Functional genomics of mountain pine beetle (Dendroctonus ponderosae) midguts and fat bodies

<p>Abstract</p> <p>Background</p> <p>The mountain pine beetle (<it>Dendroctonus ponderosae</it>) is a significant coniferous forest pest in western North America. It relies on aggregation pheromones to colonize hosts. Its three major pheromone components, <it>trans</it>-verbenol, <it>exo</it>-brevicomin, and frontalin, are thought to arise via different metabolic pathways, but the enzymes involved have not been identified or characterized. We produced ESTs from male and female midguts and associated fat bodies and used custom oligonucleotide microarrays to study gene expression patterns and thereby made preliminary identification of pheromone-biosynthetic genes.</p> <p>Results</p> <p>Clones from two un-normalized cDNA libraries were directionally sequenced from the 5' end to yield 11,775 ESTs following sequence cleansing. The average read length was 550 nt. The ESTs clustered into 1,201 contigs and 2,833 singlets (4,034 tentative unique genes). The ESTs are broadly distributed among GO functional groups, suggesting they reflect a broad spectrum of the transcriptome. Among the most represented genes are representatives of sugar-digesting enzymes and members of an apparently Scolytid-specific gene family of unknown function. Custom NimbleGen 4-plex arrays representing the 4,034 tentative unique genes were queried with RNA from eleven different biological states representing larvae, pupae, and midguts and associated fat bodies of unfed or fed adults. Quantitative (Real-Time) RT-PCR (qRT-PCR) experiments confirmed that the microarray data accurately reflect expression levels in the different samples. Candidate genes encoding enzymes involved in terminal steps of biosynthetic pathways for <it>exo</it>-brevicomin and frontalin were tentatively identified.</p> <p>Conclusions</p> <p>These EST and microarray data are the first publicly-available functional genomics resources for this devastating forestry pest.</p

Keldysh Green's function approach to coherence in a non-equilibrium steady state: connecting Bose-Einstein condensation and lasing

Solid state quantum condensates often differ from previous examples of condensates (such as Helium, ultra-cold atomic gases, and superconductors) in that the quasiparticles condensing have relatively short lifetimes, and so as for lasers, external pumping is required to maintain a steady state. On the other hand, compared to lasers, the quasiparticles are generally more strongly interacting, and therefore better able to thermalise. This leads to questions of how to describe such non-equilibrium condensates, and their relation to equilibrium condensates and lasers. This chapter discusses in detail how the non-equilibrium Green's function approach can be applied to the description of such a non-equilibrium condensate, in particular, a system of microcavity polaritons, driven out of equilibrium by coupling to multiple baths. By considering the steady states, and fluctuations about them, it is possible to provide a description that relates both to equilibrium condensation and to lasing, while at the same time, making clear the differences from simple lasers

The effects of CO2, climate and land-use on terrestrial carbon balance, 1920-1992: An analysis with four process-based ecosystem models

