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The specificity of the PCR product was confirmed by sequencing with BigDyeTM terminator chemistry using the genetic analyser ABI Prism 310 (Applied Biosystems), β-2-microglobulin (as control for sample integrity) was amplified in the amplification mixture described above and using the following primers: 5'-TCTGGGTTTCATCCATCCGA-3' and 5'-CCCCAAATTCTAAGCAGAGTATGTAA-3'.
Five hundred μL of lysed cells (1 50) were added to 2.45 mL of the mixture described above; then 50 μL of xanthine oxidase, at a final concentration of 2.8 U/L, were added and incubated in a water bath at 27°C for 15 min. The reaction was stopped with 1 mL of 0.8 mM cupric chloride and the optical density was read at 560 nm.
The ligation mixture described above was electroporated into ElectroMAX DH5α-E competent cells (Invitrogen) and the transformed cells plated on 10 cm LB agar plates containing 50 ug/ml carbenicillin.
The N-AMF treatment was not analyzed in experiment 1 but the soil was used as a non-mycorrhizal control in experiment 2. Each rectangular mesocosm (45 cm long×30 cm wide×20 cm high) with a volume of 27 L was filled with 16 kg of the sterilized loam-sand mixture described above.
Because the primer pairs Pq3469, Pq3423 and Pq3313 are suitable for multiplex PCR, they were added to one tube with 1/3 concentrates of the mixture described above.
For the second round of PCR, 2 μL of the PCR product from the first round was added to the 23-μL reaction mixture described above.
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Data analysis After software baseline subtraction, the ratio of peak heights for derivatized natural AA-AMP and d15-AA-AMP was determined for the assay mixtures described above.
Cell lines seeded in 24 well plates in quadruplicates at 1×104 cells/well were incubated with Ad5 gl) in the mixtures described above for 30min.
A459 cells were seeded in 12 well plates in quadruplicates at 15×104 cells/well were incubated with virus in mixtures described above for 30 min. Infection media was replaced with fresh growth media containing 10% FCS and cell monolayers were incubated for 2h, 6h, 18h, 30h, 42h, 54 or 66h.
Samples from reaction mixtures described above were applied to a holey carbon film 400 mesh copper grid (Quantifoil Micro Tools GmbH, Jena, Germany) and manually plunge-frozen in liquid-nitrogen-cooled liquified ethane.
To test for the elicitation of human BLyS-specific antibodies following immunization of mice with the BLyS-containing recombinant proteins and mixtures described above, ELISA assays were performed as described above, except that the microtiter plates were coated with recombinant BLyS (2 μg/ml, 100 μl/well).
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