186 research outputs found
Electron Scattering from Gaseous OCS (1Sigma ): comparing measured and computed angular distributions
No full textERRATUM: The Ionic Pathways of Lithium Chemistry in the Early Universe: Quantum Calculations for LiH+ Reacting with H
No full textLow-Electron Scattering from Gaseous CS2: angular distributions and effect of exchange forces
No full textAbstract: Ab initio calculations are reported for the quantum scattering of electrons from CS2 molecules in the gas phase and for energies which range from near threshold up to about 100 eV. Angular distributions are examined in detail and an extensive comparison is made with existing experiments and earlier calculations. The agreement found with the latter data is fairly good and results are further discussed in terms of a physical mechanism of "exchange level shifting" to explain the disappearance of a Pi(u) resonance suggested by earlier studies
Low-energy electron scattering from CS(1Σ): role of short-range forces on the near-threshold resonance.
No full textThe Ionic Pathways of Lithium Chemistry in the Early Universe: Quantum Calculations for LiH+ Reacting with H
No full textTo better understand the overall role of lithium chemistry in the early universe, reactive quantum calculations involving LiH(+) have been carried out and rate coefficients have been obtained. The reactive quantum calculations have been performed using a negative imaginary potential method. Infinite-order sudden approximation and the coupled state approximation have been used to simplify the angular coupling dynamics. Rate coefficients are obtained from the reactive cross sections by further integration over Boltzmann distribution of velocities. The results from the present calculations suggest that, at low redshifts (z), LiH(+) should be amenable to observation as imprinted on the cosmic background radiation, in contrast with its neutral counterpart. At higher z, the ionic species may disappear through both depletion reaction and three-body break-up processes
J. Chem. Phys.: Supplementary Download of He-CrH(X) RCCSD(T) and MRCISD+Q Potential Energy Surfaces
No full text<p> ZENODO Supporting Information for J. Chem. Phys. Article #A16.06.0146:<br>
"Theoretical Study of the buffer gas cooling<br>
and trapping of CrH(X6Sigma+) by 3He atoms"<br>
by J. Klos, M. Hapka, G. Chalasinski<br>
P. Halvick and T. Stoecklin<br>
submitted to J. Chem. Phys. June 2016 Accepted 9 November 2016 </p>
<p>Reference: J. Chem. Phys. 145, 214305, (2016)</p>
<p>List of files: <br>
crhhe_mrcisdq_fit_export.f : FORTRAN MRCISD+Q PES Routine<br>
crhhe_rccsdt_fit_export.f : FORTRAN RCCSD(T) PES Routine</p>
<p>Sample of the output inside routines top comment</p>
<p>Compilation: ifort crhhe_rccsdt_fit_export.f -o crhhe_rccsdt_fit_export.exe</p>
<p>Units <br>
Input: R in a0, Theta in degrees<br>
Output: Interaction energy in cm-1</p>
AU-rich element-mediated mRNA decay can occur independently of the miRNA machinery in mouse embryonic fibroblasts and Drosophila S2-cells.
No full textAU-rich elements (AREs) are regulatory sequences located in the 3' untranslated region of many short-lived mRNAs. AREs are recognized by ARE-binding proteins and cause rapid mRNA degradation. Recent reports claimed that the function of AREs may be--at least in part--relayed through the miRNA pathway. We have revisited this hypothesis using dicer knock-out mouse embryonic fibroblasts and cultured Drosophila cells. In contrast to the published results, we find no evidence for a general requirement of the miRNA pathway in the function of AREs. Endogenous ier3 mRNA, which is known to contain a functional ARE, was degraded rapidly at indistinguishable rates in wild type and dicer knock-out mouse embryonic fibroblasts. In cultured Drosophila cells, both ARE-containing GFP reporter mRNAs and the endogenous cecA1 mRNA were resistant to depletion of the mi/siRNA factors dcr-1, dcr-2, ago1 and ago2. Furthermore, the Drosophila miRNA originally proposed to recognize AU-rich elements, miR-289, is not detectably expressed in flies or cultured S2 cells. Even our attempts to overexpress this miRNA from its genomic hairpin sequence failed. Thus, this sequence cannot serve as link between the miRNA and the AU-rich element mediated silencing pathways. Taken together, our studies in mammalian and Drosophila cells strongly argue that AREs can function independently of miRNAs
Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm
