Matching Items (101)
168531-Thumbnail Image.png
Description
Understanding why animals form social groups is a fundamental aim of sociobiology. To date, the field has been dominated by studies of kin groups, which have emphasized indirect fitness benefits as key drivers of grouping among relatives. Nevertheless, many animal groups are comprised of unrelated individuals. These cases provide unique

Understanding why animals form social groups is a fundamental aim of sociobiology. To date, the field has been dominated by studies of kin groups, which have emphasized indirect fitness benefits as key drivers of grouping among relatives. Nevertheless, many animal groups are comprised of unrelated individuals. These cases provide unique opportunities to illuminate drivers of social evolution beyond indirect fitness, especially ecological factors. This dissertation combines behavioral, physiological, and ecological approaches to explore the conditions that favor group formation among non-kin, using as a model the facultatively social carpenter bee, Xylocopa sonorina. Using behavioral and genetic techniques, I found that nestmates in this species are often unrelated, and that non-kin groups form following extensive inter-nest migration.Group living may arise as a strategy to mitigate constraints on available breeding space. To test the hypothesis that nest construction is prohibitively costly for carpenter bees, I measured metabolic rates of excavating bees and used imaging techniques to quantify nest volumes. From these measurements, I found that nest construction is highly energetically costly, and that bees who inherit nests through social queuing experience substantial energetic savings. These costs are exacerbated by limitations on the reuse of existing nests. Using repeated CT scans of nesting logs, I examined changes in nest architecture over time and found that repeatedly inherited tunnels become indefensible to intruders, and are subsequently abandoned. Together, these factors underlie intense competition over available breeding space. The imaging analysis of nesting logs additionally revealed strong seasonal effects on social strategy, with social nesting dominating during winter. To test the hypothesis that winter social nesting arises from intrinsic physiological advantages of grouping, I experimentally manipulated social strategy in overwintering bees. I found that social bees conserve heat and body mass better than solitary bees, suggesting fitness benefits to grouping in cold, resource-scarce conditions. Together, these results suggest that grouping in X. sonorina arises from dynamic strategies to maximize direct fitness in response to harsh and/or competitive conditions. These studies provide empirical insights into the ecological conditions that favor non-kin grouping, and emphasize the importance of ecology in shaping sociality at its evolutionary origins.
ContributorsOstwald, Madeleine (Author) / Fewell, Jennifer H (Thesis advisor) / Amdam, Gro (Committee member) / Harrison, Jon (Committee member) / Pratt, Stephen (Committee member) / Kapheim, Karen (Committee member) / Arizona State University (Publisher)
Created2022
171582-Thumbnail Image.png
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

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
190974-Thumbnail Image.png
Description
Advancements in high-throughput biotechnologies have generated large-scale multi-omics datasets encompassing diverse dimensions such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and phenomics. Traditionally, statistical and machine learning-based approaches utilize single-omics data sources to uncover molecular signatures, dissect complicated cellular mechanisms, and predict clinical results. However, to capture the multifaceted pathological

Advancements in high-throughput biotechnologies have generated large-scale multi-omics datasets encompassing diverse dimensions such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and phenomics. Traditionally, statistical and machine learning-based approaches utilize single-omics data sources to uncover molecular signatures, dissect complicated cellular mechanisms, and predict clinical results. However, to capture the multifaceted pathological mechanisms, integrative multi-omics analysis is needed that can provide a comprehensive picture of the disease. Here, I present three novel approaches to multi-omics integrative analysis. I introduce a single-cell integrative clustering method, which leverages multi-omics to enhance the resolution of cell subpopulations. Applied to a Cellular Indexing of Transcriptomes and Epitopes (CITE-Seq) dataset from human Acute Myeloid Lymphoma (AML) and control samples, this approach unveiled nuanced cell populations that otherwise remain elusive. I then shift the focus to a computational framework to discover transcriptional regulatory trios in which a transcription factor binds to a regulatory element harboring a genetic variant and subsequently differentially regulates the transcription level of a target gene. Applied to whole-exome, whole-genome, and transcriptome data of multiple myeloma samples, this approach discovered synergetic cis-acting and trans-acting regulatory elements associated with tumorigenesis. The next part of this work introduces a novel methodology that leverages the transcriptome and surface protein data at the single-cell level produced by CITE-Seq to model the intracellular protein trafficking process. Applied to COVID-19 samples, this approach revealed dysregulated protein trafficking associated with the severity of the infection.
ContributorsMudappathi, Rekha (Author) / Liu, Li (Thesis advisor) / Dinu, Valentin (Committee member) / Sun, Zhifu (Committee member) / Arizona State University (Publisher)
Created2023
190882-Thumbnail Image.png
Description
Speciation, or the process by which one population diverges into multiple populations that can no longer interbreed with each other, has brought about the incredible diversity of life. Mechanisms underlying this process can be more visible in the early stages of the speciation process. The mechanisms that restrict gene flow

Speciation, or the process by which one population diverges into multiple populations that can no longer interbreed with each other, has brought about the incredible diversity of life. Mechanisms underlying this process can be more visible in the early stages of the speciation process. The mechanisms that restrict gene flow in highly mobile species with no absolute barriers to dispersal, especially marine species, are understudied. Similarly, human impacts are reshaping ecosystems globally, and we are only just beginning to understand the implications of these rapid changes on evolutionary processes. In this dissertation, I investigate patterns of speciation and evolution in two avian clades: a genus of widespread tropical seabirds (boobies, genus Sula), and two congeneric passerine species in an urban environment (cardinals, genus Cardinalis). First, I explore the prevalence of gene flow across land barriers within species and between sympatric species in boobies. I found widespread evidence of gene flow over all land barriers and between 3 species pairs. Next, I compared the effects of urbanization on the spatial distributions of two cardinal species, pyrrhuloxia (Cardinalis sinuatus) and northern cardinals (Cardinalis cardinalis), in Tucson, Arizona. I found that urbanization has different effects on the spatial distributions of two closely related species that share a similar environmental niche, and I identified environmental variables that might be driving this difference. Then I tested for effects of urbanization on color and size traits of these two cardinal species. In both of these species, urbanization has altered traits involved in signaling, heat tolerance, foraging, and maneuverability. Finally, I tested for evidence of selection on the urban populations of both cardinal species and found evidence of both parallel selection and introgression between the species, as well as selection on different genes in each species. The functions of the genes that experienced positive selection suggest that light at night, energetics, and air pollution may have acted as strong selective pressures on these species in the past. Overall, my dissertation emphasizes the role of introgression in the speciation process, identifies environmental stressors faced by wildlife in urban environments, and characterizes their evolutionary responses to those stressors.
ContributorsJackson, Daniel Nelson (Author) / McGraw, Kevin J (Thesis advisor) / Amdam, Gro (Committee member) / Sweazea, Karen (Committee member) / Taylor, Scott (Committee member) / Arizona State University (Publisher)
Created2023
Description
The objective of this meta-analysis is to holistically evaluate the existing body of literature on the anti-neoplastic potential of snake and bee venom. In recent years, venom-based therapeutics have emerged as a promising solution for combating cancer, generating a notable rise in publications on the topic. Consequently, this comprehensive study

The objective of this meta-analysis is to holistically evaluate the existing body of literature on the anti-neoplastic potential of snake and bee venom. In recent years, venom-based therapeutics have emerged as a promising solution for combating cancer, generating a notable rise in publications on the topic. Consequently, this comprehensive study aims to assess the current state of research and identify trends that may guide future investigations. Following the guidelines established by PRISMA, a total sample of 26 research papers were extracted from the electronic databases, PubMed and Scopus. These papers were categorized based on their publication dates, and research questions were formulated regarding three main topics: venom type, cancer-targeting mechanism, and cancer type. Statistical analysis of the research questions was performed using 2x2 contingency tables for a chi-square test. The results of the analysis reveal a statistically significant increase in publications focused on cell death mechanisms and breast cancer in recent years. This increase in publications reflects a growing interest in the potential for venom to induce apoptosis in cancer cells and target the unique biological properties of breast cancer. Overall, this meta-analysis offers insight into the evolving sphere of venom-based cancer research, providing a glimpse into the potential trajectory of this field.
ContributorsHolder, Marina (Author) / Amdam, Gro (Thesis director) / Mana, Miyeko (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Economics Program in CLAS (Contributor)
Created2023-12
Description

