Reference genome assembly for Australian Ascochyta rabiei Isolate ArME14

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters

On The Pomeron at Large 't Hooft Coupling

We begin the process of unitarizing the Pomeron at large 't Hooft coupling. We do so first in the conformal regime, which applies to good accuracy to a number of real and toy problems in QCD. We rewrite the conformal Pomeron in the $J$-plane and transverse position space, and then work out the eikonal approximation to multiple Pomeron exchange. This is done in the context of a more general treatment of the complex $J$-plane and the geometric consequences of conformal invariance. The methods required are direct generalizations of our previous work on single Pomeron exchange and on multiple graviton exchange in AdS space, and should form a starting point for other investigations. We consider unitarity and saturation in the conformal regime, noting elastic and absorptive effects, and exploring where different processes dominate. Our methods extend to confining theories and we briefly consider the Pomeron kernel in this context. Though there is important model dependence that requires detailed consideration, the eikonal approximation indicates that the Froissart bound is generically both satisfied and saturated.Comment: 63 pages, 7 figures; published version: references updated and several typos correcte

Dissipation from a heavy quark moving through N=4 super-Yang-Mills plasma

Using AdS/CFT, we compute the Fourier space profile of generated by a heavy quark moving through a thermal plasma of strongly coupled N=4 super-Yang-Mills theory. We find evidence of a wake whose description includes gauge fields with large momenta. We comment on the possible relevance of our results to relativistic heavy ion collisions.Comment: 17 pages, 2 figures. v2: reference added, other minor improvements. v3: improved the phrasing describing directional structure

On unquenched N=2 holographic flavor

The addition of fundamental degrees of freedom to a theory which is dual (at low energies) to N=2 SYM in 1+3 dimensions is studied. The gauge theory lives on a stack of Nc D5 branes wrapping an S^2 with the appropriate twist, while the fundamental hypermultiplets are introduced by adding a different set of Nf D5-branes. In a simple case, a system of first order equations taking into account the backreaction of the flavor branes is derived (Nf/Nc is kept of order 1). From it, the modification of the holomorphic coupling is computed explicitly. Mesonic excitations are also discussed.Comment: 25 pages, 4 figure

Glueballs of Super Yang-Mills from Wrapped Branes

In this paper we study qualitative features of glueballs in N=1 SYM for models of wrapped branes in IIA and IIB backgrounds. The scalar mode, 0++ is found to be a mixture of the dilaton and the internal part of the metric. We carry out the numerical study of the IIB background. The potential found exhibits a mass gap and produces a discrete spectrum without any cut-off. We propose a regularization procedure needed to make these states normalizable.Comment: 22 pages plus a appendixes, 2 figure

Energy Loss of Gluons, Baryons and k-Quarks in an N=4 SYM Plasma

We consider different types of external color sources that move through a strongly-coupled thermal N=4 super-Yang-Mills plasma, and calculate, via the AdS/CFT correspondence, the dissipative force (or equivalently, the rate of energy loss) they experience. A bound state of k quarks in the totally antisymmetric representation is found to feel a force with a nontrivial k-dependence. Our result for k=1 (or k=N-1) agrees at large N with the one obtained recently by Herzog et al. and Gubser, but contains in addition an infinite series of 1/N corrections. The baryon (k=N) is seen to experience no drag. Finally, a heavy gluon is found to be subject to a force which at large N is twice as large as the one experienced by a heavy quark, in accordance with gauge theory expectations.Comment: Latex 2e, 24 pages, 1 eps figure; v2: slightly amplified discussion on the relation between the drag force and the tension of a spatial Wilson loop; v3: minor changes, version to appear in JHE

A limiting velocity for quarkonium propagation in a strongly coupled plasma via AdS/CFT

We study the dispersion relations of mesons in a particular hot strongly coupled supersymmetric gauge theory plasma. We find that at large momentum k the dispersion relations become omega = v_0 k + a + b/k + ..., where the limiting velocity v_0 is the same for mesons with any quantum numbers and depends only on the ratio of the temperature to the quark mass T/m_q. We compute a and b in terms of the meson quantum numbers and T/m_q. The limiting meson velocity v_0 becomes much smaller than the speed of light at temperatures below but close to T_diss, the temperature above which no meson bound states at rest in the plasma are found. From our result for v_0, we find that the temperature above which no meson bound states with velocity v exist is T_diss(v) \simeq (1-v^2)^(1/4) T_diss, up to few percent corrections.We thus confirm by direct calculation of meson dispersion relations a result inferred indirectly in previous work via analysis of the screening length between a static quark and antiquark in a moving plasma. Although we do not do our calculations in QCD, we argue that the qualitative features of the dispersion relation we compute, including in particular the relation between dissociation temperature and meson velocity, may apply to bottomonium and charmonium mesons propagating in the strongly coupled plasma of QCD. We discuss how our results can contribute to understanding quarkonium physics in heavy ion collisions.Comment: 57 pages, 12 figures; references adde

Odderon in Gauge/String Duality

At high energies, elastic hadronic cross sections, such as $pp, \overline p p, \pi^{\pm} p$, are dominated by vacuum exchange, which in leading order of the $1/N_c$ expansion has been identified as the BFKL Pomeron or its strong AdS dual the closed string Reggeized graviton \cite{Brower:2006ea}. However the difference of particle anti-particle cross sections are given by a so-called Odderon, carrying C = -1 vacuum quantum numbers identified in weak coupling with odd numbers of exchanged gluons. Here we show that in the dual description the Odderon is the Reggeized Kalb-Ramond field ($B_{\mu\nu}$) in the Neveu-Schwartz sector of closed string theory. To first order in strong coupling, the high energy contribution of Odderon is evaluated for ${\cal N} = 4$ Super Yang-Mills by a generalization of the gravity dual analysis for Pomeron in Ref. \cite{Brower:2006ea}. The consequence of confinement on the Odderon are estimated in the confining QCD-like $AdS^5$ hardwall model of Polchinski and Strassler \cite{Polchinski:2001tt}.Comment: 69 pages, 6 figures. Title change to better reflect the content of the paper. More discussion added in the Comments section. To be published in JHE

Holographic Duals of Quark Gluon Plasmas with Unquenched Flavors

We review the construction of gravitational solutions holographically dual to N=1 quiver gauge theories with dynamical flavor multiplets. We focus on the D3-D7 construction and consider the finite temperature, finite quark chemical potential case where there is a charged black hole in the dual solution. Discussed physical outputs of the model include its thermodynamics (with susceptibilities) and general hydrodynamic properties.Comment: Lecture presented at the Workshop "AdS/CFT and Novel Approaches to Hadron and Heavy Ion Physics", Kavli Institute of Theoretical Physics (KITPC), Beijing, China, 13 October 2010. Review article to be published in Communications in Theoretical Physics. 27 pages, 2 figure