Xylem function of arid-land shrubs from California, USA: an ecological and evolutionary analysis

Xylem traits were examined among 22 arid-land shrub species, including measures of vessel dimensions and pit area. These structural measures were compared with the xylem functional traits of transport efficiency and safety from cavitation. The influence of evolution on trait relationships was examined using phylogenetic independent contrasts (PICs). A trade-off between xylem safety and efficiency was supported by a negative correlation between vessel dimensions and cavitation resistance. Pit area was correlated with cavitation resistance when cross species data were examined, but PICs suggest that these traits have evolved independently of one another. Differences in cavitation resistance that are not explained by pit area may be related to differences in pit membrane properties or the prevalence of tracheids, the latter of which may alter pit area through the addition of vessel-to-tracheid pits or through changes in xylem conduit connectivity. Some trait relationships were robust regardless of species ecology or evolutionary history. These trait relationships are likely to be the most valuable in predictive models that seek to examine anatomical and functional trait relationships among extant and fossil woods and include the relationship among hydraulic conductivity and vessel diameter, between vessel diameter and vessel length, and between hydraulic conductivity and wood density.     

Genetic variation and drought response in two Populus × euramericana genotypes through 2-DE proteomic analysis of leaves from field and glasshouse cultivated plants

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides × Populus nigra, cv. ‘Agathe_F’ and ‘Cima’, were analysed over a short-term period of 18 days in glasshouse using 4-month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra.A reliable genotype effect was observed in the leaf proteome over experiment locations, water regimes and sampling dates. Quantitative differences between genotypes were found. Most of them corresponded to proteins matching isoforms or post-translational modification variants. However, ‘Cima’ displayed the highest abundance of antioxidant enzymes.In response to water deficit, about 10% of the reproducible spots significantly varied regardless of the experiment location, among which about 25% also displayed genotype-dependent variations. As a whole, while ‘Cima’ differed from ‘Agathe_F’ by increased abundance of enzymes involved in photorespiration and in oxidative stress, ‘Agathe_F’ was mainly differentiated by increased abundance of enzymes involved in photosynthesis.     

Behavior of free-ranging common dolphins (Delphinus sp.) in the Hauraki Gulf, New Zealand

Here we present the first data describing the behavior of common dolphins ( Delphinus sp.) in the Hauraki Gulf, New Zealand. Activity budgets are used to assess the effects of diel, season, depth, sea surface temperature, group size, and composition on dolphin behavior. Additionally, the presence/absence of Bryde's whale ( Balaenoptera brydei ) and Australasian gannet ( Morus serrator ) is examined in relation to dolphin behavior. Behavioral data were collected from 686 independent dolphin groups during boat-based surveys conducted between February 2002 and January 2005. Foraging (46.7%) and social (7.2%) were the most and least frequently observed behaviors, respectively. Travel (28.9%), mill (9.5%), and rest (7.7%) accounted for the remainder of the activity budget. Behavior varied seasonally, with the highest proportion of foraging and resting groups observed during the spring and autumn, respectively. Behavior also varied with water depth, with foraging animals observed in the deepest and resting groups recorded in the shallowest regions of the Hauraki Gulf. A correlation between group size and behavior was evident, although behavior did not vary with the composition of dolphin groups. Resting, milling, and socializing animals were more frequently observed in smaller group sizes. Foraging behavior was prevalent in both small and large group sizes, suggesting foraging plasticity exists within this population. Behavior differed between single- and multispecies groups, with foraging more frequent in multispecies groups. Resting, milling, or socializing was rarely observed in the presence of any associated species, indicating the primary mechanism for association is likely prey related.     

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.     

The content of total sulphur and sulphur forms in birch (Betula pendula Roth) leaves in the air-polluted Krusne hory mountains

In leaves of birch (Betula pendula Roth), changes in the content of total sulphur and its inorganic and organic forms were determined in relation to the decreasing air-pollution load (SO₂) in the air-polluted Krusne hory mountains and the Decin sandstone highlands in 1995, 1998, 2001 and 2004. Results have shown that birch is able to use considerable amounts of sulphur taken through leaves from air-pollution load. Birch responds fast to changes in air-pollution load by fall in the content of total and inorganic forms of sulphur in leaves.     

