818 research outputs found
The architecture of RNA polymerase fidelity
The basis for transcriptional fidelity by RNA polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. A study just published in BMC Biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. See research article http://www.biomedcentral.com/1741-7007/8/5
A review of wetting versus adsorption, complexions, and related phenomena: the rosetta stone of wetting
This paper reviews the fundamental concepts and the terminology of wetting. In particular, it focuses on high temperature wetting phenomena of primary interest to materials scientists. We have chosen to split this review into two sections: one related to macroscopic (continuum) definitions and the other to a microscopic (or atomistic) approach, where the role of chemistry and structure of interfaces and free surfaces on wetting phenomena are addressed. A great deal of attention has been placed on thermodynamics. This allows clarification of many important features, including the state of equilibrium between phases, the kinetics of equilibration, triple lines, hysteresis, adsorption (segregation) and the concept of complexions, intergranular films, prewetting, bulk phase transitions versus âinterface transitionsâ, liquid versus solid wetting, and wetting versus dewetting.Seventh Framework Programme (European Commission) (Grant FP7-NMP-2009-CSA-23348-MACAN
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High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier.
Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Recent evidence suggests that transcript elongation by RNA polymerase II (RNAPII) is regulated by mechanical cues affecting the entry into, and exit from, transcriptionally inactive states, including pausing and arrest. We present a single-molecule optical-trapping study of the interactions of RNAPII with transcription elongation factors TFIIS and TFIIF, which affect these processes. By monitoring the response of elongation complexes containing RNAPII and combinations of TFIIF and TFIIS to controlled mechanical loads, we find that both transcription factors are independently capable of restoring arrested RNAPII to productive elongation. TFIIS, in addition to its established role in promoting transcript cleavage, is found to relieve arrest by a second, cleavage-independent mechanism. TFIIF synergistically enhances some, but not all, of the activities of TFIIS. These studies also uncovered unexpected insights into the mechanisms underlying transient pauses. The direct visualization of pauses at near-base-pair resolution, together with the load dependence of the pause-entry phase, suggests that two distinct mechanisms may be at play: backtracking under forces that hinder transcription and a backtrack-independent activity under assisting loads. The measured pause lifetime distributions are inconsistent with prevailing views of backtracking as a purely diffusive process, suggesting instead that the extent of backtracking may be modulated by mechanisms intrinsic to RNAPII. Pauses triggered by inosine triphosphate misincorporation led to backtracking, even under assisting loads, and their lifetimes were reduced by TFIIS, particularly when aided by TFIIF. Overall, these experiments provide additional insights into how obstacles to transcription may be overcome by the concerted actions of multiple accessory factors
Flavor Mediation Delivers Natural SUSY
If supersymmetry (SUSY) solves the hierarchy problem, then naturalness
considerations coupled with recent LHC bounds require non-trivial superpartner
flavor structures. Such "Natural SUSY" models exhibit a large mass hierarchy
between scalars of the third and first two generations as well as degeneracy
(or alignment) among the first two generations. In this work, we show how this
specific beyond the standard model (SM) flavor structure can be tied directly
to SM flavor via "Flavor Mediation". The SM contains an anomaly-free SU(3)
flavor symmetry, broken only by Yukawa couplings. By gauging this flavor
symmetry in addition to SM gauge symmetries, we can mediate SUSY breaking via
(Higgsed) gauge mediation. This automatically delivers a natural SUSY spectrum.
