389 research outputs found
UV friendly T-parity in the SU(6)/Sp(6) little Higgs model
Electroweak precision tests put stringent constraints on the parameter space
of little Higgs models. Tree-level exchange of TeV scale particles in a generic
little Higgs model produce higher dimensional operators that make contributions
to electroweak observables that are typically too large. To avoid this problem
a discrete symmetry dubbed T-parity can be introduced to forbid the dangerous
couplings. However, it was realized that in simple group models such as the
littlest Higgs model, the implementation of T-parity in a UV completion could
present some challenges. The situation is analogous to the one in QCD where the
pion can easily be defined as being odd under a new symmetry in the
chiral Lagrangian, but this is not a symmetry of the quark Lagrangian. In
this paper we examine the possibility of implementing a T-parity in the low
energy model that might be easier to realize in the UV. In our
model, the T-parity acts on the low energy non-linear sigma model field in way
which is different to what was originally proposed for the Littlest Higgs, and
lead to a different low energy theory. In particular, the Higgs sector of this
model is a inert two Higgs doublets model with an approximate custodial
symmetry. We examine the contributions of the various sectors of the model to
electroweak precision data, and to the dark matter abundance.Comment: 21 pages,4 figures. Clarifications added, typos corrected and
references added. Published in JHE
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al
Heavy fermions and two loop electroweak corrections to
Applying effective Lagrangian method and on-shell scheme, we analyze the
electroweak corrections to the rare decay from some
special two loop diagrams in which a closed heavy fermion loop is attached to
the virtual charged gauge bosons or Higgs. At the decoupling limit where the
virtual fermions in inner loop are much heavier than the electroweak scale, we
verify the final results satisfying the decoupling theorem explicitly when the
interactions among Higgs and heavy fermions do not contain the nondecoupling
couplings. Adopting the universal assumptions on the relevant couplings and
mass spectrum of new physics, we find that the relative corrections from those
two loop diagrams to the SM theoretical prediction on the branching ratio of
can reach 5% as the energy scale of new physics
GeV.Comment: 30 pages,4 figure
Secondary contact and admixture between independently invading populations of the Western corn rootworm, diabrotica virgifera virgifera in Europe
The western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is one of the most destructive pests of corn in North America and is currently invading Europe. The two major invasive outbreaks of rootworm in Europe have occurred, in North-West Italy and in Central and South-Eastern Europe. These two outbreaks originated from independent introductions from North America. Secondary contact probably occurred in North Italy between these two outbreaks, in 2008. We used 13 microsatellite markers to conduct a population genetics study, to demonstrate that this geographic contact resulted in a zone of admixture in the Italian region of Veneto. We show that i) genetic variation is greater in the contact zone than in the parental outbreaks; ii) several signs of admixture were detected in some Venetian samples, in a Bayesian analysis of the population structure and in an approximate Bayesian computation analysis of historical scenarios and, finally, iii) allelic frequency clines were observed at microsatellite loci. The contact between the invasive outbreaks in North-West Italy and Central and South-Eastern Europe resulted in a zone of admixture, with particular characteristics. The evolutionary implications of the existence of a zone of admixture in Northern Italy and their possible impact on the invasion success of the western corn rootworm are discussed
Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote
The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research
Testing Little Higgs Mechanism at Future Colliders
In the framework of the little higgs scenario, coupling constants of several
interactions are related to each other to guarantee the stability of the higgs
boson mass at one-loop level. This relation is called the little higgs
mechanism. We discuss how accurately the relation can be tested at future e+e-
colliders, with especially focusing on the top sector of the scenario using a
method of effective lagrangian. In order to test the mechanism at the top
sector, it is important to measure the Yukawa coupling of the top partner. We
consider higgs associated production and threshold production of the top
partner, and find that the mechanism can be tested precisely using the
associate production when the center of mass energy is large enough. The
threshold production also allows us to test it even if the center mass energy
is not so large.Comment: 22 pages, 5 figures, 2 tables ; v2 minor correction
EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly
This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Data files of wing spot sizes and AFLP genotypes available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.j7v42.Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns reflected island-specific selection and that there was little migration between islands. However, genetic studies to test the underlying assumption of restricted migration are lacking and it is also unknown whether the originally described wing-spot patterns have persisted over time. We therefore collected female butterflies from five of Ford's original study locations, including three large islands (St Mary's, St Martin's and Tresco) and two small islands (Tean and St Helen's). Wing-spot patterns had not changed appreciably over time on three of the islands (two large and one small), but were significantly different on the other two. Furthermore, analysis of 176 amplified fragment length polymorphisms revealed significant genome-wide differentiation among the five islands. Our findings are consistent with Ford's conclusions that despite the close proximity of these islands, there is restricted gene flow among them.Heredity advance online publication, 2 November 2016; doi:10.1038/hdy.2016.94.We thank the Genetics Society for a fieldwork grant (to DJH) that funded the collection trip and DJH thanks Mike Johnson for sparking interest in this area. SWB is supported by the Australian Research Council and a Ramsay Fellowship, NW by a Royal Society Wolfson Fellowship and NERC and DJH by the Leverhulme Trust
Genetic Affinities of the Central Indian Tribal Populations
Background: The central Indian state Madhya Pradesh is often called as âheart of India â and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. Methodology/Principal Findings: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. Conclusions/Significance: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic labe
A systematic, large-scale comparison of transcription factor binding site models
Background The modelling of gene regulation is a major challenge in biomedical
research. This process is dominated by transcription factors (TFs) and
mutations in their binding sites (TFBSs) may cause the misregulation of genes,
eventually leading to disease. The consequences of DNA variants on TF binding
are modelled in silico using binding matrices, but it remains unclear whether
these are capable of accurately representing in vivo binding. In this study,
we present a systematic comparison of binding models for 82 human TFs from
three freely available sources: JASPAR matrices, HT-SELEX-generated models and
matrices derived from protein binding microarrays (PBMs). We determined their
ability to detect experimentally verified ârealâ in vivo TFBSs derived from
ENCODE ChIP-seq data. As negative controls we chose random downstream exonic
sequences, which are unlikely to harbour TFBS. All models were assessed by
receiver operating characteristics (ROC) analysis. Results While the area-
under-curve was low for most of the tested models with only 47 % reaching a
score of 0.7 or higher, we noticed strong differences between the various
position-specific scoring matrices with JASPAR and HT-SELEX models showing
higher success rates than PBM-derived models. In addition, we found that while
TFBS sequences showed a higher degree of conservation than randomly chosen
sequences, there was a high variability between individual TFBSs. Conclusions
Our results show that only few of the matrix-based models used to predict
potential TFBS are able to reliably detect experimentally confirmed TFBS. We
compiled our findings in a freely accessible web application called ePOSSUM
(http:/mutationtaster.charite.de/ePOSSUM/) which uses a Bayes classifier to
assess the impact of genetic alterations on TF binding in user-defined
sequences. Additionally, ePOSSUM provides information on the reliability of
the prediction using our test set of experimentally confirmed binding sites
A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ~4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ~60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.National Human Genome Research Institute (U.S.)National Institute of General Medical Sciences (U.S.) (Grant number GM82901)National Science Foundation (U.S.). Postdoctural Fellowship (Award 0905968)National Science Foundation (U.S.). Career (0644282)National Institutes of Health (U.S.) (R01-HG004037)Alfred P. Sloan Foundation.Austrian Science Fund. Erwin Schrodinger Fellowshi
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