Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks

It has been generally acknowledged that the module structure of protein interaction networks plays a crucial role with respect to the functional understanding of these networks. In this paper, we study evolutionary aspects of the module structure of protein interaction networks, which forms a mesoscopic level of description with respect to the architectural principles of networks. The purpose of this paper is to investigate limitations of well known gene duplication models by showing that these models are lacking crucial structural features present in protein interaction networks on a mesoscopic scale. This observation reveals our incomplete understanding of the structural evolution of protein networks on the module level. © 2012 Emmert-Streib.

Structure and interactions of ultracold Yb ions and Rb atoms

In order to study ultracold charge-transfer processes in hybrid atom-ion traps, we have mapped out the potential-energy curves and molecular parameters for several low-lying states of the Rb, Yb+ system. We employ both a multireference configuration interaction and a full configuration interaction (FCI) approach. Turning points, crossing points, potential minima, and spectroscopic molecular constants are obtained for the lowest five molecular states. Long-range parameters, including the dispersion coefficients, are estimated from our ab initio data. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom (ad=128.4 atomic units) are in good agreement with experiment and previous calculations. We present some dynamical calculations for (adiabatic) scattering lengths for the two lowest (Yb, Rb+) channels that were carried out in our work. However, we find that the pseudopotential approximation is rather limited in validity and only applies to nK temperatures. The adiabatic scattering lengths for both the triplet and singlet channels indicate that both are large and negative in the FCI approximation.

Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

The relationships among organisms and their surroundings can be of immense complexity. To describe and understand an ecosystem as a tangled bank, multiple ways of interaction and their effects have to be considered, such as predation, competition, mutualism and facilitation. Understanding the resulting interaction networks is a challenge in changing environments, e.g. to predict knock-on effects of invasive species and to understand how climate change impacts biodiversity. The elucidation of complex ecological systems with their interactions will benefit enormously from the development of new machine learning tools that aim to infer the structure of interaction networks from field data. In the present study, we propose a novel Bayesian regression and multiple changepoint model (BRAM) for reconstructing species interaction networks from observed species distributions. The model has been devised to allow robust inference in the presence of spatial autocorrelation and distributional heterogeneity. We have evaluated the model on simulated data that combines a trophic niche model with a stochastic population model on a 2-dimensional lattice, and we have compared the performance of our model with L1-penalized sparse regression (LASSO) and non-linear Bayesian networks with the BDe scoring scheme. In addition, we have applied our method to plant ground coverage data from the western shore of the Outer Hebrides with the objective to infer the ecological interactions. (C) 2012 Elsevier B.V. All rights reserved.

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Effects of very low birthweight on brain structure in adulthood

Very-low-birthweight (VLBW) individuals are at high risk of brain injury in the perinatal period. We wished to determine how such early brain lesions affect brain structure in adulthood. Thirty-two VLBW adults (20 female, 12 male) and, 18 term, normal birthweight sibling control individuals (nine female, nine male) underwent structural MRI at a mean age of 23 years 4 months (range 17 to 33 years; SD 3.4). Images were analyzed using an automated tissue segmentation algorithm in order to estimate whole brain tissue class volumes in native space. Images were then warped to a template image in standard space. There was no significant between-group difference in whole brain, greymatter, white matter, or total cerebral spinal fluid (CSF) volumes. However, lateral ventricular volume was significantly increased by 41% in those with VLBW. The ratio of grey to white matter was also significantly increased (by 10%) in those with VLBW. Group comparison maps showed widespread changes in the distribution of grey and white matter, and relative excess of ventricular CSF, in the brains of VLBW individuals. Increased ventricular volume predicted decreased grey matter in subcortical nuclei and limbic cortical structures, and decreased periventricular white matter. We conclude that these diffuse abnormalities of grey and white matter are a consequence,of the interaction of perinatal brain injury and ongoing neurodevelopmental processes.

Mimicking the colourful wing scale structure of the Papilio blumei butterfly

The brightest and most vivid colours in nature arise from the interaction of light with surfaces that exhibit periodic structure on the micro- and nanoscale. In the wings of butterflies, for example, a combination of multilayer interference, optical gratings, photonic crystals and other optical structures gives rise to complex colour mixing. Although the physics of structural colours is well understood, it remains a challenge to create artificial replicas of natural photonic structures(1-3). Here we use a combination of layer deposition techniques, including colloidal self-assembly, sputtering and atomic layer deposition, to fabricate photonic structures that mimic the colour mixing effect found on the wings of the Indonesian butterfly Papilio blumei. We also show that a conceptual variation to the natural structure leads to enhanced optical properties. Our approach offers improved efficiency, versatility and scalability compared with previous approaches(4-6).

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Indigenous Arbuscular Mycorrhizal Fungal Assemblages Protect Grassland Host Plants from Pathogens

Plant roots can establish associations with neutral, beneficial and pathogenic groups of soil organisms. Although it has been recognized from the study of individual isolates that these associations are individually important for plant growth, little is known about interactions of whole assemblages of beneficial and pathogenic microorganisms associating with plants. We investigated the influence of an interaction between local arbuscular mycorrhizal (AM) fungal and pathogenic/saprobic microbial assemblages on the growth of two different plant species from semi-arid grasslands in NE Germany (Mallnow near Berlin). In a greenhouse experiment each plant species was grown for six months in either sterile soil or in sterile soil with one of three different treatments: 1) an AM fungal spore fraction isolated from field soil from Mallnow; 2) a soil pathogen/saprobe fraction consisting of a microbial community prepared with field soil from Mallnow and; 3) the combined AM fungal and pathogen/saprobe fractions. While both plant species grew significantly larger in the presence of AM fungi, they responded negatively to the pathogen/saprobe treatment. For both plant species, we found evidence of pathogen protection effects provided by the AM fungal assemblages. These results indicate that interactions between assemblages of beneficial and pathogenic microorganisms can influence the growth of host plants, but that the magnitude of these effects is plant species-specific.

Dietary switching of collembola in grassland soil food webs

Soil food webs are characterised by complex direct and indirect effects among the organisms. Consumption of microorganisms by soil animals is considered as an important factor that contributes to the stability of communities, though cascading effects within the food web can be difficult to detect. In a greenhouse experiment, an addition of a high number the fungal feeding collembola Folsomia quadrioculata was applied to grassland soil food webs in monocultures of three plant species: Plantago lanceolato (forb), Lotus corniculatus (legume) and Holcus lanatus (grass). The abundance of microorganisms, determined as the abundances of phospholipid fatty acids (PLFAs) and the abundances of resident invertebrates, nematodes and collembolans, did not change due to the addition of E quadrioculata. Trophic positions of collembolans were determined by analyses of natural abundances of N-15 stable isotopes. The use of food resources by microorganisms and collembolans was determined by C-13 analysis of microbial PLFAs and solid samples of collembolans. delta C-13 values of the resident collembola Folsomia fimetaria were lower in the presence of E quadrioculata than in the control food webs indicating a use of more depleted C-13 food resources by E fimetaria. The delta N-15 values of E fimetaria did not change at the addition of E quadrioculata thus no change of trophic levels was detected. The switch of E fimetaria to a different food resource could be due to indirect interactions in the food web as the two collembolan species were positioned on different trophic positions, according to different delta N-15 values. (c) 2008 Elsevier Ltd. All rights reserved.

Micro-arthropod communities under human disturbance: is taxonomic aggregation a valuable tool for detecting multivariate change? Evidence from Mediterranean soil oribatid coenoses

Animal communities are sensitive to environmental disturbance, and several multivariate methods have recently been developed to detect changes in community structure. The complex taxonomy of soil invertebrates constrains the use of the community level in monitoring environmental changes, since species identification requires expertise and time. However, recent literature data on marine communities indicate that little multivariate information is lost in the taxonomic aggregation of species data to high rank taxa. In the present paper, this hypothesis was tested on two oribatid mite (oribatida, Acari) assemblages under two different kinds of disturbance: metal pollution and fires. Results indicate that data sets built at the genus and family systematic rank can detect the effects of disturbance with little loss of information. This is an encouraging result in view of the use of the community level as a preliminary tool for describing patterns of human-disturbed soil ecosystems. (c) 2006 Elsevier SAS. All rights reserved.

High energy resolution fluorescence detection XANES - an in situ method to study the interaction of adsorbed molecules with metal catalysts in the liquid phase

The change in the Pt electronic structure following the adsorption of an a,ß-unsaturated aldehyde and ketone was followed by in situ HERFD-XANES in the liquid phase. The resulting shift in the Pt Fermi energy is in good agreement with the molecule adsorption energy trends calculated by DFT and provides insight into the reaction selectivity.

Atomistic investigation on the structure-property relationship during thermal spray nanoparticle impact

During thermal spraying, hot particles impact on a colder substrate. This interaction of crystalline copper nanoparticles and copper substrate is modelled, using MD simulation. The quantitative results of the impacts at different velocities and temperatures are evaluated using a newly defined flattening aspect ratio. This ratio between the maximum diameter after the impact and the height of the splat increases with increasing Reynolds numbers until a critical value is reached. At higher Reynolds numbers the flattening aspect ratio decreases again, as the kinetic energy of the particle leads to increasing substrate temperature and, therefore, decreases the substrate resistance. Thus, the particle penetrates into the substrate and deforms less.

Whose statistical reasoning is improved by information about causal structure?

People often struggle when making Bayesian probabilistic estimates on the basis of competing sources of statistical evidence. Recently, Krynski and Tenenbaum (Journal of Experimental Psychology: General, 136, 430–450, 2007) proposed that a causal Bayesian framework accounts for peoples’ errors in Bayesian reasoning and showed that, by clarifying the causal relations among the pieces of evidence, judgments on a classic statistical reasoning problem could be significantly improved. We aimed to understand whose statistical reasoning is facilitated by the causal structure intervention. In Experiment 1, although we observed causal facilitation effects overall, the effect was confined to participants high in numeracy. We did not find an overall facilitation effect in Experiment 2 but did replicate the earlier interaction between numerical ability and the presence or absence of causal content. This effect held when we controlled for general cognitive ability and thinking disposition. Our results suggest that clarifying causal structure facilitates Bayesian judgments, but only for participants with sufficient understanding of basic concepts in probability and statistics.

Asymmetric Total Synthesis of (+)-Inthomycin C Via O-Directed Free Radical Alkyne Hydrostannation with Ph3SnH and Catalytic Et3B: Reinstatement of the Zeeck-Taylor (3R)-Structure for (+)-Inthomycin C

A new pathway to (+)-inthomycin C is reported that exploits an O-directed free radical hydrostannation reaction on (−)-12 and a Stille cross-coupling as key steps. Significantly, the latter process was effected on 19 where a gauche-pentane repulsive interaction could interfere. Our stereochemical studies on the alkynol (−)-12 and the enyne (+)-7 confirm that Ryu and Hatakeyama’s (3S)-stereochemical revision of (+)-inthomycin C is invalid and that Zeeck and Taylor’s original (3R)-stereostructure for (+)-inthomycin C is correct.

Community structure, diversity and spatial organization of enchytraeids in Mediterranean urban holm oak stands

There is a strong northern bias in Europe as regards enchytraeid community ecology, particularly in urban settings. We approached the enchytraeid assemblages of urban holm oak stands in Naples and Siena adopting a high intensity sampling that, for the first time in the Mediterranean climate zone, would ensure that the data collected be representative of the target populations. Structural parameters (diversity and evenness, biomass, size classes, aggregation) were compared across different spatial (regional, urban district, within habitat) and temporal scales (season and year). Species richness was found to change significantly only at regional scale; background data suggest that this may depend on the higher environmental heterogeneity occurring at Naples. Differences in size class structure were significant only on a seasonal scale and within either city separately. With one exception (Fridericia bulbosa s.s.), the patterns of spatial aggregation of the common species were fairly robust and the total range of patchiness was consistent with previous studies, despite the different sampling methodologies. The size of the sampling unit, the number of replicates per plot and the number of plots proposed in this study appear suitable to obviate the difficulties of evaluating Mediterranean enchytraeid communities.