The guardian's little helper: MicroRNAs in the p53 tumor suppressor network

Several microRNAs (miRNAs) have been implicated in tumor development based on both changes in their expression patterns and gene structural alterations in human tumors. However, we are only now beginning to see how miRNAs interact with classic oncogene and tumor suppressor mechanisms. Several recent studies have implicated the miR-34 family of miRNAs in the p53tumor suppressor network. The expression of miR-34a, miR-34b, and miR-34c is robustly induced by DNA damage and oncogenic stress in a p53-dependent manner. When overexpressed, miR-34 leads to apoptosis or cellular senescence, whereas reduction of miR-34 function attenuates p53-mediated cell death. These findings, together with the fact that miR-34 is down-regulated in several types of human cancer, show that miRNAs can affect tumorigenesis by working within the confines of well-known tumor suppressor pathways. ©2007 American Association for Cancer Research

The Atomic Slide Puzzle: Self-Diffusion of an Impure Atom

In a series of recent papers van Gastel et al have presented first experimental evidence that impure, Indium atoms, embedded into the first layer of a Cu(001) surface, are not localized within the close-packed surface layers but make concerted, long excursions visualized in a series of STM images. Such excursions occur due to continuous reshuffling of the surface following the position exchanges of both impure and host atoms with the naturally occuring surface vacancies. Van Gastel et al have also formulated an original lattice-gas type model with asymmetric exchange probabilities, whose numerical solution is in a good agreement with the experimental data. In this paper we propose an exact lattice solution of several versions of this model.Comment: Latex, 4 pages, 2 figures, to appear in Phys. Rev. E (RC

Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization

The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. Here we apply this strategy during RasV12 immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, we generated a gene network based on temporal expression profile similarities. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retained the capacity for myogenic differentiation when treated with the steroid hormone ecdysone. Further, we validated in vivo the transcription factor CG9650, the ortholog of mammalian Bcl11a/b, as a regulator of AMP proliferation predicted by our analysis. Our study demonstrates the power of time series synexpression analysis to characterize Drosophila embryonic progenitor lines and identify stem/progenitor cell regulators

Molecular Dynamics Simulation of Compressible Fluid Flow in Two-Dimensional Channels

We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream reservoir is kept at vacuum. The channel is sufficiently long in the direction of the flow that the finite length has little effect on the properties of the fluid in the central region. The simulated system is represented by an efficient data structure, whose internal elements are created and manipulated dynamically in a layered fashion. Consequently the code is highly efficient and manifests completely linear performance in simulations of large systems. We obtain the steady-state velocity, temperature, and density distributions in the system. The velocity distribution across the channel is very nearly a quadratic function of the distance from the center of the channel and reveals velocity slip at the boundaries; the temperature distribution is only approximately a quartic function of this distance from the center to the channel. The density distribution across the channel is non-uniform. We attribute this non-uniformity to the relatively high Mach number, approximately 0.5, in the fluid flow. An equation for the density distribution based on simple compressibility arguments is proposed; its predictions agree well with the simulation results. Validity of the concept of local dynamic temperature and the variation of the temperature along the channel are discussed.Comment: 16 pages (in latex) + 8 figures (in a single ps file). Submitted to the Physical Review

Dicer-2 Processes Diverse Viral RNA Species

RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double-stranded (ds)RNA precursors by Dicer and guide the RNA-induced silencing complex (RISC) to targets. Although principles governing small RNA sorting into RISC have been uncovered, the spectrum of RNA species that can be targeted by Dicer proteins, particularly the viral RNAs present during an infection, are poorly understood. Dicer-2 potently restricts viral infection in insects by generating virus-derived siRNAs from viral RNA. To better characterize the substrates of Dicer-2, we examined the virus-derived siRNAs produced during the Drosophila antiviral RNAi response to four different viruses using high-throughput sequencing. We found that each virus was uniquely targeted by the RNAi pathway; dicing substrates included dsRNA replication intermediates and intramolecular RNA stem loops. For instance, a putative intergenic RNA hairpin encoded by Rift Valley Fever virus generates abundant small RNAs in both Drosophila and mosquito cells, while repetitive sequences within the genomic termini of Vaccinia virus, which give rise to abundant small RNAs in Drosophila, were found to be transcribed in both insect and mammalian cells. Moreover, we provide evidence that the RNA species targeted by Dicer-2 can be modulated by the presence of a viral suppressor of RNAi. This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi. © 2013 Sabin et al

Azacytidine Enhances Regulatory T-Cells In Vivo and Prevents Experimental Xenogeneic Graft-Versus-Host Disease

