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

Treatment of Helicobacter pylori infections: Mitigating factors and prospective natural remedies

Helicobacter pylori is a Gram-negative, microaerophilic spiral or motile rod that infects about half the world’s population with a very high prevalence in the developing world. It is an important aetiological factor in the development of gastritis, peptic ulcer disease, gastric atrophy and B cell mucosa associated lymphoid tissue (MALT) lymphoma. H. pylori infection is responsible for a significant cause of morbidity and mortality imposing a major burden on health care systems world wide. The high prevalence of infection in the developing countries has been attributed to poor socioeconomic status and sanitation as well as an increased trend of antibiotic resistance. Antimicrobial chemotherapy (two antibiotics and a proton pump inhibitor) employed for the treatment of H. pylori infections has emerged as the most important means to resolve these infections. However, antimicrobial therapy is fraught with a number of inherent limitations such as resistance, cost of treatment, unavailability of drugs in rural areas and undesirable side effects necessitating the need to search for alternative approaches from natural sources including vegetables, honey and probiotics amongst others. These could form the basis of novel low cost, efficient, large-scale and alternative/complementary solutions with minimal side effects to decrease or eradicate H. pylori infections in the future

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

Helicobacter pylori infection and transmission in Africa: Household hygiene and water sources are plausible factors exacerbating spread

Helicobacter pylori (H. pylori) is a microaerophilic motile curve rod that inhabits the gastric mucosa of the human stomach. The organism chronically infects billions of people worldwide and is one of themost genetically diverse of bacterial species. Infection with the bacterium which leads to chronic gastritis, peptic ulceration, gastric cancers and gastric malt lymphoma has been reported to follow a pattern linked to geographic and socio-demographic factors. Studies have documented a higherprevalence in Africa than elsewhere although the pathological outcomes do not correlate with infection. H. pylori transmission pathways are still vague, but the risks of transmission include precarious hygiene standards, over-crowding and contaminated environment and water sources amongst others. The possible routes of transmission include oral-oral, faecal-oral and person- to -person, either with or without transitional transmission steps during episodes of diarrhoea or gastro-oral contact in the eventof vomiting. Use of contaminated water including municipal tap water has also been suspected to have a high impact in the transmission of the organism. To generate the data presented in this paper, we conducted an internet based search on relevant literature pertaining to H. pylori epidemiology in general and Africa in particular. Sites such as Pubmed, AJOL, Scopus and Goggle scholar were mainly used. This paper therefore attempts to appraise the role of household hygiene and water sources in the transmission of this organism in the developing world context