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- Member of: Barrett, The Honors College Thesis/Creative Project Collection
Description
Soiled: An Environmental Podcast is a six episode series where common environmental topics are discussed and misconceptions surrounding these topics are debunked.
ContributorsJones, Cassity Rachelle (Co-author) / Kuta, Tiffany (Co-author) / Turner, Natalie (Co-author) / Boyer, Mackenzie (Thesis director) / Ward, Kristen (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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 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
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
Introduction: Human papillomavirus (HPV) infection is seen in up to 90% of cases of cervical cancer, the third leading cancer cause of death in women. Current HPV screening focuses on only two HPV types and covers roughly 75% of HPV-associated cervical cancers. A protein based assay to test for antibody biomarkers against 98 HPV antigens from both high and low risk types could provide an inexpensive and reliable method to screen for patients at risk of developing invasive cervical cancer. Methods: 98 codon optimized, commercially produced HPV genes were cloned into the pANT7_cGST vector, amplified in a bacterial host, and purified for mammalian expression using in vitro transcription/translation (IVTT) in a luminescence-based RAPID ELISA (RELISA) assay. Monoclonal antibodies were used to determine immune cross-reactivity between phylogenetically similar antigens. Lastly, several protein characteristics were examined to determine if they correlated with protein expression. Results: All genes were successfully moved into the destination vector and 86 of the 98 genes (88%) expressed protein at an adequate level. A difference was noted in expression by gene across HPV types but no correlation was found between protein size, pI, or aliphatic index and expression. Discussion: Further testing is needed to express the remaining 12 HPV genes. Once all genes have been successfully expressed and purified at high concentrations, DNA will be printed on microscope slides to create a protein microarray. This microarray will be used to screen HPV-positive patient sera for antibody biomarkers that may be indicative of cervical cancer and precancerous cervical neoplasias.
ContributorsMeshay, Ian Matthew (Author) / Anderson, Karen (Thesis director) / Magee, Mitch (Committee member) / Katchman, Benjamin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The Intercellular Adhesion Molecule-1 (ICAM-1, known as CD54) is a cell surface type I transmembrane glycoprotein with a molecular weight of 85 to 110 kDa. The primary function of ICAM-1 is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 is used as a receptor for various pathogens such as rhinoviruses, coxsackievirus A21 and the malaria parasite Plasmodium falciparum. ICAM-1 contains five immunoglobulin (Ig) domains in its long N-terminal extracellular region, a hydrophobic transmembrane domain, and a small C-terminal cytoplasmic domain. The Ig domains 1-2 and Ig domains 3-4-5 have been crystallized separately and their structure solved, however the full ICAM-1 structure has not been solved. Because ICAM-1 appears to be important for the mediation of cell-to-cell communication in physiological and pathological conditions, gaining a structural understanding of the full-length membrane anchored ICAM-1 is desirable. In this context, we have transiently expressed a plant-optimized gene encoding human ICAM-1 in Nicotiana benthamiana plants using the MagnICON expression system. The plant produced ICAM-1 is forming aggregates according to previous data. Thus, the current extraction and purification protocols have been altered to include TCEP, a reducing agent. The protein was purified using TALON metal affinity resin and partially characterized using various biochemical techniques. Our results show that there is a reduction in aggregation formation with the use of TCEP.
ContributorsPatel, Heeral (Author) / Mor, Tsafrir (Thesis director) / Mason, Hugh (Committee member) / Kannan, Latha (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Variants of human butyrylcholinesterase (BChE) have been designed to have high cocaine hydrolytic activity. These variants have potential pharmacological applications toward treating cocaine overdose and addiction. These enzymes must be stable in the human body over fairly long periods of time in order to be effective at treating cocaine addiction. Recombinantly expressed BChE, however, tends to be in monomer or dimer oligomeric forms, which are far less stable than the tetramer form of the enzyme. When BChE is transiently expressed in Nicotiana benthamiana, it is produced mainly as monomers and dimers. However, when the protein is expressed through stable transformation, it produces much greater proportions of tetramers. Tetramerization of WT human plasma derived BChE is facilitated by the binding of a proline rich peptide. In this thesis, I investigated if a putative plant-derived analog of the mammalian proline-rich attachment domain caused stably expressed cocaine hydrolase variants of human BChE to undergo tetramerization. I also examined if co-expression of peptides with known proline-rich attachment domains further shifted the monomer-tetramer ratio toward the tetramer.
