Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape

A Pb-mine site situated on acidic soil, but comprising of Ca-enriched islands around derelict buildings was used to study the spatial pattern of genetic diversity in Lumbricus rubellus. Two distinct genetic lineages ('A' and 'B'), differentiated at both the mitochondrial (mtDNA COII) and nuclear level (AFLPs) were revealed with a mean inter-lineage mtDNA sequence divergence of approximately 13%, indicative of a cryptic species complex. AFLP analysis indicates that lineage A individuals within one central 'ecological island' site are uniquely clustered, with little genetic overlap with lineage A individuals at the two peripheral sites. FTIR microspectroscopy of Pb-sequestering chloragocytes revealed different phosphate profiles in residents of adjacent acidic and calcareous islands. Bioinformatics found over-representation of Ca pathway genes in ESTPb libraries. Subsequent sequencing of a Ca-transport gene, SERCA, revealed mutations in the protein's cytosolic domain. We recommend the mandatory genotyping of all individuals prior to field-based ecotoxicological assays, particularly those using discriminating genomic technologies.

Right ventromedial and dorsolateral prefrontal cortices mediate adaptive decisions under ambiguity by integrating choice utility and outcome evaluation.

The Iowa gambling task (IGT) is one of the most influential behavioral paradigms in reward-related decision making and has been, most notably, associated with ventromedial prefrontal cortex function. However, performance in the IGT relies on a complex set of cognitive subprocesses, in particular integrating information about the outcome of choices into a continuously updated decision strategy under ambiguous conditions. The complexity of the task has made it difficult for neuroimaging studies to disentangle the underlying neurocognitive processes. In this study, we used functional magnetic resonance imaging in combination with a novel adaptation of the task, which allowed us to examine separately activation associated with the moment of decision or the evaluation of decision outcomes. Importantly, using whole-brain regression analyses with individual performance, in combination with the choice/outcome history of individual subjects, we aimed to identify the neural overlap between areas that are involved in the evaluation of outcomes and in the progressive discrimination of the relative value of available choice options, thus mapping the two fundamental cognitive processes that lead to adaptive decision making. We show that activation in right ventromedial and dorsolateral prefrontal cortex was predictive of adaptive performance, in both discriminating disadvantageous from advantageous decisions and confirming negative decision outcomes. We propose that these two prefrontal areas mediate shifting away from disadvantageous choices through their sensitivity to accumulating negative outcomes. These findings provide functional evidence of the underlying processes by which these prefrontal subregions drive adaptive choice in the task, namely through contingency-sensitive outcome evaluation.

Urban smoke concentrations at Kew, London, 1898-2004

Historical smoke concentrations at monthly resolution for the early twentieth century are found for Kew Observatory, London, using the atmospheric electricity proxy technique. Smoke particles modify the electrical properties of urban air: an increase in smoke concentration reduces air's electrical conductivity and increases the Potential Gradient (PG). Calibrated PG data are available from Kew since 1898, and air conductivity was measured routinely between 1909 and 1979 using the technique developed by C.T.R. Wilson. Automated smoke observations at the same site overlap with the atmospheric electrical measurements from 1921, providing an absolute calibration to smoke concentration. This shows that the late nineteenth century winter smoke concentrations at Kew were approximately 100 times greater than contemporary winter smoke concentrations. Following smoke emission regulations reducing the smoke concentration, the electrical parameters of the urban air did not change dramatically. This is suggested to be due to a composition change, with an increase in the abundance of small aerosol compensating for the decrease in smoke. (c) 2006 Elsevier Ltd. All rights reserved.

Origin and structure of Devensian depressions at Letton, Herefordshire

Groups of circular to oval enclosed depressions in soft sediments of Pleistocene age are relatively common in north-west Europe. These features are normally interpreted as being either glacial or periglacial in origin. Where these features are developed in glacial sediments, a glacial (and specifically ‘kettle hole’) genesis is considered most likely. Some groups of features, however, have been re-interpreted as being periglacial in origin and are thought to be the remains of cryogenic mounds (former pingos or palsas/lithalsas). The problem at many sites, of course, is correct identification and previously this was often resolved through extensive trenching of the sediments. The use of geophysics in the form of electrical resistivity tomography and ground probing radar, however, can aid investigation and interpretation and is less invasive. A group of enclosed depressions in the Letton area of Herefordshire within the Last Glacial Maximum ice limit (Late Devensian) have been investigated in this way. The morphology and internal structure of the features and their existence in glaciolacustrine sediments of Late Devensian age strongly suggests that these depressions are kettle holes resulting from ice block discharge into a shallow lakes or lakes, and hence a glacial origin is supported. The lack of any ramparts surrounding the depressions (at the surface or any evidence of these at depth) and the fact that they do not overlap (‘mutually interfere’) indicates that they are not the remains of cryogenic mounds.

