Analysis of prion strains by PrPSc profiling in sporadic Creutzfeldt-Jakob disease.

BACKGROUND: Prion diseases are a group of invariably fatal neurodegenerative disorders affecting humans and a wide range of mammals. An essential part of the infectious agent, termed the prion, is composed of an abnormal isoform (PrPSc) of a host-encoded normal cellular protein (PrPC). The conversion of PrPC to PrPSc is thought to play a crucial role in the development of prion diseases and leads to PrPSc deposition, mainly in the central nervous system. Sporadic Creutzfeldt-Jakob disease (sCJD), the most common form of human prion disease, presents with a marked clinical heterogeneity. This diversity is accompanied by a molecular signature which can be defined by histological, biochemical, and genetic means. The molecular classification of sCJD is an important tool to aid in the understanding of underlying disease mechanisms and the development of therapy protocols. Comparability of classifications is hampered by disparity of applied methods and inter-observer variability. METHODS AND FINDINGS: To overcome these difficulties, we developed a new quantification protocol for PrPSc by using internal standards on each Western blot, which allows for generation and direct comparison of individual PrPSc profiles. By studying PrPSc profiles and PrPSc type expression within nine defined central nervous system areas of 50 patients with sCJD, we were able to show distinct PrPSc distribution patterns in diverse subtypes of sCJD. Furthermore, we were able to demonstrate the co-existence of more than one PrPSc type in individuals with sCJD in about 20% of all patients and in more than 50% of patients heterozygous for a polymorphism on codon 129 of the gene encoding the prion protein (PRNP). CONCLUSION: PrPSc profiling represents a valuable tool for the molecular classification of human prion diseases and has important implications for their diagnosis by brain biopsy. Our results show that the co-existence of more than one PrPSc type might be influenced by genetic and brain region-specific determinants. These findings provide valuable insights into the generation of distinct PrPSc types.

Upper Triassic foraminifers from Panthalassan carbonate buildups of Southwestern Japan and their paleobiogeographic implications

Detailed sampling of the Upper Triassic atoll-type carbonates of the Sambosan Accretionary Complex throughout Southwest Japan yielded highly abundant and diversified porcelaneous, microgranular, agglutinated and hyaline foraminifers of Carnian-Rhaetian age, as well as some microproblematica and ostracods. The foraminiferal assemblages were collected from shallow-water carbonates originated upon volcanic seamounts surrounded by deep-water radiolarian chert in a mid-open oceanic realm of the Panthalassan Ocean during Triassic time. Because most studies of the Upper Triassic microfauna come from the former Tethys, counterparts of the Panthalassan Ocean are pivotal to decipher the micropalaeontological biodiversity of the western circum Pacific, as well as to evaluate the distribution patterns of organisms and their evolution trends throughout the Tethys and Panthalassa. This study reports on 42 genera and 60 species whose associations can be used as sedimentary facies indicators of carbonate buildup environments. Japanese specimens show a strong Tethyan affinity, and especially with the Peri- and Southern Tethyan forms. A palaeobiogeographic distribution analysis using a large foraminiferal database is led, in order to evaluate the extraordinary spreading of these Upper Triassic foraminifers between the Neo-Tethys and the Panthalassa. Data are finally integrated in a new plate tectonic model, where six faunistic provinces are defined, each containing a characteristic foraminiferal assemblage. This map provides for the first time a useful and visual synthesis of the Upper Triassic foraminifer palaeobiogeographic distribution.

Seismic attenuation and velocity dispersion in heterogeneous partially saturated porous rocks

