Juvenile-mature wood transition in pine: correlation between wood properties and candidate gene expression profiles

There is a strong desire to exploit transcriptomics data from model species for the genetic improvement of non-model crops. Here, we use gene expression profiles from the commercial model Pinus taeda to identify candidate genes implicated in juvenile-mature wood transition in the non-model relative, P. sylvestris. Re-analysis of 'public domain' SAGE data from xylem tissues of P. taeda revealed 283 mature-abundant and 396 juvenile-abundant tags (P < 0.01), of which 70 and 137, respectively matched to genes with known function. Based on sequence similarity, we then isolated 16 putative homologues of genes that in P. taeda exhibited widest divergence in expression between juvenile and mature samples. Candidate expression levels in P. sylvestris were almost invariably differential between juvenile and mature woody tissue samples among two cohorts of five trees collected from the same seed source and selected for genetic uniformity by genetic distance analysis. However, the direction of differential expression was not always consistent with that described in the original P. taeda SAGE data. Correlation was observed between gene expression and juvenile-mature wood anatomical characteristics by OPLS analysis. Four candidates (alpha-tubulin, porin MIP1, lipid transfer protein and aquaporin like protein) apparently had greatest influence on the wood traits measured. Speculative function of these genes in relation to juvenile-mature wood transition is briefly explored. Thus, we demonstrate the feasibility of exploiting SAGE data from a model species to identify consistently differentially expressed candidates in a related non-model species.

Correlation between regioselectivity and site charge in propene polymerisation catalysed by metallocene

The reactions of propene with [Zr(cyclopentadienyl)(2)Me](+) have been investigated using density functional theory in order to study the correlation between regioselectivity and site charge in propene polymerisation. The reaction paths of the 1,2 and 2,1 additions of the methyl group to propene have been established. The geometries and energies of the reactants, transition states and products have been obtained using both PBEPBE/LANL2DZ and B3LYP/LANL2DZ methodologies. The results with both density functionals show that the activation energy for 1,2-insertion is lower than that for 2,1-insertion (Fig. 5) and this is consistent with the experiment results. Also for both density functionals, the difference of the thermal dynamic driving forces between the 2,1 product named 2-21 and the 1,2 product named 2-12 is significantly lower than the difference between the energy barriers. It is noted that in the reactants, the Mulliken partial charge on the central carbon atom C2 is positive and it can be concluded that 1,2-insertion is favoured because it can proceed via a cationic reaction.

Conditional symmetric instability in sting-jet storms

Sting jets are transient mesoscale jets of air that descend from the tip of the cloud head towards the top of the boundary layer in severe extratropical cyclones and can lead to damaging surface wind gusts. This recently identified jet is distinct from the well-documented jets associated with the cold and warm conveyor belts. One mechanism proposed for their development is the release of conditional symmetric instability (CSI). Here the spatial distribution and temporal evolution of several CSI diagnostics in four severe storms are analysed. A sting jet has been identified in three of these storms; for comparison, we also analysed one storm that did not have a sting jet, even though it hadmany of the apparent features of sting-jet storms. The sting-jet storms are distinct from the non-sting-jet storms by having much greater andmore extensive conditional instability (CI) and CSI. CSI is released by ascending air parcels in the cloud head in two of the sting-jet storms and by descending air parcels in the other sting-jet storm. By contrast, only weak CI to ascending air parcels is present at the cloud-head tip in the non-sting-jet storm. CSI released by descending air parcels, as diagnosed by decaying downdraught slantwise convective available potential energy (DSCAPE), is collocated with the sting jets in all three sting-jet storms and has a localisedmaximum in two of them. Consistent evolutions of saturated moist potential vorticity are found.We conclude that CSI release has a role in the generation of the sting jet, that the sting jet may be driven by the release of instability to both ascending and descending parcels, and that DSCAPE could be used as a discriminating diagnostic for the sting jet based on these four case-studies.

Selecting from amongst non–nested conditional variance models: information criteria and portfolio determination

We consider the finite sample properties of model selection by information criteria in conditionally heteroscedastic models. Recent theoretical results show that certain popular criteria are consistent in that they will select the true model asymptotically with probability 1. To examine the empirical relevance of this property, Monte Carlo simulations are conducted for a set of non–nested data generating processes (DGPs) with the set of candidate models consisting of all types of model used as DGPs. In addition, not only is the best model considered but also those with similar values of the information criterion, called close competitors, thus forming a portfolio of eligible models. To supplement the simulations, the criteria are applied to a set of economic and financial series. In the simulations, the criteria are largely ineffective at identifying the correct model, either as best or a close competitor, the parsimonious GARCH(1, 1) model being preferred for most DGPs. In contrast, asymmetric models are generally selected to represent actual data. This leads to the conjecture that the properties of parameterizations of processes commonly used to model heteroscedastic data are more similar than may be imagined and that more attention needs to be paid to the behaviour of the standardized disturbances of such models, both in simulation exercises and in empirical modelling.