Later Pleistocene evolution of the Exe valley: a chronostratigraphic model of terrace formation and its implications for Palaeolithic archaeology

This paper presents the first systematic chronostratigraphic study of the river terraces of the Exe catchment in South West England and a new conceptual model for terrace formation in unglaciated basins with applicability to terrace staircase sequences elsewhere. The Exe catchment lay beyond the maximum extent of Pleistocene ice sheets and the drainage pattern evolved from the Tertiary to the Middle Pleistocene, by which time the major valley systems were in place and downcutting began to create a staircase of strath terraces. The higher terraces (8-6) typically exhibit altitudinal overlap or appear to be draped over the landscape, whilst the middle terraces show greater altitudinal separation and the lowest terraces are of a cut and fill form. The terrace deposits investigated in this study were deposited in cold phases of the glacial-interglacial Milankovitch climatic cycles with the lowest four being deposited in the Devensian Marine Isotope Stages (MIS) 4-2. A new cascade process-response model is proposed of basin terrace evolution in the Exe valley, which emphasises the role of lateral erosion in the creation of strath terraces and the reworking of inherited resistant lithological components down through the staircase. The resultant emergent valley topography and the reworking of artefacts along with gravel clasts, have important implications for the dating of hominin presence and the local landscapes they inhabited. Whilst the terrace chronology suggested here is still not as detailed as that for the Thames or the Solent System it does indicate a Middle Palaeolithic hominin presence in the region, probably prior to the late Wolstonian Complex or MIS 6. This supports existing data from cave sites in South West England.

A well-characterised peak identification list of MALDI MS profile peaks for human blood serum

MALDI MS profiling, using easily available body fluids such as blood serum, has attracted considerable interest for its potential in clinical applications. Despite the numerous reports on MALDI MS profiling of human serum, there is only scarce information on the identity of the species making up these profiles, particularly in the mass range of larger peptides. Here, we provide a list of more than 90 entries of MALDI MS profile peak identities up to 10 kDa obtained from human blood serum. Various modifications such as phosphorylation were detected among the peptide identifications. The overlap with the few other MALDI MS peak lists published so far was found to be limited and hence our list significantly extends the number of identified peaks commonly found in MALDI MS profiling of human blood serum.

Estimating technical efficiency of Australian dairy farms using alternative frontier methodologies

Technical efficiency is estimated and examined for a cross-section of Australian dairy farms using various frontier methodologies; Bayesian and Classical stochastic frontiers, and Data Envelopment Analysis. The results indicate technical inefficiency is present in the sample data. Also identified are statistical differences between the point estimates of technical efficiency generated by the various methodologies. However, the rank of farm level technical efficiency is statistically invariant to the estimation technique employed. Finally, when confidence/credible intervals of technical efficiency are compared significant overlap is found for many of the farms' intervals for all frontier methods employed. The results indicate that the choice of estimation methodology may matter, but the explanatory power of all frontier methods is significantly weaker when interval estimate of technical efficiency is examined.

The changing structure of diets in the European Union in relation to healthy eating guidelines

Objective: Our objective in this paper is to assess diets in the European Union (EU) in relation to the recommendations of the recent World Health Organization/Food and Agriculture Organization expert consultation and to show how diets have changed between 1961 and 2001. Data and methods: Computations make use of FAOSTAT data on food availability at country level linked to a food composition database to convert foods to nutrients. We further explore the growing similarity of diets in the EU by making use of a consumption similarity index. The index provides a single number measure of dietary overlap between countries. Results: The data confirm the excessive consumption by almost all countries of saturated fats, cholesterol and sugars, and the convergence of nutrient intakes across the EU. Whereas in 1961 diets in several European countries were more similar to US diets than to those of other European countries, this is no longer the case; moreover, while EU diets have become more homogeneous, the EU as a whole and the USA have become less similar over time. Conclusions: Although the dominant cause of greater similarity in EU diets over the period studied is increased intakes in Mediterranean countries of saturated fats, cholesterol and sugar, also important are reductions in saturated fat and sugar in some Northern European countries. This suggests that healthy eating messages are finally having an impact on diets; a distinctly European diet may also be emerging.

