A temporal switch model for estimating transcriptional activity in gene expression

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation

Near-surface remote sensing of spatial and temporal variation in canopy phenology

There is a need to document how plant phenology is responding to global change factors, particularly warming trends. “Near-surface” remote sensing, using radiometric instruments or imaging sensors, has great potential to improve phenological monitoring because automated observations can be made at high temporal frequency. Here we build on previous work and show how inexpensive, networked digital cameras (“webcams”) can be used to document spatial and temporal variation in the spring and autumn phenology of forest canopies. We use two years of imagery from a deciduous, northern hardwood site, and one year of imagery from a coniferous, boreal transition site. A quantitative signal is obtained by splitting images into separate red, green, and blue color channels and calculating the relative brightness of each channel for “regions of interest” within each image. We put the observed phenological signal in context by relating it to seasonal patterns of gross primary productivity, inferred from eddy covariance measurements of surface–atmosphere CO2 exchange. We show that spring increases, and autumn decreases, in canopy greenness can be detected in both deciduous and coniferous stands. In deciduous stands, an autumn red peak is also observed. The timing and rate of spring development and autumn senescence varies across the canopy, with greater variability in autumn than spring. Interannual variation in phenology can be detected both visually and quantitatively; delayed spring onset in 2007 compared to 2006 is related to a prolonged cold spell from day 85 to day 110. This work lays the foundation for regional- to continental-scale camera-based monitoring of phenology at network observatory sites, e.g., National Ecological Observatory Network (NEON) or AmeriFlux

Resonance energy transfer: The unified theory revisited

Resonanceenergy transfer (RET) is the principal mechanism for the intermolecular or intramolecular redistribution of electronic energy following molecular excitation. In terms of fundamental quantum interactions, the process is properly described in terms of a virtual photon transit between the pre-excited donor and a lower energy (usually ground-state) acceptor. The detailed quantum amplitude for RET is calculated by molecular quantum electrodynamical techniques with the observable, the transfer rate, derived via application of the Fermi golden rule. In the treatment reported here, recently devised state-sequence techniques and a novel calculational protocol is applied to RET and shown to circumvent problems associated with the usual method. The second-rank tensor describing virtual photon behavior evolves from a Green’s function solution to the Helmholtz equation, and special functions are employed to realize the coupling tensor. The method is used to derive a new result for energy transfer systems sensitive to both magnetic- and electric-dipole transitions. The ensuing result is compared to that of pure electric-dipole–electric-dipole coupling and is analyzed with regard to acceptable transfer separations. Systems are proposed where the electric-dipole–magnetic-dipole term is the leading contribution to the overall rate

Lifting of Ir{100} reconstruction by CO adsorption: An ab initio study

The adsorption of CO on unreconstructed and reconstructed Ir{100} has been studied, using a combination of density functional theory and thermodynamics, to determine the relative stability of the two phases as a function of CO coverage, temperature and pressure. We obtain good agreement with experimentaldata. At zero temperature, the (1X5) reconstruction becomes less stable than the unreconstructed (1X1) surface when the CO coverage exceeds a critical value of 0.09 ML. The interaction between CO molecules is found to be repulsive on the reconstructed surface, but attractive on the unreconstructed, explaining the experimental observation of high CO coverage on growing (1X1) islands. At all temperatures and pressures, we find only two possible stable states: 0.05 ML CO c(2X2) overlayer on the (1X1) substrate, and the clean (1$\times$5) reconstructed surface.Comment: 31 page

Trends in antibacterial resistance among Streptococcus pneumoniae isolated in the USA: update from PROTEKT US Years 1–4

© 2008 Jenkins et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Influence of playing standard and physical fitness on activity profiles and post-match fatigue during intensified junior rugby league competition

BACKGROUND: The aim of this study was to determine whether the fatigue responses to the same intensified rugby league competition differed depending on playing standard and physical fitness. METHODS: Players from a high-standard (n = 15) and a low-standard (n = 16) junior rugby league team had lower body neuromuscular fatigue, perceptual wellbeing, and blood creatine kinase (CK) assessed over an intensified competition. Global positioning system units measured match activity profiles and rating of perceived exertion-assessed internal loads. Players were divided into high- and low-fitness groups across the two standards based on Yo-Yo intermittent recovery test performance. RESULTS: Playing intensity increased with playing standard and fitness levels (high-standard = 92 +/- 6 m.min(-1) vs. 88 +/- 6 m.min(-1); low-standard = 88 +/- 2 m.min(-1) vs. 83 +/- 6 m.min(-1)). Despite greater internal and external loads, high-fitness players showed smaller reductions in lower body power (high-standard effect size [ES] = -0.74; low-standard ES = -0.41). High-standard players had smaller increases in blood CK (77% +/- 94% vs. 113% +/- 81%; ES = -0.41), primarily due to very small increases in the high-fitness group (50% +/- 45%). CONCLUSIONS: Increased fitness leads to greater internal and external workloads during intensified competition, smaller increases in blood CK, and less neuromuscular fatigue. Maximising player fitness should be a primary goal of coaches in order to increase match workloads and reduce post-match fatigue during intensified competition. KEY POINTS: Increased physical fitness results in greater relative and absolute match workloads.Increased physical fitness results in less fatigue and muscle damage during an intensified competition.Coaching staff should aim to maximise physical fitness in order to optimise match performance and reduce player fatigue