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The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern

The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
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Description
Lactase persistence is the ability of adults to digest lactose in milk (Segurel & Bon, 2017). Mammals are generally distinguished by their mammary glands which gives females the ability to produce milk and feed their newborn children. The new born therefore requires the ability to breakdown the lactose in the

Lactase persistence is the ability of adults to digest lactose in milk (Segurel & Bon, 2017). Mammals are generally distinguished by their mammary glands which gives females the ability to produce milk and feed their newborn children. The new born therefore requires the ability to breakdown the lactose in the milk to ensure its proper digestion (Segurel & Bon, 2017). Generally, humans lose the expression of lactase after weaning, which prevents them being able to breakdown lactose from dairy (Flatz, 1987).
My research is focused on the people of Turkana, a human pastoral population inhabiting Northwest Kenya. The people of Turkana are Nilotic people that are native to the Turkana district. There are currently no conclusive studies done on evidence for genetic lactase persistence in Turkana. Therefore, my research will be on the evolution of lactase persistence in the people of Turkana. The goal of this project is to investigate the evolutionary history of two genes with known involvement in lactase persistence, LCT and MCM6, in the Turkana. Variants in these genes have previously been identified to result in the ability to digest lactose post-weaning age. Furthermore, an additional study found that a closely related population to the Turkana, the Massai, showed stronger signals of recent selection for lactase persistence than Europeans in these genes. My goal is to characterize known variants associated with lactase persistence by calculating their allele frequencies in the Turkana and conduct selection scans to determine if LCT/MCM6 show signatures of positive selection. In doing this, we conducted a pilot study consisting of 10 female Turkana individuals and 10 females from four different populations from the 1000 genomes project namely: the Yoruba in Ibadan, Nigeria (YRI); Luhya in Webuye, Kenya; Utah Residents with Northern and Western European Ancestry (CEU); and the Southern Han Chinese. The allele frequency calculation suggested that the CEU (Utah Residents with Northern and Western European Ancestry) population had a higher lactase persistence associated allele frequency than all the other populations analyzed here, including the Turkana population. Our Tajima’s D calculations and analysis suggested that both the Turkana population and the four haplotype map populations shows signatures of positive selection in the same region. The iHS selection scans we conducted to detect signatures of positive selection on all five populations showed that the Southern Han Chinese (CHS), the LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations had stronger signatures of positive selection than the Turkana population. The LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations showed the strongest signatures of positive selection in this region. This project serves as a first step in the investigation of lactase persistence in the Turkana population and its evolution over time.
ContributorsJobe, Ndey Bassin (Author) / Wilson Sayres, Melissa (Thesis director) / Paaijmans, Krijn (Committee member) / Taravella, Angela (Committee member) / School of Earth and Space Exploration (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
While specific resistance mechanisms to targeted inhibitors in BRAF-mutant cutaneous melanoma have been identified, surprisingly little is known about the rate at which resistance develops under different treatment options. There is increasing evidence that resistance arises from pre-existing clones rather than from de novo mutations, but there remains the need

While specific resistance mechanisms to targeted inhibitors in BRAF-mutant cutaneous melanoma have been identified, surprisingly little is known about the rate at which resistance develops under different treatment options. There is increasing evidence that resistance arises from pre-existing clones rather than from de novo mutations, but there remains the need for a better understanding of how different drugs affect the fitness of clones within a tumor population and promote or delay the emergence of resistance. To this end, we have developed an assay that defines the in vitro rate of adaptation by analyzing the progressive change in sensitivity of a melanoma cell line to different treatments. We performed a proof-of-theory experiment based on the hypothesis that drugs that cause cell death (cytotoxic) impose a higher selection pressure for drug-resistant clones than drugs that cause cell-cycle arrest (cytostatic drugs), thereby resulting in a faster rate of adaptation. We tested this hypothesis by continuously treating the BRAFV600E melanoma cell line A375 with the cytotoxic MEK inhibitor E6201 and the cytostatic MEK inhibitor trametinib, both of which are known to be effective in the setting of constitutive oncogenic signaling driven by the BRAF mutation. While the identification of confounding factors prevented the direct comparison between E6201-treated and trametinib-treated cells, we observed that E6201-treated cells demonstrate decreased drug sensitivity compared to vehicle-treated cells as early as 18 days after treatment begins. We were able to quantify this rate of divergence at 2.6% per passage by measuring the increase over time in average viability difference between drug-treated and vehicle-treated cells within a DDR analysis. We argue that this value correlates to the rate of adaptation. Furthermore, this study includes efforts to establish a barcoded cell line to allow for individual clonal tracking and efforts to identify synergistic and antagonist drug combinations for use in future experiments. Ultimately, we describe here a novel system capable of quantifying adaptation rate in cancer cells undergoing treatment, and we anticipate that this assay will prove helpful in identifying treatment options that circumvent or delay resistance through future hypothesis-driven experiments.
ContributorsDe Luca, Valerie Jean (Author) / Wilson Sayres, Melissa (Thesis director) / Trent, Jeff (Committee member) / Hendricks, William (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to

Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Tremendous phenotypic variation exists across people with Turner syndrome (45,X). This variation likely stems from differential dosage of genes on the X chromosome. X-inactivation is the process whereby all X chromosomes in excess of one are silenced. However, about 15% of the genes on the silenced X chromosome escape this

Tremendous phenotypic variation exists across people with Turner syndrome (45,X). This variation likely stems from differential dosage of genes on the X chromosome. X-inactivation is the process whereby all X chromosomes in excess of one are silenced. However, about 15% of the genes on the silenced X chromosome escape this inactivation and are candidates for affecting phenotype in people with Turner syndrome. In this study we take an evolutionary approach to rank candidate genes that may contribute to phenotypic variation among people with Turner Syndrome. We incorporate analysis of patterns of DNA methylation from 46,XX and 45,X individuals, and estimates of variable X-inactivation status across 46,XX individuals, with patterns of gene expression conservation on the X chromosomes across five tissues and ten species. We find that genes that escape XCI are possible candidate genes for Turner syndrome phenotype, indicated by the constant levels of expression in escape genes and inactivated genes. Variation in these genes is expected to affect phenotype when dosage is altered from typical levels.
ContributorsSchaffer, Kara Nina (Author) / Wilson Sayres, Melissa (Thesis director) / Crook, Sharon (Committee member) / Narang, Pooja (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description

The academic environment has historically been somewhat slow to implement and adopt new technologies. However, developments in video games have created an opportunity for students to learn new skills and topics through nontraditional mediums of education. The disruption caused by the COVID-19 pandemic further highlighted the need for flexible learning

The academic environment has historically been somewhat slow to implement and adopt new technologies. However, developments in video games have created an opportunity for students to learn new skills and topics through nontraditional mediums of education. The disruption caused by the COVID-19 pandemic further highlighted the need for flexible learning opportunities. Joystick Education is our approach to addressing this need. Through online, game-based tutoring and a database of video games with high educational value, Joystick Education creates a learning environment that is effective, fun, and engaging for students. We analyzed popular, mainstream video games for educational content and selected nine games that teach concepts like history, biology, or physics while playing the game. Through promotion on social media, we generated buzz around our website which led to 103 unique visitors over our first month online and two customers requesting to book our tutoring service. We are confident that given more time to grow, Joystick Education can generate profit and become a successful business.

ContributorsVanlue, Aleczander Bryce (Co-author) / Bartels, Parker (Co-author) / Barrong, Tanner (Co-author) / Byrne, Jared (Thesis director) / Pierce, John (Committee member) / Department of Marketing (Contributor) / Department of Management and Entrepreneurship (Contributor, Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Brundtland’s definition of sustainability is the ability to “meet the needs of the present<br/>without compromising the ability of future generations to meet their needs” (IISD, 2021). But<br/>what if there are no future generations? Social sustainability, the sector of sustainability that<br/>foregrounds the well-being and livelihoods of people (and thereby continuation of

