Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent Genomes and Ecophysiologies

A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. A set of 11 strains of Brevundimonas alba were isolated from a bacterial freshwater community by conventional plating or by using a liquid most-probable-number (MPN) dilution series. These strains had identical 16S rRNA gene sequences and represented the dominant phylotype in the plateable fraction, as well as in the highest positive dilutions of the MPN series. However, internally transcribed spacer and enterobacterial repetitive intergenic consensus PCR fingerprinting analyses, as well as DNA-DNA hybridization analyses, revealed great genetic diversity among the 11 strains. Each strain utilized a specific combination of 59 carbon substrates, and the niche overlap indices were low, suggesting that each strain occupied a different ecological niche. In dialysis cultures incubated in situ, each strain had a different growth rate and cell yield. We thus demonstrated that the B. alba strains represent distinct populations with genetically determined adaptations and probably occupy different ecological niches. Our results have implications for assessment of the diversity and biogeography of bacteria and increase the perception of natural diversity beyond the level of 16S rRNA gene sequences.     

Measurement of Biologically Available Naphthalene in Gas and Aqueous Phases by Use of a Pseudomonas putida Biosensor

Genetically constructed microbial biosensors for measuring organic pollutants are mostly applied in aqueous samples. Unfortunately, the detection limit of most biosensors is insufficient to detect pollutants at low but environmentally relevant concentrations. However, organic pollutants with low levels of water solubility often have significant gas-water partitioning coefficients, which in principle makes it possible to measure such compounds in the gas rather than the aqueous phase. Here we describe the first use of a microbial biosensor for measuring organic pollutants directly in the gas phase. For this purpose, we reconstructed a bioluminescent Pseudomonas putida naphthalene biosensor strain to carry the NAH7 plasmid and a chromosomally inserted gene fusion between the sal promoter and the luxAB genes. Specific calibration studies were performed with suspended and filter-immobilized biosensor cells, in aqueous solution and in the gas phase. Gas phase measurements with filter-immobilized biosensor cells in closed flasks, with a naphthalene-contaminated aqueous phase, showed that the biosensor cells can measure naphthalene effectively. The biosensor cells on the filter responded with increasing light output proportional to the naphthalene concentration added to the water phase, even though only a small proportion of the naphthalene was present in the gas phase. In fact, the biosensor cells could concentrate a larger proportion of naphthalene through the gas phase than in the aqueous suspension, probably due to faster transport of naphthalene to the cells in the gas phase. This led to a 10-fold lower detectable aqueous naphthalene concentration (50 nM instead of 0.5 μM). Thus, the use of bacterial biosensors for measuring organic pollutants in the gas phase is a valid method for increasing the sensitivity of these valuable biological devices.     

The HhH domain of the human DNA repair protein XPF forms stable homodimers

The human XPF-ERCC1 protein complex plays an essential role in nucleotide excision repair by catalysing positioned nicking of a DNA strand at the 5' side of the damage. We have recently solved the structure of the heterodimeric complex of the C-terminal domains of XPF and ERCC1 (Tripsianes et al., Structure 2005;13:1849-1858). We found that this complex comprises a pseudo twofold symmetry axis and that the helix-hairpin-helix motif of ERCC1 is required for DNA binding, whereas the corresponding domain of XPF is functioning as a scaffold for complex formation with ERCC1. Despite the functional importance of heterodimerization, the C-terminal domain of XPF can also form homodimers in vitro. We here compare the stabilities of homodimeric and heterodimeric complexes of the C-terminal domains of XPF and ERCC1. The higher stability of the XPF HhH complexes under various experimental conditions, determined using CD and NMR spectroscopy and mass spectrometry, is well explained by the structural differences that exist between the HhH domains of the two complexes. The XPF HhH homodimer has a larger interaction interface, aromatic stacking interactions, and additional hydrogen bond contacts as compared to the XPF/ERCC1 HhH complex, which accounts for its higher stability.     

Glutathione as an endogenous sulphur source in the yeast Saccharomyces cerevisiae.

