Dissipative electro-elastic network model of protein electrostatics

We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins

Methylmercury degradation and exposure pathways in streams and wetlands impacted by historical mining

The authors acknowledge financial support from the National Science Foundation: EAR-1226741 (to M.B.S.) and EAR-1225630 (to J.D.B.).Monomethyl mercury (MMHg) and total mercury (THg) concentrations and Hg stable isotope ratios (δ202Hg and Δ199Hg) were measured in sediment and aquatic organisms from Cache Creek (California Coast Range) and Yolo Bypass (Sacramento Valley). Cache Creek sediment had a large range in THg (87 to 3870 ng/g) and δ202Hg (− 1.69 to − 0.20‰) reflecting the heterogeneity of Hg mining sources in sediment. The δ202Hg of Yolo Bypass wetland sediment suggests a mixture of high and low THg sediment sources. Relationships between %MMHg (the percent ratio of MMHg to THg) and Hg isotope values (δ202Hg and Δ199Hg) in fish and macroinvertebrates were used to identify and estimate the isotopic composition of MMHg. Deviation from linear relationships was found between %MMHg and Hg isotope values, which is indicative of the bioaccumulation of isotopically distinct pools of MMHg. The isotopic composition of pre-photodegraded MMHg (i.e., subtracting fractionation from photochemical reactions) was estimated and contrasting relationships were observed between the estimated δ202Hg of pre-photodegraded MMHg and sediment IHg. Cache Creek had mass dependent fractionation (MDF; δ202Hg) of at least − 0.4‰ whereas Yolo Bypass had MDF of + 0.2 to + 0.5‰. This result supports the hypothesis that Hg isotope fractionation between IHg and MMHg observed in rivers (− MDF) is unique compared to + MDF observed in non-flowing water environments such as wetlands, lakes, and the coastal ocean.PostprintPeer reviewe

Seed mass and seed nutrient content as predictors of seed output variation between species

In patch-occupancy models for vegetation, propagule output per area occupied is a key species trait, influencing the potential to colonize vacant patches, and hence species dynamics and coexistence. We estimated seed output across a range of species and quantified its relationship to seed dry mass, seed N and P content, and accessory costs in fruiting structures. Fruiting and seed production data were obtained for 47 woody perennial species, spanning an almost 3000-fold range of seed mass, over a period of one year in Ku-ring-gai Chase National Park, New South Wales, Australia. Seed output was measured as numbers per m² canopy outline and per m² leaf area. Of cross-species variation in seed output per m² canopy outline per year, 72% could be predicted from seed mass alone, with a directly inverse relationship (log-log slope not significantly different from −1). Seed output per m² leaf area could be predicted somewhat more tightly (75%), indicating leaf area per canopy outline area accounted for some cross-species variation. Reproductive production per m² occupied per year varied much less than seed mass and accounted for the remaining variation in seed output. Although accessory costs were about equal in magnitude to seed mass as a component of aggregate investment per seed, they were strongly correlated with seed mass, and consequently did not add substantially to the predictive power. Total mass of N or P per seed were found to be slightly but significantly better predictors of seed output variation than dry seed mass (83% and 78%, respectively). This supports the idea that mineral nutrients are a more fundamental currency for seed production than dry mass. Seed mass, whether measured as dry mass or as N or P, appears to be the principal driver of variation in seed output per m² occupied, and consequently is among the most important dimensions of ecological variation across coexisting species.12 page(s

Differential defoliation of Eucalyptus grandis arises from indiscriminant oviposition and differential larval survival

1 The influence of six open-pollinated families (OPFs) of Eucalyptus grandis on both the growth and development of larvae and the oviposition preference of a paropsine chrysomelid (Paropsis atomaria) was investigated. The OPFs had previously been identified as differing in their susceptibility to defoliation by P. atomaria in forestry progeny trials. 2 Oviposition preference for resistant and susceptible foliage was tested using binary choice tests. These tests did not demonstrate any significant preference for either resistant or susceptible open-pollinated material indicating that adult host preference for susceptible trees was not a likely cause of differential defoliation. 3 Quantification and analysis of growth and development parameters for all larval stages of P. atomaria showed that feeding on genetic material identified as resistant resulted in a significant reduction of relative growth rate of first instar larvae and an alteration to normal feeding behaviour. There was also a trend towards increased larval mortality on resistant E. grandis. 4 We argue that although the magnitude of these effects was minor, interactions with additional biotic and abiotic sources of mortality in the field have the potential, when magnified over successive generations, to result in significant variation in defoliation of host genotypes in the field

Does soil nitrogen influence growth, water transport and survival of snow gum (Eucalyptus pauciflora Sieber ex Sprengel.) under CO2 enrichment?

