Digital Commons Network^™

The Transcriptome Of The Veiled Chameleon (Chamaeleo Calyptratus): A Resource For Studying The Evolution And Development Of Vertebrates, Brendan John Pinto, Daren C. Card, Todd A. Castoe, Raul E. Diaz Jr., Stuart V. Nielsen, Paul A. Trainor, Tony Gamble

Biological Sciences Faculty Research and Publications

Purpose

The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo‐devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking.

Methods

To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) …

Semi-Automatic Extraction Of Liana Stems From Terrestrial Lidar Point Clouds Of Tropical Rainforests, Sruthi M. Krishna Moorthy, Yunfei Bao, Kim Calders, Stefan A. Schnitzer, Hans Verbeeck

Biological Sciences Faculty Research and Publications

Lianas are key structural elements of tropical forests having a large impact on the global carbon cycle by reducing tree growth and increasing tree mortality. Despite the reported increasing abundance of lianas across neotropics, very few studies have attempted to quantify the impact of lianas on tree and forest structure. Recent advances in high resolution terrestrial laser scanning (TLS) systems have enabled us to quantify the forest structure, in an unprecedented detail. However, the uptake of TLS technology to study lianas has not kept up with the same pace as it has for trees. The slower technological adoption of TLS …

Structural Characterization Of A Prolyl Aminodipeptidase (Pepx) From Lactobacillus Helveticus, Deanna Dahlke Ojennus

Chemistry Faculty Scholarship

Prolyl aminodipeptidase (PepX) is an enzyme that hydrolyzes peptide bonds from the N-terminus of substrates when the penultimate amino-acid residue is a proline. Prolyl peptidases are of particular interest owing to their ability to hydrolyze food allergens that contain a high percentage of proline residues. PepX from Lactobacillus helveticus was cloned and expressed in Escherichia coli as an N-terminally His-tagged recombinant construct and was crystallized by hanging-drop vapor diffusion in a phosphate buffer using PEG 3350 as a precipitant. The structure was determined at 2.0 Å resolution by molecular replacement using the structure of PepX from Lactococcus lactis (PDB entry …

The Synthesis And Characterization Of 2-Arachidonoyl Glycerol, Shawn Alan Bydalek

Master's Theses

Cannabinoids are a structurally diverse class of compounds that act as ligands at the cannabinoid receptors, CB1 and CB2, through which the majority of the physiological effects of these compounds are mediated. Endocannabinoids (endogenous cannabinoids) are a subset of the cannabinoid family and include 2-arachidonoyl glycerol (2-AG) and N-arachidonoyl ethanolamide, and like most cannabinoids, these compounds have been shown to have anti-neoplastic effects on various cancer lines. The synthesis of 2-AG from dihydroxyacetone was selected as a research goal to try to improve yield over older published synthetic methods, to keep 2-AG in a protected form to avoid isomerization and …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Bioengineering Extracellular Matrix Scaffolds For Volumetric Muscle Loss, Kevin Roberts

Graduate Theses and Dissertations

Volumetric muscle loss overwhelms skeletal muscle’s ordinarily capable regenerative machinery, resulting in fibrosis and severe functional deficits which have defied clinical repair strategies. My work spans the design and preclinical evaluation of implants intended to drive the cell community of injured muscle toward a regenerative state, as well as the development of an understanding of the molecular responses of this cell community to biomaterial interventions. I demonstrate a new class of biomaterial by leveraging the productive capacity of sacrificial hollow fiber membrane cell culture; I show specifically that unique threads of whole extracellular matrix can be isolated by solvent degradation …

Representations Of Domestic Workers In Modern Arabic Fiction, Samaher Aldhamen

Graduate Theses and Dissertations

In this study, I have examined the representations of domestic workers in a number of Arabic mid-century and contemporary novels, using feminism and intersectionality as my overarching framework. I employed several scholarships of feminism such as Marxist and postcolonial feminism to examine the discourse on working-class women. The initial assumption of this study is that there is a noticeable invisibility of domestic workers in Arabic novels. If these characters manage to find their way into a text, they are typically ahistorical figures whose subjectivity is not centered.