The representation of conditional expectations of non-Gaussian noise

For Wiener spaces conditional expectations and $L^{2}$-martingales w.r.t. the natural filtration have a natural representation in terms of chaos expansion. In this note an extension to larger classes of processes is discussed. In particular, it is pointed out that orthogonality of the chaos expansion is not required.

Consistent Dirichlet Boundary Conditions for Numerical Solution of Moving Boundary Problems

We consider the imposition of Dirichlet boundary conditions in the finite element modelling of moving boundary problems in one and two dimensions for which the total mass is prescribed. A modification of the standard linear finite element test space allows the boundary conditions to be imposed strongly whilst simultaneously conserving a discrete mass. The validity of the technique is assessed for a specific moving mesh finite element method, although the approach is more general. Numerical comparisons are carried out for mass-conserving solutions of the porous medium equation with Dirichlet boundary conditions and for a moving boundary problem with a source term and time-varying mass.

Sox1-deficient mice suffer from epilepsy associated with abnormal ventral forebrain development and olfactory cortex hyperexcitability

Mutations in several classes of embryonically-expressed transcription factor genes are associated with behavioral disorders and epilepsies. However, there is little known about how such genetic and neurodevelopmental defects lead to brain dysfunction. Here we present the characterization of an epilepsy syndrome caused by the absence of the transcription factor SOX1 in mice. In vivo electroencephalographic recordings from SOX1 mutants established a correlation between behavioral changes and cortical output that was consistent with a seizure origin in the limbic forebrain. In vitro intracellular recordings from three major forebrain regions, neocortex, hippocampus and olfactory (piriform) cortex (OC) showed that only the OC exhibits abnormal enhanced synaptic excitability and spontaneous epileptiform discharges. Furthermore, the hyperexcitability of the OC neurons was present in mutants prior to the onset of seizures but was completely absent from both the hippocampus and neocortex of the same animals. The local inhibitory GABAergic neurotransmission remained normal in the OC of SOX1-deficient brains, but there was a severe developmental deficit of OC postsynaptic target neurons, mainly GABAergic projection neurons within the olfactory tubercle and the nucleus accumbens shell. Our data show that SOX1 is essential for ventral telencephalic development and suggest that the neurodevelopmental defect disrupts local neuronal circuits leading to epilepsy in the SOX1-deficient mice

MJO Simulation Diagnostics

The Madden–Julian oscillation (MJO) interacts with and influences a wide range of weather and climate phenomena (e.g., monsoons, ENSO, tropical storms, midlatitude weather), and represents an important, and as yet unexploited, source of predictability at the subseasonal time scale. Despite the important role of the MJO in climate and weather systems, current global circulation models (GCMs) exhibit considerable shortcomings in representing this phenomenon. These shortcomings have been documented in a number of multimodel comparison studies over the last decade. However, diagnosis of model performance has been challenging, and model progress has been difficult to track, because of the lack of a coherent and standardized set of MJO diagnostics. One of the chief objectives of the U.S. Climate Variability and Predictability (CLIVAR) MJO Working Group is the development of observation-based diagnostics for objectively evaluating global model simulations of the MJO in a consistent framework. Motivation for this activity is reviewed, and the intent and justification for a set of diagnostics is provided, along with specification for their calculation, and illustrations of their application. The diagnostics range from relatively simple analyses of variance and correlation to more sophisticated space–time spectral and empirical orthogonal function analyses. These diagnostic techniques are used to detect MJO signals, to construct composite life cycles, to identify associations of MJO activity with the mean state, and to describe interannual variability of the MJO.

Pb-210-Ra-226 and Ra-228-Th-232 systematics in young arc lavas: implications for magma degassing and ascent rates

