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8 protocols using xylene

1

Histologic Evaluation of Myocardial Damage

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Heart tissues were fixed at room temperature in buffered formaldehyde solution (10% in PBS) (Sigma, St. Louis, MO, USA) for 24 h, dehydrated using a graded series of ethanol solutions (Sigma, St. Louis, MO, USA), embedded in Paraplast (Sherwood Medical, Mahwah, NJ, USA), and cut into 7-micrometer-thick sections with a pfm rotary 3004 microtome (Leica Microsystems SpA, Milan, Italy) [34 (link)]. Sections were deparaffinized with xylene (Bio-Optica, Milano, Italy) and stained with hematoxylin and eosin (Bio-Optica, Milano, Italy) [35 (link)], Furthermore, Masson’s trichrome staining was performed for the detection of collagen according to the manufacturer’s protocol (Bio-Optica, Milan, Italy), as reported previously [36 (link)]. Sections were evaluated using a Leica DM6 microscope (Leica Microsystems SpA, Milan, Italy) equipped with a motorized stage and associated with the Leica LAS X Navigator software (Leica Microsystems SpA, Milan, Italy) [37 (link)]. Histologic score was evaluated as described above [38 (link)]. Based on the score value, it is interpreted as:

Negative score (score 0 or 1), the absence of myocardial damage.

Positive score (score 2–7), the existence of damage

Mild myocardial damage (score 2–3),

Moderate myocardial damage (score 4–5),

Extensive myocardial damage (score 6–7).

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2

Determining Bacterial Hydrophobicity via BATH

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The hydrophobicity of the investigated bacteria was determined using an in vitro method to detect the bacterial adhesion to hydrocarbons [25 (link),26 (link)]. Canine and chicken E. faecalis and E. faecium were grown in BHI broth at +37 °C for 18 h. The bacterial cells harvested by centrifugation (5000× g, +4 °C, 15 min) were washed twice with PBS (pH7.0) and resuspended in the same solution to an optical density (OD600) of 0.552–0.606 (A0). In total, 1 mL of xylene (Bio-Optica, Milan, Italy) was added to 3 mL of cell suspension in a glass tube and vortexed for 2 min after 10 min of incubation at RT. After phase separation, the aqueous phase was removed after 2 h of incubation at RT, and the OD600 nm was determined (A1) and compared with the initial value. Due to the destructive effect of xylene on plastic cuvettes, both optical density measurements (A0 and A1) were performed using glass cuvettes. The percentage of hydrophobicity (%H) was calculated using the equation %H = [(A0 − A1)/A0] × 100, and was expressed as follows: 0–35%, low hydrophobicity; 36–70%, medium hydrophobicity; and 71–100%, high hydrophobicity [27 (link)]. All measurements were made in triplicate and the mean hydrophobicity percentage was reported.
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3

Histological Evaluation of GAGs Deposition

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After fixation, HS were dehydrated in an increasing scale of ethanol (70%, 95%, 100%, Bio-Optica, Milan, Italy), clarified in xylene (Bio-Optica, Milan, Italy) and embedded in paraffin (VWR International Srl, Milan, Italy) and 4 µm sections were cut. Standard stain protocol was used to evaluate morphology and GAGs deposition. Briefly, the slices were hydrated to water using xylene and a decreasing ethanol scale (100%, 95%, 70%, 50%). The sections were stained by 1 min incubation of hematoxylin (Bio-Optica, Milan, Italy), followed by 10 min of washing in tap water. Then, the sections were incubated for 5 min in a 0.05% solution of Fast Green (FCF, Sigma-Aldrich, St. Louis, MA, USA) in distilled water, and quickly rinsed in 1% acetic acid (Sigma-Aldrich, St. Louis, MA, USA) solution in distilled water. A 5 min counterstain was performed with a 0.1% Safranin-O solution (Sigma-Aldrich, St. Louis, MA, USA). Finally, slices were dehydrated in alcohol solution (95%, 100%) and clarified with xylene.
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4

Histological Analysis of Embryos and Hatchlings

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Histological analysis was performed following the method described by Chemello et al. [25 (link)]. Samples in 70% ethanol were processed to perform the histological analysis. At first, samples were dehydrated in increasing solutions of ethanol (80, 95, and 100%), then washed with xylene (Bio-Optica, Milan, Italy) and embedded in paraffin (Bio-Optica). The paraffin embedding was performed by arranging embryo and hatchling samples to obtain both longitudinal (5 embryos and 5 hatchlings) and transversal (5 embryos and 5 hatchlings) sections for each site. Solidified paraffin blocks were cut into 5 µm sections using a microtome (Leica RM2125 RTS, Nussloch, Germany) and then stained using 3 different staining protocols: Mayer’s haematoxylin and eosin Y stain (Merck KGaA), Alcian blue stain (Bio-Optica) and Masson’s trichrome stain (Bio-Optica). Sections were observed with an optical microscope (Zeiss Axio Imager.A2, Oberkochen, Germany) and images were acquired with a combined color digital camera Axiocam 503 (Zeiss, Oberkochen, Germany).
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5

