The Alps Vegetation Database - a geo-referenced community-level archive of all terrestrial plants occurring in the Alps.

Mountain ranges are biodiversity hotspots worldwide and provide refuge to many organisms under contemporary climate change. Gathering field information on mountain biodiversity over time is of primary importance to understand the response of biotic communities to climate changes. For plants, several long-term observation sites and networks of mountain biodiversity are emerging worldwide to gather field data and monitor altitudinal range shifts and community composition changes under contemporary climate change. Most of these monitoring sites, however, focus on alpine ecosystems and mountain summits, such as the global observation research initiative in alpine environments (GLORIA). Here we describe the Alps Vegetation Database, a comprehensive community level archive (GIVD ID EU-00-014) which aims at compiling all available geo-referenced vegetation plots from lowland forests to alpine grasslands across the greatest mountain range in Europe: the Alps. This research initiative was funded between 2008 and 2011 by the Danish Council for Independent Research and was part of a larger project to compare cross-scale plant community structure between the Alps and the Scandes. The Alps Vegetation Database currently harbours 35,731 geo-referenced vegetation plots and 5,023 valid taxa across Mediterranean, temperate and alpine environments. The data are mainly used by the main contributors of the Alps Vegetation Database in an ecoinformatics approach to test hypotheses related to plant macroecology and biogeography, but external proposals for joint collaborations are welcome.

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

BACKGROUND: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. RESULTS: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility. CONCLUSIONS: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

Regulation of phosphate starvation responses in plants: signaling players and cross-talks.

Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.

Prevalence and factors associated with use of smokeless tobacco in young Swiss men.

BACKGROUND: Smokeless tobacco is of increasing interest to public health researchers and policy makers. This study aims to measure prevalence of smokeless tobacco use (nasal dry snuff, snus and chewing tobacco) among young Swiss men, and to describe its correlates. METHODS: We invited 13 245 young men to participate in this survey on socio-economic and substance use data. Response rate was 45.2%. We included 5720 participants. Descriptive statistics and multivariable-adjusted logistic regression were performed. RESULTS: Mean age of participants was 19.5 years. Self-reported use once a month or more often was 8% for nasal dry snuff, 3% for snus and negligible for chewing tobacco. In multivariable-adjusted logistic regression, the odds for nasal dry snuff use increased in non daily smokers [odds ratio (OR) 2.41, 95% confidence interval (CI) 1.90-3.05], compared with non smokers, participants reporting risky weekly drinking volume (OR 3.93, 95% CI 1.86-8.32), compared with abstinents, and binge drinking once a month or more often (OR 7.41, 95% CI 4.11-13.38), compared with never binge drinking. Nasal dry snuff use was positively associated with higher BMI, average or above family income and German language, compared with French, and negatively associated with academic higher education, compared with non higher education, and occasional cannabis use, compared with no cannabis use. Correlates of snus were similar to those of nasal dry snuff. CONCLUSION: One in 12 young Swiss men use nasal dry snuff and 3% use snus. Consumption of smokeless tobacco is associated with a cluster of other risky behaviours, especially binge drinking.

The serine-rich N-terminal region of Arabidopsis phytochrome A is required for protein stability.

Deletion or substitution of the serine-rich N-terminal stretch of grass phytochrome A (phyA) has repeatedly been shown to yield a hyperactive photoreceptor when expressed under the control of a constitutive promoter in transgenic tobacco or Arabidopsis seedlings retaining their native phyA. These observations have lead to the proposal that the serine-rich region is involved in negative regulation of phyA signaling. To re-evaluate this conclusion in a more physiological context we produced transgenic Arabidopsis seedlings of the phyA-null background expressing Arabidopsis PHYA deleted in the sequence corresponding to amino acids 6-12, under the control of the native PHYA promoter. Compared to the transgenic seedlings expressing wild-type phyA, the seedlings bearing the mutated phyA showed normal responses to pulses of far-red (FR) light and impaired responses to continuous FR light. In yeast two-hybrid experiments, deleted phyA interacted normally with FHY1 and FHL, which are required for phyA accumulation in the nucleus. Immunoblot analysis showed reduced stability of deleted phyA under continuous red or FR light. The reduced physiological activity can therefore be accounted for by the enhanced destruction of the mutated phyA. These findings do not support the involvement of the serine-rich region in negative regulation but they are consistent with a recent report suggesting that phyA turnover is regulated by phosphorylation.

