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While ChIP protocols generally include bovine serum albumin as a carrier (e.g. [ 30]), Zwart and coworkers speculate that combined oligonucleotide RNA and histones mimic chromatin better, and hence offer improved blocking of spurious binding.
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The avoidance of spurious binding could represent considerable energetic savings by allowing transcription to proceed with minimal numbers of RNAP molecules per cell.
The different response to selection suggests that the deleterious fitness effects of spurious binding are much larger than the potential benefits of finely tuned regulation of gene expression via over-representation of −10 sites, at least in host-associated bacteria.
Clearly, the present model also allows for pathways of negative selection leading to the elimination of spurious binding sites in regulatory or non-regulatory DNA where the binding has an adverse fitness effect.
The NEXT-peak program also provides a goodness-of-fit test, automating screening of the spurious binding, and work is in progress to extend its model to locate multiple binding events in a region.
By an analogous reasoning, the low numbers of tRNA genes and the absence of adaptive codon biases in these species suggest that avoidance of RNAP spurious binding is a stronger constraint than optimization of speed and accuracy during translation.
Most of the analyzed genomes having minimum generation times between 40 minutes and 3 hours do not display any evidence of selection against spurious binding, suggesting that high efficiency during transcription is not critical at intermediate growth rates.
Because there is no reason to expect any selection for −10 σ70 motifs in nonfunctional regions, these NSD values may be interpreted as the baseline strength of selection against spurious binding in a given genome.
Blocking of unspecific binding was performed with FCS/TRIS 20%.
Blocking of unspecific binding sites was not necessary.
Blocking of unspecific binding was performed with 2% BSA/PBS.
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