Detecting predators and locating competitors while foraging: an experimental study of a medium-sized herbivore in an African savanna

Vigilance allows individuals to escape from predators, but it also reduces time for other activities which determine fitness, in particular resource acquisition. The principles determining how prey trade time between the detection of predators and food acquisition are not fully understood, particularly in herbivores because of many potential confounding factors (such as group size), and the ability of these animals to be vigilant while handling food. We designed a fertilization experiment to manipulate the quality of resources, and compared awareness (distinguishing apprehensive foraging and vigilance) of wild impalas (Aepyceros melampus) foraging on patches of different grass height and quality in a wilderness area with a full community of predators. While handling food, these animals can allocate time to other functions. The impalas were aware of their environment less often when on good food patches and when the grass was short. The animals spent more time in apprehensive foraging when grass was tall, and no other variable affected apprehensive behavior. The probability of exhibiting a vigilance posture decreased with group size. The interaction between grass height and patch enrichment also affected the time spent in vigilance, suggesting that resource quality was the main driver when visibility is good, and the risk of predation the main driver when the risk is high. We discuss various possible mechanisms underlying the perception of predation risk: foraging strategy, opportunities for scrounging, and inter-individual interference. Overall, this experiment shows that improving patch quality modifies the trade-off between vigilance and foraging in favor of feeding, but vigilance remains ultimately driven by the visibility of predators by foragers within their feeding patches.     

Daphnia magna, a host for evaluation of bacterial virulence

We show that Daphnia magna can be used to assess acute virulence of pathogens relevant to human health, such as Pseudomonas aeruginosa or Photorhabdus asymbiotica. Analysis of bacterial mutants suggests that P. aeruginosa uses similar mechanisms to infect Daphnia and other hosts.     

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture

Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.     

Seasonality of peak metabolic rate in non‐migrant tropical birds

Birds that are year‐round residents of temperate and tropical regions have divergent life histories. Tropical birds have a slower ‘pace of life’, one characteristic of which includes lower peak metabolic rate and daily activity levels. Temperate resident birds are faced with seasonal variation in thermogenic demand. This challenge is met with seasonally increased peak metabolic rate during winter. These thermogenic demands are much lower in birds that are year‐round tropical residents. By measuring peak (summit) metabolic rate in tropical and temperate resident bird species during summer and winter, we asked whether tropical birds exhibit seasonality in peak metabolic rate, and if the direction of seasonality differs between tropical and temperate species. We measured summit metabolism in seven tropical and one temperate species during the winter and during the summer breeding season to test the hypothesis that summit metabolism of tropical residents would change seasonally. We consider whether metabolic seasonality is associated with breeding season for tropical species. We found that summit metabolism was significantly greater during the summer for most tropical residents, while the temperate resident matched several previous reports with higher summit metabolism in winter. We conclude that metabolic seasonality occurs in tropical residents and differs from temperate residents, suggesting that breeding during the summer may be driving relatively higher metabolism as compared to winter thermogenesis in temperate birds.     

Accounting for uncertainty in colonisation times: a novel approach to modelling the spatio‐temporal dynamics of alien invasions using distribution data

A novel, yet generic, Bayesian approach to parameter inference in a stochastic, spatio‐temporal model of dispersal and colonisation is developed and applied to the invasion of a region by an alien plant species. The method requires species distribution data from multiple time points, and accounts for temporal uncertainty in colonisation times inherent in such data. Covariates, such as climate parameters, altitude and land use, which capture variation in the suitability of sites for plant colonisation, are easily incorporated into the model. The method assumes no local extinction of occupied sites and thus is primarily applicable to modelling distribution data at relatively coarse spatial resolutions of plant species whose range is expanding over time. The implementation of the model and inference algorithm are illustrated through application to British floristic atlas data for the widespread alien Heracleum mantegazzianum (giant hogweed) assessed at a 10 × 10 km resolution in 1970 and 2000. We infer key characteristics of this species, predict its future spread, and use the resulting fitted model to inform a simulation‐based assessment of the methodology. Simulated distribution data are used to validate the inference algorithm. Our results suggest that the accuracy of inference is not sensitive to the number of distribution time points, requiring only that there are at least two points in time when distributions are mapped. We demonstrate the utility of the modelling approach by making future forecasts and historic hindcasts of the distribution of giant hogweed in Great Britain. Giant hogweed is one of the worst alien plants in Britain and has rapidly increased its range since 1970, yet we highlight that a further 20% of land area remains susceptible to colonisation by this species. We use the robustness of this case study to discuss the potential for modelling distribution data for other species and at different spatial scales.     

