Novel structural insights into rotavirus recognition of ganglioside glycan receptors

Rotaviruses ubiquitously infect children under the age of 5, being responsible for more than half a million diarrhoeal deaths each year worldwide. Host cell oligosaccharides containing sialic acid(s) are critical for attachment by rotaviruses. However, to date, no detailed three-dimensional atomic model showing the exact rotavirus interactions with these glycoconjugate receptors has been reported. Here, we present the first crystallographic structures of the rotavirus carbohydrate-recognizing protein VP8^? in complex with ganglioside G_M3 glycans. In combination with assessment of the inhibition of rotavirus infectivity by N-acetyl and N-glycolyl forms of this ganglioside, our results reveal key details of rotavirus-ganglioside G_M3 glycan recognition. In addition, they show a direct correlation between the carbohydrate specificities exhibited by VP8^? from porcine and by monkey rotaviruses and the respective infectious virus particles. These novel results also indicate the potential binding interactions of rotavirus VP8^? with other sialic acid-containing gangliosides.     

The surface exposed amino acid residues of monomeric proteins determine the partitioning in aqueous two-phase systems

It is of great interest and importance how different amino acid residues contribute to and affect the properties of a protein surface. Partitioning in aqueous two-phase systems has the potential to be used as a rapid and simple method for studying the surface properties of proteins. The influence on partitioning of the surface exposed amino acid residues of eight structurally determined monomeric proteins has been studied. The proteins were characterized in terms of surface exposed residues with a computer program, Graphical Representation and Analysis of Surface Properties (GRASP), and partitioned in two EO30PO70-dextran aqueous two-phase systems, only differing in polymer concentrations (system I: 6.8% EO30PO70, 7.1% dextran; system II: 9% EO30PO70, 9% dextran). We show for the first time that the partitioning behaviour of different monomeric proteins can be described by the differences in surface exposed amino acid residues. The contribution to the partition coefficient of the residues was found to be best characterized by peptide partitioning in the aqueous two-phase system. Compared to hydrophobicity scales available in the literature, each amino acid contribution is characterized by the slope given by the graph of log K against peptide chain length, for peptides of different length containing only one kind of residue. It was also shown that each amino acid contribution is relative to the total protein surface and the other residues on the surface. Surface hydrophobicity calculations realized for systems I and II gave respectively correlation coefficients of 0.961 and 0.949 for the linear relation between log K and calculated hydrophobicity values. To study the effect on the partition coefficient of different amino acids, they were grouped into classes according to common characteristics: the presence of an aromatic group, a long aliphatic chain or the presence of charge. Using these groups it was possible to confirm that aromatic residues have the strongest effect on the partition coefficient, giving preference to the upper EO30PO70 phase of the system; on the other hand the presence of charged amino acids on the protein surface enhances the partition of the protein to the lower dextran phase. It is also important to note that the sensitivity of the EO30PO70-dextran system for the surface exposed residues was increased by increasing the polymer concentrations. The partition coefficient of a monomeric protein can thus be predicted from its surface exposed amino acid residues and the system can also be used to characterize protein surfaces of monomeric proteins in general.     

Donning your enemy's cloak: ground squirrels exploit rattlesnake scent to reduce predation risk

Ground squirrels (Spermophilus spp.) have evolved a battery of defences against the rattlesnakes (Crotalus spp.) that have preyed on them for millions of years. The distinctive behavioural reactions by these squirrels to rattlesnakes have recently been shown to include self-application of rattlesnake scent-squirrels apply scent by vigorously licking their fur after chewing on shed rattlesnake skins. Here, we present evidence that this behaviour is a novel antipredator defence founded on exploitation of a foreign scent. We tested three functional hypotheses for snake scent application--antipredator, conspecific deterrence and ectoparasite defence--by examining reactions to rattlesnake scent by rattlesnakes, ground squirrels and ectoparasites (fleas). Rattlesnakes were more attracted to ground squirrel scent than to ground squirrel scent mixed with rattlesnake scent or rattlesnake scent alone. However, ground squirrel behaviour and flea host choice were not affected by rattlesnake scent. Thus, ground squirrels can reduce the risk of rattlesnake predation by applying rattlesnake scent to their bodies, potentially as a form of olfactory camouflage. Opportunistic exploitation of heterospecific scents may be widespread; many species self-apply foreign odours, but few such cases have been demonstrated to serve in antipredator defence.     

Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension

Genome-wide association studies (GWASs) have identified many genetic variants underlying complex traits. Many detected genetic loci harbor variants that associate with multiple—even distinct—traits. Most current analysis approaches focus on single traits, even though the final results from multiple traits are evaluated together. Such approaches miss the opportunity to systemically integrate the phenome-wide data available for genetic association analysis. In this study, we propose a general approach that can integrate association evidence from summary statistics of multiple traits, either correlated, independent, continuous, or binary traits, which might come from the same or different studies. We allow for trait heterogeneity effects. Population structure and cryptic relatedness can also be controlled. Our simulations suggest that the proposed method has improved statistical power over single-trait analysis in most of the cases we studied. We applied our method to the Continental Origins and Genetic Epidemiology Network (COGENT) African ancestry samples for three blood pressure traits and identified four loci (CHIC2, HOXA-EVX1, IGFBP1/IGFBP3, and CDH17; p < 5.0 × 10⁻⁸) associated with hypertension-related traits that were missed by a single-trait analysis in the original report. Six additional loci with suggestive association evidence (p < 5.0 × 10⁻⁷) were also observed, including CACNA1D and WNT3. Our study strongly suggests that analyzing multiple phenotypes can improve statistical power and that such analysis can be executed with the summary statistics from GWASs. Our method also provides a way to study a cross phenotype (CP) association by using summary statistics from GWASs of multiple phenotypes.     

Bioenergetic Constraints on Microbial Hydrogen Utilization in Precambrian Deep Crustal Fracture Fluids

Precambrian Shield rocks host the oldest fracture fluids on Earth, with residence times up to a billion years or more. Water–rock reactions in these fracture systems over geological time have produced highly saline fluids, which can contain millimolar concentrations of H₂. Mixing of these ancient Precambrian fluids with meteoric or palaeo-meteoric water can occur through tectonic fracturing, providing microbial inocula and redox couples to fuel blooms of subsurface growth. Here, we present geochemical and microbiological data from a series of borehole fluids of varying ionic strength (0.6–6.4 M) from the Thompson Mine (Manitoba) within the Canadian Precambrian Shield. Thermodynamic calculations demonstrate sufficient energy for H₂-based catabolic reactions across the entire range of ionic strengths during mixing of high ionic strength fracture fluids with meteoric water, although microbial H₂ consumption and cultivable H₂-utilizing microbes were only detected in fluids of ≤1.9 M ionic strength. This pattern of microbial H₂ utilization can be explained by the higher potential bioenergetic cost of organic osmolyte synthesis at increasing ionic strengths. We propose that further research into the bioenergetics of osmolyte regulation in halophiles is warranted to better constrain the habitability zones of hydrogenotrophic ecosystems in both terrestrial subsurface, including potential future radioactive waste disposal sites, and other planetary body crustal environments, including Mars.     

The Bromeliad Microcosm and the Assessment of Faunal Diversity in a Neotropical Forest1

The faunas of tank bromeliads were sampled over two years in three forest types at different elevations in the Luquillo Experimental Forest, Puerto Rico, and the diversity of their animal communities compared. Bromeliad plants behaved as islands in that, within forests, the species richness and abundance of their animal communities were significantly and positively correlated with increase in plant size. The amount of canopy debris they accumulated was similarly correlated with increase in plant size. Overall diversity was lowest in the dwarf forest, where plants were uniformly small. Animal communities were stable from year to year, and could be characterised for each forest type and for compartments within the plant. They showed a pattern of high dominance, which increased with elevation (Mc-Naughton index 37, 54, and 73, respectively, for the tabonuco, palo Colorado, and dwarf forest). Alpha-diversity for sites sampled in each year reflected net primary productivity (NPP) of the forest, declining with increasing elevation when animal abundance measures were used (jackknife estimates of Simpson's diversity index 6.54 & 11.04 [tabonuco], 3.53 & 6.22 [palo Colorado], and 2.75 & 2.17 [dwarf forest]). Species richness over the two years, however, was highest in the intermediate palo Colorado forest (187 species), compared to 146 and 88 in the tabonuco and dwarf forests, respectively. These figures were close to jackknife estimates of maximum species richness. The difference in species richness between tabonuco and palo Colorado forests was significant in one year only. In addition to NPP, other factors, such as litter quality and the structural complexity of the habitat in the palo Colorado forest, may have influenced species richness. The most abundant species in individual plants were also the most widely occurring, confirming known patterns of abundance and distribution in other functional groups. Diversity within bromeliad microcosms at different elevations supported known relationships between diversity, productivity, and habitat complexity along gradients and was not related to differences in the total bromeliad habitat available for colonization.     

