The largest database of trusted experimental protocols

37 protocols using gcdca

1

Norovirus Infectivity Assay in HIE Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
We performed all infections in triplicate on 100% confluent 4-day-old differentiated HIE (J3 line) monolayers, except when specified that the J2 line was used. In some experiments, we pretreated monolayers with 1% sow bile included in the differentiation medium 48 h before infection. In other experiments, we differentiated HIE monolayers without pretreatment, and infected them in the presence of 500 μmol/L of glycochenodeoxycholic acid (GCDCA; Sigma, St. Louis, MO, USA) or with 500 μM GCDCA plus 50 μM ceramide.
To determine viral infectivity, we inoculated duplicate 96-well plates with 100 μL of fecal filtrate (Technical Appendix) at 1:10, 1:100, and 1:1000 dilution. After 1 h incubation at 37°C in 5% CO2, we washed the monolayers twice with CMGF and added 100 μL of differentiation medium containing 1% sow bile, 500 μmol/L GCDCA, or 500 μM GCDCA plus 50 μmol/L ceramide to each well. For each set of infections, we immediately froze 1 plate at −70°C and incubated a duplicate plate at 37°C in 5% CO2 for 72 h and froze it at −70°C. We used quantitative reverse transcription real-time PCR to determine the amount of norovirus RNA from input virus and from HIE monolayers at 1 hour postinfection (hpi) and at 72 hpi. Standard curve based on quantified RNA transcripts was included.
+ Open protocol
+ Expand
2

Oxidative Stress Modulation in Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cells were plated at 150,000 cells/cm2 and 0.5 mM GCDCA (Sigma-Aldrich) was administered after 48 h of cell culture. The SOD mimetic MnTBAP (manganese (III) tetrakis (4-benzoic acid) porphyrin chloride) (Calbiochem, Darmstadt, Germany) and the mitochondria-targeted antioxidant MitoQ were administered at concentration of 0.1 mg/ml and 1 μM, respectively. Curcumin (diferuloylmethane), Quercetin (Sigma-Aldrich, Missouri, USA), the NOS inhibitor Nω-Nitro-L-arginine methyl ester hydrochloride (L-NAME; Sigma-Aldrich) and the specific AP-1 inhibitor SR 11302 (Santa Cruz Biotechnology, California, USA) were used at 4 μM, 20 μM, 5 mM and 50 μM, respectively. Cells were harvested at different times according to the parameter under study. MitoQ was synthesized according to the procedure described by Kelso et al. [13 (link)].
+ Open protocol
+ Expand
3

Inflammatory Bowel Disease Biomarker Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
OEA was purchased from Santa Cruz Biotechnology (Santa Cruz, CA); DSS (molecular weight=36,000–50,000 kDa) was obtained from MP Biochemical (Santa Ana, CA). MPA O-glucuronide and naloxone 3-β-D-glucuronide were obtained from Toronto Research Chemicals Inc. (ON, Canada). β-MCA, UDCA, HDCA, G-LCA, G-UDCA, G-DCA, T-β-MCA, T-UDCA, T-HDCA and T-LCA were purchased from Steraloids Inc. (Newport, RI). α-MCA, CA, DCA, CDCA, lithocholic acid (LCA), G-CDCA, G-CA, T-CDCA, T-DCA, T-CA, dehydrocholic acid and propranolol were purchased from Sigma-Aldrich (St Louis, MO). The anti-UGT1A, anti-FXR, anti-FGF15 and anti-CYP7A1 antibodies were purchased from Santa Cruz Biotechnology. The anti-PPARα antibody was from Abcam (Cambridge, UK). The anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) antibody was purchased from SunShine Biotechnology (Nanjing, China). The secondary antibodies and recombinant human FGF19 was obtained from Bioworld Technology (St Louis Park, MN). Other reagents, unless mentioned, were obtained from Sigma-Aldrich. RNA extracts of colon biopsies from 8 healthy humans and 13 ulcerative colitis and Crohn’s disease patients were previously described51 (link). The ulcerative colitis and Crohn’s disease samples were collected from consented patients and approved by the University of Michigan IRB committee (approval number HUM00042210).
+ Open protocol
+ Expand
4

