Degradation of phenanthrene-analogue azaarenes by Mycobacterium gilvum strain LB307T under aerobic conditions

A polycyclic aromatic hydrocarbon degrading Mycobacterium gilvum, strain LB307T, was able to degrade the azaarenes 5,6-benzoquinoline, 7,8-benzoquinoline, and phenanthridine (nitrogen-containing heterocyclic aromatic hydrocarbons) under aerobic conditions. The strain was able to use 5,6-benzoquinoline as sole sources of carbon, nitrogen, and energy. However, inhibition of degradation and growth was observed with increasing substrate concentration. During degradation, metabolites built up transiently. One of the metabolites detected during 5,6-benzoquinoline degradation is suggested to be 2-oxo-5,6-benzoquinoline. This is the first report on bacterial degradation of phenanthrene-analogue azaarenes.     

Gating of amiloride-sensitive Na(+) channels: subunit-subunit interactions and inhibition by the cystic fibrosis transmembrane conductance regulator

In search of the structural basis for gating of amiloride-sensitive Na(+) channels, kinetic properties of single homo and heterooligomeric ENaCs formed by the subunits with individual truncated cytoplasmic domains were studied in a cell-free planar lipid bilayer reconstitution system. Our results identify the N-terminus of the alpha-subunit as a major determinant of kinetic behavior of both homooligomeric and heterooligomeric ENaCs, although the carboxy-terminal domains of beta- and gamma-ENaC subunits play important role(s) in modulation of the kinetics of heterooligomeric channels. We also found that the cystic fibrosis transmembrane conductance regulator (CFTR) inhibits amiloride-sensitive channels, at least in part, by modulating their gating. Comparison of these data suggests that the modulatory effects of the beta- and gamma-ENaC subunits, and of the CFTR, may involve the same, or closely related, mechanism(s); namely, "locking" the heterooligomeric channels in their closed state. These mechanisms, however, do not completely override the gating mechanism of the alpha-channel.     

Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities

A workshop with the aim to compare classical and molecular techniques for phytoplankton enumeration took place at Kristineberg Marine Research Station, Sweden, in August 2005. Seventeen different techniques – nine classical microscopic-based and eight molecular methods – were compared. Alexandrium fundyense was the target organism in four experiments. Experiment 1 was designed to determine the range of cell densities over which the methods were applicable. Experiment 2 tested the species specificity of the methods by adding Alexandrium ostenfeldii, to samples containing A. fundyense. Experiments 3 and 4 tested the ability of the methods to detect the target organism within a natural phytoplankton community. Most of the methods could detect cells at the lowest concentration tested, 100 cells L⁻¹, but the variance was high for methods using small volumes, such as counting chambers and slides. In general, the precision and reproducibility of the investigated methods increased with increased target cell concentration. Particularly molecular methods were exceptions in that their relative standard deviation did not vary with target cell concentration. Only two of the microscopic methods and three of the molecular methods had a significant linear relationship between their cell count estimates and the A. fundyense concentration in experiment 2, where the objective was to discriminate that species from a morphologically similar and genetically closely related species. None of the investigated methods were affected by the addition of a natural plankton community background matrix in experiment 3. The results of this study are discussed in the context of previous intercomparisons and the difficulties in defining the absolute, true target cell concentration.     

Degradation of PCB congeners by bacterial strains

Biological in situ methods are options for the remediation of contaminated sites. An approach to quantify biodegradation by soil bacteria was developed, combining experiment with mathematical modelling. We performed in vitro assays to investigate the potential and kinetics of the wild-type degrader, Burkholderia sp. strain LB400 (expressing bph) and the genetically modified Pseudomonas fluorescens strains F113pcb and F113L::1180 (expressing bph under different promoters) to metabolise individual congeners of polychlorinated biphenyls (PCBs). Kinetics of metabolism was analysed using the Monod model. Results revealed similar patterns of degradable PCB congeners for LB400 and F113L::1180. The degree of PCB degradation was comparable for LB400 and F113L::1180 but was much lower for F113rifpcb. In additional mesocosm experiments with PCB-contaminated soil, the F113 derivatives demonstrated a good survival ability in willow (Salix sp.) rhizosphere. Strain F113L::1180 in combination with willow plants is expected to degrade a large spectrum of PCB congeners in soil. The data from the experiments were used to calculate the time scale of the degradation process in a PCB-contaminated soil. The uncertainty of the model predictions due to the uncertainties of experimental removal velocities and bacterial cell density in soil was quantified.     

Spatio-temporal variation in stable isotope and elemental composition of key-species reflect environmental changes in the Baltic Sea

Biogeochemistry - Carbon and nitrogen stable isotope ratios are increasingly used to study long-term change in food web structure and nutrient cycling. We retrospectively analyse elemental...     

Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.