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Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While

Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Extrachromosomal circular DNA (eccDNA) has been identified in a broad range of eukaryotes and have been shown to carry genes and regulatory sequences. Additionally, they can amplify within a cell by autonomous replication or reintegration into the genome, effectively influencing copy number in cells. This has significant implications for cancer,

Extrachromosomal circular DNA (eccDNA) has been identified in a broad range of eukaryotes and have been shown to carry genes and regulatory sequences. Additionally, they can amplify within a cell by autonomous replication or reintegration into the genome, effectively influencing copy number in cells. This has significant implications for cancer, where oncogenes are frequently amplified on eccDNA. However, little is known about the exact molecular mechanisms governing eccDNA functionality. To this end, we constructed a fluorescent reporter at an eccDNA-prone locus of the yeast genome, CUP1. It is our hope that this reporter will contribute to a better understanding of eccDNA formation and amplification within a cell.

ContributorsKeal, Tula Ann (Author) / Wang, Xiao (Thesis director) / Tian, Xiaojun (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description
YAP/TAZ is the key effector in the Hippo pathway, but it is also involved in many other regulatory pathways to control tissue and organ size. To better understand its regulation and effects in tumorigenesis and degeneration, a preliminary feedback network was created with the species YAP/TAZ, phosphorylated YAP/TAZ, LATS, miR-130a,

YAP/TAZ is the key effector in the Hippo pathway, but it is also involved in many other regulatory pathways to control tissue and organ size. To better understand its regulation and effects in tumorigenesis and degeneration, a preliminary feedback network was created with the species YAP/TAZ, phosphorylated YAP/TAZ, LATS, miR-130a, VGLL4, and β-catenin. From this network a set of ordinary differential equations were written and analyzed for parameter effects. A model showing the healthy, tumorigenic, and degenerative states was created and preliminary parameter analysis identified the effects of parameter modifications on the overall levels of YAP/TAZ. Further analysis is required and connections with the underlying biology should continue to be pursued to better understand how parameter modifications could improve disease treatments.
ContributorsSussex, Erin Nicole (Author) / Tian, Xiaojun (Thesis director) / Wang, Xiao (Committee member) / School of International Letters and Cultures (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05