X-Chromosome Inactivation Counting and Choice: Change or Design

Placental mammalian female cells have two X chromosomes. One of these chromosomes is randomly inactivated in each nucleus so that females are functionally mosaic for genes expressed from their X chromosomes. The evolutionary basis for this phenomenon is based on the fact that females would have twice the number of X-linked gene product compared to their male counterpart. This unequal distribution of X-linked genes requires gene dosage compensation. Species that have distinguishable sex chromosomes have evolved different ways to prevent a difference in dosage of the sex chromosome-encoded proteins between the two sexes. In female mammals one X chromosome is transcriptionally inactivated in female somatic cells by a process called X chromosome inactivation (XCI)

Buccal swab as a reliable predictor for X inactivation ratio in inaccessible tissues

Background As a result of the epigenetic phenomenon of X chromosome inactivation (XCI) every woman is a mosaic of cells with either an inactive paternal X chromosome or an inactive maternal X chromosome. The ratio between inactive paternal and maternal X chromosomes is different for every female individual, and can influence an X-encoded trait or disease. A multitude of X linked conditions is known, and for many of them it is recognised that the phenotype in affected female carriers of the causative mutation is modulated by the XCI ratio. To predict disease severity an XCI ratio is usually determined in peripheral blood samples. However, the correlation between XCI ratios in peripheral blood and disease affected tissues, that are often inaccessible, is poorly understood. Here, we tested several tissues obtained from autopsies of 12 female individuals for patch size and XCI ratio. Methods XCI ratios were analysed using methylsensitive PCR-based assays for the AR, PCSK1N and SLITRK4 loci. XCI patch size was analysed by testing the XCI ratio of tissue samples with decreasing size. Results XCI patch size was analysed for liver, muscle, ovary and brain samples and was found too small to confound testing for XCI ratio in these tissues. XCI ratios were determined in the easily accessible tissues, blood, buccal epithelium and hair follicle, and compared with ratios in several inaccessible tissues. Conclusions Buccal epithelium is preferable over peripheral blood for predicting XCI ratios of inaccessible tissues. Ovary is the only inaccessible tissue showing a poor correlation to blood and buccal epithelium, but has a good correlation to hair follicle instead

Generation and characterization of an inducible transgenic model for studying mouse esophageal biology

Background: To facilitate the in vivo study of esophageal (stem) cell biology in homeostasis and cancer, novel mouse models are necessary to elicit expression of candidate genes in a tissue-specific and inducible fashion. To this aim, we developed and studied a mouse model to allow labeling of esophageal cells with the histone 2B-GFP (H2B-GFP) fusion protein. Results: First, we generated a transgenic mouse model expressing the reverse tetracycline transactivator rtTA2-M2 under control of the promoter (ED-L2) of the Epstein-Barr virus (EBV) gene encoding the latent membrane protein-1 (LMP-1). The newly generated ED-L2-rtTA2-M2 (ED-L2-rtTA) mice were then bred with the previously developed tetO-HIST1H2BJ/GFP (tetO-H2B-GFP) model to assess inducibility and tissue-specificity. Expression of the H2B-GFP fusion protein was observed upon doxycycline induction but was restricted to the terminally differentiated cells above the basal cell layer. To achieve expression in the basal compartment of the esophagus, we ubsequently employed a different transgenic model expressing the reverse transactivator rtTA2S-M2 under the control of the ubiquitous, methylation-free CpG island of the human hnRNPA2B1-CBX3 gene (hnRNP-rtTA). Upon doxycycline administration to the compound hnRNP-rtTA/tetO-H2B-GFP mice, near-complete labeling of all esophageal cells was achieved. Pulse-chase experiments confirmed that complete turnover of the esophageal epithelium in the adult mouse is achieved within 710 days. Conclusions: We show that the esophagus-specific promoter ED-L2 is expressed only in the differentiated cells above the basal layer. oreover, we confirmed that esophageal turn-over in the adult mouse does not exceed 710 days

Molecular adsorption study of nicotine and caffeine on the single-walled carbon nanotube from first principles