Third-generation scalar masses are suppressed due to the dominant breaking of
the flavor gauge symmetry in the top direction. More subtly, the
first-two-generation scalars remain highly degenerate due to a custodial U(2)
symmetry, where the SU(2) factor arises because SU(3) is rank two. This
custodial symmetry is broken only at order (m_c/m_t)^2. SUSY gauge coupling
unification predictions are preserved, since no new charged matter is
introduced, the SM gauge structure is unaltered, and the flavor symmetry treats
all matter multiplets equally. Moreover, the uniqueness of the anomaly-free
SU(3) flavor group makes possible a number of concrete predictions for the
superpartner spectrum.Comment: 17 pages, 7 figures, 2 tables. v2 references added, minor changes to
flavor constraints and a little discussion adde
Organismal benefits of transcription speed control at gene boundaries
RNA polymerase II (RNAPII) transcription is crucial for gene expression. RNAPII density peaks at gene boundaries, associating these key regions for gene expression control with limited RNAPII movement. The connections between RNAPII transcription speed and gene regulation in multicellular organisms are poorly understood. Here, we directly modulate RNAPII transcription speed by point mutations in the second largest subunit of RNAPII in Arabidopsis thaliana. A RNAPII mutation predicted to decelerate transcription is inviable, while accelerating RNAPII transcription confers phenotypes resembling autoâimmunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in readâthrough transcription. The accelerated transcription mutant NRPB2âY732F exhibits increased association with 5âČ splice site (5âČSS) intermediates and enhanced splicing efficiency. Our findings highlight potential advantages of RNAPII stalling through local reduction in transcription speed to optimize gene expression for the development of multicellular organisms.SynopsisRNAPII mutations that accelerate transcription cause autoâimmunityâlike phenotypes, readâthrough transcription at RNAPII stalling sites and enhanced splicing in Arabidopsis, indicating that controlled transcription speed is required for optimal gene expression and plant development.A point mutation in RNAPII that increases the speed of RNAPII transcription triggers autoâimmunityâlike phenotypes.plaNETâseq reveals reduced RNAPII stalling at gene boundaries in fast transcription mutants.Increasing the speed of transcription reduces the efficiency of transcriptional termination, resulting in readâthrough transcription that blurs the spatial separation of genes.Accelerating RNAPII transcription enhances splicing efficiency in the multiâcellular context.RNAPII mutations that accelerate transcription cause autoâimmunityâlike phenotypes, readâthrough transcription at RNAPII stalling sites and enhanced splicing in Arabidopsis, indicating that controlled transcription speed is required for optimal gene expression and plant development.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154978/1/embr201949315-sup-0001-EVFigs.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154978/2/embr201949315.reviewer_comments.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154978/3/embr201949315.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154978/4/embr201949315_am.pd
Bounds on SCFTs from Conformal Perturbation Theory
The operator product expansion (OPE) in 4d (super)conformal field theory is
of broad interest, for both formal and phenomenological applications. In this
paper, we use conformal perturbation theory to study the OPE of nearly-free
fields coupled to SCFTs. Under fairly general assumptions, we show that the OPE
of a chiral operator of dimension with its complex
conjugate always contains an operator of dimension less than . Our
bounds apply to Banks-Zaks fixed points and their generalizations, as we
illustrate using several examples.Comment: 36 pages; v2: typos fixed, minor change
The X-ray Position and Optical Counterpart of the Accretion-Powered Millisecond Pulsar XTE J1814-338
We report the precise optical and X-ray localization of the 3.2 ms
accretion-powered X-ray pulsar XTE J1814-338 with data from the Chandra X-Ray
Observatory as well as optical observations conducted during the 2003 June
discovery outburst. Optical imaging of the field during the outburst of this
soft X-ray transient reveals an R = 18 star at the X-ray position. This star is
absent (R > 20) from an archival 1989 image of the field and brightened during
the 2003 outburst, and we therefore identify it as the optical counterpart of
XTE J1814-338. The best source position derived from optical astrometry is R.A.
= 18h13m39.s04, Dec.= -33d46m22.3s (J2000). The featureless X-ray spectrum of
the pulsar in outburst is best fit by an absorbed power-law (with photon index
= 1.41 +- 0.06) plus blackbody (with kT = 0.95 +- 0.13 keV) model, where the
blackbody component contributes approximately 10% of the source flux. The
optical broad-band spectrum shows evidence for an excess of infrared emission
with respect to an X-ray heated accretion disk model, suggesting a significant
contribution from the secondary or from a synchrotron-emitting region. A
follow-up observation performed when XTE J1814-338 was in quiescence reveals no
counterpart to a limiting magnitude of R = 23.3. This suggests that the
secondary is an M3 V or later-type star, and therefore very unlikely to be
responsible for the soft excess, making synchroton emission a more reasonable
candidate.Comment: Accepted for publication in ApJ. 6 pages; 3 figure
Reconstruction and thermal stability of the cubic SiC(001) surfaces
The (001) surfaces of cubic SiC were investigated with ab-initio molecular
dynamics simulations. We show that C-terminated surfaces can have different
c(2x2) and p(2x1) reconstructions, depending on preparation conditions and
thermal treatment, and we suggest experimental probes to identify the various
reconstructed geometries. Furthermore we show that Si-terminated surfaces
exhibit a p(2x1) reconstruction at T=0, whereas above room temperature they
oscillate between a dimer row and an ideal geometry below 500 K, and sample
several patterns including a c(4x2) above 500 K.Comment: 12 pages, RevTeX, figures 1 and 2 available in gif form at
http://irrmawww.epfl.ch/fg/sic/fig1.gif and
http://irrmawww.epfl.ch/fg/sic/fig2.gi
Flavor of quiver-like realizations of effective supersymmetry
We present a class of supersymmetric models which address the flavor puzzle
and have an inverted hierarchy of sfermions. Their construction involves
quiver-like models with link fields in generic representations. The magnitude
of Standard-Model parameters is obtained naturally and a relatively heavy Higgs
boson is allowed without fine tuning. Collider signatures of such models are
possibly within the reach of LHC in the near future.Comment: LaTeX, 17 pages, 3 figures. V2: reference adde
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