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38 protocols using rm2125 microtome

1

Chili Plant Leaf Anatomy Analysis

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The tested specimens, including the upper leaf developed on the third branch from the base of the main stem of chili plants, were selected during the second growing season of 2022, 10 days after the third foliar application. A sample of approximately 1 cm of the specimens was taken from each treatment, killed, and fixed in FAA solution (5 mL of glacial acetic, 10 mL of formalin, 35 mL of water, and 50 mL of ethyl alcohol 70%), for 48 h at least. The chosen sample was washed in ethyl alcohol at 30%, dehydrated in a normal ethanol and butyl alcohol chain, buried in paraffin wax with a melting point of 56 °C, sliced to a thickness of 15 μm, stained with crystal violet and erythrosin, clarified in xylene, and mounted in Canada balsam. Transverse sections were obtained using a Leica Microtome RM 2125, micrographed, and measured using a Leica Light Image Analysis System DM 750 at the Research Park (CURP), Faculty of Agriculture, Cairo University. The following parameters were recorded: the thickness of the midvein (μm), lamina (μm), palisade tissue (μm), spongy tissue (μm), upper and lower epidermis (μm), bundles dimension (μm), and mean vessels diameter (μm).
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2

Tomato Leaf Anatomy Under Low Temp

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Tested specimens included the blade of the terminal leaflet of the fourth compound leaf developed on the main stem of tomato plants under low-temperature conditions, were taken throughout the second growing season of 2021/2022, 60 days after sowing. Approximately 1.0 cm of the specimens were killed and fixed in FAA solution (5 mL glacial acetic, 10 mL formalin, 35 mL water, and 50 mL ethyl alcohol 70%) for at least 48 h. The selected materials were washed in 30% ethyl alcohol, dehydrated in a normal ethanol and butyl alcohol series, embedded in paraffin wax with a melting point of 56 °C, sectioned to a thickness of 15 μm stained with crystal violet erythrosin, cleared in xylene, and mounted in Canada balsam in accordance with [70 ]. Transverse sections were completed with a Leica Microtome RM 2125 and then micrographed and measured using a Leica Light Image Analysis System DM 750 at the Faculty of Agriculture, Cairo University-Research Park (CURP). The following parameters were recorded: thickness of the midvein (μm), lamina (μm), palisade tissue (μm), spongy tissue (μm), upper and lower epidermis, bundle dimension (length and width) (μm), and mean vessels diameter (μm).
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Zebrafish Histology Preparation Protocol

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Histology was performed using an established protocol (Sullivan-Brown et al., 2011 (link)) with the following modifications. Whole adult zebrafish were fixed in Dietrich's fixative (ZIRC Health Services Sample/Specimen Preparation) (30:10:2:58 ratio of 95% ethanol:formalin:glacial acetic acid:distilled water) for 1-2 weeks, followed by dehydration (20 min incubation step in 50% ethanol in PBS, followed by a 20 min incubation step in 75% ethanol in PBS and two 20 min incubation steps in 100% ethanol, all at room temperature), JB-4 infiltration and embedding. Embedding was performed overnight under static vacuum at 4°C. Then, 4-µm sections were collected on a Leica microtome (RM2125) with 8 mm glass blades and stained with H&E based on a previously published protocol (Sullivan-Brown et al., 2011 (link)).
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4

Histological Analysis of Distal Colon

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Samples of the distal colons were fixed immediately in 10% formaldehyde, embedded in liquid paraffin, cut into transverse sections of 5 μm thick using a Leica RM 2125 Microtome (Leica Biosystems, Wetzlar, Germany), and then mounted on glass slides and stained with haematoxylin and eosin (H&E). Microscopic changes such as necrosis, fibrosis, hyperemia, epithelial damage, ulceration, infiltration, and submucosal abscesses were scored on a 0-4 scale where 0 denotes no detectable damage and 4 denotes most severe damage [1 (link)].
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5

Histological Analysis of Distal Colon

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Samples of the distal colons were fixed immediately in 10% formaldehyde, embedded in liquid paraffin, cut into transverse sections of 5 μm thick using a Leica RM 2125 Microtome (Leica Biosystems, Wetzlar, Germany), and then mounted on glass slides and stained with haematoxylin and eosin (H&E). Microscopic changes such as necrosis, fibrosis, hyperemia, epithelial damage, ulceration, infiltration, and submucosal abscesses were scored on a 0–4 scale where 0 denotes no detectable damage and 4 denotes most severe damage [40 (link)]. Microscopy images for each group obtained with a magnification of 50X.
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6

