Immunogenic peptides corresponding to the dominant antigenic region alanine-597 to cysteine-619 in the transmembrane protein of simian immunodeficiency virus have a propensity to fold in aqueous solution.

Two synthetic peptides corresponding to the N- and C-terminal halves of a 23 amino acid sequence representing an immunodominant domain of the simian immunodeficiency virus of macaque origin (SIVmac) were examined for conformational preferences in aqueous solution by proton nuclear magnetic resonance methods. The two constituent peptides, termed A12-7 (Ala597-Ile-Glu-Lys-Tyr-Leu-Glu-Asp-Gln-Ala-Gln607) and A12-9 (Leu608-Asn-Ala-Trp-Gly-Cys-Ala-Phe-Arg-Gln-Val-Ser619), were found to contain a considerable conformational preference for states in which the backbone phi and psi angles populate the alpha region of the Ramachandran plot. Further, for peptide A12-9, the types and intensities of the nuclear Overhauser effect (NOE) connectivities between protons in the polypeptide backbone suggest that these states appear to include helical turns. The temperature dependence of the amide proton chemical shifts indicates that some degree of intramolecular hydrogen bonding occurs in these peptides. These results are consistent with a model in which immunogenic peptides which induce antibodies reactive with the intact protein from which the peptide sequence was derived contain conformational preferences in water solution for states other than the extended-chain forms typically found in "random coil" peptides.     

bioRad: biological analysis and visualization of weather radar data

Weather surveillance radars are increasingly used for monitoring the movements and abundances of animals in the airspace. However, analysis of weather radar data remains a specialised task that can be technically challenging. Major hurdles are the difficulty of accessing and visualising radar data on a software platform familiar to ecologists and biologists, processing the low‐level data into products that are biologically meaningful, and summarizing these results in standardized measures. To overcome these hurdles, we developed the open source R package bioRad, which provides a toolbox for accessing, visualizing and analyzing weather radar data for biological studies. It provides functionality to access low‐level radar data, process these data into meaningful biological information on animal speeds and directions at different altitudes in the atmosphere, visualize these biological extractions, and calculate further summary statistics. The package aims to standardize methods for extracting and reporting biological signals from weather radars. Here we describe a roadmap for analyzing weather radar data using bioRad. We also define weather radar equivalents for familiar measures used in the field of migration ecology, such as migration traffic rates, and recommend several good practices for reporting these measures. The bioRad package integrates with low‐level data from both the European radar network (OPERA) and the radar network of the United States (NEXRAD). bioRad aims to make weather radar studies in ecology easier and more reproducible, allowing for better inter‐comparability of studies.     

A plasma membrane Ca(2+)-ATPase (PMCA) from the liver fluke, Fasciola hepatica

Fasciolosis is a parasitic infection by the liver fluke Fasciola hepatica, which costs the global agricultural community over US $2 billion per year. Its prevalence is rising due to factors such as climate change and drug resistance. ATP-dependent membrane transporters are considered good potential drug targets as they are essential for cellular processes and are in an exposed, accessible position in the cell. Immunolocalisation studies demonstrated that a plasma membrane calcium ATPase (PMCA) was localised to the parenchymal tissue in F. hepatica. The coding sequence for a F. hepatica PMCA (FhPMCA) has been obtained. This sequence encodes a 1,163 amino acid protein which contains motifs which are commonly conserved in PMCAs. Molecular modelling predicted that the protein has 10 transmembrane segments which include a potential calcium ion binding site and phosphorylation motif. FhPMCA interacts with the calmodulin-like protein FhCaM1, but not the related proteins FhCaM2 or FhCaM3, in a calcium-ion dependent manner. This interaction occurs through a region in the C-terminal region of FhPMCA which most likely adopts an α-helical conformation. When FhPMCA was heterologously expressed in a budding yeast strain deleted for its PMCA (Pmc1p), it restored viability. Microsomes prepared from these yeast cells had calcium ion stimulated ATPase activity which was inhibited by the known PMCA inhibitors, bisphenol and eosin. The potential of FhPMCA as a new drug target is discussed.     

Sleeping functional group drives coral-reef recovery

The world's coral reefs are in decline, with many exhibiting a phase shift from coral to macroalgal dominance . This change is often associated with habitat loss and overharvesting of herbivorous fishes, particularly parrotfishes and surgeonfishes . The challenge is to reverse this decline and enhance the resilience of coral-reef ecosystems . We demonstrate, by using a large-scale experimentally induced phase shift, that the rapid reversal from a macroalgal-dominated to a coral- and epilithic algal-dominated state was not a result of herbivory by parrotfishes or surgeonfishes. Surprisingly, phase-shift reversal was primarily driven by a single batfish species (Platax pinnatus), a fish previously regarded as an invertebrate feeder. The 43 herbivorous fishes in the local fauna played only a minor role, suggesting that biodiversity may not offer the protection we hoped for in complex ecosystems. Our findings highlight the dangers faced by coral reefs and other threatened complex ecosystems: Species or functional groups that prevent phase shifts may not be able to reverse phase shifts once they occur. Nevertheless, reversal is possible. The critical issue is to identify and protect those groups that underpin the resilience and regeneration of complex ecosystems.     

Functional versatility supports coral reef biodiversity

We explore the role of specialization in supporting species coexistence in high-diversity ecosystems. Using a novel ordination-based method to quantify specialist and generalist feeding structures and diets we examined the relationship between morphology and diet in 120 wrasses and parrotfishes from the Great Barrier Reef. We find that wrasses, despite their morphological diversity, exhibit weak links between morphology and diet and that specialist morphologies do not necessarily equate to specialized diets. The dominant pattern shows extensive overlap in morphology (functional morphospace occupation) among trophic groups; fish with a given morphology may have a number of feeding modes. Such trophic versatility may lay the foundation for both the origins and maintenance of high biodiversity on coral reefs.