Among the Arabic novels I have examined, I found that the tradition of …

The Functional Conservation Of Frazzled In Insects, Benjamin Wadsworth

Graduate Theses and Dissertations

Axons in the developing embryo receive and react to signals that direct their growth to reach target tissues at specified locations. The signal pathways that direct midline crossing of axons during embryonic development have been comprehensively examined in the past years using the Drosophila ventral nerve cord or the spinal cord as a model system. A number of these signaling mechanisms are conserved, however disparities have been found between species in general strategy or the molecular signals controlling the response of axons to guidance cues.

The Netrin-Frazzled pathway has been shown to aid in midline crossing of axons in the …

Microbial Rhodopsins Are Major Contributors To The Solar Energy Captured In The Sea, Laura Gómez-Consarnau, John A. Raven, Naomi M. Levine, Lynda S. Cutter, Deli Wang, Brian Seegers, Javier Arístegui, Jed A. Fuhrman, Josep M. Gasol, Sergio A. Sañudo-Wilhelmy

Research outputs 2014 to 2021

All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to …

Ltc Newsletter, University Of Dayton. Ryan C. Harris Learning Teaching Center

LTC Newsletter

Fall 2019

Predicting Residency Match Outcomes For Fourth-Year Medical Students., Jacob Shreffler

Electronic Theses and Dissertations

An important goal for undergraduate medical education program leaders is to prepare their medical students to successfully match during the National Residency Match Program (Gauer & Jackson, 2017). Due to the recent increase in applications submitted during the residency process, it is critical for medical education programs to better understand the factors and attributes of those medical students who are successfully matching (Liang, Curtin, Signer, & Sawoia, 2017). As there is a larger number of medical students now enrolled than positions available for residency, the number of unmatched seniors is expected to rise (Bumsted, Schenider, & Deiorio, 2017). Additionally, the …

Cognitive Satellite Communications And Representation Learning For Streaming And Complex Graphs., Wenqi Liu

Electronic Theses and Dissertations

This dissertation includes two topics. The first topic studies a promising dynamic spectrum access algorithm (DSA) that improves the throughput of satellite communication (SATCOM) under the uncertainty. The other topic investigates distributed representation learning for streaming and complex networks. DSA allows a secondary user to access the spectrum that are not occupied by primary users. However, uncertainty in SATCOM causes more spectrum sensing errors. In this dissertation, the uncertainty has been addressed by formulating a DSA decision-making process as a Partially Observable Markov Decision Process (POMDP) model to optimally determine which channels to sense and access. Large-scale networks have attracted …

Cannabidiol And The Remainder Of The Plant Extract Modulate The Effects Of Δ9-Tetrahydrocannabinol On Fear Memory Reconsolidation, Anthony Murkar, Pam Kent, Christian Cayer, Jon James, Tony Durst, Zul Merali

Brain and Mind Institute

Background: Δ9-Tetrahydrocannabinol (THC, a CB1 receptor agonist) and Cannabidiol (CBD, a non-competitive antagonist of endogenous CB1 and CB2 ligands) are two primary components of Cannabis species, and may modulate fear learning in mammals. The CB1 receptor is widely distributed throughout the cortex and some limbic regions typically associated with fear learning. Humans with posttraumatic disorder (PTSD) have widespread upregulation of CB1 receptor density and reduced availability of endogenous cannabinoid anandamide, suggesting a role for the endocannabinoid system in PTSD. Pharmacological blockade of memory reconsolidation following recall of a conditioned response modulates the expression of learned fear and may represent …

Molecular Phylogeny Provides New Insights On The Taxonomy And Composition Of Lyperosomum Looss, 1899 (Digenea, Dicrocoeliidae) And Related Genera, Joanna Hildebrand, Ewa Pyrka, Jiljí Sitko, Witold Jeżewski, Grzegorz Zaleśny, Vasyl V. Tkach, Zdzisław Laskowski

