Directed seed dispersal towards areas with low conspecific tree density by a scatter‐hoarding rodent

Scatter‐hoarding animals spread out cached seeds to reduce density‐dependent theft of their food reserves. This behaviour could lead to directed dispersal into areas with lower densities of conspecific trees, where seed and seedling survival are higher, and could profoundly affect the spatial structure of plant communities. We tested this hypothesis with Central American agoutis and Astrocaryum standleyanum palm seeds on Barro Colorado Island, Panama. We radio‐tracked seeds as they were cached and re‐cached by agoutis, calculated the density of adult Astrocaryum trees surrounding each cache, and tested whether the observed number of trees around seed caches declined more than expected under random dispersal. Seedling establishment success was negatively dependent on seed density, and agoutis carried seeds towards locations with lower conspecific tree densities, thus facilitating the escape of seeds from natural enemies. This behaviour may be a widespread mechanism leading to highly effective seed dispersal by scatter‐hoarding animals.     

The heat is on: Genetic adaptation to urbanization mediated by thermal tolerance and body size

Worldwide, urbanization leads to tremendous anthropogenic environmental alterations, causing strong selection pressures on populations of animals and plants. Although a key feature of urban areas is their higher temperature (“urban heat islands”), adaptive thermal evolution in organisms inhabiting urban areas has rarely been studied. We tested for evolution of a higher heat tolerance (CT_MAX) in urban populations of the water flea Daphnia magna, a keystone grazer in freshwater ecosystems, by carrying out a common garden experiment at two temperatures (20°C and 24°C) with genotypes of 13 natural populations ordered along a well‐defined urbanization gradient. We also assessed body size and haemoglobin concentration to identify underlying physiological drivers of responses in CT_MAX. We found a higher CT_MAX in animals isolated from urban compared to rural habitats and in animals reared at higher temperatures. We also observed substantial genetic variation in thermal tolerance within populations. Overall, smaller animals were more heat tolerant. While urban animals mature at smaller size, the effect of urbanization on thermal tolerance is only in part caused by reductions in body size. Although urban Daphnia contained higher concentrations of haemoglobin, this did not contribute to their higher CT_MAX. Our results provide evidence of adaptive thermal evolution to urbanization in the water flea Daphnia. In addition, our results show both evolutionary potential and adaptive plasticity in rural as well as urban Daphnia populations, facilitating responses to warming. Given the important ecological role of Daphnia in ponds and lakes, these adaptive responses likely impact food web dynamics, top‐down control of algae, water quality, and the socio‐economic value of urban ponds.     

Integration of biological networks and gene expression data using Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.     

RESTRICTION FRAGMENT ANALYSIS OF CHLOROPLAST DNA AND THE SYSTEMATICS OF VIGUIERA AND RELATED GENERA (ASTERACEAE: HELIANTHEAE)

Phylogenetic relationships among 31 species representing variously Helianthus, Helianthopsis, Heliomeris, Simsia, Viguiera, and Tithonia were assessed by chloroplast DNA restriction site mapping. A total of 147 mutations including 92 informative ones was detected using 16 restriction enzymes, with an estimated sequence divergence within the group of 1.4%. Parsimony analysis produced a single most parsimonious tree with a length of 161 steps and a consistency index of 0.91. Statistically significant clades, as assessed by the bootstrap method, correspond to a number of taxa recognized previously, including Helianthus (3 species), Helianthopsis (5 species), and several groups within Viguiera, including sect. Maculatae (4 species), the Baja California group (6 species), sect. Paradosa (2 species) and V. dentata (3 samples). However, species of Viguiera collectively form a highly paraphyletic group relative to species of other genera. Helianthus and Helianthopsis were separated into different clades, supporting their recent segregation. Placement of H. porteri in Helianthus rather than Heliomeris was confirmed; the single sample of the latter genus was most similar to the Baja California group of Viguiera. An expected relationship between Simsia (2 species) and one member of Viguiera ser. Grammatoglossae was confirmed (although not with two other putatively related members of Viguiera) and an unexpected relationship between Simsia and Tithonia was suggested. The presence of Mexican taxa as the more basal groups in the tree points toward a possible Mexican origin for Viguiera and related genera. A molecular clock hypothesis is rejected in many pairwise comparisons involving woody taxa with herbaceous ones, although it could not be rejected in most pairwise comparisons involving taxa of similar habit.     

Potential Effects of Climate Warming on Fish Habitats in Temperate Zone Lakes with Special Reference to Lake 239 of the Experimental Lakes Area (ELA), North-Western Ontario

We used simple statistics (e.g. mean temperature, degree days, cumulative volume days) to describe present thermal habitats for cool water (yellow perch, Perca flavescens) and cold water (lake trout, Salvelinus namaycush) fish of a small boreal lake. We then modelled changes in the vertical and temporal extent of these habitats under various scenarios of climatic change that included increases in air temperature of 2°C, 4°C, and 9°C, and positive and negative deviations from present levels of 10% in solar radiation and relative humidity, and 20% in wind speed and the lake water extinction coefficient. Model simulations indicated pronounced changes in the temporal and vertical availability of fish thermal niche space. These changes were mainly driven by the large increases in mean mixed layer temperatures that corresponded to 85% of the increases in air temperature, but, in particular, changes in light attenuation also resulted in some non-linear, unexpected effects in the distribution and seasonal availability of thermal niche space. As expected, classical lake trout thermal habitat (5–15°C) was progressively reduced and almost disappeared in littoral areas in spring and early summer. Perch thermal niche space expanded for air temperature increases of up to 4°C, but largely disappeared for the 9°C increase. We discuss changes in thermal habitat with regard to the life history of lake trout and yellow perch, and include other determinants of fish habitat to evaluate the potential of these species for long-term ecological success under climatic warming.     

