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10 protocols using dmd108 microscope

1

Histological Validation of Semiquantitative MSUS Scoring

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For validation of the semiquantitative MSUS score, histology was used as a gold standard applying a semiquantitative score of 1–3 as used for the MSUS assessments.
The histological samples were obtained from the previously marked area of the cadaver specimens and were fixated in blocks with a 20% formalin solution. These blocks were then processed for H&E staining to obtain histological slices for general morphological analysis. All preparations were examined and measured with a Leica DMD 108 microscope.
The histological scoring was carried out independently by the same two assessors that performed the MSUS examinations together with a third external observer who was an experienced histologist. All were blinded to the others’ evaluation and blinded to the results of the MSUS and the gross anatomy measurements. The same process was repeated after half an hour by each investigator to assess inter-and intra-observer reliability.
The histological characteristics of the muscle, the fat/fibrous infiltration and the organisation of muscular tissue were considered for semiquantitatively scoring of the muscles as follows: (1) normal, (2) moderate sarcopenia (moderate fat infiltration and fibrosis) and (3) severe sarcopenia (severe fat infiltration and fibrosis) (figures 1–3).
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2

Enzymatic Histochemistry of Extracellular Nucleotide Metabolism

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A protocol based on the Wachstein/Meisel lead phosphate method was used [8 (link),11 (link),44 (link),45 ]. The sections were washed twice with 50 mM Tris-maleate buffer pH 7.4 and pre-incubated for 30 min at RT with 50 mM Tris-maleate buffer pH 7.4 containing 2 mM MgCl2 and 0.25 mM sucrose. The enzymatic reaction was carried out by incubating tissue sections for 1 h at 37 °C with 50 mM Tris-maleate buffer pH 7.4 supplemented with 0.25 mM sucrose, 2 mM MgCl2, 5 mM MnCl2, 3 % Dextran, 2 mM Pb(NO3)2, and 2 mM CaCl2. All experiments were performed in the presence of 2.5 mM levamisole, as an inhibitor of alkaline phosphatase (AP) activity, and in the presence of 1 mM AMP, ADP, ATP, or TPP as a substrate. TPP is a false substrate, which can be cleaved by the pyrophosphatase activity of E-NPPs. Control assays were performed in the absence of nucleotide. For E-NTPDase inhibition experiments, 1 mM POM 1 was added to pre-incubation and enzymatic reaction buffers. For CD73 inhibition experiments, 1 mM α, β-meADP was added to pre-incubation and enzymatic reaction buffers. The reaction was revealed by incubation with 1% (NH4)2S (v/v) for exactly 1 min. Nuclei were counterstained with haematoxylin. Samples were mounted with aqueous mounting medium (FluoromountTM, Sigma-Aldrich), observed under a light Nikon Eclipse E200 microscope, and photographed under a light Leica DMD 108 microscope.
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3

Liver Immunohistochemistry for ITGB3

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Liver samples for immunohistochemical analyses were selected from the tissue archives of the Institute of Pathology, Ludwig Maximilian University of Munich, Germany. Liver samples originated from patients with clinical indication for liver biopsy. Tissue sections were stained with anti-ITGB3 (Ventana) on an automated slide staining platform from Ventana, according to manufacturer’s instructions. For analysis, representative brightfield images were taken on a Leica DMD 108 microscope at the indicated magnifications. ITGB3-positive infiltration spots at inflammation sites were counted at 40× magnification.
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4

Histological and Immunofluorescence Analysis of Rag2−/− Mice

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The palate, esophagus, and skin of Rag2−/− mice with the experimental autoimmune dermatitis phenotype or CHS responses were fixed in 10% formalin and stained with hematoxylin and eosin. Sections were observed under a DMD108 microscope (Leica, Wetzlar, Germany). For immunofluorescence staining, 10 μm cryosections of the palate were fixed with paraformaldehyde and stained with anti-CD4 and DAPI. Sections were observed under a fluorescence microscope (Axio Observer.Z1; Carl Zeiss, Oberkochen, Germany). Briefly, for Ch25h staining, differentiated T cells were spun onto microscope slides using a cytospin apparatus and fixed with acetone. Sections were stained with rat anti-Ch25h monoclonal antibody (185-1; BML) and stained with Alexa488-conjugated goat anti-rat IgG antibody, Alexa647-conjugated anti-CD4 antibody (RM4-5), and DAPI.
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5

