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23 protocols using molecular analyst

1

Quantifying Neurogenic Markers in Dentate Gyrus

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For confirming the expressions of BDNF and TrkB, the detected bands were calculated densitometrically using Molecular Analyst, version 1.4.1 (Bio-Rad). The numbers of BrdU-positive cells in the dentate gyrus were counted hemilaterally under a light microscope (Olympus, Tokyo, Japan). The area of the dentate gyrus was measured by Image-Pro Plus image analysis system (Media Cyberbetics Inc., Silver Spring, MD, USA). The numbers of BrdU-positive cells were expressed as the numbers of cells per mm2 in the hippocampal dentate gyrus.
The data were analyzed with one-way analysis of variance and then Duncan post hoc tests. All values are expressed as the mean± standard error of the mean. P<0.05 was considered as significant.
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2

Western Blot Analysis of NLRP3 Inflammasome

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Approximately 100 mg of frozen rat kidney tissues was homogenised in 1 ml of RIPA buffer and then centrifuged at 10,000g for 20 min. The protein concentrations of the supernatants were measured according to the Bradford method. Total proteins were denaturalized in boiling water for 5 min. Equal amounts of total protein were separated onto 6%–12% SDS-PAGE and electrophoretically transferred to a polyvinylidenedifluoride (PVDF) membrane (Millipore, Shanghai, China) which was preactivated with methanol in the transferring buffer. Membranes were blocked with 5% skim milk for 2 h and incubated overnight with specific primary antibodies at 4°C. Immunoreactive bands were detected using HRP-conjugated goat anti-rabbit IgG as the secondary antibody (1 : 5000) (Jackson, Shanghai, China). Immunoreactive bands were visualised using a phototope-horseradish peroxidase Western blotting detection system (Cell Signaling Technologies, Beverly, MA) and quantified through densitometry with Molecular Analyst (Bio-Rad Laboratories, Hercules, CA). Primary antibodies included rabbit polyclonal antibodies against rTXNIP, rNLRP3, rASC, rCaspase-1, rpro-IL-1β, rIL-1β, and pro-IL-18, and rIL-18 (all 1 : 1000).
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3

Analyzing Neurobiological Markers in Tissue Samples

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For confirming expression of Bax, Bcl-2, and cytochrome c, the detected bands were calculated densitometrically using Molecular Analyst (version 1.4.1, Bio-Rad). The number of TPH-positive and 5-HT-positive cells in the dorsal raphe and the number of DCX-positive and TUNEL-positive cells in dentate gyrus were counted hemilaterally under a light microscope (Olympus, Tokyo, Japan). The data were analyzed with one-way analysis of variance and then Tukey post hoc test. All values are expressed as the mean±standard error of the mean, and P-value<0.05 was considered significant.
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4

Quantifying BDNF and BrdU in Dentate Gyrus

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For confirming the expressions of BDNF and TrkB, the detected bands were calculated densitometrically using Molecular Analyst™, version 1.4.1 (Bio-Rad). The number of BrdU-positive cells in the dentate gyrus were counted hemilaterally under a light microscope (Olympus, Tokyo, Japan), and expressed as the numbers of cells per mm2 in the dentate gyrus. The area of the dentate gyrus was measured by Image-Pro® Plus image analysis system (Media Cyberbetics Inc., Silver Spring, MD, USA). Statistical analysis was performed using one-way ANOVA followed by Duncan’s post-hoc test, and the results are expressed as the mean±standard error of the mean (SEM). Significances were accepted at P<0.05.
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5

Quantitative Densitometry Analysis

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The respective RNA bands were analysed using a model GS-700 Imaging Densitometer and Molecular Analyst software (version 1.5; Bio-Rad Laboratories, Hercules, CA, USA).
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6

BDNF, TrkB, pCREB, and 5-HT1A Expression Analysis

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For confirming the expressions of BDNF, TrkB, pCREB, and 5-HT1A, the detected bands were calculated densitometrically using Molecular Analyst™ (Bio-Rad). The data were analyzed with one-way ANOVA and then Duncan post-hoc tests. All values are expressed as the mean±standard error of the mean (SEM), and P value<0.05 was considered significant.
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7

