ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data.

Genomic variations are in the focus of research to uncover mechanisms of host-pathogen interactions and diseases such as cancer. Nowadays, next-generation sequencing (NGS) data are analyzed through dedicated pipelines to detect them. Surrogate NGS data in conjunction with genomic variations help to evaluate pipelines and validate their outcomes, fostering selection of proper tools for a given scientific question. I describe how existing approaches for simulating NGS data in conjunction with genomic variations fail to model local enrichments of single nucleotide polymorphisms (SNPs), so called SNP clusters. Two distributions for count data are applied to publicly available collections of genomic variations. The results suggest modeling of SNP cluster sizes by overdispersion-aware distributions.

Men and women differ in their diurnal expression of monocyte peroxisome proliferator-activated receptor-α in the fed but not in the fasted state.

Peroxisome proliferator-activated receptor-α (PPARα) plays a pivotal role in regulating metabolic response to fasting and is an inhibitor of inflammatory pathways in immune cells. It represents a therapeutic target for treatment of several diseases, mainly hyperlipidemia. To shed light on PPARα expression changes in response to fasting, young healthy male and female volunteers were fed or fasted for 24 hours. Monocytes were analyzed every 2 hours to compile both profiles of mRNA and protein expression of PPARα and its interactive partner, the circadian pacemaker brain and muscle aryl hydrocarbon receptor nuclear translocator like-1 (BMAL1). We found that women change their diurnal expression profiles of PPARα and BMAL1 when switching from the fed to the fasted state, whereas men do not. Interestingly, the PPARα and BMAL1 profiles of men and women in the fed state are different, whereas the profiles in the fasted state are virtually identical. The finding of diametrically opposite responses of male and female PPARα expression in the fed state might have practical implication in human medicine as PPARα activators like fibrates are used for the therapy of chronic lymphocytic leukemia, microvascular complications in diabetes, and kidney diseases.