A tool for mapping research skills in undergraduate curricula

There has been considerable interest recently in the teaching of skills to undergraduate students. However, existing methods for collating data on how much, where and when students are taught and assessed skills have often been shown to be time-consuming and ineffective. Here, we outline an electronic research skills audit tool that has been developed to map both transferable and discipline-specific skills teaching and assessment within individual modules, the results of which can be collated and analysed across entire degree programmes. The design and use of the audit tool is described in detail and a bioscience case study is presented to illustrate the types of data that can be collected. The audit tool has been designed as a time-effective way of collecting information on skills teaching and assessment, but also actively encourages staff to reflect on their teaching and learning practices. Conclusions are drawn about the practicalities of using the audit tool and its importance in both curriculum design and as a resource to encourage dialogue with graduate employers.

Phenotyping parents of mapping populations of rice for heat tolerance during anthesis

Seed set of rice (Oryza sativa L.) is highly sensitive to short episodes of high temperature at anthesis events that are likely to be more frequent in future climates. Breeding for tolerance is therefore an essential component of adaptation to climate variability and change. Experiments were conducted in 2003 and 2004 at optimum (30 degrees C daytime) and high (35 and 38 degrees C) air temperature using parents of some prominent mapping populations (i) to determine whether there were differences in the daily flowering pattern and hence a potential heat avoidance mechanism, and (ii) to identify rice genotypes having true heat tolerance during anthesis, that is, high seed set in spikelets exposed to high temperature. Rice cultivar CG14 (O. glaberrima) reached peak anthesis earlier in the morning (1.5 h after dawn) under both control (30 degrees C) and high (38 degrees C) temperature conditions than O. sativa genotypes (>= 3 h after dawn). Exposure to high temperature (centered on the time of peak anthesis) for 6 h reduced spikelet fertility more than exposure for 2 h, and fertility was lower at 38 degrees C than at 35 degrees C. Genotypic ranking for spikelet fertility at 35 and 38 degrees C was highly correlated in both 2003 and 2004. Fertility was also highly correlated across years, suggesting a consistent and reproducible response of spikelet fertility to temperature. The check cultivar N22 was the most heat tolerant genotype (64-86% fertility at 38 degrees C) and cultivars Azucena and Moroberekan the most susceptible (<8%).

The economic dimensions of integrating flood management and agri-environment through washland creation: a case from Somerset, England

In many river floodplains in the UK, there has been a long history of flood defence, land reclamation and water regime management for farming. In recent years, however, changing European and national policies with respect to farming, environment and flood management are encouraging a re-appraisal of land use in rural areas. In particular, there is scope to develop, through the use of appropriate promotional mechanisms, washland areas, which will simultaneously accommodate winter inundation, support extensive farming methods, deliver environmental benefits, and do this in a way which can underpin the rural economy. This paper explores the likely economic impacts of the development of flood storage and washland creation. In doing so, consideration is given to feasibility of this type of development, the environmental implications for a variety of habitats and species, and the financial and institutional mechanisms required to achieve implementation. (C) 2007 Elsevier Ltd. All rights reserved.

Effects of grazing management on beetle and plant assemblages during the re-creation of a flood-plain meadow

Flood-plain meadows (Alopecurus-Sanguisorba grassland) are a floristically rich community of conservation importance throughout Europe. Declines in their distribution due in part to modern farming practices mean they now cover less than 1500 ha in the UK. To investigate the effect of grazing regime during the re-creation of this grassland type, target plant species were sown onto ex-arable land during 1985. Traditional management, based on a July hay cut followed by aftermath grazing was subsequently instigated, and the site was divided into replicated grazing regimes of cattle, sheep and an un-grazed control. Plant and beetle assemblages were sampled and compared to those of target flood-plain meadows and improved grassland communities. Within the re-creation treatments the absence of aftermath grazing reduced beetle abundances and species richness. Assemblages of plants were closest to that of the target flood-plain meadow under sheep grazing, although this differed little from cattle grazing. Beetle species assemblages and functional group structure were, however, closest to the target grassland under cattle grazing. For all taxa the greatest resilience to succession to the target flood-plain meadow occurred when grazing was not part of the management prescription. Although successful re-creation had not been achieved for either the plants or beetles, cutting followed by aftermath cattle grazing has provided the best management to date. (c) 2006 Elsevier B.V. All rights reserved.

Mapping the immune response to the outer domain of a human immunodeficiency virus-1 clade C gp120

The outer domain (OD) of human immunodeficiency virus (HIV)-1 gp120 represents an attractive, if difficult, target for a beneficial immune response to HIV infection. Unlike the entire gp120, the OD is structurally stable and contains the surfaces that interact with both the primary and secondary cellular receptors. The primary strain-specific neutralizing target, the V3 loop, lies within the OD, as do epitopes for two cross-reactive neutralizing monoclonal antibodies (mAbs), b12 and 2G12, and the contact sites for a number of inhibitory lectins. The OD is poorly immunogenic, at least in the context of complete gp120, but purposeful OD immunization can lead to a substantial antibody response. Here, we map the antibody generated following immunization with a clade C OD. In contrast to published data for the clade B OD, the majority of the polyclonal response to the complete clade C OD is to the V3 loop; deletion of the loop substantially reduces immunogenicity. When the loop sequence was substituted for the epitope for 2F5, a well-characterized human cross-neutralizing mAb, a polyclonal response to the epitope was generated. A panel of mAbs against the clade C OD identified two mAbs that reacted with the loop and were neutralizing for clade C but not B isolates. Other mAbs recognized both linear and conformational epitopes in the OD. We conclude that, as for complete gp120, V3 immunodominance is a property of OD immunogens, that the responses can be neutralizing and that it could be exploited for the presentation of other epitopes.

