Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is change

Synthesis and characterization of poly(vinyl alcohol)-chitosan-hydroxyapatite scaffolds: a promising alternative for bone tissue regeneration

Scaffolds can be considered as one of the most promising treatments for bone tissue regeneration. Herein, blends of chitosan, poly(vinyl alcohol), and hydroxyapatite in different ratios were used to synthesize scaffolds via freeze-drying. Mechanical tests, FTIR, swelling and solubility degree, DSC, morphology, and cell viability were used as characterization techniques. Statistical significance of the experiments was determined using a two-way analysis of variance (ANOVA) with p < 0.05. Crosslinked and plasticized scaffolds absorbed five times more water than non-crosslinked and plasticized ones, which is an indicator of better hydrophilic features, as well as adequate resistance to water without detriment of the swelling potential. Indeed, the tested mechanical properties were notably higher for samples which were undergone to crosslinking and plasticized process. The presence of chitosan is determinant in pore formation and distribution which is an imperative for cell communication. Uniform pore size with diameters ranging from 142 to 519m were obtained, a range that has been described as optimal for bone tissue regeneration. Moreover, cytotoxicity was considered as negligible in the tested conditions, and viability indicates that the material might have potential as a bone regeneration system. © 2018 MDPI AG. All rights reserved.Ministry of Education, Youth and Sports of the Czech Republic-Program NPU I [LO1504]; Universidad Distrital Francisco Jose de Calda

Four-point renormalized coupling constant and Callan-Symanzik beta-function in O(N) models

We investigate some issues concerning the zero-momentum four-point renormalized coupling constant g in the symmetric phase of O(N) models, and the corresponding Callan-Symanzik beta-function. In the framework of the 1/N expansion we show that the Callan- Symanzik beta-function is non-analytic at its zero, i.e. at the fixed-point value g^* of g. This fact calls for a check of the actual accuracy of the determination of g^* from the resummation of the d=3 perturbative g-expansion, which is usually performed assuming analyticity of the beta-function. Two alternative approaches are exploited. We extend the \epsilon-expansion of g^* to O(\epsilon^4). Quite accurate estimates of g^* are then obtained by an analysis exploiting the analytic behavior of g^* as function of d and the known values of g^* for lower-dimensional O(N) models, i.e. for d=2,1,0. Accurate estimates of g^* are also obtained by a reanalysis of the strong-coupling expansion of lattice N-vector models allowing for the leading confluent singularity. The agreement among the g-, \epsilon-, and strong-coupling expansion results is good for all N. However, at N=0,1, \epsilon- and strong-coupling expansion favor values of g^* which are sligthly lower than those obtained by the resummation of the g-expansion assuming analyticity in the Callan-Symanzik beta-function.Comment: 35 pages (3 figs), added Ref. for GRT, some estimates are revised, other minor change

Improved high-temperature expansion and critical equation of state of three-dimensional Ising-like systems

High-temperature series are computed for a generalized $3d$ Ising model with arbitrary potential. Two specific ``improved'' potentials (suppressing leading scaling corrections) are selected by Monte Carlo computation. Critical exponents are extracted from high-temperature series specialized to improved potentials, achieving high accuracy; our best estimates are: $\gamma=1.2371(4)$, $\nu=0.63002(23)$, $\alpha=0.1099(7)$, $\eta=0.0364(4)$, $\beta=0.32648(18)$. By the same technique, the coefficients of the small-field expansion for the effective potential (Helmholtz free energy) are computed. These results are applied to the construction of parametric representations of the critical equation of state. A systematic approximation scheme, based on a global stationarity condition, is introduced (the lowest-order approximation reproduces the linear parametric model). This scheme is used for an accurate determination of universal ratios of amplitudes. A comparison with other theoretical and experimental determinations of universal quantities is presented.Comment: 65 pages, 1 figure, revtex. New Monte Carlo data by Hasenbusch enabled us to improve the determination of the critical exponents and of the equation of state. The discussion of several topics was improved and the bibliography was update

Status of the CRESST-II Experiment for Direct Dark Matter Search

The CRESST-II (Cryogenic Rare Event Search with Superconducting Thermometers) experiment aims for the direct detection of dark matter in form of WIMPs. Scintillating CaWO$_4$ single crystals are used as target material. We present the results of a low-threshold analysis of one single detector module employing a crystal (m~$\sim$~250~g) grown at the Technische Universit{\"a}t M{\"u}nchen with an improved radiopurity and excellent properties of the phonon detector. With an exposure of 29~kg~days new parameter space could be explored for WIMP masses below 3~GeV/c$^2$. In addition, the high potential of CRESST in the low WIMP-mass regime will be shown in a projection employing detectors that are further improved in performance and radiopurity

Galileo Galilei (1564-1642) Acknowledgements

Die Neugier steht immer an erster Stelle eines Problems, das gelöst werden will

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed