Codon ambiguities as a mechanism to alter the genetic code in Saccharomyces cerevisiae

Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

Singlet extensions of the standard model at LHC Run 2: benchmarks and comparison with the NMSSM

The Complex singlet extension of the Standard Model (CxSM) is the simplest extension that provides scenarios for Higgs pair production with different masses. The model has two interesting phases: the dark matter phase, with a Standard Model-like Higgs boson, a new scalar and a dark matter candidate; and the broken phase, with all three neutral scalars mixing. In the latter phase Higgs decays into a pair of two different Higgs bosons are possible. In this study we analyse Higgs-to-Higgs decays in the framework of singlet extensions of the Standard Model (SM), with focus on the CxSM. After demonstrating that scenarios with large rates for such chain decays are possible we perform a comparison between the NMSSM and the CxSM. We find that, based on Higgs-to-Higgs decays, the only possibility to distinguish the two models at the LHC run 2 is through final states with two different scalars. This conclusion builds a strong case for searches for final states with two different scalars at the LHC run 2. Finally, we propose a set of benchmark points for the real and complex singlet extensions to be tested at the LHC run 2. They have been chosen such that the discovery prospects of the involved scalars are maximised and they fulfil the dark matter constraints. Furthermore, for some of the points the theory is stable up to high energy scales. For the computation of the decay widths and branching ratios we developed the Fortran code sHDECAY, which is based on the implementation of the real and complex singlet extensions of the SM in HDECAY.