Phylogenetic classification of short environmental DNA fragments

Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.     

Kinase array design, back to front: biaryl amides

New kinase inhibitors can be found by synthesis of targeted arrays of compounds designed using system-based knowledge as well as through screening focused or diverse compounds. Most array strategies aim to add functionality to a fragment that binds in the purine subpocket of the ATP-site. Here, an alternative pharmacophore-guided array approach is described which set out to discover novel purine subpocket-binding groups. Results are shown for p38alpha and cFMS kinase, for which multiple distinct series with nanomolar potency were discovered. Some of the compounds showed potency in cell-based assays and good pharmacokinetic properties.     

Management of threatened insect species in Australia, with particular reference to butterflies

Abstract   Advances in determination of conservation status of insects through evaluation of threats (rather than simple 'rarity' alone) help to set priorities for allocation of conservation resources, and formulate effective legislative treatment and field management for the most needy species. Summaries of several recent conservation studies on butterflies exemplify the variety of practical needs, amongst which habitat protection and enhancement is paramount. However, the paucity of biological and distributional information on most Australian insects necessitates considerable flexibility in approach, so that perceptions of conservation need may be highly subjective. Listing species for protection and conservation priority must be viewed as a dynamic process, with opportunity for rapid action, either to list or de-list taxa as research and recovery actions lead to change in perceived or real status and conservation need.     

What can experience add to early medical education? Consensus survey

Objective To provide a rationale for integrating experience into early medical education (“early experience”).Design Small group discussions to obtain stakeholders'' views. Grounded theory analysis with respondent, internal, and external validation.Setting Problem based, undergraduate medical curriculum that is not vertically integrated.Participants A purposive sample of 64 students, staff, and curriculum leaders from three university medical schools in the United Kingdom.Results Without early experience, the curriculum was socially isolating and divorced from clinical practice. The abruptness of students'' transition to the clinical environment in year 3 generated positive and negative emotions. The rationale for early experience would be to ease the transition; orientate the curriculum towards the social context of practice; make students more confident to approach patients; motivate them; increase their awareness of themselves and others; strengthen, deepen, and contextualise their theoretical knowledge; teach intellectual skills; strengthen learning of behavioural and social sciences; and teach them about the role of health professionals.Conclusion A rationale for early experience would be to strengthen and deepen cognitively, broaden affectively, contextualise, and integrate medical education. This is partly a process of professional socialisation that should start earlier to avoid an abrupt transition. “Experience” can be defined as “authentic human contact in a social or clinical context that enhances learning of health, illness or disease, and the role of the health professional.”     

Standing crop and aboveground biomass partitioning of a dwarf mangrove forest in Taylor River Slough,Florida

The structure and standing crop biomass of a dwarf mangrove forest, located in the salinity transition zone ofTaylor River Slough in the Everglades National Park, were studied. Although the four mangrove species reported for Florida occurred at the study site, dwarf Rhizophora mangle trees dominated the forest. The structural characteristics of the mangrove forest were relatively simple: tree height varied from 0.9 to 1.2 meters, and tree density ranged from 7062 to 23 778 stems ha^–1. An allometric relationship was developed to estimate leaf, branch, prop root, and total aboveground biomass of dwarf Rhizophora mangle trees. Total aboveground biomass and their components were best estimated as a power function of the crown area times number of prop roots as an independent variable (Y = B × X^–0.5083). The allometric equation for each tree component was highly significant (p<0.0001), with all r² values greater than 0.90. The allometric relationship was used to estimate total aboveground biomass that ranged from 7.9 to 23.2 ton ha^–1. Rhizophora mangle contributed 85% of total standing crop biomass. Conocarpus erectus, Laguncularia racemosa, and Avicennia germinans contributed the remaining biomass. Average aboveground biomass allocation was 69% for prop roots, 25% for stem and branches, and 6% for leaves. This aboveground biomass partitioning pattern, which gives a major role to prop roots that have the potential to produce an extensive root system, may be an important biological strategy in response to low phosphorus availability and relatively reduced soils that characterize mangrove forests in South Florida.     

Extensive Aggregations of Wild Fish at Coastal Sea-Cage Fish Farms

We present evidence of a largely undocumented environmental effect of coastal sea-cage fish farms on wild fish. We estimated the total abundance and biomass of wild fish aggregated in the immediate vicinity of nine fish farms in the Mediterranean Sea and one farm off the east coast of Australia. Estimates of wild fish aggregations ranged from 2000 to 86000 individuals and from 100 kg to 38.5 tons of fish per farm and were always greater than control locations. Particularly large aggregations (>30000 fish, > 12 tons) occurred at half of the farms. Aggregations were temporally stable for weeks to months and most wild fish associated with farms (88%) were of adult size. Potential effects of such large aggregations of wild fish in the immediate vicinity of fish farms include increased vulnerability to fishing and pathogen transfer between caged and wild fish. We suggest specific legislation should be enacted wherever large aggregations of wild fish occur around fish farms to enhance the positive and reduce the negative effects of association.     

Rapid preliminary characterisation of host specificity of leaf-beetles (Coleoptera: Chrysomelidae)

Rapid characterisation of host specificity is important both in biological control of weeds and studies in ecology and evolution. A means for doing this was developed and tested on four species of leaf beetles of interest for biological control of the weed Mimosa pigra (Mimosaceae). We identified the most promising for the more detailed tests necessary to obtain release approval. The impact of time-dependent effects and effects of experience were also investigated as part of this study but were not detected. Short-term host specificity tests on adult feeding accurately predicted the results of longer term trials. The long-term trial showed that survival on a plant species depended on feeding on it. Hence short-term feeding trials can predict the longer term survival of adults on other plant species. Different feeding results were obtained in cut foliage versus entire plants but no consistent pattern was shown: of the two insect species tested, one species ate more of the cut material while the opposite was demonstrated for the second species. Species in order of priority for further consideration as biocontrol agents were Syphrea bibiana, Genaphthona sp., Syphrea sp. and Paria sp. The latter three species were probably not sufficiently specific for release. The tests done here allow the identification of the most likely species upon which to conduct the more laborious and difficult larval developmental tests, saving considerable resources.     

Hormonal and metabolic responses to nesting activities in the green turtle, Chelonia mydas

We examined the association between green turtle nesting activities and plasma profiles of hormones that are widely implicated in aspects of heightened metabolism and energy regulation; epinephrine (EPI), norepinephrine (NE) and corticosterone. In conjunction, we examined plasma profiles of glucose and lactate to infer metabolic processes associated with green turtle nesting behaviour. Finally, because these hormones are also involved in mediating behaviour and physiology associated with stressful situations, we examined the effect of a stressor encountered during nesting, physical disturbance, on hormone levels. Plasma profiles of epinephrine, norepinephrine and corticosterone were not significantly altered across different stages of nesting. Plasma glucose and lactate both exhibited significant increases related to nesting activity; glucose increased dramatically during the emergence stage of nesting before stabilizing, and lactate levels continued to increase throughout the nesting process. There was no significant association between plasma hormones and glucose. For female turtles that abandoned nesting activities due to competition for nest space, there was no significant difference in plasma levels of epinephrine, norepinephrine and corticosterone compared to females that persisted with nesting activities. Overall, while distinct metabolic changes took place in nesting females, there was little association in profiles of hormones typically considered important for regulating heightened metabolism and nesting activity. This disassociation could arise because hormonal action may be altered in breeding female green turtles to facilitate reproductive processes.