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Bacteria have been shown to possess a large array of regulatory mechanisms to not just respond to a diverse array of environmental stresses, but to injurious artificial proteins as well. A previous investigation introduced DX, a man-made ATP sequestering protein into Escherichia coli (E. coli) which resulted in the formation

Bacteria have been shown to possess a large array of regulatory mechanisms to not just respond to a diverse array of environmental stresses, but to injurious artificial proteins as well. A previous investigation introduced DX, a man-made ATP sequestering protein into Escherichia coli (E. coli) which resulted in the formation of novel endoliposome structures and induced a viable but non-culturable state (VBNC) that was not easily reversed. It was hypothesized that the broadly conserved bacterial stringent response pathway may have been responsible for the observed phenotypic changes. With the goal of unveiling the molecular mechanism behind this novel response, changes in cellular morphology and physiology upon DX expression were assessed in a population of E. coli encoding a dysfunctional relA gene, one of the two genes controlling the induction of the stringent response. It was ultimately shown that RelA directly contributed to cellular filamentation, endoliposome structure formation, and the induction of a VBNC state. While the stringent response has been extensively shown to induce a VBNC state, to our knowledge, relA has not yet been shown to induce filamentation or coordinate the formation of endoliposome structures in bacteria. As the stringent response has been shown to be increasingly involved in antibiotic tolerance, this study provided an exciting opportunity to further characterize this adaptive response pathway to aid in the future development of novel therapeutics. In addition to this, this study continued to highlight that the DX protein may serve one of the first tools to allow for the direct selection of bacteria in a VBNC state by morphologically distinguishing non-culturable cells through cellular filamentation.
ContributorsFrost, Fredrick Charles (Author) / Chaput, John (Thesis director) / Wachter, Rebekka (Committee member) / Korch, Shaleen (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-12
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Description
Nucleic acids encode the information required to create life, and polymerases are the gatekeepers charged with maintaining the storage and flow of this genetic information. Synthetic biologists utilize this universal property to modify organisms and other systems to create unique traits or improve the function of others. One of the

Nucleic acids encode the information required to create life, and polymerases are the gatekeepers charged with maintaining the storage and flow of this genetic information. Synthetic biologists utilize this universal property to modify organisms and other systems to create unique traits or improve the function of others. One of the many realms in synthetic biology involves the study of biopolymers that do not exist naturally, which is known as xenobiology. Although life depends on two biopolymers for genetic storage, it may be possible that alternative molecules (xenonucleic acids – XNAs), could be used in their place in either a living or non-living system. However, implementation of an XNA based system requires the development of polymerases that can encode and decode information stored in these artificial polymers. A strategy called directed evolution is used to modify or alter the function of a protein of interest, but identifying mutations that can modify polymerase function is made problematic by their size and overall complexity. To reduce the amount of sequence space that needs to be samples when attempting to identify polymerase variants, we can try to make informed decisions about which amino acid residues may have functional roles in catalysis. An analysis of Family B polymerases has shown that residues which are involved in substrate specificity are often highly conserved both at the sequence and structure level. In order to validate the hypothesis that a strong correlation exists between structural conservation and catalytic activity, we have selected and mutated residues in the 9°N polymerase using a loss of function mutagenesis strategy based on a computational analysis of several homologues from a diverse range of taxa. Improvement of these models will hopefully lead to quicker identification of loci which are ideal engineering targets.
ContributorsHaeberle, Tyler Matthew (Author) / Chaput, John (Thesis director) / Chen, Julian (Committee member) / Larsen, Andrew (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Description
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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Description
This study sought to identify traits that act as possible predictors of academic science proficiency of highly gifted adolescent students. A combination of cognitive, personality, and conative traits were selected for evaluation as predictors of scientific proficiency using student General Ability Index (GAI), Revised NEO Personality Index (NEO-PI R), and

This study sought to identify traits that act as possible predictors of academic science proficiency of highly gifted adolescent students. A combination of cognitive, personality, and conative traits were selected for evaluation as predictors of scientific proficiency using student General Ability Index (GAI), Revised NEO Personality Index (NEO-PI R), and Kolbe Index scores to evaluate each, respectively. Statistical correlational analyses revealed that high expressions of the conative trait Fact Finder and the personality traits Ideas and Straight-forwardness predicted higher degrees of academic science proficiency. In contrast, lower expressions of the personality traits Excitement Seeking and Order predicted higher degrees of scientific proficiency. Further, stepwise regression confirmed that the NEO-PI R facets of Excitement Seeking and Ideas traits were significant predictors of science proficiency and suggested that the personality trait Vulnerability may also be a predictor. The repeated appearance of the Excitement Seeking and Ideas facets and the dependence of the other identified traits suggests that these traits were the most promising possible predictors of scientific proficiency in highly gifted students and should be the target of future research.
ContributorsRoss, Christian Hamilton (Author) / Lansdowne, Kimberly (Thesis director) / Oakes, Wendy (Committee member) / Young, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
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Description
In Mexico, the female adolescent population is made up from two groups, single women and married or cohabitating women. Throughout the past decade there has been an increase in the fertility rate amongst the adolescent population in the state of Sonora. Several factors were analyzed to determine their impact on

In Mexico, the female adolescent population is made up from two groups, single women and married or cohabitating women. Throughout the past decade there has been an increase in the fertility rate amongst the adolescent population in the state of Sonora. Several factors were analyzed to determine their impact on adolescent fertility rate and unplanned pregnancies but ultimately it was found that sexual education was the most influential factor. Comprehensive sexual education has been found to decrease the number of adolescent pregnancies in schools or cities where that curriculum is taught. Many experts believe that this occurs because adolescents are better educated in the proper usage of contraception. Increased contraceptive use directly causes a decrease in unplanned pregnancy rate. With respect to Mexico, it was found that comprehensive sexual education is taught in Sonora but there is no standardized program. Few institutions provide comprehensive sexual education and the programs range between a level 0 and level 3 with respect to the strictness of the abstinence only curricula. Four interviews were conducted between December of 2013 and March of 2014. The purpose of the interviews was to gain a better understanding about how sexual education is perceived in Hermosillo, Sonora, Mexico and what sort of programs are available to adolescents. The questions that comprised the interview consisted of three general parts: background, demographics and sexual education. The interviewees were selected based on their level of expertise reproductive health among adolescents. Two programs were selected for research: Programa Gente Joven (PGJ) and Vive Prevenido. Based on research and data analysis several conclusions were reached. The average age a Mexican woman first has sex, gets married and has her first child within less than 5 years starting in their adolescence. Many years pass between the age of a woman's first childbirth and when she first uses contraception. This is caused by an unmet or unsatisfied need for contraception where the national level is higher than that of Sonora. With respect to sexual education the Guttmacher Institute data suggests that comprehensive sexual education is more effective than abstinence only education. And finally, the experts interviewed all agreed that comprehensive sexual education is what should be taught on a state wide level. The views and opinions of these four interviewees do not reflect those of all who work with adolescents. To gain a more generalized idea on the situation surrounding unplanned pregnancies in adolescents more interviews would need to be conducted. This project was purely exploratory and does not aim to analyze or evaluate either program.
ContributorsGalaz, Mayra Alejandra (Author) / Garcia Perez, Maria (Thesis director) / Lara-Valencia, Francisco (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05