Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

<p>Abstract</p> <p>Background</p> <p>Rainbow trout (<it>Oncorhynchus mykiss</it>) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents.</p> <p>Results</p> <p>A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study.</p> <p>Conclusions</p> <p>The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.</p

On hypercharge flux and exotics in F-theory GUTs

We study SU(5) Grand Unified Theories within a local framework in F-theory with multiple extra U(1) symmetries arising from a small monodromy group. The use of hypercharge flux for doublet-triplet splitting implies massless exotics in the spectrum that are protected from obtaining a mass by the U(1) symmetries. We find that lifting the exotics by giving vacuum expectation values to some GUT singlets spontaneously breaks all the U(1) symmetries which implies that proton decay operators are induced. If we impose an additional R-parity symmetry by hand we find all the exotics can be lifted while proton decay operators are still forbidden. These models can retain the gauge coupling unification accuracy of the MSSM at 1-loop. For models where the generations are distributed across multiple curves we also present a motivation for the quark-lepton mass splittings at the GUT scale based on a Froggatt-Nielsen approach to flavour.Comment: 38 pages; v2: emphasised possibility of avoiding exotics in models without a global E8 structure, added ref, journal versio

Non-geometric flux vacua, S-duality and algebraic geometry

The four dimensional gauged supergravities descending from non-geometric string compactifications involve a wide class of flux objects which are needed to make the theory invariant under duality transformations at the effective level. Additionally, complex algebraic conditions involving these fluxes arise from Bianchi identities and tadpole cancellations in the effective theory. In this work we study a simple T and S-duality invariant gauged supergravity, that of a type IIB string compactified on a $T^6/(Z_2 x Z_2)$ orientifold with O3/O7-planes. We build upon the results of recent works and develop a systematic method for solving all the flux constraints based on the algebra structure underlying the fluxes. Starting with the T-duality invariant supergravity, we find that the fluxes needed to restore S-duality can be simply implemented as linear deformations of the gauge subalgebra by an element of its second cohomology class. Algebraic geometry techniques are extensively used to solve these constraints and supersymmetric vacua, centering our attention on Minkowski solutions, become systematically computable and are also provided to clarify the methods.Comment: 47 pages, 10 tables, typos corrected, Accepted for Publication in Journal of High Energy Physic

A toy model of fractal glioma development under RF electric field treatment

A toy model for glioma treatment by a radio frequency electric field is suggested. This low-intensity, intermediate-frequency alternating electric field is known as the tumor-treating-field (TTF). In the framework of this model the efficiency of this TTF is estimated, and the interplay between the TTF and the migration-proliferation dichotomy of cancer cells is considered. The model is based on a modification of a comb model for cancer cells, where the migration-proliferation dichotomy becomes naturally apparent. Considering glioma cancer as a fractal dielectric composite of cancer cells and normal tissue cells, a new effective mechanism of glioma treatment is suggested in the form of a giant enhancement of the TTF. This leads to the irreversible electroporation that may be an effective non-invasive method of treating brain cancer.Comment: Submitted for publication in European Physical Journal

Froggatt-Nielsen models from E8 in F-theory GUTs

This paper studies F-theory SU(5) GUT models where the three generations of the standard model come from three different curves. All the matter is taken to come from curves intersecting at a point of enhanced E8 gauge symmetry. Giving a vev to some of the GUT singlets naturally implements a Froggatt-Nielsen approach to flavour structure. A scan is performed over all possible models and the results are filtered using phenomenological constraints. We find a unique model that fits observations of quark and lepton masses and mixing well. This model suffers from two drawbacks: R-parity must be imposed by hand and there is a doublet-triplet splitting problem.Comment: 42 pages; v2:journal version; v3:corrected typo in neutrino masse

Building SO(10) models from F-theory

We revisit local F-theory SO(10) and SU(5) GUTs and analyze their properties within the framework of the maximal underlying E_8 symmetry in the elliptic fibration. We consider the symmetry enhancements along the intersections of seven-branes with the GUT surface and study in detail the embedding of the abelian factors undergoing monodromies in the covering gauge groups. We combine flux data from the successive breaking of SO(10) to SU(5) gauge symmetry and subsequently to the Standard Model one, and further constrain the parameters determining the models' particle spectra. In order to eliminate dangerous baryon number violating operators we propose ways to construct matter parity like symmetries from intrinsic geometric origin. We study implementations of the resulting constrained scenario in specific examples obtained for a variety of monodromies.Comment: 53 page

Towards Realistic String Vacua From Branes At Singularities

We report on progress towards constructing string models incorporating both realistic D-brane matter content and moduli stabilisation with dynamical low-scale supersymmetry breaking. The general framework is that of local D-brane models embedded into the LARGE volume approach to moduli stabilisation. We review quiver theories on del Pezzo $n$ ($dP_n$) singularities including both D3 and D7 branes. We provide supersymmetric examples with three quark/lepton families and the gauge symmetries of the Standard, Left-Right Symmetric, Pati-Salam and Trinification models, without unwanted chiral exotics. We describe how the singularity structure leads to family symmetries governing the Yukawa couplings which may give mass hierarchies among the different generations. We outline how these models can be embedded into compact Calabi-Yau compactifications with LARGE volume moduli stabilisation, and state the minimal conditions for this to be possible. We study the general structure of soft supersymmetry breaking. At the singularity all leading order contributions to the soft terms (both gravity- and anomaly-mediation) vanish. We enumerate subleading contributions and estimate their magnitude. We also describe model-independent physical implications of this scenario. These include the masses of anomalous and non-anomalous U(1)'s and the generic existence of a new hyperweak force under which leptons and/or quarks could be charged. We propose that such a gauge boson could be responsible for the ghost muon anomaly recently found at the Tevatron's CDF detector.Comment: 40 pages, 10 figure

Poly-instanton Inflation

We propose a new inflationary scenario in type IIB Calabi-Yau compactifications, where the inflaton is a K\"ahler modulus parameterising the volume of an internal four-cycle. The inflaton potential is generated via poly-instanton corrections to the superpotential which give rise to a naturally flat direction due to their double exponential suppression. Given that the volume mode is kept stable during inflation, all the inflaton-dependent higher dimensional operators are suppressed. Moreover, string loop effects can be shown to be negligible throughout all the inflationary dynamics for natural values of the underlying parameters. The model is characterised by a reheating temperature of the order $T_{\rm rh}\simeq 10^6$ GeV which requires $N_e \simeq 54$ e-foldings of inflation. All the inflationary observables are compatible with current observations since the spectral index is $n_s \simeq 0.96$, while the tensor-to-scalar ratio is $r\simeq 10^{-5}$. The volume of the Calabi-Yau is of order $10^3$ in string units, corresponding to an inflationary scale around $10^{15}$ GeVComment: 20 pages, 4 figure

Wavefunctions and the Point of E8 in F-theory

In F-theory GUTs interactions between fields are typically localised at points of enhanced symmetry in the internal dimensions implying that the coefficient of the associated operator can be studied using a local wavefunctions overlap calculation. Some F-theory SU(5) GUT theories may exhibit a maximum symmetry enhancement at a point to E8, and in this case all the operators of the theory can be associated to the same point. We take initial steps towards the study of operators in such theories. We calculate wavefunctions and their overlaps around a general point of enhancement and establish constraints on the local form of the fluxes. We then apply the general results to a simple model at a point of E8 enhancement and calculate some example operators such as Yukawa couplings and dimension-five couplings that can lead to proton decay.Comment: 46 page