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14 protocols using xylene

1

Quantifying Bacterial Cell Hydrophobicity

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The degree of cell surface hydrophobicity of the LAB isolates was assessed via measuring microbial adhesion to hydrocarbons (MATH) in xylene (Macklin, Shanghai, China) according to the method in Zhang et al. (2022) (link). Briefly, overnight cultures of four isolates were centrifuged at 5,000 × g for 3 min at 4 °C. The pellets were washed twice with PBS and resuspended in PBS, then the OD600 of the isolates was adjusted by spectrophotometry (Biochrom genequant, UK) in the range of 1.0 ± 0.1. Each bacterial suspension (3 mL) was mixed with 1 mL of xylene (Macklin, Shanghai, China), swirled for 2 min, then incubated at 37 °C for 1 h. The water layer was carefully aspirated and measured at OD600 (Biochrom genequant, UK). Cell surface hydrophobicity (%) was calculated the equation as follows:
Where A0 denotes the optical density at 0 h and At stands for the optical density at 1 h (Zeng et al., 2021 (link)).
The affinity of LAB to solvent was divided into hydrophilicity (< 10%), medium hydrophilicity (10-34%), medium hydrophobicity (35-70%) or high hydrophobicity (71-100%) (Qureshi et al., 2020 (link))
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2

Spinal Cord Tissue Preparation for Analysis

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The SC from segments 7 to 9 of the trunk vertebrae (approximately 0.5 cm in length) was isolated, and the SC fragments from all 10 animals in each group were placed in a single tube containing RNA storage solution. Then, the SC fragments were transferred to 4% paraformaldehyde (Sangon Biotech, Shanghai, China) for 24 hours, fully rinsed with 0.1 M phosphate buffer solution (Servicebio, Wuhan, Hubei, China), decalcificated using ethylene diamine tetra acetic acid (EDTA) decalcifying solution (Servicebio) for 40 days, rinsed in running water for 2 hours followed by gradient alcohol dehydration (75%, 85%, 95%, 100%) (Wuxi Zhanwang Chemical Reagent CO., Ltd., Wuxi, Jiangsu, China), and cleared using xylene (Macklin, Shanghai, China).
Subsequently, the tissues were embedded in paraffin and sliced into coronal sections with a thickness of 5 μm for all experiments, except for nerve fiber staining, which was performed using 12-μm sagittal sections.
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3

Spinal Cord Histological Analysis

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After cardiac perfusion 28 days after surgery, mice were sedated with 0.3% pentobarbital, and carefully removed the spinal cord tissue. The samples were first dehydrated with varying levels of alcohol, made transparent with xylene (Macklin), and then embedded in paraffin wax. Once the wax blocks had fully hardened, the samples were divided into sections. The sections were sealed with neutral gum after being stained with hematoxylin and eosin (LEAGENE, Beijing). An N2-Ni-U ortho-fluorescence microscope (Nikon, Shanghai) was used to capture the images.
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4

Microbial Adhesion to Hydrocarbon Assay

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To assess the degree of surface hydrophobicity, the microbial adhesion to hydrocarbon (MATH) method was adopted with minor modifications (Rosenberg, Judes & Weiss, 1983 (link); Slizewska, Chlebicz-Wojcik & Nowak, 2021 (link)). LAB strains were washed twice in PBS, harvested by centrifugation (5,000×g, 10 min, 4 °C), and re-suspended in PBS. We measured the optical density of bacterial suspension using spectrophotometry (Biochrom GeneQuant, Cambridge, UK) and adjusted the OD600nm within the range of 1.0 ± 0.1. Each bacterial suspension (3 mL) was mixed with xylene, ethyl acetate, and n-hexadecane (1 mL, Macklin, Shanghai, China), vortexed for 2 min for emulsion formation, and incubated at 37 °C for 1 h. We then measured the OD600nm of the aqueous layer. The hydrophobicity was calculated using the following equation:
Hydrophobicity%=[(A0At)/A0]×100
where A0 represented the absorbance at time t = 0 h, and At represented the absorbance taken at 1 h (Rastogi, Mittal & Singh, 2020 (link)).
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5

