The Difficult Case of Crystallization and Structure Solution for the ParC55 Breakage-Reunion Domain of Topoisomerase IV from Streptococcus pneumoniae

BACKGROUND: Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. METHODOLOGY/PRINCIPAL FINDINGS: Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. CONCLUSIONS/SIGNIFICANCE: The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution

Crossover Scales at the Critical Points of Fluids with Electrostatic Interactions

Criticality in a fluid of dielectric constant D that exhibits Ising-type behavior is studied as additional electrostatic (i.e., ionic) interactions are turned on. An exploratory perturbative calculation is performed for small ionicity as measured by the ratio of the electrostatic energy to the strength of the short-range nonionic (i.e., van der Waals) interactions in the uncharged fluid. With the aid of distinct transformations for the short-range and for the Coulombic interactions, an effective Hamiltonian with coefficients depending on the ionicity is derived at the Debye-Hueckel limiting-law level for a fully symmetric model. The crossover between classical (mean-field) and Ising behavior is then estimated using a Ginzburg criterion. This indicates that the reduced crossover temperature depends only weakly on the ionicity (and on the range of the nonionic potentials); however, the trends do correlate with the, much stronger, dependence observed experimentally.Comment: 25 pages, 4 figure; submitted to J. Chem. Phy

Probabilistic analysis and comparison of stress-dependent rock physics models

A rock physics model attempts to account for the nonlinear stress dependence of seismic velocity by relating changes in stress and strain to changes in seismic velocity and anisotropy. Understanding and being able to model this relationship is crucial for any time-lapse geophysical or geohazard modelling scenario. In this study, we take a number of commonly used rock physics models and assess their behaviour and stability when applied to stress versus velocity measurements of a large (dry) core data set of different lithologies. We invert and calibrate each model and present a database of models for over 400 core samples. The results of which provide a useful tool for setting a priori parameter constraints for future model inversions. We observe that some models assume an increase in VP/VS ratio (hence Poisson’s ratio) with stress. A trait not seen for every sample in our data set. We demonstrate that most model parameters are well constrained. However, third-order elasticity models become ill-posed when their equations are simplified for an isotropic rock. We also find that third-order elasticity models are limited by their approximation of an exponential relationship via functions that lack an exponential term. We also argue that all models are difficult to parametrize without the availability of core data. Therefore, we derive simple relationships between model parameters, core porosity and clay content. We observe that these relationship are suitable for estimating seismic velocities of rock but poor when comes to predicting changes related to effective stress. The findings of this study emphasize the need for improvement to models if quantitatively accurate predictions of time-lapse velocity and anisotropy are to be made. Certain models appear to better fit velocity depth log data than velocity–stress core data. Thus, there is evidence to suggest a limitation in core data as a representation of the stress dependence of the subsurface. The differences in the stress dependence of the subsurface compared to that measured under laboratory conditions could potentially be significant. Although potentially difficult to investigate, its importance is of great significance if we wish to accurately interpret the stress dependence of subsurface seismic velocities

Wearing colored glasses can influence the exercise performance and testosterone concentration

Perception of red color is associated with higher testosterone concentration and better human performance. Thus, we evaluated the acute effects of wearing colored-lens glasses on the YoYo intermittent endurance exercise test 2 (YoYoIE2) performance indicators and testosterone concentration. Ten soccer players performed three YoYoIE2 (counterbalanced crossover) wearing colorless (control), blue- or red-lensed glasses (2–4 days of rest in between). YoYoIE2 performance did not differ among the trials (p>0.05), but blood testosterone increased post-exercise in red compared to red baseline (red=14%, effect size=0.75). Analysis showed faster heart rate recovery (p0.05) among the trials. Wearing red-colored lenses during high-intensity intermittent exercise increased testosterone concentration, but do not influence performance

Managing the trade-off implications of global supply

The cost versus response trade-off is a growing logistics issue due to many markets being increasingly characterized by demand uncertainty and shorter product life cycles. This is exacerbated further with supply increasingly moving to low cost global sources. However, the poor response implications of global supply are often not addressed or even acknowledged when undertaking such decisions. Consequently, various practical approaches to minimising, postponing or otherwise managing the impact of the demand uncertainty are often only adopted retrospectively. Even though such generic solutions are documented through case examples we lack effective tools and concepts to support the proactive identification and resolution of such trade-offs. This paper reports on case-based theory building research, involving three cases from the UK and USA used in developing a conceptual model with associated tools, in support of such a process

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. We benchmark this method against other SNP callers using our FDR method with three fungal genomes, finding that it was able achieve a high level of accuracy. These tools are available at http://cfdr.sourceforge.net/.R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study

Mixed initial conditions to estimate the dynamic critical exponent in short-time Monte Carlo simulation

We explore the initial conditions in short-time critical dynamics to propose a new method to evaluate the dynamic exponent z. Estimates are obtained with high precision for 2D Ising model and 2D Potts model for three and four states by performing heat-bath Monte Carlo simulations.Comment: Latex paper, 2 eps figure

A simple mathematical model for anomalous diffusion via Fisher's information theory

Starting with the relative entropy based on a previously proposed entropy function $S_q[p]=\int dx p(x)(-\ln p(x))^q$, we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the $q\to 1$ limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization of the functions in the Barenblatt-Pattle solution. We find that the mean squared displacement, up to a $q$-dependent constant, has a time dependence according to $\sim K^{1/q}t^{1/q}$, where the parameter $q$ takes values $q=\frac{2n-1}{2n+1}$ (superdiffusion) and $q=\frac{2n+1}{2n-1}$ (subdiffusion), $\forall n\geq 1$.Comment: 13 pages,3 figure