Effect of salt bridges on the energy landscape of a model protein

The effect of introducing salt bridges (gatekeepers) into an off-lattice three-color, 46-bead model protein is investigated in terms of the effect on global optimization statistics. The global minima for all the gatekeepers that exhibited faster folding in previous molecular dynamics studies are located more rapidly than for the original potential, although the global minimum itself may change. Visualization of the underlying potential energy surface using disconnectivity graphs reveals that the gatekeepers exhibit structure intermediate between the original potential and a Go model. Competition between low-lying minima and the global minimum is reduced in the gatekeepers compared to the original potential, and interconversion barriers are generally smaller.     

Semi-targeted analysis of metabolites using capillary-flow ion chromatography coupled to high-resolution mass spectrometry

This work describes a novel application of capillary-flow ion chromatography mass spectrometry for metabolomic analysis, and comparison of the technique to octadecyl silica and hydrophilic interaction chromatography (HILIC)-based mass spectrometry. While liquid chromatography/mass spectrometry (LC/MS) is rapidly becoming the standard technique for metabolomic analysis, metabolomic samples are extremely heterogeneous, leading to a requirement for multiple methods of analysis and separation techniques to perform a 'global' metabolomic analysis. While C18 is suitable for hydrophobic metabolites and has been used extensively in pharmaceutical drug metabolism studies, HILIC is, in general, efficient at separating polar metabolites. Phosphorylated species and organic acids are challenging to analyse and effectively quantitate on both systems. There is therefore a requirement for an MS-compatible analytical technique that can separate negatively charged compounds, such as ion-exchange chromatography. Evaluation of capillary flow ion chromatography with electrolytic suppression was performed on a library of metabolite standards and was shown to effectively separate organic acids and sugar di- and tri-phosphates. Limits of detection for these compounds range from 0.01 to 100 pmol on-column. Application of capillary ion chromatography to a comparative analysis of energy metabolism in procyclic forms of the parasitic protozoan Trypanosoma brucei where cells were grown on glucose or proline as a carbon source was demonstrated to be more effective than HILIC for detection of the organic acids that comprise glucose central metabolism and the tricarboxylic acid (TCA) cycle.     

HARVESTING ECONOMIC MODELS AND CATCH‐TO‐BIOMASS DEPENDENCE: THE CASE OF SMALL PELAGIC FISH

Abstract In the case of small pelagic fish, it seems reasonable to consider harvest functions depending nonlinearly on fishing effort and fish stock. Indeed, empirical evidence about these fish species suggests that marginal catch does not necessarily react in a linear way neither to changes in fishing effort nor in fish stock levels. This is in contradiction with traditional fishery economic models where catch‐to‐input marginal productivities are normally assumed to be constant. While allowing for nonlinearities in both catch‐to‐effort and catch‐to‐stock parameters, this paper extends the traditional single‐stock harvesting economic model by focusing on the dependence of the stationary solutions upon the nonlinear catch‐to‐stock parameter. Thus, we analyze equilibrium responses to changes in this parameter, which in turn may be triggered either by climatic or technological change. Given the focus in this study on the case of small pelagic fish, the analysis considers positive but small values for the catch‐to‐stock parameter.