Vertical plates were scanned using a flatbed scanner (Epson Expression 1680Pro, Epson, UK) at resolution 600 dpi. Primary root (PR) length, lateral root (LR) number, and LR length were analyzed from these images using ImageJ (Schneider et al., 2012 ) with the plugin SmartRoot (Lobet et al., 2011 (link)). All LRs were measured when they were long enough to be identified by the analysis software (ca. >200 µm). Data from ImageJ were then transferred to Microsoft Excel to produce graphs. Anchor roots (defined as roots emerging from the hypocotyl–root junction; Ingram et al., 2011 (link)) were discounted from analysis. The auxin reporter DR5::GUS (Sabatini et al., 1999 (link)) was used as a marker for early LR development in LR progression analysis. Tissue localization of GUS enzyme activity was performed as described by Topping and Lindsey (1997) (link), and roots were examined using compound light microscopy.
Expression 1680 pro
Manufactured by Epson
Sourced in United States
The Expression 1680 Pro is a professional-grade flatbed scanner designed for high-resolution scanning. It features a maximum optical resolution of 1600 x 3200 dpi and can capture images up to 8.5 x 11.7 inches in size. The scanner utilizes Epson's advanced CCD technology to deliver accurate color reproduction and detailed scans.
Automatically generated - may contain errors
11 protocols using expression 1680 pro
1
Quantitative Root Morphology Analysis
2
Gel Electrophoresis and Protein Analysis
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Gels were fixed for 1 h in 10% (v/v) ethanol-7% (v/v) acetic acid, rinsed with water and stained with Sypro Ruby (Invitrogen, Eugene, OR, USA) for 1 day. Background fluorescence was washed off and Sypro Ruby images were analyzed as described below. Imaged gels were washed with water, stained with Colloidal G-250 Coomassie Blue [22 (link)] and scanned at 300 dpi in an Epson Expression 1680 Pro (Epson, Long Beach, CA, USA).
Isoelectric point values were calculated according to the pI curve of 3–11 non-linear Immobiline DryStrip gels [35 ]. Experimental molecular masses were calculated from semi-logarithmic (log10) curves of molecular mass vs. migration distance.
Isoelectric point values were calculated according to the pI curve of 3–11 non-linear Immobiline DryStrip gels [35 ]. Experimental molecular masses were calculated from semi-logarithmic (log10) curves of molecular mass vs. migration distance.
3
Quantitative Proteomic Analysis Pipeline
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Coomassie-stained gels were scanned in transmission mode in an Epson Expression 1680 Pro (Epson, Long Beach, CA, USA), at 300 dpi, in conditions of linear intensity response. Images were analysed using Redfin 3 Solo software (Ludesi AB, Lund, Sweden, http://www.ludesi.com) for professional image analysis. The features of this programme are as follows: spot detection, segmentation and matching followed a strict protocol ensuring a high level of correctness. All-to-all spot matching avoided the bias caused by the use of a reference gel. Quantification consisted of measuring the cumulative staining intensity contained within each spot, which is proportional to protein volume. Spot intensities were corrected for background level and noise. Gels were normalized according to their total protein content, taken as the sum of the intensities of all the spots contained in each gel. Normalization as performed made spot volumes comparable between gel images, removing differences that may originate from variations in staining, protein loading or scanning velocity by mathematically minimizing the median expression difference between matched spots. A comprehensive total of 1028 spots per gel were detected. Proteins were considered to be differentially expressed when their mean spot intensity differed by over 1.5-fold between groups, with P < 0.05 (analysis of variance).
4
Staining of Infected Endothelial Cells
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Primary ovine and bovine endothelial cells were infected in 12-well plates as described previously. Infected cells were incubated at 37°C and fixed in 4% (wt/vol) formaldehyde in phosphate-buffered saline (PBS) (FS) at 24, 48, 72, and 96 hpi. Monolayers were stained with Coomassie blue staining solution (0.1% [wt/vol] Coomassie brilliant blue R-250, 45% [vol/vol] methanol, 10% [vol/vol] glacial acetic acid) and imaged with a photo scanner (Epson Expression 1680 Pro).
5
Panoramic Radiographic Analysis of Apical Root Resorption
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The classification of patients’ skeletal pattern was based on pre-treatment lateral cephalometric radiographs. Both panoramic radiographs (before and after treatment) were performed with the same equipment with the standard quality criteria of a panoramic X-ray. Panoramic radiographs were digitalized (300 dpi, 256 grey levels) using a scanner (Expression 1680 Pro, Epson) and saved in TIFF. The evaluation of OIEARR was performed by measuring root length variation in pre- and post-treatment panoramic radiographs using a specific software prototype (ARIAS for Apical Resorption Image Analysis System) as previously described [25 (link)]. A correction factor (CF) corresponding to the ratio between the initial (C1) and final crown lengths (C2), was applied, as it is accepted that during orthodontic treatment, the crown length does not change [25 (link)]. The applied formula was based on the Linge & Linge method [5 (link)] (1991) modified by Brezniak et al. [26 (link)] (2004) and calculates the percentage of root length variation (%OIEARR). where R1 and R2 are the initial and final root length, respectively, and CF = C1/C2
To better assess %OIEARR in each patient, the maximum value of %OIEARR obtained in the six teeth, %OIEARRmax, was considered as a dependent variable. All measurement procedures were executed by the same operator, a specialist in orthodontics.
