Matching Items (52)
Description
“Tell It to the Frogs: Fukushima’s nuclear disaster and its impact on the Japanese Tree Frog” is a representation of the work from Giraudeau et. al’s “Carotenoid distribution in wild Japanese tree frogs (Hyla japonica) exposed to ionizing radiation in Fukushima.” This paper looked to see if carotenoid levels in

“Tell It to the Frogs: Fukushima’s nuclear disaster and its impact on the Japanese Tree Frog” is a representation of the work from Giraudeau et. al’s “Carotenoid distribution in wild Japanese tree frogs (Hyla japonica) exposed to ionizing radiation in Fukushima.” This paper looked to see if carotenoid levels in the tree frog’s vocal sac, liver, and blood were affected by radiation from Fukushima’s power plant explosion. Without carotenoids, the pigment that gives the frogs their orange color on their necks, their courtship practices would be impacted and would not be as able to show off their fitness to potential mates. The artwork inspired by this research displayed the tree frog’s degradation over time due to radiation, starting with normal life and ending with their death and open on the table. The sculptures also pinpoint where the carotenoids were being measured with a brilliant orange glaze. Through ceramic hand building, the artist created larger than life frogs in hopes to elicit curiosity about them and their plight. While the paper did not conclude any changes in the frog’s physiology after 18 months of exposure, there are still questions that are left unanswered. Why did these frogs not have any reaction? Could there be any effects after more time has passed? Is radiation leakage as big of a problem as previously thought? The only way to get the answers to these questions is to be aware of these amphibians, the circumstances that led them to be involved, and continued research on them and radiation.
ContributorsWesterfield, Savannah (Author) / Beiner, Susan (Thesis director) / McGraw, Kevin (Committee member) / School of Life Sciences (Contributor) / School of Art (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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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 develo

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
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Description
Among the most ornate animal traits in nature are the angle-dependent (i.e. iridescent) structural colors of many birds, beetles, and butterflies. Though we now have a solid understanding of the mechanisms, function, and evolution of these features in several groups, less attention has been paid to the potential for angle-dependent

Among the most ornate animal traits in nature are the angle-dependent (i.e. iridescent) structural colors of many birds, beetles, and butterflies. Though we now have a solid understanding of the mechanisms, function, and evolution of these features in several groups, less attention has been paid to the potential for angle-dependent reflectance in otherwise matte-appearing (i.e. not thought to be structurally colored) tissues. Here for the first time we describe non-iridescent angle-dependent coloration from the tail and wing feathers of several parrot species (Psittaciformes). We employed a novel approach \u2014 by calculating chromatic and achromatic contrasts (in just noticeable differences, JNDs) of straight and angled measurements of the same feather patch \u2014 to test for perceptually relevant angle-dependent changes in coloration on dorsal and ventral feather surfaces. We found, among the 15 parrot species studied, significant angle dependence for nearly all parameters (except chromatic JNDs on the ventral side of wing feathers). We then measured microstructural features on each side of feathers, including size and color of barbs and barbules, to attempt to predict interspecific variation in degree of angle-dependent reflectance. We found that hue, saturation, and brightness of feather barbs, barbule saturation, and barb:barbule coverage ratio were the strongest predictors of angle-dependent coloration. Interestingly, there was significant phylogenetic signal in only one of the seven angle-dependence models tested. These findings deepen our views on the importance of microscopic feather features in the production of directional animal coloration, especially in tissues that appear to be statically colored.
ContributorsReed, Steven Andrew (Co-author) / McGraw, Kevin (Thesis director) / Pratt, Stephen (Committee member) / Simpson, Richard (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal

Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We measured carotenoid-based plumage coloration and coccidian (Isospora spp) parasite burden in desert and city populations of house finches to examine urban impacts on male and female health and attractiveness. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected that pattern in this study for males. However, though city females are also less colorful than their rural counterparts, we found that rural females were more parasitized. Also, regardless of sex and unlike rural birds, more colorful birds in the city were more heavily infected with coccidia. These results show that urban environments can disrupt signal honesty in female animals and highlight the need for more studies on how cities affect disease and condition-dependent traits in both male and female animals.
ContributorsSykes, Brooke Emma (Author) / McGraw, Kevin (Thesis director) / Sweazea, Karen (Committee member) / Hutton, Pierce (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Description
There are two electrophysiological states of sleep in birds (rapid-eye-movement sleep [REM] and slow-wave sleep [SWS]), which have different functions and costs. REM improves memory consolidation, while SWS is neuro-restorative but also exposes the animal to more risk during this deep-sleep phase. Birds who sleep in more exposed microsites are known

