Modular epistasis in yeast metabolism

Epistatic interactions, manifested in the effects of mutations on the phenotypes caused by other mutations, may help uncover the functional organization of complex biological networks. Here, we studied system-level epistatic interactions by computing growth phenotypes of all single and double knockouts of 890 metabolic genes in Saccharomyces cerevisiae, using the framework of flux balance analysis. A new scale for epistasis identified a distinctive trimodal distribution of these epistatic effects, allowing gene pairs to be classified as buffering, aggravating or noninteracting. We found that the ensuing epistatic interaction network could be organized hierarchically into function-enriched modules that interact with each other 'monochromatically' (i.e., with purely aggravating or purely buffering epistatic links). This property extends the concept of epistasis from single genes to functional units and provides a new definition of biological modularity, which emphasizes interactions between, rather than within, functional modules. Our approach can be used to infer functional gene modules from purely phenotypic epistasis measurements.     

The German Federal Republic: Annual report for 1990 of the Deutsche Forschungsgemeinschaft (DFG; German Research Association)

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The German Federal Republic: Annual report for 1990 of the Deutsche Forschungsgemeinschaft (DFG; German Research Association)     

Evaluating volatility dynamics and the forecasting ability of Markov switching models

This paper uses Markov switching models to capture volatility dynamics in exchange rates and to evaluate their forecasting ability. We identify that increased volatilities in four euro‐based exchange rates are due to underlying structural changes. Also, we find that currencies are closely related to each other, especially in high‐volatility periods, where cross‐correlations increase significantly. Using Markov switching Monte Carlo approach we provide evidence in favour of Markov switching models, rejecting random walk hypothesis. Testing in‐sample and out‐of‐sample Markov trading rules based on Dueker and Neely (Journal of Banking and Finance, 2007) we find that using econometric methodology is able to forecast accurately exchange rate movements. When applied to the Euro/US dollar and the euro/British pound daily returns data, the model provides exceptional out‐of‐sample returns. However, when applied to the euro/Brazilian real and the euro/Mexican peso, the model loses power. Higher volatility exercised in the Latin American currencies seems to be a critical factor for this failure. Copyright © 2009 John Wiley & Sons, Ltd.     

Invariant density,Lapunov exponent,and almost sure stability of Markovian-regime-switching linear systems

This paper is concerned with stability of a class of randomly switched systems of ordinary differential equations. The system under consideration can be viewed as a two-component process (X(t), α(t)), where the system is linear in X(t) and α(t) is a continuous-time Markov chain with a finite state space. Conditions for almost surely exponential stability and instability are obtained. The conditions are based on the Lyapunov exponent, which in turn, depends on the associate invariant density. Concentrating on the case that the continuous component is two dimensional, using transformation techniques, differential equations satisfied by the invariant density associated with the Lyapunov exponent are derived. Conditions for existence and uniqueness of solutions are derived. Then numerical solutions are developed to solve the associated differential equations.     

Understanding supercapacitors based on nano-hybrid materials with interfacial conjugation

The recent fast development of supercapacitors,also known scientifically as electrochemical capacitors,has benefited significantly from synthesis,characterisations and electrochemistry of nanomaterials.Herein,the principle of supercapacitors is explained in terms of performance characteristics and charge storage mechanisms,i.e.double layer(or interfacial) capacitance and pseudo-capacitance.The semiconductor band model is applied to qualitatively account for the pseudo-capacitance in association with rectangular cyclic voltammograms(CVs) and linear galvanostatic charging and discharging plots(GCDs),aiming to differentiate supercapacitors from rechargeable batteries.The invalidity of using peak shaped CVs and non-linear GCDs for capacitance measurement is highlighted.A selective review is given to the nano-hybrid materials between carbon nanotubes and redox active materials such as electronically conducting polymers and transition metal oxides.A new concept,"interfacial conjugation",is introduced to reflect the capacitance enhancement resulting from π-π stacking interactions at the interface between two materials with highly conjugated chemical bonds.The prospects of carbon nanotubes and graphenes for supercapacitor applications are briefly compared and discussed.Hopefully,this article can help readers to understand supercapacitors and nano-hybrid materials so that further developments in materials design and synthesis,and device engineering can be more efficient and objective.