Plants were grown for 3 weeks under short-day conditions (8 h light, 16 h dark), and then shifted to long-day conditions (16 h light, 8 h dark) to induce flowering. JA treatments were performed by watering plants with either tap water (mock) or 0.5 mm jasmonic acid after moving plants to long days. Due to the asymmetric effects of side shoots on tissue patterning, only plants in which the first internode was at least 3.5 cm long were analysed. For histological analyses, stem fragments were fixed in FAA (formalin/acetic acid/alcohol) and embedded in paraffin. Subsequently, 10 μm sections were produced using a microtome, deparaffinized, stained with 0.05% toluidine blue (AppliChem, http://www.applichem.com ), and fixed with Entellan (Merck, http://www.merck.com ) or Dako Ultramount (Dako, http://www.dako.com ) (Figure 6 ) on microscope slides. For quantitative analyses, at least five plants were evaluated for each data point. The standard errors of means were used to visualize variation. Data were subjected to statistical analysis, using a two-tailed independent Student’s t test with SPSS 15.0 software (http://www.spss.com ). Significance levels of P<0.05, P<0.01 and P<0.001 are indicated in the figures by single, double and triple asterisks, respectively. Phloroglucinol staining and analysis of GUS reporter activity were performed as described previously (Ruzin, 1999 ; Scarpella et al., 2004 (link)). For analysis of signal distribution in cross-sections (Figure 7 ), stained samples were left in 30% sucrose overnight at 4°C, then embedded in 5% low-melting-point agarose (Sigma, http://www.sigmaaldrich.com/ ) and sectioned using a vibratome (HM430, Microm, http://www.microm-online.com ). The resulting 30 μm sections were observed using DIC optics. Alternatively, samples were embedded in Technovit 7100 (Kulzer, http://www.kulzer.com ) using the manufacturer’s protocol, and 5 μm sections were produced with a microtome, fixed with Entellan and observed using dark-field optics (Figure S3 ).
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