There are two electrophysiological states of sleep in birds (rapid-eye-movement sleep [REM] and slow-wave sleep [SWS]), which have different functions and costs. REM improves memory consolidation, while SWS is neuro-restorative but also exposes the animal to more risk during this deep-sleep phase. Birds who sleep in more exposed microsites are known to invest proportionally less in SWS (presumably to ensure proper vigilance), but otherwise little else is known about the ecological or behavioral predictors of how much time birds devote to REM v. SWS sleep. In this comparative analysis, we examine how proportional time spent in SWS v. REM is related to brain mass and duration of the incubation period in adults. Brain mass and incubation period were chosen as predictors of sleep state investment because brain mass is positively correlated with body size (and may show a relationship between physical development and sleep) and incubation period can be a link used to show similarities and differences between birds and mammals (using mammalian gestation period). We hypothesized that (1) species with larger brains (relative to body size and also while controlling for phylogeny) would have higher demands for information processing, and possibly proportionally outweigh neuro-repair, and thus devote more time to REM and that (2) species with longer incubation periods would have proportionally more REM due to the extended time required for overnight predator vigilance (and not falling into deep sleep) while on the nest. We found, using neurophysiological data from literature on 27 bird species, that adults from species with longer incubation periods spent proportionally more time in REM sleep, but that relative brain size was not significantly associated with relative time spent in REM or SWS. We therefore provide evidence that mammalian and avian REM in response to incubation/gestation period have convergently evolved. Our results suggest that overnight environmental conditions (e.g. sleep site exposure) might have a greater effect on sleep parameters than gross morphological attributes.
ContributorsRaiffe, Joshua Sapell (Author) / McGraw, Kevin (Thesis director) / Deviche, Pierre (Committee member) / Hutton, Pierce (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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Humans have greatly altered the night-time photic environment via the production of artificial light at night (ALAN; e.g. street lights, car traffic, billboards, lit buildings). ALAN is problematic because it may significantly alter the seasonal/daily physiological rhythms or behaviors of animals. There has been considerable interest in the impacts of

Humans have greatly altered the night-time photic environment via the production of artificial light at night (ALAN; e.g. street lights, car traffic, billboards, lit buildings). ALAN is problematic because it may significantly alter the seasonal/daily physiological rhythms or behaviors of animals. There has been considerable interest in the impacts of ALAN on health in humans and lab animals, but most such work has centered on adults and we know comparatively little about effects on young animals. We exposed 3-week-old king quail (Excalfactoria chinensis) to a constant overnight blue-light regime for 6 weeks and assessed weekly bactericidal activity of plasma against Escherichia coli - a commonly employed metric of innate immunity in animals. We found that chronic ALAN exposure significantly increased immune function, and that this elevation in immune performance manifested at different developmental time points in males and females. These results counter the pervasive notion that overnight light exposure is universally physiologically harmful to diurnal organisms and indicate that ALAN can provide sex-specific, short-term immunological boosts to developing animals.
ContributorsSaini, Chandan (Author) / McGraw, Kevin (Thesis director) / Hutton, Pierce (Committee member) / Sweazea, Karen (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
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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
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Description
Beta-Amyloid(Aβ) plaques and tau protein tangles in the brain are now widely recognized as the defining hallmarks of Alzheimer’s disease (AD), followed by structural atrophy detectable on brain magnetic resonance imaging (MRI) scans. However, current methods to detect Aβ/tau pathology are either invasive (lumbar puncture) or quite costly and not