The concurrent effects of increasing atmospheric CO2 concentration, climate variability, and cropland establishment and abandonment on terrestrial carbon storage between 1920 and 1992 were assessed using a standard simulation protocol with four process-based terrestrial biosphere models. Over the long-term(1920–1992), the simulations yielded a time history of terrestrial uptake that is consistent (within the uncertainty) with a long-term analysis based on ice core and atmospheric CO2 data. Up to 1958, three of four analyses indicated a net release of carbon from terrestrial ecosystems to the atmosphere caused by cropland establishment. After 1958, all analyses indicate a net uptake of carbon by terrestrial ecosystems, primarily because of the physiological effects of rapidly rising atmospheric CO2. During the 1980s the simulations indicate that terrestrial ecosystems stored between 0.3 and 1.5 Pg C yr−1, which is within the uncertainty of analysis based on CO2 and O2 budgets. Three of the four models indicated (in accordance with O2 evidence) that the tropics were approximately neutral while a net sink existed in ecosystems north of the tropics. Although all of the models agree that the long-term effect of climate on carbon storage has been small relative to the effects of increasing atmospheric CO2 and land use, the models disagree as to whether climate variability and change in the twentieth century has promoted carbon storage or release. Simulated interannual variability from 1958 generally reproduced the El Niño/Southern Oscillation (ENSO)-scale variability in the atmospheric CO2 increase, but there were substantial differences in the magnitude of interannual variability simulated by the models. The analysis of the ability of the models to simulate the changing amplitude of the seasonal cycle of atmospheric CO2 suggested that the observed trend may be a consequence of CO2 effects, climate variability, land use changes, or a combination of these effects. The next steps for improving the process-based simulation of historical terrestrial carbon include (1) the transfer of insight gained from stand-level process studies to improve the sensitivity of simulated carbon storage responses to changes in CO2 and climate, (2) improvements in the data sets used to drive the models so that they incorporate the timing, extent, and types of major disturbances, (3) the enhancement of the models so that they consider major crop types and management schemes, (4) development of data sets that identify the spatial extent of major crop types and management schemes through time, and (5) the consideration of the effects of anthropogenic nitrogen deposition. The evaluation of the performance of the models in the context of a more complete consideration of the factors influencing historical terrestrial carbon dynamics is important for reducing uncertainties in representing the role of terrestrial ecosystems in future projections of the Earth system

Capturing differences in dental training using a virtual reality simulator

Virtual reality simulators are becoming increasingly popular in dental schools across the world. But to what extent do these systems reflect actual dental ability? Addressing this question of construct validity is a fundamental step that is necessary before these systems can be fully integrated into a dental school's curriculum. In this study, we examined the sensitivity of the Simodont (a haptic virtual reality dental simulator) to differences in dental training experience. Two hundred and eighty-nine participants, with 1 (n = 92), 3 (n = 79), 4 (n = 57) and 5 (n = 61) years of dental training, performed a series of tasks upon their first exposure to the simulator. We found statistically significant differences between novice (Year 1) and experienced dental trainees (operationalised as 3 or more years of training), but no differences between performance of experienced trainees with varying levels of experience. This work represents a crucial first step in understanding the value of haptic virtual reality simulators in dental education

Moment Closure - A Brief Review

Moment closure methods appear in myriad scientific disciplines in the modelling of complex systems. The goal is to achieve a closed form of a large, usually even infinite, set of coupled differential (or difference) equations. Each equation describes the evolution of one "moment", a suitable coarse-grained quantity computable from the full state space. If the system is too large for analytical and/or numerical methods, then one aims to reduce it by finding a moment closure relation expressing "higher-order moments" in terms of "lower-order moments". In this brief review, we focus on highlighting how moment closure methods occur in different contexts. We also conjecture via a geometric explanation why it has been difficult to rigorously justify many moment closure approximations although they work very well in practice.Comment: short survey paper (max 20 pages) for a broad audience in mathematics, physics, chemistry and quantitative biolog

Should prospective dental students be screened for colour vision deficits?

A perennial question in dental education is: what skills and aptitudes should be assessed in prospective dental students? Intellectual capacity and manual dexterity understandably rank highly, but are there minimum thresholds for visual perception that applicants need be able to demonstrate before they enter the profession? We have recently flagged this issue with regard to the thresholds of stereoscopic acuity required for a dentist when operating on teeth. In the present article, we highlight the issue of identifying a minimum acceptable level of colour vision

Collective coherence in planar semiconductor microcavities

Semiconductor microcavities, in which strong coupling of excitons to confined photon modes leads to the formation of exciton-polariton modes, have increasingly become a focus for the study of spontaneous coherence, lasing, and condensation in solid state systems. This review discusses the significant experimental progress to date, the phenomena associated with coherence which have been observed, and also discusses in some detail the different theoretical models that have been used to study such systems. We consider both the case of non-resonant pumping, in which coherence may spontaneously arise, and the related topics of resonant pumping, and the optical parametric oscillator.Comment: 46 pages, 12 figure