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10 protocols using lide110 scanner

1

Protein Extraction and Western Blot Analysis

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Total cellular protein was extracted using lysis buffer, and protein levels were quantified using a BCA kit (ASPEN Biotechnology, Wuhan, China). Proteins were separated on a 10% SDS-PAGE before being probed with the appropriate primary antibodies for CD9, CD63 TSG101, PI3Kγ (#ab154598, Abcam, Cambridge, UK, 1:500), PIK3R1 (#4257, CST, MA, US, 1:1000), P-Akt (#4060, CST, MA, US, 1:1000), IL-17 (#sc-374218, Santa Cruz, Texas, US, 1:500), PTEN (#ab267787, Abcam, Cambridge, UK, 1:2000) and Bcl-2 (#ab182858, Abcam, Cambridge, UK, 1:1000) and then transferred to polyvinylidene fluoride (PVDF) membranes. The blots were then probed with secondary antibodies, and protein was identified using a LiDE110 scanner (Canon, Japan). GAPDH (#ab37168, Abcam, Cambridge, UK, 1:10,000) was used for normalization, and the AlphaEaseFC software was used to measure protein band density.
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2

Examining Protein Expression with AZD6738 and Cisplatin

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Cells were treated with the indicated doses of AZD6738, cisplatin, combination, or mock for 24 h. Protein lysates were generated by scraping adherent cells in lysis buffer (150 mM NaCl, 50 mM Tris-HCL, 5 mM NaF, 1% Tween 20, 0.5% IGEPAL CA-630, protease inhibitor cocktail, pH 7.5) and incubating on ice for 30 min. For AZD6738 + cisplatin experiments, detached cells were pelleted from the media and combined with the adherent cell lysate. SDS-PAGE using 4–12% Bis-Tris gels (NuPAGE Novex) and Western blotting were performed using standard techniques. Antibody details are provided in the supplementary methods. Following detection of phospho-proteins, membranes were stripped for 25 min at room temperature in Restore stripping buffer (Thermo Scientific) and re-probed for corresponding total protein. Images of blots were acquired at 24-bit depth using a Canon LiDE110 scanner and were processed (converted to 8-bit, cropped) using ImageJ.
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3

Leaf Morphology and Phytochemical Analysis

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Leaf morphometrics were measured using ImageJ software (version 1.47; Abramoff et al., 2004 ). Leaves from each depth, were scanned (Canon Lide 110 scanner) and images were used to measure leaf length (mm), width (mm) and area (mm2); at least 10 leaves from each plant were used for these morphometric measurements. Total phenols were extracted from the leaves (200 mg fresh weight) and rhizomes (200 mg fresh weight) of each plant in duplicate to increase confidence and quantified according to Migliore et al. (2007) (link). Photosynthetic pigments (Chlorophyll a and Chlorophyll b, total Carotenoids) were extracted in duplicate from leaves (250 mg) of each plant, according to Wellburn (1994) (link), modified by Rotini et al. (2013) (link). Both phenols and photosynthetic pigment contents are expressed as mg/g of fresh weight (FW).
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4

Converted Flatbed Scanner for Fluorescence

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More detailed instructions on converting our Canon LiDE 110 scanner (Canon USA, Melville, NY) to fluorescence detection are given in Supporting Information. Briefly, the scanner was disassembled and a Kodak number 15 filter was carefully taped across a region of the scanner bed. The control pins on the ribbon cable for the green and red illumination sources were covered with tape in order to insulate them from their contacts. Conductive ink was then used to bridge the blue control contact to the red and green control contacts so that blue LEDs were eliminated irrespective of the connection to which current was applied. The white background and the portion of the glass panel not covered by the yellow filter were blacked out with flat black spray paint. We added additional side on illumination with a string of high intensity blue LEDs. These LEDs were connected to a separate, 12 v external power source during scanning.
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5

Western Blot Analysis of Bone Markers

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Samples were diluted at a ratio of 1:5 and heated at 95 °C for 5 minutes. Proteins were separated by SDS-PAGE and transferred to polyvinylidene fluoride membranes. 5% milk was used to block the membranes in TBST for 1 hour at room temperature, incubated with primary antibodies at 4°C overnight, and incubated with horseradish peroxidase-conjugated secondary antibodies at 37 °C for 1 hour. Primary antibodies and dilutions were as follows: anti-TLR4 (1:1000; #ab13556, Abcam, Cambridge, UK), anti-Collagen I (1:1000; #ab138492, Abcam, Cambridge, UK), anti-OCN (1:1000; #ab133612, Abcam, Cambridge, UK), anti-Runx2 (1:1000; #ab236639, Abcam, Cambridge, UK), and anti-GAPDH (1:10000; #ab37168, Abcam, Cambridge, UK). Secondary antibodies were used to probe the blots, and protein was detected with a LiDE110 scanner (Canon, Tokyo, Japan).
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6