Beta-Amyloid(Aβ) plaques and tau protein tangles in the brain are now widely recognized as the defining hallmarks of Alzheimer’s disease (AD), followed by structural atrophy detectable on brain magnetic resonance imaging (MRI) scans. However, current methods to detect Aβ/tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (positron emission tomography (PET)). And one of the particular neurodegenerative regions is the hippocampus to which the influence of Aβ/tau on has been one of the research projects focuses in the AD pathophysiological progress. In this dissertation, I proposed three novel machine learning and statistical models to examine subtle aspects of the hippocampal morphometry from MRI that are associated with Aβ /tau burden in the brain, measured using PET images. The first model is a novel unsupervised feature reduction model to generate a low-dimensional representation of hippocampal morphometry for each individual subject, which has superior performance in predicting Aβ/tau burden in the brain. The second one is an efficient federated group lasso model to identify the hippocampal subregions where atrophy is strongly associated with abnormal Aβ/Tau. The last one is a federated model for imaging genetics, which can identify genetic and transcriptomic influences on hippocampal morphometry. Finally, I stated the results of these three models that have been published or submitted to peer-reviewed conferences and journals.
ContributorsWu, Jianfeng (Author) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Liang, Jianming (Committee member) / Wang, Junwen (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2022
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Description

Animals use diverse signal types (e.g. visual, auditory) to honestly advertise their genotypic and/or phenotypic quality to prospective mates or rivals. Behavioral displays and other dynamically updateable signals (e.g. songs, vibrations) can reliably reveal an individual’s quality in real-time, but it is unclear whether more fixed traits like feather coloration,

Animals use diverse signal types (e.g. visual, auditory) to honestly advertise their genotypic and/or phenotypic quality to prospective mates or rivals. Behavioral displays and other dynamically updateable signals (e.g. songs, vibrations) can reliably reveal an individual’s quality in real-time, but it is unclear whether more fixed traits like feather coloration, which is often developed months before breeding, still reveal an individual’s quality at the time of signal use. To address this gap, we investigated if various indices of health and condition – including body condition (residual body mass), poxvirus infection, degree of habitat urbanization, and circulating levels of ketones, glucose, vitamins, and carotenoids – were related to the expression of male plumage coloration at the start of the spring breeding season in wild male house finches (Haemorhous mexicanus), a species in which many studies have demonstrated a link between plumage redness and the health and condition of individuals at the time the feathers are grown in late summer and autumn. We found that, at the time of pair formation, plumage hue was correlated with body condition, such that redder males were in better condition (i.e. higher residual mass). Also, as in previous studies, we found that rural males had redder plumage; however, urban males had more saturated plumage. In sum, these results reveal that feather coloration developed long before breeding still can be indicative to choosy mates of a male’s current condition and suggest that females who prefer to mate with redder males may also gain proximate material benefits (e.g. better incubation provisioning) by mating with these individuals in good current condition.

ContributorsDepinto, Kathryn (Author) / McGraw, Kevin (Thesis director) / Sweazea, Karen (Committee member) / Webb, Emily (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor)
Created2021-12
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Bioindicators of wildlife health are useful tools for studying the viability of various organisms and populations, and can include a range of phenotypic variables, such as behavior, body size, and physiological parameters, such as circulating hormones and nutrients. Few studies have investigated the utility of total plasma protein as a

Bioindicators of wildlife health are useful tools for studying the viability of various organisms and populations, and can include a range of phenotypic variables, such as behavior, body size, and physiological parameters, such as circulating hormones and nutrients. Few studies have investigated the utility of total plasma protein as a predictor of environmental or nutritional variation among birds, as well as variation across different seasons and life-history stages. Here I examined relationships between plasma protein and season, urbanization, sex, body condition, molt status, and disease state in house finches (Haemorhous mexicanus). I sampled blood from house finches across three seasons (winter, summer and fall 2021) and measured plasma protein levels using a Bradford assay. I also collected data including condition, sex, and poxvirus infection state at capture, as well as fecal samples to assess gut parasitism (coccidiosis). During the fall season I also estimated molt status, as number of actively growing feathers. I found circulating plasma protein concentration to be lower in the fall during molt than during winter or summer. I also found a significant relationship between circulating protein levels and capture site, as well as novel links to molt state and pox presence, with urban birds, those infected with pox, and those in more intense molt having higher protein levels. My results support the hypotheses that plasma protein concentration can be indicative of a bird’s body molt (which demands considerable protein for feather synthesis) and degree of habitat urbanization, although future work is needed to determine why protein levels were higher in virus-infected birds.

ContributorsDrake, Dean (Author) / McGraw, Kevin (Thesis director) / Sweazea, Karen (Committee member) / Jackson, Daniel (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05