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1

Evaluating Bacterial Modulation of Intestinal Cell Inflammation

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The IPEC-J2 cell monolayers seeded into 12-well plates were preincubated with sterile PBS, Lac16 (MOI = 100) or BaSC06 (MOI = 100, positive control) with 3 wells per group for 12 h. After washing with sterile PBS for 3 times to remove bacteria, the treated IPEC-J2 cells were then treated with LPS (40 µg/mL) for another 12 h. After capturing using Leica DMIRB, the supernatant of the treated cells was then collected to analysis the release of LDH and NO from cells using LDH kits (Beyotime, Shanghai, China) and NO kits (Beyotime, Shanghai, China) according to the manufacturer’s instructions. After washing with sterile PBS 3 times, the cells were collected by RNAiso Plus for total RNA extraction and qPCR. The primers of IPEC-J2 cells are shown in Table S2. Fold changes were calculated after normalizing to two housekeeping genes (β-actin and GAPDH) using the 2−ΔΔCt method.
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2

Extraction and Characterization of D. officinale Polysaccharides

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Dendrobium officinale was purchased from Longanba Green Spring Agricultural Development Co., Ltd. (Guiding, China). The samples were dried at 60 °C, crushed, passed through an 80-mesh sieve and set aside.
Saccharomyces cerevisiae FBKL2.8022 (Sc) and Wickerhamomyces anomalous FBKL2.8023 (Wa) were derived from the Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province. The CCTCC NO. was M2019406 and M2019412, respectively [13 (link)]. Monosaccharide standards were purchased from Aladdin Reagent Co., Ltd. (Shanghai, China), including mannose, ribose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose, arabinose, and fucose. Amyloglucosidase and anhydrous D-glucose were purchased from Beijing Solarbio Science & Technology Co., Ltd. (Beijing, China). NO kits were purchased from Beyotime Biotechnology Co., Ltd. (Shanghai, China). TNF-α, IL-1β, IL-6, and IL-10 ELISA kits were purchased from Shanghai Jianglai Biological Co., Ltd. (Shanghai, China). The relative Mw of polysaccharides was calculated according to calibration curves of the dextran standards purchased from Sigma-Aldrich (St. Louis, MO, USA). DEAE-Sepharose Fast Flow (DEAE-QFF) and Sephacryl S-300 HR were purchased from GE Healthcare. A G4000SWXL column (7.8 × 300 mm, Tosoh Co., Ltd., Tokyo, Japan) was used. The other chemicals and reagents were analytical grade.
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3

PDGF-BB and Ferulic Acid Regulate Cell Cycle

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PDGF-BB was purchased from R&D Systems, Inc. (Minneapolis, MN, USA) and dissolved in 4 mM HCl containing 0.1% bovine serum albumin (BSA). FA (purity greater than 99%) was purchased from Sigma (St. Louis, MO, USA), dissolved in dimethyl sulfoxide (DMSO) at a concentration of 200 mM and stored at 4 ℃. The final concentration of DMSO was less than 0.1% [v/v] in all of the experiments. NO kits (catalog no. S0021) were purchased from Beyotime Biotechnology (Nanjing, China). 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was supplied by Sigma (St. Louis, MO, USA). Dulbecco’s modified Eagle’s medium (DMEM) was purchased from Life Technologies (Carlsbad, CA, USA). Primary antibodies against endothelial nitric oxide synthase (eNOS), p-eNos, p21CIP1, p27Kip1, Cyclin D1, CDK4, CyclinE, CDK2, proliferating cell nuclear antigen (PCNA), and β-actin and horseradish peroxidase-conjugated anti-rabbit antibodies were obtained from Cell Signaling Technology. PI3K, p-PI3K was purchased from abcam(UK)and AKT, p-AKT was purchased from proteintech(USA).
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4

Vascular Function Assessment Protocol

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After one week adaptive training, systolic blood pressure (SBP) was measured via tail-cuff method weekly during waking hours (BP-2010A, Softron Beijing Biotechnology Co., Ltd, Beijing, China). SBP was measured three times under rest state, and then average values were obtained. Blood samples were collected 8 weeks later. Within 4 hours, whole blood viscosity was detected. Vascular contractility was preliminarily measured by relevant vasoactive substances in serum. ABC-ELISA kits (Westang Biotechnology Co., Ltd, Shanghai, China) were used to detect angiotensin II (Ang II) and epinephrine (EPI) levels in serum. In addition, vascular relaxant factor, nitric oxide (NO) in serum, was measured by NO kit (Beyotime Biotechnology, China) with Griess reagent. All of the experimental procedures were followed in accordance with the rules designated by the manufacturer.
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5