New data show that island arc rocks have (Pb-210/Ra-226)(o) ratios which range from as low as 0.24 up to 2.88. In contrast, (Ra-22S/Th-232) appears always within error of I suggesting that the large Ra-226-excesses observed in arc rocks were generated more than 30 years ago. This places a maximum estimate on melt ascent velocities of around 4000 m/year and provides further confidence that the Ra-226 excesses reflect deep (source) processes rather than shallow level alteration or seawater contamination. Conversely, partial melting must have occurred more than 30 years prior to eruption. The Pb-210 deficits are most readily explained by protracted magma degassing. Using published numerical models, the data suggest that degassing occurred continuously for periods up to several decades just prior to eruption but no link with eruption periodicity was found. Longer periods are required if degassing is discontinuous, less than 100% efficient or if magma is recharged or stored after degassing. The long durations suggest much of this degassing occurs at depth with implications for the formation of hydrothermal and copper-porphyry systems. A suite of lavas erupted in 1985-1986 from Sangeang Api volcano in the Sunda arc are characterised by deficits of Pb-210 relative to Ra-226 from which 6-8 years of continuous Rn-222 degassing would be inferred from recent numerical models. These data also form a linear (Pb-210)/Pb-(Ra-226)/Pb array which might be interpreted as a 71-year isochron. However, the array passes through the origin suggesting displacement downwards from the equiline in response to degassing and so the slope of the array is inferred not to have any age significance. Simple modelling shows that the range of (Ra-226)/Pb ratios requires thousands of years to develop consistent with differentiation occurring in response to cooling at the base of the crust. Thus, degassing post-dated, and was not responsible for magma differentiation. The formation, migration and extraction of gas bubbles must be extremely efficient in mafic magma whereas the higher viscosity of more siliceous magmas retards the process and can lead to Pb-210 excesses. A possible negative correlation between (Pb-210/Ra-226)(o) and SO2 emission rate requires further testing but may have implications for future eruptions. (C) 2004 Elsevier B.V. All rights reserved.

Spatial covariation of Azotobacter abundance and soil properties: A case study using the wavelet transform

The soil microflora is very heterogeneous in its spatial distribution. The origins of this heterogeneity and its significance for soil function are not well understood. A problem for understanding spatial variation better is the assumption of statistical stationarity that is made in most of the statistical methods used to assess it. These assumptions are made explicit in geostatistical methods that have been increasingly used by soil biologists in recent years. Geostatistical methods are powerful, particularly for local prediction, but they require the assumption that the variability of a property of interest is spatially uniform, which is not always plausible given what is known about the complexity of the soil microflora and the soil environment. We have used the wavelet transform, a relatively new innovation in mathematical analysis, to investigate the spatial variation of abundance of Azotobacter in the soil of a typical agricultural landscape. The wavelet transform entails no assumptions of stationarity and is well suited to the analysis of variables that show intermittent or transient features at different spatial scales. In this study, we computed cross-variograms of Azotobacter abundance with the pH, water content and loss on ignition of the soil. These revealed scale-dependent covariation in all cases. The wavelet transform also showed that the correlation of Azotobacter abundance with all three soil properties depended on spatial scale, the correlation generally increased with spatial scale and was only significantly different from zero at some scales. However, the wavelet analysis also allowed us to show how the correlation changed across the landscape. For example, at one scale Azotobacter abundance was strongly correlated with pH in part of the transect, and not with soil water content, but this was reversed elsewhere on the transect. The results show how scale-dependent variation of potentially limiting environmental factors can induce a complex spatial pattern of abundance in a soil organism. The geostatistical methods that we used here make assumptions that are not consistent with the spatial changes in the covariation of these properties that our wavelet analysis has shown. This suggests that the wavelet transform is a powerful tool for future investigation of the spatial structure and function of soil biota. (c) 2006 Elsevier Ltd. All rights reserved.

Preparation of consistent soil data sets for modelling purposes: Secondary SOTER data for four case study areas

The common GIS-based approach to regional analyses of soil organic carbon (SOC) stocks and changes is to define geographic layers for which unique sets of driving variables are derived, which include land use, climate, and soils. These GIS layers, with their associated attribute data, can then be fed into a range of empirical and dynamic models. Common methodologies for collating and formatting regional data sets on land use, climate, and soils were adopted for the project Assessment of Soil Organic Carbon Stocks and Changes at National Scale (GEFSOC). This permitted the development of a uniform protocol for handling the various input for the dynamic GEFSOC Modelling System. Consistent soil data sets for Amazon-Brazil, the Indo-Gangetic Plains (IGP) of India, Jordan and Kenya, the case study areas considered in the GEFSOC project, were prepared using methodologies developed for the World Soils and Terrain Database (SOTER). The approach involved three main stages: (1) compiling new soil geographic and attribute data in SOTER format; (2) using expert estimates and common sense to fill selected gaps in the measured or primary data; (3) using a scheme of taxonomy-based pedotransfer rules and expert-rules to derive soil parameter estimates for similar soil units with missing soil analytical data. The most appropriate approach varied from country to country, depending largely on the overall accessibility and quality of the primary soil data available in the case study areas. The secondary SOTER data sets discussed here are appropriate for a wide range of environmental applications at national scale. These include agro-ecological zoning, land evaluation, modelling of soil C stocks and changes, and studies of soil vulnerability to pollution. Estimates of national-scale stocks of SOC, calculated using SOTER methods, are presented as a first example of database application. Independent estimates of SOC stocks are needed to evaluate the outcome of the GEFSOC Modelling System for current conditions of land use and climate. (C) 2007 Elsevier B.V. All rights reserved.

