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19 protocols using mak080

1

Permeability Assay for C. parvum Infection

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IPEC-J2 monolayers were grown to confluence on 12-mm diameter, 0.4-μm pore size polycarbonate filters. A subset of monolayers was infected with C parvum, and the permeability of uninfected control and C parvum–infected monolayers was measured at 24 and 48 hours after infection by concurrent transepithelial passage of 3 permeability probes: creatinine, fluorescein isothiocyanate–4 kilodalton dextran, and rhodamine–70 kilodalton dextran (catalog C4255, 46944, and R9379; Millipore Sigma). Probes were prepared in cell culture media at a final concentration of 11 mg/mL. At the beginning of each flux period, 100 μL of the flux solution was added to the apical side of each insert to give a final volume and concentration of 500 μL and 2.2 mg/mL, respectively. After 2 hours of incubation, basolateral recovery of each probe was measured in a plate reader (Synergy HT; BioTek, Winooski, VT) using freshly prepared standards. Fluorescence of fluorescein and rhodamine B were measured at 490 and 555 nm using emission wavelengths of 520 and 585 nm, respectively. Creatinine was measured separately using a colorimetric assay (catalog MAK080; Millipore Sigma).
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2

Creatinine-Normalized Molecule Quantification

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All molecule abundances were additionally normalized to creatinine concentrations of corresponding urine samples using a creatinine colorimetric assay kit (MilliporeSigma, catalog MAK080). Absorbance at 570 nm was measured using a Spectramax M2 microplate reader. Each sample was measured in duplicates, and all measured creatinine concentrations were within range of the standard curve.
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3

Serum Creatinine and AST Analysis

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Serum creatinine (Millipore Sigma, MAK080) and aspartate aminotransferase (AST) (Millipore Sigma, MAK055) levels were measured by commercial kits according to the manufacturer’s protocols.
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4

Serum Creatinine and AST Assays

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Serum creatinine (Millipore Sigma; MAK080) and aspartate aminotransferase (AST) (Millipore Sigma; MAK055) levels were measured by commercial kits according to the manufacturer's protocols.
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5

Creatinine Quantification Protocol

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Urine creatinine was measured using creatinine assay kit (MAK080; Sigma-Aldrich Corp., St Louis, MO) according to the manufacturer's instructions. Briefly, samples were passed through 10 KDa cut off filter to sieve out unwanted proteins. The urine creatinine concentration was measured by a colorimetric assay at 530 nm using a microplate reader (Synergy MX; Biotek Instruments Inc., VT). Serum creatinine concentration was measured with a serum-specific assay (700460; Cayman Chemical, Ann Arbor, MI), according to the manufacturer's protocol. This kit uses Jaffe's reaction, where picric acid in an alkaline condition reacts with creatinine to give a concentration dependent color.
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6

Hematological and Biochemical Profiling

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Red blood cell (RBC) counts were established as specified by Brown (1976). Hemoglobin (Hb) concentration was quantified according to [17 ]. The serum concentrations of creatinine, urea alanine transaminase (ALT) and aspartate transaminase (AST) were calculated using standard kits (Sigma-Aldrich; MAK052, MAK055, MAK080 and MAK006, respectively). C-reactive protein (CRP) levels were evaluated according to the guidelines of a commercial kit (AG723-M; Sigma-Aldrich).
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7

Serum Biomarker Quantification in Mice

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Mouse blood samples were collected at the end of experiments. Serum urea, urea nitrogen (BUN), and creatinine were respectively assessed by Urea assay kit (MAK006, Sigma-Aldrich, St. Louis, MO, USA), Urea Nitrogen (BUN) colorimetric detection kit (EIABUN, Thermo Fisher Scientific, Waltham, MA), and Creatinine assay kit (MAK080, Sigma-Aldrich) according to the manufacturer’s instructions.
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8

Urine Creatinine Normalization Protocol

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A random subset of urine samples from the discover and validation cohort were selected and urine molecule abundance was compared prior to and after creatinine normalization. Urine creatinine concentration was measured using a creatinine colorimetric assay kit (Sigma Aldrich Catalog number MAK080). Absorbance was measured using a Spectramax M2 microplate reader at 570 nm (fluorometric (λex = 535/λem = 587 nm). If the creatinine concentration was out of the measurable range, the sample was excluded from the analysis. Creatinine measurement was done in triplicate for each urine sample. Statistical analysis was performed as described in statistical methods section. A random sample of 66 participants from the discovery (Haitian) cohort and 88 from the validation (Vietnam) cohort was analyzed before and after creatinine normalization. There was no difference in overall metabolite abundance or ROC characteristics when comparing samples that were normalized to osmolality alone vs. those that were normalized to both osmolality and creatinine. (Supplementary Table 1).
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9

Glycosaminoglycan Quantification in Tissues and Urine

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Tissue lysates were digested in proteinase K (20 mg/mL) at a ratio of 1:10 (ProK:tissue lysate) at 55 °C overnight. Proteinase K was inactivated by boiling for 10 minutes the next day. Samples were then incubated with 200 units of DNase and 2 mg of RNase per 50 μL tissue lysate at room temperature overnight and heat inactivated the next day by boiling for 10 minutes. GAG levels were then assayed using the Blyscan Sulfated Glycosaminoglycan Assay kit (Biocolor Life Science Assays, Accurate Chemical, NY Inc. Cat # CLRB1000) according to the manufacturer’s instructions. For tissues, GAG levels were normalized to protein as determined using the Pierce protein assay (Cat #: 22660, ThermoFisher). The results are expressed as μg GAG/mg protein. For urine, GAG levels were normalized to creatinine as determined using a creatinine assay kit from Sigma (MAK080). The results are expressed as μg GAG/mg creatinine.
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10

Urinary ß-CTX Measurement Protocol

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Human cross-linked C-terminal telopeptides of type I collagen (ß-CTX) were measured by an enzyme-linked immunosorbent assay (Catalog Number: EH3989, Fine-Biotech), as previously reported [46 (link)]. Assay values were corrected for urinary dilution by urinary creatinine concentration. The intra- and interassay coefficients of variation were <8% and <10%, respectively. All samples were analyzed in duplicates in the same assay to prevent interassay variation. Urinary creatinine was determined by a standard colorimetric method (Catalog Number: MAK080, Sigma-Aldrich, St. Louis, MO, USA).
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