Movement, impacts and management of plant distributions in response to climate change: insights from invasions

A major challenge in this era of rapid climate change is to predict changes in species distributions and their impacts on ecosystems, and, if necessary, to recommend management strategies for maintenance of biodiversity or ecosystem services. Biological invasions, studied in most biomes of the world, can provide useful analogs for some of the ecological consequences of species distribution shifts in response to climate change. Invasions illustrate the adaptive and interactive responses that can occur when species are confronted with new environmental conditions. Invasion ecology complements climate change research and provides insights into the following questions: i) how will species distributions respond to climate change? ii) how will species movement affect recipient ecosystems? and iii) should we, and if so how can we, manage species and ecosystems in the face of climate change? Invasion ecology demonstrates that a trait-based approach can help to predict spread speeds and impacts on ecosystems, and has the potential to predict climate change impacts on species ranges and recipient ecosystems. However, there is a need to analyse traits in the context of life-history and demography, the stage in the colonisation process (e.g., spread, establishment or impact), the distribution of suitable habitats in the landscape, and the novel abiotic and biotic conditions under which those traits are expressed. As is the case with climate change, invasion ecology is embedded within complex societal goals. Both disciplines converge on similar questions of "when to intervene?" and "what to do?" which call for a better understanding of the ecological processes and social values associated with changing ecosystems.

Towards Integrated Governance of Landscape Development : The Swiss Model of Regional Nature Parks

Coherent regulation of landscape as a resource is a major challenge. How can the development interests of some actors (eg cable car operators and property developers) be reconciled with those of others (agriculture, forestry) and with conservation of biodiversity and scenic value? To help understand how the newly introduced Regional Nature Parks (RNPs) can improve the coherence of the regulation regime in Switzerland, we highlight current direct mechanisms for regulation of landscape as a resource (bans, inventories, subsidies) as well as indirect mechanisms (taking place through the regulation of the physical basis of landscapes, eg forest, land, and water planning policies). We show that RNPs are fundamentally innovative because they make it possible to manage and coordinate indirect strategies for appropriate regulation of resources at a landscape scale. In other words, RNPs enable organization of governance of landscape as a resource in a perimeter that is not necessarily restricted to administrative boundaries.

Landscape of transcription in human cells.

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Mineralogical, petrographic and geochemical characterisation of white and coloured Iberian marbles in the context of the provenancing of some artefacts from Thamusida (Kenitra, Morocco)

A multi-analytical study has been carried out on a collection of white and coloured Iberian marbles. A total of 135 marble specimens were collected in Spain and Portugal from the Betic chain (Alhaurin de la Torre, Mijas, Macael), Ossa Morena (Alconera, Almaden de la Plata and Viana do Alentejo), and the Estremoz Anticline (Bencatel, Borba and Estremoz) areas. X-ray diffractometry and carbon and oxygen stable isotope analysis were carried out on these samples; 38 samples were also investigated by optical and scanning electron microscopy. The results provide a set of diagnostic parameters that allow discriminating the sampled marble quarries. The carbonate minerals composition is distinctive for the Mijas and Alhaurin de la Torre marbles; the isotopic analysis allows discriminating also between these two dolomitic marble quarries. The Ossa Morena and Estremoz Anticline marbles share a similar stable isotope composition; the accessory mineral content, the maximum grain size (MGS) and the fabric are particularly useful in the distinction between them. In the framework of archaeometric provenance studies on Thamusida (Kenitra, Morocco) Roman marble artefacts, a specific comparison between this new Iberian database and archaeological findings has been carried out. The hypothesis of commercial exchanges between the Iberian regions and Roman Morocco is supported by the results of the provenance study, which suggested the Almaden de la Plata and Mijas quarries as possible sources of raw materials for the production of archaeological artefacts.

Clinicopathologic and molecular analysis of a choroidal pigmented schwannoma in the context of a PTEN hamartoma tumor syndrome.

