0000000000187617
AUTHOR
Miguel Nebot
Viral Mutation Rates
Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 108 to106 s/n/c for DNA viruses and from 106 to 104 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mut…
Singlet Heavy Fermions as the Origin of B Anomalies in Flavour Changing Neutral Currents
We show that a simple extension of the Standard Model involving the introduction of vector-like quarks and heavy neutrinos, provides an explanation of the so called B-anomalies in $b\to s\ell\bar\ell$ transitions. Vector-like quarks can explain, in the context of a discrete flavour symmetry, all the relevant characteristics of the Cabibbo-Kobayashi-Maskawa sector. It is in this framework that we study the requirements on the masses of the vector like quarks and the heavy neutrinos leading to viable models with sufficient deviations of lepton flavour universality and which simultaneously avoid too large Flavour Changing Neutral Current effects. Related predictions on $b\to d\ell\bar\ell$ and…
The Demise of Flavour Tagging and its Delta-T Dependence
In this work we discuss how the loss of particle-antiparticle identity due to CPT violation affects the observables in the decay of two neutral EPR-correlated $B$-mesons. We study this possible new effect in the context of equal-sign flavour specific decays and we find a considerable modification in the $\Delta t$-dependence of the equal-sign dilepton charge asymmetry, $A_{sl}$. Although the more important changes occur right outside the $\Dt$ region that has been up-to-the-date effectively explored, we show that a deeper experimental research may be able to distinguish a possible existence of this new CPT violating parameter, $\w$. In any case, using the available data for $A_{sl}$, we put…
Prospects for the Zee-Babu Model at the LHC and low energy experiments
We analyze the viability of the Zee-Babu model as an explanation of observed neutrino masses and mixings and the possibility that the model is confirmed or discarded in experiments planned for the very close future. The allowed parameter space is studied analytically by using some approximations and partial data. Then, a complete scanning of all parameters and constraints is performed numerically by using Monte Carlo methods. The cleanest signal of the model will be the detection of the doubly charged scalar at the LHC and its correlation with measurements of the branching ratio of $\mu\to e\gamma$ at the MEG experiment. In addition, the model offers interesting predictions for $\tau^{-}\to…
Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1
Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal dist…
Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1.
The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4(+) helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient l…
CPT Violation in $\boldsymbol{B^0_s}$--$\boldsymbol{\bar B^0_s}$ mixing and the measurement of CP Violation in $\boldsymbol{B_s\to K^+K^-}$
A simple analysis of time-dependent $B_s\to K^+K^-$ transitions, based on recent results from the LHCb experiment, is presented. The benefits of adopting a fully consistent theoretical description of the $B^0_s$--$\bar B^0_s$ mixing are stressed. It is shown that bounds on CPT violation in the $B^0_s$--$\bar B^0_s$ system can be consistently obtained and that direct CP violation in $B_s\to K^+K^-$ can be robustly established, even in the presence of CPT violation in the mixing.
Small violations of 3 × 3 unitarity, the phase inB0s–B̄0smixing and visiblet → cZdecays at the LHC
We show that it is possible to accommodate the observed size of the phase in Bs0?s0 mixing in the framework of a model with violation of 3 ? 3 unitarity. This violation is associated to the presence of a new Q = 2/3 isosinglet quark T, which mixes both with t and c and has a mass not exceeding 500 GeV. The crucial point is the fact that this framework allows for ? ? arg(?VtsVcbV*tbV*cs) of order ?, to be contrasted with the situation in the Standard Model, where ? is constrained to be of order ?2. We point out that this scenario implies rare top decays t?cZ at a rate observable at the LHC and |Vtb| significantly different from unity. In this framework, one may also account for the observed …
Novel T-violation observable open to any decay channel at meson factories
Two genuine Quantum phenomena: Entanglement and Filtering Measurement are at the origin of the first direct observation of Time-Reversal-Violation in the time evolution of the B neutral meson system by BaBar. The used meson transitions are directly connected to semileptonic and CP-eigenstate decay channels. We analyse the possibility of extending the observable asymmetries to more decay channels. We propose an alternative T-Violation Asymmetry in the meson factories which allows its opening to any pair of decay channels. The new asymmetry needs also the measurement of the time dependent total survival probability of the initial tagged states. By combining several asymmetries these total sur…
Physical constraints on a class of two-Higgs doublet models with FCNC at tree level
We analyse the constraints and some of the phenomenological implications of a class of two Higgs doublet models where there are flavour-changing neutral currents (FCNC) at tree level but the potentially dangerous FCNC couplings are suppressed by small entries of the CKM matrix V. This class of models have the remarkable feature that, as a result of a discrete symmetry of the Lagrangian, the FCNC couplings are entirely fixed in the quark sector by V and the ratio v 2/v 1 of the vevs of the neutral Higgs. The discrete symmetry is extended to the leptonic sector, so that there are FCNC in the leptonic sector with their flavour structure fixed by the leptonic mixing matrix. We analyse a large n…
