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32 protocols using dmrb light microscope

1

Histological Analysis of Linho Plant Organs

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Shoot tips, segments of leaves (immature and mature), internodes and inflorescence meristems of linho and WT plants were collected from potted plants. Explants were collected at different plant ages during both vegetative stages V4-V6 (Schneiter and Miller, 1981) and early reproductive stage R1 (Schneiter and Miller, 1981) . Plant material was fixed for 24 h in FAA solution [5% (v/v) acetic acid, 50% (v/v) ethanol, 10% (v/v) formaldehyde, and 35% distilled water], dehydrated using a graded ethanol series, and then cleared in Noxil (Italscientifica S.p.A., Genova, Italy) in a five stepprocess according to Ruzin (1999). Samples were embedded in Paraplast Plus (Sigma-Aldrich Co. LLC, St. Louis, USA) and sectioned at 8 m using a manual rotary microtome (Reichert, Vienna, Austria). The serial transverse sections were stained with a solution containing Alcian Blue 8GX, Bismarck Brown Y, and Safranin O according to Graham and Trentham (1998) . Sections were
observed with a Leica DMRB light microscope (Leica Microsystems, Wetzlar, Germany) and images were recorded with a digital camera. To determine cell length (m) in cross and longitudinal sections of eighth-ninth internode of potted plants, slides were observed with a Leica DMRB light microscope (Leica Microsystems) and images were recorded with a digital camera. ImageJ was utilized to collect data.
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2

Immunohistochemical Analysis of Septic Lung Tissue

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Paraffin-embedded lung tissue of septic and critically ill, non-septic patients obtained by autopsy was provided by the Department of Pathology of our hospital (Amsterdam University Medical Center, location VUmc, Amsterdam, The Netherlands). Paraffin slices (5µm) were de-paraffinized with xylene and incubated with H2O2 to block endogenous peroxidase. After antigen retrieval (TRIS/EDTA 10 mM pH 9.0, 15 min at 100 °C), slices were incubated with primary antibody against p(Y207)CrkL (o/n at 4 °C). Detection of primary antibody was performed with Powervision® (Immunologic, Duiven, The Netherlands), according to the manufacturers protocol. After counterstaining with hematoxylin, slices were evaluated with a Leica DMRB light microscope (Leica Microsystems, Wetzlar, Germany) at 20x (air, NA 0.40) and 40x (air, NA 0.65) magnification. For imaging, a Nikon D50 digital camera (Nikon Corporation, Tokyo, Japan) was used.
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3

Colon Histological Analysis Protocol

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Colon macroscopic and microscopic damage were assessed in accordance with the criteria reported previously [24 (link)]. Colon segments were fixed in 4% paraformaldehyde for 24 h, dehydrated in alcohol, embedded in paraffin, and finally cut into 5 μm sections. Microscopic evaluations were carried out on haematoxylin-eosin stained sections of full-thickness samples obtained from the distal colon. GIEMSA staining (Sigma-Aldrich, Milan, Italy) was used to analyse mast cells (MCs) density (cell number/respective arbitrary field) in the submucosal layer of colon [25 (link)]. Digitalized images were collected at 40× magnification by a Leica DMRB light microscope, equipped with a DFC480 digital camera (Leica Microsystems, Milan, Italy), and analysed quantitatively using the ImageJ software. At least five independent arbitrary optical fields (0.1 mm2) were analysed for each animal.
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4

Quantitative Claudin-1 Immunohistochemistry

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Sections (epithelial cells) were incubated overnight at 4 °C with the primary anti-claudin-1 antibody. Sections were then exposed to appropriate biotinylated immunoglobulins, peroxidase-labelled streptavidin complex and 3.3′-diaminobenzidine tetrahydrochloride, counterstained and examined by a Leica DMRB light microscope equipped with a DFC480 digital camera (Leica Microsystems, Cambridge, UK). For each group, representative photomicrographs were shot and analysed quantitatively using the Image Analysis System “L.A.S. software version 4.5” (Leica Microsystems, Cambridge, UK). Two blind investigators (C.I. and C.S.) carried out cell-counting independently and assessed the colorimetric threshold values to detect antigen expression levels. Immunostaining expression was calculated as ratio between area of the stained fields and the total tissue area examined (percentage positive pixels (PPP)), as previously reported [58 (link),61 (link)]. Data obtained from all the examined fields for each rat were averaged and used to calculate mean values ± SEM for each experimental group, which were plotted in graphs.
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5

Macroscopic and Microscopic Colon Evaluation

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The animals were sacrificed 15 days after DNBS injection, and the colon was macroscopically analysed to assess the damage. To quantify the injury, a macroscopic damage score (MDS) was assigned to each colon in accordance with the criteria previously reported [25 (link)] The macroscopic criteria were the following: presence of adhesions between the colon and other intra-abdominal organs (0–2); consistency of colonic faecal material (indirect marker of diarrhoea; 0–2); thickening of colonic wall (mm); presence and extension of hyperaemia and macroscopic mucosal damage (0–5). A colon segment (around 1 cm) was fixed in 4% paraformaldehyde for 24 h, dehydrated in alcohol, encased in paraffin, and finally cut into 5 μm sections. Microscopic evaluations were carried out on haematoxylin/eosin-stained sections of full-thickness samples obtained from the distal colon. Digitalised images were collected at 10, 20, and 40× magnification by a Leica DMRB light microscope equipped with a DFC480 digital camera (Leica Microsystems, Milan, Italy), and analysed quantitatively using the ImageJ software.
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6

