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- Creators: School of Life Sciences
- Creators: Tollis, Marc
Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
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
Dogs' health and wellbeing is of great importance to their owners. The most common nutritional problem for pet dogs is obesity, with 22-40% of pet dogs being classified as overweight or obese. With many adverse health effects associated with obesity, this is a major concern for owners and veterinarians. The degree to which dogs enjoy consuming certain foods can have substantial implications for their body weight, so it is important to understand which aspects of foods make them appealing to dogs. This study aimed to determine whether nutritional aspects of commercial dog foods predict dogs' preferences for those foods. It was found that consumption preference is positively correlated with protein content (p < .001), therefore implying that the protein content of commercial dry dog foods may predict dogs' consumption preferences. Consumption preferences were not predicted by other available measures of food content or caloric value. Dogs' preference for foods high in protein content may be due to the satiating effect of protein. Since foods high in protein both reduce the amount of energy consumed and are found to be palatable to dogs, high-protein dog foods may offer a way for dog food manufacturers, veterinarians, and pet owners to combat obesity in pet dogs.
ContributorsPrevost, Emily Danielle (Author) / Wynne, Clive (Thesis director) / Hall, Nathaniel (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
This thesis explores how we can harness new technology to improve our relationship with companion animals and promote shelter animal welfare. The study looked into using the photo-sharing application Instagram to increase adoption rates at the Arizona Animal Welfare League & SPCA. An Instagram page was created and managed for the shelter, and data was collected regarding the impact the page had on adoption rates. The results were mixed, but overall it was determined that the Instagram page has unique value for the shelter.
ContributorsBautista-Hobin, Elena Maria (Author) / Minteer, Ben (Thesis director) / Ellison, Karin (Committee member) / Morefield, Michael (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Valley Fever, also known as coccidioidomycosis, is a respiratory disease that affects 10,000 people annually, primarily in Arizona and California. Due to a lack of gene annotation, diagnosis and treatment of Valley Fever is severely limited. In turn, gene annotation efforts are also hampered by incomplete genome sequencing. We intend to use proteogenomic analysis to reannotate the Coccidioides posadasii str. Silveira genome from protein-level data. Protein samples extracted from both phases of Silveira were fragmented into peptides, sequenced, and compared against databases of known and predicted proteins sequences, as well as a de novo six-frame translation of the genome. 288 unique peptides were located that did not match a known Silveira annotation, and of those 169 were associated with another Coccidioides strain. Additionally, 17 peptides were found at the boundary of, or outside of, the current gene annotation comprising four distinct clusters. For one of these clusters, we were able to calculate a lower bound and an estimate for the size of the gap between two Silveira contigs using the Coccidioides immitis RS transcript associated with that cluster's peptides \u2014 these predictions were consistent with the current annotation's scaffold structure. Three peptides were associated with an actively translated transposon, and a putative active site was located within an intact LTR retrotransposon. We note that gene annotation is necessarily hindered by the quality and level of detail in prior genome sequencing efforts, and recommend that future studies involving reannotation include additional sequencing as well as gene annotation via proteogenomics or other methods.
ContributorsSherrard, Andrew (Author) / Lake, Douglas (Thesis director) / Grys, Thomas (Committee member) / Mitchell, Natalie (Committee member) / Computing and Informatics Program (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Bats (order Chiroptera) are the longest lived mammals for their size, with particularly extreme longevity evolving in the family Vespertilionidae, or vesper bats. Because of this, researchers have proposed using bats to study ageing and cancer suppression. Here, we study gene duplications across mammalian genomes and show that, similar to previous findings in elephants, bats have experienced duplications of the tumor suppressor gene TP53, including five genomic copies in the genome of the little brown bat (Myotis lucifugus) and two copies in Brandt's bat (Myotis brandtii). These species can live 37 and 41 years, respectively, despite having an adult body mass of only ~7 grams. We use evolutionary genetics and next generation sequencing approaches to show that positive selection has acted on the TP53 locus across bats, and two recently duplicated TP53 gene copies in the little brown bat are both highly conserved and expressed, suggesting they are functional. We also report an extraordinary genomic copy number expansion of the tumor suppressor gene FBXO31 in the common ancestor of vesper bats which accelerated in the Myotis lineage, leading to 34\u201457 copies and the expression of 20 functional FBXO31 homologs in Brandt's bat. As FBXO31 directs the degradation of MDM2, which is a negative regulator of TP53, we suggest that increased expression of both FBXO31 and TP53 may be related to an enhanced DNA-damage response to genotoxic stress brought on by long lifespans and rapid metabolic rates in bats.
