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To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
One of the largest problems facing modern medicine is drug resistance. Many classes of drugs can be rendered ineffective if their target is able to acquire beneficial mutations. While this is an excellent showcase of the power of evolution, it necessitates the development of increasingly stronger drugs to combat resistant pathogens. Not only is this strategy costly and time consuming, it is also unsustainable. To contend with this problem, many multi-drug treatment strategies are being explored. Previous studies have shown that resistance to some drug combinations is not possible, for example, resistance to a common antifungal drug, fluconazole, seems impossible in the presence of radicicol. We believe that in order to understand the viability of multi-drug strategies in combating drug resistance, we must understand the full spectrum of resistance mutations that an organism can develop, not just the most common ones. It is possible that rare mutations exist that are resistant to both drugs. Knowing the frequency of such mutations is important for making predictions about how problematic they will be when multi-drug strategies are used to treat human disease. This experiment aims to expand on previous research on the evolution of drug resistance in S. cerevisiae by using molecular barcodes to track ~100,000 evolving lineages simultaneously. The barcoded cells were evolved with serial transfers for seven weeks (200 generations) in three concentrations of the antifungal Fluconazole, three concentrations of the Hsp90 inhibitor Radicicol, and in four combinations of Fluconazole and Radicicol. Sequencing data was used to track barcode frequencies over the course of the evolution, allowing us to observe resistant lineages as they rise and quantify differences in resistance evolution across the different conditions. We were able to successfully observe over 100,000 replicates simultaneously, revealing many adaptive lineages in all conditions. Our results also show clear differences across drug concentrations and combinations, with the highest drug concentrations exhibiting distinct behaviors.
A mutation rate refers to the frequency at which DNA mutations occur in an organism over time. In organisms, mutations are the ultimate source of genetic variation on which selection may act. However, a large number of mutations over time can be detrimental to the cell. Mutation rates are the frequency at which these new mutations arise over time. This can give great insight into DNA repair mechanisms abilities as well as the mutagenic abilities of selected factors. CRISPR-Cas9 is a powerful tool for genome editing, but its off-target effects are not yet fully understood and studied. With its increasing implementation in science and medicine, it is crucial to understand the mutagenic potential of the tool. S. cerevisiae is a model organism for studying genetics due to its fast growth rate and eukaryotic nature. By integrating CRISPR-Cas9 systems into S. cerevisiae, the mutational burden of the technology can be measured and quantified using fluctuation assays. In this experiment, a fluctuation assay using canavanine selective plates was conducted to determine the mutational burden of CRISPR-Cas9 in S. cerevisiae. Multiple trials revealed that various strains of CRISPR-Cas9 had a mutation rate up to 3-fold higher than that of wild-type S. cerevisiae. This information is essential in improving the precision and safety of CRISPR-Cas9 editing in various applications, including gene therapy and biotechnology.
The transcriptome of an organism is a collection of the various messenger RNAs that the genes of an organism produce. As the level of gene expression is different between different tissues of an organism, understanding the transcriptome serves as a way to better understand the differences between the functions and abilities of tissues and cells in an organism. This understanding of the transcriptome can aid further research in targeted disease treatments and indentifying new biomarkers. This study aims to gather the transcriptome from various tissues of the organism Daphnia pulex. This will be done by using a combination of single cell RNA sequencing (scRNA-seq), which involves the isolation and sequencing of single cells, and single nuclei RNA sequencing (snRNA-seq), which involves the isolation and sequencing of single nuclei. Here we show the viability of isolating single cells and single nuclei from various Daphnia pulex tissues using different techniques and enzymes including trypLE, trypsin EDTA, accutase, etc by using microscopy and automatic cell counting. The results show that each tissue is best isolated using different techniques.
Protein misfolding is a problem across all organisms, but the reasons behind misfolded protein (MP) toxicity to cells are largely unknown. To better understand toxicity, I investigate if toxicity from MPs affects all cells equally or affects some cell subpopulations more than others, such as older cells. To define cell subpopulations, I optimized a cutting-edge single-cell RNA sequencing platform (scRNAseq) for yeast. By using scRNAseq in yeast, I studied the expression variability of many genes across populations of thousands of cells. I studied how the transcriptomes of single cells differ from one another in various conditions: at different stages in the growth phase and with different engineered MPs. Differences in gene expression between strains expressing misfolded vs. properly folded proteins were found, confirming previous proteomic data. Further, I found a greater number of cell subpopulations in a MP expressing strain compared to a properly folded protein expressing strain, implying more differentiated subpopulations, potentially in response to toxicity from MPs. This observation is consistent with previous observations that heterogeneity within microbial populations can be beneficial to their fitness by allowing that population to thrive in stressful environments. Thus, my data provide insights about evolutionary biology and how strains respond to stress. Further, after identifying subpopulations with a more severe transcriptional response to MPs, I studied the cells’ physiology to gain insights about why that subpopulation is sensitive to MPs and found an upregulation of markers of aging, stress response, and shortening of lifespan. Observing characteristics of cell subpopulations, I also found differences dependent on stages of the cell cycle. Overall, this study provides insights on the gene regulatory responses associated with MP toxicity by revealing which type of cells are most sensitive to this intracellular threat.
Pathogenic drug resistance is a major global health concern. Thus, there is great interest in modeling the behavior of resistant mutations–how quickly they will rise in frequency within a population, and whether they come with fitness tradeoffs that can form the basis of treatment strategies. These models often depend on precise measurements of the relative fitness advantage (s) for each mutation and the strength of the fitness tradeoff that each mutation suffers in other contexts. Precisely quantifying s helps us create better, more accurate models of how mutants act in different treatment strategies. For example, P. falciparum acquires antimalarial drug resistance through a series of mutations to a single gene. Prior work in yeast expressing this P. falciparum gene demonstrated that mutations come with tradeoffs. Computational work has demonstrated the possibility of a treatment strategy which enriches for a particular resistant mutation that then makes the population grow poorly once the drug is removed. This treatment strategy requires knowledge of s and how it changes when multiple mutants are competing across various drug concentrations. Here, we precisely quantified s in varying drug concentrations for five resistant mutants, each of which provide varying degrees of drug resistance to antimalarial drugs. DNA barcodes were used to label each strain, allowing the mutants to be pooled together for direct competition in different concentrations of drug. This will provide data that can make the models more accurate, potentially facilitating more effective drug treatments in the future.