Immunohistochemical Staining Protocol

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DAB-peroxidase IHC was performed as described by Kwakowsky et al. (2018 (link)). In brief, sections were washed in PBS with 0.2% Triton X-100 (PBST) before blocking for endogenous peroxidases (50% methanol and 1% H2O2) for 20 min, followed by three 10-min washes in PBST and incubated for 72 h in primary antibody in immunobuffer at 4°C (Table 3). Following three 10-min washes in PBST the sections were incubated for 24 h with the biotinylated secondary antibody (anti-mouse IgG-Biotin antibody produced in goat 1:1,000) in immunobuffer at room temperature (RT). The sections were then washed in PBST before incubation with ExtrAvidin (1:1,000, E2886; Sigma, St. Louis, MO, USA) in immunobuffer for 4 h at RT, followed by three 10-min washes in PBST before development in 0.05% DAB and 0.01% H2O2 in 0.1 M phosphate buffer. Sections were washed in PBST, mounted onto glass slides, dried, dehydrated through a graded series of ethanol, and cleared in xylene. The slides were coverslipped with DPX mountant (1019790500; Merck, Whitehouse Station, NJ, USA). The sections were imaged on either a Leica DMRB light microscope or a Leica MZ6 dissecting microscope (Wetzlar, Germany).
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7

Nissl Staining for Cortex Identification

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Nissl staining was performed for identification of the sensory and motor cortex regions on each block. Fresh frozen section were stained with a cresyl violet solution (2% Cresyl violet in 0.1 M glacial acetic acid and 0.0136 M sodium acetate solution) for a period of 45 min, mounted onto glass slides, dried, dehydrated through a graded series of ethanol, and cleared in xylene. Sections were examined using a Leica (Wetzlar, Germany) DMRB light microscope. Tissue sections were examined for features such as cortical thickness and the presence of large motor neurons.
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8

Colonic Histomorphometric Analysis

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8-μm-thick slices from full-thickness, formalin-fixed, paraffin-embedded colonic samples were processed to evaluate the morphology of colonic wall by haematoxylin/eosin and immunoperoxidase staining (see below). The severity and extent of inflammatory infiltrations were evaluated on the basis of the percentage of leucocytes per microscopic field and their presence through the colonic wall layers, respectively, as previously described [18 (link)]. The density of eosinophils was estimated within the tunica mucosa/submucosa and expressed as cell number per square millimeter as described in detail previously by Pellegrini and coworkers [19 (link)]. The microscopic analyses were performed by three different histologists (NB, CS, CI), blinded to the experimental group, using a Leica DMRB light microscope equipped with a computer image analysis software (L.A.S. software v.4.5), and following histomorphological scores for intestinal inflammation in mice [20 (link)].
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9

Histological Analysis of N. guentheri Heads

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In this study, we used adult specimens of N. guentheri found dead by unknown causes (1-year-old, 1 male, and 2 females) in ornamental aquariums (freshwater, 22 °C, pH 6.8–7.0). The heads were quickly removed, fixed in 4% paraformaldehyde in phosphate-buffered saline (PBS) (AAJ19943K2, Thermo Scientific) 0.1 m (pH = 7.4) for 12–18 h, dehydrated through graded ethanol series, and clarified in xylene for paraffin wax embedding. Included tissues were then cut into 7 μm thick serial sections and collected on gelatin-coated microscope slides. Then, serial sections were deparaffinized and rehydrated, washed in distilled water, and stained with hematoxylin and eosin (H&E) (Carazzi’s Hematoxylin Nuclear staining, 05-M06012; Eosin Y 1% aqueous solution cytoplasmic staining, 05-M10002, Bio-Optica Milano s.p.a.) and Masson Trichrome with aniline blue method (04-010802, Bio-Optica Milano s.p.a.). Sections were examined under a Leica DMRB light microscope.
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10

Glycosaminoglycan Staining of Cartilage

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Sections were stained for glycosaminoglycans using both toluidine blue and safranin O. Whereas both stain for glycosaminoglycans, the staining pattern can be different for different cartilage types.10 (link) Samples were fixed in 10% normal buffered formalin solution (10%; Sigma) for 10 minutes before being rinsed in running water for 2 minutes. For toluidine blue staining, sections were placed in 0.001 mg/mL toluidine blue (Sigma) for 1 minute and rinsed in running water for 5 minutes. Excess water was removed with filter paper and cover-slips were placed over the sample and mounted with DPX (RA Lamb).
For safranin O staining, sections were placed in hematoxylin (RA Lamb, UK) for 2 minutes and then washed again in water for 5 minutes. They were then placed into 0.1% safranin O solution (BDH, UK) for a further 2 minutes before being washed for 30 seconds in water. Finally, the sections were passed through a series of increasing industrial methylated spirit concentrations (IMS; Fisher Scientific; 70% to 100%) for 2 minutes at each concentration. The slides were then cleared in xylene for 2 minutes (× 2). Cover-slips were placed over the sample and mounted with DPX (RA Lamb). Slides were then viewed and images taken using a Leica DMRB light microscope.
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