A general model of error-prone PCR

In this paper, we generalise a previously-described model of the error-prone polymerase chain reaction (PCR) reaction to conditions of arbitrarily variable amplification efficiency and initial population size. Generalisation of the model to these conditions improves the correspondence to observed and expected behaviours of PCR, and restricts the extent to which the model may explore sequence space for a prescribed set of parameters. Error-prone PCR in realistic reaction conditions is predicted to be less effective at generating grossly divergent sequences than the original model. The estimate of mutation rate per cycle by sampling sequences from an in vitro PCR experiment is correspondingly affected by the choice of model and parameters. (c) 2005 Elsevier Ltd. All rights reserved.

Development and experimental identification of a biomechanical model of the trunk for functional electrical stimulation control in paraplegia

Objectives. Theoretic modeling and experimental studies suggest that functional electrical stimulation (FES) can improve trunk balance in spinal cord injured subjects. This can have a positive impact on daily life, increasing the volume of bimanual workspace, improving sitting posture, and wheelchair propulsion. A closed loop controller for the stimulation is desirable, as it can potentially decrease muscle fatigue and offer better rejection to disturbances. This paper proposes a biomechanical model of the human trunk, and a procedure for its identification, to be used for the future development of FES controllers. The advantage over previous models resides in the simplicity of the solution proposed, which makes it possible to identify the model just before a stimulation session ( taking into account the variability of the muscle response to the FES). Materials and Methods. The structure of the model is based on previous research on FES and muscle physiology. Some details could not be inferred from previous studies, and were determined from experimental data. Experiments with a paraplegic volunteer were conducted in order to measure the moments exerted by the trunk-passive tissues and artificially stimulated muscles. Data for model identification and validation also were collected. Results. Using the proposed structure and identification procedure, the model could adequately reproduce the moments exerted during the experiments. The study reveals that the stimulated trunk extensors can exert maximal moment when the trunk is in the upright position. In contrast, previous studies show that able-bodied subjects can exert maximal trunk extension when flexed forward. Conclusions. The proposed model and identification procedure are a successful first step toward the development of a model-based controller for trunk FES. The model also gives information on the trunk in unique conditions, normally not observable in able-bodied subjects (ie, subject only to extensor muscles contraction).

Linking the coevolutionary and population dynamics of host-parasitoid interactions

The interplay between coevolutionary and population or community dynamics is currently the focus of much empirical and theoretical consideration. Here, we develop a simulation model to study the coevolutionary and population dynamics of a hypothetical host-parasitoid interaction. In the model, host resistance and parasitoid virulence are allowed to coevolve. We investigate how trade-offs associated with these traits modify the system's coevolutionary and population dynamics. The most important influence on these dynamics comes from the incorporation of density-dependent costs of resistance ability. We find three main outcomes. First, if the costs of resistance are high, then one or both of the players go extinct. Second, when the costs of resistance are intermediate to low, cycling population and coevolutionary dynamics are found, with slower evolutionary changes observed when the costs of virulence are also low. Third, when the costs associated with resistance and virulence are both high, the hosts trade-off resistance against fecundity and invest little in resistance. However, the parasitoids continue to invest in virulence, leading to stable host and parasitoid population sizes. These results support the hypothesis that costs associated with resistance and virulence will maintain the heritable variation in these traits found in natural populations and that the nature of these trade-offs will greatly influence the population dynamics of the interacting species.

CAMCR: Computer-Assisted Mixture model analysis for Capture–Recapture count data

Population size estimation with discrete or nonparametric mixture models is considered, and reliable ways of construction of the nonparametric mixture model estimator are reviewed and set into perspective. Construction of the maximum likelihood estimator of the mixing distribution is done for any number of components up to the global nonparametric maximum likelihood bound using the EM algorithm. In addition, the estimators of Chao and Zelterman are considered with some generalisations of Zelterman’s estimator. All computations are done with CAMCR, a special software developed for population size estimation with mixture models. Several examples and data sets are discussed and the estimators illustrated. Problems using the mixture model-based estimators are highlighted.

Molecular dynamics simulations of proteins: can the explicit water model be varied?

