Project description:Laboratory evolution experiments of yeast cells impaired for microtubule dynamics. The sequencing was done at two time-points, early and late, to identify compensatory mutations. For details see Macaluso et al, Cell Reports, 2025.
Project description:The metabolome of a cell is the integration point of an organism's environment, genetics, and gene expression pattern. The metabolic phenotype can be under selection and is known to contribute to adaption. However, the metabolome's inherent networked and convoluted nature makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long Term Evolution Experiment (LTEE) as a model to understand how mutations can transduce themselves through a cellular network, eventually affecting metabolism and perhaps fitness. We used mass-spectropscopy to broadly survey the metabolomes of both ancestors and all 12 evolved lines and combined this with genomic and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work brings the field closer to a complete genotype-phenotype map for the LTEE and a better understanding of how mutations might affect fitness through the metabolome. We used mass-spectroscopy to profile metabolic changes in the Long Term Evolution Experiment and link these change to upstream changes in gene expression and mutations.
Project description:We used microarrays to study the evolution of gene expression in two bacterial ecotypes that coexisted for more than 35000 generations of experimental evolution in an extremely simple environment We sampled four clones from each of two lineages at generations 6,500, 17,000 and 40,000 from the polymorphic Ara-2 population of the E. coli long-term evolution experiment. The four clones from each lineage and generation were mixed equally and used for global expression profiling, growth assays and competition experiments. Global expression profiles and growth assays were also performed on the ancestral strain. RNA extractions were done using cells in mid-exponential growth in the same glucose-limited minimal medium used in the evolution experiment. Global expression profiles were obtained by using Affymetrix arrays, with 5 or 6 biological replicates for each lineage-generation sample.
Project description:We used microarrays to study the evolution of gene expression in two bacterial ecotypes that coexisted for more than 35000 generations of experimental evolution in an extremely simple environment
Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Using REPLACE, we attempted continuous intracellular evolution of the negative dominant mutant KRAS (S17N). To analyze the process of mutation accumulation, we performed amplicon sequencing on experimental materials at different stages and under different treatment conditions. The results indicated that the mutations generated by this system were primarily induced by Monanunavir, and the addition of Monanunavir significantly accelerated the rate of evolution.
Project description:We used microarrays to study the changes in whole-genome expression profiles accompanying the evolution of one bacterial population propagated in glucose minimal medium for 20,000 generations.
