Bonilla, C., Nebot, M., Valle, J. W. F., & Srivastava, R. (2016). Flavor physics scenario for the 750 GeV diphoton anomaly. Phys. Rev. D, 93(7), 073009–5pp.
Abstract: A simple variant of a realistic flavor symmetry scheme for fermion masses and mixings provides a possible interpretation of the diphoton anomaly as an electroweak singlet “flavon.” The existence of TeV scale vectorlike T-quarks required to provide adequate values for Cabibbo-Kobayashi-Maskawa (CKM) parameters can also naturally account for the diphoton anomaly. Correlations between V-ub and V-cb with the vectorlike T-quark mass can be predicted. Should the diphoton anomaly survive in a future run, our proposed interpretation can also be tested in upcoming B and LHC studies.
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Sanjuan, R., Nebot, M., Chirico, N., Mansky, L. M., & Belshaw, R. (2010). Viral Mutation Rates. J. Virol., 84(19), 9733–9748.
Abstract: 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 10(-8) to 10(-6) s/n/c for DNA viruses and from 10(-6) to 10(-4) s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut.
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Morisi, S., Nebot, M., Patel, K. M., Peinado, E., & Valle, J. W. F. (2013). Quark-lepton mass relation and CKM mixing in an A(4) extension of the minimal supersymmetric standard model. Phys. Rev. D, 88(3), 036001–8pp.
Abstract: An interesting mass relation between down-type quarks and charged leptons has been recently predicted within a supersymmetric SU(3)(c) circle times SU(2)(L) circle times U(1)(Y) model based on the A(4) flavor symmetry. Here we propose a simple extension which provides an adequate full description of the quark sector. By adding a pair of vectorlike up quarks, we show how the CKM entries V-ub, V-cb, V-td and V-ts arise from deviations of the unitarity. We perform an analysis including the most relevant observables in the quark sector, such as oscillations and rare decays of kaons, B-d and B-s mesons. In the lepton sector, the model predicts an inverted hierarchy for the neutrino masses, leading to a potentially observable rate of neutrinoless double beta decay.
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Bernabeu, J., Botella, F. J., Nebot, M., & Segarra, A. (2022). B-0 – (B)over-bar(0) entanglement for an ideal experiment for the direct CP violation phi(3)/gamma phase. Phys. Rev. D, 106(5), 054026–7pp.
Abstract: B-0-(B) over bar0 entanglement offers a conceptual alternative to the single charged B-decay asymmetry for the measurement of the direct CP-violating gamma/phi(3) phase. With f = J/Psi(L); J/Psi K-S and g = (pi pi)(0); (rho(L)rho(L))(0), the 16 time-ordered double-decay rate intensities to (f, g) depend on the relative phase between the f- and g-decay amplitudes given by gamma at tree level. Several constraining consistencies appear. An intrinsic accuracy of the method at the level of +/- 1 degrees could be achievable at Belle-II with an improved determination of the penguin amplitude to g channels from existing facilities.
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Peris, J. B., Davis, P., Cuevas, J. M., Nebot, M., & Sanjuan, R. (2010). Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1. Genetics, 185(2), 603–U308.
Abstract: 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 distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria.
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