Responses of foliage‐living spider assemblage composition and traits to a climatic gradient in Themeda grasslands

For speciose, but poorly known groups, such as terrestrial arthropods, functional traits present a potential avenue to assist in predicting responses to environmental change. Species turnover is common along environmental gradients, but it is unclear how this is reflected in species traits. Community‐level change in arthropod traits, other than body size, has rarely been explored across spatial scales comparable to those examined here. We hypothesized that the composition and morphological traits of spider assemblages would differ across a gradient of climate and habitat structure. We examined foliage‐living spider assemblages associated with Themeda triandra grasslands along a 900 km climatic gradient in south‐eastern Australia. We used sweep‐netting to collect T. triandra‐associated spiders and counted juveniles and identified adults. We also measured morphological traits of adult spiders and noted their hunting mode. Associations with measures of habitat structure were less consistent than relationships with climate. Both juvenile and adult spiders were more abundant in warmer sites, although species richness was not affected by temperature. We found distinct turnover in species composition along the climatic gradient, with hunting spiders, particularly crab spiders (Thomisidae), making up a greater proportion of assemblages in warmer climates. A range of traits of spiders correlated with the climatic gradient. For example, larger spider species and species that were active hunters were more common in warmer climates. Changes in morphological traits across species, rather than within species drove the morphology‐climate relationship. Strong climate‐trait correlations suggest that it may be possible to predict changes in functional traits of assemblages in response to anthropogenic disturbances such as climate change.     

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.     

The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

The genome of the cold-adapted bacterium Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct monomeric hemoglobins exhibiting a 2/2 ??-helical fold. In the present work, one of these hemoglobins is studied by resonance Raman, electronic absorption and electronic paramagnetic resonance spectroscopies, kinetic measurements, and different bioinformatic approaches. It is the first cold-adapted bacterial hemoglobin to be characterized. The results indicate that this protein belongs to the 2/2 hemoglobin family, Group II, characterized by the presence of a tryptophanyl residue on the bottom of the heme distal pocket in position G8 and two tyrosyl residues (TyrCD1 and TyrB10). However, unlike other bacterial hemoglobins, the ferric state, in addition to the aquo hexacoordinated high-spin form, shows multiple hexacoordinated low-spin forms, where either TyrCD1 or TyrB10 can likely coordinate the iron. This is the first example in which both TyrCD1 and TyrB10 are proposed to be the residues that are alternatively involved in heme hexacoordination by endogenous ligands.     

The agmatine-degrading enzyme agmatinase: a key to agmatine signaling in rat and human brain?

Agmatinase, an ureohydrolase belonging to the arginase family, is widely expressed in mammalian tissues including the brain. Here, it may serve two different functions, the inactivation of the arginine derivative agmatine, a putative neurotransmitter, and the formation of the diamine putrescine. In order to identify the cellular sources of agmatinase expression in the brain, we generated a polyclonal monospecific antibody against recombinant rat agmatinase. With immunocytochemistry, selected areas of rat and human brain were screened. Clearly, in both species agmatinase-like immunoreactivity was predominantly detected in distinct populations of neurons, especially cortical interneurons. Also, principal neurons in limbic regions like the habenula and in the cerebellum robustly expressed agmatinase protein. When comparing the overall agmatinase expression with immunocytochemical data available for agmatine and polyamine biosynthetic enzymes, the observed pattern may argue in favor of an agmatine inactivating function rather than fueling the alternative pathway of polyamine synthesis. The putative neurotransmitter agmatine is seemingly involved with mental disorders. Therefore, agmatinase may be similarly important for pathogenesis. The normal expression profile of the protein as described here may therefore be altered under pathological conditions.     

Genetic mapping of the interface between the ArsD metallochaperone and the ArsA ATPase

The ArsD metallochaperone delivers trivalent metalloids, As(III) or Sb(III), to the ArsA ATPase, the catalytic subunit of the ArsAB As(III) efflux pump. Transfer of As(III) increases the affinity of ArsA for As(III), allowing resistance to environmental arsenic concentrations. As(III) transfer is channelled from chaperone to ATPase, implying that ArsD and ArsA form an interface at their metal binding sites. A genetic approach was used to test this hypothesis. Thirteen ArsD mutants exhibiting either weaker or stronger interaction with ArsA were selected by either repressed transactivator yeast two-hybrid or reverse yeast two-hybrid assays. Additionally, Lys-37 and Lys-62 were identified as being involved in ArsD function by site-directed mutagenesis and chemical modification. Substitution at either position with arginine was tolerated, suggesting participation of a positive charge. By yeast two-hybrid analysis K37A and K62A mutants lost interaction with ArsA. All 15 mutations were mapped on the surface of the ArsD structure, and their locations are consistent with a structural model generated by in silico docking. Four are close to metalloid binding site residues Cys-12, Cys-13 and Cys-18, and seven are on the surface of helix 1. These results suggest that the interface involves one surface of helix 1 and the metalloid binding site.     