Background The demethylating agent 5-azacytidine (AZA) has proven its efficacy as treatment for myelodysplastic syndrome and acute myeloid leukemia. In addition, AZA can demethylate FOXP3 intron 1 (FOXP3i1) leading to the generation of regulatory T cells (Tregs). Objective We investigated the impact of AZA on xenogeneic graft-versus-host disease (xGVHD) in a humanized murine model of transplantation, and described the impact of the drug on human T cells in vivo. Methods In order to induce xGVHD, human peripheral blood mononuclear cells (huPBMC) were administered intravenously in NOD-scid IL-2Rγnull (NSG) mice. Results AZA successfully improved both survival (p<0.0001) and xGVHD scores (p<0.0001). Further, AZA significantly decreased human T-cell proliferation as well as INF-γ and TNF-α serum levels, and reduced the expression of GRANZYME B and PERFORIN 1 by cytotoxic T cells. In addition, AZA administration significantly increased the function, proliferation and frequency of Tregs through demethylation of FOXP3i1 and higher secretion of IL-2 by conventional T cells due to IL2 gene promoter site 1 demethylation. Interestingly, among AZA-treated mice surviving the acute phase of xGVHD, there was an inverse correlation between the presence of Tregs and signs of chronic GVHD. Finally, Tregs harvested from the spleen of AZA-treated mice were suppressive and stable over time since they persisted at high frequency in secondary transplant experiments. Conclusion These findings emphasize a potential role for AZA as prevention or treatment of GVHD

LEEM Investigation of the Faceting of the Pt Covered W (111) Surface

A low energy electron microscope (LEEM) has been used to investigate the faceting of W(111) as induced by Pt. The atomically rough W(111) surface, when fully covered with a monolayer film of Pt and annealed to temperatures higher than {approximately} 750 K, experiences a significant morphological restructuring: the initially planar surface undergoes a faceting transition and forms three-sided pyramids with {211} faces. The experiments demonstrate the capability of LEEM for imaging both the fully and partially faceted surface. In addition, we have observed the formation of the facets in real time, when Pt is dosed onto the heated surface. We find that the transition from planar surface, to partially faceted surface, and to fully faceted surface proceeds through the nucleation and growth of spatially separated faceted regions

Weak selection and stability of localized distributions in Ostwald ripening

We support and generalize a weak selection rule predicted recently for the self-similar asymptotics of the distribution function (DF) in the zero-volume-fraction limit of Ostwald ripening (OR). An asymptotic perturbation theory is developed that, when combined with an exact invariance property of the system, yields the selection rule, predicts a power-law convergence towards the selected self-similar DF and agrees well with our numerical simulations for the interface- and diffusion-controlled OR.Comment: 4 pages, 2 figures, submitted to PR

Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy

shRNAs can trigger effective silencing of gene expression in mammalian cells, thereby providing powerful tools for genetic studies, as well as potential therapeutic strategies. Specific shRNAs can interfere with the replication of pathogenic viruses and are currently being tested as antiviral therapies in clinical trials. However, this effort is hindered by our inability to systematically and accurately identify potent shRNAs for viral genomes. Here we apply a recently developed highly parallel sensor assay to identify potent shRNAs for HIV, hepatitis C virus (HCV), and influenza. We observe known and previously unknown sequence features that dictate shRNAs efficiency. Validation using HIV and HCV cell culture models demonstrates very high potency of the top-scoring shRNAs. Comparing our data with the secondary structure of HIV shows that shRNA efficacy is strongly affected by the secondary structure at the target RNA site. Artificially introducing secondary structure to the target site markedly reduces shRNA silencing. In addition, we observe that HCV has distinct sequence features that bias HCV-targeting shRNAs toward lower efficacy. Our results facilitate further development of shRNA based antiviral therapies and improve our understanding and ability to predict efficient shRNAs

Examining the moderating effect of individual-level cultural values on users’ acceptance of E-learning in developing countries: a structural equation modeling of an extended technology acceptance model

In this study, we examine the effects of individual-level culture on the adoption and acceptance of e-learning tools by students in Lebanon using a theoretical framework based on the Technology Acceptance Model (TAM). To overcome possible limitations of using TAM in developing countries, we extend TAM to include subjective norms (SN) and quality of work life constructs as additional constructs and a number of cultural variables as moderators. The four cultural dimensions of masculinity/femininity (MF), individualism/collectivism, power distance and uncertainty avoidance were measured at the individual level to enable them to be integrated into the extended TAM as moderators and a research model was developed based on previous literature. To test the hypothesised model, data were collected from 569 undergraduate and postgraduate students using e-learning tools in Lebanon via questionnaire. The collected data were analysed using the structural equation modelling technique in conjunction with multi-group analysis. As hypothesised, the results of the study revealed perceived usefulness (PU), perceived ease of use (PEOU), SN and quality of work life to be significant determinants of students’ behavioural intention (BI) towards e-learning. The empirical results also demonstrated that the relationship between SN and BI was particularly sensitive to differences in individual-cultural values, with significant moderating effects observed for all four of the cultural dimensions studied. Some moderating effects of culture were also found for both PU and PEOU, however, contrary to expectations the effect of quality of work life was not found to be moderated by MF as some previous authors have predicted. The implications of these results to both theory and practice are explored in the paper