Matching Items (457)
Filtering by
- Language: English
- Creators: Ira A. Fulton Schools of Engineering
Description
This research project investigated known and novel differential genetic variants and their associated molecular pathways involved in Type II diabetes mellitus for the purpose of improving diagnosis and treatment methods. The goal of this investigation was to 1) identify the genetic variants and SNPs in Type II diabetes to develop a gene regulatory pathway, and 2) utilize this pathway to determine suitable drug therapeutics for prevention and treatment. Using a Gene Set Enrichment Analysis (GSEA), a set of 1000 gene identifiers from a Mayo Clinic database was analyzed to determine the most significant genetic variants related to insulin signaling pathways involved in Type II Diabetes. The following genes were identified: NRAS, KRAS, PIK3CA, PDE3B, TSC1, AKT3, SOS1, NEU1, PRKAA2, AMPK, and ACC. In an extensive literature review and cross-analysis with Kegg and Reactome pathway databases, novel SNPs located on these gene variants were identified and used to determine suitable drug therapeutics for treatment. Overall, understanding how genetic mutations affect target gene function related to Type II Diabetes disease pathology is crucial to the development of effective diagnosis and treatment. This project provides new insight into the molecular basis of the Type II Diabetes, serving to help untangle the regulatory complexity of the disease and aid in the advancement of diagnosis and treatment. Keywords: Type II Diabetes mellitus, Gene Set Enrichment Analysis, genetic variants, KEGG Insulin Pathway, gene-regulatory pathway
ContributorsBucklin, Lindsay (Co-author) / Davis, Vanessa (Co-author) / Holechek, Susan (Thesis director) / Wang, Junwen (Committee member) / Nyarige, Verah (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
An intimate view of the unique architecture of Harpegnathos saltwater nest using aluminum nest casts
Description
Abstract:
Given the incredible variety in ant nest architecture, this experiment sought to evaluate how the nest architecture of Harpegnathos saltator differs from other species’ nests. To achieve the ability to evaluate the structure of H. saltator nest, we created experimental colonies varying in size from 20, 40, 60, 80 workers of Harpegnathos saltator in five-gallon buckets of sand and then allowing the colonies to grow for four months and twelve days. To create the nest casts, we developed a charcoal kiln out of a galvanized trash can and used a ceramic crucible to hold the aluminum being melted. Using molten aluminum to create nest casts of each colony produced, we obtained three poorly developed nests and one decent nest. The decent nest cast, the 80 worker H. saltator nest, was lacking key features of H. saltator nests that have been excavated in the field. However, they do share many of the same structures such as the shaping of the chambers. The ability of the experimental colonies to excavate the soil provided in the buckets to them was likely halted by poor penetration of water into superficial layers of the soil, thus making the soil too difficult to excavate and form the structures that are key elements of the species nest architecture. Despite these key challenges which the colonies faced, the 80-worker colony showed extensive vertical development and did display features associated with natural H. saltator colonies. Thus, given the display of some key features associated with characteristics of the H. saltator nests excavated in the field, it can be said that with some modification to technique that this is a viable avenue for future study of nest architecture and colony structure.
Given the incredible variety in ant nest architecture, this experiment sought to evaluate how the nest architecture of Harpegnathos saltator differs from other species’ nests. To achieve the ability to evaluate the structure of H. saltator nest, we created experimental colonies varying in size from 20, 40, 60, 80 workers of Harpegnathos saltator in five-gallon buckets of sand and then allowing the colonies to grow for four months and twelve days. To create the nest casts, we developed a charcoal kiln out of a galvanized trash can and used a ceramic crucible to hold the aluminum being melted. Using molten aluminum to create nest casts of each colony produced, we obtained three poorly developed nests and one decent nest. The decent nest cast, the 80 worker H. saltator nest, was lacking key features of H. saltator nests that have been excavated in the field. However, they do share many of the same structures such as the shaping of the chambers. The ability of the experimental colonies to excavate the soil provided in the buckets to them was likely halted by poor penetration of water into superficial layers of the soil, thus making the soil too difficult to excavate and form the structures that are key elements of the species nest architecture. Despite these key challenges which the colonies faced, the 80-worker colony showed extensive vertical development and did display features associated with natural H. saltator colonies. Thus, given the display of some key features associated with characteristics of the H. saltator nests excavated in the field, it can be said that with some modification to technique that this is a viable avenue for future study of nest architecture and colony structure.