Histomorphometric Analysis of Tibialis Anterior Muscle

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Tibialis anterior muscle samples were washed in phosphate-buffered saline (PBS, Bio-Optica, Milano, Italy), fixed in 10% buffered-formalin (Bio-Optica, Milan, Italy) for 24 h at room temperature. Afterwards, the samples were dehydrated in graded ethanol (Bio-Optica, Milan, Italy), cleaned in xylene (Bio-Optica, Milan, Italy) and paraffin-embedded (Bio-Optica, Milan, Italy), being careful to preserve the desired anatomical orientation. Slides of 5 μm thickness were cut from the obtained paraffin blocks and hematoxylin and eosin-stained (H&E, Bio-Optica, Milan, Italy) following a protocol described elsewhere [59 (link)]. The samples were then examined in triplicate for morphological evaluation with a Zeiss Axioplan light microscope (Carl Zeiss, Oberkochen, Germany) and by a digital camera (AxioCam MRc5, Carl Zeiss, Oberkochen, Germany), used to take images.
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6

Localization of TGF-β and IL-10 in Tissues

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To localize TGF-β and IL-10 positive cells, tissues were analyzed with RNAscope assay (Advanced Cell Diagnostics, Newark) using RNAscope 2.5 HD Assay-RED kit. The Hs-IL10 probe (cat no. 602051) recognizes the nt 122–1,163 of the IL-10 mRNA (reference sequence NM_000572.2), and the Hs-TGFB1 probe (cat. no. 400881) recognizing the nt 170–1,649 of the TGF-β mRNA (reference sequence NM_000660.4). The sections from fixed human tissue blocks were treated following the manufacturer’s instructions. Briefly, freshly cut 3-mm sections were deparaffinized in xylene (Bio-Optica, cat. no. 06- 1304F) and treated with the peroxidase block solution (ACD, cat. no. 322335) for 10 minutes at room temperature followed by the retrieval solution for 15 minutes at 98°C and by protease plus (ACD, cat. no. 322331) at 40°C for 30 minutes. Hs-POLR2a-C2 (cat. no. 310451) and dapB-C2 (cat. no. 310043-C2) were used as control probes. The hybridization was performed for 2 hours at 40°C. The signal was revealed using RNAscope 2.5 HD Detection Reagent and FAST RED.
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7

Cuttlefish Histological Analysis Protocol

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Histological analyses were performed according to [23] (link). Briefly, cuttlefish (n = 5 for each experimental tank) were fixed in Bouin's solution (Sigma Aldrich, MO, USA) and stored at 4 • C for 24 h. Samples were then dehydrated by graded ethanol solutions, washed with xylene (Bio-Optica, Milan, Italy), and embedded in solid paraffin (Bio-Optica, Milan, Italy). Moreover, 5 µm sections were obtained by a rotary microtome (Leica RM2125 RTS, GmbH, Wetzlar, Germany) and stained using Mayer hematoxylin and eosin Y (H&E) (Sigma Aldrich, MO, USA). Slides were examined under a Zeiss Axio Imager. We used an A2 microscope (Zeiss, Oberkochen, Germany) combined with a color digital camera Axiocam 503 (Zeiss, Oberkochen, Germany). Histo-morphometric parameters such as fold height and width, as well as cilia length, were measured.
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8

Histological Evaluation of Cartilage Repair

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Cartilage samples were washed in phosphate-buffered saline (PBS, Bio-Optica, Milano, Italy), fixed in 10% buffered-formalin (Bio-Optica, Milan, Italy) for 24 h at room temperature. Afterwards, the samples were dehydrated in graded ethanol (Bio-Optica, Milan, Italy), cleaned in xylene (Bio-Optica, Milan, Italy) and paraffin-embedded (Bio-Optica, Milan, Italy), being careful to preserve the desired anatomical orientation. For the general evaluation of the morphological structure of the cartilage, the slides of 4–5 µm thickness were cut from the obtained paraffin blocks and haematoxylin and eosin-stained (H&E; Bio-Optica, Milan, Italy) as previously described [33 (link)]. The samples were then examined with a Zeiss Axioplan light microscope (Carl Zeiss, Oberkochen, Germany) and by a digital camera (AxioCam MRc5, Carl Zeiss), used to take images.
For qualitative histological analysis the following parameters were analysed:

The type of repaired tissue on the lesion surface (cartilaginous, fibrous or calcified);

Capability of the collagen I-based scaffold to recruit host cells and promote cartilaginous matrix deposition;

The scaffold biocompatibility and reabsorption of the collagen I-based scaffold.

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