A comparison of cross-hole electrical and seismic data in fractured rock

Cross-hole anisotropic electrical and seismic tomograms of fractured metamorphic rock have been obtained at a test site where extensive hydrological data were available. A strong correlation between electrical resistivity anisotropy and seismic compressional-wave velocity anisotropy has been observed. Analysis of core samples from the site reveal that the shale-rich rocks have fabric-related average velocity anisotropy of between 10% and 30%. The cross-hole seismic data are consistent with these values, indicating that observed anisotropy might be principally due to the inherent rock fabric rather than to the aligned sets of open fractures. One region with velocity anisotropy greater than 30% has been modelled as aligned open fractures within an anisotropic rock matrix and this model is consistent with available fracture density and hydraulic transmissivity data from the boreholes and the cross-hole resistivity tomography data. However, in general the study highlights the uncertainties that can arise, due to the relative influence of rock fabric and fluid-filled fractures, when using geophysical techniques for hydrological investigations.

Variograms of ancillary data to aid sampling for soil surveys

To provide reliable estimates for mapping soil properties for precision agriculture requires intensive sampling and costly laboratory analyses. If the spatial structure of ancillary data, such as yield, digital information from aerial photographs, and soil electrical conductivity (EC) measurements, relates to that of soil properties they could be used to guide the sampling intensity for soil surveys. Variograins of permanent soil properties at two study sites on different parent materials were compared with each other and with those for ancillary data. The ranges of spatial dependence identified by the variograms of both sets of properties are of similar orders of magnitude for each study site, Maps of the ancillary data appear to show similar patterns of variation and these seem to relate to those of the permanent properties of the soil. Correlation analysis has confirmed these relations. Maps of kriged estimates from sub-sampled data and the original variograrns showed that the main patterns of variation were preserved when a sampling interval of less than half the average variogram range of ancillary data was used. Digital data from aerial photographs for different years and EC appear to show a more consistent relation with the soil properties than does yield. Aerial photographs, in particular those of bare soil, seem to be the most useful ancillary data and they are often cheaper to obtain than yield and EC data.

Interactions between mass balance, atmospheric circulation, and recent climate change on the Djankuat Glacier, Caucasus Mountains, Russia

This paper reports recent changes in the mass balance record from the Djankuat Glacier, central greater Caucasus, Russia, and investigates possible relationships between the components of mass balance, local climate, and distant atmospheric forcing. The results clearly show that a strong warming signal has emerged in the central greater Caucasus, particularly since the 1993/1994 mass balance year, and this has led to a significant increase in the summer ablation of Djankuat. At the same time, there has been no compensating consistent increase in winter precipitation and accumulation leading to the strong net loss of mass and increase in glacier runoff. Interannual variability in ablation and accumulation is partly associated with certain major patterns of Northern Hemisphere climatic variability. The positive phase of the North Pacific (NP) teleconnection pattern forces negative geopotential height and temperature anomalies over the Caucasus in summer and results in reduced summer melt, such as in the early 1990s, when positive NP extremes resulted in a temporary decline in ablation rates. The positive phase of the NP is related to El Nino-Southern Oscillation, and it is possible that a teleconnection between the tropical Pacific sea surface temperatures and summer air temperatures in the Caucasus is bridged through the NP pattern. More recently, the NP pattern was predominantly negative, and this distant moderating forcing on summer ablation in the Caucasus was absent. Statistically significant correlations are observed between accumulation and the Scandinavian (SCA) teleconnection pattern. The frequent occurrence of the positive SCA phase at the beginning of accumulation season results in lower than average snowfall and reduced accumulation. The relationship between the North Atlantic Oscillation (NAO), Arctic Oscillation, and accumulation is weak, although positive precipitation anomalies in the winter months are associated with the negative phase of the NAO. A stronger positive correlation is observed between accumulation on Djankuat and geopotential height over the Bay of Biscay unrelated to the established modes of the Northern Hemisphere climatic variability. These results imply that the mass balance of Djankuat is sensitive to the natural variability in the climate system. Distant forcing, however, explains only 16% of the variance in the ablation record and cannot fully explain the recent increase in ablation and negative mass balance.