Insect pheromones are crucial for survival and reproduction because they influence insect behavior, communication, and interactions within and outside the colony. Honey bees (Apis mellifera) have one of the most complex pheromonal communication systems. One pheromone, known as Queen Mandibular Pheromone (QMP), is released by the queen bee to regulate

Insect pheromones are crucial for survival and reproduction because they influence insect behavior, communication, and interactions within and outside the colony. Honey bees (Apis mellifera) have one of the most complex pheromonal communication systems. One pheromone, known as Queen Mandibular Pheromone (QMP), is released by the queen bee to regulate physiology, behavior, and gene expression in the female worker caste. The pheromone acts as a signal of queen presence that suppresses worker reproduction. In the absence of reproduction, young workers focus on taking care of the queen and larvae, known as nurse tasks, while older workers forage. In nurse bees, QMP has fundamental physiological impacts, including increasing abdominal lipid stores and increasing the protein content of hypopharyngeal glands (HPG). The HPG are worker-specific glands that can synthesize royal jelly used in colony nourishment. In workers, larger HPG signifies the ability to secrete royal jelly, while shrunken glands are characteristic of foragers that do not make jelly. While it is known that QMP increases abdominal lipid stores, the underlying mechanism is unclear: Does the pheromone simply make workers consume more pollen which provides lipids and protein, or does QMP also increase lipogenesis? In this study, I measured abdominal lipogenesis as fatty acid synthase (FAS) activity and monitored abdominal protein content and HPG size in caged, nurse-aged worker bees. In cages, workers were exposed to QMP or not, and they were provided with a lipid less diet in a full factorial design experiment. I found that QMP did not influence abdominal FAS activity or protein, but significantly increased HPG size. The data also revealed a significant positive correlation between abdominal protein and HPG size. My results do not support the idea that QMP modulates lipogenesis in worker bees, but my data can be interpreted to reflect that QMP mobilizes abdominal protein for the production of jelly in the HPG. This finding is in line with a previous study revealing a role of honey bee Brood Pheromone in mobilization of a major protein used in jelly production. Overall, my results support a fundamental role of QMP in worker metabolic processes associated with colony nourishment.

ContributorsOreshkova, Angela (Author) / Amdam, Gro (Thesis director) / Scofield, Sebastian (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor) / School of Life Sciences (Contributor)
Created2023-05
Description

Although social hierarchies are commonly found all throughout nature, the underlying mechanisms of their formation are still ambiguous. Hierarchies form through a wide range of interactions between subordinate and dominant individuals, and the ponerine ant Harpegnathos saltator provides the perfect model to explore such dominance behaviors. When the queen is

Although social hierarchies are commonly found all throughout nature, the underlying mechanisms of their formation are still ambiguous. Hierarchies form through a wide range of interactions between subordinate and dominant individuals, and the ponerine ant Harpegnathos saltator provides the perfect model to explore such dominance behaviors. When the queen is absent or her fecundity levels drop below a certain threshold, H. saltator workers undergo a dominance tournament, in which several individuals emerge as gamergates, reproductive workers that are not queens. During this tournament, several characterizable dominance behaviors are exhibited (antennal dueling, dominance biting, and policing), which can be used to study the behavioral and social dynamics in the formation of a reproductive hierarchy. Colonies of 15, 30, 60, and 120 workers were created in duplicate, and their dominance tournaments were recorded to study how these interactions impact gamergate establishment. Rather than studying these behaviors as isolated incidents, responses to policing behaviors (timid, neutral, or aggressive) and their duration were recorded along with the frequency of dueling. Three groups were determined: dueling future gamergates (DFG), dueling future non-gamergates (DFNG) and non-dueling individuals (ND). DFNG received many more policing attacks and the duration of these interactions lasted much longer. DFG consistently exhibited the most dueling. Timid and neutral responses were more common than aggressive responses, perhaps due to energy conversation purposes. Peaks in dueling correspond to peaks in policing, highlighting the dynamic behavioral interactions necessary for the formation of a reproductive hierarchy.