PURPOSE: To report the first case of choroidal schwannoma in a patient affected by PTEN hamartoma tumor syndrome (PHTS) and investigate the molecular involvement of the phosphatase and tensin homolog (PTEN) and neurofibromin 2 (NF2) genes in this rare intraocular tumor. DESIGN: Observational case report. PARTICIPANT: A 10-year-old girl diagnosed with PHTS. METHODS: The enucleated specimen underwent histologic, immunohistochemical, and transmission electronic microscopy. The expression of PTEN and NF2 and their protein products were evaluated by reverse transcription-polymerase chain reaction and immunohistochemistry. Somatic mutations of PTEN and NF2, as well as allelic loss, were investigated by direct sequencing of DNA extracted from the tumor. PTEN epigenetic silencing was investigated by pyrosequencing. MAIN OUTCOME MEASURES: Histopathologic and molecular characterization of a choroidal pigmented schwannoma. RESULTS: Histopathologic, immunohistochemical, and electron microscopic analysis demonstrated features consistent with a pigmented cellular schwannoma of the choroid. We found no loss of heterozygosity at the genomic level for the PTEN germline mutation and no promoter hypermethylation or other somatic intragenic mutations. However, we observed an approximate 40% reduction of PTEN expression at both the mRNA and the protein level, indicating that the tumor was nonetheless functionally deficient for PTEN. Although DNA sequencing of NF2 failed to identify any pathologic variants, its expression was abolished within the tumor. CONCLUSIONS: We report the first description of a pigmented choroidal schwannoma in the context of a PHTS. This rare tumor showed a unique combination of reduction of PTEN and absence of NF2 expression.

Cartographier les géomorphosites : objectifs, publics et propositions méthodologiques

Related to the raise of the awareness of the importance of the Earth heritage, geomorphosites receive increasing attention from the scientific community. Assessment methods, classification and conservation strategies have been developed to safeguard the geomorphological heritage for present and future generations. On the other hand, Earth heritage offers opportunities to develop educational and recreational programs as well as tourism projects. Various interpretive supports and local development projects have been engendered in the past few years to promote geoheritage.¦Be it for the assessment, conservation or promotion of geomorphosites, maps are valuable from many standpoints. They can provide fundamental data for detailed geomorphosite description, serve as visual communication tools helping to guide the selection process in defining protection priority or supporting Earth heritage promotion and interpretàtion.¦This study reviews the main achievements and the objectives yet to be accomplished in the field of geomorphosite mapping and proposes a general framework for the mapping of geomorphosites that takes into account the different aims and publics. The main focus is on mapping geomorphosites for non-specialists in the field of Earth heritage promotion (Geotourism). In this context, maps are often employed to show itineraries or points of interest. Like a scheme or a diagram, a map can also be used as a method for visualising geoscientific information. This function is particularly important since some processes, which contributed to the formation of a geomorphosite or a geomorphological landscape are no longer or not always clearly visible in the landscape. In this case, maps become interpretive media that serve popularisation purposes.¦Mapping for non-specialists holds the challenging task to ensure the information transfer between the cartographer and the user. We therefore focus on both the implementation of the map by the cartographer (which information? which visualisation?) and the interpretation of the map by the user (effectiveness of the knowledge transfer). The research is based on empirical studies carried out in the Maderan valley (Canton of Uri) and in classes of the Cantons of Uri and Tessin that aim to gain knowledge about the familiarity and interests of non- specialists for geoheritage as well as about their map reading skills. The final objective is to formulate methodological proposals for geomorphosite mapping for interpretive purpose.

Old ferricrete landscape dismantling in Central Africa rain forest zone: formation of the present downslope iron accumulations.

Present downslope iron accumulations were investigated in the rainforest zone in southern Cameroon. Six clay and Fe-hydroxide dominated patterns have been identified and occur on the lower part of hill slopes. They can be subdivided in three different sequences, related to gentle, moderate or steep slopes. They are discontinuous with respect to the dismantling zone of the old ferricrete cap formed at Cretaceous period. They show a gradual development from a soft Fe-crust (carapace) to a vesicular facies that will, with time, cover the whole landscape again.

Shaping the interaction landscape of bioactive molecules.

