Matching Items (45)
Filtering by

Clear all filters

156042-Thumbnail Image.png
Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial

The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.

My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.

1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.

2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
134327-Thumbnail Image.png
Description
The Mexican gray wolf (Canis lupus baileyi) is a genetically distinct subspecies of the gray wolf (Canis lupus) that was driven to the brink of extinction as a result of human persecution. The wolf is listed as Endangered under the Endangered Species Act, and a recovery program is underway in

The Mexican gray wolf (Canis lupus baileyi) is a genetically distinct subspecies of the gray wolf (Canis lupus) that was driven to the brink of extinction as a result of human persecution. The wolf is listed as Endangered under the Endangered Species Act, and a recovery program is underway in Arizona and New Mexico to restore its population. However, the wolf is struggling to recover due to high mortality, which is a result of continued human hostility toward it. This thesis examines historical and current human attitudes toward the wolf and the implications that they have had on the extermination and recovery of the subspecies. An overview is given of wolf biology, the history of wolf extermination and recovery, and recent events relating to the recovery of the wolf. Negative impacts on ranching, hunting, and human safety are the main reasons for opposition toward wolves and wolf recovery; these concerns are analyzed, and solutions to them are proposed, with the goal of addressing them while fostering non-lethal coexistence with the wolf. In addition, opposition to wolves and wolf recovery is tied in with larger socio-political issues and is influenced by the representation of the wolf in culture; these issues in the context of wolves are also analyzed.
ContributorsLenk, Heather Nicole (Author) / Smith, Andrew (Thesis director) / Minteer, Ben (Committee member) / Brown, David E. (Committee member) / School of Life Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
136419-Thumbnail Image.png
Description
A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai)

A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai) species proceeded by an analysis of if and how the ESA should apply to the Sonoran population. Analysis of current plans and interagency cooperations followed by a multi-step proposal on how best to conserve the Sonoran population of Desert tortoise.
ContributorsKulik, Elise Chikako (Author) / Kusumi, Kenro (Thesis director) / Tollis, Marc (Committee member) / Wilson Sayres, Melissa (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
136133-Thumbnail Image.png
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
133855-Thumbnail Image.png
Description
The International Union for Conservation of Nature's Red List of Threatened Species is the most comprehensive and objective global approach to evaluate the conservation status of species by categorizing species based on relative extinction risk. For the Global Muranidae IUCN Red List assessment, all known, taxonomically valid species of Muraenidae

The International Union for Conservation of Nature's Red List of Threatened Species is the most comprehensive and objective global approach to evaluate the conservation status of species by categorizing species based on relative extinction risk. For the Global Muranidae IUCN Red List assessment, all known, taxonomically valid species of Muraenidae were assessed for their extinction risk using the IUCN Red List Global Categories and Criteria. Of all 208 Muraenidae species, it was concluded that 86% of species qualified for Least Concern, 13% of species are Data Deficient, and 1% of species qualified for a threatened category. Channomuraena bauchotae is listed as threatened under VU D2 and Gymnothorax parini qualified for VU B2ab(iii). This study will have brought the International Union for the Conservation of Nature one step closer to their goal of conducting Red List assessments of all the world's species(not including microorganisms). Future implications of this study may include future monitoring of key habitat areas and species or conducting further research to gain a more in depth understanding of the life history and threats to Muraenidae.
ContributorsLaurence, Paige Marie (Author) / Polidoro, Beth (Thesis director) / Ralph, Gina (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
137215-Thumbnail Image.png
Description
Conservation is a complicated entity consisting of a multitude of professional fields including social issues, cultural issues, and physical science. This thesis evaluates the positive and negative aspects of two broad types of conservation: top down fortress conservation and bottom up community-based conservation. Fortress conservation has many negative aspects, such

Conservation is a complicated entity consisting of a multitude of professional fields including social issues, cultural issues, and physical science. This thesis evaluates the positive and negative aspects of two broad types of conservation: top down fortress conservation and bottom up community-based conservation. Fortress conservation has many negative aspects, such as displacing human communities and preventing utilization of resources. However, it also has positive aspects, such as preventing the destruction of delicate ecosystems and slowing down extinctions. Community-based conservation is more inclusive and focuses on including the indigenous populations located within the proposed conservation site in the decision-making process. Its negatives include having an anthropocentric goal instead of valuing nature's intrinsic values. Understanding the differences inherent in these two methods is necessary in order to implement a conservation network with the highest chance for success.
ContributorsFink, Laurel Berylline (Author) / Smith, Andrew (Thesis director) / Collins, James (Committee member) / Minteer, Ben (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
137202-Thumbnail Image.png
Description
Zoos are doing amazing projects to help wildlife globally and locally. A lot of people aren't aware of what goes on with these conservation projects because much of it happens behind the scenes. So I decided to make a film to explain how zoos facilitate our world's wildlife. My film

Zoos are doing amazing projects to help wildlife globally and locally. A lot of people aren't aware of what goes on with these conservation projects because much of it happens behind the scenes. So I decided to make a film to explain how zoos facilitate our world's wildlife. My film can be viewed at this link: https://www.youtube.com/watch?v=_JmLGf138zY
ContributorsRossman, Chloe June (Author) / Sandler, Kevin (Thesis director) / Wells, Stuart (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Film, Dance and Theatre (Contributor)
Created2014-05
137107-Thumbnail Image.png
Description
The purpose of my thesis is to illustrate the story of the black-footed ferret's conservation, and to provide my own suggestions for how to eventually get the species removed from the Endangered Species List, marking a successful rebound in population numbers. I highlight my personal experience working at the Phoenix

The purpose of my thesis is to illustrate the story of the black-footed ferret's conservation, and to provide my own suggestions for how to eventually get the species removed from the Endangered Species List, marking a successful rebound in population numbers. I highlight my personal experience working at the Phoenix Zoo's black-footed ferret breeding center. In the first chapter, I present the species by describing its morphology, diet, reproduction, behaviors, range, and habitat. In the second chapter, I recount the chronological history of the conservation of the species, starting with its rediscovery following its putative "extinction", and ending with its present status. In the third chapter, I discuss the threats that have led to the species' overall decline and continue to affect its persistence today. In the fourth and final chapter, I conclude by making recommendations regarding what needs to occur in order to eventually get the species delisted.
ContributorsGeer, Emily Maren (Author) / Smith, Andrew T. (Thesis director) / Minteer, Ben (Committee member) / Wells, Stuart (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
137125-Thumbnail Image.png
Description
Globally, many species of shark are facing rapid population decline. This is due to increasing fishing pressures, primarily from the booming demand in China for shark fins for soup. In recent years there has also been an increase in international shark conservation efforts, but there is still a long way

Globally, many species of shark are facing rapid population decline. This is due to increasing fishing pressures, primarily from the booming demand in China for shark fins for soup. In recent years there has also been an increase in international shark conservation efforts, but there is still a long way to go in gathering support for those efforts. Public perception of sharks in America has been greatly influenced by negative media representations of them, Jaws being one of the most influential. Many of these representations are based on inaccurate information that has been disproven by science, but still lingers in popular culture. Symbolic Interactionism Theory proved to be a useful framework for unpacking the connections between public perception, mainstream culture and media, and conservation regarding sharks. A social psychological theory, Symbolic Interactionism describes the ways that people construct meaning about a topic through direct and indirect interactions, and how this meaning can change on individual, social, and cultural levels. By changing the way sharks are perceived and represented to the public, these important and incredible animals may gather the support they need to continue living in the world's oceans.
ContributorsCressler, Christina Nancy (Author) / Minteer, Ben (Thesis director) / Gerber, Leah (Committee member) / Ellison, Karin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
137162-Thumbnail Image.png
Description
Consumption of seafood poses a substantial threat to global biodiversity. Chemical contamination found in both wild-caught and farmed seafood also presents significant health risks to consumers. Flame retardants, used in upholstery, plastics, clothing, and other products to reduce fire danger, are of particular concern as they are commonly found in

Consumption of seafood poses a substantial threat to global biodiversity. Chemical contamination found in both wild-caught and farmed seafood also presents significant health risks to consumers. Flame retardants, used in upholstery, plastics, clothing, and other products to reduce fire danger, are of particular concern as they are commonly found in the marine environment and permeate the tissues of fish that are sold for consumption via multiple pathways. By summarizing various metrics of sustainability and the mercury content in consumed species of fish and shellfish, researchers have found that high levels of chemical contamination was linked with lesser fishery sustainability. I conducted a literature review of flame retardant content in seafood to further compare contamination and sustainability in addition to the initial analysis with mercury. My review suggests that the widespread issue of fishery collapse could be alleviated by demonstrating to stakeholders that many unsustainable fish stocks are mutually disadvantageous for both human consumers and the environment. Future research should address the need for the collection of data that better represent actual global contaminant concentrations in seafood.
ContributorsNoziglia, Andrea Joyce (Author) / Gerber, Leah (Thesis director) / Smith, Andrew (Committee member) / Pratt, Stephen (Committee member) / Barrett, The Honors College (Contributor) / Herberger Institute for Design and the Arts (Contributor) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor)
Created2014-05