ContributorsAnderson, Clayton Edward (Author) / Liebig, Juergen (Thesis director) / Pratt, Stephen (Committee member) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
This research project investigated known and novel differential genetic variants and their associated molecular pathways involved in Type II diabetes mellitus for the purpose of improving diagnosis and treatment methods. The goal of this investigation was to 1) identify the genetic variants and SNPs in Type II diabetes to develop a gene regulatory pathway, and 2) utilize this pathway to determine suitable drug therapeutics for prevention and treatment. Using a Gene Set Enrichment Analysis (GSEA), a set of 1000 gene identifiers from a Mayo Clinic database was analyzed to determine the most significant genetic variants related to insulin signaling pathways involved in Type II Diabetes. The following genes were identified: NRAS, KRAS, PIK3CA, PDE3B, TSC1, AKT3, SOS1, NEU1, PRKAA2, AMPK, and ACC. In an extensive literature review and cross-analysis with Kegg and Reactome pathway databases, novel SNPs located on these gene variants were identified and used to determine suitable drug therapeutics for treatment. Overall, understanding how genetic mutations affect target gene function related to Type II Diabetes disease pathology is crucial to the development of effective diagnosis and treatment. This project provides new insight into the molecular basis of the Type II Diabetes, serving to help untangle the regulatory complexity of the disease and aid in the advancement of diagnosis and treatment.
ContributorsDavis, Vanessa Brooke (Co-author) / Bucklin, Lindsay (Co-author) / Holechek, Susan (Thesis director) / Wang, Junwen (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Complex animal societies consist of a plethora of interactions between members. To successfully thrive they must be able to recognize members and their kin, and to understand how they do this we need sufficient and reliable methods of testing. Eusocial insects are especially good at recognizing their nestmates, but the exact mechanism or how well they can discriminate is unknown. Ants achieve nestmate recognition by identifying varying proportions of cuticular hydrocarbons. Previous studies have shown ants can be trained to discriminate between pairs of hydrocarbons. This study aims to compare two methodologies previously shown to demonstrate odor learning to identify which one is the most promising to use for future odor learning experiments. The two methods tested were adapted from Sharma et al. (2015) and Guerrieri and d’Ettorre (2010). The results showed that the Guerrieri method demonstrated learning better and was more reliable and faster than the Sharma method. The Guerrieri method should be used in future experiments regarding odor learning discrimination
ContributorsDavis, Cole (Author) / Liebig, Juergen (Thesis director) / Stephen, Pratt (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
Description
For colonies of ponerine ant species, sterility regulation after a founding queen's death is not totally achieved in the worker caste, and the possibility of sexual reproduction is opened to workers. The persisting survival of these colonies is dependent on capturing the optimal reproductive ratio; yet, an informational gap bounds the mechanisms detailing the selection of new reproductives and the suppression of ovarian development in rejected reproductives. We investigated the mechanisms of worker policing, one of the primary methods of ovarian suppression, through continuous video observation for a period of five days at the start of colony instability. Observations suggest policing in H. saltator is performed by a majority of a colony, including potential reproductives, and requires multiple events to fully discourage ovarian growth.
ContributorsChien, Jeffrey (Co-author) / Barat Ali, Fatima (Co-author) / Kang, Yun (Thesis director) / Liebig, Juergen (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Due to the widely accepted trend of urbanization displacing wildlife from their natural habitats and niches, many wildlife conservation organizations have sprouted up, even in Phoenix. Liberty Wildlife Foundation is one that rehabilitates avian wildlife. Several studies have mentioned an opposing theory: that urbanization helps conserve those species that have turned urban environments into a niche of their own. Since these wildlife conservation centers are localized in cities themselves, this brings into question these organizations' definitions of the term "wildlife." This study examined injury and recovery statistics to determine just how many of the patients admitted were conventional wildlife versus urban-dwelling city birds, and whether this classification had any effect on their likeliness of recovery and release. The data showed that out of over 130 species, a few key urban species contributed to an overwhelmingly large majority of injured birds admitted to the center in 2017; urban and non-urban birds, however, had relatively equal average release frequencies, demonstrating then that their likelihood of recovery was predominantly dependent on the injury borne by them.
