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14 protocols using ascent software v2

1

Microplate Fluorometer Data Analysis

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For each of the methods performed on the Fluoroskan Ascent™ (Thermo Scientific, Vantaa, Finland) Microplate Fluorometer (Cat#1506450, Thermo Scientific, Vantaa, Finland), data was collected using Ascent® Software v2.6 (Thermo Scientific, Vantaa, Finland). All raw data were firstly blank corrected using the Ascent® software (v2.6, Thermo Scientific, Vantaa, Finland) package and then exported for further analysis using Windows Excel 2016 and GraphPad PRISM 7.0 (GraphPad Prism Inc., La Jolla, CA, USA).
Graphs: Using Excel, averages of blank corrected data triplicates were calculated. From these averages, maximum absorbance was calculated and absorbance value plotted in a column graph for relative percentages.
Two-way (RM) ANOVA and Tukey’s Post-hoc test: the blank corrected data was transformed, setting the top value as 100 and lowest as 0 across sub columns within a data set. A two-way repeated measures (RM) ANOVA was performed, followed by a Tukey’s post-hoc multiple comparison test, comparing every mean with every other mean.
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2

Fluorometric Assay of Venom-Mediated Coagulation

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Activation of human Factor X (FX) and prothrombin by the venoms were measured with a Fluoroskan Ascent™ Microplate Fluorometer with Ascent® Software v2.6 (Thermo Fisher Scientific, Vantaa, Finland) using the following protocol: 10 µL venom (0.01, 0.05, and 0.1 µg/μL) in dilution buffer (150 mM NaCl, 50 mM Tris-HCl, pH 7.4) was plated in at least triplicate on a 384-well plate along with 10 µL phospholipid (Stago Cat#00597 in O.K. Buffer) and 10 µL of human recombinant FX or prothrombin (0.01 μg/mL) (Haematologic Technologies, VT, USA) in dilution buffer. Venom controls substituted 10 μL coagulation factor with 10 μL dilution buffer. Vehicle controls substituted 10 μL venom and 10 μL coagulation factor with 20 μL dilution buffer. Positive controls substituted 10 μL venom with dilution buffer and 10 μL coagulation factor with 10 µL (0.01 μg/mL) of human recombinant FXa or thrombin (Haematologic Technologies, Inc.). Plates were loaded into the fluorometer (pre-incubated to 37 °C), and 70 µL quenched substrate was dispensed into each well (1 µL substrate in 500 μL enzyme buffer: 150 mM NaCl, 50 mM Tris-HCl, 5 mM CaCl, pH 7.4. Fluorogenic Peptide Substrate Cat#ES002 used for FX activation assay; Cat#ES011 for prothrombin). Fluorescence was monitored (excitation/emission: FX–390 nm/460 nm, prothrombin–390 nm/460 nm) for 300 cycles over ~150 min.
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3

Enzymatic Activity of Snake Venom

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A working stock solution of freeze dried venom was reconstituted in a buffer containing 50% MilliQ/50% glycerol (>99.9%, Sigma, St. Louis, MO, USA) at a 1:1 ratio to preserve enzymatic activity and reduce enzyme degradation. Varying concentrations of crude venom (10 ng/µL and 50 ng/µL) were plated out in triplicates on a 384-well plate (black, Lot#1171125, nunc™ Thermo Scientific, Rochester, NY, USA) and measured by adding 90 µL quenched fluorescent substrate per well (total volume 100 µL/well, 10 µL/5mL enzyme buffer, 150 mM NaCl, and 50 mM Tri-HCl (pH 7.3), Fluorogenic Peptide Substrate, R&D systems, Cat#ES001 & ES011, Minneapolis, MI, USA). Fluorescence was monitored by a Fluoroskan Ascent™ (Thermo Scientific, Vantaa, Finland) Microplate Fluorometer (Cat#1506450, Thermo Scientific, Vantaa, Finland) (Cat#ES001 for Matrix Metalloprotease at an excitation of 320 nm, emission at 405 nm; Cat#ES011 for Kallikrein at an excitation of 390 nm, emission at 460 nm) over 400 mins or until activity had ceased. Data was collected using Ascent® Software v2.6 (Thermo Scientific, Vantaa, Finland).
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4

Serum Cortisol Measurement by EIA

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Laboratory analysis for cortisol was conducted by enzyme immunoassay (EIA). Serum samples were thawed, and cortisol concentrations were measured with commercial enzyme immunoassay kits (Immunotech, Moscow, Russia), following the manufacturer guidelines. Cortisol antibody cross-reactivity to other steroids was 6% to prednisolone and <1% for all other tested steroids. We used the flatbed spectrophotometer Multiscan EX with the Ascent Software v.2.6 (Thermo Fisher Scientific, Vantaa, Finland) for measuring the optical density in the wells at 450 and 620 nm and comparing it with the standard values. Serum samples were analyzed in duplicates (n = 220), and the coefficient of variation (CV) was calculated. If the CV was more than 10%, the samples were re-assayed. When CV was less than 10%, the mean cortisol concentration was taken for further analysis. The interassay coefficient of variation for the standard concentration of 7.25 ng/mL was 1.99% (n = 6) (n is the number of used plates). The mean intraassay coefficient of variation of paired samples was 3.03 ± 0.19% (n = 173) (n is the number of measured samples). All details are shown in Table S1.
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5

Mink IgG Standard Curve Protocol

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The standard curve (Fig. 2) was constructed from a seven point twofold dilution series of the purified mink IgG standard using a four-parametric logistic curve fit [Ascent software v. 2.6 (Thermo Scientific, Waltham, MA, USA)]. Concentrations of mink serum and milk samples were interpolated and calculated from the within-assay standard curve. To account for background signal all absorbance readings were adjusted by subtraction of the mean absorbance of wells not containing sample (blanks with only buffer).

