Matching Items (6)
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- All Subjects: ethics
- All Subjects: Synthetic Biology
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 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
Description
The prospect of anti-aging or life extension technology is controversial in biogerentology but deemed even by skeptical experts to warrant discussion. I discuss the justifications that the probability of life extension technology being developed in the near future is reasonably high and that this research justifies the time and money it receives. I investigate potential ethical and societal issues anti-aging technology might create. This paper addresses inequality of access, economic cost, changes in quality of life, the role of death in human life, if and how the technology should be regulated and how parties who choose not to undergo treatment can be fairly treated, even when they are a minority.
ContributorsGlesener, Julia Hannah (Author) / McGregor, Joan (Thesis director) / DeSerpa, Allan (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
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 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
Description
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
Description
This thesis aims to address the ethics of keeping the big cats, such as lions, tigers, and leopards, in zoos. It is a practice that has generated some controversy in light of scientific studies reporting stress among wide-ranging animals in captive enclosures, as well as in the context of wider discussions in animal welfare and conservation ethics in zoos. A driving question for this project, therefore, was "What are the arguments for and against keeping large felids in zoos/captivity?" This thesis examines the historical and current ethical approaches to evaluating the ethics of maintaining big cats in zoos. Due to many of the big cat species listed as endangered species on the IUCN redlist, the species-centered approach to zoo ethics is becoming the common viewpoint, and, as a result, zoos are deemed ethical because of their contribution to ex situ conservation practices. Further, the ethical arguments against zoos are minimized when the zoos provide suitable and appropriate enclosures for their large felids. Of course, not all zoos are created equal; the ethics of zoos need to be evaluated on a case-by-case basis, but in general, it is ethical to maintain big cats in zoos.
ContributorsZeien, Krista Marie (Author) / Minteer, Ben (Thesis director) / Smith, Andrew (Committee member) / Ellison, Karin (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Joseph Rotblat (1908-2005) was the only physicist to leave the Manhattan Project for moral reasons before its completion. He would spend the rest of his life advocating for nuclear disarmament. His activities for disarmament resulted in the formation, in 1957, of the Pugwash conferences, which emerged as the leading global forum to advance limits on nuclear weapons during the Cold War. Rotblat's efforts, and the activities of Pugwash, resulted in both being awarded the Nobel Peace Prize in 1995. Rotblat is a central figure in the global history of resistance to the spread of nuclear weapons. He also was an important figure in the emergence, after World War II, of a counter-movement to introduce new social justifications for scientific research and new models for ethics and professionalism among scientists. Rotblat embodies the power of the individual scientist to say "no" and thus, at least individually, put limits of conscience on his or her scientific activity. This paper explores the political and ethical choices scientists make as part of their effort to behave responsibly and to influence the outcomes of their work. By analyzing three phases of Rotblat's life, I demonstrate how he pursued his ideal of beneficial science, or science that appears to benefit humanity. The three phases are: (1) his decision to leave the Manhattan Project in 1944, (2) his role in the creation of Pugwash in 1957 and his role in the rise of the organization into international prominence and (3) his winning the Nobel Peace Prize in 1995. These three phases of Rotblat's life provide a singular window of the history of nuclear weapons and the international movement for scientific responsibility in the 50 years since the bombing of Hiroshima in 1945. While this paper does not provide a complete picture of Rotblat's life and times, I argue that his experiences shed important light on the difficult question of the individual responsibility of scientists.
ContributorsEvans, Alison Dawn (Author) / Zachary, Gregg (Thesis director) / Hurlbut, Ben (Committee member) / Francis, Sybil (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05