The C-terminus of the transmembrane MUC17 mucin binds to the scaffold protein PDZK1 that stably localizes it to the enterocyte apical membrane in the small intestine

The membrane bound mucins have a heavily O-glycosylated extracellular domain, a single pass membrane domain and a short cytoplasmic tail. Three of the membrane bound mucins, MUC3, MUC12 and MUC17, are clustered on chromosome 7 and found in the gastrointestinal tract. These mucins have C-terminal sequences typical for PDZ domain binding proteins. To identify PDZ proteins able to interact with the mucins, we screened PDZ domain arrays using YFP-tagged proteins. MUC17 exhibited a strong binding to PDZK1 whereas the binding to NHERF1 was weak. Furthermore, we showed weak binding of MUC12 to PDZK1, NHERF1 and NHERF2. GST pull-down experiments confirmed that the C-terminal tail of MUC17 co-precipitates with the scaffold protein PDZK1 as identified by mass spectrometry. This was mediated through the C-terminal PDZ-interaction site in MUC17 which was capable of binding to three of the four PDZ domains in PDZK1. Immunostaining of wild-type or Pdzk1-/- mouse jejunum with an antiserum against Muc3(17), the mouse orthologue of human MUC17, revealed strong brush border membrane staining in the wild-type mice compared to an intracellular Muc3(17) staining in the Pdzk1-/- mice. This suggests that Pdzk1 plays a specific role in stabilizing Muc3(17) in the apical membrane of small intestinal enterocytes

Designing forest biodiversity experiments : general considerations illustrated by a new large experiment in subtropical China

Funded by German Research Foundation. Grant Number: DFG FOR 891/1 and 2 National Natural Science Foundation of China. Grant Numbers: NSFC 30710103907, 30930005, 31170457 , 31210103910 Swiss National Science Foundation (SNSF) Sino-German Centre for Research Promotion in BeijingPeer reviewedPublisher PD

Early subtropical forest growth is driven by community mean trait values and functional diversity rather than the abiotic environment

While functional diversity (FD) has been shown to be positively related to a number of ecosystem functions including biomass production, it may have a much less pronounced effect than that of environmental factors or species specific properties. Leaf and wood traits can be considered particularly relevant to tree growth, as they reflect a trade-off between resources invested into growth and persistence. Our study focussed on the degree to which early forest growth was driven by FD, the environment (11 variables characterizing abiotic habitat conditions), and community-weighted mean (CWM) values of species traits in the context of a large-scale tree diversity experiment (BEF-China). Growth rates of trees with respect to crown diameter were aggregated across 231 plots (hosting between one and 23 tree species) and related to environmental variables, FD, and CWM, the latter two of which were based on 41 plant functional traits. The effects of each of the three predictor groups were analyzed separately by mixed model optimization and jointly by variance partitioning. Numerous single traits predicted plot-level tree growth, both in the models based on CWMs and FD, but none of the environmental variables was able to predict tree growth. In the best models, environment and FD explained only 4 and 31% of variation in crown growth rates, respectively, while CWM trait values explained 42%. In total, the best models accounted for 51% of crown growth. The marginal role of the selected environmental variables was unexpected, given the high topographic heterogeneity and large size of the experiment, as was the significant impact of FD, demonstrating that positive diversity effects already occur during the early stages in tree plantations

Testing macroecological abundance patterns: The relationship between local abundance and range size, range position and climatic suitability among European vascular plants

Aim: A fundamental question in macroecology centres around understanding the relationship between species' local abundance and their distribution in geographical and climatic space (i.e. the multi‐dimensional climatic space or climatic niche). Here, we tested three macroecological hypotheses that link local abundance to the following range properties: (a) the abundance-range size relationship, (b) the abundance-range centre relationship and (c) the abundance-suitability relationship. Location: Europe. Taxon: Vascular plants. Methods: Distribution range maps were extracted from the Chorological Database Halle to derive information on the range and niche sizes of 517 European vascular plant species. To estimate local abundance, we assessed samples from 744,513 vegetation plots in the European Vegetation Archive, where local species' abundance is available as plant cover per plot. We then calculated the 'centrality', that is, the distance between the location of the abundance observation and each species' range centre in geographical and climatic space. The climatic suitability of plot locations was estimated using coarse‐grain species distribution models (SDMs). The relationships between centrality or climatic suitability with abundance was tested using linear models and quantile regression. We summarized the overall trend across species' regression slopes from linear models and quantile regression using a meta‐analytical approach. Results: We did not detect any positive relationships between a species' mean local abundance and the size of its geographical range or climatic niche. Contrasting yet significant correlations were detected between abundance and centrality or climatic suitability among species. Main conclusions: Our results do not provide unequivocal support for any of the relationships tested, demonstrating that determining properties of species' distributions at large grains and extents might be of limited use for predicting local abundance, including current SDM approaches. We conclude that environmental factors influencing individual performance and local abundance are likely to differ from those factors driving plant species' distribution at coarse resolution and broad geographical extents