The heat shock response in moss plants is regulated by specific calcium-permeable channels in the plasma membrane.

Land plants are prone to strong thermal variations and must therefore sense early moderate temperature increments to induce appropriate cellular defenses, such as molecular chaperones, in anticipation of upcoming noxious temperatures. To investigate how plants perceive mild changes in ambient temperature, we monitored in recombinant lines of the moss Physcomitrella patens the activation of a heat-inducible promoter, the integrity of a thermolabile enzyme, and the fluctuations of cytoplasmic calcium. Mild temperature increments, or isothermal treatments with membrane fluidizers or Hsp90 inhibitors, induced a heat shock response (HSR) that critically depended on a preceding Ca(2+) transient through the plasma membrane. Electrophysiological experiments revealed the presence of a Ca(2+)-permeable channel in the plasma membrane that is transiently activated by mild temperature increments or chemical perturbations of membrane fluidity. The amplitude of the Ca(2+) influx during the first minutes of a temperature stress modulated the intensity of the HSR, and Ca(2+) channel blockers prevented HSR and the onset of thermotolerance. Our data suggest that early sensing of mild temperature increments occurs at the plasma membrane of plant cells independently from cytosolic protein unfolding. The heat signal is translated into an effective HSR by way of a specific membrane-regulated Ca(2+) influx, leading to thermotolerance.

Diplostigmaty in plants: a novel mechanism that provides reproductive assurance.

Differentiation of female sexual organs in flowering plants is rare and contrasts with the wide range of male reproductive strategies. An unusual example involves diplostigmaty, the possession of spatially and temporally distinct stigmas in Sebaea (Gentianaceae). Here, the single pistil within a flower has an apical stigma, as occurs in most flowering plants, but also a secondary stigma that occurs midway down the style, which is physically discrete and receptive several days after the apical stigma. We examined the function of diplostigmaty in Sebaea aurea, an insect-pollinated species of the Western Cape of South Africa. Floral manipulations and measurements of fertility and mating patterns provided evidence that basal stigmas function to enable autonomous delayed self-pollination, without limiting opportunities for outcrossing and thus avoiding the costs of seed discounting. We suggest that delayed selfing serves as a mechanism of reproductive assurance in populations with low plant density. The possession of dimorphic stigma function provides a novel example of a flexible mixed-mating strategy in plants that is responsive to changing demographic conditions.

Interaction between tobacco and alcohol use and the risk of head and neck cancer: pooled analysis in the International Head and Neck Cancer Epidemiology Consortium.

BACKGROUND: The magnitude of risk conferred by the interaction between tobacco and alcohol use on the risk of head and neck cancers is not clear because studies have used various methods to quantify the excess head and neck cancer burden. METHODS: We analyzed individual-level pooled data from 17 European and American case-control studies (11,221 cases and 16,168 controls) participating in the International Head and Neck Cancer Epidemiology consortium. We estimated the multiplicative interaction parameter (psi) and population attributable risks (PAR). RESULTS: A greater than multiplicative joint effect between ever tobacco and alcohol use was observed for head and neck cancer risk (psi = 2.15; 95% confidence interval, 1.53-3.04). The PAR for tobacco or alcohol was 72% (95% confidence interval, 61-79%) for head and neck cancer, of which 4% was due to alcohol alone, 33% was due to tobacco alone, and 35% was due to tobacco and alcohol combined. The total PAR differed by subsite (64% for oral cavity cancer, 72% for pharyngeal cancer, 89% for laryngeal cancer), by sex (74% for men, 57% for women), by age (33% for cases <45 years, 73% for cases >60 years), and by region (84% in Europe, 51% in North America, 83% in Latin America). CONCLUSIONS: Our results confirm that the joint effect between tobacco and alcohol use is greater than multiplicative on head and neck cancer risk. However, a substantial proportion of head and neck cancers cannot be attributed to tobacco or alcohol use, particularly for oral cavity cancer and for head and neck cancer among women and among young-onset cases.