Representative standard curve with seven twofold dilutions of the purified mink IgG standard fitted using a four-parametric logistic curve fit (y = b + (a − b)/(1 + xc)^d and R2 = 0.998). The y-axis displays the absorbance at 450 nm after subtraction of the absorbance at 650 nm. Mean ± SD for duplicate determinations of each concentration is indicated on a log-scale

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6

Continuous Phospholipase A2 Activity Assay

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We assessed the continuous Phospholipase A2 (PLA2) activity of the venoms using a fluorescence substrate assay (EnzChek® Phospholipase A2 Assay Kit, Cat#E10217, Thermo Scientific, Rochester, NY, USA), measured on a Fluoroskan Ascent® Microplate Fluorometer (Cat#1506450, Thermo Scientific, Vantaa, Finland). As above, we used a working stock solution of freeze dried venom reconstituted in a buffer containing 50% MilliQ/50% glycerol (>99.9%, Sigma) at a 1:1 ratio. A concentration of enzyme activity in venom (50 ng/µL) was brought up in 12.5 µL 1× PLA2 reaction buffer (50 mM Tris-HCL, 100 mM NaCl, 1 mM CaCl2, pH 8.9) and plated out in triplicates on a 384-well plate (black, Lot#1171125, nunc™ Thermo Scientific, Rochester, NY, USA). The triplicates were measured by dispensing 12.5 µL quenched 1 mM EnzChek® (Thermo Scientific, Rochester, NY, USA) Phospholipase A2 Substrate per well (total volume 25 µL/well) over 100 min or until activity had ceased (at an excitation of 485 nm, emission 538 nm). Purified PLA2 from bee venom (1 U/mL) was used as a positive control and data was collected using Ascent® Software v2.6 (Thermo Scientific, Vantaa, Finland).
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7

Fluorometric Venom Enzyme Assay

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Venom enzyme activity was assessed by combining venoms with fluorescent substrates using a Fluoroskan Ascent™ Microplate Fluorometer with Ascent® Software v2.6 (Thermo Fisher Scientific, Vantaa, Finland). Unless otherwise stated, venom working stocks were diluted to the desired concentration in dilution buffer (150 mM NaCl, 50 mM Tris-HCl, pH 7.4), each condition was tested in triplicate using 384-well plates, and machine incubation temperature was set at 37 °C.
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8

Serum S100B Protein ELISA Assay

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A commercially available S100B ELISA kit was used (CanAg EIA S100, Fujirebio Diagnostics AB, Göteborg, Sweden). Serum samples where thawed overnight at 4°C and were transferred (50 μL per well) to a pre-coated 96-well plate (in duplicates) and run according to manufacturer’s protocol. The results were analyzed using a Multiskan EX and Ascent Software V2.6 (ThermoLabSystems, Thermo Scientific, Waltham, MA, USA). Absorbance was measured at 620 nm, and cubic spline curve fit method was used to fit the absorbance as recommended by the manufacturer. Extrapolation was used for sample levels outside the calibration reference levels. Outliers (deviating more than 5 SD) were excluded (n = 2) (both normoxic, day 7), as well as animals with an inadequate sample volume (n = 1) (hypoxic, day 7).
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9

Quantifying Serum sST2 in AL Amyloidosis

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All blood samples taken from AL amyloidosis patients were collected into a 5-ml vacutainer and centrifuged at 3,000 rpm for 5 min. The serum was stored at −80°C. All samples were analyzed using the same reagent lot. The serum levels of sST2 were measured using a Presage ST2 sandwich ELISA kit (Presage® ST2; Critical Diagnostics, San Diego, CA, USA). The signals were detected by a Labsystems Multiskan MS spectrophotometer (Thermo Labsystems) and calculated using Ascent software v2.6 (Thermo Labsystems). The mean absorbance value (OD450) was measured for standard substances, samples and controls, and the concentration of ST2 (ng/ml) was calculated via a standard curve.
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10

Quantifying CCL17 and CCL22 Cytokines

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CCL17 serum levels in humans and mice were measured using a human or mouse CCL17/TARC ELISA kit, respectively (#PDDN00, #MCC170; R&D Systems), according to the manufacturer’s instructions. CCL22 serum levels in mice were measured using a mouse CCL22/MDC ELISA kit, according to the manufacturer’s instructions (#MCC220; R&D Systems). Standard cytokine dilutions were initially prepared, with subsequent additions of 50 μl of standard, control, or sample per well. Thereafter, each well was aspirated and washed, repeating the process four times and adding 100 μl of mouse or human TARC conjugate to each well. Finally, 100 μl of substrate solution and 100 μl of stop solution were added to each well. The signals were detected using a Labsystems Multiskan mass spectrometry spectrophotometer (Thermo Labsystems) and calculated using Ascent software v2.6 (Thermo Labsystems).
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