877 research outputs found

    Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1

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    In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1+ gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1¿ strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression

    Environmentally friendly analysis of emerging contaminants by pressurized hot water extraction-stir bar sorptive extraction-derivatization and gas chromatography-mass spectrometry

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    This work describes the development, optimiza- tion, and validation of a new method for the simultaneous determination of a wide range of pharmaceuticals (beta- blockers, lipid regulators ... ) and personal care products (fragrances, UV filters, phthalates ... ) in both aqueous and solid environmental matrices. Target compounds were extracted from sediments using pressurized hot water ex- traction followed by stir bar sorptive extraction. The first stage was performed at 1,500 psi during three static extrac- tion cycles of 5 min each after optimizing the extraction temperature (50 – 150 °C) and addition of organic modifiers (% methanol) to water, the extraction solvent. Next, aqueous extracts and water samples were processed using polydime- thylsiloxane bars. Several parameters were optimized for this technique, including extraction and desorption time, ionic strength, presence of organic modifiers, and pH. Fi- nally, analytes were extracted from the bars by ultrasonic irradiation using a reduced amount of solvent (0.2 mL) prior to derivatization and gas chromatography – mass spectrome- try analysis. The optimized protocol uses minimal amounts of organic solvents (<10 mL/sample) and time ( ≈ 8 h/sam- ple) compared to previous ex isting methodologies. Low standard deviation (usually below 10 %) and limits of de- tection (sub-ppb) vouch for the applicability of the method- ology for the analysis of target compounds at trace levels. Once developed, the method was applied to determin

    The number of transmission channels through a single-molecule junction

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    We calculate transmission eigenvalue distributions for Pt-benzene-Pt and Pt-butadiene-Pt junctions using realistic state-of-the-art many-body techniques. An effective field theory of interacting π\pi-electrons is used to include screening and van der Waals interactions with the metal electrodes. We find that the number of dominant transmission channels in a molecular junction is equal to the degeneracy of the molecular orbital closest to the metal Fermi level.Comment: 9 pages, 8 figure

    Phase-Locked Spatial Domains and Bloch Domain Walls in Type-II Optical Parametric Oscillators

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    We study the role of transverse spatial degrees of freedom in the dynamics of signal-idler phase locked states in type-II Optical Parametric Oscillators. Phase locking stems from signal-idler polarization coupling which arises if the cavity birefringence and/or dichroism is not matched to the nonlinear crystal birefringence. Spontaneous Bloch domain wall formation is theoretically predicted and numerically studied. Bloch walls connect, by means of a polarization transformation, homogeneous regions of self-phase locked solutions. The parameter range for their existence is analytically found. The polarization properties and the dynamics of walls in one- and two transverse spatial dimensions is explained. Transition from Bloch to Ising walls is characterized, the control parameter being the linear coupling strength. Wall dynamics governs spatiotemporal dynamical states of the system, which include transient curvature driven domain growth, persistent dynamics dominated by spiraling defects for Bloch walls, and labyrinthine pattern formation for Ising walls.Comment: 27 pages, 16 figure

    Stabilization of Spatial Solitons by Gain Diffusion

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    It is shown, that diffusion of saturated gain (e.g. diffusion of population inversion in lasers) causes, and/or enhances a modulational instability of generated light field. In case of a subcritical system (e.g. a laser with saturable absorber) the enhancement of the modulational instability stabilizes spatial solitons. These predictions are made for general nonlinear optical systems, and are illustrated by numerical simulation of lasers with saturable absorber.Comment: 10 pages, 4 figures, submitted to Phys.Rev.

    VERITAS Observations of the gamma-Ray Binary LS I +61 303

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    LS I +61 303 is one of only a few high-mass X-ray binaries currently detected at high significance in very high energy gamma-rays. The system was observed over several orbital cycles (between September 2006 and February 2007) with the VERITAS array of imaging air-Cherenkov telescopes. A signal of gamma-rays with energies above 300 GeV is found with a statistical significance of 8.4 standard deviations. The detected flux is measured to be strongly variable; the maximum flux is found during most orbital cycles at apastron. The energy spectrum for the period of maximum emission can be characterized by a power law with a photon index of Gamma=2.40+-0.16_stat+-0.2_sys and a flux above 300 GeV corresponding to 15-20% of the flux from the Crab Nebula.Comment: accepted for publication in The Astrophysical Journa

    Virtual Northern Analysis of the Human Genome

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    BACKGROUND: We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale. METHODOLOGY/PRINCIPAL FINDINGS: We used separation by gel electrophoresis followed by hybridization to cDNA microarrays to measure 8,774 mRNA transcript lengths representing at least 6,238 genes at high (>90%) confidence. By comparing these transcript lengths to the Refseq and H-Invitational full-length cDNA databases, we found that nearly half of our measurements appeared to represent novel transcript variants. Comparison of length measurements determined by hybridization to different cDNAs derived from the same gene identified clones that potentially correspond to alternative transcript variants. We observed a close linear relationship between ORF and mRNA lengths in human mRNAs, identical in form to the relationship we had previously identified in yeast. Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and yeast. CONCLUSIONS/SIGNIFICANCE: Human transcript diversity is extensive and largely unannotated. Our length dataset can be used as a new criterion for judging the completeness of cDNAs and annotating mRNA sequences. Similar relationships between the lengths of the UTRs in human and yeast mRNAs and the functions of the proteins they encode suggest that UTR sequences serve an important regulatory role among eukaryotes

    VERITAS Observations of the BL Lac Object 1ES 1218+304

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    The VERITAS collaboration reports the detection of very-high-energy (VHE) gamma-ray emission from the high-frequency-peaked BL Lac object 1ES 1218+304 located at a redshift of z=0.182. A gamma-ray signal was detected with high statistical significance for the observations taken during several months in the 2006-2007 observing season. The photon spectrum between ~160 GeV and ~1.8 TeV is well described by a power law with an index of Gamma = 3.08 +/- 0.34(stat) +/- 0.2(sys). The integral flux above 200 GeV corresponds to ~6% of that of the Crab Nebula. The light curve does not show any evidence for VHE flux variability. Using lower limits on the density of the extragalactic background light (EBL) in the near-IR to mid-IR we are able to limit the range of intrinsic energy spectra for 1ES 1218+304. We show that the intrinsic photon spectrum is harder than a power law with an index of Gamma = 2.32 +/- 0.37. When including constraints from the spectra of 1ES 1101-232 and 1ES 0229+200, the spectrum of 1ES 1218+304 is likely to be harder than Gamma = 1.86 +/- 0.37.Comment: Submitted to Proceedings of "4th Heidelberg International Symposium on High Energy Gamma-Ray Astronomy 2008
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