Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension

The role of alternative promoter usage in tissue-specific gene expression has been well established, however, its role in complex diseases is poorly understood. We performed cap analysis of gene expression (CAGE) sequencing from the left ventricle (LV) of a rat model of hypertension, the spontaneously hypertensive rat (SHR), and a normotensive strain, Brown Norway (BN) to understand the role of alternative promoter usage in complex disease. We identified 26,560 CAGE-defined transcription start sites (TSS) in the rat LV, including 1,970 novel cardiac TSSs. We identified 28 genes with alternative promoter usage between SHR and BN, which could lead to protein isoforms differing at the amino terminus between two strains and 475 promoter switching events altering the length of the 5’ UTR. We found that the shift in Insr promoter usage was significantly associated with insulin levels and blood pressure within a panel of HXB/BXH recombinant inbred rat strains, suggesting that hyperinsulinemia due to insulin resistance might lead to hypertension in SHR. Our study provides a preliminary evidence of alternative promoter usage in complex diseases

Private hospital workflow optimization via secure k-means clustering

Optimizing the workflow of a complex organization such as a hospital is a difficult task. An accurate option is to use a real-time locating system to track locations of both patients and staff. However, privacy regulations forbid hospital management to assess location data of their staff members. In this exploratory work, we propose a secure solution to analyze the joined location data of patients and staff, by means of an innovative cryptographic technique called Secure Multi-Party Computation, in which an additional entity that the staff members can trust, such as a labour union, takes care of the staff data. The hospital, owning location data of patients, and the labour union perform a two-party protocol, in which they securely cluster the staff members by means of the frequency of their patient facing times. We describe the secure solution in detail, and evaluate the performance of our proof-of-concept. This work thus demonstrates the feasibility of secure multi-party clustering in this setting

Inception and propagation of positive streamers in high-purity nitrogen: effects of the voltage rise-rate

Controlling streamer morphology is important for numerous applications. Up to now, the effect of the voltage rise rate was only studied across a wide range. Here we show that even slight variations in the voltage rise can have significant effects. We have studied positive streamer discharges in a 16 cm point-plane gap in high-purity nitrogen 6.0, created by 25 kV pulses with a duration of 130 ns. The voltage rise varies by a rise rate from 1.9 kV/ns to 2.7 kV/ns and by the first peak voltage of 22 to 28 kV. A structural link is found between smaller discharges with a larger inception cloud caused by a faster rising voltage. This relation is explained by the greater stability of the inception cloud due to a faster voltage rise, causing a delay in the destabilisation. Time-resolved measurements show that the inception cloud propagates slower than an earlier destabilised, more filamentary discharge. This explains that the discharge with a faster rising voltage pulse ends up to be shorter. Furthermore, the effect of remaining background ionisation in a pulse sequence has been studied, showing that channel thickness and branching rate are locally affected, depending on the covered volume of the previous discharge.Comment: 16 pages, 9 figure

Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

RNA-binding proteins (RBPs) are key regulators of RNA metabolism. Many RBPs possess uncharacterized RNA-binding domains and localize to multiple subcellular compartments, suggesting their involvement in multiple biological processes. We searched for such multifunctionality within a set of 143 RBPs by integrating experimentally validated target genes with the transcriptomes and translatomes of 80 human hearts. This revealed that RBP abundance is predictive of the extent of target regulation in vivo, leading us to newly associate 27 RBPs with translational control. Amongst those were several splicing factors, of which the muscle specific RBM20 modulated target translation rates through switches in isoform production. For 21 RBPs, we newly observed dual regulatory effects impacting both mRNA levels and translation rates, albeit for virtually independent sets of target genes. We highlight a subset, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved by differential affinity for targets of distinct length and functionality. Strikingly, in a manner very similar to DDX3X, the known splicing factors EFTUD2 and PRPF8 selectively influence target translation rates depending on 5’ UTR structure. Our results indicate unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression and implicate multiple core splicing factors as key regulators of translational output

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8 - all identified as multifunctional RBPs by our analysis - selectively influence target translation rates depending on 5' UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression

Probing photo-ionization: simulations of positive streamers in varying N2:O2 mixtures

Photo-ionization is the accepted mechanism for the propagation of positive streamers in air though the parameters are not very well known; the efficiency of this mechanism largely depends on the presence of both nitrogen and oxygen. But experiments show that streamer propagation is amazingly robust against changes of the gas composition; even for pure nitrogen with impurity levels below 1 ppm streamers propagate essentially with the same velocity as in air, but their minimal diameter is smaller, and they branch more frequently. Additionally, they move more in a zigzag fashion and sometimes exhibit a feathery structure. In our simulations, we test the relative importance of photo-ionization and of the background ionization from pulsed repetitive discharges, in air as well as in nitrogen with 1 ppm O2 . We also test reasonable parameter changes of the photo-ionization model. We find that photo- ionization dominates streamer propagation in air for repetition frequencies of at least 1 kHz, while in nitrogen with 1 ppm O2 the effect of the repetition frequency has to be included above 1 Hz. Finally, we explain the feather-like structures around streamer channels that are observed in experiments in nitrogen with high purity, but not in air.Comment: 12 figure

Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension

The role of alternative promoter usage in tissue-specific gene expression has been well established; however, its role in complex diseases is poorly understood. We performed cap analysis of gene expression (CAGE) sequencing from the left ventricle of a rat model of hypertension, the spontaneously hypertensive rat (SHR), and a normotensive strain, Brown Norway to understand the role of alternative promoter usage in complex disease. We identified 26,560 CAGE-defined transcription start sites in the rat left ventricle, including 1,970 novel cardiac transcription start sites. We identified 28 genes with alternative promoter usage between SHR and Brown Norway, which could lead to protein isoforms differing at the amino terminus between two strains and 475 promoter switching events altering the length of the 5' UTR. We found that the shift in Insr promoter usage was significantly associated with insulin levels and blood pressure within a panel of HXB/BXH recombinant inbred rat strains, suggesting that hyperinsulinemia due to insulin resistance might lead to hypertension in SHR. Our study provides a preliminary evidence of alternative promoter usage in complex diseases