In molecular mechanics simulations of biological systems, the solvation water is typically represented by a default water model which is an integral part of the force field. Indeed, protein nonbonding parameters are chosen in order to obtain a balance between water-water and protein-water interactions and hence a reliable description of protein solvation. However, less attention has been paid to the question of whether the water model provides a reliable description of the water properties under the chosen simulation conditions, for which more accurate water models often exist. Here we consider the case of the CHARMM protein force field, which was parametrized for use with a modified TIP3P model. Using quantum mechanical and molecular mechanical calculations, we investigate whether the CHARMM force field can be used with other water models: TIP4P and TIP5P. Solvation properties of N-methylacetamide (NMA), other small solute molecules, and a small protein are examined. The results indicate differences in binding energies and minimum energy geometries, especially for TIP5P, but the overall description of solvation is found to be similar for all models tested. The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.

Geodetic mass balance of Azarova glacier, Kodar Mountains, eastern Siberia, and its links to observed and projected climatic change

The Kodar Mountains in eastern Siberia accommodate 30 small, cold-based glaciers with a combined surface area of about 19 km2. Very little is known about these glaciers, with the first survey conducted in the late 1950s. In this paper, we use terrestrial photogrammetry to calculate changes in surface area, elevation, volume and geodetic mass balance of the Azarova Glacier between 1979 and 2007 and relate these to meteorological data from nearby Chara weather station (1938-2007). The glacier surface area declined by 20±6.9% and surface lowered on average by 20±1.8 m (mean thinning: 0.71 m a-1) resulting in a strongly negative cumulative and average mass balance of -18±1.6 m w.e. and -640±60 mm w.e.a-1 respectively. The July-August air temperature increased at a rate of 0.036oC a-1 between 1979 and 2007 and the 1980-2007 period was, on average, around 1oC warmer than 1938-1979. The regional climate projections for A2 and B2 CO2 emission scenarios developed using PRECIS regional climate model indicate that summer temperatures will increase in 2071–2100 by 2.6-4.7°C and 4.9-6.2°C respectively in comparison with 1961–1990. The annual total of solid precipitation will increase by 20% under B2 scenario but decline by 3% under A2 scenario. The length of the ablation season will extend from July–August to June-September. The Azarova Glacier exhibits high sensitivity to climatic warming due to its low elevation, exposure to comparatively high summer temperatures, and the absence of a compensating impact of cold season precipitation. Further summer warming and decline of solid precipitation projected under the A2 scenario will force Azarova to retreat further while impacts of an increase in solid precipitation projected under the B2 scenario require further investigation.

The International Urban Energy Balance Models Comparison Project: First Results from Phase 1

A large number of urban surface energy balance models now exist with different assumptions about the important features of the surface and exchange processes that need to be incorporated. To date, no com- parison of these models has been conducted; in contrast, models for natural surfaces have been compared extensively as part of the Project for Intercomparison of Land-surface Parameterization Schemes. Here, the methods and first results from an extensive international comparison of 33 models are presented. The aim of the comparison overall is to understand the complexity required to model energy and water exchanges in urban areas. The degree of complexity included in the models is outlined and impacts on model performance are discussed. During the comparison there have been significant developments in the models with resulting improvements in performance (root-mean-square error falling by up to two-thirds). Evaluation is based on a dataset containing net all-wave radiation, sensible heat, and latent heat flux observations for an industrial area in Vancouver, British Columbia, Canada. The aim of the comparison is twofold: to identify those modeling ap- proaches that minimize the errors in the simulated fluxes of the urban energy balance and to determine the degree of model complexity required for accurate simulations. There is evidence that some classes of models perform better for individual fluxes but no model performs best or worst for all fluxes. In general, the simpler models perform as well as the more complex models based on all statistical measures. Generally the schemes have best overall capability to model net all-wave radiation and least capability to model latent heat flux.

Relation between neuronal morphology and electrophysiology in the Kainate lesion model of Alzheimer's Disease

This paper describes a computational and statistical study of the influence of morphological changes on the electrophysiological response of neurons from an animal model of Alzheimer's Disease (AD). We combined experimental morphological data from rat hippocampal CA1 pyramidal cells with a well-established model of active membrane properties. Dendritic morphology and the somatic response to simulated current clamp conditions were then compared for cells from the control and the AD group. The computational approach allowed us to single out the influences of neuromorphology on neuronal response by eliminating the effects of active channel variability. The results did not reveal a simple relationship between morphological changes associated with AD and changes in neural response. However, they did suggest the existence of more complex than anticipated relationships between dendritic morphology and single-cell electrophysiology.