ContributorsVirdee, Rishika Kaur (Author) / Liebig, Juergen (Thesis director) / Lynch, John (Committee member) / Haight, Kevin (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Insects have intricate systems they depend on for survival. They live in societies where every individual plays an important role. Ants are a great example of this observation. They are known for having structurally sound societies that ensure the livelihood of the colony. The ant species analyzed for this research, Harpegnathos saltator, portrays a structured colony and serves as a useful example of levels of hierarchy. In the colony of H. saltator, one can find a queen, gamergates, workers, and male ants living underground in Southern India. Recording and analyzing egg-laying rates are important in this study because of the amount of information it provides. It is used especially when observing the relationship among the gamergates in colonies with varying colony sizes. Three different methods were used to record the egg-laying rates, each providing insight into valuable information. Results show that the smaller colonies with fewer identified gamergates do share an equal amount of egg-laying. In larger colonies, it appears that there are more active identified gamergates than others. Egg-laying duration times are smaller in colonies with fewer gamergates. It is also found that the presence of brood does not affect egg-laying rates and reproductive inhibition could be a possibility based on two of the colonies observed F65 and F21. Based on the data found, a more active colony that attempts to maintain stability by demonstrating aggression may be affecting the reproduction of gamergates. Future work that would further strengthen the research and conclusions made would involve further observation of colonies, both large and small, with varying numbers of gamergates. More observation involving behavior among gamergates and workers would also be beneficial. Mathematical modeling could also be incorporated to create equations that could determine information about colonies based on size, number of gamergates, and egg-laying rates.
ContributorsMayoral, Alejandra (Author) / Kang, Yun (Thesis director) / Liebig, Juergen (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Insects are able to navigate their environments because they can detect hydrocarbons and volatile odors, but it is not clear which one has the fastest reaction when detected, or how much of a response can be produced due to either one. In order to determine which category of odorant is detected first as well as which one causes the highest response rate, data on electrophysiological responses from ants was analyzed. While the statistical tests can be done to understand and answer the questions raised by the study, there are various hydrocarbons and volatile odors that were not used in the data. Conclusive evidence only applies to the odorants used in the experiments.
ContributorsDarden, Jaelyn (Author) / Gerkin, Richard (Thesis director) / Liebig, Juergen (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
High throughput transcriptome data analysis like Single-cell Ribonucleic Acid sequencing (scRNA-seq) and Circular Ribonucleic Acid (circRNA) data have made significant breakthroughs, especially in cancer genomics. Analysis of transcriptome time series data is core in identifying time point(s) where drastic changes in gene transcription are associated with homeostatic to non-homeostatic cellular transition (tipping points). In Chapter 2 of this dissertation, I present a novel cell-type specific and co-expression-based tipping point detection method to identify target gene (TG) versus transcription factor (TF) pairs whose differential co-expression across time points drive biological changes in different cell types and the time point when these changes are observed. This method was applied to scRNA-seq data sets from a SARS-CoV-2 study (18 time points), a human cerebellum development study (9 time points), and a lung injury study (18 time points). Similarly, leveraging transcriptome data across treatment time points, I developed methodologies to identify treatment-induced and cell-type specific differentially co-expressed pairs (DCEPs). In part one of Chapter 3, I presented a pipeline that used a series of statistical tests to detect DCEPs. This method was applied to scRNA-seq data of patients with non-small cell lung cancer (NSCLC) sequenced across cancer treatment times. However, this pipeline does not account for correlations among multiple single cells from the same sample and correlations among multiple samples from the same patient. In Part 2 of Chapter 3, I presented a solution to this problem using a mixed-effect model. In Chapter 4, I present a summary of my work that focused on the cross-species analysis of circRNA transcriptome time series data. I compared circRNA profiles in neonatal pig and mouse hearts, identified orthologous circRNAs, and discussed regulation mechanisms of cardiomyocyte proliferation and myocardial regeneration conserved between mouse and pig at different time points.
ContributorsNyarige, Verah Mocheche (Author) / Liu, Li (Thesis advisor) / Wang, Junwen (Thesis advisor) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2022