Using a numerical approach, we explore wave-induced fluid flow effects in partially saturated porous rocks in which the gas-water saturation patterns are governed by mesoscopic heterogeneities associated with the dry frame properties. The link between the dry frame properties and the gas saturation is defined by the assumption of capillary pressure equilibrium, which in the presence of heterogeneity implies that neighbouring regions can exhibit different levels of saturation. To determine the equivalent attenuation and phase velocity of the synthetic rock samples considered in this study, we apply a numerical upscaling procedure, which permits to take into account mesoscopic heterogeneities associated with the dry frame properties as well as spatially continuous variations of the pore fluid properties. The multiscale nature of the fluid saturation is taken into account by locally computing the physical properties of an effective fluid, which are then used for the larger-scale simulations. We consider two sets of numerical experiments to analyse such effects in heterogeneous partially saturated porous media, where the saturation field is determined by variations in porosity and clay content, respectively. In both cases we also evaluate the seismic responses of corresponding binary, patchy-type saturation patterns. Our results indicate that significant attenuation and modest velocity dispersion effects take place in this kind of media for both binary patchy-type and spatially continuous gas saturation patterns and in particular in the presence of relatively small amounts of gas. The numerical experiments also show that the nature of the gas distribution patterns is a critical parameter controlling the seismic responses of these environments, since attenuation and velocity dispersion effects are much more significant and occur over a broader saturation range for binary patchy-type gas-water distributions. This analysis therefore suggests that the physical mechanisms governing partial saturation should be accounted for when analysing seismic data in a poroelastic framework. In this context, heterogeneities associated with the dry frame properties, which do not play important roles in wave-induced fluid flow processes per se, should be taken into account since they may determine the kind of gas distribution pattern taking place in the porous rock.

Nonshivering thermogenesis capacity associated to mitochondrial DNA haplotypes and gender in the greater white-toothed shrew, Crocidura russula.

A selection gradient was recently suggested as one possible cause for a clinal distribution of mitochondrial DNA (mtDNA) haplotypes along an altitudinal transect in the greater white-toothed shrew, Crocidura russula (Ehinger et al. 2002). One mtDNA haplotype (H1) rare in lowland, became widespread when approaching the altitudinal margin of the distribution. As H1 differs from the main lowland haplotype by several nonsynonymous mutations (including on ATP6), and as mitochondria play a crucial role in metabolism and thermogenesis, distribution patterns might stem from differences in the thermogenic capacity of different mtDNA haplotypes. In order to test this hypothesis, we measured the nonshivering thermogenesis (NST) associated with different mtDNA haplotypes. Sixty-two shrews, half of which had the H1 haplotype, were acclimated in November at semioutdoor conditions and measured for NST throughout winter. Our results showed the crucial role of NST for winter survival in C. russula. The individuals that survived winter displayed a higher significant increase in NST during acclimation, associated with a significant gain in body mass, presumably from brown fat accumulation. The NST capacity (ratio of NST to basal metabolic rate) was exceptionally high for such a small species. NST was significantly affected by a gender x haplotype interaction after winter-acclimation: females bearing the H1 haplotype displayed a better thermogenesis at the onset of the breeding season, while the reverse was true for males. Altogether, our results suggest a sexually antagonistic cyto-nuclear selection on thermogenesis.

Transmission Fourier transform infrared microspectroscopy allows simultaneous assessment of cutin and cell-wall polysaccharides of Arabidopsis petals.

A procedure for the simultaneous analysis of cell-wall polysaccharides, amides and aliphatic polyesters by transmission Fourier transform infrared microspectroscopy (FTIR) has been established for Arabidopsis petals. The combination of FTIR imaging with spectra derivatization revealed that petals, in contrast to other organs, have a characteristic chemical zoning with high amount of aliphatic compounds and esters in the lamina and of polysaccharides in the stalk of the petal. The hinge region of petals was particular rich in amides as well as in vibrations potentially associated with hemicellulose. In addition, a number of other distribution patterns have been identified. Analyses of mutants in cutin deposition confirmed that vibrations of aliphatic compounds and esters present in the lamina were largely associated with the cuticular polyester. Calculation of spectrotypes, including the standard deviation of intensities, allowed detailed comparison of the spectral features of various mutants. The spectrotypes not only revealed differences in the amount of polyesters in cutin mutants, but also changes in other compound classes. For example, in addition to the expected strong deficiencies in polyester content, the long-chain acyl CoA synthase 2 mutant showed increased intensities of vibrations in a wavelength range that is typical for polysaccharides. Identical spectral features were observed in quasimodo2, a cell-wall mutant of Arabidopsis with a defect in pectin formation that exhibits increased cellulose synthase activity. FTIR thus proved to be a convenient method for the identification and characterization of mutants affected in the deposition of cutin in petals.

