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 report a measurement of the ratio of the t (t) over bar to Z/gamma* production cross sections in root s = 1.96 TeV p (p) over bar collisions using data corresponding to an integrated luminosity of up to 4.6 fb(-1), collected by the CDF II detector. The t (t) over bar cross section ratio is measured using two complementary methods, a b-jet tagging measurement and a topological approach. By multiplying the ratios by the well-known theoretical Z/gamma* -> ll cross section predicted by the standard model, the extracted t (t) over bar cross sections are effectively insensitive to the uncertainty on luminosity. A best linear unbiased estimate is used to combine both measurements with the result sigma(t (t) over bar) = 7.70 +/- 0.52 pb, for a top-quark mass of 172.5 GeV/c(2).

Abstract: We report the results of a study of the exclusive charmless semileptonic decays, B+ -> eta(l)l(+)nu and B-0 -> pi(-)l(+)nu undertaken with approximately 464 x 10(6) B (B) over bar pairs collected at the Y(4S) resonance with the BABAR detector. The analysis uses events in which the signal B decays are reconstructed with a loose neutrino reconstruction technique. We obtain partial branching fractions for B+ -> eta l(+)nu and B-0 -> pi(-)l(+)nu decays in three and 12 bins of q(2), respectively, from which we extract the f (+)(q(2)) form-factor shapes and the total branching fractions B(B+ -> eta l(+)nu)= (0.36 +/- 0.05(stat) +/- 0.04(syst)) x 10(-4) and B(B-0 -> pi(-)l(+)nu) = (1.42 +/- 0.05(stat) +/- 0.07(syst)) x 10(-4). We also measure B(B+ -> eta'l(+)nu) = (0.24 +/- 0.08(stat) +/- 0.03(syst)) x 10(-4). We obtain values for the magnitude of the CKM matrix element |V-ub| using three different QCD calculations.

Abstract: We investigate the Lambda (1520) photoproduction in the (gamma) over right arrowp -> K+ Lambda(1520) reaction within the effective Lagrangian method near threshold. In addition to the “background” contributions from the contact, t-channel K-exchange, and s-channel nucleon pole terms, which were already considered in previous studies, the contribution from the nucleon resonance N*(2080) (spin-parity J(P) = 3/2(-)) is also considered. We show that the inclusion of the nucleon resonance N*(2080) leads to a fairly good description of the new LEPS differential cross-section data, and that these measurements can be used to determine some of the properties of this latter resonance. However, serious discrepancies appear when the predictions of the model are compared to the photon-beam asymmetry, which was also measured by the LEPS Collaboration.

Abstract: The identification of the correct model for physics beyond the Standard Model requires the determination of the spin of new particles. We investigate to which extent the spin of a new particle X can be identified in scenarios where it decays dominantly in three-body decays X -> f (f) over barY. Here we assume that Y is a candidate for dark matter and escapes direct detection at a high energy collider such as the LHC. We show that in the case that all intermediate particles are heavy, one can get information on the spins of X and Y at the LHC by exploiting the invariant mass distribution of the two standard model fermions. We develop a model-independent strategy to determine the spins without prior knowledge of the unknown couplings and test it in a series of Monte Carlo studies.