The dusty AGB star RS CrB: first mid-infrared interferometric observations with the Keck Telescopes

We report interferometric observations of the semi-regular variable star RS CrB, a red giant with strong silicate emission features. The data were among the first long baseline mid-infrared stellar fringes obtained between the Keck telescopes, using parts of the new nulling beam combiner. The light was dispersed by a low-resolution spectrometer, allowing simultaneous measurement of the source visibility and intensity spectra from 8 to 12 microns. The interferometric observations allow a non-ambiguous determination of the dust shell spatial scale and relative flux contribution. Using a simple spherically-symmetric model, in which a geometrically thin shell surrounds the stellar photosphere, we find that ~30% to ~70% of the overall mid-infrared flux - depending on the wavelength - originates from 7-8 stellar radii. The derived shell opacity profile shows a broad peak around 11 microns (tau ~ 0.06), characteristic of Mg-rich silicate dust particles.Comment: Accepted for publication in ApJ Letter

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

BACKGROUND: Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. RESULTS: We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. CONCLUSION: Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases

Design, development and validity testing of the Gang Affiliation Risk Measure (GARM)

This study aimed to create a measure of risk for gang affiliation, for use in the UK. A pilot stage invited gang affiliated and non-gang affiliated participants between the ages of 16–25 years to retrospectively self-report on 58 items of risk exposure at the age of 11 years. Based on performance of these items, a 26-item measure was developed and administered to a main study sample (n=185) of gang affiliated and non-gang affiliated participants. Categorical Principal Component Analysis was applied to data, yielding a single-factor solution (historic lack of safety and current perception of threat). A 15-item gang affiliation risk measure (GARM) was subsequently created. The GARM demonstrated good internal consistency, construct validity and discriminative ability. Items from the GARM were then transformed to read prospectively, resulting in a test measure for predictive purposes (T-GARM). The T-GARM requires further validation regarding its predictive utility and generalisability. However, this study has resulted in the first measure of gang affiliation, with promising results

The Bacillus subtilis Minimal Genome Compendium

To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology