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

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-

Heterovalent and A-atom effects in A(B'B'')O3 perovskite alloys

Using first-principles supercell calculations, we have investigated energetic, structural and dielectric properties of three different A(B'B'')O_3 perovskite alloys: Ba(Zn_{1/3}Nb_{2/3})O_3 (BZN), Pb(Zn_{1/3}Nb_{2/3})O_3 (PZN), and Pb(Zr_{1/3}Ti_{2/3})O_3 (PZT). In the homovalent alloy PZT, the energetics are found to be mainly driven by atomic relaxations. In the heterovalent alloys BZN and PZN, however, electrostatic interactions among B' and B'' atoms are found to be very important. These electrostatic interactions are responsible for the stabilization of the observed compositional long-range order in BZN. On the other hand, cell relaxations and the formation of short Pb--O bonds could lead to a destabilization of the same ordered structure in PZN. Finally, comparing the dielectric properties of homovalent and heterovalent alloys, the most dramatic difference arises in connection with the effective charges of the B' atom. We find that the effective charge of Zr in PZT is anomalous, while in BZN and PZN the effective charge of Zn is close to its nominal ionic value.Comment: 7 pages, two-column style with 2 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#lb_he

Basis Functions for Linear-Scaling First-Principles Calculations

In the framework of a recently reported linear-scaling method for density-functional-pseudopotential calculations, we investigate the use of localized basis functions for such work. We propose a basis set in which each local orbital is represented in terms of an array of `blip functions'' on the points of a grid. We analyze the relation between blip-function basis sets and the plane-wave basis used in standard pseudopotential methods, derive criteria for the approximate equivalence of the two, and describe practical tests of these criteria. Techniques are presented for using blip-function basis sets in linear-scaling calculations, and numerical tests of these techniques are reported for Si crystal using both local and non-local pseudopotentials. We find rapid convergence of the total energy to the values given by standard plane-wave calculations as the radius of the linear-scaling localized orbitals is increased.Comment: revtex file, with two encapsulated postscript figures, uses epsf.sty, submitted to Phys. Rev.

RNF12 Activates Xist and Is Essential for X Chromosome Inactivation

In somatic cells of female placental mammals, one of the two X chromosomes is transcriptionally silenced to accomplish an equal dose of X-encoded gene products in males and females. Initiation of random X chromosome inactivation (XCI) is thought to be regulated by X-encoded activators and autosomally encoded suppressors controlling Xist. Spreading of Xist RNA leads to silencing of the X chromosome in cis. Here, we demonstrate that the dose dependent X-encoded XCI activator RNF12/RLIM acts in trans and activates Xist. We did not find evidence for RNF12-mediated regulation of XCI through Tsix or the Xist intron 1 region, which are both known to be involved in inhibition of Xist. In addition, we found that Xist intron 1, which contains a pluripotency factor binding site, is not required for suppression of Xist in undifferentiated ES cells. Analysis of female Rnf12−/− knockout ES cells showed that RNF12 is essential for initiation of XCI and is mainly involved in the regulation of Xist. We conclude that RNF12 is an indispensable factor in up-regulation of Xist transcription, thereby leading to initiation of random XCI

Relation between intra-abdominal pressure and early intestinal ischemia in rats

Background: Little is known on early irreversible effects of increased intra-abdominal pressure (IAP). Therefore, timing of abdominal decompression among patients with abdominal compartment syndrome remains challenging. The study objective was to determine the relation between IAP and respiratory parameters, hemodynamic parameters, and early intestinal ischemia. Methods: Twenty-five anesthetized and ventilated male Sprague-Dawley rats were randomly assigned to five groups exposed to IAPs of 0, 5, 10, 15, or 20 mm Hg for 3 hours. Respiratory parameters, hemodynamic parameters, and serum albumin-cobalt binding (ACB) capacity as measure for systemic ischemia were determined. Intestines were processed for histopathology. Results: IAP was negatively associated with mean arterial pressure at 90 (Spearman correlation coefficient; Rs=-0.446, p=0.025) and 180 min (Rs=-0.466, p=0.019), oxygen saturation at 90 min (Rs=-0.673, p<0.001) and 180 min (Rs=-0.882, p<0.001), and pH value at 90 (Rs=-0.819, p<0.001) and 180 min (Rs=-0.934, p<0.001). There were no associations between IAP and lactate level or ACB capacity. No histological signs for intestinal ischemia were found. Discussion: Although increasing IAP was associated with respiratory and hemodynamic difficulties, no signs for intestinal ischemia were found. Level of evidence: Prognostic and epidemiologic study, level II

Electronic and structural properties of vacancies on and below the GaP(110) surface

We have performed total-energy density-functional calculations using first-principles pseudopotentials to determine the atomic and electronic structure of neutral surface and subsurface vacancies at the GaP(110) surface. The cation as well as the anion surface vacancy show a pronounced inward relaxation of the three nearest neighbor atoms towards the vacancy while the surface point-group symmetry is maintained. For both types of vacancies we find a singly occupied level at mid gap. Subsurface vacancies below the second layer display essentially the same properties as bulk defects. Our results for vacancies in the second layer show features not observed for either surface or bulk vacancies: Large relaxations occur and both defects are unstable against the formation of antisite vacancy complexes. Simulating scanning tunneling microscope pictures of the different vacancies we find excellent agreement with experimental data for the surface vacancies and predict the signatures of subsurface vacancies.Comment: 10 pages, 6 figures, Submitted to Phys. Rev. B, Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Maximally-localized generalized Wannier functions for composite energy bands

We discuss a method for determining the optimally-localized set of generalized Wannier functions associated with a set of Bloch bands in a crystalline solid. By ``generalized Wannier functions'' we mean a set of localized orthonormal orbitals spanning the same space as the specified set of Bloch bands. Although we minimize a functional that represents the total spread sum_n [ _n - _n^2 ] of the Wannier functions in real space, our method proceeds directly from the Bloch functions as represented on a mesh of k-points, and carries out the minimization in a space of unitary matrices U_mn^k describing the rotation among the Bloch bands at each k-point. The method is thus suitable for use in connection with conventional electronic-structure codes. The procedure also returns the total electric polarization as well as the location of each Wannier center. Sample results for Si, GaAs, molecular C2H4, and LiCl will be presented.Comment: 22 pages, two-column style with 4 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#nm_wan