Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT... Show moreNucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family. Show less
We abstract the concept of a randomized controlled trial as a triple (beta,b,s), where beta is the primary efficacy parameter, b the estimate, and s the standard error (s>0). If the parameter... Show moreWe abstract the concept of a randomized controlled trial as a triple (beta,b,s), where beta is the primary efficacy parameter, b the estimate, and s the standard error (s>0). If the parameter beta is either a difference of means, a log odds ratio or a log hazard ratio, then it is reasonable to assume that b is unbiased and normally distributed. This then allows us to estimate the joint distribution of the z-value z=b/s and the signal-to-noise ratio SNR=beta/s from a sample of pairs (bi,si). We have collected 23 551 such pairs from the Cochrane database. We note that there are many statistical quantities that depend on (beta,b,s) only through the pair (z,SNR). We start by determining the estimated distribution of the achieved power. In particular, we estimate the median achieved power to be only 13%. We also consider the exaggeration ratio which is the factor by which the magnitude of beta is overestimated. We find that if the estimate is just significant at the 5% level, we would expect it to overestimate the true effect by a factor of 1.7. This exaggeration is sometimes referred to as the winner's curse and it is undoubtedly to a considerable extent responsible for disappointing replication results. For this reason, we believe it is important to shrink the unbiased estimator, and we propose a method for doing so. We show that our shrinkage estimator successfully addresses the exaggeration. As an example, we re-analyze the ANDROMEDA-SHOCK trial. Show less
