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Reference genes are used to normalize target genes for relative quantification in gene expression studies. However, different experimental conditions may affect the expression of reference genes, which could lead to erroneous quantitative results. In this study, we performed real-time polymerase chain to investigate the expression of eight reference genes (rpoN, rpoD, dbhA, phaF, 16S rRNA, gst, lexA, and atkA) in Pseudomonas putida mt-2 during degradation of p-xylene. According to their expression stability, geNorm software analysis revealed that rpoN, rpoD, 16S rRNA, and atkA were suitable reference genes with highly stable expression, whereas phaF and dbhA were not suitable due to unstable expression. When normalized either to phaF or dbhA, xylA and xylE expression were significantly different compared to the expression levels normalized with the normalization factor (NF(4)) obtained from the four most stable reference genes (rpoN, -rpoD, -16S rRNA, and -atkA). The use of unstably expressing reference genes resulted in an over- or underestimation of target gene expression, a delay in maximal gene expression, and an increase in gene expression in the absence of inducer. While experimental results indicated that the relative maximum expression of xylA and xylE occurred at different times, unstable reference genes indicated that the maximum expression occurred at the same time. Our study indicates that a valid set of reference genes covering a broad expression range is recommended to accurately normalize and quantify the relative expression levels of the target gene(s) transcripts in many microbial processes.

We present a minimal two-component model that can exhibit various types of spatial patterns including patchiness. The model, comprising nutrients and phytoplankton, includes the effect of nutrient uptake by phytoplankton as a Holling type II functional response, and also includes the effect of zooplankton grazing on phytoplankton as a Holling type II non-dynamical term. The mean-field model without the diffusion and advection terms shows both bistability and limit-cycle oscillations as a few parameters such as the input rate of nutrients and the maximum feeding rate of zooplankton are changed. If the parameter values are chosen from the limit-cycle oscillation region, the corresponding reaction-advection-diffusion equations show spatial pattern formations by the combined effects of advection and diffusion by turbulent stirring and mixing, and biological interactions. As the nutrient input is increased, the system behaviour changes from the extinction of the entire phytoplankton to the formation of filamentous patterns, patchiness patterns and homogeneous distributions. These observations suggest that the spatial pattern of phytoplankton can function as an indicator to evaluate the eutrophication level in aquatic ecosystems.

Visible-light-driven TiO2 photocatalysts doped with nitrogen have been prepared as powders and thin films in a cylindrical tubular furnace under a stream of ammonia gas. The photocatalysts thus obtained were found to have a band-gap energy of 2.95 eV. Electron spin resonance (ESR) under irradiation with visible light (lambda > or = 430 nm) afforded the increase in intensity in the visible-light region. The concentration of trapped holes was about fourfold higher than that of trapped electrons. Nitrogen-doped TiO2 has been used to investigate mechanistically the photocatalytic oxidation of trichloroethylene (TCE) under irradiation with visible light (lambda > or = 420 nm). Cl and O radicals, which contribute significantly to the generation of dichloroacetyl chloride (DCAC) in the photocatalytic oxidation of TCE under UV irradiation, were found to be deactivated under irradiation with visible light. As the main by-product, only phosgene was detected in the photocatalytic oxidation of TCE under irradiation with visible light. Thus, the reaction mechanism of TCE photooxidation under irradiation with visible light clearly differs markedly from that under UV irradiation. Based on the results of the present study, we propose a new reaction mechanism and adsorbed species for the photocatalytic oxidation of TCE under irradiation with visible light. The energy band for TiO2 by doping with nitrogen may involve an isolated band above the valence band.

Experimental and computational studies of the formation and evolution of scroll waves in three-dimensional excitable media are presented. Scroll waves are initiated in the photosensitive Belousov-Zhabotinsky reaction by perturbing traveling waves transverse to their direction of propagation. Scroll rings are generated by perturbing circular waves, which expand or contract depending on the strength of an imposed excitability gradient and its direction relative to the rotational direction of the scroll wave. (c) 1998 American Institute of Physics.