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8 protocols using cellsens standard v1

1

Multicolor Immunofluorescence Staining Protocol

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Immunofluorescence was performed as described previously2 (link). The following antibodies or chemical compounds were used: COL17A1 (Abcam, ab186415, 1:400), Keratin 14 (Biolegend, 906004, 1:500), ITGA6 (BD, 555734, 1:200), Keratin 15 (Biolegend, 833904, 1:300), NFκB (Santa Cruz, sc-101749, 1:50), CD11b (BD, 557686, 1:100), F4/80 (Bio-Rad, MCA497A488, 1:100), KI67 (Invitrogen, 14-5698-82, 1:300), CD3 (Biolegend, 100235, 1:100), MHC2 (Biolegend, 107605, 1:100), CD31(BD Biosciences, 557355, 1:200), anti-DNA/RNA Damage (Abcam, ab62623, 1:2000), Tom20 (Thermo Fisher, 11802-1-AP, 1:30), Keratin 1 (Abcam, ab185628, 1:300), survivin (Cell signaling, 2808, 1:100), casp3 (Cell signaling, 9661, 1:200), Tuj1 (Covance, PRB-435P, 1:500), CD34-FITC (Invitrogen, 11-0341-85, 1:100), ITGA6-PE (BD, 555736, 1:100), Sca1-APC (Miltenyi Biotec, 130-102-343, 1:100), CD45-APC-cy7 (BioLegend, 103116, 1:100). FV10-ASW4.2 was used for capturing confocal images. CellSens Standard v1.13 (Olympus) was used for collecting HE data.
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2

Rabbit Brain Fixation and Imaging

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After the completion of training, rabbits were anesthetized with a solution containing ketamine HCl (83.3 mg/ml) and xylazine (16.7 mg/ml), followed by a lethal dose of Euthasol (sodium pentobarbital, 390 mg/ml) and transcardial perfusion with 0.9% saline followed by 10% formalin. The brains were post-fixed in 10% formalin and prior to sectioning, cryoprotected in a 15% sucrose, 2% formalin solution for a minimum of 24 h. Coronal sections were cut at 40 μm using a freezing microtome. Sections were placed on slides and digitally imaged while wet (1.5X) with an Olympus BX51 microscope equipped with a computer assisted camera and software (monochrome Olympus FVII, cellSens Standard v1.13). The digital images were then used to determine the placement of the guide cannula, verified by consulting two rabbit brain atlases (Lavond and Steinmetz, 2003 ; McBride and Klemm, 1968 ).
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3

Seahorse Intestine Histomorphometry

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After 24 hr, formalin fixed seahorse specimens were rinsed with deionized distilled water, patted dried and decalcified (Decalcifying Solution-Lite D 0818, Sigma-Aldrich, Inc.) before the routine processing for paraffin embedment and histological sections (LePage et al., 2015) . Sagittal sections measuring 5.0-6.0 µm thickness were cut with a rotary microtome (Microm HM 340E, Thermo Scientific). Sections were stained with haematoxylin and eosin and periodic acid-Schiff (PAS), and then mouted with DPX. All slides were examined and photographed under a compound microscope (Olympus BX43F) with a digital camera (Olympus DP22) linked to a computer with image-processing software (Olympus cellSens Standard V1.14). The length of intestine was measured (proximate length from the beginning of foregut to the end of hindgut) while the intestine length to height ratio (IL:H) was calculated (Yip et al., 2015) .
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4

Seahorse Intestine Histomorphometry

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After 24 hr, formalin fixed seahorse specimens were rinsed with deionized distilled water, patted dried and decalcified (Decalcifying Solution-Lite D 0818, Sigma-Aldrich, Inc.) before the routine processing for paraffin embedment and histological sections (LePage et al., 2015) . Sagittal sections measuring 5.0-6.0 µm thickness were cut with a rotary microtome (Microm HM 340E, Thermo Scientific). Sections were stained with haematoxylin and eosin and periodic acid-Schiff (PAS), and then mouted with DPX. All slides were examined and photographed under a compound microscope (Olympus BX43F) with a digital camera (Olympus DP22) linked to a computer with image-processing software (Olympus cellSens Standard V1.14). The length of intestine was measured (proximate length from the beginning of foregut to the end of hindgut) while the intestine length to height ratio (IL:H) was calculated (Yip et al., 2015) .
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5

Histological Analysis of Aortic Tissue

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Aortic fragments were embedded in paraffin blocks, cut into 4-µm-thick transverse sections, and placed on glass slides. The preparations were stained with the routine hematoxylin and eosin (H&E) method and viewed using an Olympus BX 53 light microscope coupled with a camera model UC90. To take measurements, the cellSens Standard V1 software was used (Olympus, Tokyo, Japan). The thickness of the foamy cell depositions was evaluated as described previously by Brant et al. [28 (link)] and El-Sheakh et al. [29 (link)].
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6

Canine Post-Operative Monitoring and Histopathology

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On the second day after discharge, the patients were under the supervision of the referring veterinarian most of the time. The operated dogs had a follow-up visit to perform a physical examination and remove sutures only on the 10th day after the surgery. There were additional phone consultations with the owners of the dogs and their attending veterinarians before and after the control visit in cases that required it. The owners were questioned about any information regarding the health of their dogs, which may be the result of the surgical procedure as well as the previously diagnosed neoplastic disease. In the event of animal death, owners were also asked to inform the authors of the time and possible causes.
Cytological preparations, made from the biopsy material taken during the endoscopic examination, were stained with hematoxylin and eosin.
The resected fragments of the urethra as well as the fragments excised during the evening of the edges of the urethra were fixed in 10% formalin, and after obtaining histopathological preparations, they were also stained with hematoxylin and eosin.
The cytological and histopathological slides were observed under an Olympus BX53 microscope coupled with an Olympus UC90 camera (Olympus, Tokyo, Japan). For acquisition, the cellSens Standard V1 software was used (Olympus, Tokyo, Japan).
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7

Quantitative Fluorescence Imaging Protocol

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Images were captured by cellSens Imaging Software (Cellsens Standard v1.16, Evident, Olympus Life Science Solutions, Tokyo, Japan) and semi-qualified by ImageJ. A constant threshold value of each marker was pre-adjusted and determined through preliminary imaging of various sections. Integrated density (stained area × mean gray value) of the images was measured and normalized to the number of cells (DAPI counting) to determine a final mean fluorescence density per cell. An average was quantified from at least 3 random images per non-consecutive triplicate section (n = 3) per group. Relative expressions between the groups were calculated for analysis.
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8

Floral Morphology and Pollinator Accessibility

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Since flowers are the resources for the pollinators, the morphology or the outlook place a great role during pollination. Therefore, key morphological attributes of flowers and inflorescences were measured to characterize the visual display and the resource accessibility of the reproductive units. The length of flowering inflorescences and the number of inflorescences was determined in the field on selected individuals with a ruler. The number of flowers in inflorescences and the number of inflorescences in inflorescence clusters were counted in the field. Three selected inflorescences clusters were tagged. We recorded the number of opened and closed flowers in an inflorescence, flowering period, and flower lifespan, and measured the length of the stigma, petal, stamen, and corolla taking the mean values of 10 replicates.
Floral morphology was studied with fresh flowers using a Stereomicroscope (Kruss Opironic and Olympus SZX10). The images were captured from the software AmScope V/ 3.7.2776 and Olympus Cell Sens Standard V 1.16). Dimensions of single floral organs and their position within the flower were determined with size differenced micrographs using the ImageJ software [20 ].
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