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30 protocols using microm hm 325

1

Histological Analysis of Mouse Intestine

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Immediately after sacrificing, the intestines of mice were fixed with 10% (v/v) formaldehyde. Fixed tissues were taken out and soaked in distilled water overnight. Then, they were dehydrated with 70% and 80% ethanol for 2 h, immersed in xylene, and embedded in melted paraffin for 16 h. After vacuum infiltration at 60 °C, embedded wax blocks were cut into 5 μm sections with Thermo Scientific Microm HM325 rotary microtome (Thermo, USA). Tissue sections were dewaxed with xylene twice, placed in absolute ethanol, 95% ethanol, 80% ethanol and 70% ethanol for 1–2 min and then washed with distilled water for 3 min. After being stained with hematoxylin solution for 5 min and differentiated with 1% acid ethanol, sections were washed in running water for at least 15 min until the nucleus turned blue. Then, sections were stained with eosin solution and dehydrated twice with 95% ethanol and absolute ethanol. Finally, the sections were immersed in phenol xylene and xylene in sequence, and sealed with neutral gum.
After paraffin embedding, sectioning, and H&E staining, images for histological slides were taken at 200× magnification by Nikon Eclipse E400 biological microscope (Nikon, Tokyo, Japan) with Nikon Digital Camera DXM1200F (Nikon, Japan). Villus length and crypt depth of the intestine were analyzed by Image J 1.52v (Wayne Rasband National Institutes of Health, Bethesda, MD, USA).
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2

Tissue Preparation for Histological Analysis

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Fresh frozen and paraffin embedded tissue were used for histological analysis. For fresh frozen tissue, whole eyes were embedded in OCT compound (TissueTek) using standard protocols. 8μm sections were cut using a Leica CM1850 cryostat. Cryosections were stored at -80°C.
For paraffin embedded tissue, whole eyes were fixed in 4% PFA overnight at 4°C. Fixed tissue was then processed using standard protocols and embedded in paraffin wax. 4μm sections were cut using a Thermo Scientific Microm HM325 microtome. Sectioned tissue was dried at 37°C overnight and then stored at 4°C.
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3

Leaf Anatomy Quantification

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The young leaves that emerged under the experimental conditions for 7 days (5–8 mm leaf length) were fixed with FAA fixative (ethanol:acetic acid:formaldehyde:distilled water = 10:1:2:7). The fixed samples were dehydrated using an ethanol series and embedded in Technovit resin (Kulzer and Co., Wehrheim, Germany). The samples were sectioned into 4 µm slices with a Microm HM 325 microtome (Thermo Fisher Scientific, Waltham, MA, USA) and stained with 0.1% toluidine blue. The samples obtained from ten biological replicate leaves were photographed under a microscope; and the leaf thickness, area of mesophyll cells and density of intercellular regions were determined using the ImageJ software version 1.52 (http://rsb.info.nih.gov/ij/, Bethesda, MD, USA). Statistical analyses among the experimental conditions were performed with the Tukey–Kramer method using the multcomp package [24 (link)] in an R environment. The data were presented as a box plot using ggplot2 [25 ] in R.
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4

Cardiac Fibrosis and Structure Analysis

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Subgroups of hearts were harvested at 4 and 14 weeks after TAC for analyses of structure, fibrosis, and biochemistry. Trichrome staining was performed as previously described (44 (link)). Briefly, mice were euthanized, and after cardioperfusion, hearts were fixed for 1 to 3 days in 4% paraformaldehyde at 4°C. Hearts were dehydrated and paraffinized using the Microm STP 120 from Thermo Fisher Scientific, embedded in paraffin using a HistoStar apparatus (Thermo Fisher), and sectioned (4 to 6 μm) using the Microm HM 325 (Thermo Fisher). Tissue sections were then stained with Weigert’s iron hematoxylin and Masson trichrome (Sigma-Aldrich) according to the manufacturer’s instructions. Interstitial fibrosis was quantified by color threshold measures using ImageJ. Alternatively, tissue sections were deparaffinized and rehydrated according to the trichrome staining protocol, but after the wash with deionized water, heart sections were washed three times for 5 min with 1× phosphate-buffered saline (PBS) followed by staining with Alexa Fluor 488–conjugated WGA (1:10 in 1× PBS) (Invitrogen) for 1 hour at room temperature in a humidified chamber in the dark. Sections were again washed three times for 5 min with 1× PBS followed by mounting with coverslips using Fluoromount-G mounting media containing DAPI nuclear stain (Southern Biotech).
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5

Callogenesis in Asteraceae: Phytohormone Effects

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The callogenesis process was tested using various combinations of phytohormones considering several concentrations and information referring to callogenesis processes in the genus Asteraceae (see Table 2), observing the effect of these on callus induction of material from lateral leaves and internodal segments obtained from plantlets multiplied in vitro. The induction conditions used considered periods of darkness for 30 days and subsequently, a photoperiod regime of 16 h light/8 h darkness (16/8), or an immediate period of 16/8, without going through the 30 days in darkness. In addition, variables such as temperature (23 ± 2 °C) and humidity (50–70% RH) remained constant. According to the structure’s evolution, media renovation proceeded every 2 to 3 months. Callus formation response was determined according to callus induction index (CIF) [47 ]. Variables were volume (wet weight/dry weight), callification time, morphology (friable, compact, oxidized), and the presence or absence of organogenesis or other structures [25 (link)] (Table 2). Histological sections were performed using widely described protocols [48 ]. Structures fixed in a FAA solution were embedded in paraffin and subsequently, cuts between 8 to 10 µm were made using microtome (Microm HM325, ThermoFisher, Waltham, MA, USA). These were stained with Safranin-O according to published protocols [49 ].
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6

