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This was followed by a melting programme of 30 s at 95°C, 30 s at 67°C and 0 s at 95°C at rates of 20, 20, and 0.1°C/s, respectively, and cooling at 40°C for at least 30 s. Multilocus sequence typing (MLST) of 81 isolates was carried out as described previously.
The temperature transition rate was 20°C s−1, except in the melting programme, which was 0.4°C s−1 between 40 and 90°C.
The following programme conditions were applied for qrt-PCR running: denaturation programme, consisting of one cycle at 95°C for 8 min; amplification programme, consisting of 45 cycles at 95°C for 5 s, 60°C for 10 s and 72°C for 15 s; melting programme, one cycle at 95°C for 0 s, 40°C for 60 s and 90°C for 0 s; and cooling programme, one cycle at 40°C for 60 s.
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The melting curve programme was set from 60 °C to 95 °C with a 2%% heating rate and a continuous fluorescence measurement.
For reactions using SYBR Green, a melting curve programme was then performed to check the presence of a single product with a specific melting temperature.
The melting curve programme was 95°C × 5 s and 65°C × 1 min, and then readings were acquired while increasing the temperature by 0.11°C/s to 97°C.
Thermal cycling conditions consisted of polymerase activation at 95 °C for 30 s, followed by 40 cycles of 95 °C for 5 s, 63 °C for 15 s, and 72 °C for 10 s and then a melt programme of 95 °C for 15 s, 55 °C for 15 s, and 95 °C for 15 s.
Additionally, templates were folded and secondary structures avoided using MFold programme and beacon hairpin melting temperatures were calculated using the Zucker software.
The programme was completed after a melting curve analysis in the temperature range of 55 °C to 95 °C.
Analysis of real time PCR reactions and melting point dissociation curve reactions were performed using the programme Rotorgene version 6.0 (Corbett).
Phébus-FP is a multi-national collaborative programme comprising four integral and one debris bed melting and fission product release experiments.
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