The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Comparative study of GeO2/Ge and SiO2/Si structures on anomalous charging of oxide films upon water adsorption revealed by ambient-pressure X-ray photoelectron spectroscopy

The energy difference between the oxide and bulk peaks in X-ray photoelectron spectroscopy (XPS) spectra was investigated for both GeO2/Ge and SiO2/Si structures with thickness-controlled water films. This was achieved by obtaining XPS spectra at various values of relative humidity (RH) of up to ∼15%. The increase in the energy shift is more significant for thermal GeO2 on Ge than for thermal SiO2 on Si above ∼10-4% RH, which is due to the larger amount of water molecules that infiltrate into the GeO2 film to form hydroxyls. Analyzing the origins of this energy shift, we propose that the positive charging of a partially hydroxylated GeO2 film, which is unrelated to X-ray irradiation, causes the larger energy shift for GeO2/Ge than for SiO2/Si. A possible microscopic mechanism of this intrinsic positive charging is the emission of electrons from adsorbed water species in the suboxide layer of the GeO2 film to the Ge bulk, leaving immobile cations or positively charged states in the oxide. This may be related to the reported negative shift of flat band voltages in metal-oxide-semiconductor diodes with an air-exposed GeO2 layer.Mori D., Oka H., Hosoi T., et al. Comparative study of GeO2/Ge and SiO2/Si structures on anomalous charging of oxide films upon water adsorption revealed by ambient-pressure X-ray photoelectron spectroscopy. Journal of Applied Physics, 120, 9, 095306. https://doi.org/10.1063/1.4962202.https://doi.org/10.1063/1.496220

The efficient detection of membrane protein with immunoblotting: lessons from cold-temperature denaturation

　Transmembrane proteins play essential roles in cell signaling, transport of membrane-impermeable molecules, cell-cell communication, and cell adhesion. Our recent work demonstrated that reactive oxygen species-generating NADPH oxidase 4 (Nox4), a protein with multiple transmembrane domains, is involved in cell migration by stabilizing vascular endothelial growth factor receptor 2 (VEGFR-2), a single-span transmembrane protein. During this study and with further verification, we developed a simple method to prepare protein samples without aggregating these membrane proteins for SDS-PAGE, immunoblotting, and deglycosylation assay. We found that heating was unnecessary for protein denaturation for SDS-PAGE and deglycosylation assay. Also, the detectable amounts of VEGFR-2 and Nox4 were increased in the sample treated at 4℃ compared with the sample treated at 98℃ . Moreover, the N-glycan of VEGFR-2 was digested by glycosidase at reaction temperature 4℃