Design methodology accounting for the effects of porous medium heterogeneity on hydraulic residence time and biodegradation in horizontal subsurface flow constructed wetlands

Horizontal flow constructed wetlands are engineered systems capable of eliminating a wide range of pollutants from the aquatic environment. Nevertheless, poor hydrodynamic behavior is commonly found resulting in preferential pathways and variations in both (i) the hydraulic residence time distribution (HRTD) and, consequently, (ii) the wetland's treatment efficiency. The aim of this work was to outline a methodology for wetland design that accounts for the effect of heterogeneous hydraulic properties of the porous substrate on the HRTD and treatment efficiency. Biodegradation of benzene was used to illustrate the influence of hydraulic conductivity heterogeneity on wetland efficiency. Random, spatially correlated hydraulic conductivity fields following a log-normal distribution were generated and then introduced in a subsurface flow numerical model. The results showed that the variance of the distribution and the correlation length in the longitudinal direction are key indicators of the extent of heterogeneity. A reduction of the mean hydraulic residence time was observed as the extent of heterogeneity increased, while the HRTD became broader with increased skewness. At the same time, substrate heterogeneity induced preferential flow paths within the wetland bed resulting in variations of the benzene treatment efficiency. Further to this it was observed that the distribution of biomass within the porous bed became heterogeneous, rising questions on the representativeness of sampling. It was concluded that traditional methods for wetland design based on assumptions such as a homogeneous porous medium and plug flow are not reliable. The alternative design methodology presented here is based on the incorporation of heterogeneity directly during the design phase. The same methodology can also be used to optimize existing systems, where the HRTD has been characterized with tracer experiments.     

Mechanism of hydrogen peroxide-induced keratinocyte migration in a scratch-wound model

Recent studies have shown that low concentrations of H₂O₂ are produced endogenously by nonphagocytes after wounding. We observed that H₂O₂ at such concentrations can stimulate proliferation as well as migration of keratinocytes in a scratch-wound assay. Both wounding and H₂O₂ can induce phosphorylation of ERK1/2 via EGFR, but the activation of ERK1/2 by H₂O₂ is more sustained and can last more than 8 h. Sustained ERK1/2 activation is required for the increased proliferation and migration induced by H₂O₂. The p38 MAPK was also found to be phosphorylated upon treatment with H₂O₂ but it was not required for H₂O₂-induced migration or proliferation. Furthermore, it was observed that there is a cross talk between the ERK1/2 and the p38 pathways whereby inhibition of either pathway can lead to activation of the other. As a result, the motogenic effects of H₂O₂ were further enhanced when p38 was inhibited. Our data are consistent with the view that H₂O₂ may play an important signaling role in wound healing.     

Radial stem variations of Tabebuia chrysantha (Bignoniaceae) in different tropical forest ecosystems of southern Ecuador

Stem diameter increments of the broadleaved deciduous tree species Tabebuia chrysantha were measured with high-resolution dendrometers in a tropical lower montane forest and in a dry forest in southern Ecuador, the latter showing a distinct dry season. Those analyses were complemented by wood anatomical studies on regularly collected microcores to determine the season of active cambial growth and the time of formation of annual growth boundaries. The length of the cambial active period varied between 3 and 7 months at the tropical lower montane forest and 2 and 4 months in the dry forest, respectively. During dry days, amplitudes of daily stem diameter variations correlated with vapour pressure deficit. During October and November, inter-annual climate variations may lead to dry and sunny conditions in the tropical lower montane forest, causing water deficit and stem diameter shrinkage in T. chrysantha. The results of the climate–growth analysis show a positive relationship between tree growth and rainfall as well as vapour pressure deficit in certain periods of the year, indicating that rainfall plays a major role for tree growth.