Immunohistochemical Analysis of NB Samples

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The tissue microarray containing 27 samples of NB patients and 5 peripheral nerve tissues was purchased from Biomax (MC642, Derwood, USA). NB xenograft tumor tissues and mouse organ tissues obtained from animal experiments were fixed in 4% paraformaldehyde (Beyotime, Shanghai, China) and embedded in paraffin. Sections were deparaffinized in xylene (MACKLIN, Shanghai, China), rehydrated in graded alcohols (Sinopharm, Beijing, China), and washed in distilled water. Antigens were retrieved by boiling the sections in citric acid-based antigen unmasking solution (Thermo Fisher, Waltham, MA, US) for 30 min, then incubated with primary anti-BRD4 (1:200, ab128874, Abcam, Cambridge, UK) or Ki-67 (1:200, ab15580, Abcam, Cambridge, UK) overnight at 4 °C followed by rabbit specific HRP/DAB detection kit (Cat: ab64261, Abcam, Cambridge, UK) and hematoxylin (Beyotime, Shanghai, China) in compliance with protocols. Staining results were independently evaluated by two experienced pathologists. The total scoring (TS) results were scored by multiplying the percentage of positive cells (P) by the intensity (I). Formula: TS = P × I.
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6

Brain Tissue Cresyl Violet Staining

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Brain sections (14 μm) were processed through incubation in the following solutions in this order: 100% ethanol (30 s), 95% ethanol (30 s), distilled water (30 s, twice), cresyl violet (Sigma-Aldrich, St Louis, MO, USA) (3–5 min), distilled water (2 min, three times), 50% ethanol (2 min), 95% ethanol (5–30 min), 100% ethanol (5 min, twice), and xylene (MACKLIN, Shanghai, China) (3 min, twice). Thereafter, the sections were mounted with a coverslip.
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7

Shikonin Modulates Acute Ear Edema

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Shikonin (Meilunbio, S0921AS; purity, >98%) was occupied to treat the experimental group with 20 mg/kg for each mouse, while dexamethasone (Plant Chem Medicine company, Xi’an, China, PCM20356; purity, >98%) was used as positive control in the current study. Xylene (Macklin, X821391; purity, >99%) was utilized to induce a mouse model of acute ear edema. IL-6 (Cell signaling Technology, 12912), IL-1β (Bioteche, AF401-NA), and β-actin (ABclonal, AC026) antibodies were prepared for Western blot assay.
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8

Tissue Preparation and Histological Staining

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The colon was embedded, frozen at −20°C, and 3 μm sections were cut, water-bath spread, and baked. Sections were stained with hematoxylin (Beyotime, Shanghai, China) for 5 min, followed by rinsing under running tap water for 3 min first and then for 20 s. Sections were then counterstained with eosin (Solarbio, Beijing, China) for 4 min, followed by cleaning with 80% and 95% ethanol (Macklin, Shanghai, China) for 40 s each. Sections were then cleared in xylene (Macklin, Shanghai, China) for 5 s and mounted with neutral balsam. After staining, the sections were observed under a microscope, and the Leica Application Suite was used to collect and analyze the relevant parts of the samples.
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9

Synthesis of Chlorinated Hydrocarbons

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Methanol (99.9%, HPLC grade, Concord), xylene (99%, Macklin), TCE (99%, Kermel), palladium acetate (Pd ≥ 47.4%, Mascot), iron nitrate nonahydrate (98.5%, Huaxueshiji Co., Tianjin), trans-dichloroethene (standard grade, AccuStandard) cis-dichloroethene (standard grade, AccuStandard), 1,1-dichloroethene (standard grade, AccuStandard), vinyl chloride (2 g l−1 in methanol, AccuStandard) and CNTs (Chengdu Organic Chemicals Co., Ltd, Chinese Academy of Sciences) were purchased from commercial sources in China and used as received. The chemicals are analytical grade reagents and used without any further purification unless otherwise specified. All the reagents were prepared with deionized water.
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10

Histological Analysis of Shrimp Hepatopancreas

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For each group, the whole hepatopancreas from 5 shrimps were collected for histological analysis. After being fixed in 4% paraformaldehyde for 24 h, the hepatopancreas tissues were dehydrated using a gradient solution of methanol (25%, 50%, and 75%) with each step lasting 30 min and embedded in paraffin using embedding equipment (Leica Biosystems HistoCore Arcadia, Leica Biosystems, Wetzlar, Germany). The sections were continuously sliced with a fully automated rotary microtome HistoCore AUTOCUT (Leica Biosystems, Wetzlar, Germany) to 4~5 μm thicknesses, spread in a water bath at 40 °C, mounted on glass slides (three to four serial sections per slide), and dried at 37 °C overnight. The wax was removed from the hepatopancreas tissue sections using xylene and ethanol, rehydrated in a decreasing ethanol gradient (100%, 95%, 80%, 70%, 50%, and 30%; 2 min for each step), and stained with hematoxylin–eosin (H&E) (Njjcbio, Nanjing, China). All the stained slides were dehydrated in ethanol and xylene (Macklin, Shanghai, China) for 5 min each, sealed with neutral gum (Solarbio, Beijing, China), and then observed under a BX43 manual light microscope (Olympus, Tokyo, Japan).
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