Histological Evaluation of Rat Lung Tissue

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Lung tissues were carefully removed from the rats and fixed in formalin (10%). Tissues were serially dehydrated in increasing concentrations of ethanol, cleared in xylene in a TP 1020 Tissue processor (Leica Biosystems, Wetzlar, Germany), and embedded in paraffin using a Leica EG 1160 Embedding machine (Leica Biosystems, Wetzlar, Germany). Transverse sections of 5 μm were cut with a Leica RM 2125 Microtome (Leica Biosystems, Wetzlar, Germany), deparaffinized, and hydrated to distilled water and stained with haematoxylin and eosin (H&E). The slides were viewed under a digital light microscope (DM 750, Leica Microsystems, Wetzlar, Germany) fitted with a digital camera (ICC 50 HD, Leica Microsystems, Wetzlar, Germany).
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Histopathological Analysis of Fish Tissues

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Five fish were chosen at random from each fish group after eight weeks of feeding trials and five days of being exposed to A. hydrophila for a histopathological analysis. The abdomen was dissected after being deeply antisepticized with 70% ethyl alcohol, and tissue samples from the hepatopancreas, spleen, kidney, and middle part of the small intestine were preserved for at least 24 h in 10% neutral buffered formalin. The tissue samples were cleaned in xylene, embedded in paraffin wax, and dehydrated using increasing concentrations of ethanol (70–100%). Leica RM 2125 microtome (Leica DM 5000, Leica Biosystems, Richmond, IL, USA) was used to slice tissues into 5 mm thick slices, which were subsequently stained with hematoxylin and eosin (H&E) and viewed under a light microscope (Leica DM 5000).
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8

Airway Smooth Muscle Hyperplasia Assessment

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Lung tissues were carefully removed and fixed in 10% formalin. Tissues were serially dehydrated in increasing concentrations of ethanol, cleared in xylene in a TP 1020 tissue processor (Leica Biosystems, Wetzlar, Germany), and embedded in paraffin using a Leica EG 1160 embedding machine (Leica Biosystems, Wetzlar, Germany). Transverse sections of 3 μm were cut with a Leica RM 2125 Microtome (Leica Biosystems, Wetzlar, Germany), deparaffinized, and hydrated with distilled water. Tissue sections were stained with H and E appropriately for airway integrity examination and observed under light microscope for assessment of smooth muscle hyperplasia of the airway.
Scoring was done according to Gibson–Corley [21 (link)]. Scoring adopted was 0—normal smooth muscle hyperplasia, 1—mild smooth muscle hyperplasia, 2—moderate smooth muscle hyperplasia, and 3—severe smooth muscle hyperplasia.
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9

Laser Capture Microdissection of Lung Biopsies

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All FFPE biopsies were selected by a specialist thoracic pathologist, sectioned using a Leica RM2125 microtome and stained with Hematoxylin and Eosin. PSCC, ISCC cell clusters and normal epithelia were microdissected as follows: each FFPE biopsy was used to produce a series of a single 5μm section, transferred to a standard glass slide for diagnostic evaluation by specialist thoracic pathologists, and on average ten 10μm sections were each placed on 1mm PEN membrane slides (Carl Zeiss, Germany) for LCM using a Leica LMD6000 (Additional file 1: Figure S1). RNA was isolated using the Ambion Recover All Kit. Isolated RNA was quantified using a Qubit fluorometer (Qubit RNA assay kit) and RNA integrity was examined using an Agilent Bioanalyser. Samples with RIN values in the range 2–3 were employed for microarray analysis. All donors gave written informed consent and the conducted research was approved by the South Manchester Ethics Committee
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10

Mouse Tissue Fixation and Staining Protocol

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Mouse tissues were collected, perfused with 4% PFA, and incubated on an end-to-end shaker at 4 °C overnight. The next day, the tissues were embedded in paraffin or OCT (Tissue-Tek; Sakura Finetek USA, Cat#4583) and sectioned with a Leica RM2125 Microtome for paraffin sections or a Leica CM1950 for frozen sections. The tissues were rinsed with rinse buffer: 0.1 M sodium phosphate dibasic (Sigma-Aldrich, Cat#S7907), 5.0 mM sodium phosphate monobasic (Sigma-Aldrich, Cat#S9638), 3.0 mM magnesium chloride hexahydrate (Sigma-Aldrich, Cat#M2670), 1.5 mM sodium deoxycholate (Sigma-Aldrich, Cat#30970), and 3.0% IGEPAL CA-630 (Sigma-Aldrich, Cat#I8896) for 30 min at 4 °C, and washed with rinse buffer two more times at room temperature for 30 min each. The tissues were then stained with staining buffer: 5.0 mM potassium ferricyanide (Sigma-Aldrich, Cat#702587), 5.0 mM potassium ferrocyanide (Sigma-Aldrich, Cat#P3289), and 1.0 mg/mL X-gal (Sigma-Aldrich, Cat# B4252) at 37 °C overnight. After staining overnight, wash the tissue with 70% ethanol for two times, each times 30 min, and then the tissues fixed in 4% PFA45 (link).
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