ABSTRACTmRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease.

Abstract. The Whole Atmosphere Community Climate Model (WACCM) is utilised to study the daily ozone cycle and underlying photochemical and dynamical processes. The analysis is focused on the daily ozone cycle in the middle stratosphere at 5 hPa where satellite-based trend estimates of stratospheric ozone are most biased by diurnal sampling effects and drifting satellite orbits. The simulated ozone cycle shows a minimum after sunrise and a maximum in the late afternoon. Further, a seasonal variation of the daily ozone cycle in the stratosphere was found. Depending on season and latitude, the peak-to-valley difference of the daily ozone cycle varies mostly between 3 and 5 % (0.4 ppmv) with respect to the midnight ozone volume mixing ratio. The maximal variation of 15 % (0.8 ppmv) is found at the polar circle in summer. The global pattern of the strength of the daily ozone cycle is mainly governed by the solar zenith angle and the sunshine duration. In addition, we find synoptic-scale variations in the strength of the daily ozone cycle. These variations are often anti-correlated to regional temperature anomalies and are due to the temperature dependence of the rate coefficients k 2 and k 3 of the Chapman cycle reactions. Further, the NO x catalytic cycle counteracts the accumulation of ozone during daytime and leads to an anti-correlation between anomalies in NO x and the strength of the daily ozone cycle. Similarly, ozone recombines with atomic oxygen which leads to an anti-correlation between anomalies in ozone abundance and the strength of the daily ozone cycle. At higher latitudes, an increase of the westerly (easterly) wind cause a decrease (increase) in the sunshine duration of an air parcel leading to a weaker (stronger) daily ozone cycle.

Abstract. The ground-based radiometer GROMOS, stationed in Bern (47.95 • N, 7.44 • E), Switzerland, has a unique data set: it obtains ozone profiles from November 1994 to present with a time resolution of 30 min and equivalent quality during night-and daytime. Here, we derive a monthly climatology of the daily ozone cycle from 17 years of GRO-MOS observation. We present the diurnal ozone variation of the stratosphere and mesosphere. Characterizing the diurnal cycle of stratospheric ozone is important for correct trend estimates of the ozone layer derived from satellite observations. The diurnal ozone cycle from GROMOS is compared to two models: the Whole Atmosphere Community Climate Model (WACCM) and the Hamburg Model of Neutral and Ionized Atmosphere (HAMMONIA). Generally, observation and models show a good agreement: in the lower mesosphere, daytime ozone is for both GROMOS and models around 25 % less than midnight ozone. In the stratosphere, ozone reaches its maximum in the afternoon showing values several percent larger than the midnight value. Further, GROMOS and models indicate a seasonal behaviour of the diurnal ozone variations in the stratosphere with a larger afternoon maximum during daytime in summer than in winter. Using the 17 years of ozone profiles from GROMOS, we find strong interannual variations in the diurnal ozone cycle for both the stratosphere and the mesosphere. Interannual variability in temperature, atmospheric circulation and composition may explain the observed interannual variability of the diurnal ozone cycle above Bern.