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For all SPR assays, the surfaces were regenerated between sample injections at 50 µl min−1 with a 30 s single pulse of 0.4 M NaCl followed by a stabilization time after regeneration of 3 min. The assays were performed in duplicates with different batches of purified proteins.
AGS cells, (3.2×106) maintained in RPMI 1640 medium (Gibco BRL, Life Technologies, Grand Island, USA) were transiently transfected in duplicates with different amounts of DNA as required for the specific experiment by using Lipofectamine2000 Reagent (Invitrogen, Life Technologies, Carlsbad, USA) according to the manufacturer's protocol.
Both copies evolved further tandem duplicates with different substrate specificities (Li et al. 2008).
In other words, 2R-WGD most likely resulted in retention of duplicates with different signalling inputs but similar outputs.
Hence we took this into consideration in this study by defining gene duplicates with different identity criteria.
Sequence duplicates with different names were identified using BLASTCLUST [ 62] with the threshold set at 99% sequence identity.
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The experiments were performed at least twice, each at least in duplicate (with different batches of cells and at different time periods).
In this study, 14 experiments were designed and carried out in duplicate with different range of the independent variables, reflux temperature (X 1 °C50–80 °C) and extraction time (X 2 : 2–4 h).
Transfected cells were incubated in duplicate with different concentrations (10-6 to 10-11M) of the human VIP, PACAP38 and secretin (SCT) peptides and ovine PACAP27 peptide for 30 minutes (Sigma-Aldrich, Spain).
In this study, 20 experiments were designed and carried out in duplicate with different ranges of ultrasonic power, methanol concentration, and extraction temperature, which are presented in Table 1.
We categorized duplicate pairs as either relocalized (duplicate proteins with different predicted subcellular locations) or nonrelocalized (duplicates with identical predicted subcellular locations).
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