Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.

The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information

A Factorization Algorithm for G-Algebras and Applications

It has been recently discovered by Bell, Heinle and Levandovskyy that a large class of algebras, including the ubiquitous $G$-algebras, are finite factorization domains (FFD for short). Utilizing this result, we contribute an algorithm to find all distinct factorizations of a given element $f \in \mathcal{G}$, where $\mathcal{G}$ is any $G$-algebra, with minor assumptions on the underlying field. Moreover, the property of being an FFD, in combination with the factorization algorithm, enables us to propose an analogous description of the factorized Gr\"obner basis algorithm for $G$-algebras. This algorithm is useful for various applications, e.g. in analysis of solution spaces of systems of linear partial functional equations with polynomial coefficients, coming from $\mathcal{G}$. Additionally, it is possible to include inequality constraints for ideals in the input

Modeling and control of UAV bearing formations with bilateral high-level steering

In this paper we address the problem of controlling the motion of a group of unmanned aerial vehicles (UAVs) bound to keep a formation defined in terms of only relative angles (i.e. a bearing formation). This problem can naturally arise within the context of several multi-robot applications such as, e.g. exploration, coverage, and surveillance. First, we introduce and thoroughly analyze the concept and properties of bearing formations, and provide a class of minimally linear sets of bearings sufficient to uniquely define such formations. We then propose a bearing-only formation controller requiring only bearing measurements, converging almost globally, and maintaining bounded inter-agent distances despite the lack of direct metric information.The controller still leaves the possibility of imposing group motions tangent to the current bearing formation. These can be either autonomously chosen by the robots because of any additional task (e.g. exploration), or exploited by an assisting human co-operator. For this latter 'human-in-the-loop' case, we propose a multi-master/multi-slave bilateral shared control system providing the co-operator with some suitable force cues informative of the UAV performance. The proposed theoretical framework is extensively validated by means of simulations and experiments with quadrotor UAVs equipped with onboard cameras. Practical limitations, e.g. limited field-of-view, are also considered. © The Author(s) 2012

Rapid and selective absorption of plant defense compounds from the gut of a sequestering insect

Many herbivorous insects exploit defense compounds produced by their host plants for protection against predators. Ingested plant defense compounds are absorbed via the gut epithelium and stored in the body, a physiological process that is currently not well understood. Here, we investigated the absorption of plant defense compounds from the gut in the horseradish flea beetle, Phyllotreta armoraciae, a specialist herbivore known to selectively sequester glucosinolates from its brassicaceous host plants. Feeding experiments using a mixture of glucosinolates and other glucosides not found in the host plants showed a rapid and selective uptake of glucosinolates in adult beetles. In addition, we provide evidence that this uptake mainly takes place in the foregut, whereas the endodermal midgut is the normal region of absorption. Absorption via the foregut epithelium is surprising as the apical membrane is covered by a chitinous intima. However, we could show that this cuticular layer differs in its structure and overall thickness between P. armoraciae and a non-sequestering leaf beetle. In P. armoraciae, we observed a thinner cuticle with a less dense chitinous matrix, which might facilitate glucosinolate absorption. Our results show that a selective and rapid uptake of glucosinolates from the anterior region of the gut contributes to the selective sequestration of glucosinolates in P. armoraciae

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria