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1

Biochemical Assays for Inflammatory Markers

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Dulbecco's modified Eagle's medium (DMEM) and foetal bovine serum (FBS) were purchased from Gibco‐BRL (NY, USA). The assay kits for tumour necrosis factor alpha (TNFα), interleukin‐6 (IL‐6), soluble intercellular adhesion molecule‐1 (sICAM‐1), soluble vascular cellular adhesion molecule‐1 (sVCAM‐1) and endothelin‐1 (ET‐1) were bought from R&D Systems, Inc. (MN, USA), and NO assay kit from Beyotime Institute of Biotech (Shanghai, CHN). Streptozotocin (STZ), acetylcholine (Ach), sodium nitroprusside (SNP), phenylephrine (PE) and dimethyl sulfoxide (DMSO) and all other chemicals were commercially obtained from Sigma‐Aldrich (St. Louis, MO, USA) unless indicated elsewhere. Antibodies against PPARγ, endothelial nitric oxide synthase (eNOS), AKT and phosphor‐AKT (p‐AKT), inhibitory κB kinase alpha/beta (IKKα/β) and phosphorylated‐inhibitory κB kinase alpha/beta (p‐IKKα/β) and inhibitory κB alpha (IκBα) were purchased from Cell Signaling Technology, Inc. (MA, USA), and antibody against β‐actin from Santa Cruz (CA, USA).
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2

Comprehensive Metabolic Biomarker Assessment

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Plasma calcium, phosphate, urea and lipid fractions were measured by automated bioanalyzer (Beckman Coulter DxC). Whole blood fasting glucose concentration was measured using a portable glucometer (Optium Xceed, Medisense, UK) and commercial ELISAs were used to quantify plasma parathyroid hormone (Immutopics, USA), 25(OH)D (Immunodiagnostic Systems, UK), soluble vascular cell adhesion molecule-1 (sVCAM-1) (R and D Systems, USA) and insulin (Crystalchem, USA). Insulin resistance was measured by homeostatic model assessment (HOMA-IR), calculated as fasting plasma insulin (ng/mL)×fasting plasma glucose (mg/dL)/405. The total plasma nitric oxide oxidation product concentration was measured by Sievers analyser (GE Analytical Instruments, UK).
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3

Inflammatory Pathway Modulation Assay

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Calcein O, where O = -diacetate tetrakis (acetoxymethyl) ester (calcein AM)), RPMI-1640; and DMEM medium were purchased from Life Technologies (Grand Island, NY). Enzyme-linked immunosorbent assay (ELISA) kits for human and mouse soluble adhesion molecules ICAM-1 (sICAM-1), VCAM-1 (sVCAM-1) and E-selectin (sE-Selectin) and mouse chemokines MCP-1/JE and KC ELISA kits for the determination of human IL-8 and MCP-1 were from R&D Systems (Minneapolis, MN). Goat anti-rabbit IgG, DyLight 488 conjugated secondary antibody and Goat anti-rabbit HRP-IgG secondary antibody were purchased from Thermo Fisher Scientific Inc. (Waltham, MA, USA). NF-κB p65, VCAM-1 and F4/80 primary antibodies were obtained from Cell Signaling Technology, Inc. (Danvers, MA, USA), Santa Cruz Biotechnology (Santa Cruz, CA, USA) and BMA Biomedicals (Augst, Switzerland), respectively. Sulforaphane was from Toronto Research Chemicals (Toronto, CA, ≥98%, HPLC) and other general chemicals were from Sigma-Aldrich (St. Louis, MO).
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4

Biomarkers of Intestinal Injury in Ugandan Children

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Serum or plasma samples were analyzed for biomarkers of intestinal injury in Uganda on all cryopreserved samples. Children were considered to have intestinal injury if they had either elevated TFF3 or I-FABP compared to the population reference levels (>99th percentile for the population was used as the upper limit of normal). Markers were assessed using a custom Luminex MagPix panel including plasma trefoil factor 3 (TFF3), angiopoietin 2 (Angpt-2), soluble Fms-related receptor tyrosine kinase 1 (sFlt-1), P-selectin, sE-selectin, soluble vascular cell adhesion molecule 1 (sVCAM-1), chitinase-3-like protein 1 (CHI3L1), and procalcitonin (R&D Systems, Minneapolis, MN). A modified cytokine Luminex panel was used to measure serum levels of selected cytokines, including tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), interleukin-8 (IL-8), interleukin-6 (IL-6), interleukin-10 (IL-10), and interleukin-4 (IL-4), vascular endothelial growth factor (VEGF), granzyme B, Fractalkine, and sFlt-3 (R&D Systems, Minneapolis, MN). Intestinal fatty acid binding protein (I-FABP), soluble CD14 (sCD14), LPS binding protein (LBP), C-reactive protein (CRP), and soluble intercellular adhesion molecule 1 (sICAM-1) were measured by enzyme-linked immunosorbent assay (ELISA) using DuoSets by R&D Systems.
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5

Cardiac Protein Quantification in Immunized Mice

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Proteins were extracted from hearts of immunized mice and healthy controls. After digestion in 0.1% collagenase for 45 minutes, cells were lysed by ultrasonic pulse echo instrument. cVCAM-1, interleukin-6 (IL-6) and transforming growth factor-β (TGF-β) proteins were quantified using commercially available kits (VCAM-1: RayBiotech, Norcross, GA, Cat# ELM-VCAM1-001; IL-6: Cat#M6000B, TGF-β: Cat#MB100B, R&D Systems, Minneapolis, MN) according to the manufacturer’s instructions. For cVCAM-1, each value represents a pooled analysis of two hearts. sVCAM-1 (R&D Systems, Minneapolis, MN, Cat# MVC00, and RayBiotech, Norcross, GA, Cat# ELM-VCAM1-001) was quantified in plasma of immunized mice, sham immunized mice and healthy controls according to the manufacturer’s instructions. For both cardiac and soluble proteins, values represent mean of 2 consecutive measurements.
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6

Plasma and Urine Biomarkers After BMT

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Platelet-poor plasma was used for analysis of thrombin-antithrombin (TAT) complexes (Siemens Diagnostica), interleukin-6 (IL-6; R&D Systems), and soluble vascular cell adhesion molecular (sVCAM-1; R&D Systems). Urine was collected 240 days after BMT for 24 hours in metabolic cages (Hatteras Instruments). Urine analysis was performed as previously described.33 (link)
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7

Biomarker Profiling in Clinical Study

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Total platelet counts were determined with an automated cell counter (XN9000; Sysmex Corporation, Kobe, Japan). Enzyme-linked immunosorbent assay kits were used to measure serum concentrations of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) (R&D Systems, Minneapolis, MN), and high-mobility group box 1 (HMGB1) (Shino-test, Kanagawa, Japan). Plasma concentrations of sRAGE, matrix metalloproteinase 9 (MMP-9), soluble vascular adhesion molecule 1 (sVCAM-1), plasminogen activator inhibitor 1 (PAI-1) (R&D Systems), endogenous secreted form of RAGE (esRAGE) (B-Bridge International, Sunnyvale, CA), advanced glycation end products (AGEs) (Cusabio Biotech, Wuhan, China), and a disintegrin and metalloproteinase domain 10 (ADAM10) (Abnova Corporation, Taipei, Taiwan) were also measured with enzyme-linked immunosorbent assay. The frozen samples were thawed and subsequently processed according to manufacturers' instructions. Absorbance was measured with a microplate reader (SH-9000Lab; Corona Electric Co., Ltd., Ibaraki, Japan).
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