No full textIn mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs. AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level. Based on the number of AUUUA pentamers, their proximity, and surrounding AU-rich regions, we generated an algorithm termed AREScore that identifies AREs and provides a numerical assessment of their strength. By analyzing the AREScore distribution in the transcriptomes of 14 metazoan species, we provide evidence that AREs were selected for in several vertebrates and Drosophila melanogaster. We then measured mRNA expression levels genome-wide to address the importance of AREs in SL2 cells derived from D. melanogaster hemocytes. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, was found to target ARE-containing reporter mRNAs for rapid degradation in SL2 cells. Drosophila mRNAs whose expression is elevated upon knock down of Tis11 were found to have higher AREScores. Moreover high AREScores correlate with reduced mRNA expression levels on a genome-wide scale. The precise measurement of degradation rates for 26 Drosophila mRNAs revealed that the AREScore is a very good predictor of short-lived mRNAs. Taken together, this study introduces AREScore as a simple tool to identify ARE-containing mRNAs and provides compelling evidence that AREs are widespread regulatory elements in Drosophila
Investigation of the posttranscriptional regulator BRF1 in embryonic stem cells by inducible RNA interference
No full textPluripotency in murine embryonic stem (ES) cells is maintained by a hierarchy of transcription factors (Nanog, Oct4, Sox2, etc.) but nothing is known to date if ES cell self-renewal or differentiation may also involve mechanisms that act posttranscriptionally at the level of mRNA turnover. Around 8% of all transcipts contain in their 3'-untranslated region a so-called AU-rich element (ARE), a destabilizing motif, which is a key target for proteins regulating dynamic mRNA turnover control, and many of these transcripts code for growth and cell cycle regulatory genes. Our longstanding interest in the laboratory is the ARE-mRNA regulator Brf1 (Zfp36L1), and we were interested to see if this protein is also involved in ES cell pluripotency or differentiation. In early experiments we found Brf1 to be expressed in undifferentiated ES cells (CCE, CGR-8) and under positive regulation by the LIF (leukemia inhibitory factor) and Stat3 axis. As LIF removal or targeting of Stat3 by siRNA led to downregulation of Brf1, we wished to explore the consequences of only downregulating Brf1.
To do so, we developed a cassette system where a small hairpin RNA (shRNA) of choice can be introduced into a defined frt (flip-recombinase target)-site by co-transfection with the recombinase, and which can, in addition, be induced by doxycycline. CCE ES cells already expressing the Tet-repressor (TR) for doxycycline inducibility were transfected with a construct expressing both GFP and neomycin resistance markers linked to a frt-site, allowing Flp-recombinase mediated integration of the plasmid encoding the inducible shRNA. For systems control, we targetet Stat3 by shRNA and observed in response to doxycycline, as exptected, the morphological and biochemical (Oct-4, Fgf4, Rex-1) signs of differentiation of ES cells even in presence of LIF, thus verifying the validity of the system.
Addition of doxycycline to clones with induvible Brf1 shRNA led to a distinct alteration of the morphology of plated embryoid bodies formed in hanging drops. Unexpectedly, downregulation of Brf1 strongly stimulated the formation of cardiac markers (Nkx2.5, Gata4) as well as the formation of beating bodies observed around day 9. To trigger these changes and to enhance cardiomyocyte formation, 4 days of doxycycline addition following LIF removal was sufficient.
A DNA microarray chip analysis was conducted to identify ARE-bearing transcripts with altered expression upon LIF removal and Brf1 downregulation by RNA interference. Based on our hypothesis, we hoped to identify ARE-bearing transcripts that would be increased by these changes. Unfortunately we could not identify any such transcripts suggesting that the effect may be subtle, or could be masked by the simultaneous changes in transcriptional regulation that accompanies these changes.
In a series of preliminary experiments to establish if posttranscriptional regulation is operating in undifferentiated ES cells, an EGFP reporter linked to the destabilizing ARE from the IL3 gene was transduced into CCE cells. The amount of EGFP expresion, as a marker for steady-state mRNA levels, was consistently lower in cells transduced with a reporter bearing the wild-type ARE when compared to cells bearing a non-functional mutant ARE suggesting reporter mRNA destabilization. In addition, when the reporter was expressed in cells bearing the Brf1 shRNA, a slight but significant increase in EGFP expression was observed upon Brf1 downregulation. These results suggest that posttranscriptional regulation of mRNAs is also active in murine ES cells.
Taken together, these findings raise the possibility that Brf1 could be a novel potential regulator of cardiomyocyte formation and suggest that posttranscriptional mechanisms may play an important role in early development. In addition, the inducible RNA interference system developed for this study can be used to investigate any gene of interest and its role in ES cell development
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