MOTIVATION: Most bioactive molecules perform their action by interacting with proteins or other macromolecules. However, for a significant fraction of them, the primary target remains unknown. In addition, the majority of bioactive molecules have more than one target, many of which are poorly characterized. Computational predictions of bioactive molecule targets based on similarity with known ligands are powerful to narrow down the number of potential targets and to rationalize side effects of known molecules. RESULTS: Using a reference set of 224 412 molecules active on 1700 human proteins, we show that accurate target prediction can be achieved by combining different measures of chemical similarity based on both chemical structure and molecular shape. Our results indicate that the combined approach is especially efficient when no ligand with the same scaffold or from the same chemical series has yet been discovered. We also observe that different combinations of similarity measures are optimal for different molecular properties, such as the number of heavy atoms. This further highlights the importance of considering different classes of similarity measures between new molecules and known ligands to accurately predict their targets. CONTACT: olivier.michielin@unil.ch or vincent.zoete@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

'Toxic' and 'Nontoxic': confirming critical terminology concepts and context for clear communication

If 'the dose makes the poison', and if the context of an exposure to a hazard shapes the risk as much as the innate character of the hazard itself, then what is 'toxic' and what is 'nontoxic'? This article is intended to help readers and communicators: anticipate that concepts such as 'toxic' and 'nontoxic' may have different meanings to different stakeholders in different contexts of general use, commerce, science, and the law; recognize specific situations in which terms and related information could potentially be misperceived or misinterpreted; evaluate the relevance, reliability, and other attributes of information for a given situation; control actions, assumptions, interpretations, conclusions, and decisions to avoid flaws and achieve a desired outcome; and confirm that the desired outcome has been achieved. To meet those objectives, we provide some examples of differing toxicology terminology concepts and contexts; a comprehensive decision-making framework for understanding and managing risk; along with a communication and education message and audience-planning matrix to support the involvement of all relevant stakeholders; a set of CLEAR-communication assessment criteria for use by both readers and communicators; example flaws in decision-making; a suite of three tools to assign relevance vs reliability, align know vs show, and refine perception vs reality aspects of information; and four steps to foster effective community involvement and support. The framework and supporting process are generally applicable to meeting any objective.

The Mont-Mort metapelites: Variscan metamorphism and geodynamic context (Brianconnais basement, Western Alps, Switzerland)

The Mont-Mort metapelites are one of the best preserved relies of the Variscan unit in the Brianconnais basement. These micaschists crystallized during a poly-phase metamorphic cycle, under amphibolite facies conditions. Mineral parageneses and geothermobarometric calculations indicate a two-stage evolution. Stage (1) (550-600 degrees C and 5-8 kbar) is documented by assemblages of zoned garnet, staurolite, kyanite(?), biotite, muscovite, quartz and pla gioclase. Stage (2) (550-600 degrees C and 2 kbar) is illustrated by assemblages of andalusite, sillimanite, muscovite, biotite. This metamorphic evolution is characterized by a nearly isothermal decompression path, terminating with the formation of andalusite-bearing veins. U-Pb monazite dates at 330 Ma and Ar-40/Ar-39 muscovite dates at 290-310 Ma (without substantial evidence of argon resetting) point to Variscan metamorphism and yield an estimate of the time interval between the thermal peak and the retrogression stage within this part of the Brianconnais basement. Restoring the Brianconnais and other Alpine basement units within an existing geodynamic model of Cordillera construction and destruction, it is possible to understand better the transition from a medium pressure/high temperature regime (collision with a peak metamorphism around 330 Ma) to low-P/high-T conditions (decompression in an extensional regime) with high geothermal gradient, as recorded by the successive Variscan parageneses within the Mont-Mort metapelites.

Geomorphological heritage, conservation and promotion in high-alpine protected areas

In recent decades, recognition of both cultural and natural heritage has grown in the Alps. This tendency illustrates a collective identity building (local, national, alpine), but it also highlights, in the current context of global change, a renewed reflection of man's relationship with the environment. Thus, a fundamental and scientific intrinsic value (as a part of wilderness) tends to be recognized in the natural heritage as a whole. However, geoheritage (and geodiversity) is still often perceived as a secondary natural component, compared with bioheritage (and biodiversity). In this context, we study the geomorphological heritage (landforms and the processes that shape them) of Les Contamines-Montjoie Natural Reserve. Indeed, despite the high geomorphological richness (especially glacial) of the reserve, which covers more than 4000 ha of the Mont-Blanc Massif, local recognition of this heritage is still limited. In order to recognize and protect it, and starting with a scientific study, this research identifies the main local richness and assesses the geotourist and educational potentials. Finally, several tools to educate and promote geoheritage (educational paths and website) are proposed.

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and "roughness" (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.