Characterization of the active site and calcium binding in cytochromecnitrite reductases

The decahaem homodimeric cytochrome c nitrite reductase (NrfA) is expressed within the periplasm of a wide range of Gamma-, Delta- and Epsilon-proteobacteria and is responsible for the six-electron reduction of nitrite to ammonia. This allows nitrite to be used as a terminal electron acceptor, facilitating anaerobic respiration while allowing nitrogen to remain in a biologically available form. NrfA has also been reported to reduce nitric oxide (a reaction intermediate) and sulfite to ammonia and sulfide respectively, suggesting a potential secondary role as a detoxification enzyme. The protein sequences and crystal structures of NrfA from different bacteria and the closely related octahaem nitrite reductase from Thioalkalivibrio nitratireducens (TvNir) reveal that these enzymes are homologous. The NrfA proteins contain five covalently attached haem groups, four of which are bis-histidine-co-ordinated, with the proximal histidine being provided by the highly conserved CXXCH motif. These haems are responsible for intraprotein electron transfer. The remaining haem is the site for nitrite reduction, which is ligated by a novel lysine residue provided by a CXXCK haem-binding motif. The TvNir nitrite reductase has five haems that are structurally similar to those of NrfA and three extra bis-histidine-coordinated haems that precede the NrfA conserved region. The present review compares the protein sequences and structures of NrfA and TvNir and discusses the subtle differences related to active-site architecture and Ca2+ binding that may have an impact on substrate reduction

Molecular microbial ecology of lignocellulose mobilisation as a carbon source in mine drainage wastewater treatment

The community structure of complex microbial consortia which develop in lignocellulose packed passive treatment systems for acid mine drainage remediation were investigated. An understanding of interactions between these populations is important in determining mechanisms by which such systems operate. A degrading packed bed reactor was packed with lignocellulositic material as a sole carbon source and fed continuously with simulated acid mine drainage. Samples were collected every two months at different depths of the reactor to isolate the total genomic DNA and PCR amplify section of 16S rDNA gene. PCR primers, GM5F and 907R incorporating GC clamp were used to amplify 586-bp region of 16S rDNA gene. Denaturing gradient gel electrophoresis (DGGE) indicated clearly a highly differentiated pattern of r-DNA – derived amplificates between different depths of the bioreactor. Predominant DGGE bands were further excised, reamplified, cloned and sequenced. Sequencing analysis revealed phylogenetic affiliation of specific bacterial populations in different depths of the bioreactor. Water SA Vol. 30 (5) 2005: pp.658-66

How many independent bets are there?

The benefits of portfolio diversification is a central tenet implicit to modern financial theory and practice. Linked to diversification is the notion of breadth. Breadth is correctly thought of as the number of in- dependent bets available to an investor. Conventionally applications us- ing breadth frequently assume only the number of separate bets. There may be a large discrepancy between these two interpretations. We uti- lize a simple singular-value decomposition (SVD) and the Keiser-Gutman stopping criterion to select the integer-valued effective dimensionality of the correlation matrix of returns. In an emerging market such as South African we document an estimated breadth that is considerably lower than anticipated. This lack of diversification may be because of market concentration, exposure to the global commodity cycle and local currency volatility. We discuss some practical extensions to a more statistically correct interpretation of market breadth, and its theoretical implications for both global and domestic investors.Comment: Less technical rewrite. 12 Pages, 6 Figures (.eps

Elastic-plastic solutions for expanding cavities embedded in two different cohesive-frictional materials

An analytical solution of cavity expansion in two different concentric regions of soil is developed and investigated in this paper. The cavity is embedded within a soil with finite radial dimension and surrounded by a second soil, which extends to infinity. Large-strain quasi-static expansion of both spherical and cylindrical cavities in elastic-plastic soils is considered. A non-associated Mohr–Coulomb yield criterion is used for both soils. Closed-form solutions are derived, which provide the stress and strain fields during the expansion of the cavity from an initial to a final radius. The analytical solution is validated against finite element simulations, and the effect of varying geometric and material parameters is studied. The influence of the two different soils during cavity expansion is discussed by using pressure–expansion curves and by studying the development of plastic regions within the soils. The analytical method may be applied to various geotechnical problems, which involve aspects of soil layering, such as cone penetration test interpretation, ground-freezing around shafts, tunnelling, and mining

RexAB promotes the survival of staphylococcus aureus exposed to multiple classes of antibiotics

Antibiotics inhibit essential bacterial processes, resulting in arrest of growth and, in some cases, cell death. Many antibiotics are also reported to trigger endogenous production of reactive oxygen species (ROS), which damage DNA, leading to induction of the mutagenic SOS response associated with the emergence of drug resistance. However, the type of DNA damage that arises and how this triggers the SOS response are largely unclear. We found that several different classes of antibiotic triggered dose-dependent induction of the SOS response in Staphylococcus aureus, indicative of DNA damage, including some bacteriostatic drugs. The SOS response was heterogenous and varied in magnitude between strains and antibiotics. However, in many cases, full induction of the SOS response was dependent upon the RexAB helicase/nuclease complex, which processes DNA double-strand breaks to produce single-stranded DNA and facilitate RecA nucleoprotein filament formation. The importance of RexAB in repair of DNA was confirmed by measuring bacterial survival during antibiotic exposure, with most drugs having significantly greater bactericidal activity against rexB mutants than against wild-type strains. For some, but not all, antibiotics there was no difference in bactericidal activity between wild type and rexB mutant under anaerobic conditions, indicative of a role for reactive oxygen species in mediating DNA damage. Taken together, this work confirms previous observations that several classes of antibiotics cause DNA damage in S. aureus and extends them by showing that processing of DNA double-strand breaks by RexAB is a major trigger of the mutagenic SOS response and promotes bacterial survival