Tomato GDSL1 Is Required for Cutin Deposition in the Fruit Cuticle

The plant cuticle consists of cutin, a polyester of glycerol, hydroxyl, and epoxy fatty acids, covered and filled by waxes. While the biosynthesis of cutin building blocks is well documented, the mechanisms underlining their extracellular deposition remain unknown. Among the proteins extracted from dewaxed tomato (Solanum lycopersicum) peels, we identified GDSL1, a member of the GDSL esterase/acylhydrolase family of plant proteins. GDSL1 is strongly expressed in the epidermis of growing fruit. In GDSL1-silenced tomato lines, we observed a significant reduction in fruit cuticle thickness and a decrease in cutin monomer content proportional to the level of GDSL1 silencing. A significant decrease of wax load was observed only for cuticles of the severely silenced transgenic line. Fourier transform infrared (FTIR) analysis of isolated cutins revealed a reduction in cutin density in silenced lines. Indeed, FTIR-attenuated total reflectance spectroscopy and atomic force microscopy imaging showed that drastic GDSL1 silencing leads to a reduction in ester bond cross-links and to the appearance of nanopores in tomato cutins. Furthermore, immunolabeling experiments attested that GDSL1 is essentially entrapped in the cuticle proper and cuticle layer. These results suggest that GDSL1 is specifically involved in the extracellular deposition of the cutin polyester in the tomato fruit cuticle.     

The conserved glutamate (Glu136) in transmembrane domain 2 of the serotonin transporter is required for the conformational switch in the transport cycle

The alternate access model provides the theoretical framework for understanding how transporters translocate hydrophilic substrates across the lipid bilayer. The model postulates at least two conformations of a transporter, an outward and an inward facing conformation, which seal the translocation pathway to the interior and exterior of the cell, respectively. It is not clear how the conformational switch is triggered in neurotransmitter/sodium symporters, but Na+ is likely to play an essential role. Here, we focused on Glu136 of the serotonin transporter (SERT); this residue is conserved in transmembrane domain 2 of neurotransmitter/sodium symporters and related proteins. Three substitutions were introduced, resulting in SERT-E136D, SERT-E136Q, and SERT-E136A, which were all correctly inserted into the plasma membrane. SERT-E136Q and SERT-E136A failed to support substrate influx into cells, whereas SERT-E136D did so at a reduced rate. Binding experiments with the inhibitor 2beta-[3H]carbomethoxy-3beta-(4-iodophenyl)tropane (beta-[3H]CIT) supported the conjecture that the mutant transporters preferentially adopted the inward facing conformation: beta-[3H]CIT interacted with SERT in a manner consistent with binding to the outward facing state. Accordingly, the Na+-induced acceleration of beta-[3H]CIT association was most pronounced in wild-type SERT, followed by SERT-E136D > SERT-E136Q > SERT-E136A. Similarly, SERT-E136Q supported substrate efflux in a manner indistinguishable from wild-type SERT, whereas SERT-E136A was inactive. Thus, in the absence of Glu136, the conformational equilibrium of SERT is shifted progressively (SERT-E136D > SERT-E136Q > SERT-E136A) to the inward facing conformation.     

Molecular architecture and ligand recognition determinants for T4 RNA ligase

RNA ligase type 1 from bacteriophage T4 (Rnl1) is involved in countering a host defense mechanism by repairing 5'-PO4 and 3'-OH groups in tRNA(Lys). Rnl1 is widely used as a reagent in molecular biology. Although many structures for DNA ligases are available, only fragments of RNA ligases such as Rnl2 are known. We report the first crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,beta-methylenetriphosphate) (AMPcPP). The N-terminal domain is related to the equivalent region of DNA ligases and Rnl2 and binds AMPcPP but with further interactions from the additional N-terminal 70 amino acids in Rnl1 (via Tyr37 and Arg54) and the C-terminal domain (Gly269 and Asp272). The active site contains two metal ions, consistent with the two-magnesium ion catalytic mechanism. The C-terminal domain represents a new all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding.     

Expression of type XXIII collagen mRNA and protein

Collagen XXIII is a member of the transmembranous subfamily of collagens containing a cytoplasmic domain, a membrane-spanning hydrophobic domain, and three extracellular triple helical collagenous domains interspersed with non-collagenous domains. We cloned mouse, chicken, and humanalpha1(XXIII) collagen cDNAs and showed that this non-abundant collagen has a limited tissue distribution in non-tumor tissues. Lung, cornea, brain, skin, tendon, and kidney are the major sites of expression. In contrast, five transformed cell lines were tested for collagen XXIII expression, and all expressed the mRNA. In vivo the alpha1(XXIII) mRNA is found in mature and developing organs, the latter demonstrated using stages of embryonic chick cornea and mouse embryos. Polyclonal antibodies were generated in guinea pig and rabbit and showed that collagen XXIII has a transmembranous form and a shed form. Comparison of collagen XXIII with its closest relatives in the transmembranous subfamily of collagens, types XIII and XXV, which have the same number of triple helical and non-collagenous regions, showed that there is a discontinuity in the alignment of domains but that striking similarities remain despite this.