Quantification of Serotonergic Neurons in Dorsal Raphe

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The numbers of 5-HT and TPH-positive cells in the dorsal raphe were counted hemilaterally through a light microscope (Olympus, Tokyo, Japan). The area of the dorsal raphe was measured using an Image-Pro plus computer-assisted image analysis system (Media Cybernetics Inc., Silver Spring, MD, USA) attached to a light microscope (Olympus). Molecular Analyst (ver. 1.4.1, Bio-Rad) was used for analyzing of detected bands.
Differences among the groups were evaluated using SPSS Statistics ver. 21.0 (IBM Co., Armonk, NY, USA) by the one-way analysis of variance followed by Duncan post hoc test. All values are expressed as the mean±standard error of the mean. Statistically significant differences were established at P<0.05.
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8

Western Blot Analysis of Rat Kidney OATs

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Approximately 20 mg of frozen rat kidney tissues was homogenised in 200 µl of RIPA buffer and then centrifuged at 12,000 rpm for 10 min. The protein concentrations of the supernatants were measured according to the BCA method. Total proteins were denaturalized in boiling water for 5 min. Equal amounts of total protein were separated onto 10% SDS-PAGE and electrophoretically transferred to a polyvinylidenedifluoride (PVDF) membrane (Millipore, Shanghai, China) which preactivated with methanol in the transferring buffer. Membranes were blocked with 5% skim milk for 2 h and incubated overnight with specific primary antibodies at 4°C. Immunoreactive bands were detected using HRP-conjugated goat anti-rabbit IgG as the secondary antibody (1:5000) (Jackson, Shanghai, China). Immunoreactive bands were visualised using a phototope-horseradish peroxidase Western blotting detection system (Cell Signaling Technologies, Beverly, MA) and quantified through densitometry with Molecular Analyst (Bio-Rad Laboratories, Hercules, CA). Primary antibodies included rabbit polyclonal antibodies against rOAT1 (dilution 1:1000) and rOAT3 (dilution 1:500).
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9

Quantifying COX-2 and Perilipin-2 in Macrophages

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COX-2 and perilipin-2 protein levels in cultured macrophages were detected by Western blotting. Aliquots of MT-III-stimulated and non-stimulated cells (1.5×106 cells) were lysed with 100 μL sample buffer (0.5 M Tris-HCl, pH 6.8, 20% SDS, 1% glycerol, 1 M β-mercapto ethanol, 0.1% bromophenol blue) and boiled for 10 min. Samples were resolved by SDS-PAGE on 10% bis-acrylamide gels overlaid with a 5% stacking gel. Proteins were then transferred to nitrocellulose membranes using a Mini Trans-Blot (Bio-Rad Laboratories, Richmond, CA, USA). The membranes were blocked for 1 h with 5% nonfat dry milk in Tris-buffered saline (TBS) (20 mM Tris, 100 mM NaCl, and 0.5% Tween 20, pH 7.2), and incubated with primary antibodies against COX-2 (1∶1000 dilution), perilipin-2 (1∶2000) and β-actin (1∶3000) for 1 h. They were then washed and incubated with the appropriate secondary antibody conjugated to horseradish peroxidase. The immunonereactive bands were detected by the entry-level peroxidase substrate for enhanced chemiluminescence (ECL), according to the instructions of the manufacturer (GE Healthcare). Band densities were quantified with a GS 700 densitometer (Bio- Rad Laboratories) using the image analysis software Molecular Analyst (Bio-Rad Laboratories).
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10

Hippocampal Neurogenesis and Apoptosis Analysis

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For the analysis of the expression of BDNF, Bax, Bcl-2, cytochrome c, and caspase-3, the detected bands were calculated densitometrically using Molecular Analyst ver 1.4.1 (Bio-Rad). The numbers of BrdU-positive, TUNEL-positive, and caspase-3-positive cells in the hippocampal dentate gyrus were counted hemilaterally under a light microscope (Olympus, Tokyo, Japan), and they were expressed as the number of cells per mm2 in the hippocampal dentate gyrus. The area of the hippocampal dentate gyrus was measured using Image-Pro Plus image analysis system (Media Cyberbetics Inc., Silver Spring, MD, USA). The data were analyzed with one-way analysis of variance followed by Duncan post hoc tests. All values are expressed as the mean±standard error of the mean, and a P-value of <0.05 was considered significant.
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