Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes.

Although genes with similar expression patterns are sometimes found in the same genomic regions, almost nothing is known about the relative organization in genomes of genes and transposable elements (TEs), which might influence each other at the regulatory level. In this study, we used transcriptomic data from male and female gonads of the Japanese medaka Oryzias latipes to define sexually biased genes and TEs and analyze their relative genomic localization. We identified 20,588 genes expressed in the adult gonads of O. latipes. Around 39% of these genes are differentially expressed between male and female gonads. We further analyzed the expression of TEs using the program SQuIRE and showed that more TE copies are overexpressed in testis than in ovaries (36% vs. 10%, respectively). We then developed a method to detect genomic regions enriched in testis- or ovary-biased genes. This revealed that sex-biased genes and TEs are not randomly distributed in the genome and a part of them form clusters with the same expression bias. We also found a correlation of expression between TE copies and their closest genes, which increases with decreasing intervening distance. Such a genomic organization suggests either that TEs hijack the regulatory sequences of neighboring sexual genes, allowing their expression in germ line cells and consequently new insertions to be transmitted to the next generation, or that TEs are involved in the regulation of sexual genes, and might therefore through their mobility participate in the rewiring of sex regulatory networks.

Shear relaxation of imidazolium-based room-temperature ionic liquids.

The frequency-dependent shear viscosities of four representative imidazolium-based room-temperature ionic liquids, 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([bmim][TFSA]), 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]), 1-hexyl-3-methylimidazolium hexafluorophosphate ([hmim][PF(6)]), and 1-methyl-3-octylimidazolium hexafluorophosphate ([omim][PF(6)]), are measured from 5 to 205 MHz with shear impedance spectroscopy. A relaxation is observed in the measured frequency range in all cases. This is the first report on the shear relaxation of ionic liquids at room temperature, to our best knowledge. Comparing the spectra of the common cations, [bmim][TFSA] and [bmim][PF(6)], the normalized relaxation spectra, eta(nu)/eta(0), reduce to a single curve when plotted against eta(0)nu, where nu and eta(0) stand for the frequency and shear viscosity, respectively. The lower viscosity of the TFSA salt is thus elucidated by the shorter relaxation time. The lower viscosity at higher temperature is also attributed to the shorter relaxation time. On the other hand, the increase in the length of the alkyl chain of the cation leads to the lower-frequency shift of the relaxation frequency on the eta(0)nu scale. Therefore, the higher viscosity of the omim salt is the result of the compensation of the longer relaxation time for the smaller high-frequency shear modulus. In addition, the relaxation time distribution becomes broader with increasing chain length, which can be ascribed to the heterogeneity of the liquid structure.