Glutathione-deficient mutants (gshA) of the yeast Saccharomyces cerevisiae, impaired in the first step of glutathione (GSH) biosynthesis were studied with respect to the regulation of enzymes involved in GSH catabolism and cysteine biosynthesis. Striking differences were observed in the content of the sulphur amino acids when gshA mutants were compared to wild-type strains growing on the same minimal medium. Furthermore, all mutants examined showed a derepression of gamma-glutamyltranspeptidase (gamm-GT), the enzyme initiating GSH degradation. However, gamma-cystathionase and cysteine synthase were unaffected by the GSH deficiency as long as the nutrient sulphate source was not exhausted. The results suggest that the mutants are probably not impaired in the sulphate assimilation pathway, but that the gamma-glutamyl cycle could play a leading role in the regulation of the sulphur fluxes. Studies of enzyme regulation showed that the derepression of gamma-GT observed in the gshA strains was most probably due to an alteration of the thiol status. The effectors governing the biosynthesis of cysteine synthase and gamma-cystathionase seemed different from those playing a role in gamma-GT regulation and it was only under conditions of total sulphate deprivation that all these enzymes were derepressed. As a consequence the endogenous pool of GSH was used in the synthesis of cysteine. GSH might, therefore, fulfil the role of a storage compound.     

Acute effects of intramuscular aponeurotomy on rat gastrocnemius medialis: force transmission, muscle force and sarcomere length

Acute effects of intramuscular aponeurotomy on muscle force and geometry as a function to muscle length were studied in rat m. gastrocnemius medialis (GM). Acutely after aponeurotomy, activation of the muscle at increasing lengths (acute trajectory) showed a spontaneous and progressive but patial tearing of the connective tissue interface between the fibres inserting directly proximally and distally to the location of the section. After this the muscle consisted morphologically of a stable proximal and a distal part (post-aponeurotomy). Post-aponeurotomy mean active sarcomere length within fibres of the proximal part was shown to be unaffected. In contrast, mean sarcomere length within the distal part was reduced substantially after aponeurotomy. However active sarcomeres in the distal part were still attaining higher lengths with increasing muscle lengths (p<0.005), indicating myofascial force transmission through the intact part of the connective tissue interface of the muscle parts. Post-aponeurotomy optimum muscle force was reduced substantially to less than 45% of pre-aponeurotomy values. During the acute trajectory the muscle yielded approximately 20% higher forces than post-aponeurotomy, indicating that myofascial force transmission was related to the area of connective tissue interface. It is concluded that after aponeurotomy of the proximal aponeurosis of rat GM, fibres without direct myotendinous connection to the origin of the muscle are still able to contribute to muscle force. As the magnitude of reduction in muscle force can only be explained partially by the spontaneous rupture of the connective tissue interface between proximal and distal muscle part, other factors causing a decrease of muscle force are present. Clinical implication of acute effects of intramuscular aponeurotomy are discussed.     

Genetic heterogeneity in patients having ataxia telangiectasia

UV-irradiated Chinese hamster cells on post-irradiation treatment with caffeine in growth medium for 24 h gave rise to biphasic UV-survival curves. At caffeine concentrations between 0.001 and 0.1 mM, control and caffeine-grown cells had similar survival curves initially from 0 to 30 J/m². At fluences greater than 30 J/m², there was effectively only little further killing of caffeine-grown cells beyond that observed at 30 J/m². At concentrations of caffeine greater than 0.5 mM, there was a gradual sensitization in the early part of the survival curve with increasing caffeine concentrations; but at fluences greater than 3 J/m², the slopes in the survival curves decreased very much.It has been proposed that the initial sensitization observed at low UV fluences is due to the suppression of post-replication repair by caffeine. After high fluences of UV exposures in these excision-deficient cells, in the presence of caffeine, the possibility of an induced ‘SOS’-like repair process has been suggested. This suggestion was supported by the observation that caffeine increased the yield of the UV-induced 8-azaguanine-resistant mutants only for the cell population exposed to UV fluences greater than 30 J/m².