Phylogeny and the hierarchical organization of plant diversity

R. H. Whittaker's idea that plant diversity can be divided into a hierarchy of spatial components from alpha at the within-habitat scale through beta for the turnover of species between habitats to gamma along regional gradients implies the underlying existence of alpha, beta, and gamma niches. We explore the hypothesis that the evolution of a, (3, and gamma niches is also hierarchical, with traits that define the a niche being labile, while those defining a and 7 niches are conservative. At the a level we find support for the hypothesis in the lack of close significant phylogenetic relationship between meadow species that have similar a niches. In a second test, a niche overlap based on a variety of traits is compared between congeners and noncongeners in several communities; here, too, there is no evidence of a correlation between a niche and phylogeny. To test whether beta and gamma niches evolve conservatively, we reconstructed the evolution of relevant traits on evolutionary trees for 14 different clades. Tests against null models revealed a number of instances, including some in island radiations, in which habitat (beta niche) and elevational maximum (an aspect of the gamma niche) showed evolutionary conservatism.

The phenology and potential for self-pollination of two Australian monoecious fig species

In this preliminary study, the reproductive phenology of two monoecious fig species, Ficus racemosa and F. rubiginosa, was examined in tropical Australia. Syconia (inflorescences) occurred on both species all year round, but pre-floral and interfloral syconia were much commoner than the wasp-receptive and wasp-emitting phases in both species. The temporal overlap of the wasp-receptive and wasp-emitting phases on a single tree indicated that self-pollination was possible in both species and that pollinators may sometimes persist through multiple generations on one tree. This sexual phase overlap was commoner in F. rubiginosa than in F racemosa. The two species also differed in their general within-tree asynchrony, with a higher diversity of phases on F. rubiginosa than on F. racemosa. The time from syconium initiation to ripening was very similar in F. rubiginosa (mean = 48.51 days) and F. racemosa (mean = 43.53 days). However, there was much more variation within and between trees for F. rubiginosa. In addition, the wasp-receptive phase was found to last up to 5 days (rnean = 4.38) in F. rubiginosa. Such longevity should contribute substantially to local pollinator population persistence. Future work should use genetic studies to determine whether self-pollination is common in these fig species.

Inhibition of coxsackie B virus infection by soluble forms of its receptors: Binding affinities, altered particle formation, and competition with cellular receptors

We previously reported that soluble decay-accelerating factor (DAF) and coxsackievirus-adenovirus receptor (CAR) blocked coxsackievirus 133 (CVB3) myocarditis in mice, but only soluble CAR blocked CVB3-mediated pancreatitis. Here, we report that the in vitro mechanisms of viral inhibition by these soluble receptors also differ. Soluble DAF inhibited virus infection through the formation of reversible complexes with CVB3, while binding of soluble CAR to CVB induced the formation of altered (A) particles with a resultant irreversible loss of infectivity. A-particle formation was characterized by loss of VP4 from the virions and required incubation of CVB3-CAR complexes at 37 degrees C. Dimeric soluble DAF (DAF-Fc) was found to be 125-fold-more effective at inhibiting CVB3 than monomeric DAF, which corresponded to a 100-fold increase in binding affinity as determined by surface plasmon resonance analysis. Soluble CAR and soluble dimeric CAR (CAR-Fc) bound to CVB3 with 5,000- and 10,000-fold-higher affinities than the equivalent forms of DAF. While DAF-Fc was 125-fold-more effective at inhibiting virus than monomeric DAF, complement regulation by DAF-Fc was decreased 4 fold. Therefore, while the virus binding was a cooperative event, complement regulation was hindered by the molecular orientation of DAF-Fc, indicating that the regions responsible for complement regulation and virus binding do not completely overlap. Relative contributions of CVB binding affinity, receptor binding footprint on the virus capsid, and induction of capsid conformation alterations for the ability of cellular DAF and CAR to act as receptors are discussed.

