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By consequence, potential iron binding sites close to carbonylatable sites promote the effective oxidation of these sites.
We identified 98 binding sites close to 94 unique genes which differ at least 1.2 fold in expression between Actinomycin D and Etoposide (Table S4).
Specifically, we generated mutants for binding sites close to nucleotide 15 (CCTGAACACTGTGA to CCTGAACgggcTGA), nucleotide 236 (GGTTAACCACTGTG to GGTTAACCgggGTG) and nucleotide 465 (TGGGAGCACTTTG to TGGGAGCACgggG).
In addition to that, another important implication for the prediction of CRM or cis-motifs is the overlap between transcription factors which have binding sites close to each other.
According to the data presented here, this model seems to apply for a number of known LXR binding sites close to target genes, such as ABCA1.
We conclude that the higher frequency of CUX1 binding sites close to TSS reflects the preferential recruitment of CUX1 to promoter regions.
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This is presumably because binding sites closer to the edge of the PSD are first to capture mobile receptors.
When probes in every probe set are ordered according to the localization of their binding site in target transcript, the average signal of probes with binding sites closer to the 5′ end of transcripts is shifted toward lower values.
If we assume that the rise was due to simple addition of cofilin molecules at the two binding sites closest to the crossover point, and if the cofilin clusters grow in perfect synchrony along two strands of the double helix, then the crossover points should rise abruptly in one step.
In line with this, we observed a trend of finding ER binding sites closer to the significantly differentially expressed miRNAs between ER-positive and ER-negative cell lines than nonsignificant miRNAs (see Table S19 in Additional file 1 and Figure S4 in Additional file 2).
However, turnover/binding of short chain substrates is dramatically increased by introducing a novel substrate carboxylate binding site close to the heme.
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