Effect of increased Populus cover on Abies regeneration in the Picea–feathermoss boreal forest

Question: Does the increase in Populus tremuloides cover within the Picea mariana–feathermoss domain enhance establishment and growth conditions for Abies balsamea regeneration? Location: Boreal forest of northwest Quebec, Canada. Method: To document the effect of Populus tremuloides on A. balsamea regeneration, mixed stands with a heterogeneous presence of P. tremuloides adjacent to Picea mariana‐dominated stands were selected. Abies balsamea regeneration, understorey environment and canopy composition were characterized from 531 sampling units distributed along transects covering the mixed–coniferous gradient. Abundance of understorey A. balsamea regeneration was described using three height groups: seedling (<30 cm), small sapling (30 to <100 cm) and tall sapling (100 to 300 cm). Growth characteristics were measured from 251 selected individuals of A. balsamea (<3 m). Results: Results showed that A. balsamea regeneration was generally more abundant when P. tremuloides was present in the canopy. Differences between seedling and sapling abundance along the mixed–coniferous gradient suggest that while establishment probably occurs over a wide range of substrates, the better growth conditions found under mixed stands ensure a higher survival rate for A. balsamea seedlings. Conclusions: The abundant A. balsamea regeneration observed within mixed stands of the Picea mariana–feathermoss domain suggests that the increase in P. tremuloides cover, favoured by intensive management practices and climatic change, could contribute to acceleration of the northward expansion of the A. balsamea–Betula papyrifera domain into the northern boreal forest dominated by Picea mariana.     

Mixed glucose and lactate uptake by Corynebacterium glutamicum through metabolic engineering

The Corynebacterium glutamicum ATCC 13032 lysC(fbr) strain was engineered to grow fast on racemic mixtures of lactate and to secrete lysine during growth on lactate as well as on mixtures of lactate and glucose. The wild-type C. glutamicum only grows well on L-lactate. Overexpression of D-lactate dehydrogenase (dld) achieved by exchanging the native promoter of the dld gene for the stronger promoter of the sod gene encoding superoxide dismutase in C. glutamicum resulted in a duplication of biomass yield and faster growth without any secretion of lysine. Elementary mode analysis was applied to identify potential targets for lysine production from lactate as well as from mixtures of lactate and glucose. Two targets for overexpression were pyruvate carboxylase and malic enzyme. The overexpression of these genes using again the sod promoter resulted in growth-associated production of lysine with lactate as sole carbon source with a carbon yield of 9% and a yield of 15% during growth on a lactate-glucose mixture. Both substrates were taken up simultaneously with a slight preference for lactate. As surmised from the elementary mode analysis, deletion of glucose-6-phosphate isomerase resulted in a decreased production of lysine on the mixed substrate. Elementary mode analysis together with suitable objective functions has been found a very useful tool guiding the design of strains producing lysine on mixed substrates.     

Inference for the Break Point in Segmented Regression with Application to Longitudinal Data

This paper considers inference for the break point in the segmented regression or piece‐wise regression model. Standard likelihood theory does not apply because the break point is absent under the null hypothesis. We use results by Davies for this type of non‐standard set‐up [Biometrika 64 (1977), 247–254 and 74 (1987), 33–43] to obtain a test for the null hypothesis of no break point. A confidence interval can be constructed provided replicate data are available. The methods are exemplified using two longitudinal datasets, the one from ecology, the other from pharmacology.     

Variance Component Estimation for Mixed Model Analysis of cDNA Microarray Data

Microarrays provide a valuable tool for the quantification of gene expression. Usually, however, there is a limited number of replicates leading to unsatisfying variance estimates in a gene‐wise mixed model analysis. As thousands of genes are available, it is desirable to combine information across genes. When more than two tissue types or treatments are to be compared it might be advisable to consider the array effect as random. Then information between arrays may be recovered, which can increase accuracy in estimation. We propose a method of variance component estimation across genes for a linear mixed model with two random effects. The method may be extended to models with more than two random effects. We assume that the variance components follow a log‐normal distribution. Assuming that the sums of squares from the gene‐wise analysis, given the true variance components, follow a scaled χ²‐distribution, we adopt an empirical Bayes approach. The variance components are estimated by the expectation of their posterior distribution. The new method is evaluated in a simulation study. Differentially expressed genes are more likely to be detected by tests based on these variance estimates than by tests based on gene‐wise variance estimates. This effect is most visible in studies with small array numbers. Analyzing a real data set on maize endosperm the method is shown to work well. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Forecasting spatially structured populations: the role of dispersal and scale

We forecasted spatially structured population models with complex dynamics, focusing on the effect of dispersal and spatial scale on the predictive capability of nonlinear forecasting (NLF). Dispersal influences NLF ability by its influence on population dynamics. For simple 2-cell models, when dispersal is small, our ability to predict abundance in subpopulations decreased and then increased with increasing dispersal. Spatial heterogeneity, dispersal manner, and environmental noise did not qualitatively change this result. But results are not clear for complex spatial configurations because of complicated dispersal interactions across subpopulations. Populations undergoing periodic fluctuations could be forecasted perfectly for all deterministic cases that we studied, but less reliably when environmental noise was incorporated. More importantly, for all models that we have examined, NLF was much worse at larger spatial scales as a consequence of the asynchronous dynamics of subpopulations when the dispersal rate was below some critical value. The only difference among models was the critical value of dispersal rate, which varied with growth rate, carrying capacity, mode of dispersal, and spatial configuration. These results were robust even when environmental noise was incorporated. Intermittency, common in the dynamics of spatially structured populations, lowered the predictive capability of NLF. Forecasting population behaviour is of obvious value in resource exploitation and conservation. We suggest that forecasting at local scales holds promise, whereas forecasting abundance at regional scales may yield poor results. Improved understanding of dispersal can enhance the management and conservation of natural resources, and may help us to understand resource-exploitation strategies employed by local indigenous humans.     

