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 “interface transitions”, liquid versus solid wetting, and wetting versus dewetting.Seventh Framework Programme (European Commission) (Grant FP7-NMP-2009-CSA-23348-MACAN

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 auto‐immunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in read‐through transcription. The accelerated transcription mutant NRPB2‐Y732F exhibits increased association with 5′ splice site (5′SS) 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 auto‐immunity‐like phenotypes, read‐through 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 auto‐immunity‐like phenotypes.plaNET‐seq reveals reduced RNAPII stalling at gene boundaries in fast transcription mutants.Increasing the speed of transcription reduces the efficiency of transcriptional termination, resulting in read‐through transcription that blurs the spatial separation of genes.Accelerating RNAPII transcription enhances splicing efficiency in the multi‐cellular context.RNAPII mutations that accelerate transcription cause auto‐immunity‐like phenotypes, read‐through 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 $\Delta = 1+\epsilon$ with its complex conjugate always contains an operator of dimension less than $2 \Delta$. 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