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.

Abstract: We analyse the possible presence of New Physics (NP) in the Flavour Sector and evaluate its potential for solving the tension between the experimental values of A(J/Psi KS) and Br(B+ -> tau(+)v(tau)) with respect to the Standard Model (SM) expectations. Updated model independent analyses, where NP contributions are allowed in B-d(0) – (B) over bar (0)(d) and B-s(0) – (B) over bar (0)(s) transitions, suggest the need of New Physics in the bd sector. A detailed analysis of recent Flavour data is then presented in the framework of a simple extension of the SM, where a Q = 2/3 vector-like isosinglet quark is added to the spectrum of the SM. Special emphasis is given to the implications of this model for correlations among various measurable quantities. We include constraints from all the relevant quark flavour sectors and give precise predictions for selected rare processes. We find important deviations from the SM in observables in the bd sector like the semileptonic asymmetry A(SL)(d), B-d(0) -> mu(+)mu(-) and A(SL)(s) – A(SL)(d). Other potential places where NP can show up include A(J/Psi Phi), gamma, K-L(0) -> pi(0)v (v) over bar, t -> Zq and D-0 -> mu(+)mu(-) among others. The experimental data favours in this model the existence of an up vector-like quark with a mass below 600(1000) GeV at 1(2) sigma.

Abstract: The precise connection between the theoretical T, CP, CPT asymmetries, in terms of transition probabilities between the filtered neutral meson B-d states, and the experimental asymmetries, in terms of the double decay rate intensities for Flavour-CP eigenstate decay products in a B-d-factory of entangled states, is established. This allows the identification of genuine Asymmetry Parameters in the time distribution of the asymmetries and their measurability by disentangling genuine and possible fake terms. We express the nine asymmetry parameters three different observables for each one of the three symmetries in terms of the ingredients of the Weisskopf-Wigner dynamical description of the entangled B-d-meson states and we obtain a global fit to their values from the BaBar collaboration experimental results. The possible fake terms are all compatible with zero and the information content of the nine asymmetry parameters is indeed different. The non -vanishing Delta l(c)(T) = 0.687 +/- 0.020 and Delta l(c)(CP) = 0.680 +/- 0.021 are impressive separate direct evidence of Time -Reversal -violation and CP-violation in these transitions and compatible with Standard Model expectations. An intriguing 2 sigma effect for the Re(theta) parameter responsible of CPT -violation appears which, interpreted as an upper limit, leads to vertical bar M (B) over baro (B) over baro vertical bar MBoBo < 4.0 x 10(-5) eV at 95% C.L. for the diagonal flavour terms of the mass matrix. It contributes to the CP-violating Delta l(c)(CP) asymmetry parameter in an unorthodox manner – in its cos(Delta M t) time dependence-, and it is accessible in facilities with non-entangled B-d's, like the LHCb experiment.