Mapping the landscape of the lymphocytic choriomeningitis virus stable signal peptide reveals novel functional domains

The stable signal peptide (SSP) of the lymphocytic choriomeningitis virus surface glycoprotein precursor has several unique characteristics. The SSP is unusually long, at 58 amino acids, and contains two hydrophobic domains, and its sequence is highly conserved among both Old and New World arenaviruses. To better understand the functions of the SSP, a panel of point and deletion mutants was created by in vitro mutagenesis to target the highly conserved elements within the SSP. We were also able to confirm critical residues required for separate SSP functions by trans-complementation. Using these approaches, it was possible to resolve functional domains of the SSP. In characterizing our SSP mutants, we discovered that the SSP is involved in several distinct functions within the viral life cycle, beyond translocation of the viral surface glycoprotein precursor into the endoplasmic reticulum lumen. The SSP is required for efficient glycoprotein expression, posttranslational maturation cleavage of GP1 and GP2 by SKI-1/S1P protease, glycoprotein transport to the cell surface plasma membrane, formation of infectious virus particles, and acid pH-dependent glycoprotein-mediated cell fusion.

Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome

The number of solute-binding protein-dependent transporters in rhizobia is dramatically increased compared with the majority of other bacteria so far sequenced. This increase may be due to the high affinity of solute-binding proteins for solutes, permitting the acquisition of a broad range of growth-limiting nutrients from soil and the rhizosphere. The transcriptional induction of these transporters was studied by creating a suite of plasmid and integrated fusions to nearly all ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) transporters of Sinorhizobium meliloti. In total, specific inducers were identified for 76 transport systems, amounting to approximate to 47% of the ABC uptake systems and 53% of the TRAP transporters in S. meliloti. Of these transport systems, 64 are previously uncharacterized in Rhizobia and 24 were induced by solutes not known to be transported by ABC- or TRAP-uptake systems in any organism. This study provides a global expression map of one of the largest transporter families (transportome) and an invaluable tool to both understand their solute specificity and the relationships between members of large paralogous families.

Mapping quantitative trait loci for flag leave senescence as a yield determinant in winter wheat under optimal and drought stressed environments

The timing of flag leaf senescence (FLS) is an important determinant of yield under stress and optimal environments. A doubled haploid population derived from crossing the photo period-sensitive variety Beaver,with the photo period-insensitive variety Soissons, varied significantly for this trait, measured as the percent green flag leaf area remaining at 14 days and 35 days after anthesis. This trait also showed a significantly positive correlation with yield under variable environmental regimes. QTL analysis based on a genetic map derived from 48 doubled haploid lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, revealed the genetic control of this trait. The coincidence of QTL for senescence on chromosomes 2B and 2D under drought-stressed and optimal environments, respectively, indicate a complex genetic mechanism of this trait involving the re-mobilisation of resources from the source to the sink during senescence.

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and ArnphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.

Mapping CD55 function: the structure of two pathogen-binding domains at 1.7 A

Decay-accelerating factor (CD55), a regulator of the alternative and classical pathways of complement activation, is expressed on all serum-exposed cells. It is used by pathogens, including many enteroviruses and uropathogenic Escherichia coli, as a receptor prior to infection. We describe the x-ray structure of a pathogen-binding fragment of human CD55 at 1.7 A resolution containing two of the three domains required for regulation of human complement. We have used mutagenesis to map biological functions onto the molecule; decay-accelerating activity maps to a single face of the molecule, whereas bacterial and viral pathogens recognize a variety of different sites on CD55.

Mapping antimalarial pharmacophores as a useful tool for the rapid discovery of drugs effective in vivo: design, construction, characterization, and pharmacology of metaquine

Resistant strains of Plasmodium falciparum and the unavailability of useful antimalarial vaccines reinforce the need to develop new efficacious antimalarials. This study details a pharmacophore model that has been used to identify a potent, soluble, orally bioavailable antimalarial bisquinoline, metaquine (N,N'-bis(7-chloroquinolin-4-yl)benzene-1,3-diamine) (dihydrochloride), which is active against Plasmodium berghei in vivo (oral ID50 of 25 mu mol/kg) and multidrug-resistant Plasmodium falciparum K1 in vitro (0.17 mu M). Metaquine shows strong affinity for the putative antimalarial receptor, heme at pH 7.4 in aqueous DMSO. Both crystallographic analyses and quantum mechanical calculations (HF/6-31+G*) reveal important regions of protonation and bonding thought to persist at parasitic vacuolar pH concordant with our receptor model. Formation of drug-heme adduct in solution was confirmed using high-resolution positive ion electrospray mass spectrometry. Metaquine showed strong binding with the receptor in a 1: 1 ratio (log K = 5.7 +/- 0.1) that was predicted by molecular mechanics calculations. This study illustrates a rational multidisciplinary approach for the development of new 4-aminoquinoline antimalarials, with efficacy superior to chloroquine, based on the use of a pharmacophore model.