Designing forest biodiversity experiments: general considerations illustrated by a new large experiment in subtropical China


 Biodiversity-ecosystem functioning (BEF) experiments address ecosystem-level consequences of species loss by comparing communities of high species richness with communities from which species have been gradually eliminated. BEF experiments originally started with microcosms in the laboratory and with grassland ecosystems. A new frontier in experimental BEF research is manipulating tree diversity in forest ecosystems, compelling researchers to think big and comprehensively.
 We present and discuss some of the major issues to be considered in the design of BEF experiments with trees and illustrate these with a new forest biodiversity experiment established in subtropical China (Xingangshan, Jiangxi Province) in 2009/2010. Using a pool of 40 tree species, extinction scenarios were simulated with tree richness levels of 1, 2, 4, 8 and 16 species on a total of 566 plots of 25.8 × 25.8 m each.
 The goal of this experiment is to estimate effects of tree and shrub species richness on carbon storage and soil erosion; therefore, the experiment was established on sloped terrain. The following important design choices were made: (i) establishing many small rather than fewer larger plots, (ii) using high planting density and random mixing of species rather than lower planting density and patchwise mixing of species, (iii) establishing a map of the initial 'ecoscape' to characterize site heterogeneity before the onset of biodiversity effects and (iv) manipulating tree species richness not only in random but also in trait-oriented extinction scenarios.
 Data management and analysis are particularly challenging in BEF experiments with their hierarchical designs nesting individuals within-species populations within plots within-species compositions. Statistical analysis best proceeds by partitioning these random terms into fixed-term contrasts, for example, species composition into contrasts for species richness and the presence of particular functional groups, which can then be tested against the remaining random variation among compositions.
 We conclude that forest BEF experiments provide exciting and timely research options. They especially require careful thinking to allow multiple disciplines to measure and analyse data jointly and effectively. Achieving specific research goals and synergy with previous experiments involves trade-offs between different designs and requires manifold design decisions.&#13

Assessing sampling coverage of species distribution in biodiversity databases

Abstract Aim Biodiversity databases are valuable resources for understanding plant species distributions and dynamics, but they may insufficiently represent the actual geographic distribution and climatic niches of species. Here we propose and test a method to assess sampling coverage of species distribution in biodiversity databases in geographic and climatic space. Location Europe. Methods Using a test selection of 808,794 vegetation plots from the European Vegetation Archive (EVA), we assessed the sampling coverage of 564 European vascular plant species across both their geographic ranges and realized climatic niches. Range maps from the Chorological Database Halle (CDH) were used as background reference data to capture species geographic ranges and to derive species climatic niches. To quantify sampling coverage, we developed a box-counting method, the Dynamic Match Coefficient (DMC), which quantifies how much a set of occurrences of a given species matches with its geographic range or climatic niche. DMC is the area under the curve measuring the match between occurrence data and background reference (geographic range or climatic niche) across grids with variable resolution. High DMC values indicate good sampling coverage. We applied null models to compare observed DMC values with expectations from random distributions across species ranges and niches. Results Comparisons with null models showed that, for most species, actual distributions within EVA are deviating from null model expectations and are more clumped than expected in both geographic and climatic space. Despite high interspecific variation, we found a positive relationship in DMC values between geographic and climatic space, but sampling coverage was in general more random across geographic space. Conclusion Because DMC values are species-specific and most biodiversity databases are clearly biased in terms of sampling coverage of species occurrences, we recommend using DMC values as covariates in macroecological models that use species as the observation unit. This article is protected by copyright. All rights reserved.Peer reviewe

Impact of tree diversity and environmental conditions on the survival of shrub species in a forest biodiversity experiment in subtropical China

Aims Although shrubs are an important component of forests, their role has not yet been considered in forest biodiversity experiments. In the biodiversity-ecosystem functioning (BEF) experiment with subtropical tree species in south-east China (BEF-China), we factorially combined tree with shrub species-diversity treatments. Here, we tested the hypotheses that shrub survival differs between the 10 planted shrub species, with lower survival rates of late- than early-successional species and is affected by environmental conditions, such as topography and top soil characteristics, as well as by biotic factors, represented by tree, shrub and herb layer characteristics. Methods We analyzed the survival of 42 000 shrub individuals in 105 plots varying in tree and shrub species richness of the BEF-China project four years after planting. Shrub survival was analyzed with generalized linear mixed effects models at the level of individuals and with variance partitioning at the plot level. Random intercept and random slope models of different explanatory variables were compared with respect to the Bayesian Information Criterion (BIC). Important Findings Survival rates differed largely between the 10 shrub species, ranging from 26% to 91% for Ardisia crenata and Distylium buxifolium, respectively. Irrespective of species identity, single abiotic factors explained up to 5% of species survival, with a negative effect of altitude and slope inclination and a positive effect of the topsoil carbon to nitrogen ratio, which pointed to drought as the major cause of shrub mortality. In contrast, neither tree nor shrub richness affected shrub survival at this early stage of the experiment. Among the biotic predictors, only herb layer species richness and cover of the dominant fern species (Dicranopteris pedata) affected shrub survival. Overall, our models that included all variables could explain about 65% in shrub survival, with environmental variables being most influential, followed by shrub species identity, while tree species diversity (species richness and identity) and herb layer characteristics contributed much less. Thus, in this early stage of the experiment the biotic interactions among shrubs and between shrubs and trees have not yet overruled the impact of abiotic environmental factors

Impact of tree diversity and environmental conditions on the survival of shrub species in a forest biodiversity experiment in subtropical China

Aims Although shrubs are an important component of forests, their role has not yet been considered in forest biodiversity experiments. In the biodiversity-ecosystem functioning (BEF) experiment with subtropical tree species in south-east China (BEF-China), we factorially combined tree with shrub species-diversity treatments. Here, we tested the hypotheses that shrub survival differs between the 10 planted shrub species, with lower survival rates of late-than early-successional species and is affected by environmental conditions, such as topography and top soil characteristics, as well as by biotic factors, represented by tree, shrub and herb layer characteristics. Methods We analyzed the survival of 42 000 shrub individuals in 105 plots varying in tree and shrub species richness of the BEF-China project four years after planting. Shrub survival was analyzed with generalized linear mixed effects models at the level of individuals and with variance partitioning at the plot level. Random intercept and random slope models of different explanatory variables were compared with respect to the Bayesian Information Criterion (BIC). Important Findings Survival rates differed largely between the 10 shrub species, ranging from 26% to 91% for Ardisia crenata and Distylium buxifolium, respectively. Irrespective of species identity, single abiotic factors explained up to 5% of species survival, with a negative effect of altitude and slope inclination and a positive effect of the topsoil carbon to nitrogen ratio, which pointed to drought as the major cause of shrub mortality. In contrast, neither tree nor shrub richness affected shrub survival at this early stage of the experiment. Among the biotic predictors, only herb layer species richness and cover of the dominant fern species (Dicranopteris pedata) affected shrub survival. Overall, our models that included all variables could explain about 65% in shrub survival, with environmental variables being most influential, followed by shrub species identity, while tree species diversity (species richness and identity) and herb layer characteristics contributed much less. Thus, in this early stage of the experiment the biotic interactions among shrubs and between shrubs and trees have not yet overruled the impact of abiotic environmental factors

Impact of tree diversity and environmental conditions on the survival of shrub species in a forest biodiversity experiment in subtropical China

Aims: Although shrubs are an important component of forests, their role has not yet been considered in forest biodiversity experiments. In the biodiversity–ecosystem functioning (BEF) experiment with subtropical tree species in south-east China (BEF-China), we factorially combined tree with shrub species-diversity treatments. Here, we tested the hypotheses that shrub survival differs between the 10 planted shrub species, with lower survival rates of late- than early-successional species and is affected by environmental conditions, such as topography and top soil characteristics, as well as by biotic factors, represented by tree, shrub and herb layer characteristics. Methods: We analyzed the survival of 42 000 shrub individuals in 105 plots varying in tree and shrub species richness of the BEF-China project four years after planting. Shrub survival was analyzed with generalized linear mixed effects models at the level of individuals and with variance partitioning at the plot level. Random intercept and random slope models of different explanatory variables were compared with respect to the Bayesian Information Criterion (BIC). Important Findings: Survival rates differed largely between the 10 shrub species, ranging from 26% to 91% for Ardisia crenata and Distylium buxifolium, respectively. Irrespective of species identity, single abiotic factors explained up to 5% of species survival, with a negative effect of altitude and slope inclination and a positive effect of the topsoil carbon to nitrogen ratio, which pointed to drought as the major cause of shrub mortality. In contrast, neither tree nor shrub richness affected shrub survival at this early stage of the experiment. Among the biotic predictors, only herb layer species richness and cover of the dominant fern species (Dicranopteris pedata) affected shrub survival. Overall, our models that included all variables could explain about 65% in shrub survival, with environmental variables being most influential, followed by shrub species identity, while tree species diversity (species richness and identity) and herb layer characteristics contributed much less. Thus, in this early stage of the experiment the biotic interactions among shrubs and between shrubs and trees have not yet overruled the impact of abiotic environmental factors