Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain

The bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16S rRNA gene pool, isolation and identification of strains, and biodegradation assays. Three strains, Variovorax sp. strain WDL1, Delftia acidovorans WDL34, and Pseudomonas sp. strain WDL5, were isolated directly from the linuron-degrading culture. In addition, subculture of this enrichment culture on potential intermediates in the degradation pathway of linuron (i.e., N,O-dimethylhydroxylamine and 3-chloroaniline) resulted in the isolation of, respectively, Hyphomicrobium sulfonivorans WDL6 and Comamonas testosteroni WDL7. Of these five strains, only Variovorax sp. strain WDL1 was able to use linuron as the sole source of C, N, and energy. WDL1 first converted linuron to 3,4-dichloroaniline (3,4-DCA), which transiently accumulated in the medium but was subsequently degraded. To the best of our knowledge, this is the first report of a strain that degrades linuron further than the aromatic intermediates. Interestingly, the rate of linuron degradation by strain WDL1 was lower than that for the consortium, but was clearly increased when WDL1 was coinoculated with each of the other four strains. D. acidovorans WDL34 and C. testosteroni WDL7 were found to be responsible for degradation of the intermediate 3,4-DCA, and H. sulfonivorans WDL6 was the only strain able to degrade N,O-dimethylhydroxylamine. The role of Pseudomonas sp. strain WDL5 needs to be further elucidated. The degradation of linuron can thus be performed by a single isolate, Variovorax sp. strain WDL1, but is stimulated by a synergistic interaction with the other strains isolated from the same linuron-degrading culture.     

Essential role for CD40 ligand interactions in T lymphocyte-mediated modulation of the murine immune response to pneumococcal capsular polysaccharides

Protection against infection with pneumococci is provided by anti-capsular polysaccharide (caps-PS) Abs. We investigated whether CD40 ligand (CD40L) plays a role in T lymphocyte-mediated regulation of the immune response to caps-PS, which are considered thymus-independent Ags. Administration of MR1, an antagonist mAb against murine CD40L, in BALB/c mice immunized with Pneumovax resulted in an inhibition of the IgM and IgG Ab response for various caps-PS serotypes. Evidence for the involvement of CD4(+) T lymphocytes in the Ab response to caps-PS was obtained in SCID/SCID mice that, when reconstituted with B lymphocytes and CD4(+) T lymphocytes, mounted a higher specific IgM response compared with SCID/SCID mice reconstituted with only B lymphocytes. This helper effect of CD4(+) T lymphocytes was abrogated by MR1. Blocking CD40L in vitro decreased the IgM response to caps-PS and abolished the helper effect of CD4(+) T lymphocytes. CD8(+) T lymphocyte-depleted murine spleen cells mounted a higher in vivo immune response than total murine spleen cells, which provided evidence for a suppressive role of CD8(+) T lymphocytes on the anti-caps-PS immune response. CD4(+) T lymphocyte-depleted murine spleen cells, leaving a B and CD8(+) T lymphocyte fraction, elicited only a weak in vivo and in vitro Ab response, which was enhanced after MR1 administration. In summary, our data provide evidence that T lymphocytes contribute to the regulation of the anti-caps-PS immune response in a CD40L-dependent manner.     

MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues

Background  

Serial analysis of gene expression using small amounts of starting material (microSAGE) has not yet been conclusively shown to be representative, reproducible or accurate.     

Eggshell matrix protein mimics: designer peptides to induce the nucleation of calcite crystal aggregates in solution

Ansocalcin is a novel goose eggshell matrix protein with 132 amino acid residues, which induces the formation of polycrystalline calcite aggregates in in vitro crystallization experiments. The central region of ansocalcin is characterized by the presence of multiplets of charged amino acids. To investigate the specific role of charged amino acid multiplets in the crystal nucleation, three short peptides REWD-16, REWDP-17 (containing charged doublets), and RADA-16 (alternating charged residues) were synthesized and characterized. The aggregation of these peptides in solution was investigated using circular dichroism, intrinsic tryptophan fluorescence, and dynamic light scattering experiments. The peptides REWD-16 and REWDP-17 induced the polycrystalline calcite crystal aggregates, whereas RADA-16 did not induce significant changes in calcite crystal morphology or aggregate formation in in vitro crystallization experiments. The lattice and morphology of the calcite crystals were characterized using X-ray diffraction and scanning electron microscope. The results discussed in this paper reveal the importance of multiplets of charged amino acid residues toward the nucleation of polycrystalline calcite crystal aggregates in solution.     