Brundtland’s definition of sustainability is the ability to “meet the needs of the present<br/>without compromising the ability of future generations to meet their needs” (IISD, 2021). But<br/>what if there are no future generations? Social sustainability, the sector of sustainability that<br/>foregrounds the well-being and livelihoods of people (and thereby continuation of humanity), is<br/>included in definitions within the sustainability field, but less developed in sustainability<br/>practice. In an effort to bridge this gap of knowledge, 14 U.S. cities and over 100 sustainability<br/>policies were analyzed for their social sustainability performance. An eight-item analytical<br/>framework that deals with differing areas of social equity guided the analysis. Results found that<br/>most cities’ sustainability departments fell short of truly addressing social sustainability<br/>concerns. Out of the eight items, the most frequently addressed were housing security and racial<br/>and gender equality whereas few, if any, cities addressed the more specific social concerns of<br/>immigration, technology and media, or arts/cultural preservation. Future research is<br/>recommended to gain a better understanding of the ways existing cities can improve in this area.

ContributorsWeekes, Daniel Buckner (Co-author) / Tam, Joey (Co-author) / Brian, Jennifer (Thesis director) / Keeler, Lauren Withycombe (Thesis director) / N/A, N/A (Committee member) / Dean, W.P. Carey School of Business (Contributor) / Department of Economics (Contributor) / Department of Supply Chain Management (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

A deep dive on digital education solutions in the current and post-COVID education industry. Specific attention was given Interactive Flat Panel Display solutions in K-12 and higher education classrooms.

ContributorsHauck, Tanner (Co-author) / Morales, Herwin (Co-author) / Phillips, Maya (Co-author) / Koroli, Eri (Co-author) / Simonson, Mark (Thesis director) / Rakosi, Rock (Committee member) / Department of Finance (Contributor) / Department of Management and Entrepreneurship (Contributor) / The Design School (Contributor) / Economics Program in CLAS (Contributor) / Watts College of Public Service & Community Solut (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

The academic environment has historically been somewhat slow to implement and adopt new technologies. However, developments in video games have created an opportunity for students to learn new skills and topics through nontraditional mediums of education. The disruption caused by the COVID-19 pandemic further highlighted the need for flexible learning

The academic environment has historically been somewhat slow to implement and adopt new technologies. However, developments in video games have created an opportunity for students to learn new skills and topics through nontraditional mediums of education. The disruption caused by the COVID-19 pandemic further highlighted the need for flexible learning opportunities. Joystick Education is our approach to addressing this need. Through online, game-based tutoring and a database of video games with high educational value, Joystick Education creates a learning environment that is effective, fun, and engaging for students. We analyzed popular, mainstream video games for educational content and selected nine games that teach concepts like history, biology, or physics while playing the game. Through promotion on social media, we generated buzz around our website which led to 103 unique visitors over our first month online and two customers requesting to book our tutoring service. We are confident that given more time to grow, Joystick Education can generate profit and become a successful business.

ContributorsBarrong, Tanner Allen (Co-author) / Bartels, Parker (Co-author) / VanLue, Aleczander (Co-author) / Byrne, Jared (Thesis director) / Pierce, John (Committee member) / Industrial, Systems & Operations Engineering Prgm (Contributor, Contributor) / Industrial, Systems & Operations Engineering Prgm (Contributor, Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Intellectual property (IP) is the lifeblood of the U.S. economy. Despite being an important motivator for innovation, IP laws and IP protections are largely unknown by most individuals outside of the legal field. The purpose of this work is to condense some of the most fundamental concepts in U.S. intellectual

Intellectual property (IP) is the lifeblood of the U.S. economy. Despite being an important motivator for innovation, IP laws and IP protections are largely unknown by most individuals outside of the legal field. The purpose of this work is to condense some of the most fundamental concepts in U.S. intellectual property law and describe them in an understandable way for non-lawyers. This thesis covers basic information on U.S. patents, copyrights, trademarks, trade secrets, and the ways in which they impact both science and society. Additionally, this thesis discusses the need for better IP education and presents a solution to this problem in the form of a partly completed draft for an educational book. The book itself is meant to illustrate how the research of this thesis can be utilized in introductory educational materials while also demonstrating the potential for presenting IP law concepts in a fun and visual way.

ContributorsFarmer, Bethany (Author) / Blanks, Zachary (Co-author) / Martin, Thomas (Thesis director) / Prosser, Eric (Committee member) / Irving, Tom (Committee member) / Barrett, The Honors College (Contributor) / Dean, W.P. Carey School of Business (Contributor)
Created2023-05