Histological Examination of Excised Segments

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The proximal segment was fixed in two changes of 10% neutral phosphate buffered formalin (B06-003, ErgoProduction, Saint Petersburg, Russia) for 24 h at 4 °C, embedded into paraffin (Histomix Extra, 10342, ErgoProduction, Saint Petersburg, Russia), and cut (8 µm sections) on a microtome (Microm HM 325, Thermo Scientific, Waltham, MA, USA) as previously described [25 (link)]. To ensure proper histological examination, we prepared 8 sections, evenly distributed across the entire excised segment, per slide. Upon the deparaffinisation in three changes of xylene (X0053, Diapath, Martinengo, Italy) and three changes of 95% ethanol (Kemerovo Pharmaceutical Plant, Kemerovo, Russia), sections were stained with: (1) haematoxylin and eosin (05-003 and 05-011, ErgoProduction, Saint Petersburg, Russia) as described in [34 (link)] for the general examination; (2) van Gieson stain (21-020, ErgoProduction, Saint Petersburg, Russian Federation) as described in [34 (link)] to distinguish connective and smooth muscle tissue; (3) 2 % aqueous alizarin red S (6-09-1749-77, Reachim, Moscow, Russia) and 4′,6-diamidino-2-phenylindole (DAPI, 10 μg/mL, D9542, Sigma-Aldrich, Saint Louis, MO, USA) as described in [34 (link)] for the detection of calcium deposits within the grafts. Visualisation was performed by light or fluorescent microscopy (AxioImager.A1, Carl Zeiss, Oberkochen, Germany).
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7

Cartilage-Bone Sample Decalcification and Histology

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A 1-cm2 cartilage–subchondral bone sample was fixed using 4% paraformaldehyde (PFA) solution (USB, USA) for three days. Twenty-two samples were recruited for histology (derived from 11 female and 11 male donors, 16 of them suffering from FNF and 6 from OA). The samples were placed in a volume 20 times their own volume of formic acid to ensure satisfactory decalcification. The acid solution was changed every 24 hours, while a chemical end point test was also carried out on the supernatant to access the rate of decalcification. When chemical testing exhibited no significant residual calcium, the samples were rinsed in water and incubated in 5% ammonia solution (Merck KGaA) for 30 minutes to ensure neutralization. Samples were then rinsed under running tap water for 24 hours to remove any residual acid. Dehydration involving a series of ascending ethanol solutions was completed over a 48-hour period. Following this, each sample was embedded in paraffin at 60 °C with subsequent sectioning using a microtome Microm HM 325 (Thermo Fisher Scientific).
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8

Histological Analysis of Rat Skin

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Samples of rat skin that were 20 ± 3 mm in size were fixed using a mixture of formalin, ethanol and acetic acid in a volume ratio of 4:1:0.3 and were embedded into paraffin. Paraffin blocks were sliced; sections with thicknesses of 10 μm were obtained by rotary microtome Microm HM 325 (Thermo Scientific, Waltham, MA, USA), stained with hematoxylin-eosin, embedded in Canada balsam and analyzed by Carl Zeiss Axio Vert.A1 microscope (Zeiss, Jena, Germany). Images were obtained by Axiocam 305 color digital camera (Zeiss, Jena, Germany) and processed by ZEN 2.3 (blue edition) software (Zeiss, Jena, Germany).
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9

Glomerular Morphometry in Diabetic Kidney

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The right kidneys were removed 7 days after STZ (n = 6), vehicle treatment (n = 6), or insulin treatment (n = 6). The kidney wet and dry weights were measured. The dry weights of the right kidneys were taken after being placed in an oven at 105°C for 72 h. The left kidneys were perfusion fixed as described previously [2 ]. Four-micrometer-thick sections were cut using a microtome (MICROM HM 325; Thermo Scientific, Walldorf, Germany) and placed on APES-coated slides. The sections were stained with periodic acid-Schiff (PAS; Schiff's reagent; Sigma-Aldrich) for measurement of the total glomerular tuft area (GTA) and mesangial matrix area (MMA) [6 ]. A total of 15-20 glomeruli showing their tuft attached at the hilum were selected randomly from all renal cortical zones in each animal. The morphometry of glomeruli was performed with a CAS 200 cell analysis system (Becton & Dickinson Image Cytometry Systems, Franklin Lakes, NJ, USA). The contour of the tuft midsection was manually traced, and the total GTA (mm2) was calculated. The glomerular tuft volume (GTV) was estimated from:
GTV = b/k × (GA) 3/2,
where b = 1.38, a shape coefficient for a sphere, and k = 1.1, a size distribution coefficient [7 (link)]. The MMA in each glomerular tuft was measured using a threshold method that selectively highlighted all PAS-positive areas within the tuft as previously described [2 ].
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10

Immunohistochemical Analysis of Medaka Brains

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Paraffin sections were used for immunohistochemical analysis as reported previously [33 (link)]. Medaka brains were collected by surgery. The collected brains were fixed with 4% (w/v) paraformaldehyde in PBS at 4 °C for 1 day and stored in 70% ethanol until use. The fixed samples were dehydrated and embedded in paraffin using Surgipath FSC22 (Leica, Wetzlar, Germany), and sections were acquired using a Microm HM 325 (Thermo Fisher Scientific). The thickness of the sections was set at 20 µm for tyrosine hydroxylase (TH) -positive cell counting and 8 µm for other analysis. The following antibodies were used as the primary antibody: anti-TH (#MAB318, 1:1000; Merck Millipore, Burlington, MA) and anti-medaka asyn (1:2000) [33 (link)]. The sections were incubated with the primary antibody at 4 °C for 1 day after blocking with 4% skim milk. Histofine (#414322; Nichirei Bioscience Inc., Tokyo, Japan) was used as the secondary antibody for diaminobenzidine staining.
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