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9 protocols using bovine hemin

1

Spiroplasma Quantification in Flies

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An 18 nL injection of each product (or PBS as mock control) was performed in the thorax of young females using a Nanoject II (Drummond). Spiroplasma was quantified by qPCR 7 days after the treatment. FAC (Sigma F5879) was injected at 50 mM, BPS (Sigma 146617) at 10 mM and bovine hemin (Sigma H9039) at 10 mM, bovine holo-Tsf (Sigma T1283, Saint-Louis, MO, USA) and human apo-Tsf (Sigma T1147) at 300 µg per fly. Spiroplasma quantification was performed 7 days after the treatment in a least four biological replicates.
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2

Crithidia fasciculata Culturing Protocol

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The CfC1 genome reference strain of Crithidia fasciculata was used for our experiments. The line was obtained from the laboratory of Dr. Stephen Beverley (Washington University). For these experiments, cells were maintained in complete brain heart infusion medium (BHI) made by dissolving 37 g of powder (Sigma) per liter of water and supplementing with bovine hemin (Sigma) to a final concentration of 20 μg/ml. Cells were passaged every 2–3 days and cultured between 27–28 °C at a density of 105−108 cells/ml in non-treated tissue culture flasks. For cultures of swimming cells, flasks were placed on a rocker, while flasks for adherent cells were left stationary on the incubator shelf. All washes of adherent cultures were performed by pipetting the wash solution directly onto the flask surface, then rocking the flask. Swimming cells were counted by fixing in 0.3% formalin followed by staining with Gentian violet (Harleco) in 0.2 M NaCl, 0.7 mM EDTA. Fixed, stained cells were then counted on a hemocytometer.
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3

Cultivation and Cloning of Crithidia fasciculata

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C. fasciculata strain CfC1 was grown in brain heart infusion (BHI) medium supplemented with 20 μg/ml bovine hemin (Sigma) at 27°C. Cells grown on a rocker were passaged as nectomonads every 2–3 days to maintain a density between 105 and 108 cells/ml. Cell densities were determined by mixing a small sample of cells with an equal volume of 3% formalin, followed by staining with crystal violet before loading samples on a hemacytometer for counting. To generate adherent haptomonads for imaging, 2 ml of culture at a density of 1 x 107 cells/ml was seeded in a 35 mm poly-L-lysine-coated MatTek dish. The cells were allowed to adhere for 2 hours without rocking. Following 3 washes with BHI, fresh media was added, and dishes were incubated without rocking for 24 hours prior to imaging. To obtain clonal C. fasciculata cell lines, serial dilutions of culture were plated on BHI plates made with 0.65% agarose and supplemented with hygromycin (Amresco) [35 (link)]. After 4–5 days of growth, parasite colonies were transferred with a pipet tip to a standard liquid culture containing hygromycin.
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4

Fermentation of Rice Bran with Probiotics

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Rice bran was a gift from Riceland Foods (Stuttgart, AR, USA), and FOS was obtained from Megazyme International Ireland Ltd. (Wicklow, Ireland). For fermentation medium, yeast extract and resazurin from Alfa Aesar (Ward Hill, MA, USA), peptone from Fisher Scientific (Waltham, WA, USA), bile salts from Oxoid (Hampshire, UK), sodium bicarbonate, sodium chloride, potassium hydrogen phosphate, magnesium sulfate heptahydrate, calcium chloride hexahydrate, L-cysteine hydrochloride, vitamin K, bovine hemin and Tween 80 from Sigma (St. Louis, MO, USA) were purchased. SCFA standards (acetic acid, propionic acid and butyric acid) were purchased from MilliporeSigma Corporate (St. Louis, MO, USA).
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5

Visualizing RCA Reaction Products

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To visualise the products of the RCA reaction with the naked eye, pH of the reaction was adjusted to pH 5 using 10 μL (citric acid-Na2HPO4) before adding 2.68 μL of 100 μM hemin (bovine hemin, Sigma Aldrich), 8.7 μL of 50 mM 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS, Sigma Aldrich) and 8.7 μL of RefectoCil Oxidant 3%, GW cosmetics to the RCA reaction at room temperature. Thereafter, the color change was recorded with a digital camera. Quantification of the color intensity of the beads (and not the liquid in the tube) was performed using ImageJ. Quantified numbers were tested for significance (one-way, paired T-test) using GraphPad Prism software (version 9.3.0).
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6

