Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity.

Underuse of statins for secondary prevention of atherosclerotic cardiovascular disease events among ambulatory surgical patients.

Although statins are highly effective for reducing cardiovascular disease events, prior studies demonstrate their significant underuse in the US population, including among those with known atherosclerotic disease. It is unknown whether this finding applies to the subset of patients who present for outpatient surgery, as such patients would be expected to have recent exposures to healthcare providers during the preoperative referral period. The primary aim of this manuscript was to ascertain the prevalence of statin underuse and associated risk-factors for such underuse among ambulatory surgical patients with documented atherosclerotic cardiovascular disease.

Characterizing the DNA binding site specificity of NF-κB with protein-binding microarrays (PBMs).

NF-κB transcription factors control a wide array of important cellular and organismal processes in eukaryotes. All NF-κB transcription factors bind to DNA target sites as dimers. In vertebrates, there are five NF-κB subunits, p50, p52, RelA (p65), c-Rel, and RelB, that can form almost all combinations of homodimers and heterodimers, which recognize distinct, but overlapping, target sequences.

Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.

A major challenge in obtaining a full molecular description of evolutionary adaptation is to characterize how transcription factor (TF) DNA-binding specificity can change. To identify mechanisms of TF diversification, we performed detailed comparisons of yeast C2H2 ZF proteins with identical canonical recognition residues that are expected to bind the same DNA sequences. Unexpectedly, we found that ZF proteins can adapt to recognize new binding sites in a modular fashion whereby binding to common core sites remains unaffected.