303 research outputs found
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 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 () 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 GeV which requires e-foldings of inflation. All the inflationary observables are compatible
with current observations since the spectral index is , while
the tensor-to-scalar ratio is . The volume of the Calabi-Yau
is of order in string units, corresponding to an inflationary scale
around 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
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