Comprehensive Histopathological Evaluation of MIA Samples

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All samples taken during the MIA procedure were evaluated using an Olympus BX51 light microscope. H&E sections of all the tissues were initially evaluated. When necessary, ancillary histochemical (i.e. Zieh-Neelsen, PAS, Grocott stain, etc.) and immunohistochemical stains were performed in selected blocks to confirm or exclude specific lesions suspected on the H&E stains. Immunohistochemical staining for CD45 (leukocyte common antigen) was performed in all cases in the CNS samples in order to exclude/confirm minimal leukocyte infiltrates.
All the cylinders present in each block were carefully evaluated, recording all the organs present and measuring the area (in mm2) of each organ obtained in the MIA procedure after drawing the perimeter of each tissue cylinder in a Leica dmd 108 microscope.
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6

Brain Tissue Histological Processing

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Brain tissue fixed in 10% buffered formalin was subjected to standard procedures for fixing, washing, dehydration and paraffin embedding as previously described by us [34 ]. Following fixing of the brain tissue, 5-μm sections were cut and mounted on clean slides. Slides were stained with haematoxylin and counterstained with eosin for light microscopic examination. Images were taken using a digital Leica DMD108 microscope (Wetzlar, Germany).
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7

Histological Analysis of Visceral Fat

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Visceral fat pad was removed from the peritoneal cavity and fixed in 10% Neutral Buffered Formalin (Leica Biosystems), embedded in paraffin and cut in 5 μm sections. Tissue sections were stained with Hematoxylin and Eosin. Stained sections were imaged with Leica DMD108 microscope using 20X objective (for Ripk3gfpfl/fl and Ripk3ΔR/ΔR mice) or 10X objective (for Mlkl−/− mice). Representative images are shown in Figure 7D and S7C.
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8

Staining Amyloid and Lipid Deposits in C. elegans

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X‐34 dye (Sigma‐Aldrich‐Merck) stains specifically amyloid deposits. One‐day synchronised adults were incubated in a drop containing 1 mM X‐34 and 10 mM TRIS pH 7.5 solution. Stained animals were washed with PBS‐Tween and transferred to fresh NGM plates. We used the Oil Red O (Sigma‐Aldrich‐Merck) dye to stain triglycerides and lipoproteins for semi‐quantitative purposes. Young adults were stained with diluted 3:2 Oil Red O stock solution for 2 h at room temperature in a rotator. After this, animals were washed two times with PBS‐Tween (0.1%) for 30 min. Stained animals were mounted in 2% agarose pads with sodium azide (0.05 M) to count amyloid deposits using a DM2500 fluorescent microscope (Leica). To quantify the stained area of worms, with the Oild Red O stain, we used a DMD108 microscope (Leica). We analysed the pictures obtained from these animals using the Image J software.
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9

Immunohistochemical Analysis of Endometrial Tumors

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Cre:ER+/−Pten f/f mice were euthanized by cervical dislocation after 3 weeks of NP137 treatment. Endometrial samples were collected and formalin fixed overnight at 4 °C. Tumours were paraffin embedded for further histologic analysis. Paraffin blocks were sectioned at 3 µm and dried for 1 h at 65 °C before the pretreatment procedures of deparaffinization, rehydration and epitope retrieval in the pretreatment module at 95 °C for 20 min in 50× Tris/EDTA buffer. Before staining of sections, endogenous peroxidase was blocked. Representative images were taken with a Leica DMD108 microscope.
Immunohistochemistry was performed on an automated immunostainer (Ventana discoveryXT, Roche) using the rabbit Omni map DAB Kit. Sections were incubated with specific antibodies targeting EpCAM (no. ab71916, abcam), cleaved caspase-3 (no. 9661, Cell Signaling Technologies), netrin-1 (no. CPA2389, Cohesion Biosciences), Unc5B (no. 13851S, Cell Signaling Technologies) and CD8 (no. 4SM15, eBioscience). Staining was by anti-rabbit horseradish peroxidase, visualized with 3,3′-diaminobenzidine as a chromogenic substrate and counterstained with Gill’s haematoxylin. Histological quantifications were performed with Halo software (Indica Labs).
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10

Bone Marrow Cell Cytospin and Staining

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2 × 105 bone marrow cells were spun on slides for 5 min at 600 rpm using Shandon Cytospin 3 Cytocentrifuge (Thermo Fisher Scientific). Slides were stained with May-Grünwald Giemsa solution (Sigma). 40× images were acquired using a Leica DMD 108 microscope. Scale bar = 50 µm.
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