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 present an efficient method of reconstructing the parameters of the constrained MSSM from assumed future LHC data, applied both on their own right and in combination with the cosmological determination of the relic dark matter abundance. Focusing on the ATLAS SU3 benchmark point, we demonstrate that our simple Gaussian approximation can recover the values of its parameters remarkably well. We examine two popular noninformative priors and obtain very similar results, although when we use an informative, naturalness-motivated prior, we find some sizeable differences. We show that a further strong improvement in reconstructing the SU3 parameters can by achieved by applying additional information about the relic abundance at the level of WMAP accuracy, although the expected data from Planck will have only a very limited additional impact. Further external data may be required to break some remaining degeneracies. We argue that the method presented here is applicable to a wide class of low-energy effective supersymmetric models, as it does not require one to deal with purely experimental issues, e.g., detector performance, and has the additional advantages of computational efficiency. Furthermore, our approach allows one to distinguish the effect of the model's internal structure and of the external data on the final parameters constraints.

Abstract: We use a theoretical model of the gamma d --> K+K- np reaction adapted to the experiment done at LEPS where a peak was observed and associated with the Theta(+)(1540) pentaquark. The study shows that the method used in the experiment to assign momenta to the undetected proton and neutron, together with the chosen cuts, necessarily creates an artificial broad peak in the assumed K(+)n invariant mass in the region of the claimed Theta(+)(1540), such that the remaining strength seen for the experimental peak is compatible with a fluctuation of 2 sigma significance.