Prospects for photostimulation of nisin biosynthesis

The purpose of the article was to study the effect of blue spectrum light on the nisin producer Lactobacillus lactis. It was found that photostimulation of a Lactobacillus Lactis culture with blue spectrum light (435-470 nm) with a light flux intensity of 1800 mcd for 50-60 minutes positively affects the activity of nisin (increases by 60.1%), while the titer of the Lactobacillus culture lactis is 2 times higher. At the same time, there is a slight decrease in nisin titer after 24 hours of incubation, which is explained by the peculiarities of nisin biosynthesis: nisin is less active at the beginning of biosynthesis; during the period of the exponential growth phase, an increase in the biosynthesis of nisin is noted; the greatest activity of nisin is noted at the beginning of the stationary phase; nisin synthesis is reduced in the middle of the stationary phase of the cells; self-regulation of nisin synthesis (increased nisin synthesis leads to increased competition for metabolites of the substrate and energy material, nisin molecules act as an external factor that regulates synthesis). Light treatment of the nisin producer Lactobacillus lactis increases its resistance to oxidative stress and enhances its viability. As a result of studies during storage of the Lactobacillus lactis culture in skimmed milk, the positive effect of light on the high preservation of nisin activity was proved. Thus, photostimulation of the bioproducer of nisin - Lactobacillus Lactis culture with blue light with a light flux intensity of 1800 mcd for 50-60 minutes has a positive effect on its viability and allows us to recommend the use of blue light to increase nisin production. © Published under licence by IOP Publishing Ltd

GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks

Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GR aNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation