Utilization of tmRNA sequences for bacterial identification

In recent years, molecular approaches based on nucleotide sequences of ribosomal RNA (rRNA) have become widely used tools for identification of bacteria [1-4]. The high degree of evolutionary conservation makes 16S and 23S rRNA molecules very suitable for phylogenetic studies above the species level [3-5]. More than 16,000 sequences of 16S rRNA are presently available in public databases [4,6]. The 16S rRNA sequences are commonly used to design fluorescently labeled oligonucleotide probes. Fluorescence in situ hybridization (FISH) with these probes followed by observation with epifluorescence microscopy allows the identification of a specific microorganism in a mixture with other bacteria [2-4]. By shifting probe target sites from conservative to increasingly variable regions of rRNA, it is possible to adjust the probe specificity from kingdom to species level. Nevertheless, 16S rRNA sequences of closely related strains, subspecies, or even of different species are often identical and therefore can not be used as differentiating markers [3]. Another restriction concerns the accessibility of target sites to the probe in FISH experiments. The presence of secondary structures, or protection of rRNA segments by ribosomal proteins in fixed cells can limit the choice of variable regions as in situ targets for oligonucleotide probes [7,8]. One way to overcome the limitations of in situ identification of bacteria is to use molecules other than rRNA for phylogenetic identification of bacteria, for which nucleotide sequences would be sufficiently divergent to design species specific probes, and which would be more accessible to oligonucleotide probes. For this purpose we investigated the possibility of using tmRNA (also known as 10Sa RNA; [9-11]). This molecule was discovered in E. coli and described as small stable RNA, present at ~1,000 copies per cell [9,11]. The high copy number is an important prerequisite for FISH, which works best with naturally amplified target molecules. In E. coli, tmRNA is encoded by the ssrA gene, is 363 nucleotides long and has properties of tRNA and mRNA [12,13]. tmRNA was shown to be involved in the degradation of truncated proteins: the tmRNA associates with ribosomes stalled on mRNAs lacking stop codons, finally resulting in the addition of a C-terminal peptide tag to the truncated protein. The peptide tag directs the abnormal protein to proteolysis [14,15]. 165 tmRNA sequences have so far (August 2001; The tmRNA Website: http://www.indiana.edu/~tmrna/) been determined [16,17]. The tmRNA is likely to be present in all bacteria and has also been found in algae chloroplasts, the cyanelle of Cyanophora paradoxa and the mitochondrion of the flagellate Reclinomonas americana[10,17,18]

Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification

The substrate fluorescein-tyramide was combined with oligonucleotide probes directly labeled with horseradish peroxidase to improve the sensitivity of in situ hybridization of whole fixed bacterial cells. Flow cytometry and quantitative microscopy of cells hybridized by this technique showed 10- to 20-fold signal amplifications relative to fluorescein-manolabeled probes. The application of the new technique to the detection of natural bacterial communities resulted in very bright signals; however, the number of detected cells was significantly lower than that detected with fluorescently monolabeled, rRNA-targeted oligonucleotide probes

Simulation of polarimetric radar variables in rain at S-, C- and X-band wavelengths

International audiencePolarimetric radar variables of rainfall events, like differential reflectivity ZDR, or specific differential phase KDP, are better suited for estimating rain rate R than just the reflectivity factor for horizontally polarized waves, ZH. A variety of physical and empirical approaches exist to estimate the rain rate from polarimetric radar observables. The relationships vary over a wide range with the location and the weather conditions. In this study, the polarimetric radar variables were simulated for S-, C- and X-band wavelengths in order to establish radar rainfall estimators for the alpine region of the form R(KDP), R(ZH, ZDR), and R(KDP), ZDR. For the simulation drop size distributions of hundreds of 1-minute-rain episodes were obtained from 2D-Video-Distrometer measurements in the mountains of Styria, Austria. The sensitivity of the polarimetric variables to temperature is investigated, as well as the influence of different rain drop shape models ? including recently published ones ? on radar rainfall estimators. Finally it is shown how the polarimetric radar variables change with the elevation angle of the radar antenna

Sugden’s team preferences

In this paper, I presented Sugden’s theory of team reasoning. I argued that (A), Sugden’s theory is not able to sufficiently account for challenges between individual self-interest and team goals. The point I made is that there is a difference between saying that individuals engage in team-directed reasoning and have to solve a coordination or cooperation problem together, and claiming that, because of engaging in team-directed reasoning, self-interest will be ignored. (B) Exploiting this argument, I proposed to think of team-directed reasoning as an agent being aware of the group goal, but that this way of thinking does not lead one to ignore their self-interest. However, I showed that on this account, teamdirected reasoning does not solve coordination problems anymore. Hence, I conclude that team-directed reasoning does not offer a solution to coordination and cooperation problems

Simulation of polarimetric radar variables in rain at S-, C- and X-band wavelengths

International audience(clôture d'une controverse non ouverte)

Further evidence for superterminal raindrops

A network of optical disdrometers (including laser precipitation monitors and a two‐dimensional video disdrometer) was utilized to determine whether the recent reports of “superterminal” raindrops were spurious results of drop breakup occurring on instrumentation. Results unequivocally show that superterminal raindrops at small (less than 1 mm) sizes are ubiquitous, are measurable over an extended area, and appear in every rain event investigated. No evidence was found to suggest that superterminal drops are the result of drop breakup due to impact with the measurement instrument; thus, if the superterminal drops are the result of drop fragmentation, this fragmentation happens in the ambient atmosphere during all rain events measured in this study. The ubiquity of superterminal drops at small drop sizes raises natural questions regarding rain accumulation estimations, estimates of drop size distributions, and erosion characterization