Sensitivity analysis of a cyanobacterial growth and movement model under two different flow regimes

Bloom-forming and toxin-producing cyanobacteria remain a persistent nuisance across the world. Modelling cyanobacterial behaviour in freshwaters is an important tool for understanding their population dynamics and predicting the location and timing of the bloom events in lakes, reservoirs and rivers. A new deterministic–mathematical model was developed, which simulates the growth and movement of cyanobacterial blooms in river systems. The model focuses on the mathematical description of the bloom formation, vertical migration and lateral transport of colonies within river environments by taking into account the major factors that affect the cyanobacterial bloom formation in rivers including light, nutrients and temperature. A parameter sensitivity analysis using a one-at-a-time approach was carried out. There were two objectives of the sensitivity analysis presented in this paper: to identify the key parameters controlling the growth and movement patterns of cyanobacteria and to provide a means for model validation. The result of the analysis suggested that maximum growth rate and day length period were the most significant parameters in determining the population growth and colony depth, respectively.

Ensemble prediction for nowcasting with a convection-permitting model - II: forecast error statistics

A 24-member ensemble of 1-h high-resolution forecasts over the Southern United Kingdom is used to study short-range forecast error statistics. The initial conditions are found from perturbations from an ensemble transform Kalman filter. Forecasts from this system are assumed to lie within the bounds of forecast error of an operational forecast system. Although noisy, this system is capable of producing physically reasonable statistics which are analysed and compared to statistics implied from a variational assimilation system. The variances for temperature errors for instance show structures that reflect convective activity. Some variables, notably potential temperature and specific humidity perturbations, have autocorrelation functions that deviate from 3-D isotropy at the convective-scale (horizontal scales less than 10 km). Other variables, notably the velocity potential for horizontal divergence perturbations, maintain 3-D isotropy at all scales. Geostrophic and hydrostatic balances are studied by examining correlations between terms in the divergence and vertical momentum equations respectively. Both balances are found to decay as the horizontal scale decreases. It is estimated that geostrophic balance becomes less important at scales smaller than 75 km, and hydrostatic balance becomes less important at scales smaller than 35 km, although more work is required to validate these findings. The implications of these results for high-resolution data assimilation are discussed.

Limitations of the MRL mouse as a model for cardiac regeneration

Objective Myocardial repair following injury in mammals is restricted such that damaged areas are replaced by scar tissue, impairing cardiac function. MRL mice exhibit exceptional regenerative healing in an ear punch wound model. Some myocardial repair with restoration of heart function has also been reported following cryoinjury. Increased cardiomyocyte proliferation and a foetal liver stem cell population were implicated. We investigated molecular mechanisms facilitating myocardial repair in MRL mice to identify potential therapeutic targets in non-regenerative species. Methods Expressions of specific cell-cycle regulators that might account for regeneration (CDKs 1, 2, 4 and 6; cyclins A, E, D1 and B1; p21, p27 and E2F5) were compared by immunoblotting in MRL and control C57BL/6 ventricles during development. Flow cytometry was used to investigate stem cell populations in livers from foetal mice, and infarct sizes were compared in coronary artery-ligated and sham-treated MRL and C57BL/6 adult mice. Key findings No differences in the expressions of cell cycle regulators were observed between the two strains. Expressions of CD34+Sca1+ckit-, CD34+Sca1+ckit+ and CD34+Sca1-ckit+ increased in livers from C57BL/6 vs MRL mice. No differences were observed in infarct sizes, levels of fibrosis, Ki67 staining or cardiac function between MRL and C57BL/6 mice. Conclusions No intrinsic differences were observed in cell cycle control molecules or stem cell populations between MRL and control C57BL mouse hearts. Pathophysiologically relevant ischaemic injury is not repaired more efficiently in MRL myocardium, questioning the use of the MRL mouse as a reliable model for cardiac regeneration in response to pathophysiologically relevant forms of injury.