Meliponini neotropicais: o gênero Partamona Schwarz, 1939 (Hymenoptera, Apidae)

Neotropical Meliponini: the genus Partamona Schwarz, 1939 (Hymenoptera, Apidae). The systematics and biogeography of Partamona Schwarz, a Neotropical genus of stingless bees (Meliponini, Apinae, Apidae), are revised. Seventeen new species are described: P. epiphytophila sp. nov., P. subtilis sp. nov., P. nhambiquara sp. nov., P. batesi sp. nov., P. yungarum sp. nov., P. vitae sp. nov., P. ferreirai sp. nov., P. gregaria sp. nov., P. auripennis sp. nov., P. nigrilabris sp. nov., P. combinata sp. nov., P. chapadicola sp. nov., P. seridoensis sp. nov., P. littoralis sp. nov., P. criptica sp. nov., P. rustica sp. nov. and P. sooretamae sp. nov. Partamona pseudomusarum Camargo, 1980, is considered as junior synonym of P. vicina Camargo, 1980. Types of P. grandipennis (Schwarz, 1951), P. xanthogastra Pedro & Camargo, 1996-1997, P. pearsoni (Schwarz, 1938), P. ailyae Camargo, 1980, P. pseudomusarum, P. vicina, P. mulata Moure in Camargo, 1980, P. aequatoriana Camargo, 1980, P. mourei Camargo, 1980, P. peckolti, (Friese, 1901), P. testacea (Klug, 1807), P. helleri (Friese, 1900) and P. musarum (Cockerell, 1917) were examined. Lectotypes of P. orizabaensis (Strand, 1919), and P. cupira (Smith, 1863) are designated. An identification key for the species and drawings of morphological characters are presented. A phylogenetic hypothesis, based mainly on morphological characters is proposed. Four groups are defined, considering the shape of mandible of workers and sternum VII of males: bilineata / epiphytophila group (western Amazon to México), including P. bilineata (Say), P. grandipennis, P. xanthogastra P. orizabaensis P. peckolti P. epiphytophila sp. nov., P. subtilis sp. nov., P. nhambiquara sp. nov., P. batesi sp. nov., P. yungarum sp. nov. and P. vitae sp. nov.; musarum group (Central Brazil, north of South America to Central America), including P. musarum, P. aequatoriana, P. vicina, P. mourei, P. pearsoni, P. ferreirai sp. nov., P. gregaria sp. nov. and P. testacea; nigrior group (Central Brazil to northeast of South America) including P. nigrior (Cockerell, 1925), P. auripennis sp. nov., P. nigrilabris sp. nov., P. combinata sp. nov., P. chapadicola sp. nov., P. seridoensis sp. nov. and P. littoralis sp. nov., and cupira group (southeastern and Central Brazil), including P. cupira, P. mulata, P. ailyae, P. sooretamae sp. nov., P. criptica sp. nov., P. rustica sp. nov. and P. helleri. Some geographic distribution patterns, congruent with that of other Meliponini bees, are commented.

Padrões de Distribuição da Flora Exótica em Cabo Verde: o Papel dos Factores Antrópicos e Ecológicos

