Current topics in genome evolution: Molecular mechanisms of new gene formation

Comparative genome analyses reveal that most functional domains of human genes have homologs in widely divergent species. These shared functional domains, however, are differentially shuffled among evolutionary lineages to produce an increasing number of domain architectures. Combined with duplication and adaptive evolution, domain shuffling is responsible for the great phenotypic complexity of higher eukaryotes. Although the domain-shuffling hypothesis is generally accepted, determining the molecular mechanisms that lead to domain shuffling and novel gene creation has been challenging, as sequence features accompanying the formation of known genes have been obscured by accumulated mutations. The growing availability of genome sequences and EST databases allows us to study the characteristics of newly emerged genes. Here we review recent genome-wide DNA and EST analyses, and discuss the three major molecular mechanisms of gene formation: (1) atypical spicing, both within and between genes, followed by adaptation, (2) tandem and interspersed segmental duplications, and (3) retrotransposition events. Received 18 October 2006; received after revision 18 November 2006; accepted 28 November 2006     

Volatility impulse response analysis for DCC-GARCH models: The role of volatility transmission mechanisms

This study introduces volatility impulse response functions (VIRF) for dynamic conditional correlation–generalized autoregressive conditional heteroskedasticity (DCC-GARCH) models. In addition, the implications with respect to network analysis—using the connectedness approach of Diebold and Y lmaz (Journal of Econometrics, 2014, 182(1), 119–134)—is discussed. The main advantages of this framework are (i) that the time-varying dynamics do not underlie a rolling-window approach and (ii) that it allows us to test whether the propagation mechanism is time varying or not. An empirical analysis on the volatility transmission mechanism across foreign exchange rate returns is illustrated. The results indicate that the Swiss franc and the euro are net transmitters of shocks, whereas the British pound and the Japanese yen are net volatility receivers of shocks. Finally, the findings suggest a high degree of comovement across European currencies, which has important portfolio and risk management implications.     

Reticulate evolution and cladism: Tests for the direction of evolution

Summary Reticulate evolution between ancestral-descendant lineages can be critically tested for by investigating the relationship between out-group and mid-point roots on numerically derived cladograms. The western grass-snake provides a worked example for the theoretical test.     

Modification of the skin feeding site by tick saliva mediates virus transmission

A tick vector of Thogoto (THO) virus was shown to secrete a factor in saliva which potentiates the transmission of THO virus to uninfected ticks feeding on an apparently non-viraemic host. The effect of the saliva activated transmission (SAT) factor on the virus occurred at the site of inoculation in the skin and was apparent even when the virus was introduced 3 days after the SAT factor. The results suggest that tick saliva can play an important role in disease transmission by virtue of host modification at the site of feeding.     

Non-viraemic transmission of tick-borne encephalitis virus: a mechanism for arbovirus survival in nature

The vectors of arthropod-borne viruses (arboviruses) become infected by feeding on the viraemic blood of an infected animal. This theory is based on transmission studies involving artificial infection of vertebrate hosts by syringe inoculation. To reproduce natural conditions of virus transmission, infected and uninfected vectors (ticks) of tick-borne encephalitis virus, the most important arbovirus in Europe, were allowed to feed together on uninfected wild vertebrate hosts. The greatest numbers of infected ticks were obtained from susceptible host species that had undetectable or very low levels of viraemia. The results suggest that nonviremic transmission is an important mechanism for the survival of certain arboviruses in nature.     

Modification of the skin feeding site by tick saliva mediates virus transmission.

A tick vector of Thogoto (THO) virus was shown to secrete a factor in saliva which potentiates the transmission of THO virus to uninfected ticks feeding on an apparently non-viraemic host. The effect of the saliva activated transmission (SAT) factor on the virus occurred at the site of inoculation in the skin and was apparent even when the virus was introduced 3 days after the SAT factor. The results suggest that tick saliva can play an important role in disease transmission by virtue of host modification at the site of feeding.     

Oxygen consumption and the evolution of order: negentropy criteria applied to the evolution of ants

Optimization of energy use by evolving organisms, predicted by theoretical extensions of the neo-Darwinian theory, i. contrasted with that of irreversible thermodynamics, which predicts an increase in orderliness and thus an increase in energy consumption per unit of biomass. We compared this index with estimates of social complexity among ant genera and species. Our results show that simple optimization models cannot explain experimental data, and that social complexity correlates differently with negentropy at different levels of analysis. Comparing the genera among Formicidae, workers (not colonies) from genera with highly social species are less negentropic than those of socially primitive ones. At the sub-generic level, social complexity correlated positively with negentropy among species, for major workers inAcromyrmex and for minor workers inAtta. The results illustrate the complexity of thermodynamic criteria in the study of evolution but also hint at their usefulness. In this case, they show that two different evolutionary routes to the complex Attini ant societies may exist.     

The metabolism, pharmacokinetics and mechanisms of antiviral activity of ribavirin against hepatitis C virus

Ribavirin, a broad spectrum antiviral agent, in conjunction with interferon forms the current standard of treatment for hepatitis C virus (HCV) infection in humans. While ribavirin alone fails to induce a significant antiviral response, in combination with interferon, ribavirin dramatically improves the long-term outcome of therapy. The predominant mechanism(s) of ribavirin action against HCV, are yet to be established. In this review, we examine the current status of our understanding of the metabolism, pharmacokinetics and mechanisms of the antiviral activity of ribavirin against HCV, all of which are central to the rational identification of improved treatment protocols. Received 30 September 2005; received after revision 20 November 2005; accepted 7 December 2005     

Detrending economic time series: a Bayesian generalization of the Hodrick–Prescott filter

This article develops a new method for detrending time series. It is shown how, in a Bayesian framework, a generalized version of the Hodrick–Prescott filter is obtained by specifying prior densities on the signal‐to‐noise ratio (q) in the underlying unobserved components model. This helps ensure an appropriate degree of smoothness in the estimated trend while allowing for uncertainty in q. The article discusses the important issue of prior elicitation for time series recorded at different frequencies. By combining prior expectations with the likelihood, the Bayesian approach permits detrending in a way that is more consistent with the properties of the series. The method is illustrated with some quarterly and annual US macroeconomic series. Copyright © 2006 John Wiley & Sons, Ltd.