Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin a6b4

Integrin alpha6beta4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin alpha6beta4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin beta4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron– electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes

A trophic interaction framework for identifying the invasive capacity of novel organisms

1. The likelihood and impacts of invasions by novel organisms (e.g. non-native species, genetically modified organisms) on the composition and functioning of receiving biological communities hinges on their capacity to exploit resources and/or avoid predation relative to resident counterparts. While assessment of invasion risk based on the comparison of functional responses (per-capita consumption rate as a function of resource density) of novel species with native analogues has been gaining popularity, it may be undermined if alternative prey and potential predators are not represented realistically. 2. Here, we propose a conceptual framework that enables rigorous identification of trophic traits conducive to invasion success by novel organisms—irrespective of their trophic position—and their likely ecological impacts, given their arrival and establishment. We focus on consumption here, but our framework can also be used for autotrophic energy acquisition, and extended to non-trophic and indirect interactions. 3. The framework enables a structured and prioritized selection of subsets of trophic links for invasion risk assessment. It is based on foraging theory and advances in comparative functional responses in invasion ecology. It can even be used in the absence of a resident comparator organism and when resources or predators are only partly known. 4. Our approach enhances the predictive power of species screening, and thus advances prevention and management of invasions under a common framework for all types of novel organisms

Functional responses can unify invasion ecology.

We contend that invasion ecology requires a universal, measurable trait of species and their interactions with resources that predicts key elements of invasibility and ecological impact; here, we advocate that functional responses can help achieve this across taxonomic and trophic groups, among habitats and contexts, and can hence help unify disparate research interests in invasion ecology

The ecogenetic link between demography and evolution : can we bridge the gap between theory and data?

Calls to understand the links between ecology and evolution have been common for decades. Population dynamics, i.e. the demographic changes in populations, arise from life history decisions of individuals and thus are a product of selection, and selection, on the contrary, can be modified by such dynamical properties of the population as density and stability. It follows that generating predictions and testing them correctly requires considering this ecogenetic feedback loop whenever traits have demographic consequences, mediated via density dependence (or frequency dependence). This is not an easy challenge, and arguably theory has advanced at a greater pace than empirical research. However, theory would benefit from more interaction between related fields, as is evident in the many near-synonymous names that the ecogenetic loop has attracted. We also list encouraging examples where empiricists have shown feasible ways of addressing the question, ranging from advanced data analysis to experiments and comparative analyses of phylogenetic data

Comparing factors associated with total and dead sooty shearwater bycatch in New Zealand trawl fisheries

Incidental capture of seabirds is a conservation concern because such periodic ‘bycatch’ may cause population declines. Not all birds die upon capture, but distinctions between total and dead captures are rarely done. Thus, it is currently unclear whether using total captures is an adequate simplification, for example when studying factors associated with bycatch. We investigated this question by analysing total and dead procellariiform seabird captures of 663 trawling operations between 1996 and 2008 in the Exclusive Economic Zone of New Zealand. As potential factors associated with bycatch, we considered eleven technical and seven environmental characteristics recorded by onboard observers during commercial trawling. A total of 1 231 procellariids were recovered as bycatch, with sooty shearwaters (Puffinus griseus) comprising 98% of the bycatch sample. Our analyses indicated that specific technical (headline height) and environmental factors (month, daylight, sea state, area code) influenced both total and dead captures of sooty shearwaters, with similar results for both response variables. Using total captures may thus be an adequate simplification in the interpretation of sooty shearwater captures in New Zealand trawl fisheries, and practices that mitigate the overall capture of birds will be most effectiv

Are exotic species red queens?

<div><p>We combined two general hypotheses from the fields of invasion biology and evolutionary biology, the enemy release hypothesis and the Red Queen hypothesis, into the new invasive queens hypothesis. This hypothesis predicts that if species with the principal ability to reproduce both sexually and asexually are introduced to an exotic range, they show a shift towards asexual reproduction in the exotic range. The reasoning behind this hypothesis is that (1) species tend to leave behind their natural enemies when being introduced to an exotic range (enemy release hypothesis) and (2) sexual reproduction is less advantageous in the absence of natural enemies due to its high costs (inverted Red Queen hypothesis). We tested the invasive queens hypothesis against data from 70 animal species, based on information from the literature and unpublished information provided by 105 experts from various continents. As predicted, the investigated species showed a significant shift towards asexual reproduction in their exotic as compared to their native range.</p></div

Parametrized Model Predictive Control Approaches for Urban Traffic Networks

Model Predictive Control (MPC) has shown promising results in the control of urban traffic networks, but unfortunately it has one major drawback. The, often nonlinear, optimization that has to be performed at every control time step is computationally too complex to use MPC controllers for real-time implementations (i.e. when the online optimization is performed within the control time interval of the controlled network). This paper proposes an effective parametrized MPC approach to lower the computational complexity of the MPC controller. Two parametrized control laws are proposed that can be used in the parametrized MPC framework, one based on the prediction model of the MPC controllers, and another is constructed using Grammatical Evolution (GE). The performance and computational complexity of the parametrized MPC approach is compared to a conventional MPC controller by performing an extensive simulation-based case study. The simulation results show that for the given case study the parametrized MPC approach is real-time implementable while the performance decreases with less than 3% with respect to the conventional MPC controller.Team DeSchutte

Limiting similarity and Darwin’s naturalization hypothesis: understanding the drivers of biotic resistance against invasive plant species.

Several hypotheses have been proposed to explain biotic resistance of a recipient plant community based on reduced niche opportunities for invasive alien plant species. The limiting similarity hypothesis predicts that invasive species are less likely to establish in communities of species holding similar functional traits. Likewise,Darwin’s naturalization hypothesis states that invasive species closely related to the native community would be less successful. We tested both using the invasive alien Ambrosia artemisiifolia L. and Solidago gigantea Aiton, and grassland species used for ecological restoration in central Europe. We classified all plant species into groups based on functional traits obtained from trait databases and calculated the phylogenetic distance among them. In a greenhouse experiment, we submitted the two invasive species at two propagule pressures to competition with communities of ten native species from the same functional group. In another experiment, they were submitted to pairwise competition with native species selected from each functional group. At the community level, highest suppression for both invasive species was observed at low propagule pressure and not explained by similarity in functional traits. Moreover, suppression decreased asymptotically with increasing phylogenetic distance to species of the native community. When submitted to pairwise competition, suppression for both invasive species was also better explained by phylogenetic distance. Overall, our results support Darwin’s naturalization hypothesis but not the limiting similarity hypothesis based on the selected traits. Biotic resistance of native communities against invasive species at an early stage of establishment is enhanced by competitive traits and phylogenetic relatedness