5-μl of 10× reaction buffer [200 mM Tris/HCl (pH 8.8), 100 mM KCl, 100 mM (NH4)2SO4, 1% Tween 20], 3.5-μl 10 mM dNTPs, 4.0-μl 5 M betaine (Sigma, St Louis, MI), 1.5-μl 100 mM MgSO4, 2.0-μl primer mixture (20 μM each of FIP, BIP, LF, and LB primers, and 2.5 μM each of F3 and B3
primers for the pCS20 LAMP; or 20 μM each of FIP, BIP, and LF primers, and 35 μM of LB primers, and 2.5 Ensartinib cost μM each of F3 and B3 primers for the sodB LAMP), 9.5-μl DDW, 1.0-μl (8 U) Bst DNA polymerase (New England Biolabs, Beverly, MA), and 1.0-μl template DNA. To find the optimal reaction temperatures for the two LAMP assays, the reaction mixtures were incubated for 120 min at 58 to 66°C in a Loopamp real-time turbidimeter (LA-200; Teramecs, Kyoto, Japan). For the field samples, LAMP reactions were conducted in a heating block. Preparation of plasmid standard The pCS20 and sodB genes of E. ruminantium were amplified by PCR using the F3 and B3 primers of each LAMP primer set. PCR was carried out using
high-fidelity KOD plus DNA polymerase (Toyobo, Tokyo, Japan) in 25-μl reaction mixture containing 1.0 μM of each primer, 200 μM dNTPs, 1.0 unit of KOD plus DNA polymerase, and genomic DNA from E. ruminantium, isolate Welgevonden. Amplification was performed for 25 cycles of 95°C for 15 s, 55°C for 15 s, and 72°C for 1 min, followed by a final extension at 72°C for 2 min. The PCR products were poly-A tailed and Fludarabine research buy then cloned into a pGEM-T vector (Promega, Madison, WI). Each plasmid clone was sequenced on an ABI Prism 3130 genetic analyzer (Applied Fulvestrant Biosystems, Foster City, CA) with BigDye Terminator version 1.1 (Applied Biosystems), to confirm identity, and was used as the standard plasmid for determining the specificity of the respective LAMP assay. The concentrations of plasmid DNA were measured with a Quant-iT dsDNA
BR and Qubit Fluorometer (Invitrogen, Carlsbad, CA) and the corresponding copy numbers were calculated. Assessment of LAMP inhibitors in DNA prepared from blood or ticks Five bovine blood samples and five individual A. variegatum ticks were obtained from heartwater free areas and verified negative for E. ruminantium by LAMP. Total DNA was extracted as described above. The concentrations of DNA were 0.40-16.56 ng/μl and 1.97-4.20 ng/μl for those extracted from bovine blood and A. variegatum, respectively. The standard plasmid was diluted with DNA solution prepared from bovine blood or A. variegatum to give final concentrations of 1, 10, 102, 103, 104 copies of plasmid DNA per microliter. LAMP sensitivity and specificity The sensitivity of each LAMP assay was assessed using each standard plasmid (104, 103, 102, 10, 5, and 1 copies/reaction) in a Loopamp real-time turbidimeter (Model & Maker).