Perfection v700 scanner

The root systems of three plants per pot were scanned with an Epson Perfection V700 scanner, and the images were analyzed with the WinRHIZO^TM software, 2015a Pro version (Regent Instruments Inc.), using the “root morphology” mode. This software analyses the digital images, estimating parameters such as total root length and root surface area, making it possible to estimate the effects of the treatments on root development.

Measurements and quantifications were performed using the LAS×Leica Software. For studying the RAM length, seedlings were mounted in PI (0.02 mg/ml). We measured the distance from quiescent center until the uppermost first cortical cell, which was twice as long as wide as described by Feraru et al. (2019) (link). For epidermal cell patterning, lengths of four consecutive epidermal cells from neighboring (tricho/atrichoblast) files in the late meristem were measured (Löfke et al., 2015 (link)). For analyzing the patterning frequency in GL2::4xYFP, we checked for its expression in cell division and transition zones. We defined the occurrence of trichoblast cells in an atrichoblast cell file, and vice versa, as a patterning defect and counted the number of such patterning events in each seedling. For root length measurements, ½ MS plates with seedlings were scanned using Epson Perfection V700 scanner and the root lengths were measured using ImageJ.

HEK-293 and MCF7 cells were seeded in 6-well plates at an initial seeding density of 500 cells/well. After 3–4 days, cells were treated with Complex V or Complex III inhibitors at the previously-indicated concentrations, or incubated with galactose-containing DMEM for 2–3 weeks. After each week, cells were treated with fresh media containing the inhibitors. After gently rinsing the cells with 1X PBS, cells were fixed in 4% PFA for 10 min at room temperature. Cells were then washed twice with 1X PBS and stained with 0.2% (w/v) crystal violet for 10 min. Excess of dye was removed by washing the cells with 1X PBS, before letting the wells dry at room temperature. Then, plates were scanned on Epson Perfection V700 scanner and colonies were counted using the Colony Counter plugin of the Image J software (NIH).

2D gels were stained with silver nitrate according to Rajjou et al. (2008) (link). Stained gels were placed within two layers of cellophane membrane stretched on cassette frames for drying. Images of dry gels were obtained with an Epson Perfection V700 scanner. Quantitative image analysis was conducted using Progenesis Samespot software (v3.2, NonLinear Dynamics) to quantify proteins spots and to detect changes in protein accumulation.
The PCA was performed based on the abundance of the differentially-accumulated protein spots.
Pair-wise statistics were used to detect protein spots that significantly changed in abundance. Two categories were defined; physiological state and genotype and four physiological state comparisons were made between the protein profiles of the two physiological states (aged versus AR) within each genotype. The AR seed proteome profiles of the NILs were also compared to that the Ler genetic background. Protein spots were considered to have been significantly different in abundance if they were higher than or equal to 1.5-fold up or down accumulated and when the P-value was equal or smaller than 0.05 according to one-way ANOVA test (Progenesis Samespot software) between the means of the four replicates.

Fungal isolates were cultured on four media types; PDA, oatmeal agar (OA), malt extract agar (MEA) (Boerema et al. 2004 (link); Chen et al. 2015a (link)), and carnation leaf agar (CLA). The colonies were measured at 7 d, and morphology examined after 12–14 d incubation in the same light and temperature conditions described above. Images of the colonies were captured by an Epson Perfection V700 scanner at a 300 dpi resolution. Colony colour was determined on surface and reverse using the colour charts of Rayner (1970) . Isolates were characterised microscopically from the PDA plates. Lactic acid (100 % v/v) was used as the mounting fluid. Specimens were examined using a Leica DM5500B compound microscope with a Leica DFC 500 camera fitted to capture images under Nomarski differential interference contrast illumination. Micromorphological measurements and descriptions of pycnidia, pycnidial wall cells and conidia were taken from up to 20 samples, and septation and colour recorded. Images of pycnidia were taken from CLA plates using a Leica M165C stereo microscope and Lecia DFC 500 camera. The NaOH spot test on MEA culture plates helped distinguish taxa (Boerema et al. 2004 (link)).