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53 protocols using tissue extraction reagent 1

1

Quantifying Neuroinflammatory Markers in White Matter

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The CC white matter tissues were dissected from the other half of the slices mentioned above in cold ACSF under an anatomic microscope. Then, the CC tissue was quickly transferred into Tissue Extraction Reagent 1 (FNN0071, Invitrogen, Camarillo, CA) with 1:1000 protease inhibitor (P-2714, Sigma) and homogenized. Protein concentration was measured by bicinchoninic acid assay (BCA assay). Routine electrophoresis was carried out using 10% sodium dodecyl sulfate-polyamide gel. Polyclonal rabbit anti-β-APP (1:600; AB5302, Millipore, Temecula, CA), monoclonal mouse anti-inducible nitric oxide synthase (iNOS; 1:500; AB49999, Abcam, Cambridge, MA), and rabbit anti-tumor necrosis factor alpha (TNF-α; 1:1000; AB66579, Abcam) were used to identify β-APP, iNOS, and TNF-α. Mouse anti-β-actin (1:10000; Sigma, A2228) was applied as a gel loading control. Immunoreactivity bands were detected using enhanced chemiluminescence and developed with autoradiography film.
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2

LPS-Induced β-APP Accumulation in Brain

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The prepared brain slices were divided into the ACSF group and ACSF containing LPS 0.2 μg/mL group, both bathed for 3 hours or 6 hours. After an incubation that displayed significant β-APP accumulation, pre-treatment with RS-LPS (2.0 μg/mL) followed by incubation with LPS (0.2 μg/mL) or co-incubation with LPS+RS-LPS was performed for the same duration. Then, CC tissues were disseced and transferred to Tissue Extraction Reagent 1 (FNN0071, Invitrogen) with 1:1,000 protease inhibitor (P-2714, Sigma-Aldrich, St. Louis, MO, USA), and homogenized. Protein concentration was measured by bicinchoninic acid assay (BCA assay). Routine electrophoresis was carried out using 10% sodium dodecyl sulfate-polyamide gel. Polyclonal rabbit anti-β-APP antibody (1:600; #AB5302, Millipore, CA, USA) was used to detect β-APP. Mouse anti-β-actin (1:10,000, #A2228, Sigma-Aldrich) was applied as a gel loading control. Immunoreactivity bands were detected using enhanced chemiluminescence and developed with autoradiography film. Protein density of β-APP was measured using Image J and normalized to the corresponding β-actin in each sample.
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3

Western Blot Analysis of β-APP

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The rats were euthanized with isoflurane and brain slices were prepared as the same way as described in the Electrophysiology section. The CC was dissected from coronal brain slices in cold ACSF under a dissecting microscope and quickly transferred into Tissue Extraction Reagent 1 (FNN0071, Invitrogen, Camarillo, CA) with 1:1000 protease inhibitor (P-2714, Sigma). Protein homogenate concentrations were determined by bicinchoninic acid assay (BCA assay). After centrifugation, the supernatant was subjected to sodium dodecyl sulfate-polyamide gel electrophoresis and then the protein was transferred to a PVDF membrane. The membranes were then blocked with 5% non-fat milk and incubated with rabbit anti-β-APP antibody (1:500; Abcam USA), followed by HRP-conjugated secondary antibody (1:5000; Jackson Immuno Inc., West Grove, PA). Mouse anti-β-actin (1:10,000; Sigma) was used for the gel loading control. Protein bands were detected using enhanced chemiluminescence and developed with autoradiography film. Image J (NIH, Bethesda, MD) software was used to quantify the band densities and protein densities of β-APP values were normalized by corresponding β-actin in each sample.
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4

Quantification of CREB and Phospho-CREB in Mouse Hypothalamus

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Hypothalamus isolated from mice was transferred to 300μl Tissue Extraction Reagent 1 (Cat# FNN0071; Invitrogen) with 3μl protease inhibitor (Cat# P-2714; Sigma-Aldrich, St. Louis, MO, USA) and homogenized. Pierce BCA Protein Assay Kit (Cat# 23227; Thermo Fisher Scientific) was used to determine the conentration of protein samples. Each protein lysate (20μg) was run on sodium dodecyl sulfate polyacrylamide gel electrophoresis gel, transferred to a polyvinylidene fluoride membrane, blocked for 1 h at 24 °C with 5% fat-free milk in Tris-buffered saline containing 0.1% Tween 20, and incubated with monoclonal rabbit anti-CREB (1:500) (Cat# ab32515; Abcam, Cambridge, UK; RRID:AB_2292301), rabbit and anti-phospho-CREB (1:1,000) (Cat# 9198S; Cell Signaling Technology, Danvers, MA, USA; RRID:AB_2561044). Mouse anti-α-tubulin (1:10,000) (Cat# T5168, Sigma-Aldrich, St. Louis, MO, USA; RRID:AB_477579) was used as a control. Horseradish peroxidase-conjugated goat anti-rabbit secondary antibodies (1:5,000) (Cat# 7074S; Cell Signaling Technology, Danvers, MA, USA; RRID:AB_2099233) and goat anti-mouse secondary antibodies (1:10,000) (Cat# G21040; Invitrogen, Carlsbad, CA, USA; RRID:AB_2536527) were used for detection. Enhanced chemiluminescence western blot detection reagents (Amersham Pharmacia Biotech, Piscataway, NJ, USA) were used to detect the target proteins. n = 3 mice/group.
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5