Using first-principles calculations, we investigate the electronic structures and binding properties of nicotine and caffeine adsorbed on single-walled carbon nanotubes to determine whether CNTs are appropriate for filtering or sensing nicotine and caffeine molecules. We find that caffeine adsorbs more strongly than nicotine. The different binding characteristics are discussed by analyzing the modification of the electronic structure of the molecule-adsorbed CNTs. We also calculate the quantum conductance of the CNTs in the presence of nicotine or caffeine adsorbates and demonstrate that the influence of caffeine is stronger than nicotine on the conductance of the host CNT.Comment: 5 pages, 5 figure

First Principles Study of Structural, Electronic and Magnetic Interplay in Ferroelectromagnetic Yttrium Manganite

We present results of local spin density approximation pseudopotential calculations for the ferroelectromagnet, yttrium manganite (YMnO3). The origin of the differences between ferroelectric and non-ferroelectric perovskite manganites is determined by comparing the calculated properties of yttrium manganite in its ferroelectric hexagonal and non-ferroelectric orthorhombic phases. In addition, orthorhombic YMnO3 is compared with the prototypical non-ferroelectric manganite, lanthanum manganite. We show that, while the octahedral crystal field splitting of the cubic perovskite structure causes a centro-symmetric Jahn-Teller distortion around the Mn3+ ion, the markedly different splitting in hexagonal perovskites creates an electronic configuration consistent with ferroelectric distortion. We explain the nature of the distortion, and show that a local magnetic moment on the Mn3+ ion is a requirement for it to occur.Comment: Replacement of earlier version with error in pseudopotentia

A First-principles Prediction of Two-Dimensional Superconductivity in Pristine B2C Single layer

Based on first-principles lattice dynamics and electron-phonon coupling calculations, B2C sheet is predicted to be a two-dimensional (2D) phonon-mediated superconductor with a relatively high transition temperature (Tc). The electron-phonon coupling parameter calculated is 0.92, and it is mainly contributed by low frequency out-of-plane phonon modes and electronic states with a {\pi} character. When the Coulomb pseudopotential is set to 0.10, the estimated temperature Tc is 19.2 K. To be best of our knowledge, B2C is the first pristine 2D superconductor with a Tc higher than the boiling point of liquid helium.Comment: accepted by Nanoscal

Ag-Cu alloy surfaces in an oxidizing environment: a first-principles study

Recent experiments on model catalysts have shown that Ag-Cu alloys have improved selectivity with respect to pure silver for ethylene epoxidation. In this paper we review our first-principles investigations on the (111) surface of this alloy and present new findings on other low index surfaces. We find that, for every surface orientation, the presence of oxygen leads to copper segregation to the surface. Considering the alloy to be in equilibrium with an oxygen atmosphere and accounting for the effect of temperature and pressure, we compute the surface free energy and study the stability of several surface structures. Investigating the dependence of the surface free energy on the surface composition, we construct the phase diagram of the alloy for every surface orientation. Around the temperature, pressure and composition of interest for practical applications, we find that a limited number of structures can be present, including a thin layer of copper oxide on top of the silver surface and copper-free structures. Different surface orientations show a very similar behavior and in particular a single layer with CuO stoichiometry, significantly distorted when compared to a layer of bulk CuO, has a wide range of stability for all orientations. Our results are consistent with, and help explain, recent experimental measurements

Temperature-dependent Raman study of CeFeAsO0.9F0.1 Superconductor: Crystal field excitations, phonons and their coupling

We report temperature-dependent Raman spectra of CeFeAsO0.9F0.1 from 4 K to 300 K in spectral range of 60 to 1800 cm-1 and interpret them using estimates of phonon frequencies obtained from first-principles density functional calculations. We find evidence for a strong coupling between the phonons and crystal field excitations; in particular Ce3+ crystal field excitation at 432 cm-1 couples strongly with Eg oxygen vibration at 389 cm-1 . Below the superconducting transition temperature, the phonon mode near 280 cm-1 shows softening, signaling its coupling with the superconducting gap. The ratio of the superconducting gap to Tc thus estimated to be ~ 10 suggests CeFeAsO0.9F0.1 as a strong coupling superconductor. In addition, two high frequency modes observed at 1342 cm-1 and 1600 cm-