Many genes in fish have species-specific asymmetric rates of molecular evolution

BACKGROUND: Gene and genome duplication events increase the amount of genetic material that might then contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. Thus, it has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. This hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. Such a functional divergence might be caused by an increase in evolutionary rates in one ortholog, by changes in expression, regulatory evolution, insertion of repetitive elements, or due to positive Darwinian selection in one copy. We studied a set of 2466 genes that were present in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oryzias latipes to test (i) for forces of positive Darwinian selection; (ii) how frequently duplicated genes are retained, and (iii) whether novel gene functions might have evolved. RESULTS: 25% (610) of all investigated genes show significantly smaller or higher genetic distances in the genomes of particular fish species compared to their human ortholog than their orthologs in other fish according to relative rate tests. We identified 49 new paralogous pairs of duplicated genes in fish, in which one of the paralogs is under positive Darwinian selection and shows a significantly higher rate of molecular evolution in one of the four fish species, whereas the other copy apparently did not undergo adaptive changes since it retained the original rate of evolution. Among the genes under positive Darwinian selection, we found a surprisingly high number of ATP binding proteins and transcription factors. CONCLUSION: The significant rate difference suggests that the function of these rate-changed genes might be essential for the respective fish species. We demonstrate that the measurement of positive selection is a powerful tool to identify divergence rates of duplicated genes and that this method has the capacity to identify potentially interesting candidates for adaptive gene evolution

Temperature dependence of the hydrogen bond network in Trimethylamine N-oxide and guanidine hydrochloride - water solutions

We present an X-ray Compton scattering study on aqueous Trimethylamine N-oxide (TMAO) and guanidine hydrochloride solutions (GdnHCl) as a function of temperature. Independent from the concentration of the solvent, Compton profiles almost resemble results for liquid water as a function of temperature. However, The number of hydrogen bonds per water molecule extracted from the Compton profiles suggests a decrease of hydrogen bonds with rising temperatures for all studied samples, the differences between water and the solutions are weak. Nevertheless, the data indicate a reduced bond weakening with rising TMAO concentration up to 5M of 7.2% compared to 8 % for pure water. In contrast, the addition of GdnHCl appears to behave differently for concentrations up to 3.1 M with a weaker impact on the temperature response of the hydrogen bond structure

Intramolecular structure and energetics in supercooled water down to 255 K

We studied the structure and energetics of supercooled water by means of X-ray Raman and Compton scattering. Under supercooled conditions down to 255 K, the oxygen K-edge measured by X-ray Raman scattering suggests an increase of tetrahedral order similar to the conventional temperature effect observed in non-supercooled water. Compton profile differences indicate contributions beyond the theoretically predicted temperature effect and provide a deeper insight into local structural changes. These contributions suggest a decrease of the electron mean kinetic energy by 3.3 +/- 0.7 kJ (mol K)(-1) that cannot be modeled within established water models. Our surprising results emphasize the need for water models that capture in detail the intramolecular structural changes and quantum effects to explain this complex liquid.Peer reviewe

A note on the rate of convergence of local polynomial estimators in regression models

summary:Local polynomials are used to construct estimators for the value $m(x_{0})$ of the regression function $m$ and the values of the derivatives $D_{\gamma }m(x_{0})$ in a general class of nonparametric regression models. The covariables are allowed to be random or non-random. Only asymptotic conditions on the average distribution of the covariables are used as smoothness of the experimental design. This smoothness condition is discussed in detail. The optimal stochastic rate of convergence of the estimators is established. The results cover the special cases of regression models with i.i.d. errors and the case of observations at an equidistant lattice

Microsecond Structural Rheology

The relationship between the local structure of complex liquids and their response to shear is generally not well understood. This concerns, in particular, the formation of particle strings in the flow direction or hydroclusters, both important for the understanding of shear thinning and thickening phenomena. Here, we present results of a microfocus X-ray scattering experiment on spherical silica colloids in a liquid jet at high shear rates. Along and across the jet, we observe direction-dependent modifications of the structure factor of the suspension, suggesting the formation of differently ordered clusters in compression lines and as particle strings. With increasing distance from the orifice, the structure relaxes to the unsheared case with a typical relaxation 10 times larger as the time scale of Brownian motion. These results provide the first experimental flow characterization of a complex fluid at high shear rates detecting cluster formation and relaxation with micrometer and microsecond resolution

On the Usage of Cyclic Voltammetry and Impedance Spectroscopy for Measuring the Concentration of Aqueous Solutions

This article describes sensors for concentration measurement based on the electro- chemical properties of the liquid being measured. Herein two electrical methods, namely cyclic voltammetry and impedance spectroscopy, are being presented. The measurement can be performed quasi simultaneously using the same measurement medium. Further optimization of the combined methods is possible by adapting the geometric design of the electrode structure, the electrode material, the optional passivation and the electric coupling (galvanically or capacitively). In summary, by combining multiple sensory principles on a device it becomes possible to analyze mixtures of substances contained in a solution with respect to their composition