The contribution of <Emphasis Type="Italic">Potamogeton crispus</Emphasis> to the phosphorus budget of an urban shallow lake: Lake Monger,Western Australia

Lake Monger (Perth, Western Australia) is a highly eutrophic lake, characterised by very low species richness of macrophytes with the dominance of Potamogeton crispus. Mesocosm experiments were performed using water and plants collected from the lake to determine the effects of vegetation decay on the phosphorus (P) concentrations in the overlying waters. After 2 weeks of experimental incubation of mesocosms with and without re-oxygenation, P concentrations in the water column were significantly higher, showing a quite similar effect of P. crispus on the phosphorus release in different mesocosms. The results of our study provide clear evidence that the P concentrations in overlying waters mainly depend upon the plant P content and developmental stage. Although many sources contribute to the nutrient load of Lake Monger, macrophyte harvesting, prior to its senescence, might constitute a significant in-lake measure for reducing the internal P load.     

Governance options for science–policy interfaces on biodiversity and ecosystem services: comparing a network versus a platform approach

Science–policy-interfaces (SPIs) are expected to go beyond the linear model of scientific policy advice through creating spaces for exchange and dialogue between ‘policy’ and ‘knowledge’. Given that most environmental issues require inter- and transdisciplinary approaches, SPIs must take into account a variety of knowledge types, views and interests of scientists, policymakers and other decision makers. Moreover, acceptance and durability of SPIs depend largely on their perceived legitimacy and the credibility of their knowledge-gathering processes, providing additional challenges for their internal organisation. As the interplay between different knowledge types and decision making is far from neutral, a reflexive approach is required in the design of an SPI so that it is capable of learning from past experiences. The aim of this article is to discuss which governance arrangements could best support the development of an effective and legitimate SPI for European biodiversity politics. We analyse different options for facilitating the implementation of a ‘Network of Knowledge’ approach. This approach has been developed to improve the interface between diverse knowledge-holder communities and decision making processes for biodiversity and ecosystem services—a field where multi-scalar and multi-dimensional problems arise. In this article, we develop and discuss two stylized extreme governance models as our starting point: an `informal network model´, which almost entirely depends on the dedication of individuals, versus a more formalized `platform model´, predominantly based on the needs and interests of the organisations involved. We discuss the pros and cons of each of these models in reaching their objectives and in developing sound governing processes for a ‘Network of Knowledge’. From this discussion, we derive a recommended design for the reflexive governance of such a network in the context of the European Union and finish by discussing some more general lessons learnt.     

The Effect of Anti-Synaptosomal Membrane Antibodies on Neurotransmitter Uptake

Antibodies raised against synaptosomal plasma membranes of rat hippocampus (anti-HPC IgG) caused inhibition of [3H]noradrenaline, [3H]5-hydroxytryptamine, [3H]GABA and [3H]aspartate uptake into S1 fractions and slices of hippocampus and cerebral cortex, but not those of caudate nucleus and hypothalamus. Similar inhibition was not observed on using antibodies against synaptosomal membranes of rat caudate nucleus. Anti-HPC IgG raised against synaptosomal membranes of hippocampus failed to alter both spontaneous and K+-evoked release of [3H]noradrenaline. They did not interfere with the binding of [3H]desipramine (the potent noradrenaline-uptake inhibitor) and with the binding of [3H]dihydroalprenolol, thus excluding any interaction of the antibodies with drug receptors which are located on either the pre- or postsynaptic membrane. The anti-HPC IgG inhibit the enzymatic activity of [Na+-K+-]ATPase by 30% upon incubation of the antibodies with crude membrane preparations. A comparison of their inhibitory effects with those of the neurotoxin 6-hydroxydopamine suggests that the corresponding hippocampal specific antigens are located at a presynaptic site.