Dada a relevância a nível global do impacto da introdução de espécies exóticas, e tendo sido identificada uma grande escassez de estudos nesta área de investigação em Cabo Verde, pretendeu-se com este estudo actualizar a lista dos taxa exóticos naturalizados deste arquipélago, fornecendo dados sobre a sua distribuição, caracterização taxonómica e principais grupos funcionais. Com o objectivo de averiguar quais são os factores que influenciam os padrões de distribuição da flora exótica nestas ilhas, efectuaram-se correlações de Spearman entre o número de taxa exóticos e várias variáveis ambientais e antrópicas. Sendo conhecida a importância que os factores antrópicos têm na composição e distribuição da flora introduzida, procurou-se ainda perceber se a flora da única ilha desabitada do arquipélago (Santa Luzia) poderá ser indicadora de características invasoras das espécies introduzidas. Os resultados obtidos indicaram um total de 403 taxa exóticos, correspondendo a 55% da flora de Cabo Verde, sendo as Poaceae, Fabaceae e Asteraceae as famílias com maior número de espécies. Verificou-se também que predominam as espécies herbáceas e o tipo biológico mais frequente é o terófito. Além disso, a população rural é o factor que mais fortemente e positivamente correlacionado com os padrões de distribuição da flora exótica em Cabo Verde. Correlações positivas muito significativas foram também encontradas para a área e altitude máxima de cada ilha. A análise da flora exótica da ilha desabitada de Santa Luzia revelou que, embora os taxa exóticos registados nesta ilha estejam presentes em quase todas as outras ilhas, as espécies inventariadas parecem não exibir um comportamento invasor ou de ameaça à flora nativa. Para finalizar, espera-se que os resultados obtidos possam contribuir com informação que fundamente futuras estratégias de conservação da Biodiversidade das ilhas de Cabo Verde.

Origin of samples of Cannabis sativa through insect fragments associated with compacted hemp drug in South America

Origin of samples of Cannabis sativa through insect fragments associated with compacted hemp drug in South America. Insects associated with a seizure of Cannabis sativa L. may indicate the origin of the illicit drug. Nevertheless, no work regarding this subject has been previously published for South America. In the present investigation, seven kilograms of vegetal material (C. sativa) were inspected for insect fragments. Three species were identified and used to test the origin of the seizure of cannabis plant material: Euschistus heros (Fabricius, 1794), Thyanta perditor (Fabricius, 1794) (Heteroptera, Pentatomidae), and Cephalotes pusillus (Klug, 1824) (Hymenoptera, Formicidae). These insect species restricted the geographic origin of the drug to the Neotropical region, and their distribution patterns showed an overlap of the State of Mato Grosso (Brazil), Argentina, and Paraguay. Based on this information, two of the three major C. sativa growing areas in South America were excluded: (1) the Colombian territory and (2) northeastern Brazil.

What is the importance of open habitat in a predominantly closed forest area to the dung beetle (Coleoptera, Scarabaeinae) assemblage?

What is the importance of open habitat in a predominantly closed forest to the dung beetle assemblage? The Atlantic Forest in Brazil is one of the most highly disturbed ecosystems and is mainly represented by fragmented areas. However, in places where human disturbances have ceased, certain areas are showing a natural regeneration pattern. The aim of the present study was to determine how the dung beetle assemblage responds to distinct habitat structures in a fragment of Atlantic Forest. For such, open and closed forest areas were sampled in a fragment of the Atlantic Forest in the northeastern region of Brazil. Pitfall traps baited with excrement and carrion were used to collect the beetles. A total of 7,267 individuals belonging to 35 species were captured. Canthon chalybaeus and C. mutabilis were restricted to open areas. Nearly 90% of the individuals of C. aff. simulans and Deltochilum aff. irroratum were identified in these areas. A higher percentage (> 50%) of Canthon staigi, Dichotomius aff. depressicolis and D. aff. sericeus occurred in closed areas. Abundance differed between areas, with higher values in closed areas. Richness was not influenced by the habitat structure. NMDS ordination exhibited the segregation of areas and ANOSIM confirmed that this variable explained the assemblage of dung beetle species. The findings of the present study validate that open areas are associated to more restrictive conditions, limiting a higher abundance of dung beetle. Although situated near preserved fragments, the studied open areas increase the heterogeneity of the general landscape.

Comparative study of algal communities in acid and alkaline waters from Tinto, Odiel and Piedras river basins (SW Spain)

The distribution patterns of benthic algal assemblages in the Tinto, Odiel and Piedras rivers were analyzed during the winter of 2005 in 18 sampling stations. The main objective was to assess and compare the algal communities and parameters affecting them both in the zones affected by acid mine drainage (AMD) and in naturally alkaline waters. A total of 108 benthic diatom taxa and 31 non-diatom taxa were identi ed. Results showed large differences between algal communities in the two environments: Pinnularia acoricola, P. subcapitata and Eunotia exigua were the most frequent diatom taxa in regions affected by acid mine drainage, along with algae like Klebsormidium and Euglena mutabilis were the most relevant non-diatom taxa. In alkaline waters the dominant diatom taxa were Planothidium frequentissimum, Gomphonema angustum, Fragilaria capucina, and some species of Navicula (N. viridula, N. veneta or N. radiosa), accompanied by Oscillatoria and Anabaena as well as by streptophytes of the group of zygnemataceae and desmidiaceae

Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.

Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods' resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R.

Understanding the ecological niche to elucidate spatial strategies of the southernmost Tupinambis lizards

Understanding factors that shape ranges of species is central in evolutionary biology. Species distribution models have become important tools to test biogeographical, ecological and evolutionary hypotheses. Moreover, from an ecological and evolutionary perspective, these models help to elucidate the spatial strategies of species at a regional scale. We modelled species distributions of two phylogenetically, geographically and ecologically close Tupinambis species (Teiidae) that occupy the southernmost area of the genus distribution in South America. We hypothesized that similarities between these species might have induced spatial strategies at the species level, such as niche differentiation and divergence of distribution patterns at a regional scale. Using logistic regression and MaxEnt we obtained species distribution models that revealed interspecific differences in habitat requirements, such as environmental temperature, precipitation and altitude. Moreover, the models obtained suggest that although the ecological niches of Tupinambis merianae and T. rufescens are different, these species might co-occur in a large contact zone. We propose that niche plasticity could be the mechanism enabling their co-occurrence. Therefore, the approach used here allowed us to understand the spatial strategies of two Tupinambis lizards at a regional scale.

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation.

Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps.

Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ).

Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18-85years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

Trace element partitioning in HP-LT metamorphic assemblages during subduction-related metamorphism, Ile de Groix, France: a detailed LA-ICPMS study

Devolatilization reactions and subsequent transfer of fluid from subducted oceanic crust into the overlying mantle wedge are important processes, which are responsible for the specific geochemical characteristics of subduction-related metamorphic rocks, as well as those of arc magmatism. To better understand the geochemical fingerprint induced by fluid mobilization during dehydration and rehydration processes related to subduction zone metamorphism, the trace element and rare earth element (REE) distribution patterns in HP-LT metamorphic assemblages in eclogite-, blueschist- and greenschist-facies rocks of the Ile de Groix were obtained by laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) analysis. This study focuses on 10 massive basic rocks representing former hydrothermally altered mid-ocean ridge basalts (MORB), four banded basic rocks of volcano-sedimentary origin and one micaschist. The main hosts for incompatible trace elements are epidote (REE, Th, U, Pb, Sr), garnet [Y, heavy REE (HREE)], phengite (Cs, Rb, Ba, B), titanite [Ti, Nb, Ta, REE; HREE > LREE (light REE)], rutile (Ti, Nb, Ta) and apatite (REE, Sr). The trace element contents of omphacite, amphibole, albite and chlorite are low. The incompatible trace element contents of minerals are controlled by the stable metamorphic mineral assemblage and directly related to the appearance, disappearance and reappearance of minerals, especially epidote, garnet, titanite, rutile and phengite, during subduction zone metamorphism. Epidote is a key mineral in the trace element exchange process because of its large stability field, ranging from lower greenschist- to blueschist- and eclogite-facies conditions. Different generations of epidote are generally observed and related to the coexisting phases at different stages of the metamorphic cycle (e.g. lawsonite, garnet, titanite). Epidote thus controls most of the REE budget during the changing P-T conditions along the prograde and retrograde path. Phengite also plays an important role in determining the large ion lithophile element (LILE) budget, as it is stable to high P-T conditions. The breakdown of phengite causes the release of LILE during retrogression. A comparison of trace element abundances in whole-rocks and minerals shows that the HP-LT metamorphic rocks largely retain the geochemical characteristics of their basic, volcano-sedimentary and pelitic protoliths, including a hydrothermal alteration overprint before the subduction process. A large part of the incompatible trace elements remained trapped in the rocks and was recycled within the various metamorphic assemblages stable under changing metamorphic conditions during the subduction process, indicating that devolatilization reactions in massive basic rocks do not necessarily imply significant simultaneous trace element and REE release.