Neutralization of GII.4 Norovirus by mAbs

Check if the same lab product or an alternative is used in the 5 most similar protocols
Serial dilutions of each mAb were prepared in complete medium without growth factors (CMGF) and pre-incubated with GII.P16-GII.4 Sydney stool filtrate (3.1 x 105 viral genomic copies). After 1 h incubation at 37°C and 5% CO2, samples were diluted 1:2 in CMGF supplemented with 1000 μM sodium glycochenodeoxycholate (GCDCA; Sigma-Aldrich) plus 100 μM ceramide (Santa Cruz Biotechnology). Duplicated, 100% confluent 4-day old differentiated monolayers, were inoculated. After 1 h incubation at 37°C and 5% CO2, monolayers were washed twice with CMGF and 100 μl of differentiation medium containing 500 μM GCDCA plus 50 μM ceramide was added to each well. For each set of infections, one plate was immediately frozen at -70°C and a duplicate plate was incubated at 37°C, 5% CO2 for 24 h and frozen at -70°C.
For each monoclonal antibody, 4 independent experiments with 2 technical replicates for each mAb dilution on each experiment were performed. Neutralization was expressed as a measure of the reduction in viral genomic copies (as percentage) when compared to a control (no mAb) within each assay using real-time RT-qPCR.
+ Open protocol
+ Expand
5

Hepatocyte Toxicity Assay with GCDCA and DCA

Check if the same lab product or an alternative is used in the 5 most similar protocols
WT and MCJ-KO hepatocytes were treated with toxic doses of glycochenodeoxycholic acid (GCDCA) or deoxycholic acid (DCA). We seeded 500,000 cells in 6-well plates, cultured overnight in 0% FBS MEM 1% PSG medium and treated the day after. The administered dose of GCDCA (Sigma) and DCA (Sigma) was 100 μM using ethanol as a vehicle.
+ Open protocol
+ Expand
6

Visualizing Rab7-Mediated Endocytic Pathways

Check if the same lab product or an alternative is used in the 5 most similar protocols
GCDCA and CDCA were purchased from Sigma-Aldrich (St. Louis, MO) and resuspended in distilled water or dimethyl sulfoxide (DMSO), respectively, at 100 mM. Hyperimmune guinea pig sera raised against recombinant PEC 2AB, polymerase (POL) and VPg and hyperimmune swine sera raised against PEC virus-like particles (Chang et al., 2005 (link)) were used in this study. Rabbit polyclonal anti-Rab7 serum was purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Secondary antibodies including FITC conjugated rabbit anti-guinea pig or anti-pig IgG and PerCP-Cy5.5 labelled goat anti-rabbit IgG were purchased from commercial sources including Sigma-Aldrich and Santa Cruz Biotechnology. Sytox orange was obtained from Molecular Probes (Bedford, MA). Chloroquine, GW4064, and oleanolic acid were also purchased from Sigma-Aldrich. Other basic chemicals for confocal microscopy and other studies were purchased from various sources including Sigma-Aldrich.
+ Open protocol
+ Expand
7

Isolation and Characterization of Mouse Hepatic Stellate Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Isolation of primary mHSC was performed via pronase–collagenase perfusion followed by density gradient centrifugation in 13.2% Nycodenz (Axis-Shield PoC, Oslo, Norway) [33 (link)]. Purity of preparation was assessed by confirmation of vitamin A autofluorescence.
Isolated HSCs were allowed to attach for 2 h and were then stimulated with bile salts CDCA, GCDCA, TCDCA, and UDCA (Sigma-Aldrich, Darmstadt, Germany) for the time periods indicated, in the absence or presence of AG1478 (Sigma-Aldrich, Darmstadt, Germany) and PD98059 (Cayman, Ann Arbor, MI, USA). To quantify total DNA as a surrogate of cell number, HSCs were incubated with PicoGreen® (Invitrogen, Carlsbad, CA, USA) and fluorescence signals were detected with a CytoFluor 4000 system (PerSeptive Biosystems, Framingham, MA, USA). Proliferation of HSC was quantified using a BrdU-assay kit (Roche, Penzberg, Germany) according to the manufacturer’s instructions. To quantify total cell count, HSCs, seeded in Lab-Tek II Chamber Slides (Nunc, Rochester, NY, USA), were mounted on cover slides with Vectashield mounting medium including DAPI (Vector, Burlingame, CA, USA). Slides were scanned with a Pannoramic Midi Slide Scanner (3DHistech, Budapest, Hungary) and nucles count was performed with ImageJ2 software on the complete slide (0.7 cm2).
+ Open protocol
+ Expand
8