Chemical constraints on the evolution of olfactory communication channels of moths

It is estimated there are over 100,000 moth species (Lepidoptera) that produce sex pheromones comprising communication channels used in specific-mate-recognition systems (SMRS) involved in pre-zygotic mating isolation and speciation. About 1572 moth species have been found to use 377 pheromone components, the majority being alcohols, aldehydes or acetate esters of olefinic chains of 10-22 carbons. Since there are limited numbers of possible unsaturated (double bonded) E- and Z-configured isomers of these chains, there may be constraints on incipient species evolving new pheromone components, especially if they are utilized by existing species. Here I develop algorithms that count and name all possible structures of chains with or without a functional group. The results show that for acetate esters there are only seven or nine monounsaturated isomers of six or seven carbon chains, respectively, suggesting use of these compounds could limit the number of communication channels available for radiation of new species (no moths use these short chains). For commonly used 14-carbon chains with an acetate ester functional group, and 1-3 unsaturations, there are 1039 isomers. A total of 2,096,883 isomers were counted from all multiply unsaturated 10-22-carbon chain acetate esters. The number of possible signals quickly extends into millions when considering pheromone blends of 2-4 components used by most species. There should be little chemical constraint on evolution of new communication channels based on compounds of 10 or more carbons, even for closely related species (e.g. ermine moths, Yponomeuta).     

A simple model of plankton population dynamics coupled with a LES of the surface mixed layer

The concentration of phytoplankton in the sea is affected by biological processes, such as growth/mortality rates, predatory zooplankton concentrations and nutrient levels. Phytoplankton concentrations are also influenced by physical processes, in particular the mixing properties of the local fluid environment. On planktonic scales (approximately 10-1000 microm) one can assume the local turbulent flow is isotropic, with no distinction between horizontal and vertical mixing. However, agglomerations of phytoplankton into patches are observed on larger scales of up to hundreds of metres, whose formation will be influenced by the anisotropic advection/mixing properties and large-eddy structures prevalent in the surface mixed layer. This paper presents the results of the coupling of a large-eddy simulation (LES) model of the mixed layer with an advection-diffusion system of coupled equations for nitrate-phytoplankton-zooplankton (NPZ) concentration, incorporating sub-grid parameterizations of the biological processes. Typically these include phytoplankton growth due to light levels and ambient nitrate concentration, offset by grazing losses due to the presence of zooplankton. The primary goal of this work is to investigate how the characteristics of the mixed layer turbulence influence the observed distribution of phytoplankton. One novel feature is the incorporation of a 'vortex-force' term in the LES code in order to generate Langmuir circulations. It has been speculated that the enhanced mixing rates associated with 'Langmuir turbulence' play a significant role in regulating planktonic activity. Results derived from the coupled LES-NPZ model, run with and without the presence of Langmuir circulations, are presented in order to investigate these ideas.     

Arum- and Paris-type arbuscular mycorrhizas in a mixed pine forest on sand dune soil in Niigata Prefecture, central Honshu, Japan

Arbuscular mycorrhizas (AM) are the most widespread mycorrhiza in nature and form two morphologies, Arum- and Paris-type. The determining factors defining the two different morphologies are not well understood. In this study, the distribution of Arum- and Paris-type AM was determined in a mixed pine forest. A total of 35 plant species belonging to 20 families and 32 genera were identified and examined for AM colonization and morphological types. AM morphological types in 14 families were confirmed as follows: Arum-type in Rosaceae, Oleaceae, Lauraceae, Vitaceae and Compositae, Paris-type in Aquifoliaceae, Ulmaceae, Araliaceae, Theaceae, Magnoliaceae, Rubiaceae and Dioscoraceae, and both and/or intermediate types in Caprifoliaceae and Gramineae. Plant families whose AM morphological status was previously unknown were clarified as follows: Polygonaceae and Commelinaceae showed Arum-type morphology; Celastraceae, Menispermaceae and Elaeagnaceae had typical Paris-type morphology. The proportion of Arum-type to Paris-type species decreased in the following order: annuals > perennials > deciduous species > evergreen species, and pioneer group > early successional group > late successional group. Evergreen plants had a higher tendency to form Paris-type AM than annuals, perennials and deciduous plants. The results indicate that environmental changes, such as shade during plant succession, control the distribution of plant growth forms in mixed pine forest and may also play a part in the distribution of Arum- and Paris-type morphology. The identity of the plant seems to strongly influence AM morphology, though control by the fungal genome cannot be ruled out.     

Bayesian inference for stochastic kinetic models using a diffusion approximation

This article is concerned with the Bayesian estimation of stochastic rate constants in the context of dynamic models of intracellular processes. The underlying discrete stochastic kinetic model is replaced by a diffusion approximation (or stochastic differential equation approach) where a white noise term models stochastic behavior and the model is identified using equispaced time course data. The estimation framework involves the introduction of m- 1 latent data points between every pair of observations. MCMC methods are then used to sample the posterior distribution of the latent process and the model parameters. The methodology is applied to the estimation of parameters in a prokaryotic autoregulatory gene network.