Crystal Structure of BamB Bound to a Periplasmic Domain Fragment of BamA,the Central Component of the β-Barrel Assembly Machine

The β-barrel assembly machinery (BAM) mediates folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria. BAM is a five-protein complex consisting of the β-barrel OMP BamA and lipoproteins BamB, -C, -D, and -E. High resolution structures of all the individual BAM subunits and a BamD-BamC complex have been determined. However, the overall complex architecture remains elusive. BamA is the central component of BAM and consists of a membrane-embedded β-barrel and a periplasmic domain with five polypeptide translocation-associated (POTRA) motifs thought to interact with the accessory lipoproteins. Here we report the crystal structure of a fusion between BamB and a POTRA3–5 fragment of BamA. Extended loops 13 and 17 protruding from one end of the BamB β-propeller contact the face of the POTRA3 β-sheet in BamA. The interface is stabilized by several hydrophobic contacts, a network of hydrogen bonds, and a cation-π interaction between BamA Tyr-255 and BamB Arg-195. Disruption of BamA-BamB binding by BamA Y255A and probing of the interface by disulfide bond cross-linking validate the physiological relevance of the observed interface. Furthermore, the structure is consistent with previously published mutagenesis studies. The periplasmic five-POTRA domain of BamA is flexible in solution due to hinge motions in the POTRA2–3 linker. Modeling BamB in complex with full-length BamA shows BamB binding at the POTRA2–3 hinge, suggesting a role in modulation of BamA flexibility and the conformational changes associated with OMP folding and insertion.     

The effect of air-borne ammonium sulphate onPinus nigra var.maritima in the Netherlands

Summary As a result of air pollution, considerable deposition of ammonium sulphate occurs on vegetation and soil in the vicinity of chicken farms and fields dressed with animal slurry. A clear relation exists between this ammonium sulphate deposition and the distance to certain agricultural activities. Field investigations and ecophysiological experiments both show that the needles ofPinus nigra var.maritima (Ait.) Melville take up ammonium and excrete potassium, magnesium and calcium. This often results in potassium and/or magnesium deficiencies and may lead to premature shedding of needles. The high levels of nitrogen in the needles are strongly correlated to fungal diseases.Whether the observed cation leaching will result in disturbed nutrient budgets depends mainly on soil conditions. Leaching of K, Mg and Ca from the soil, caused by ammonium sulphate, may further inhibit nutrient uptake.Field investigations show a clear correlation between increased ratios of NH₄ to K, Mg and Ca in the soil solution and the damage to pine forests.     

Avian Influenza Virus (H11N9) in Migratory Shorebirds Wintering in the Amazon Region,Brazil

Aquatic birds are the natural reservoir for avian influenza viruses (AIV). Habitats in Brazil provide stopover and wintering sites for water birds that migrate between North and South America. The current study was conducted to elucidate the possibility of the transport of influenza A viruses by birds that migrate annually between the Northern and Southern Hemispheres. In total, 556 orotracheal/cloacal swab samples were collected for influenza A virus screening using real-time RT-PCR (rRT-PCR). The influenza A virus-positive samples were subjected to viral isolation. Four samples were positive for the influenza A matrix gene by rRT-PCR. From these samples, three viruses were isolated, sequenced and characterized. All positive samples originated from a single bird species, the ruddy turnstone (Arenaria interpres), that was caught in the Amazon region at Caeté Bay, Northeast Pará, at Ilha de Canelas. To our knowledge, this is the first isolation of H11N9 in the ruddy turnstone in South America.     

Fragmented Perception: Slower Space-Based but Faster Object-Based Attention in Recent-Onset Psychosis with and without Schizophrenia

Background

Schizophrenia is associated with impairments of the perception of objects, but how this affects higher cognitive functions, whether this impairment is already present after recent onset of psychosis, and whether it is specific for schizophrenia related psychosis, is not clear. We therefore tested the hypothesis that because schizophrenia is associated with impaired object perception, schizophrenia patients should differ in shifting attention between objects compared to healthy controls. To test this hypothesis, a task was used that allowed us to separately observe space-based and object-based covert orienting of attention. To examine whether impairment of object-based visual attention is related to higher order cognitive functions, standard neuropsychological tests were also administered.

Method

Patients with recent onset psychosis and normal controls performed the attention task, in which space- and object-based attention shifts were induced by cue-target sequences that required reorienting of attention within an object, or reorienting attention between objects.

Results

Patients with and without schizophrenia showed slower than normal spatial attention shifts, but the object-based component of attention shifts in patients was smaller than normal. Schizophrenia was specifically associated with slowed right-to-left attention shifts. Reorienting speed was significantly correlated with verbal memory scores in controls, and with visual attention scores in patients, but not with speed-of-processing scores in either group.

Conclusions

deficits of object-perception and spatial attention shifting are not only associated with schizophrenia, but are common to all psychosis patients. Schizophrenia patients only differed by having abnormally slow right-to-left visual field reorienting. Deficits of object-perception and spatial attention shifting are already present after recent onset of psychosis. Studies investigating visual spatial attention should take into account the separable effects of space-based and object-based shifting of attention. Impaired reorienting in patients was related to impaired visual attention, but not to deficits of processing speed and verbal memory.