Comprehensive Spectroscopic Characterization

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Specific optical rotation was measured on a PerkinElmer 341 instrument at 25°C. Cary 5000 spectrophotometer was used to record UV spectra in MeOH. ECD data were obtained by Model 420SF CD spectrometer (Aviv Biomedical Inc). In KBr discs, IR spectra were obtained using Fourier infrared IS50 spectrometer. All NMR experiments were performed at room temperature on a Bruker AVANCE 500 spectrometer using the signals of residual solvent protons (CDCl3: δH 7.26; CD3OD: δH 3.31) and carbons (CDCl3: δC 77.1; CD3OD: δC 49.2). HRESIMS spectra were tested by Waters TQ-XS mass spectrometer. Column chromatography (CC) was conducted by silica gel (200–300 mesh, Yantai Huiyou Silica gel company) and Sephadex LH-20 (CHCl2/MeOH, v/v 1:1) (Pharmacia Sweden). On silica gel plates, thin layer chromatography (TLC) was conducted (GF 254 Silica gel Thin Layer Plate Yantai Huiyou Silica company). The Typical Culture Preservation Committee Cell Bank, China provided RAW264.7 cells; the fetal bovine serum (FBS) was obtained by Gibco; ProCell provided Dulbecco's modified Eagle's medium (DMEM); Sigma supplied LPS and L-NMMA; Shanghai Beyotime Biotechnology supplied the NO kit. Thermo Fisher Scientific (Shanghai, China) provided the primers for iNOS. Cell Signaling (Beverly, MA, USA) supplied all the antibodies.
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6

Spleen Cell Stimulation Assay

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The cell supernatants from cultured BALB/c spleen cells stimulated with C57BL/6 mouse spleen cells were collected and assessed using an NO kit (Beyotime Institute of Biotechnology, Shanghai, China).
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7

Rhubarb Anthraquinones Modulate Inflammatory Markers

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Free total rhubarb anthraquinones were purchased from the Research Institute (Huaian, Jiangsu, China, batch number: 20130211) and dissolved in normal saline (NS). Sodium taurocholate (STC) was purchased from Sigma–Aldrich Co. (St. Louis, MO, United States). Rat TNF-α and IL-1β ELISA Kits were purchased from United States Systems R&D (Long Beach, CA, United States). NO Kit was purchased from Beyotime Biotechnology Research Institute (Shanghai, China). MPO kit was purchased from Nanjing Jiancheng Biological Engineering Institute (Nanjing, Jiangsu, China). Fixative solution, permeabilization wash buffer, Foxp3 fixative permeabilization wash solution, monensin, APC anti-rats CD4, FITC anti-rats IFN-γ, PE anti-rat IL-4, PE anti-rat CD25, Alexa fluor 488 anti-rat Foxp3 and goat anti-rat SIgA were purchased from Biolegend Company (San Diego, CA, United States). Rabbit anti-rat NLRP3, goat anti-rat ASC, mouse anti-rat caspase-1 were purchased from Santa Company (Santa Cruz, CA, United States). Triton, bovine serum albumin (BSA) DAB color liquid, goat super sensitive two-step reagent Kit, mouse one-step kit, TRITC labeled rabbit ant- goat secondary antibodies, fluorescein (FITC) labeled sheep anti-rabbit secondary antibodies were purchased from ZSGB Biological Company (Beijing, China).
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8

Measurement of Nitric Oxide Levels

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Nitric oxide (NO) levels were measured according to the Griess method by detecting NO3 and NO2 with a NO Kit (S0021, Beyotime, China). Standard samples were diluted into different concentrations (0, 1, 2, 5, 10, 20, 40, 60, and 100 μM) to plot the standard curve. After the above treatment, 50 μL of the culture supernatant fluid was collected and 50 μL (per well) Griess Reagent I and 50 μL (per well) Griess Reagent II were added. Then, NO production was measured using OD value readings with a microplate spectrophotometer (Tecan, Crailsheim, Germany) at an absorbance wavelength of 540 nm. The concentrations were calculated from the standard curve.
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9

Fluorescent Probes for Intracellular Analysis

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The intracellular NO content was detected using a NO kit (Beyotime). Fluorescent probes for Dihydroethidium (DHE, 10 µM), mitochondrial membrane potential [a probe of mitochondrial membrane potential (JC-1), 1x], ROS [2ʹ,7ʹ-Dichlorodihydrofluorescein diacetate (DCFH-DA), 10 µM], and a probe to enable mitochondria visualization (Mitotracker Red CMXRos, 200 nM) were used to detect the corresponding intracellular indicator. All probes were incubated for 20 min at 37 °C. RAW264.7 cells were washed with PBS buffer twice and visualised under a fluorescence microscope. Image processing was performed using ImageJ analysis software. Analyses were performed using GraphPad Prism 6.0 software.
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10

Neuroprotective Effects of Endophytic Extracts

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Dendrobine (purity ≥98%) was obtained from Shanghai yuanye Bio-Technology Co., Ltd (Shanghai, China). Two endophytic strains were isolated from Dendrobium in our previous studies and named as Pseudomonas protegens CM-YJ44 (National Center for Biotechnology Information NCBI accession No.MZ674076), Priestia megaterium D-HT207 (NCBI accession No.MK389456), respectively. The dried extract of CM-YJ44 and D-HT207 was collected following the method by Wang et al. [13 ]. The extracts were redissolved in 1 mL Dimethyl Sulfoxide (DMSO) for the following experiments.
The human neuroblastoma SH-SY5Y cells were obtained from the Cell Bank of the Chinese Academy of Sciences (Beijing, China). Dulbecco's modified Eagle's minimum (DMEM) was purchased from Thermo Scientific; fetal bovine serum (FBS) from Gibco; cell Counting Kit-8 (CCK-8) test, ROS kit, MDA kit, GSH kit, CAT kit from Solarbio; the 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethyl-benzimidazolyl-carbocyanine iodide (JC-1) fluorescent probe, SOD kit, NO kit and LDH kit from Beyotime; annexin V-FITC Apoptosis Detection Kit from BD; prime Script RT reagent Kit, SYBR Premix Ex Taq from TaKaRa.
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