Enabling comparative modeling of closely related genomes: Example genus Brucella

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this short report, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.We thank Jean Jacques Letesson, Maite Iriarte, Stephan Kohler and David O'Callaghan for their input on improving specific annotations. This project has been funded by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C, awarded to BW Sobral, and from the United States National Science Foundation under Grant MCB-1153357, awarded to CS Henry. J.P.F. acknowledges funding from [FRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) Ph.D. scholarship

Many-body interactions and melting of colloidal crystals

We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson-Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the mesoscopic colloids. This technique ensures that many-body interactions between the colloids are fully taken into account, and thus allows us to investigate how many-body interactions affect the solid-liquid phase behavior of charged colloids. Using the Lindemann criterion, we determine the melting line in a phase-diagram spanned by the colloidal charge and the salt concentration. We compare our results to predictions based on the established description of colloidal suspensions in terms of pairwise additive Yukawa potentials, and find good agreement at high-salt, but not at low-salt concentration. Analyzing the effective pair-interaction between two colloids in a crystalline environment, we demonstrate that the difference in the melting behavior observed at low salt is due to many-body interactions

Does affirming children's autonomy and prosocial intentions help? A microtrial into intervention component effects to improve psychosocial behavior

Item does not contain fulltextPrior research has related children's prosocial behavior to overall well-being, and stimulating prosocial behavior is the aim of many social-emotional skills interventions. This study assessed if affirming children's autonomy stimulates their psychosocial behavior. We conducted a three-arm microtrial with four repeated measures to assess if a social-emotional skills intervention with an autonomy affirmation component had an additive effect on children's behavior as compared to a "regular" intervention focused exclusively on teaching social-emotional skills and a no-treatment control condition. Our sample consisted of 779 children in Grades 4-6 (Mage = 10.61, SD = 0.93). Findings from latent change modeling demonstrated that the social-emotional skills intervention with an autonomy affirmation component yielded superior effects as compared to the "regular" intervention and the no-treatment control condition on the improvement of internalizing and externalizing problem behavior in the three-month period after the intervention. The intervention with autonomy affirmation did not yield superior effects on prosociality and social skills, self-efficacy, and self-esteem or self-perceived competence. The absence of these effects may be attributed to the dosage of the interventions implemented - the affirmation of children's autonomy may require more than four sessions to sort observable effects. Overall, however, the findings of this study provide an initial suggestion that it may be beneficial to affirm children's autonomy and prosocial intentions when enhancing children's behavior.22 p

A Primer on Rapid Prototyping of Genomic Databases in Prolog

This report presents a tutorial on how one might create an integrated database of genomic information. We outline the required steps for implementation, give a brief introduction to Prolog, and discuss the query facility supported by our system. Our goal is to enable researchers to being constructing their own biological information system

Numerical electrokinetics

A new lattice method is presented in order to efficiently solve the electrokinetic equations, which describe the structure and dynamics of the charge cloud and the flow field surrounding a single charged colloidal sphere, or a fixed array of such objects. We focus on calculating the electrophoretic mobility in the limit of small driving field, and systematically linearise the equations with respect to the latter. This gives rise to several subproblems, each of which is solved by a specialised numerical algorithm. For the total problem we combine these solvers in an iterative procedure. Applying this method, we study the effect of the screening mechanism (salt screening vs. counterion screening) on the electrophoretic mobility, and find a weak non-trivial dependence, as expected from scaling theory. Furthermore, we find that the orientation of the charge cloud (i. e. its dipole moment) depends on the value of the colloid charge, as a result of a competition between electrostatic and hydrodynamic effects.Comment: accepted for publication in Journal of Physics Condensed Matter (proceedings of the 2012 CODEF conference

Validation of FEM models describing moisture transport in heated concrete by Magnetic Resonance Imaging

Fire safety of buildings and structures is an important issue, and has a great impact on human life and economy. One of the processes negatively affecting the strength of a concrete building or structure during fire is spalling. Many examples exists in which spalling of concrete during fire has caused severe damage to structures, such as in the Mont Blanc and Channel Tunnel. Especially newly developed dense types of concrete such as HPC and SCC, have shown to be sensitive to spalling, hampering the application of these new concrete types. To reduce risks and building costs, the processes behind spalling need to be understood. Increasing our knowledge allows us to reliably predict the behaviour and take effective and cost friendly preventive measures. Moisture present in concrete is one of the reasons for spalling. When concrete is heated water will evaporate, which results in a high gas pressure inside the pores of concrete. This high gas pressure can induce spalling. To attain a better understanding of this process, a first step was taken to develop a finite element model (FEM) describing this transport of moisture in heated concrete. However, the validity of all current models (including our own) is unknown because of debatable input parameters and lack of experimental techniques to follow the transport process in situ. In cooperation with the Eindhoven University of Technology moisture transport in heated concrete can now be investigated with a home built dedicated 1D Magnetic Resonance Imaging (MRI) setup. Using the results of the MRI experiments the validity of our FEM models has been assessed for the first time. A general correspondence is observed. The FEM model described in this paper is a simplified FEM model compared to literature models. Already this simplified model shows a good correspondence with the MRI measurements