Comparison of the euryarchaeal microbial community in guts and food-soil of the soil-feeding termite Cubitermes fungifaber across different soil types

Termites are an important component of tropical soil communities and have a significant affect on the structure and nutrient content of soil. Digestion in termites is related to gut structure, gut physico-chemical conditions and gut symbiotic microbiota. Here we describe the use of 16S rRNA gene sequencing and Terminal-restriction Fragment Length Polymorphism (T-RFLP) analysis to examine methanogenic Archaea (MA) in the guts and food-soil of the soil-feeder Cubitermes fungifaber Sjostedt across a range of soil types. If they are strictly vertically inherited, then MA in guts should be the same in all individuals even if the soils differ across sites. In contrast, gut MA should reflect what is present in soil if populations are merely a reflection of what is ingested as the insects forage. We show clear differences between the euryarchaeal communities in termite guts and in food-soils from five different sites. Analysis of 16S rRNA gene clones indicated little overlap between the gut and soil communities. Gut clones were related to a termite-derived Methanomicrobiales cluster, to Methanobrevibacter and, surprisingly, to the haloalkaliphile Natronococcus. Soil clones clustered with Methanosarcina, Methanomicrococcus or Rice Cluster I. T-RFLP analysis indicated that the archaeal communities in the soil samples differed from site to site, whereas those in termite guts were similar between sites. There was some overlap between the gut and soil communities but these may represent transient populations in either guts or soil. Our data does not support the hypothesis that termite gut MA are derived from their food soil but also does not support a purely vertical transmission of gut microflora.

Comparison of Euryarchaea strains in the guts and food-soil of the soil-feeding termite Cubitermes fungifaber across different soil types

Termites are an important component of tropical soil communities and have a significant effect on the structure and nutrient content of soil. Digestion in termites is related to gut structure, gut physicochemical conditions, and gut symbiotic microbiota. Here we describe the use of 16S rRNA gene sequencing and terminal-restriction fragment length polymorphism (T-RFLP) analysis to examine methanogenic archaea (MA) in the guts and food-soil of the soil-feeder Cubitermes fungifaber Sjostedt across a range of soil types. If these MA are strictly vertically inherited, then the MA in guts should be the same in all individuals even if the soils differ across sites. In contrast, gut MA should reflect what is present in soil if populations are merely a reflection of what is ingested as the insects forage. We show clear differences between the euryarchaeal communities in termite guts and in food-soils from five different sites. Analysis of 16S rRNA gene clones indicated little overlap between the gut and soil communities. Gut clones were related to a termite-derived Methanomicrobiales cluster, to Methanobrevibacter and, surprisingly, to the haloalkaliphile Natronococcus. Soil clones clustered with Methanosarcina, Methanomicrococcus, or rice cluster I. T-RFLP analysis indicated that the archaeal communities in the soil samples differed from site to site, whereas those in termite guts were similar between sites. There was some overlap between the gut and soil communities, but these may represent transient populations in either guts or soil. Our data do not support the hypothesis that termite gut MA are derived from their food-soil but also do not support a purely vertical transmission of gut microflora.

A conserved basic loop in hepatitis C virus p7 protein is required for amantadine-sensitive ion channel activity in mammalian cells but is dispensable for localization to mitochondria

We previously identified the function of the hepatitis C virus (HCV) p7 protein as an ion channel in artificial lipid bilayers and demonstrated that this in vitro activity is inhibited by amantadine. Here we show that the ion channel activity of HCV p7 expressed in mammalian cells can substitute for that of influenza virus M2 in a cell-based assay. This was also the case for the p7 from the related virus, bovine viral diarrhoea virus (BVDV). Moreover, amantadine was shown to abrogate HCV p7 function in this assay at a concentration that specifically inhibits M2. Mutation of a conserved basic loop located between the two predicted trans-membrane alpha helices rendered HCV p7 non-functional as an ion channel. The intracellular localization of p7 was unaffected by this mutation and was found to overlap significantly with membranes associated with mitochondria. Demonstration of p7 ion channel activity in cellular membranes and its inhibition by amantadine affirm the protein as a target for future anti-viral chemotherapy.

Pax gene expression in the developing central nervous system of Ciona intestinalis

We compare the expression patterns in Ciona intestinalis of three members of the Pax gene family, CiPax3/7, CiPax6 and Cipax2/5/8. All three genes are expressed in restricted patterns in the developing central nervous system. At the tailbud stage, CiPax3/7 is present in three patches in the brain and along the posterior neural tube, CiPax6 throughout the anterior brain and along the posterior neural tube and CiPax2/5/8 in a restricted region of the posterior brain. Double in situ hybridisations were used to identify areas of overlap between the expression of different genes. This showed that CiPax3/7 overlaps with the boundaries of CiPax6 expression in the anterior brain, and with CiPax2/5/8 in the posterior brain. The overlap between CiPax3/7 and CiPax2/5/8 is unlike that described in the ascidian Halocynthia rorezti. (C) 2003 Elsevier B.V. All rights reserved.