Differences in daily stem size variation and growth in two hybrid eucalypt clones

Understanding daily stem size variation is important as the net increment of a forest stand is ultimately determined by the accumulation of daily increment events. In this study, measurements of stem size at high spatial and temporal resolution were made using two commercial hybrid Eucalyptus clones [E. grandis × urophylla (GU) and E. grandis × camaldulensis (GC)] over a period of more than 3.5 years in order to better understand how daily stem growth is effected by variations in environmental conditions. It was evident that GU had fewer days on which net growth occurred than GC. However, when growth did occur, GU grew for longer each day and at a higher rate than GC. Thus, it still had an overall larger net stem increment during the study period. The GU clone had a markedly intermittent pattern of growth, such that growth essentially ceased under drought conditions, but responded rapidly when water became available. This confirms other findings that E. grandis × urophylla is more susceptible to drought stress than E. grandis × camaldulensis, but emphasizes that a strategy of “rapid response” when environmental conditions become temporarily non-limiting is a good one in terms of net increment at sites such as in this study.

Are bioleaching rates determined by the available particle surface area concentration?

It is well known that pulp density and particle size determine the available surface area concentration and have an influence in the overall rate of bioleaching of minerals. As metal solubilization takes place through the surface area of the particles, it can be expected that different combinations of pulp densities and particle sizes giving the same surface area concentration would determine the same leaching rate. The objective of this work was to test this hypothesis on the effect of surface area concentration, pulp density and particle size of the biooxidation of a pyritic gold concentrate by the thermophilic Archaeon Sulfolobus metallicus in shake flasks. The gold concentrate was used at 2.5%, 5%, 10%, and 15% w/v pulp density and at four size fractions: 150–106, 106–75, 75–38 and –38 μm. Temperature was 68°C and the initial pH was 2.0. Results showed that the volumetric productivities of iron and sulfate depend not only on the surface area concentration but also on pulp density and particle size considered separately. These two variables not only determine surface area but also exert additional effects on the process, so the hypothesis was not confirmed. Maximum attained iron productivity was 1.042 g/l day with the 75–38 μm fraction at 5% pulp density. Maximum sulfate productivity was 4.279 g/l day with the 75–38 μm fraction at 10% pulp density.     

Review of the protected area network in Guinea, West Africa, and recommendations for new sites for biodiversity conservation

With only five protected areas dedicated to the conservation of biodiversity (two national parks, one strict nature reserve and two faunal reserves), Guinea has one of the smallest protected area networks in West Africa. As a result, two of the five ecoregions of the country and six of the 14 globally threatened large and medium-sized mammals occurring in Guinea are not found in the national protected area network. To identify areas with high biodiversity that could be included in the national protected area network, we used the Key Biodiversity Areas (KBA) methodology. We devised a scoring system to rank the identified KBAs according to their relative conservation significance. We identified a total of 16 KBAs throughout the country. Their proclamation as protected areas would result in the protection of all ecoregions and all but one of Guinea’s globally threatened large and medium-sized mammals. Twelve of the 16 KBAs have the legal status of classified forest, a status that should facilitate the change into formal biodiversity protected areas (IUCN category I–IV). Our analysis indicates that even if only the two areas with the highest conservation significance score, the Ziama and Diécké forests, become formal protected areas, this would provide protection to both the western Guinean lowland forests, one of the most threatened ecoregions in Africa, and to 11 of the 14 threatened large and medium-sized mammals occurring in Guinea.     

Macrofungal taxa and human population in Italy’s regions

Fungi are relatively understudied, particularly in terms of biogeographical patterns. We analyse whether there is a spatial correlation between macrofungi (Basidiomycota) and human population (both in terms of size and rate of change) in Italy’s regions. Although current fungal taxonomic richness increases with increasing number of inhabitants (censused in 1986 and 2006 and predicted for 2026) and with their density, these relationships are not significant when controlling for variations in area amongst regions. This result, along with other recent independent studies, suggests that the large-scale spatial correlation of people and species can be often explained by both variables correlating with a third factor such as area, habitat heterogeneity or energy availability. Macrofungal richness significantly increases with percentage of forest cover, but not with percentage of protected area, suggesting that the conservation of Italian fungi needs to be addressed also outside the current network of national and regional nature reserves. The absence of any significant association of the estimate of macrofungal taxa with human population change observed in the last and predicted for the next two decades implies that there is no current clear trend towards a change of the ratio between macrofungal taxa and human presence at this scale of analysis. Further work at a higher resolution is needed to assess the consequences for Italy’s fungal biodiversity of the abandonment of marginal land and the expansion of urbanized areas in regions of high environmental productivity.