Kinetic Study of Guaiacol Oxidation by Camel β-Casein

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Bovine hemin, sodium dodecyl sulfate (SDS) and imidazole were obtained from Sigma (St. Louis, MO USA). Camel milk was generously provided by the Faculty of Veterinary, University of Tehran, Iran. Camel β-casein was purified according to modified methods (Rasmussen, Due & Petersen 1995 ; Egito et al. 2002 (link)). The purity of Cβ-casein was assessed using SDS-PAGE and estimated to be greater than 95%. Other chemicals were of analytical grade (Merck, Germany) and used without further purification. Hemin, hydrogen peroxide, and guaiacol solutions were freshly prepared. Absorption spectra were collected using a model Shimadzu- 3100 spectrophotometer with 1 cm path length cells equipped with a thermostatted holder. The steady state kinetics of guaiacol oxidation by hydrogen peroxide, catalyzed by the model catalyst, were monitored at 470 nm (colored product of the reaction) in 5 mM phosphate buffer solution (PBS) pH 7.
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7

Fecal Slurry Model for Gut Microbiome Dynamics

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Cell-free culture supernatants from the proximal and distal colon, both in resting conditions (basal) and after immune challenges (LPS and IL-15), were subsequently used to explore their effect on a stable fecal population via the fecal slurry model. For this purpose, we used a basal media composed of 2 g/l peptone water [Becton, Dickinson and Company (BD), Franklin Lakes, NJ, USA] 2 g/l yeast extract (BD), 0.1 g/l NaCl, 0.04 g/l K2HPO4, 0.04 g/l KH2PO4, 0.01 g/l MgSO4, 0.01 g/l CaCl2.⋅2H2O, 2 g/l NaHCO3, 2.5 g/l l-Cysteine-HCl, 0.5 g/l bile salts, 2 ml/l Tween-80, 1 g/l arabinogalactan, 2 g/l pectin, 1 g/l xylan, 4 g/l starch, 0.4 g/l glucose, and 0.4 g/l mucin type III (all purchased to Sigma-Aldrich). The mixture was homogenized and autoclaved for 15 min at 121°C, and the following components were added to the cooled media after sterilization by filtration (0.20 μm): 0.05 g/l bovine hemin (Sigma-Aldrich) and 10 μg/l vitamin K (Sigma-Aldrich). Before use, the basal media was maintained overnight at 37°C in anaerobiosis (10% v/v H2, 10%CO2, and 80% N2) in an anaerobic chamber Mac 500 (Don Whitley Scientific, West Yorkshire, UK).
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8

Purification of Sodium Dodecyl Sulfate

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Sodium dodecyl sulfate (SDS) and bovine hemin (>90%) were procured from Sigma-Aldrich. Imidazole, Pyridine and Sodium Hydroxide were procured from Merck. Saline solution was purchased from Baxter (India) Pvt. Limited. All the above chemicals were commercially available and used as received without further purification.
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9

Enzymatic Assay for β-Glucuronidase

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DMSO, bovine hemin, vitamin K1, amoxapine, p-nitrophenol (PNP), p-nitrophenyl-β-D-glucuronide (PNPG), and E. coli β-glucuronidase (G8401) were supplied by Sigma-Aldrich (St. Louis, MO). L-cystine was purchased from Research Organics (Cleveland, OH). Purities were all >98%. Agar was purchased from Biosharp (Hirono, Japan). The BBL Brain Heart Infusion (BHI) medium was purchased from Becton Dickinson (Franklin Lakes, NJ). Dulbecco's phosphate-buffered saline (PBS) was provided by Life Technologies (Carlsbad, CA). Deionized water was purified by a Milli-Q purification system (Millipore, Bedford, MA).
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