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Thresholds chosen for WT vs. mutant analyses were 1.5-fold minimum change between WT and KO and difference ≥50, and probe sets in both Picciotto and Xu mutants had to differ from WT in the same direction (i.e., either overexpressed in WT or overexpressed in both mutants).
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Further studies using both ribosomal profiling as well as specific mutant analyses are required to advance our understanding of these novel regulatory mechanisms.
These sorts of analyses may also be used much in the same way as mutant analyses are used to identify genes involved in a specific process (i.e., R or S).
These double mutant analyses are consistent with PTRN-1 and TAC-1 acting in a common pathway in regeneration, with EFA-6 acting as a negative regulator of one or both proteins.
All the mutants analysed are affected in the hnwd gene involved in the system.
The other mutants analysed are able to bind to pRb but, with the exception of S31G/S32G in raft culture, are unable to induce tetrasomy.
Due to the absence of an RpoN deletion mutant, our analyses were restricted to the use of an RpoN over-expressing strain.
To check this suspected mutant, Southern hybridization analyses were employed using probes of SpcR gene, an internal fragment of salKR, and pUC18, respectively.
2) Clarifications re phenotypic characterization: Phenotypes were compared in detail between llg1 and fer, but double mutant and epistatic analyses were not performed.
Among these measurements, the data obtained with mutant cycle analyses are more reliable in gauging residue proximities on either side of the toxin-channel interface.
Mutant generation and molecular analyses were performed by VR SAS, VR, NMD, BCM, SMM and MR edited the manuscript.
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