Perfection v750

The gels were scanned after silver staining on a flatbed scanner (Epson perfection V750), using a 16 bits grayscale image acquisition. The gel images were then analyzed using the Delta 2D software (v 4.7). Spots that were never expressed above 100 ppm of the total spots were first filtered out. Then, significantly-varying spots were selected on the basis of their Student T-test p-value between the treated and the control groups. Spots showing a p-value lower than 0.05 were selected.
The false discovery rate was controlled by a combination of approaches, including the classical Benjamini-Hochberg FDR [59 (link)] or the more recent Sequential Goodness of Fit approaches [60 ,61 (link)]. Global analysis of the proteomic results was carried out by the PAST statistical software [62 ].

To determine the effect of HMME on plant growth and development, germinated wheat seeds were planted into medium containing non-autoclaved or autoclaved inoculum (control) from the final round of selection (e.g. 1:10 ratio inoculum to autoclaved Metro-Mix 900). Pots were watered to field capacity, given no additional watering, and maintained under the aforementioned growth chamber conditions. After 10 days, plants were harvested, and roots were washed on a fine mesh sieve to remove debris. Whole plant fresh weight (biomass) was measured, and then roots were separated from above ground tissue and scanned using a flatbed scanner (EPSON, Perfection V-750). Intact root systems were transferred to a root positioning tray (20 cm × 30 cm) with sterile water (three root systems per tray) and carefully spread out to avoid root overlap. Root scans were analyzed using WinRHIZO Arabidopsis 2017a (Regent Instruments Inc., Quebec, Canada, 2000), generating estimates of total root length, root surface area, and number of root tips as previously described [7 (link), 8 ]. Dry weights were obtained after scanning and compared as previously described [9 (link)], This experiment was repeated once.

The gels were scanned after silver staining on a flatbed scanner (Epson perfection V750), using a 16 bits grayscale image acquisition. The gel images were then analyzed using the Delta 2D software (v 4.1). The spots intensities were normalized by the software as the fraction (in percent) of the sum of all detected spots. This allowed the quantitative comparison of the various cofilin spots in all gels analyzed.
For determining the effects of LIMK inhibition on cofilin phosphorylation, statistical tests were used. As different culture batches can show quantitatively different 2D gel profiles, paired (by culture batch) and unpaired (over the complete replicate series) T-tests were used.

Four‐week‐old Rx1:4xHA plants were agroinfiltrated with DEX::CP105 and DEX::CP106. Two days after transformation, sectors were infiltrated with DAB staining solution (1 mg/mL 3,3′‐diaminobenzidine‐4HCl in 20 mm Na₂HPO₄). After infiltration, leaves were induced by brushing 20 µm DEX in 0.01% Silwet and sampled at different time points. Leaves were de‐stained by boiling for 15 min in ethanol–glycerol–acetic acid (3 : 1 : 1). Leaves were mounted in ethanol–glycerol–water (1 : 1 : 2) in Petri dishes and photographed using an Epson Perfection V750 flatbed scanner (Epson, Suwa, Nagano Prefecture, Japan).

Strain collections (the Keio collection [2 (link)] and sRNA single and double deletion libraries) were stored in 96-well plates as glycerol stocks and pinned onto LB agar using the Singer ROTOR HDA and then grown at 37°C for 18 h. Strain libraries were then upscaled to master plates at the appropriate colony density for screening (384 or 1,536 density). Master plates were used to inoculate freshly prepared assay plates, which were incubated for 18 or 24 h at 37°C to reach endpoint growth (defined as a time period where the growth of a WT strain has plateaued for at least 6 h). Plates were scanned with an Epson Perfection V750 scanner to generate a high-resolution image, and then the integrated density of each colony was extracted from the image using ImageJ (100 (link)). Kinetic growth curves on solid medium were conducted by scanning plates every 20 min until endpoint growth using scanners housed within a 37°C incubator (27 (link)). Data were normalized as previously described (27 (link)).

Three random pieces of filaments, each 20 mm in length, were scanned in an Epson Perfection V750 (Long Beach, CA, USA) for quantification of thickness variation. The images were acquired in reflection and transmission modes with a resolution of 2400 dots per inch. The images acquired in transmission mode were automatically thresholded and binarized. The variation in thickness of the binarized filaments were quantified with a plugin for ImageJ developed for this purpose. The thickness variation is considered a measurement of the filament roughness and corresponds to the variation in thickness along each single filament piece (20 mm length, 3 replicates).
Pieces of filaments were used to estimate the void fraction of the filaments considering the weight of the filaments (W_i, in g), the cross-sectional area (A_i, in cm²) and length (L_i, in cm) of the pieces, the estimated density of TMP fibers (1.56 × 10⁻⁶ g/cm³) and BioPE (0.955 g/cm³ for BioPE1 and 0.954 g/cm³ for BioPE2), and the mass fraction of fibers (X_F) and BioPE (X_BioPE) in the filaments. The void fraction was calculated as follows:


It should be noted that the cross-sectional area A_i is obtained by measuring the diameter of the filaments and assuming a circular cross-section. This is a reasonably simple approach, but it considers the surface roughness as voids.

The reproducibility of the flatbed Epson Perfection V750 scanner response was investigated by repeatedly scanning film pieces irradiated at 0, 1, 6, 15, 35, and 70 Gy at different times: 30 min, 18 hrs, and 25 days between scans.