ( n = 4) and error bars represent SD. (C, F) Callose depositions in cotyledons have been quantified 24 h after treatment. Values are means ( n = 15-20) ± SEM. ( G ) Lignification in Col-0 cotyledons was visualized 24 h after treatment by Phloroglucinol staining. The scale bar represents 1 mm. ( H ) Relative TOUCH4 ( TCH4) expression level in Col-0 seedlings 7 h after treatment. Values are means ( n = 3) ± SD. ( I ) Relative PLANT DEFENSIN1.2 ( PDF1.2) expression level in Col-0 and bak1-5 seedlings 7 h after treatment with bDri or Dri compared to non-treated (NT) seedlings. Values are means ( n = 3) ± SD. Different letters between treatments of each genotype in (A-I) indicate statistically significant differences according to one-way ANOVA and Tukey’s HSD test (α = 0.05). Asterisks in (A-F) indicate statistically significant differences to the wild type (Student’s t -test; * P < 0.05; ** P < 0.01; *** P < 0.001; ns, not significant).

Article Snippet: Fig. S4: Expression survey of glutamate like receptor ( GLR ) genes and characterization of a WAK2 T-DNA insertion line. ( A ) Changes in transcript levels of 18 GLR genes in isoxaben-treated Col-0 seedlings after 0, 4, 8, 12, 18, 20, 24, 36 h. Y-axis shows fold change in isoxaben-treated Col-0 seedlings based on normalization to transcript levels in mock-treated seedlings on the Affymetrix ATH-1 chip ( ). ( B ) Sketch of the GLR2.5 gene and results from semi-quantitative RT-PCR reactions for GLR2.5 compared to ACT1 .

Techniques: Staining, Expressing

Journal: bioRxiv

Article Title: Plant cell wall integrity maintenance and pattern-triggered immunity modulate jointly plant stress responses in Arabidopsis thaliana

doi: 10.1101/130013

Figure Lengend Snippet: ( A ) Jasmonic acid (JA), ( B ) Salicylic acid (SA) and ( C ) root tip lignification were quantified in 6 d-old mutant seedlings after 7 h (A-B; n = 4, means ± SD) or 12 h (C; n ≥ 10, means ± SD) of Isoxaben (ISX) treatment. Values are relative to a wild type control from a representative experiment selected from at least 3 independent experimental repeats per genotype. Asterisks indicate statistically significant differences to the wild type (Student’s t -test, * P < 0.05). Mutant lines are organized in functional groups (RLKs, Receptor-like kinases; Cr RLK1 Ls, Catharanthus roseus RLK1-like kinases; AHKs, Arabidopsis histidine kinases; Ion channels) and individual genotypes described in detail in Supplemental Table S2. ( D ) Hierarchical clustering of mutant phenotypes assigns functions in CWI maintenance to candidate genes based on their responses to standardized cell wall damage. Mutant phenotype data from (A-C) and Supplemental Figure S5 (RGI, root growth inhibition) have been normalized to wild type controls and log 2 transformed prior to average linkage clustering. Blue color indicates reduced ISX responses while red color is indicative of increased ISX responses compared to wild type. ( E-G ) Col-0, mca1, fei2, mca1 fei2, the1-1, the1-1 mca1, the1-1 fei2 and ( H-J ) the1-4, the1-4 mca1, the1-4 fei2 seedlings were grown for 6 d before treatment with ISX. (E, H) Jasmonic acid (JA) and (F, I) Salicylic acid (SA) were quantified 7 h after treatment ( n = 4, means ± SD), (G, J) Root tip lignification was quantified 12 h after treatment ( n ≥17, means ± SD). Different letters between genotypes indicate statistically significant differences according to one-way ANOVA and Tukey’s HSD test (α = 0.05).

Article Snippet: Fig. S4: Expression survey of glutamate like receptor ( GLR ) genes and characterization of a WAK2 T-DNA insertion line. ( A ) Changes in transcript levels of 18 GLR genes in isoxaben-treated Col-0 seedlings after 0, 4, 8, 12, 18, 20, 24, 36 h. Y-axis shows fold change in isoxaben-treated Col-0 seedlings based on normalization to transcript levels in mock-treated seedlings on the Affymetrix ATH-1 chip ( ). ( B ) Sketch of the GLR2.5 gene and results from semi-quantitative RT-PCR reactions for GLR2.5 compared to ACT1 .

Techniques: Mutagenesis, Functional Assay, Inhibition, Transformation Assay

Journal: bioRxiv

Article Title: Plant cell wall integrity maintenance and pattern-triggered immunity modulate jointly plant stress responses in Arabidopsis thaliana

doi: 10.1101/130013

Figure Lengend Snippet: ( A ) Relative expression levels of PROPEP1, 2, 3 and 4 were determined by qRT-PCR after 1 h of treatment with DMSO or Isoxaben (ISX) in Col-0 seedlings. PROPEP1 and 3 expression levels were further examined ( B ) after 0, 3, 6 and 9 h of treatment in Col-0 seedlings and ( C ) after 1 h of treatment with DMSO or ISX in Col-0 and the1-1 seedlings. Values in (A-C) are means ( n = 3) ± SD; asterisks indicate statistically significant differences to DMSO-treated controls (Student’s t -test; * P < 0.05). ( D ) Jasmonic acid (JA) and ( E ) Salicylic acid (SA) were quantified in Col-0 seedlings after 7 h of co-treatment with DMSO or ISX and 0, 1, 10 or 100 nM At Pep1 ( n = 4, means ± SD). ( F ) Root tip lignification in Col-0 after 12 h of co-treatment with DMSO or ISX and At Pep1 (0, 1, 10 nM) was visualized by Phloroglucinol staining. The scale bar represents 200 μm. ( G ) JA and ( H ) SA quantification in Col-0, pepr1 , pepr2 and pepr1 pepr2 after 7 h of co-treatment with DMSO or ISX and 10 nM At Pep1 ( n = 4, means ± SD). Different letters between treatments of each genotype in (D-H) indicate statistically significant differences according to one-way ANOVA and Tukey’s HSD test (α = 0.05). ( I ) Root tip lignification in Col-0, pepr1 , pepr2 and pepr1 pepr2 seedlings after 12 h of co-treatment with DMSO or ISX and 10 nM At Pep1 was visualized by Phloroglucinol staining. The scale bar represents 200 μm.

Article Snippet: Fig. S4: Expression survey of glutamate like receptor ( GLR ) genes and characterization of a WAK2 T-DNA insertion line. ( A ) Changes in transcript levels of 18 GLR genes in isoxaben-treated Col-0 seedlings after 0, 4, 8, 12, 18, 20, 24, 36 h. Y-axis shows fold change in isoxaben-treated Col-0 seedlings based on normalization to transcript levels in mock-treated seedlings on the Affymetrix ATH-1 chip ( ). ( B ) Sketch of the GLR2.5 gene and results from semi-quantitative RT-PCR reactions for GLR2.5 compared to ACT1 .

Techniques: Expressing, Quantitative RT-PCR, Staining