EBF1-deficient bone marrow stroma elicits persistent changes in HSC potential

Crosstalk between mesenchymal stromal cells (MSCs) and hematopoietic stem cells (HSCs) is essential for hematopoietic homeostasis and lineage output. Here, we investigate how transcriptional changes in bone marrow (BM) MSCs result in long-lasting effects on HSCs. Single-cell analysis of Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+ (PαS) cells revealed an extensive cellular heterogeneity but uniform expression of the transcription factor gene Ebf1. Conditional deletion of Ebf1 in these MSCs altered their cellular composition, chromatin structure and gene expression profiles, including the reduced expression of adhesion-related genes. Functionally, the stromal-specific Ebf1 inactivation results in impaired adhesion of HSCs, leading to reduced quiescence and diminished myeloid output. Most notably, HSCs residing in the Ebf1-deficient niche underwent changes in their cellular composition and chromatin structure that persist in serial transplantations. Thus, genetic alterations in the BM niche lead to long-term functional changes of HSCs

Coupled-barrier diffusion: the case of oxygen in silicon

Oxygen migration in silicon corresponds to an apparently simple jump between neighboring bridge sites. Yet, extensive theoretical calculations have so far produced conflicting results and have failed to provide a satisfactory account of the observed $2.5$ eV activation energy. We report a comprehensive set of first-principles calculations that demonstrate that the seemingly simple oxygen jump is actually a complex process involving coupled barriers and can be properly described quantitatively in terms of an energy hypersurface with a ``saddle ridge'' and an activation energy of $\sim 2.5$ eV. Earlier calculations correspond to different points or lines on this hypersurface.Comment: 4 Figures available upon request. Accepted for publication in Phys. Rev. Let

Structure and apparent topography of TiO2 (110) surfaces

We present self-consistent ab-initio total-energy and electronic-structure calculations on stoichiometric and non-stoichiometric TiO2 (110) surfaces. Scanning tunneling microscopy (STM) topographs are simulated by calculating the local electronic density of states over an energy window appropriate for the experimental positive-bias conditions. We find that under these conditions the STM tends to image the undercoordinated Ti atoms, in spite of the physical protrusion of the O atoms, giving an apparent reversal of topographic contrast on the stoichiometric 1x1 or missing-row 2x1 surface. We also show that both the interpretation of STM images and the direct comparison of surface energies favor an added-row structure over the missing-row structure for the oxygen-deficient 2x1 surface.Comment: 6 pages, two-column style with 5 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#ng_tio

Electron interference and entanglement in coupled 1D systems with noise

We estimate the role of noise in the formation of entanglement and in the appearance of single- and two-electron interference in systems of coupled one-dimensional channels semiconductors. Two cases are considered: a single-particle interferometer and a two-particle interferometer exploiting Coulomb interaction. In both of them, environmental noise yields a randomization of the carrier phases. Our results assess how that the complementarity relation linking single-particle behavior to nonlocal quantities, such as entanglement and environment-induced decoherence, acts in electron interferometry. We show that, in a experimental implementation of the setups examined, one- and two-electron detection probability at the output drains can be used to evaluate the decoherence phenomena and the degree of entanglement.Comment: 12 pages, 6 figures. v2: added some references and corrected tex

Structure and oxidation kinetics of the Si(100)-SiO2 interface

We present first-principles calculations of the structural and electronic properties of Si(001)-SiO2 interfaces. We first arrive at reasonable structures for the c-Si/a-SiO2 interface via a Monte-Carlo simulated annealing applied to an empirical interatomic potential, and then relax these structures using first-principles calculations within the framework of density-functional theory. We find a transition region at the interface, having a thickness on the order of 20\AA, in which there is some oxygen deficiency and a corresponding presence of sub-oxide Si species (mostly Si^+2 and Si^+3). Distributions of bond lengths and bond angles, and the nature of the electronic states at the interface, are investigated and discussed. The behavior of atomic oxygen in a-SiO2 is also investigated. The peroxyl linkage configuration is found to be lower in energy than interstitial or threefold configurations. Based on these results, we suggest a possible mechanism for oxygen diffusion in a-SiO2 that may be relevant to the oxidation process.Comment: 7 pages, two-column style with 6 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#ng_sio

On the optical properties of Ag^{+15} ion-beam irradiated TiO_{2} and SnO_{2} thin films

The effects of 200-MeV Ag^{+15} ion irradiation on the optical properties of TiO_{2} and SnO_{2} thin films prepared by using the RF magnetron sputtering technique were investigated. These films were characterized by using UV-vis spectroscopy, and with increasing irradiation fluence, the transmittance for the TiO_{2} films was observed to increase systematically while that for SnO_{2} was observed to decrease. Absorption spectra of the irradiated samples showed minor changes in the indirect bandgap from 3.44 to 3.59 eV with increasing irradiation fluence for TiO_{2} while significant changes in the direct bandgap from 3.92 to 3.6 eV were observed for SnO_{2}. The observed modifications in the optical properties of both the TiO_{2} and the SnO_{2} systems with irradiation can be attributed to controlled structural disorder/defects in the system.Comment: 6 pages, ICAMD-201

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation

The naturally occurring &Delta;40p53 isoform heterotetramerizes with wild-type p53 (WTp53) to regulate development, aging, and stress responses. How &Delta;40p53 alters WTp53 function remains enigmatic because their co-expression causes tetramer heterogeneity. We circumvented this issue with a well-tested strategy that expressed &Delta;40p53:WTp53 as a single transcript, ensuring a 2:2 tetramer stoichiometry. Human MCF10A cell lines expressing &Delta;40p53:WTp53, WTp53, or WTp53:WTp53 (as controls) from the native TP53 locus were examined with transcriptomics (precision nuclear run-on sequencing [PRO-seq] and RNA sequencing [RNA-seq]), metabolomics, and other methods. &Delta;40p53:WTp53 was transcriptionally active, and, although phenotypically similar to WTp53 under normal conditions, it failed to induce growth arrest upon Nutlin-induced p53 activation. This occurred via &Delta;40p53:WTp53-dependent inhibition of enhancer RNA (eRNA) transcription and subsequent failure to induce mRNA biogenesis, despite similar genomic occupancy to WTp53. A different stimulus (5-fluorouracil [5FU]) also showed &Delta;40p53:WTp53-specific changes in mRNA induction; however, other transcription factors (TFs; e.g., E2F2) could then drive the response, yielding similar outcomes vs. WTp53. Our results establish that &Delta;40p53 tempers WTp53 function to enable compensatory responses by other stimulus-specific TFs. Such modulation of WTp53 activity may be an essential physiological function for &Delta;40p53. Moreover, &Delta;40p53:WTp53 functional distinctions uncovered herein suggest an eRNA requirement for mRNA biogenesis and that human p53 evolved as a tetramer to support eRNA transcription. &nbsp;</p