Protein Quantification in Mouse Brains

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The prefrontal cortex, the striatum, and the cerebellum were dissected from the frozen brains. Mouse brain tissues were weighed and, for each milligram of tissue, 10 μl of PBS (Sigma-Aldrich Company Ltd, Dorset, UK) with protease inhibitors (ThermoFisher, Waltham, MA, USA) was added. Tissues were lysed on ice by using a sonication probe and to each lysate, we added an equal volume of Tissue Extraction Reagent 1 (ThermoFisher) to that of PBS that was then vortexed. Lysates were centrifuged at 13,000 rpm for 3 min and then aliquoted and stored at −20 °C. Plasma samples were prepared as per kit protocols. Assays were performed based on the instructions provided in the manual of the analyte kits. Specifically, Kcnq1, Bdnf (ABIN2101758 and ABIN2115886, respectively, from antibodies-online GmbH, Aachen, Germany) and insulin (EMINS, ThermoFisher) were detected by means of ELISA, whereas Igf1 was assessed by the Luminex Multiplex kit (LXSAMSM-02, Bio-Techne Ltd, Abingdon, UK).
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6

Tracking Salmonella Typhimurium Infection in Mice

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Mouse protocols were approved by Duke University IACUC (Protocol A200-15-07). Oral infection mouse protocols were approved by N.C. State University IACUC. Breeding stock of C57BL/6j mice were obtained from Jackson laboratories and raised in the Duke Breeding Core Facility. Male and female 6-10 week old mice were infected with S. Typhimurium intraperitoneally and monitored twice daily for morbidity. For colony-forming unit counts, tissues were weighed and homogenized in PBS using Zirconium Oxide beads (GlenMills, #7305-000031) and a Mini-BeadBeater-24 (Biospec Products). Appropriate dilutions were plated on LB agar + ampicillin (100μg/mL) or kanamycin (50μg/mL) to calculate CFUs per gram. For phosphorylated STAT3, spleens were harvested in Tissue Extraction Reagent 1 (Thermo Fisher, #FNN0071) and homogenized as above. Homogenates were diluted 1:5 and analyzed by western blot. For chronic infections, 8-10 week old CBA/J mice from Jackson Laboratories were given ~108 CFU of a 1:1 mixture of WT and ΔsarA mutant by gavage. Mice were euthanized at 14 or 24 days post-infection. Cecum, spleen, and liver were harvested, weighed, homogenized, and plated for CFUs.
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7

Quantifying Glucose and Fructose in Mouse Plasma and Liver

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Blood was collected from mice with ad libitum feeding in three dietary groups (regular chow diet, fructose-high diet, and fructose-restrict diet, Table S5). Liver tissues were frozen using a freeze clamp. Glucose and fructose levels in the plasma were measured by a modified GC-MS method (Antoniewicz et al., 2011 (link); Long and Antoniewicz, 2014 (link)). Briefly, internal standard of U-13C glucose or U-13C fructose were added for quantification. Protein in the plasma was precipitated with methanol. Samples were air-dried. Hydroxylamine/pyridine solution was added, and samples were then incubated for 60 min at 90°C, followed by adding propionic anhydride to react at 60°C for 30 min. Samples were then evaporated to dryness under airflow and re-dissolved in ethyl acetate for GC-MS analysis on the Agilent 7890B GC system. Glucose and fructose measurements used m/z 370 and m/z 401 respectively.
Liver insulin was extracted from snap frozen liver samples using Tissue Extraction Reagent I (FNN0071, ThermoFisher, USA). Insulin in both plasma and liver tissue was measured by UltraSensitive Mouse Insulin ELISA Kit (90080, Crystal Chem. Inc. USA), described previously (Kim et al., 2016 (link)).
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8

Quantifying Growth Factors in Decellularized Matrices

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Cytokines retained in the DTSs and tECM-DTSs, including transforming growth factor beta 1 (TGF-β1), vascular endothelial growth factor (VEGF), insulin-like growth factor 1 (IGF-1) and SDF-1, were measured using ELISA. Soluble molecules were extracted from the DTSs and tECM-DTSs specimens using Tissue Extraction Reagent I (FNN0071, Thermo Fisher Scientific, USA) with a protease inhibitor (1% phenylmethane sulfonyl fluoride, 1% PMSF, Sigma) at 4°C for 24 h. The extracted lysates were homogenized, and centrifuged at 10 000 rpm for 10 min at 4°C, and then the supernatants were collected. ELISA measurements of the extracted lysates were performed (n = 6 for each group) according to the manufacturer’s instructions (TGF-β1 and VEGF, NeoBioscience, China; IGF-1, RayBiotech, USA; SDF-1, DL-develop, China).
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9

Analyzing Tight Junction Proteins

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bEnd.3 cells from the urea experiments were pelleted, then lysed in Tissue Extraction Reagent I (Thermo Fisher Scientific) supplemented with protease inhibitor cocktail (Roche Applied Science). Protein concentrations were measured with a BCA protein assay kit, and Western blotting was done as described above with claudin-5 (diluted 1:500) and occludin (diluted 1:500) normalized to GAPDH internal control (diluted 1:20,000). Western blots were repeated at least three times for each sample.
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10

Lesional Cytokine Profiling via LEGENDplex

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For analysis of lesional cytokine production, total lesional protein was extracted from tissue samples using 1 mL Tissue Extraction Reagent I (Thermo Fisher Scientific, Waltham, USA) per 100 mg of tissue sample. Lesional cytokine profile was then determined using the LEGENDplex mouse inflammation panel (Biolegend, San Diego, CA) according to the manufacturer's instructions.
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