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- Creators: Mozart, Wolfgang Amadeus, 1756-1791
ContributorsMozart, Wolfgang Amadeus, 1756-1791 (Composer)
ContributorsMozart, Wolfgang Amadeus, 1756-1791 (Composer)
ContributorsMozart, Wolfgang Amadeus, 1756-1791 (Composer)
Description
Due to artificial selection, dogs have high levels of phenotypic diversity, yet, there appears to be low genetic diversity within individual breeds. Through their domestication from wolves, dogs have gone through a series of population bottlenecks, which has resulted in a reduction in genetic diversity, with a large amount of linkage disequilibrium and the persistence of deleterious mutations. This has led to an increased susceptibility to a multitude of diseases, including cancer. To study the effects of artificial selection and life history characteristics on the risk of cancer mortality, we collected cancer mortality data from four studies as well as the percent of heterozygosity, body size, lifespan and breed group for 201 dog breeds. We also collected specific types of cancer breeds were susceptible to and compared the dog cancer mortality patterns to the patterns observed in other mammals. We found a relationship between cancer mortality rate and heterozygosity, body size, lifespan as well as breed group. Higher levels of heterozygosity were also associated with longer lifespan. These results indicate larger breeds, such as Irish Water Spaniels, Flat-coated Retrievers and Bernese Mountain Dogs, are more susceptible to cancer, with lower heterozygosity and lifespan. These breeds are also more susceptible to sarcomas, as opposed to carcinomas in smaller breeds, such as Miniature Pinschers, Chihuahuas, and Pekingese. Other mammals show that larger and long-lived animals have decreased cancer mortality, however, within dog breeds, the opposite relationship is observed. These relationships could be due to the trade-off between cellular maintenance and growing fast and large, with higher expression of growth factors, such as IGF-1. This study further demonstrates the relationships between cancer mortality, heterozygosity, and life history traits and exhibits dogs as an important model organism for understanding the relationship between genetics and health.
ContributorsBalsley, Cassandra Sierra (Author) / Maley, Carlo (Thesis director) / Wynne, Clive (Committee member) / Tollis, Marc (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Mammary gland development in humans during puberty involves the enlargement of breast tissue, but this is not true in non-human primates. To identify potential causes of this difference, I examined variation in substitution rates across genes related to mammary development. Genes undergoing purifying selection show slower-than-average substitution rates, while genes undergoing positive selection show faster rates. These may be related to the difference between humans and other primates. Three genes were found to be accelerated were FOXF1, IGFBP5, and ATP2B2, but only the latter one was found in humans and it seems unlikely that it would be related to the differences between mammary gland development at puberty between humans and non-human primates.
ContributorsArroyo, Diana (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Schwartz, Rachel (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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) 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
Description
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
Description
Hepatocellular carcinoma (HCC) is a type of liver cancer common in Sub-Saharan Africa and South East Asian countries. Each year more than 700,000 new cases and more than 600,000 deaths are recorded worldwide due to HCC. According to the American Cancer Society HCC is ranked the 5th most common cancer worldwide with a male:female susceptibility ratio ranging between 2:1 and 8:1. HCC risk factors include lifestyle behaviors, such as persistent alcohol abuse and smoking, prolonged exposure to aflatoxins, chronic viral hepatitis infections, inherited metabolic diseases and non-alcoholic fatty liver diseases. To understand the genetic effects underlying sex-bias in HCC, it is necessary to include the sex chromosomes in genomics analyses. X and Y chromosomes are often discluded in genomics studies because of the technical and analytical challenges: sequence homology. The purpose of this thesis is to analyze the effects of sex chromosome complement aware read mapping to germline variant calling. 10 male and 10 female tumor adjacent samples from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA LIHC) cohort were processed using sex-aware and default reference and the concordance of the two approaches was examined. We detected a higher disconcordance of 0.69% on variants called on the X chromosome and a disconcordance of 0.51% on variants called on the Y chromosomes for the reference and alternative alleles respectively compared to autosomes. Variants called on the REF/ALT genotypes had a disconcordances of 1.00%, 1.05%, 1.35% and 12.34% for the autosomes, chromosome 7, the X, and the Y chromosome, respectively. At the end of the project we concluded that the generated datasets showed the effect of sex-aware read mapping on variant calling. Though the data did not show the sites that can be called as variants in one dataset but not in the other, rather the concordance looked at sites that were called as variants in both data sets.
ContributorsPhiri, Lovender Teresa (Co-author) / Phiri, Lovender (Co-author) / Wilson Sayres, Melissa (Thesis director) / Buetow, Kenneth (Committee member) / Natri, Heini (Committee member) / School of Life Sciences (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
This creative thesis project aimed to create career development resources that School of Life Sciences majors could use to enhance their college experience, expand the breadth of relevant career options for School of Life Sciences majors, and confront and divert career problems through the implementation of these career development resources. Students encounter career problems when their intention and action diverge. These career problems may cause a student to stop their pursuit of a given career, change majors, or even stop schooling completely. It is the objective of this project to help resolve these career problems by introducing a career development resource flyer that educates the student about a given career, provides coursework to guide a student towards this career path, familiarize students with extracurricular efforts necessary for this position, propose valuable resources that the student can utilize to learn more about the career, and offer a question and answer portion for further career and professional understanding. In order to create these career development resource flyers a variety of professionals, both with and without relationships with Arizona State University were contacted and interviewed. The answers gathered from these interviews were then utilized to create the career flyers. The project was successful in creating five distinct career development resource flyers, as well as a blank template with instructions to be used in the future by the School of Life Sciences. The career development resource flyers will be utilized by the School of Life Sciences advising staff for future exploratory majors, but is not limited to just these students. Aspirations are set to create an expansive reservoir of these resources for future generations of students to access in hopes that they will be better suited to find a career path that they are passionate about and be better prepared to attain.
ContributorsGallegos, Darius Sloan (Author) / Wilson Sayres, Melissa (Thesis director) / Downing, Virginia (Committee member) / DeNardo, Dale (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
With the rising data output and falling costs of Next Generation Sequencing technologies, research into data compression is crucial to maintaining storage efficiency and costs. High throughput sequencers such as the HiSeqX Ten can produce up to 1.8 terabases of data per run, and such large storage demands are even more important to consider for institutions that rely on their own servers rather than large data centers (cloud storage)1. Compression algorithms aim to reduce the amount of space taken up by large genomic datasets by encoding the most frequently occurring symbols with the shortest bit codewords and by changing the order of the data to make it easier to encode. Depending on the probability distribution of the symbols in the dataset or the structure of the data, choosing the wrong algorithm could result in a compressed file larger than the original or a poorly compressed file that results in a waste of time and space2. To test efficiency among compression algorithms for each file type, 37 open-source compression algorithms were used to compress six types of genomic datasets (FASTA, VCF, BCF, GFF, GTF, and SAM) and evaluated on compression speed, decompression speed, compression ratio, and file size using the benchmark test lzbench. Compressors that outpreformed the popular bioinformatics compressor Gzip (zlib -6) were evaluated against one another by ratio and speed for each file type and across the geometric means of all file types. Compressors that exhibited fast compression and decompression speeds were also evaluated by transmission time through variable speed internet pipes in scenarios where the file was compressed only once or compressed multiple times.
ContributorsHowell, Abigail (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Taylor, Jay (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05