Hydrogen sulphide: a novel inhibitor of hypochlorous acid-mediated oxidative damage in the brain?

Hydrogen sulphide (H(2)S) is a cytotoxic gas that has recently been proposed as a novel neuromodulator. Endogenous levels of H(2)S in the brain range between 50 and 160 microM, and considerably lower H(2)S levels are reported in the brains of Alzheimer's disease (AD) patients. Levels of myeloperoxidase (MPO), an enzyme that catalyses the formation of the oxidant hypochlorous acid (HOCl), are elevated in the prefrontal cortex, hippocampal microglia, and neurons of AD patients where MPO co-localised with beta-amyloid plaques. Recently 3-chlorotyrosine, a bio-marker for MPO activity (and HOCl production), was shown to be elevated threefold in hippocampal proteins from AD patients. Since H(2)S and HOCl are important mediators in brain function and disease, we investigated the effects of H(2)S on HOCl-mediated damage to bio-molecules and to cultured human SH-SY5Y cells. H(2)S significantly inhibited HOCl-mediated inactivation of alpha(1)-antiproteinase and protein oxidation to a comparable extent to reduced glutathione. H(2)S also inhibited HOCl-induced cytotoxicity, intracellular protein oxidation, and lipid peroxidation in SH-SY5Y cells. These data suggest that H(2)S has the potential to act as an inhibitor of HOCl-mediated processes in vivo and that the potential antioxidant action of H(2)S deserves further study, especially since extracellular GSH levels in the brain are very low.     

Diagnostic parameters in liquid-based cervical cytology using a coagulant suspension fixative

OBJECTIVE: To evaluate in detail the morphology of cervical cell samples suspended in the coagulant fixative BoonFix (Finetec, Tokyo, Japan) in liquid-based Papspin slides (Thermo Shandon, Pittsburgh, Pennsylvania, U.S.A) to detect shifts in diagnostic parameters for infections and neoplasia. STUDY DESIGN: Split samples of 1,010 cases were collected. All Papspin slides were scanned with neural network technology. In 849 cases the diagnosis was "within normal limits"; in 22 cases it was preneoplasia. In 151 special cases conventional smears were compared with thin-layer slides. RESULTS: In 85% of the 151 special cases, a shift of the diagnostic parameter was observed in the Papspin slide. The parameter adhesion of inflammatory cells to epithelial cells was easier to discern in 94% of the cases, and adhesion of microorganisms varied 43-100%. Koilocytosis was more visible in 79%. Prominent nucleoli in atypical and malignant cells were enhanced in 50-100% of cases with preneoplasia. The fact that the cells on the Papspin slide were no longer present in diagnostic streaks posed a problem only in the case of follicular cervicitis. CONCLUSION: The shifts in parameters facilitated the diagnostic process. BoonFix permits the screening of liquid-based Papspin slides, which have proven to be well suited to automated neural network scanning.     

Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications

A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.     

Prebiotic effects of chicory inulin in the simulator of the human intestinal microbial ecosystem

The prebiotic potential of native chicory inulin was assessed in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) by monitoring microbial community from the colon compartments, its metabolic activity and community structure. Inulin addition selected for a higher short chain fatty acid production with shifts towards propionic and butyric acid. Conventional culture-based techniques and PCR-denaturing gradient gel electrophoresis analysis showed no remarkable changes in the overall microbial community from the colon compartments of the SHIME, whereas selective effects were seen for lactic acid bacteria. Quantitative PCR with bifidobacteria-specific primers revealed a significant increase with more than 1 log CFU ml(-1) from the proximal to distal colon, in contrast to culture-based techniques, which only showed a minor bifidogenic effect in the ascending colon. Our results indicate that inulin purports prebiotic effects from the proximal to distal colon and that real-time PCR is a more precise technique to detect differences in bifidobacterial populations whereas conventional culturing techniques are much more variable.