To better assess %OIEARR in each patient, the maximum value of %OIEARR obtained in the six teeth, %OIEARRmax, was considered as a dependent variable. All measurement procedures were executed by the same operator, a specialist in orthodontics.
6
Differential Proteome Analysis of Treated Leaves
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Gels image were acquired by an Epson Expression 1680 Pro image scanner. Differentially-expressed spots were selected by Progenesis SameSpot analysis (Nonlinear Dynamics, Newcastle upon Tyne, UK). Two groups (control and treated leaves) were compared with each other by the one way ANOVA analysis. All spots were pre-filtered and manually verified before applying the statistical criteria (ANOVA p < 0.05 and fold > 1.5). Spot intensity, instead of normalized spot volumes, was used in statistical processing.
7
SARS-CoV-2 Titers via Plaque Assay
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SARS-CoV-2 titers were determined by plaque assay in either VeroE6 or VeroE6-ACE2-TMPRSS2. Cells were seeded at 2.5 x 105 cells/well in 12-well plates and plaque assays performed as described [66 (link)].The plates were fixed in 8% [w/v] formaldehyde in PBS, stained with Coomassie Blue staining solution (0.1%(w/v) Coomassie Brilliant Blue R-250; 45%(v/v) methanol; 10%(v/v) glacial acetic acid) and imaged with a photo scanner (Epson Expression 1680 Pro).
8
Eugenol Modulates Apoptosis Regulators
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The effect of eugenol on the expression of Bax, Bcl-2 and cyt-c was determined. Control and eugenol-treated cells were washed 1X-PBS and lysed via homogenization in 250 mM sucrose- 10 mM Hepes- 50 mM Tris base buffer pH 7.4 containing triton at 0.001% final concentration. Protein levels were determined using the Bio-Rad protein assay. Following standard protocols, lysates containing 50 μg of protein were loaded, resolved on 12% SDS-PAGE, electro-transferred to a nitrocellulose membrane, immuno-blotted at 4 °C overnight with proper primary antibody (Bax, Bcl-2, cyt-c or GAPDH (1:1000 dilution), washed with TBS-Tween and blotted for 1 h with the appropriate secondary anti-body. The protein bands were visualized using the ECL Kit. The films were exposed using an RP X-OMAT processor (Model M6B) and scanned using an Epson Expression 1680 Pro. The density of bands was quantified using the “ImageJ” program.
To determine whether cyt-c was released from eugenol-treated cells, the culture media of control and treated cells were collected, and lyophilized, and the resultant solid was re-suspended in lysis buffer, separated on 12% SDS-PAGE, and immune- stained as described before.
To determine whether cyt-c was released from eugenol-treated cells, the culture media of control and treated cells were collected, and lyophilized, and the resultant solid was re-suspended in lysis buffer, separated on 12% SDS-PAGE, and immune- stained as described before.
9
Plaque Assay for SARS-CoV-2 Infection
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Monolayers of A549 or Vero E6 cells and their ACE2/TMPRSS2 derivatives were prepared by seeding 2.5 × 105 cells/well in 12-well plates, and plaque assays were executed using standard conditions. Briefly, a 1-ml overlay of MEM/0.6% Avicel RC-591/2% FCS was used, and fixed plates were stained with Coomassie Blue staining solution (0.1% Coomassie Brilliant Blue R-250/45% methanol/10% acetic acid) before scanning using a photo scanner (Epson Expression 1680 Pro).
10
Radiochromic Film Dosimetry with Flatbed Scanners
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After each ART irradiation, the film was removed from the phantom and scanned in one or two flatbed scanners. A tight schedule for the dose read-out was not necessary as a relative dosimetry approach was implemented as presented in section 2.4.4. Films from centre 1 were scanned in both an Epson Expression 1680 Pro and an Epson Perfection V700 Photo scanner while films from centre 2 were scanned in an Epson Perfection V850 Pro scanner. By analysing the same data from centre 1 using digital images achieved from two different flatbed scanners, the effect of changing flatbed scanners could be investigated as described in section 2.6. In all cases, a resolution of 300 dpi and a dynamic range of 48 bit was used. A custom-made film holder was used to ensure that the film was pressed against the glass in the scanner and that a similar scan area was used for every scan. The film holder was made of 4 mm thick plastic, exactly fitting the scanner dimensions (A4), and was made with a central rectangular hole, such that it only covered the film in the outermost edges. The scanned, digital film images were analysed in an in-house developed Matlab GUI as described in the following.
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