Phenoloxidase Activity in Insect Immunity

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PO activity in S. aureus-infected T. molitor larvae, pupae and adults injected with Neb-colloostatin or an analog solution or exposed to an ND-peptide solution (ND-Neb-colloostatin, ND-[Ala1]-, [Val1]-, [Hyp4]- or [Ach4]-colloostatin) was measured on the third day of the experiment according to a modified method described previously42 (link),43 (link). In brief, 1 μl of hemolymph was placed on white filter paper (Whatman No. 52) soaked in a 10-mM sodium phosphate buffer containing 2 mg/ml DL-DOPA (Sigma Aldrich). Subsequently, the filter papers with the samples were incubated for 30 min at room temperature and air-dried. The samples were then scanned with a Canon Lide 110 scanner (600 dpi, 8 bits, gray scale). Images have been transformed so that the darker samples correspond to the highest PO activity. Images of the samples were analyzed with ImageJ (ver. 2), measuring the color intensity of the samples in their central 40 × 40 pixel area. The PO activity assessment was based on the mean pixel value of each image.
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7

Western Blot Analysis of Cell Proteins

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Lysates were prepared from cells or supernatants, were diluted 1:5 with loading buffer, and were boiled for 5 min at 95°C. Samples of protein were then separated via SDS-PAGE, transferred to PVDF membranes, and blots were blocked using 5% non-fat milk in TBST for 1 h at room temperature. Blots were then probed overnight with anti-CD81 (1:500; ab59477), anti-VEGFA (1:1000; ab52917), TSG101 (1:1000, ab83) or anti-GAPDH (1:10,000, ab37168) (all from Abcam, Cambridge, UK). Blots were then probed using HRP-linked secondary antibodies at 37°C for 1 h, and protein bands were detected via LiDE110 scanner (Canon, Tokyo, Japan), with the AlphaEaseFC software (Alpha Innotech, Genetic Technologies, Inc, FL, USA) being used to measure band density.
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8

Quantifying Liver Granuloma Formation

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Liver sections from mice of control and vaccinated groups and infected with 100 cercariae were collected 45 days post-infection to evaluate the effect of immunization in granuloma formation. The liver sections removed from the central part of the left lateral lobe were fixed with 10% buffered formaldehyde in PBS. Histological sections were performed using microtome (4 μm) and stained in a slide with Gomory's trichromic. The granulomas were counted in Axiolab Carl Zeiss microscope using 10× objective lens. All slides were digitized by the Canon Lide 110 scanner, in 300 dpi resolution. The pixels of each histological section were fully screened, with subsequent creation of a binary image and the total area of the cut was calculated. The area of the lower cutoff was used as a minimum standard of tissue to be statistically analyzed. The results were expressed by the number of granulomas per area of liver (mm2). The area of granulomas was obtained through the KS300 software contained in Carl Zeiss image analyzer. Fifteen granulomas from each mouse with a single well-defined egg were randomly chosen at a microscope with 20× objective lens and scanned through a Q-Color3 microcamera (Olympus). Using a digital pad, the total area of granulomas was measured and the results were expressed in square micrometers (μm2).
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9

Quantification of APOA1 Protein by Western Blot

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Total protein was extracted using RIPA Lysis Buffer (cat. no. AS1004; Aspen Biological) and Protease Inhibitor Cocktail (cat. no. 04693159001; Roche Diagnostics). The protein concentration was determined using the BCA Protein Quantification Kit (cat. no. AS1086; Aspen Biological). Subsequently, proteins (40 µg/lane) were separated using 10% SDS-PAGE and transferred onto PVDF membranes. The membranes were then blocked with 5% skimmed milk and 0.1% Tween-20 in Tris-buffered saline at room temperature for 1 h. After which, the membranes were incubated overnight at 4°C with primary antibodies against APOA1 (1:1,000; cat. no. 14427-1-AP; Proteintech Group, Inc.) and β-actin (1:10,000; cat. no. TDY051; Beijing TDY Biotech Co., Ltd.). After washing three times with PBS containing 0.5% Tween-20, the membranes were incubated with HRP-conjugated anti-rabbit secondary antibodies (1:10,000; cat. no. AS1107; Aspen Biological) at room temperature for 1 h. Signal visualization was performed using a Lide110 scanner (Canon, Inc.).
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10

Protein Expression Analysis of Osteoblasts

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OCCM‐30 single‐layer cells were lysed with RIPA buffer (Beyotime) containing phosphatase inhibitors (Roche) and PMSF (Beyotime). Then, lysate was centrifuged, the supernatant was collected, and the total protein concentration was determined using the BCA Protein Assay Kit (Beyotime). Forty micrograms of total protein from each group diluted in loading buffer (Beyotime) was boiled at 95°C for 10 minutes, separated by electrophoresis in 10% SDS polyacrylamide gel (Servicebio) and wetly transferred to a PVDF membrane (Millipore). The membrane was subsequently blocked with 5% non‐fat milk for 1 hour. Afterwards, the membrane was incubated at 4°C overnight with the following primary antibodies: anti‐YAP (1:2000; CST), anti‐OCN (1:1000; Proteintech) and anti‐p‐p65 (S536; 1:1000; CST).
In the next day, the membrane was washed three times with TBST buffer, incubated with corresponding horseradish peroxidase‐conjugated secondary antibody for 1 hour at room temperature and then washed with TBST buffer three times. Blots were generated using the ECL reagent (Advansta) and detected using X‐ray films (Kodak). The protein bands were scanned using the LiDE 110 scanner (Canon) and quantified with densitometry analysis by using the ImageJ software (National Institutes of Health). Western blot analysis was repeated at least three times.
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