Small mammal community maintains stability through compensatory dynamics after restoration of a ponderosa pine forest

Ecosystem stability has been of increasing interest in the past several decades as it helps predict the consequences of anthropogenic disturbances on ecosystems. Species may exhibit stability through compensation, with greatly fluctuating populations year to year but a consistent density response over time. Stability is increased when species with similar functional roles compensate for one another by responding differently to environmental change. In restoration projects, the objective is to restore stability by altering ecosystem composition, structure, and function to resemble natural (‘‘reference’’) conditions. We assessed the success of ecological restoration treatments by examining the structural and functional responses of the small mammal community before and after treatment, and compared to reference conditions. We used Royle density models to examine the responses of eight species of small mammals to restoration (thinning) treatments in ponderosa pine forests to determine if the community maintained total density, biomass, and function (represented by ectomycorrhizal fungi dispersion) after disturbance. Community composition differed in each of 6 years following treatment, but total density and biomass remained constant, suggesting the community is a stable prey base for predators. In addition, goldenmantled ground squirrels (Spermophilus lateralis) and gray-collared chipmunks (Tamias cinereicollis) appeared to play a similar role in dispersing ectomycorrhizal fungi across different forest structures. Both total species density and biomass were greater after thinning than in unthinned stands, and were similar to reference stands. These results suggest that although species composition changes from year to year after disturbance, restoration treatments can maintain ecosystem stability in terms of small mammal community-level properties

Continuation Sheaves in Dynamics: Sheaf Cohomology and Bifurcation

Continuation of algebraic structures in families of dynamical systems is described using category theory, sheaves, and lattice algebras. Well-known concepts in dynamics, such as attractors or invariant sets, are formulated as functors on appropriate categories of dynamical systems mapping to categories of lattices, posets, rings or abelian groups. Sheaves are constructed from such functors, which encode data about the continuation of structure as system parameters vary. Similarly, morphisms for the sheaves in question arise from natural transformations. This framework is applied to a variety of lattice algebras and ring structures associated to dynamical systems, whose algebraic properties carry over to their respective sheaves. Furthermore, the cohomology of these sheaves are algebraic invariants which contain information about bifurcations of the parametrized systems

One-dimensional symmetry and Liouville type results for the fourth order Allen-Cahn equation in RN^N

In this paper, we prove an analogue of Gibbons' conjecture for the extended fourth order Allen-Cahn equation in R N , as well as Liouville type results for some solutions converging to the same value at infinity in a given direction. We also prove a priori bounds and further one-dimensional symmetry and rigidity results for semilinear fourth order elliptic equations with more general nonlinearities

Cross-disciplinary evidence principles for social-environmental sustainability

Evidence-based approaches to sustainability challenges must draw on knowledge from the environment, development and health communities. To be practicable, this requires an approach to evidence that is broader and less hierarchical than the standards often applied within disciplines

Computational approach for complete Lyapunov functions

Ordinary differential equations arise in a variety of applications, including climate modeling, electronics, predator-prey modeling, etc., and they can exhibit highly complicated dynamical behaviour. Complete Lyapunov functions capture this behaviour by dividing the phase space into two disjoint sets: the chain-recurrent part and the transient part. If a complete Lyapunov function is known for a dynamical system the qualitative behaviour of the system’s solutions is transparent to a large degree. The computation of a complete Lyapunov function for a given system is, however, a very hard task. We present significant improvements of an algorithm recently suggested by the authors to compute complete Lyapunov functions. Previously this methodology was incapable to fully detect chain-recurrent sets in dynamical systems with high differences in speed. In the new approach we replace the system under consideration with another one having the same solution trajectories but such that they are traversed at a more uniform speed. The qualitative properties of the new system such as attractors and repellers are the same as for the original one. This approach gives a better approximation to the chain-recurrent set of the system under study

Computation of Lyapunov functions for systems with multiple attractors

We present a novel method to compute Lyapunov functions for continuous-time systems with multiple local attractors. In the proposed method one first computes an outer approximation of the local attractors using a graphtheoretic approach. Then a candidate Lyapunov function is computed using a Massera-like construction adapted to multiple local attractors. In the final step this candidate Lyapunov function is interpolated over the simplices of a simplicial complex and, by checking certain inequalities at the vertices of the complex, we can identify the region in which the Lyapunov function is decreasing along system trajectories. The resulting Lyapunov function gives information on the qualitative behavior of the dynamics, including lower bounds on the basins of attraction of the individual local attractors. We develop the theory in detail and present numerical examples demonstrating the applicability of our method

