Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations

Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European origin during the period 1974-1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from 1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking, haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before stocking (1950s/1960s Phi(ST) = -0.00296-0.00284), increasing considerably at the height of stocking (1980s Phi(ST) = 0.18932) and decreasing post-stocking (1990s/2002 Phi(ST) = 0.04934-0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability. Additionally, we found significant differentiation between individuals that had probably died from infectious disease and apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population declines.

The automation of nested clade phylogeographic analysis

ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis. This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation.

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

An extensible automated protein annotation tool: standardizing input and output using validated XML

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

LVB: parsimony and simulated annealing in the search for phylogenetic trees

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

PDBSprotEC: A web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.

Aldose reductase and the importance of experimental design

Kinetic studies on the AR (aldose reductase) protein have shown that it does not behave as a classical enzyme in relation to ring aldose sugars. As with non-enzymatic glycation reactions, there is probably a free radical element involved derived from monosaccharide autoxidation. in the case of AR, there is free radical oxidation of NADPH by autoxidizing monosaccharides, which is enhanced in the presence of the NADPH-binding protein. Thus any assay for AR based on the oxidation of NADPH in the presence of autoxidizing monosaccharides is invalid, and tissue AR measurements based on this method are also invalid, and should be reassessed. AR exhibits broad specificity for both hydrophilic and hydrophobic aldehydes that suggests that the protein may be involved in detoxification. The last thing we would want to do is to inhibit it. ARIs (AR inhibitors) have a number of actions in the cell which are not specific, and which do not involve them binding to AR. These include peroxy-radical scavenging and effects of metal ion chelation. The AR/ARI story emphasizes the importance of correct experimental design in all biocatalytic experiments. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has led to the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-m and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimizes the error in the parameters estimated, and is suitable for simple or complex steady-state models.

Knowledge communication and translation- A knowledge transfer model

Purpose – The purpose of this paper is to propose a process model for knowledge transfer in using theories relating knowledge communication and knowledge translation. Design/methodology/approach – Most of what is put forward in this paper is based on a research project titled “Procurement for innovation and knowledge transfer (ProFIK)”. The project is funded by a UK government research council – The Engineering and Physical Sciences Research Council (EPSRC). The discussions are mainly grounded on a thorough review of literature accomplished as part of the research project. Findings – The process model developed in this paper has built upon the theory of knowledge transfer and the theory of communication. Knowledge transfer, per se, is not a mere transfer of knowledge. It involves different stages of knowledge transformation. Depending on the context of knowledge transfer, it can also be influenced by many factors; some positive and some negative. The developed model of knowledge transfer attempts to encapsulate all these issues in order to create a holistic framework. Originality/value of paper – An attempt has been made in the paper to combine some of the significant theories or findings relating to knowledge transfer together, making the paper an original and valuable one.

When school is not enough: new initiatives in intergenerational language transmission in Wales

This paper examines language reproduction in the family in the context of a highly innovative project in Wales, where the Welsh language has been in decline for over a century. Although Welsh-medium schooling has played a pivotal role in slowing and even reversing language shift in recent decades, there is mounting evidence of the dangers of over-reliance on education. The Twf (Growth) Project was established in 2002 with funding from the National Assembly for Wales with the aim of raising awareness of the benefits of bilingualism among parents and prospective parents. Analysis of interviews with the main stakeholders in the project (managers, the Twf project officers, parents, health workers and a range of other partners), publicity materials and observations of project staff at work suggests that the achievements of the project lie in two main areas: the recognition of the need for building strong alliances with professional groups and organisations that work with families with young children; and the development of a marketing strategy appropriate for the target audience. It is argued that the experience of the project will be of interest to those addressing the issue of intergenerational transmission in a range of other minority language settings.

In-service training needs in an African context: a study of headteacher and teacher perspectives in the Gucha District of Kenya

Improving the quality of teaching is an educational priority in Kenya, as in many developing countries. The present paper considers various aspects of in-service education, including views on the effectiveness of in-service, teacher and headteacher priorities in determining in-service needs and the constraints on providing in-service courses. These issues are examined though an empirical study of 30 secondary headteachers and 109 teachers in a district of Kenya. The results show a strong felt need for in-service provision together with a firm belief in the efficacy of in-service in raising pupil achievement. Headteachers had a stronger belief in the need for in-service for their teachers than did the teachers themselves. The priorities of both headteachers and teachers were dominated by the external pressures of the schools, in particular the pressures for curriculum innovation and examination success. The resource constraints on supporting attendance at in-service courses were the major problems facing headteachers. The results reflect the difficulties that responding to an externally driven in-service agenda creates in a context of scarce resources.

Activation of pro-survival Akt and ERK1/2 signalling pathways underlie the anti-apoptotic effects of flavanones in cortical neurons

There is growing interest in the potential beneficial effects of flavonoids in the aging and diseased brain. We have investigated the potential of the flavanone hesperetin and two of its metabolites, hesperetin-7-O-beta-D-glucuronide and 5-nitro-hesperetin, to inhibit oxidative stress-induced neuronal apoptosis. Exposure of cortical neurons to hydrogen peroxide led to the activation of apoptosis signal-regulating kinase 1 via its de-phosphorylation at Ser963, the phosphorylation of c-jun N-terminal kinase and c-Jun (Ser73) and the activation of caspase 3 and caspase 9. Whilst hesperetin glucuronide failed to exert protection, both hesperetin and 5-nitro-hesperetin were effective at preventing neuronal apoptosis via a mechanism involving the activation/phosphorylation of both Akt/protein kinase B and extracellular signal-regulated kinase 1 and 2 (ERK1/2). Protection against oxidative injury and the activation of Akt and ERK1/2 followed a bell-shaped response and was most apparent at 100 nmol/L concentrations. The activation of ERK1/2 and Akt by flavanones led to the inhibition of the pro-apoptotic proteins, apoptosis signal-regulating kinase 1, by phosphorylation at Ser83 and Bad, by phosphorylation at both Ser136 and Ser112 and to the inhibition of peroxide-induced caspase 9 and caspase 3 activation. Thus, flavanones may protect neurons against oxidative insults via the modulation of neuronal apoptotic machinery.

Signaling mechanisms of GPCR ligands

G protein-coupled receptors constitute one of the major classes of drug targets, so understanding the mechanisms of signaling through these receptors is of great importance. This review covers some of the recent advances in G protein-coupled receptor signaling. A high resolution structure of the beta(2)-adrenergic receptor has been reported, as well as several molecular switches involved in receptor activation. It has also been realised that receptors and G proteins and their subunits may not always separate upon receptor activation. The definition of the ability of these receptors to signal has been expanded considerably with the realisation that some signaling may occur independently of G proteins, that some signaling events may differ in their pharmacological profiles and that formation of heterodimers of these receptors may provide new avenues for both signaling and drug design.

Grammatical collocations and verb-particle constructions in Brussels French: a corpus-linguistic approach to transfer

In this study the focus is on transfer in Brussels French, the variety of French spoken in Brussels. The methodology proposed in Jarvis (2000) and Jarvis and Pavlenko (2009) is followed to provide proof for the fact that grammatical collocations such as chercher après "to look for" are the result of contact with the source language, Brussels Dutch.