Multimodel estimate of the global terrestrial water balance: setup and first results

Six land surface models and five global hydrological models participate in a model intercomparison project (WaterMIP), which for the first time compares simulation results of these different classes of models in a consistent way. In this paper the simulation setup is described and aspects of the multi-model global terrestrial water balance are presented. All models were run at 0.5 degree spatial resolution for the global land areas for a 15-year period (1985-1999) using a newly-developed global meteorological dataset. Simulated global terrestrial evapotranspiration, excluding Greenland and Antarctica, ranges from 415 to 586 mm year-1 (60,000 to 85,000 km3 year-1) and simulated runoff ranges from 290 to 457 mm year-1 (42,000 to 66,000 km3 year-1). Both the mean and median runoff fractions for the land surface models are lower than those of the global hydrological models, although the range is wider. Significant simulation differences between land surface and global hydrological models are found to be caused by the snow scheme employed. The physically-based energy balance approach used by land surface models generally results in lower snow water equivalent values than the conceptual degree-day approach used by global hydrological models. Some differences in simulated runoff and evapotranspiration are explained by model parameterizations, although the processes included and parameterizations used are not distinct to either land surface models or global hydrological models. The results show that differences between model are major sources of uncertainty. Climate change impact studies thus need to use not only multiple climate models, but also some other measure of uncertainty, (e.g. multiple impact models).

How predation and landscape fragmentation affect vole population dynamics

Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis), we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. Significance: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results clearly demonstrate the importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics.

SATgene dietary model to implement diets of differing fat composition in prospectively genotyped groups (apoE) using commercially available foods

esponse to dietary fat manipulation is highly heterogeneous, yet generic population-based recommendations aimed at reducing the burden of CVD are given. The APOE epsilon genotype has been proposed to be an important determinant of this response. The present study reports on the dietary strategy employed in the SATgenɛ (SATurated fat and gene APOE) study, to assess the impact of altered fat content and composition on the blood lipid profile according to the APOE genotype. A flexible dietary exchange model was developed to implement three isoenergetic diets: a low-fat (LF) diet (target composition: 24 % of energy (%E) as fat, 8 %E SFA and 59 %E carbohydrate), a high-saturated fat (HSF) diet (38 %E fat, 18 %E SFA and 45 %E carbohydrate) and a HSF-DHA diet (HSF diet with 3 g DHA/d). Free-living participants (n 88; n 44 E3/E3 and n 44 E3/E4) followed the diets in a sequential design for 8 weeks, each using commercially available spreads, oils and snacks with specific fatty acid profiles. Dietary compositional targets were broadly met with significantly higher total fat (42·8 %E and 41·0 %E v. 25·1 %E, P ≤ 0·0011) and SFA (19·3 %E and 18·6 %E v. 8·33 %E, P ≤ 0·0011) intakes during the HSF and HSF-DHA diets compared with the LF diet, in addition to significantly higher DHA intake during the HSF-DHA diet (P ≤ 0·0011). Plasma phospholipid fatty acid analysis revealed a 2-fold increase in the proportion of DHA after consumption of the HSF-DHA diet for 8 weeks, which was independent of the APOE genotype. In summary, the dietary strategy was successfully implemented in a free-living population resulting in well-tolerated diets which broadly met the dietary targets set.

The impact of a seasonally ice free Arctic Ocean on the temperature, precipitation and surface mass balance of Svalbard

The observed decline in summer sea ice extent since the 1970s is predicted to continue until the Arctic Ocean is seasonally ice free during the 21st Century. This will lead to a much perturbed Arctic climate with large changes in ocean surface energy flux. Svalbard, located on the present day sea ice edge, contains many low lying ice caps and glaciers and is expected to experience rapid warming over the 21st Century. The total sea level rise if all the land ice on Svalbard were to melt completely is 0.02 m. The purpose of this study is to quantify the impact of climate change on Svalbard’s surface mass balance (SMB) and to determine, in particular, what proportion of the projected changes in precipitation and SMB are a result of changes to the Arctic sea ice cover. To investigate this a regional climate model was forced with monthly mean climatologies of sea surface temperature (SST) and sea ice concentration for the periods 1961–1990 and 2061–2090 under two emission scenarios. In a novel forcing experiment, 20th Century SSTs and 21st Century sea ice were used to force one simulation to investigate the role of sea ice forcing. This experiment results in a 3.5 m water equivalent increase in Svalbard’s SMB compared to the present day. This is because over 50 % of the projected increase in winter precipitation over Svalbard under the A1B emissions scenario is due to an increase in lower atmosphere moisture content associated with evaporation from the ice free ocean. These results indicate that increases in precipitation due to sea ice decline may act to moderate mass loss from Svalbard’s glaciers due to future Arctic warming.