ContributorsOlivas, Victoria (Author) / Liebig, Juergen (Thesis director) / Shaffer, Zachary (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / School of International Letters and Cultures (Contributor)
Created2023-05
Description
A genome wide association study (GWAS) of treatment outcomes for citalopram and escitalopram, two frontline SSRI treatments for Major Depressive Disorder, was conducted with 529 subjects on an imputed dataset. While no variants of genome-wide significance were identified, various potentially interesting variants were identified that warrant further exploration. These findings

A genome wide association study (GWAS) of treatment outcomes for citalopram and escitalopram, two frontline SSRI treatments for Major Depressive Disorder, was conducted with 529 subjects on an imputed dataset. While no variants of genome-wide significance were identified, various potentially interesting variants were identified that warrant further exploration. These findings have the potential to elucidate novel mechanisms underlying drug response for SSRIs. This work will be continued further, with machine learning and deep learning analyses to perform non-linear analyses and employing a biologist or geneticist to provide more specialized knowledge for interpretation of results.
ContributorsLeiter-Weintraub, Ethan (Author) / Dinu, Valentin (Thesis director) / Scotch, Matthew (Committee member) / Barrett, The Honors College (Contributor) / Dean, W.P. Carey School of Business (Contributor) / College of Health Solutions (Contributor) / School of Life Sciences (Contributor)
Created2024-05
168722-Thumbnail Image.png
Description
Vitamin D is a nutrient that is obtained through the diet and vitamin D supplementation and created from exposure to Ultraviolet B (UVB) radiation. While there are many factors that determine how much serum 25-hydroxyvitamin D (25(OH)D) concentration is in the body, little is known about how genetic variation in

Vitamin D is a nutrient that is obtained through the diet and vitamin D supplementation and created from exposure to Ultraviolet B (UVB) radiation. While there are many factors that determine how much serum 25-hydroxyvitamin D (25(OH)D) concentration is in the body, little is known about how genetic variation in vitamin D-related genes influences serum 25(OH)D concentrations resulting from daily vitamin D intake and exposure to direct sunlight. Previous studies show that common genetic variants rs10741657 (CYP2R1), rs4588 (GC), rs228678 (GC), and rs4516035 (VDR) act as moderators and alter the effect of outdoor time and vitamin D intake on serum 25(OH)D concentrations. The objective of this study is to analyze the associations between serum 25(OH)D concentrations resulting from outdoor time and vitamin D intake, and genetic risk scores (GRS) established from previous studies involving single nucleotide polymorphisms (SNP) located on or near genes involving vitamin D synthesis, transport, activation, and degradation in 102 Hispanic and Non-Hispanic adults in the San Diego County, California. This study is a secondary analysis of data from the Community of Mine study. Global Positioning System (GPS) data collected by the Qstarz GPS device worn by each participant was used to measure outdoor time, a proxy measurement for sun exposure time. Vitamin D intake was assessed using two 24-hour dietary recalls. Blood samples were measured for serum 25(OH)D concentrations. DNA was provided to assess each participant for the various genetic variants. Adjusted analyses of the GRS and serum 25(OH)D concentrations showed that individuals with high GRS (3-4) had lower serum 25(OH)D concentrations than individuals with low GRS (0-2) for both Nissen GRS and Rivera-Paredez GRS.
ContributorsAnderson, Heather Ray (Author) / Sears, Dorothy (Thesis advisor) / Alexon, Christy (Committee member) / Dinu, Valentin (Committee member) / Jankowska, Marta (Committee member) / Arizona State University (Publisher)
Created2022
Description

Maternal morbidity and mortality rates in the United States continues to rise, with a wide range of contributing factors such as mental illness, cardiovascular disease and systemic inequality. This metastudy provides a holistic view of the research that has been published on the issue of U.S. maternal healthcare from 2000-2022.

Maternal morbidity and mortality rates in the United States continues to rise, with a wide range of contributing factors such as mental illness, cardiovascular disease and systemic inequality. This metastudy provides a holistic view of the research that has been published on the issue of U.S. maternal healthcare from 2000-2022. The patterns of publications on specific topics over time can tell us what is perceived as a current major cause by physicians, public leaders, researchers, and the public. A deeper dive into systemic inequality as a cause of maternal morbidity and mortality highlights it as a major contributor to these high rates, but that progress is slowly being made through the implementation of detection and prevention tactics, as well as accessible prenatal programs and care.

ContributorsRettig, Lelia (Author) / Amdam, Gro (Thesis director) / Bang, Christofer (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor)
Created2023-05