ContributorsSchneider-Utaka, Aika Kunigunda (Author) / Maley, Carlo (Thesis director) / Wilson Sayres, Melissa (Committee member) / Tollis, Marc (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Alzheimer's disease affects a large number of Americans every year, and research on the causes and possible prevention continues to increase. Alzheimer's disease is a form of dementia that causes problems with memory, thinking, and behavior and is thought to be caused by beta-amyloid plaques that form in the brain. In recent years, dogs have been used more and more as an animal model looking at Alzheimer's disease and cognitive dysfunction. Dogs serve as a reliable animal model because effected dogs naturally form the same beta-amyloid plaques that affected humans do as they age. Previous research has shown that older dogs perform worse on various memory tasks than do younger dogs, however researchers have struggled to find a test for dog cognitive dysfunction that is brief and can be performed in the home. The current study aimed to find a brief memory task that requires few materials, but is still reliable. The results of this study do not support the hypothesis that older dogs would perform worse than younger dogs if tested to find a treat with varying time delays of 15, 30, and 45 seconds. The results of this experiment showed a main effect of age (F = 8.40, d.f. 1, 19, p < 0.01) and delay (F = 15.14, d.f. 2, 30, p < 0.01), but age-delay interaction was not significant (F = 2.53, d.f. 2, 30, p = 0.09). Future studies should be performed using a larger sample size and this same protocol to attempt to raise the participation level of the dogs.
ContributorsZimmerman, Megan Renee (Author) / Wynne, Clive (Thesis director) / Bimonte-Nelson, Heather (Committee member) / Department of Psychology (Contributor) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
A handheld metal cricket noisemaker known as a "clicker" is often used in dog training to teach dogs new behaviors; however, evidence for the superior efficacy of clickers as opposed to providing solely primary reinforcement or other secondary reinforcers in the acquisition of novel behavior in dogs is almost entirely anecdotal. We sought to determine under what circumstances a clicker may result in acquisition of a novel behavior to a higher level when compared to other potential reinforcement methods. In Experiment 1, three groups of 30 dogs each were trained to emit a novel sit and stay behavior with either the delivery of food alone, a verbal marker with food, or a clicker and food. The group that received only a primary reinforcer reached a significantly higher criterion of training than the group trained with a verbal secondary reinforcer. Performance of the group experiencing a clicker secondary reinforcer was intermediate between the other two groups, but not significantly different from either. In Experiment 2, three different groups of 25 dogs each were shaped to emit a nose targeting behavior and then perform that behavior at increasing distances from the experimenter using the same three methods of positive reinforcement used in Experiment 1. No statistically significant differences between the groups were found. Overall, the findings suggest that both clickers and other forms of positive reinforcement can be used successfully in training a dog to perform a novel behavior.
ContributorsGilchrist, Rachel (Author) / Wynne, Clive (Thesis director) / Conrad, Cheryl (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Dogs in animal shelters are subjected to a number of stressors during their stay, including barking which can reach 120 dB. Music has been suggested as a way to reduce this stress, however, the properties of music that result in reduced stress behavior have not been examined. An affective response to music, like that found in humans, is unlikely due to human higher cognitive function. Masking, reducing the magnitude of volume change with the presence of another sound, is one property that may be responsible for this observed stress reduction. Using white and pink noise, we examined the effects of auditory masking on stress behaviors in shelter dogs. Overall, we observed no difference in the amount of sitting, lying, head resting, or barking between the control and treatment conditions. Limitations and future directions of studies are listed.
ContributorsRedmond, Domenic Xavier Wendell (Author) / Wynne, Clive (Thesis director) / Glenberg, Arthur (Committee member) / Steele, Kenneth (Committee member) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Damage to the central nervous system due to spinal cord or traumatic brain injury, as well as degenerative musculoskeletal disorders such as arthritis, drastically impact the quality of life. Regeneration of complex structures is quite limited in mammals, though other vertebrates possess this ability. Lizards are the most closely related organism to humans that can regenerate de novo skeletal muscle, hyaline cartilage, spinal cord, vasculature, and skin. Progress in studying the cellular and molecular mechanisms of lizard regeneration has previously been limited by a lack of genomic resources. Building on the release of the genome of the green anole, Anolis carolinensis, we developed a second generation, robust RNA-Seq-based genome annotation, and performed the first transcriptomic analysis of tail regeneration in this species. In order to investigate gene expression in regenerating tissue, we performed whole transcriptome and microRNA transcriptome analysis of regenerating tail tip and base and associated tissues, identifying key genetic targets in the regenerative process. These studies have identified components of a genetic program for regeneration in the lizard that includes both developmental and adult repair mechanisms shared with mammals, indicating value in the translation of these findings to future regenerative therapies.
ContributorsHutchins, Elizabeth (Author) / Kusumi, Kenro (Thesis advisor) / Rawls, Jeffrey A. (Committee member) / Denardo, Dale F. (Committee member) / Huentelman, Matthew J. (Committee member) / Arizona State University (Publisher)
Created2015