Uranium-enrichment in soils and plants in the vicinity of a pitchblende vein at La Creusaz-Les Marecottes (W of Martigny, Valais, Switzerland)

In the NE part of the Aiguilles Rouges Massif near Martigny, at the eastern contact of the Variscan Vallorcine granite to adjacent gneisses, a series of pitchblende (UO2)-veins occur. This paper determines the level of enrichment and mobility of uranium in soils situated in the vicinity of such a UO2-vein 7 km west of Martigny. Within an area of 50 x 100 m, situated on a relatively steep slope and characterized by a strong gramma-ray anomaly, six soil profiles including their plant cover and a reference soil profile outside the influence of the UO2-vein have been examined. The soil shows pH-values between 4 and 5 and is colluvial. The applied analytical methods for the metal contents include extraction methods, common for soil studies, and bulk analysis performed with X-ray fluorescence and ICP-MS. Uranium contents found in the uppermost 20 cm of the soil profiles vary from 2,500 ppm close to the vein to 15 ppm at the lowermost point of the study area. The reference soil has around 3 ppm uranium. At greater depth (20 to 40 cm) the U-content decreases to about half of the surface values, indicating a vertical transport of uranium within the soil profile. No systematic dependance of uranium-contents to grain size (amount of clay) nor to the amount of organic matter has been found. However, the good correlation between uranium and free iron oxide concentration suggests adsorption of uranium on iron oxy-hydroxides. The ashes of grass and mosses contain up to 90 ppm U, the blueberry and redwood only up to 3 ppm. Our observations suggest that at the surface the uranium is transported by downhill creep (solifluxion) of uranium-rich rock fragments. Liberated by oxidation of the uppermost fragments in a given soil column, the uranium migrates vertically until the conditions are favourable to adsorption onto Fe-oxy-hydroxides. However, as high U-contents of local surface water show, this adsorption does not lead to a significant retention of the uranium.

Perception of tobacco, cannabis, and alcohol use of others is associated with one's own use.

BACKGROUND: Interventions have been developed to reduce overestimations of substance use among others, especially for alcohol and among students. Nevertheless, there is a lack of knowledge on misperceptions of use for substances other than alcohol. We studied the prevalence of misperceptions of use for tobacco, cannabis, and alcohol and whether the perception of tobacco, cannabis, and alcohol use by others is associated with one's own use. METHODS: Participants (n=5216) in a cohort study from a census of 20-year-old men (N=11,819) estimated the prevalence of tobacco and cannabis use among peers of the same age and sex and the percentage of their peers drinking more alcohol than they did. Using the census data, we determined whether participants overestimated, accurately estimated, or underestimated substance use by others. Regression models were used to compare substance use by those who overestimated or underestimated peer substance with those who accurately estimated peer use. Other variables included in the analyses were the presence of close friends with alcohol or other drug problems and family history of substance use. RESULTS: Tobacco use by others was overestimated by 46.1% and accurately estimated by 37.3% of participants. Cannabis use by others was overestimated by 21.8% and accurately estimated by 31.6% of participants. Alcohol use by others was overestimated by more than half (53.4%) of participants and accurately estimated by 31.0%. In multivariable models, compared with participants who accurately estimated tobacco use by others, those who overestimated it reported smoking more cigarettes per week (incidence rate ratio [IRR] [95% CI], 1.17 [range, 1.05, 1.32]). There was no difference in the number of cigarettes smoked per week between those underestimating and those accurately estimating tobacco use by others (IRR [95% CI], 0.99 [range, 0.84, 1.17]). Compared with participants accurately estimating cannabis use by others, those who overestimated it reported more days of cannabis use per month (IRR [95% CI], 1.43 [range, 1.21, 1.70]), whereas those who underestimated it reported fewer days of cannabis use per month (IRR [95% CI], 0.62 [range, 0.23, 0.75]). Compared with participants accurately estimating alcohol use by others, those who overestimated it reported consuming more drinks per week (IRR [95% CI], 1.57 [range, 1.43, 1.72]), whereas those who underestimated it reported consuming fewer drinks per week (IRR [95% CI], 0.41 [range, 0.34, 0.50]). CONCLUSIONS: Perceptions of substance use by others are associated with one's own use. In particular, overestimating use by others is frequent among young men and is associated with one's own greater consumption. This association is independent of the substance use environment, indicating that, even in the case of proximity to a heavy-usage group, perception of use by others may influence one's own use. If preventive interventions are to be based on normative feedback, and their aim is to reduce overestimations of use by others, then the prevalence of overestimation indicates that they may be of benefit to roughly half the population; or, in the case of cannabis, to as few as 20%. Such interventions should take into account differing strengths of association across substances.

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.