ContributorsKendle, Robert Player (Author) / Mor, Tsafrir (Thesis director) / Mason, Hugh (Committee member) / Larrimore, Kathy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Memory Wipe is a 22 minute, video art piece that utilizes home movie footage filmed on VHS and 8mm, as well as television and cartoon ephemera, to explore the way in which personal memory is constructed and altered through the process of recording and viewing. Three recent events in my life inspired work: the discovery of a box containing my favorite childhood media, the revelation that I am the last male of my family, and the impending sale of my family's farmland. My mother never used a video camera, insisting that her childhood was lost in footage filmed but never watched. It should also be noted that not once do I appear in this piece; therefore, I decided to extract myself from the narrative. Rather than simply guide the audience along with anecdotes from my life, I instead invite viewers to draw their own meanings and create their own nostalgias from the piece. Originally, Memory Wipe was to be accompanied by live narration, but all things considered, I thought I would let it speak for itself. Video link: https://www.youtube.com/watch?v=-E42a6Koma4
ContributorsMcDougall, Clayton Ross (Author) / Magenta, Muriel (Thesis director) / Brye, Anne (Committee member) / Barrett, The Honors College (Contributor) / School of Film, Dance and Theatre (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
Description
Efforts to quantify the diversity of the T cell repertoire have generally been unsuccessful because not all factors accounting for diversity have been considered. In order to get an accurate representation of the T cell repertoire, one must incorporate analysis of germline gene diversity, diversity from somatic recombination, joining diversity from N- and P- nucleotides, and TCR chain pairing diversity. Because of advances in high-throughput sequencing techniques, estimates have been able to account for diversity from TCR genes. However the ability to account for chain pairing diversity has been more difficult. In order to do so, single cell sorting techniques must be employed. These techniques, though effective, are time consuming and expensive. For this reason, no large-scale analyses have been done on the immune repertoires using these techniques. In this study, we propose a novel method for linking the two TCR chain sequences from an individual cell. DNA origami nanostructure technology is employed to capture and bind the TCRγ and TCRδ chain mRNA inside individual cells using probe strands complementary to the C-region of those sequences. We then use a dual-primer RT and ligation molecular strategy to link the two sequences together. The result is a single amplicon containing the CDR3 region of the TCRγ and TCRδ. This amplicon can then be easily PCR amplified using sequence specific primers, and sequenced. DNA origami nanostructures offer a rapid, cost-effective method alternative to conventional single cell sorting techniques, as both TCR mRNA can be captured on one origami molecule inside a single cell. At present, this study outlines a proof-of-principle analysis of the method to determine its functionality. Using known TCRγ and TCRδ sequences, the DNA origami and RT/PCR method was tested and resulting sequence data proved the effectiveness of the method. The original TCRγ and TCRδ sequences were linked together as a single amplicon containing both CDR3 regions of the genes. Thus, this method can be employed in further research to elucidate the γδ T cell repertoire. This technology is also easily adapted to any gene target or cell type and therefore presents a large opportunity to be used in other immune repertoire analysis and other immunological studies (such as the rapid identification and subsequent production of antibodies).
ContributorsPoindexter, Morgan Elizabeth (Author) / Blattman, Joseph (Thesis director) / Yan, Hao (Committee member) / Schoettle, Louis (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Link to website project: http://cacoope6.wix.com/tolerancemuseum The East Valley Jewish Community Center is working to build a Holocaust & Tolerance Museum adjacent to their community center campus in Chandler. As a sophomore in college I was introduced to the EVJCC and this project when I saw two Holocaust survivors who lived through Sobibor death camp speak at an EVJCC event. After that, I looked for more information online, only to find none. A series of conversations with Steve Tepper of the EVJCC later, we decided on a project - a website that would be easy for him to maintain after I passed it over when my thesis was complete. I spent a little over a year gathering materials for this project and familiarizing myself with the people and projects involved. In addition to my own original materials, I used a collection of materials I was given access to by Steve Tepper, including filmed interviews with survivors, a documentary, news stories and more. I attended events, took my own photos, talked with Holocaust survivors and learned more about the museum itself, which will be a museum not only to commemorate the Holocaust but genocide and persecution around the globe. When it came time to make the website, I chose Wix as the medium because it was something I could make to the EVJCC's standards and specifications with my own original touches and flair, and something they could easily take over and update after I pass it along. The final product is a beginning website to help them get started with their online presence as a museum.
ContributorsCooper, Clarissa Aileen (Author) / Dodge, Nancie (Thesis director) / Kiefer, Michael (Committee member) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Link to documentary: https://drive.google.com/file/d/0BxFCDFfMBwpoNVdybDZOaGhaUWc/view?usp=sharing For my thesis project, I decided to do a documentary on Special Olympic Athletes in Arizona. These individuals have always inspired me because they have faced many challenges and yet they still go through life with a smile on their face. I believe they all deserve recognition for what they have accomplished during the games and outside of them. I wanted to give them this recognition. In my documentary, I interviewed five athletes, three of which are siblings. The first athlete I interviewed was Jesse McGirl, who is a star track and field athlete. In his part of the video, I talk about his strategy as well as his involvement in the games. I also talk about him being a Global Messenger and how he travels the world in order to spread the message of the Special Olympics. The next athlete was David Fromh, who started competing in the games in 1978. In his section, I talk to him about his relationships with his coaches and teammates as well as the strategy he uses while running. He is one of the most positive athletes out there, and I really emphasize on his positivity. The last set of interviews I did was with the Meagan, Emily, and Quincy Jones, three siblings who all suffer from intellectual disabilities. David and Gena Jones adopted them when they were young and their story is a true inspiration. The family is the main focus of my documentary, so they have three parts: Early Life, Special Olympics, and Future. The Early Life focuses on how David and Gena raised their kids and their high school life. The Special Olympics section focuses on their success at the games and the Future section is about the siblings' interests outside of the games. Along with my athlete stories, I have an introduction and conclusion as well as a brief history section describing the founding of the Special Olympics. I had a great time making this project, and I am very fortunate to be able to tell such inspirational stories.
ContributorsEurich, Danielle Nikole (Author) / Dunn, Heather (Thesis director) / Kurland, Brett (Committee member) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12