Comprehensive Bile Acid Profiling Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
HPLC-grade methanol and acetonitrile were purchased from Fisher Scientific (Nepean, Ont., Canada). Ultrapure water was prepared by the Milli-Q Ultrapure water purification system (Millipore, Bedford, MA, USA). AOM was obtained from Sigma-Aldrich (St. Louis, MO, USA), and DSS (MW 36000-50000) was purchased from MP Biomedicals (Santa Ana, CA). Ammonium acetate, formic acid, glacial acetic acid and the other reagents (analytical grade) were purchased from Nanjing Chemical Factory (Nanjing, China). ‘Mouse Total Bile Acids Kit’ was purchased from Crystal Chem Inc (Downers Grove, United States). ‘MiniBEST Bacterial Genomic DNA Extraction Kit’ was from TaKaRa Bio Inc (Dalian, China). Anti-FXR, FGF15 and CYP7A1 antibodies were all purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and anti-GAPDH antibody was from Bioworld Technology (St. Louis Park, MN, USA).
CA, CDCA, DCA, and LCA, as well as their glycine [38 (link)] and taurine [45 (link)] conjugates, G-CA, G-CDCA, T-β-MCA, T-CA, T-CDCA, T-DCA, and internal standard dehydrocholic acid (dhCA) were obtained from Sigma-Aldrich (St. Louis, MO, USA). α-MCA, UDCA, HDCA, G-LCA, G-UDCA, G-DCA, T-β-MCA, T-UDCA, T-HDCA and T-LCA were purchased from Steraloids, Inc. (Newport, Rhode Island, USA).
+ Open protocol
+ Expand
9

Cathepsin Inhibitors and Viral Infection

Check if the same lab product or an alternative is used in the 5 most similar protocols
GCDCA and chloroquine were purchased from Sigma-Aldrich (St Louis, MO). Cathepsin L inhibitors, Z-FY-CHO and MDL28170, were purchased from Santa Cruz Biotech (Santa Cruz, CA), and a cathepsin B inhibitor CA074-Me was purchased from Sigma-Aldrich. Recombinant human cathepsin L and cathepsin B were purchased from R & D systems (Minneapolis, MN). The primary antibodies used in this study were anti-PEC/Cowden antibodies raised in swine (Chang et al., 2005 (link)), anti-PEC VP2 antibodies raised in guinea pig (Chang et al., 2005 (link)), anti-FCV antibodies raised in guinea pig (Sosnovtsev and Green, 1995 (link)), anti-MNV-1 antibodies raised in guinea pig (Wobus et al., 2004 (link)) and anti-Rab7 antibodies (Santa Cruz Biotech, CA). The secondary antibodies for Western blot analysis included horseradish peroxidase-conjugates of anti-swine Ig and anti-guinea pig Ig antibody (Thermo Scientific, Pittsburgh, PA). The secondary antibodies for confocal microscopy were FITC-labeled anti-swine IgG for PEC (Kirkegaard & Perry Lab Inc, MD), FITC-labeled anti-guinea pig IgG for MNV-1 (Sigma-Aldrich, MO) and anti-rabbit PerCP-Cy 5.5 (Santa Cruz Biotech, CA). Other basic chemicals for confocal microscopy and other studies were purchased from various sources including Sigma-Aldrich.
+ Open protocol
+ Expand
10

Hepatocyte Isolation and TET3 Knockdown

Check if the same lab product or an alternative is used in the 5 most similar protocols
Mouse primary hepatocytes were prepared as previously described (Zhang et al., 2018 (link)). Cells were maintained in complete culture medium (Williams’ Medium [GIBCO,12551] supplemented with 5% FBS, 10 mM HEPES buffer [GIBCO, 15630–080], 2 mM L-Glutamine [GIBCO, 25030–081], 1% SPA [GIBCO, 15240–062], 4 mg/L insulin [GIBCO, 12585–014] and 1 μM dexamethasone [Sigma, D4902]). For TET3 knockdown experiments, cells seeded in 12-well plates were infected with AAV8-scr or AAV8-siTET3 at 6,000 gc/cell at 3 h after seeding. Medium was changed the next day, and cells were stimulated with TGF-β1 at a final concentration of 5 ng/ml in insulin- and FBS-free culture medium, followed by RNA and protein extraction 48 h later.
Human primary hepatocytes were obtained through the Liver Tissue Cell Distribution System, which was funded by NIH contract N01-DK-7–0004/HHSN267200700004C. Cells were maintained in complete culture medium (HMM medium [LONZA, CC-3197] supplemented with 1% SPA [GIBCO, 15240–062], 0.1 μM insulin [GIBCO, 12585–014] and 0.1 μM dexamethasone [Sigma, D4902]). To induce hepatocyte stress, the hepatocytes were incubated with glycochenodeoxycholic acid (GCDCA) (Sigma-Aldrich, G0759) at a final concentration of 100 μM for 48 h, followed by protein extraction.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!