Eucalyptus pauciflora Sieber ex Sprengel. (snow gum) was grown under ambient (370 L-1) and elevated (700 L-1) atmospheric CO2 in open-top chambers (OTCs) in the field and temperature- controlled glasshouses. Nitrogen applications to the soil ranged from 0.1 to 2.75 g N per plant. Trees in the field at high N levels grew rapidly during summer, particularly in CO2-enriched atmosphere, but suffered high mortality during summer heatwaves. Generally, wider and more numerous secondary xylem vessels at the root-shoot junction in CO2-enriched trees conferred fourfold higher below-ground hydraulic conductance. Enhanced hydraulic capacity was typical of plants at elevated CO2 (in which root and shoot growth was accelerated), but did not result from high N supply. However, because high rates of N application consistently made trees prone to dehydration during heatwaves, glasshouse studies were required to identify the effect of N nutrition on root development and hydraulics. While the effects of elevated CO2 were again predominantly on hydraulic conductivity, N nutrition acted specifically by constraining deep root penetration into soil. Specifically, 15-40% shallower root systems supported marginally larger shoot canopies. Independent changes to hydraulics and root penetration have implications for survival of fertilized trees under elevated atmospheric CO 2, particularly during water stress

Identification of quantitative trait loci influencing foliar concentrations of terpenes and formylated phloroglucinol compounds in Eucalyptus nitens

• Leaves of eucalypt species contain a variety of plant secondary metabolites, including terpenoids and formylated phloroglucinol compounds (FPCs). Both terpene and FPC concentrations are quantitative traits that can show large variation within a popul

Methyl jasmonate does not induce changes in Eucalyptus grandis leaves that alter the effect of constitutive defences on larvae of a specialist herbivore

The up-regulation of secondary metabolic pathways following herbivore attack and the subsequent reduction in herbivore performance have been identified in numerous woody plant species. Eucalypts constitutively express many secondary metabolites in the leaves, including terpenes and formylated phloroglucinol compounds (FPCs). We used clonal ramets from six clones of Eucalyptus grandis and two clones of E. grandis × camaldulensis to determine if methyl jasmonate (MeJA) treatment could induce changes in the foliar concentrations of either of these groups of compounds. We also used bioassays to determine if any changes in the performance of larvae of Paropsis atomaria, a chrysomelid leaf beetle, could be detected in treated ramets versus the untreated controls, thus indicating whether MeJA induced the up-regulation of defences other than terpenes or FPCs. We found no significant effects of MeJA treatment on either the foliar concentrations of terpenes and FPCs or on herbivore performance. We did, however, detect dramatic differences in larval performance between Eucalyptus clones, thereby demonstrating large variations in the levels of constitutive defence. Larval feeding on clones resistant to P. atomaria resulted in high first instar mortality and disruption of normal gregarious feeding behaviour in surviving larvae. Histological examination of larvae feeding on a resistant clone revealed damage to the midgut consistent with the action of a toxin. These findings concur with mounting evidence that most evergreen perennial plants lack foliar-induced defences and suggest that constitutively expressed secondary metabolites other than those commonly examined in studies of interactions between insect herbivores and Eucalyptus may be important in plant defence

Evidence for a combination of pre-adapted traits and rapid adaptive change in the invasive plant Centaurea stoebe

1. Introduced plants have the potential to rapidly evolve traits of ecological importance that may add to their innate potential to become invasive. During invasions, selection may favour genotypes that are already pre-adapted to conditions in the new habitat and, over time, alter the characteristics of subsequent generations. 2. Spotted knapweed (Centaurea stoebe) occurs in two predominantly spatially separated cytotypes in its native range (Europe–Western Asia), but currently only the tetraploid form has been confirmed in the introduced range (North America), where it is invasive. We used several common garden experiments to examine, across multiple populations, whether tetraploids and diploids from the native range differ in life cycle, leaf traits and reproductive capacity and if such differences would explain the predominance of tetraploids and their advance into new habitats in the introduced range. We also compared the same traits in tetraploids from the native and introduced range to determine whether any rapid adaptive changes had occurred since introduction that may have enhanced invasive potential of the species in North America. 3. We found tetraploids had lower specific leaf area, less lamina dissection and fewer, narrower leaves than diploids. Diploids exhibited a monocarpic life cycle and produced few if any accessory rosettes. Diploids produced significantly more seeds per capitulum and had more capitula per plant than tetraploids. In contrast, the vast majority of European tetraploids continued to flower in both seasons by regenerating from multiple secondary rosettes, demonstrating a predominantly polycarpic life cycle. 4. During early growth tetraploids from North America achieved greater biomass than both tetraploids and diploids from the native range but this did not manifest as larger above-ground biomass at maturity. In North American tetraploids there was also evidence of a shift towards a more strictly polycarpic life cycle, less leaf dissection, greater carbon investment per leaf, and greater seed production per capitulum. 5.Synthesis: our results suggest that the characteristics of tetraploid C. stoebe pre-adapted them (compared to diploid conspecifics) for spread and persistence of the species into habitats in North America characterized by a more continental climate. After the species’ introduction, small but potentially important shifts in tetraploid biology have occurred that may have contributed significantly to successful invasion