Current Research Project
Xp Plasmid Diveristy
Principal Investigator
Dr. Erica Goss
Department
Plant Pathology
I am currently working on a project Dr. Erica Goss from the Plant Pathology Department.Plasmids are extrachromosomal DNA segments that can replicate vertically independent of their host or horizontally transfer to other organisms through horizontal gene transfer mechanisms. The project aims to analyze the diversity of plasmids in different Xp population lineages using in silico prediction tools. I have completed most of the project (presented in the research poster to the right) and currently plan on expanding by exploring factors that influence plasmid persistence within Xp populations.
Research Focus
This project focuses on studying the distribution of plasmids in different Xp bacteria groups, classifying them based on their genetic content, and investigating how key genes related to disease and antibiotic resistance spread through these plasmids. It also plans to extend this research to similar bacteria species like Xanthomonas euvesicatoria. In addition, the project aims to study how plasmids persist in a lab setting. We will test how carrying specific plasmids affects bacterial fitness, how stable plasmids are without selective pressure, and how different conditions influence plasmid persistence. We hypothesize that plasmids will be lost without selection, that larger plasmids will be lost more often than smaller ones, and that temperature changes will impact plasmid stability.
Source: National Human Genome Research Institute
Responsiblities
The project commenced in Fall 2023 during which I was learned how to use various bioinformatic tools with the help of a Aman, a graduate student working under my PI. For network analysis, some of the tools I used include NCBI Blast, MOB suite, Bindash and Cytoscape. NCBI blast helps with establishing similarity between two separate DNA sequences and finding related genomes within the ever expanding library of genomic data. MOB Suite and Bindash work to extract plasmid sequences, classify the same sequences into known classes based on several factors and use JI-values to illustrate the similarity between two sequences using numerical values. Finally, Cytoscape was used to visual the JI values obtained from the previous steps of analysis allowing for the creation of networks, like those shown below:
Background/Methods
Plasmids are mobile genetic elements that replicate independently and play a crucial role in bacterial evolution. They facilitate the transfer of genes associated with pathogenicity, antibiotic resistance, and other adaptive traits, which boosts the survival and fitness of bacterial hosts (Rodríguez-Beltrán et al., 2021). However, the plasmid paradox raises questions about whether plasmids are advantageous or burdensome to the host, given their metabolic cost and persistence in bacterial populations (Carroll and Wong, 2018). As a final part of our project, we hope to explore plasmid stability and associated fitness cost within Xp populations.
Source: Eurogentec
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Alonso-del Valle, A., León-Sampedro, R., Rodríguez-Beltrán, J., DelaFuente, J., Hernández-García, M., Ruiz-Garbajosa, P., Cantón, R., Peña-Miller, R., & San Millán, Aet al. (2021). Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nature Communications, 12(1), 2653. https://doi.org/10.1038/s41467-021-22849-y
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Carroll, A. C., & Wong, A. (2018). Plasmid persistence: Costs, benefits, and the plasmid paradox. Canadian Journal of Microbiology, 64(5), 293–304. https://doi.org/10.1139/cjm-2017-0609