The Zee–Babu model revisited in the light of new data
We update previous analyses of the Zee-Babu model in the light of new data, e.g., the mixing angle $\theta_{13}$, the rare decay $\mu\to e \gamma$ and the LHC results. We also analyse the possibility of accommodating the deviations in $\Gamma(H\to \gamma\gamma)$ hinted by the LHC experiments, and the stability of the scalar potential. We find that neutrino oscillation data and low energy constraints are still compatible with masses of the extra charged scalars accessible to LHC. Moreover, if any of them is discovered, the model can be falsified by combining the information on the singly and doubly charged scalar decay modes with neutrino data. Conversely, if the neutrino spectrum is found t…
Testing the Zee-Babu model via neutrino data, lepton flavour violation and direct searches at the LHC
We discuss how the Zee-Babu model can be tested combining information from neutrino data, low-energy experiments and direct searches at the LHC. We update previous analysis in the light of the recent measurement of the neutrino mixing angle $\theta_{13}$, the new MEG limits on $\mu \rightarrow e \gamma$, the lower bounds on doubly-charged scalars coming from LHC data, and, of course, the discovery of a 125 GeV Higgs boson by ATLAS and CMS. In particular, we find that the new singly- and doubly-charged scalars are accessible at the second run of the LHC, yielding different signatures depending on the neutrino hierarchy and on the values of the phases. We also discuss in detail the stability …
A Network Model for the Correlation between Epistasis and Genomic Complexity
The study of genetic interactions (epistasis) is central to the understanding of genome organization and evolution. A general correlation between epistasis and genomic complexity has been recently shown, such that in simpler genomes epistasis is antagonistic on average (mutational effects tend to cancel each other out), whereas a transition towards synergistic epistasis occurs in more complex genomes (mutational effects strengthen each other). Here, we use a simple network model to identify basic features explaining this correlation. We show that, in small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average. In c…
CP violation and limits on New Physics including recent B-s measurements
We analyse present constraints on the SM parameter space and derive, in a model independent way, various bounds on New Physics contributions to $B_d^0$--$\bar B_d^0$ and $B_s^0$--$\bar B_s^0$ mixings. Our analyses include information on a large set of asymmetries, leading to the measurement of the CKM phases $\gamma$ and $\bar\beta$, as well as recent data from D0 and CDF related to the $B_s^0$--$\bar B_s^0$ system such as the measurement of $\Delta M_{B_s}$, $A_{SL}$ and $\Delta\Gamma_{s}^{CP}$. We examine in detail several observables such as the asymmetries $A_{sl}^d$, $A_{SL}$, the width differences $\Delta\Gamma_{d}$ and $\Delta\Gamma_{s}^{CP}$ and discuss the r\^ole they play in estab…
Electron and muon $g-2$ anomalies in general flavour conserving two Higgs doublets models
In general two Higgs doublet models (2HDMs) without scalar flavour changing neutral couplings (SFCNC) in the lepton sector, the electron, muon and tau interactions can be decoupled in a robust framework, stable under renormalization group evolution. In this framework, the breaking of lepton flavour universality (LFU) goes beyond the mass proportionality, opening the possibility to accommodate a different behaviour among charged leptons. We analyze the electron and muon $(g-2)$ anomalies in the context of these general flavour conserving models in the leptonic sector (g$\ell$FC). We consider two different models, I-g$\ell$FC and II-g$\ell$FC, in which the quark Yukawa couplings coincide, res…
Vacuum Induced CP Violation Generating a Complex CKM Matrix with Controlled Scalar FCNC
We propose a viable minimal model with spontaneous CP violation in the framework of a two Higgs doublet model. The model is based on a generalised Branco–Grimus–Lavoura model with a flavoured Z2 symmetry, under which two of the quark families are even and the third one is odd. The lagrangian respects CP invariance, but the vacuum has a CP violating phase, which is able to generate a complex CKM matrix, with the rephasing invariant strength of CP violation compatible with experiment. The question of scalar mediated flavour changing neutral couplings is carefully studied. In particular we point out a deep connection between the generation of a complex CKM matrix from a vacuum phase and the ap…
Flavour Conservation in Two Higgs Doublet Models
In extensions of the Standard Model with two Higgs doublets, flavour changing Yukawa couplings of the neutral scalars may be present at tree level. In this work we consider the most general scenario in which those flavour changing couplings are absent. We re-analyse the conditions that the Yukawa coupling matrices must obey for such \emph{general flavour conservation} (gFC), and study the one loop renormalisation group evolution of such conditions in both the quark and lepton sectors. We show that gFC in the leptonic sector is one loop stable under the Renormalization Group Evolution (RGE) and in the quark sector we present some new Cabibbo like solution also one loop RGE stable. At a pheno…