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]

Adding low-dose antidepressants to interferon alpha treatment for chronic hepatitis C improved psychiatric tolerability in a patient with schizoaffective psychosis

Treatment of chronic hepatitis C with interferon alpha (IFN-alpha) is relatively contraindicated in patients with psychiatric disorders because of possible severe psychiatric side effects. We report on a case of a female patient with a chronic schizoaffective psychosis, who was treated for 3 months with 3 x 3 mio IE IFN-alpha s.c./week because of a chronic hepatitis C (genotype Ib). Psychosis was stable with flupentixol monotherapy. After 2 months, she developed a severe depressive syndrome which lead to suicidal ideation. Until this time, she was without any antidepressive medication. Depressive symptoms disappeared after interferon therapy was stopped. Under prophylactic treatment with low-dose trimipramine (50 mg) or nefazodone (200 mg/day) therapy with IFN-alpha 3 x 3 mio IE/week was re-established after several months and again 2 years later adding ribavirin 1200 mg/day, a virustaticum. In contrast to the symptoms during monotherapy with IFN-alpha, during the time of both combination treatments, no psychiatric side effects occurred. While for ribavirin antidepressant effects are not known, we suppose that antidepressants may in serotonergic or noradrenergic caused by IFN-alpha. prevent changes neurotransmission caused by IFN-alpha. Copyright (C) 2000 S. Karger AG, Basel

Antiphase dynamics in a multimode semiconductor laser with optical injection

A detailed experimental study of antiphase dynamics in a two-mode semiconductor laser with optical injection is presented. The device is a specially designed Fabry-Perot laser that supports two primary modes with a THz frequency spacing. Injection in one of the primary modes of the device leads to a rich variety of single and two-mode dynamical scenarios, which are reproduced with remarkable accuracy by a four dimensional rate equation model. Numerical bifurcation analysis reveals the importance of torus bifurcations in mediating transitions to antiphase dynamics and of saddle-node of limit cycle bifurcations in switching of the dynamics between single and two-mode regimes.Comment: 7 pages, 9 figure

Uniqueness of a Negative Mode About a Bounce Solution

We consider the uniqueness problem of a negative eigenvalue in the spectrum of small fluctuations about a bounce solution in a multidimensional case. Our approach is based on the concept of conjugate points from Morse theory and is a natural generalization of the nodal theorem approach usually used in one dimensional case. We show that bounce solution has exactly one conjugate point at $\tau=0$ with multiplicity one.Comment: 4 pages,LaTe

Periodic orbit theory including spin degrees of freedom

We summarize recent developments of the semiclassical description of shell effects in finite fermion systems with explicit inclusion of spin degrees of freedom, in particluar in the presence of spin-orbit interactions. We present a new approach that makes use of spin coherent states and a correspondingly enlarged classical phase space. Taking suitable limits, we can recover some of the earlier approaches. Applications to some model systems are presented.Comment: LaTeX2e, 10pp, 5 figs; contribution to 10th Nuclear Physics Workshop "Marie and Pierre Curie", 24 - 28 Sept. 2003, Kazimierz Dolny (Poland

Inverse scattering approach to multiwavelength Fabry-Pérot laser design

A class of multiwavelength Fabry-Pérot lasers is introduced where the spectrum is tailored through a patterning of the cavity effective index. The cavity geometry is obtained using an inverse scattering approach and can be designed such that the spacing of discrete Fabry-Pérot lasing modes is limited only by the bandwidth of the inverted gain medium. A specific two-color semiconductor laser with a mode spacing in the THz region is designed, and measurements are presented demonstrating the simultaneous oscillation of the two wavelengths. The nonperiodic effective index profile of the particular two-color device considered is shown to be related to a Moiré or superstructure grating

Positive solutions to indefinite Neumann problems when the weight has positive average

We deal with positive solutions for the Neumann boundary value problem associated with the scalar second order ODE $$u" + q(t)g(u) = 0, \quad t \in [0, T],$$ where $g: [0, +\infty[\, \to \mathbb{R}$ is positive on $\,]0, +\infty[\,$ and $q(t)$ is an indefinite weight. Complementary to previous investigations in the case $\int_0^T q(t) < 0$, we provide existence results for a suitable class of weights having (small) positive mean, when $g'(x) < 0$ at infinity. Our proof relies on a shooting argument for a suitable equivalent planar system of the type $$x' = y, \qquad y' = h(x)y^2 + q(t),$$ with $h(x)$ a continuous function defined on the whole real line.Comment: 17 pages, 3 figure

A Simplified Model to Predict Long-Term Ozone Concentrations in Europe

In the preparation process for the Second Sulphur Protocol of the Convention on Long-range Transboundary Air Pollution, integrated assessment models played an important role in identifying cost-effective strategies for reducing SO2 emissions in Europe. Applying this effect-based approach to other environmental problems (e.g., photo-oxidants) seems appealing. In view of the timetable adopted for the current preparation of an updated Protocol on emissions of nitrogen oxides, an integrated assessment tool for ozone is required in the very near future. The paper presents an outline of an integrated assessment model for tropospheric ozone in Europe, with modules on emissions, emission control technologies and costs, ozone formation and environmental impacts. In its central part the paper focuses on the core element of such an approach, i.e., a concise description of the relationships between the precursor emissions (nitrogen oxides and volatile organic compounds) and regional ozone levels, which must be computationally efficient for use in an integrated assessment model. Critical levels, i.e., threshold levels protecting vegetation from damage, have been recently established using long-term exposure measures. Consequently, to be suitable for integrated assessment models, source-receptor relationships should be able to describe the long-term changes of ozone, e.g., over a six-month period. Based on numerous scenario runs of the EMEP ozone model, polynomial source-receptor relationships have been statistically identified. Using national annual emissions of NO, and VOC, the model predicts regional responses of the six-month mean of early afternoon ozone concentrations. From this concentration measure, excess exposure as used in the definition of the critical levels can be derived. The paper introduces the methodology of the approach, evaluates the results and discusses areas of further work. The suggested model formulation can be incorporated into the framework of an integrated assessment model, enabling (i) the assessment of costs and environmental benefits from alternative strategies to reduce precursor emissions and (ii) the identification of cost-optimized strategies to achieve environmental targets