Design principles of a bacterial signalling network

Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology. We experimentally determine the extent of intercellular variations in the expression levels of chemotaxis proteins and use computer simulations to quantify the robustness of several hypothetical chemotaxis pathway topologies to such gene expression noise. We demonstrate that among these topologies the experimentally established chemotaxis network of Escherichia coli has the smallest sufficiently robust network structure, allowing accurate chemotactic response for almost all individuals within a population. Our results suggest that this pathway has evolved to show an optimal chemotactic performance while minimizing the cost of resources associated with high levels of protein expression. Moreover, the underlying topological design principles compensating for intercellular variations seem to be highly conserved among bacterial chemosensory systems.     

Development of DArT markers for a linkage map of flue-cured tobacco

Tobacco(Nicotiana tabacum) is one of the most economically important nonfood crops,and flue-cured tobacco accounts for approximately 80% of world tobacco production.An extremely narrow genetic diversity in the tobacco pool has led to a low efficiency of PCR-based molecular markers(such as AFLP and SSR).Diversity Arrays Technology(DArT) is a high-throughput hybridisation-based marker system that has been developed in many plants including wheat,which,like tobacco,has a complex genome.In this study,we developed a tobacco DArT chip that included 7680 representative sequence tags based on typical tobacco accessions.The 1076 DArT markers of flue-cured tobacco were identified and most(82.1%) of their polymorphism information contents(PICs) were greater than 0.4.An integrated linkage map that included 851 markers(238 DArT and 613 SSR),which is the highest density map of flue-cured tobacco to date,was constructed.This chip-based DArT system provides an alternative in high-throughput marker genotyping for tobacco.     

Supercontinent cycles and the calculation of absolute palaeolongitude in deep time

Traditional models of the supercontinent cycle predict that the next supercontinent--'Amasia'--will form either where Pangaea rifted (the 'introversion' model) or on the opposite side of the world (the 'extroversion' models). Here, by contrast, we develop an 'orthoversion' model whereby a succeeding supercontinent forms 90° away, within the great circle of subduction encircling its relict predecessor. A supercontinent aggregates over a mantle downwelling but then influences global-scale mantle convection to create an upwelling under the landmass. We calculate the minimum moment of inertia about which oscillatory true polar wander occurs owing to the prolate shape of the non-hydrostatic Earth. By fitting great circles to each supercontinent's true polar wander legacy, we determine that the arc distances between successive supercontinent centres (the axes of the respective minimum moments of inertia) are 88° for Nuna to Rodinia and 87° for Rodinia to Pangaea--as predicted by the orthoversion model. Supercontinent centres can be located back into Precambrian time, providing fixed points for the calculation of absolute palaeolongitude over billion-year timescales. Palaeogeographic reconstructions additionally constrained in palaeolongitude will provide increasingly accurate estimates of ancient plate motions and palaeobiogeographic affinities.     

Did Unexpectedly Strong Economic Growth Cause the Oil Price Shock of 2003–2008?

Recently developed structural models of the global crude oil market imply that the surge in the real price of oil between mid 2003 and mid 2008 was driven by repeated positive shocks to the demand for all industrial commodities, reflecting unexpectedly high growth mainly in emerging Asia. We evaluate this proposition using an alternative data source and a different econometric methodology. Rather than inferring demand shocks from an econometric model, we utilize a direct measure of global demand shocks based on revisions of professional real gross domestic product (GDP) growth forecasts. We show that forecast surprises during 2003–2008 were associated primarily with unexpected growth in emerging economies (in conjunction with much smaller positive GDP‐weighted forecast surprises in the major industrialized economies), that markets were repeatedly surprised by the strength of this growth, that these surprises were associated with a hump‐shaped response of the real price of oil that reaches its peak after 12–16 months, and that news about global growth predict much of the surge in the real price of oil from mid 2003 until mid 2008 and much of its subsequent decline. Copyright © 2012 John Wiley & Sons, Ltd.     

Impulse response analysis in vector autoregressions with unknown lag order

We show that the effects of overfitting and underfitting a vector autoregressive (VAR) model are strongly asymmetric for VAR summary statistics involving higher‐order dynamics (such as impulse response functions, variance decompositions, or long‐run forecasts) . Underfit models often underestimate the true dynamics of the population process and may result in spuriously tight confidence intervals. These insights are important for applied work, regardless of how the lag order is determined. In addition, they provide a new perspective on the trade‐offs between alternative lag order selection criteria. We provide evidence that, contrary to conventional wisdom, for many statistics of interest to VAR users the point and interval estimates based on the AIC compare favourably to those based on the more parsimonious Schwarz Information Criterion and Hannan – Quinn Criterion. Copyright © 2001 John Wiley & Sons, Ltd.