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

Spin-helix Larmor mode

International audienceA two-dimensional electron gas (2DEG) with equal-strength Rashba and Dresselhaus spin-orbit coupling sustains persistent helical spin-wave states, which have remarkably long lifetimes. In the presence of an in-plane magnetic field, there exist single-particle excitations that have the character of propagating helical spin waves. For magnon-like collective excitations, the spin-helix texture reemerges as a robust feature, giving rise to a decoupling of spin-orbit and electronic many-body effects. We prove that the resulting spin-flip wave dispersion is the same as in a magnetized 2DEG without spin-orbit coupling, apart from a shift by the spin-helix wave vector. The precessional mode about the persistent spin-helix state is shown to have an energy given by the bare Zeeman splitting, in analogy with Larmor’s theorem. We also discuss ways to observe the spin-helix Larmor mode experimentally

Gate-controlled persistent spin helix state in (In,Ga)As quantum wells

In layered semiconductors with spin-orbit interaction (SOI) a persistent spin helix (PSH) state with suppressed spin relaxation is expected if the strengths of the Rashba and Dresselhaus SOI terms, α and β, are equal. Here we demonstrate gate control and detection of the PSH in two-dimensional electron systems with strong SOI including terms cubic in momentum. We consider strain-free InGaAs/InAlAs quantum wells and first determine a ratio α/β≃1 for nongated structures by measuring the spin-galvanic and circular photogalvanic effects. Upon gate tuning the Rashba SOI strength in a complementary magnetotransport experiment, we monitor the complete crossover from weak antilocalization via weak localization to weak antilocalization, where the emergence of weak localization reflects a PSH-type state. A corresponding numerical analysis reveals that such a PSH-type state indeed prevails even in presence of strong cubic SOI, however no longer at α=β

In situ detection of Escherichia coli cells containing ColE1-related plasmids by hybridization to regulatory RNA II

A method is described for the in situ detection of individual whole fixed cells of Escherichia coli containing ColE1-related plasmids. It makes use of fluorescence in situ hybridization (FISH) and the regulatory RNA II as a target molecule for both, Cy3- and HRP-labeled olinucleotide probes. Various methods for signal amplification were compared. Probes targeting the regulatory RNA I did not result in the in situ detection of plasmid-bearing cells

Identification of bacteria associated with Dinoflagellates (Dinophyceae) Alexandrium spp. using tyramide signal amplification fluorescent in situ hybridization and confocal microscopy

In the marine environment, phytoplankton and bacterioplankton can be physically associated. Such association has recently been hypothesized to be involved in the toxicity of the dinoflagellate genus Alexandrium. However, the methods, which have been used so far to identify, localize, and quantify bacteria associated with phytoplankton, are either destructive, time consuming, or lack precision. In the present study we combined tyramide signal amplification–fluorescent in situ hybridization (TSA-FISH) with confocal microscopy to determine the physical association of dinoflagellate cells with bacteria. Dinoflagellate attached microflora was successfully identified with TSA-FISH, whereas FISH using monolabeled probes failed to detect bacteria, because of the dinoflagellate autofluorescence. Bacteria attached to entire dinoflagellates were further localized and distinguished from those attached to empty theca, by using calcofluor and DAPI, two fluorochromes that stain dinoflagellate theca and DNA, respectively. The contribution of specific bacterial taxa of attached microflora was assessed by double hybridization. Endocytoplasmic and endonuclear bacteria were successfully identified in the nonthecate dinoflagellate Gyrodinium instriatum. In contrast, intracellular bacteria were not observed in either toxic or nontoxic strains of Alexandrium spp. Finally, the method was successfully tested on natural phytoplankton assemblages, suggesting that this combination of techniques could prove a useful tool for the simultaneous identification, localization, and quantification of bacteria physically associated with dinoflagellates and more generally with phytoplankton

Ka-band propagation campaign in Malaysia - first months of operation and site diversity analysis

Satellite communication systems operating at high frequencies (Ka-band and above) are severely impaired by atmospheric phenomena, particularly in tropical and equatorial regions, where the climatic characteristics affect several propagation parameters, including rain, cloud and gaseous attenuation, fade duration, fade slope, sky noise emission and site diversity gain. With the support of the Austrian Research Promotion Agency, a Ka-band propagation measurement campaign is being carried out in two sites in Malaysia. The main objectives of this campaign are to improve the characterization of the radio channel modelling and ground system requirements for the development of Ka-band SatCom systems covering tropical regions, assess the accuracy of current prediction models with particular regard to the statistical distribution of rain attenuation, and improve the statistical models for the parameters describing signal fade duration, signal fade slope and gain of site and time diversity techniques. This paper presents the campaign, describing the experimental site locations, the ground propagation terminals, the ancillary equipment and the data processing. Finally, the rain, attenuation and site diversity gain statistics during the first six months of measurements are presented