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4 protocols using fast prep 24 5g machine

1

Quantitative Analysis of Intestinal Tight Junctions

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Frozen ileum tissue (ca. 100 mg) was homogenized with cell lysis buffer (500 μl) (Cat EPX-99999-000 eBioscience, San Diego, USA) with 0.1 % proteinase inhibitor cocktail (Sigma, St. Louis, MO) and 1 % NP40 in ceramic bead tubes using Fast Prep-24™ 5G machine (M.P. Biomedical LLC, California, USA) at speed 6.0 msec for 30 s (twice), and then centrifuged at 12,000 g for 15 min at 4 °C. Supernatants were collected and 100 μg of protein was used for Western blot analyses. Membranes were probed with 1:1000 dilution of rabbit anti-VE-cadherin, rabbit anti-occludin, and rabbit anti-claudin 3 (Abcam, Cambridge, MA) primary antibodies and subsequently incubated with 1:10,000 dilution of goat-anti-rabbit HRP (BioRad Laboratories Inc., California). Detection was performed using a chemilumiescence system (super signal west chemiluminescent substrate, Thermo Scientific). Immuno-quantitation was performed by densitometric scanning of the blot and normalized against the signal from β-actin (Sigma Aldrich, St Louis, MO) using Image Quant software (Image Quant TL 8.1 Version). We measured calcium levels in urine from breast-fed and formula fed piglets using colorimetric assay from Bio Vision (Catalog#K380-250) as per manufacturer’s instructions.
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2

Porcine Intestinal Cytokine Quantification

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Expression of IL-8, IL-6, and IL-10 were measured in ileum samples of pigs using porcine ELISA kit (EMD Millipore Corporation, MA) as per the manufacturer instructions. Frozen ileum tissue (100 mg) was homogenized with cell lysis buffer (500 μl) (Cat EPX-99999-000 eBioscience, San Diego, USA) in ceramic bead tubes using Fast Prep-24™ 5G machine (M.P. Biomedical LLC, California, USA) at speed 6.0 msec for 30 s, and then centrifuged at 12,000 g for 15 min at 4 °C. Clear tissue supernatant were used to measure the protein expression. Tissue cytokines data was normalized with total protein estimated by BCA method (Thermo-scientific IL, USA) and data are presented as pg/g protein.
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3

Soil Metagenomic DNA Extraction Protocol

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Soil samples (2 g/sample) were properly prepared by drying them at room temperature for a week and sifting them with a 500‐μm sieve. The dried samples were packaged and sent to SYMPLANTA laboratory in Germany (the end of March 2020). DNA used in the metagenomic analysis was extracted from the 16 soil samples using a modified protocol of the FastDNA Spin Kit for soil (MP Biomedicals, Heidelberg, Germany) and an MP FastPrep‐24 5G machine. For each sample, 500 mg of fine homogenous soil was transferred and repeated bead‐beating was performed using ¼ inch ceramic beads in lysing matrix A to insure a better DNA yield. Samples were then treated as per the manufacturer's instructions except that 2X40s disruption was used instead of 1X40s (Senés‐Guerrero et al., 2014 (link)). Extracted DNA was then stored at −20°C for further analysis.
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4

Rapid Toxoplasma DNA Extraction and Amplification

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Blood clot specimens were homogenized with 300ul guanidine hydrochloride 6M (Sigma-Aldrich, USA). After homogenization, the sample was transferred to a Lysing Matrix H 2 mL tube (MP Biomedicals, USA) followed by an agitation cycle in a FastPrep-24 5G machine (MP Biomedicals, USA) (5.5 m/s– 30”) to ensure the clot disaggregation before the treatment with proteinase K [26 (link)]. DNA was then extracted from treated clot specimen and CSF specimens using the High Pure PCR Template Preparation Kit (Roche Life Science) per manufacturer’s instructions. Target sequences were amplified using a Light Cycler (Applied Biosciences) using the following program: 2 minutes at 50°C, then 10 minutes at 95°C; and 40 cycles of 95°C for 15 seconds, 60 seconds at 58°C, and 60 seconds at 72°C; followed by a 4°C hold. Primers for 529 repeat were 5′- GCTCCTCCAGCCGTCTTG (forward) and 5′- TCCTCACCCTCGCCTTCAT (reverse), and FAM—AGGAGAGATATCAGGACTGTA—3’MGB probe was used [24 ,26 (link)]. Positive controls consist of a pool of positive patient samples and a standard logarithmic curve of RH strain tachyzoites from 1–100000 [26 (link)].
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