Inter-Species Complementation of the Translocon Beta Subunit Requires Only Its Transmembrane Domain

In eukaryotes, proteins enter the secretory pathway through the translocon pore of the endoplasmic reticulum. This protein translocation channel is composed of three major subunits, called Sec61α, β and γ in mammals. Unlike the other subunits, the β subunit is dispensable for translocation and cell viability in all organisms studied. Intriguingly, the knockout of the Sec61β encoding genes results in different phenotypes in different species. Nevertheless, the β subunit shows a high level of sequence homology across species, suggesting the conservation of a biological function that remains ill-defined. To address its cellular roles, we characterized the homolog of Sec61β in the fission yeast Schizosaccharomyces pombe (Sbh1p). Here, we show that the knockout of sbh1+ results in severe cold sensitivity, increased sensitivity to cell-wall stress, and reduced protein secretion at 23°C. Sec61β homologs from Saccharomyces cerevisiae and human complement the knockout of sbh1+ in S. pombe. As in S. cerevisiae, the transmembrane domain (TMD) of S. pombe Sec61β is sufficient to complement the phenotypes resulting from the knockout of the entire encoding gene. Remarkably, the TMD of Sec61β from S. cerevisiae and human also complement the gene knockouts in both yeasts. Together, these observations indicate that the TMD of Sec61β exerts a cellular function that is conserved across species

BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection

<p>Abstract</p> <p>Background</p> <p>Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.</p> <p>Results</p> <p>In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.</p> <p>Conclusion</p> <p>BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. The BLProt software is available at <url>http://www.inb.uni-luebeck.de/tools-demos/bioluminescent%20protein/BLProt</url></p

Functional characterization of the trans-membrane domain interactions of the Sec61 protein translocation complex beta-subunit

<p>Abstract</p> <p>Background</p> <p>In eukaryotic cells co- and post-translational protein translocation is mediated by the trimeric Sec61 complex. Currently, the role of the Sec61 complex β-subunit in protein translocation is poorly understood. We have shown previously that in <it>Saccharomyces cerevisiae </it>the trans-membrane domain alone is sufficient for the function of the β-subunit Sbh1p in co-translational protein translocation. In addition, Sbh1p co-purifies not only with the protein translocation channel subunits Sec61p and Sss1p, but also with the reticulon family protein Rtn1p.</p> <p>Results</p> <p>We used random mutagenesis to generate novel Sbh1p mutants in order to functionally map the Sbh1p trans-membrane domain. These mutants were analyzed for their interactions with Sec61p and how they support co-translational protein translocation. The distribution of mutations identifies one side of the Sbh1p trans-membrane domain α-helix that is involved in interactions with Sec61p and that is important for Sbh1p function in protein translocation. At the same time, these mutations do not affect Sbh1p interaction with Rtn1p. Furthermore we show that Sbh1p is found in protein complexes containing not only Rtn1p, but also the two other reticulon-like proteins Rtn2p and Yop1p.</p> <p>Conclusion</p> <p>Our results identify functionally important amino acids in the Sbh1p trans-membrane domain. In addition, our results provide additional support for the involvement of Sec61β in processes unlinked to protein translocation.</p

Inter-Species Complementation of the Translocon Beta Subunit Requires Only Its Transmembrane Domain

In eukaryotes, proteins enter the secretory pathway through the translocon pore of the endoplasmic reticulum. This protein translocation channel is composed of three major subunits, called Sec61α, β and γ in mammals. Unlike the other subunits, the β subunit is dispensable for translocation and cell viability in all organisms studied. Intriguingly, the knockout of the Sec61β encoding genes results in different phenotypes in different species. Nevertheless, the β subunit shows a high level of sequence homology across species, suggesting the conservation of a biological function that remains ill-defined. To address its cellular roles, we characterized the homolog of Sec61β in the fission yeast Schizosaccharomyces pombe (Sbh1p). Here, we show that the knockout of sbh1+ results in severe cold sensitivity, increased sensitivity to cell-wall stress, and reduced protein secretion at 23°C. Sec61β homologs from Saccharomyces cerevisiae and human complement the knockout of sbh1+ in S. pombe. As in S. cerevisiae, the transmembrane domain (TMD) of S. pombe Sec61β is sufficient to complement the phenotypes resulting from the knockout of the entire encoding gene. Remarkably, the TMD of Sec61β from S. cerevisiae and human also complement the gene knockouts in both yeasts. Together, these observations indicate that the TMD of Sec61β exerts a cellular function that is conserved across species