An observation of circular RNAs in bacterial RNA-seq data

Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from {\it Enterococcus faecalis} and {\it Escherichia coli} in a way similar to previous studies performed on eukaryotes. We report observations of circRNAs in RNA-seq data that are reproducible across multiple experiments performed with different protocols or growth conditions

Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends

High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when sequencing RNA fragments from one end, as it is the case on most platforms, an oscillation in the read count is observed at the other end. We further show that these oscillations can be well described by Kolmogorov's 1941 broken stick model. We investigate how the model can be used to improve predictions of gene ends (3' transcript ends) but conclude that with present data the improvement is only marginal. The results highlight subtle effects in high-throughput transcriptomics experiments which do not have a biological origin, but which may still be used to obtain biological information

Landscape of RNA polyadenylation in E-coli

Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5 '-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A) polymerase deleted Mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A) polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A) polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3 '-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.Peer reviewe

Mechanistic understanding of microstructure formation during synthesis of metal oxide/carbon nanocomposites

Nanocomposite materials consisting of metal oxide and carbon are of interest as electrode materials for both high rate intercalation-type and high capacity conversion-type charge storage processes. Facile synthesis processes like the pyrolysis of an organic carbon-source can yield a well-dispersed carbon phase within the metal oxide structure. Detailed understanding of the carbon formation process is required to tailor the resulting material microstructure. Herein, both the formation and the final microstructure of a molybdenum oxide/carbon nanocomposite are studied in detail. Octylamine assembled in the interlayer space of layered MoO3 serves as a carbon source. The structural changes during pyrolysis are characterized using a combination of in situ heating X-ray diffraction with simultaneous FTIR- and mass spectroscopy-coupled thermogravimetric analysis experiments. These reveal mobility and partial desorption of octylamine and interlayer water at low temperatures, octylamine decomposition and loss of long-range order at intermediate temperatures, and carbothermic reduction of molybdenum oxide at high temperatures during pyrolysis. The resulting nanocomposite mainly contains nanocrystalline MoO2 domains surrounded by a well-dispersed carbon phase, as observed with scanning transmission electron microscopy of focus-ion beam prepared cross-sectional lamellae. The electrochemical behavior is evaluated in organic, lithium-containing electrolyte for both intercalation and conversion-type reactions, showing good intercalation kinetics and a high first cycle efficiency for the conversion-type reaction

Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5'RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites and 352 processing sites in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding TSSs mapped. We discovered 95 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organisations. Presented data constitute a significant insight into bacterial RNA landscapes and a step towards the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner

EUropean Heliospheric FORecasting Information Asset 2.0

Aims: This paper presents a H2020 project aimed at developing an advanced space weather forecasting tool, combining the MagnetoHydroDynamic (MHD) solar wind and coronal mass ejection (CME) evolution modelling with solar energetic particle (SEP) transport and acceleration model(s). The EUHFORIA 2.0 project will address the geoeffectiveness of impacts and mitigation to avoid (part of the) damage, including that of extreme events, related to solar eruptions, solar wind streams, and SEPs, with particular emphasis on its application to forecast geomagnetically induced currents (GICs) and radiation on geospace. Methods: We will apply innovative methods and state-of-the-art numerical techniques to extend the recent heliospheric solar wind and CME propagation model EUHFORIA with two integrated key facilities that are crucial for improving its predictive power and reliability, namely (1) data-driven flux-rope CME models, and (2) physics-based, self-consistent SEP models for the acceleration and transport of particles along and across the magnetic field lines. This involves the novel coupling of advanced space weather models. In addition, after validating the upgraded EUHFORIA/SEP model, it will be coupled to existing models for GICs and atmospheric radiation transport models. This will result in a reliable prediction tool for radiation hazards from SEP events, affecting astronauts, passengers and crew in high-flying aircraft, and the impact of space weather events on power grid infrastructure, telecommunication, and navigation satellites. Finally, this innovative tool will be integrated into both the Virtual Space Weather Modeling Centre (VSWMC, ESA) and the space weather forecasting procedures at the ESA SSCC in Ukkel (Belgium), so that it will be available to the space weather community and effectively used for improved predictions and forecasts of the evolution of CME magnetic structures and their impact on Earth. Results: The results of the first six months of the EU H2020 project are presented here. These concern alternative coronal models, the application of adaptive mesh refinement techniques in the heliospheric part of EUHFORIA, alternative flux-rope CME models, evaluation of data-assimilation based on Karman filtering for the solar wind modelling, and a feasibility study of the integration of SEP models

Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer

We performed a multistage genome-wide association study including 7,683 individuals with pancreatic cancer and 14,397 controls of European descent. Four new loci reached genome-wide significance: rs6971499 at 7q32.3 (LINC-PINT, per-allele odds ratio (OR) = 0.79, 95% confidence interval (CI) 0.74-0.84, P = 3.0 x 10(-12)), rs7190458 at 16q23.1 (BCAR1/CTRB1/CTRB2, OR = 1.46, 95% CI 1.30-1.65, P = 1.1 x 10(-10)), rs9581943 at 13q12.2 (PDX1, OR = 1.15, 95% CI 1.10-1.20, P = 2.4 x 10(-9)) and rs16986825 at 22q12.1 (ZNRF3, OR = 1.18, 95% CI 1.12-1.25, P = 1.2 x 10(-8)). We identified an independent signal in exon 2 of TERT at the established region 5p15.33 (rs2736098, OR = 0.80, 95% CI 0.76-0.85, P = 9.8 x 10(-14)). We also identified a locus at 8q24.21 (rs1561927, P = 1.3 x 10(-7)) that approached genome-wide significance located 455 kb telomeric of PVT1. Our study identified multiple new susceptibility alleles for pancreatic cancer that are worthy of follow-up studies