Biology Faculty Publications

Lyperosomum Looss, 1899 is one of the largest genera of the Dicrocoeliidae and is one of the best examples of the systematic complexity and taxonomic instability within this family. We present the molecular analyses based on novel sequences of nuclear and mitochondrial genes obtained from 56 isolates of adult flukes and larval stages of dicrocoeliids belonging to Lyperosomum, Skrjabinus, Zonorchis as well as previously available sequence data. According to obtained results we propose to return Zonorchis clathratus and Z. petiolatus into Lyperosomum, and to recognize L. alagesi as a synonym of L. petiolatum. Our study shows that L. petiolatum commonly …

Maladaptation In Feral And Domesticated Animals, Eben Gering, Darren Incorvaia, R. Henriksen, Dominic Wright

Biology Faculty Articles

Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype–phenotype relationships, fitness trade‐offs, and the roles of population …

Divergent Controls On Stream Greenhouse Gas Concentrations Across A Land Use Gradient, Allison Herreid

Master's Theses and Capstones

Inland waters can be significant sources of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) to the atmosphere. However, considerable uncertainty remains in regional and global estimates of greenhouse gas (GHG) emissions from freshwater ecosystems, particularly streams. Controls on GHG production in fluvial ecosystems, such as water chemistry and sediment characteristics, are also poorly understood. The main objective of this study was to quantify spatial and temporal variability in GHG concentrations in 20 streams across a landscape with considerable variation in land use and land cover. Stream water was consistently supersaturated in CO2, CH4, and N2O, suggesting that small …

Fungal Physiological Response To Temperature And Nitrogen Availability, Shana Whitney

Master's Theses and Capstones

Microbial carbon use efficiency (CUE; the proportion of assimilated C allocated towards biomass production) is a powerful regulator of global soil C stocks, and there is a need to integrate accurate and dynamic CUE parameters into C-cycling models. However, there is uncertainty in the CUE-response to warming and increased N deposition and how this response may vary among groups of microbes. Here, we conducted a laboratory incubation of ten photogenically diverse fungal isolates grown in liquid culture to evaluate potential environmental and physiological controls over CUE. Isolates were grown at 15ºC or 25ºC and under low or high N concentrations. …

Commissioning Of Micro-Cube Thermoluminescent Dosimeters For Small Field Dosimetry Quality Assurance In Radiotherapy, Brandon Luckett

Dissertations and Theses (Open Access)

Small field dosimetry presents complications and uncertainties that could be circumvented by using detectors which are smaller than the radiation field. This study evaluates the reproducibility and accuracy of TLD micro-cubes for use in stereotactic radiosurgery (SRS) remote auditing quality assurance (QA) for treatment centers participating in clinical trials. This study tested the hypothesis that TLD micro-cubes could be commissioned to evaluate small field dosimetry, and provide reproducibility within 3%, as well as assure agreement between measured dose and calculated doses to within 5%.

The aims of this thesis were to characterize and commission TLD micro-cubes as well as to …

Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali

Dissertations and Theses (Open Access)

Recently, a novel class of muscular dystrophy has been discovered in a family due to autosomal recessive missense mutation in POGLUT1. Mutation of this enzyme leads to decreased O-glucosyltransferase activity and impaired Notch signaling, the pathways important for skeletal muscle stem cell (satellite cells) quiescence and activation. We hypothesize that reduced POGLUT1 activity and impaired Notch signaling is causative of this limb girdle muscular dystrophy through dysfunction of muscle stem cells and myogenic progenitors.

To test this, we have used iPSCs for disease modeling and rescue experiments. Using a CRISPR based gene targeting method, we aimed to correct the point …

Inhibition Of Urothelial Carcinoma By Type I Interferon Activation Of The Innate And Adaptive Immune Response, Devin Plote

Dissertations and Theses (Open Access)

Bacillus Calmette-Guerin (BCG) is the first line therapy for bladder cancer patients with non-invasive disease. However, roughly 40% of patients exhibit no response, tumor recurrence or tumor progression following BCG treatment. Type I interferon (IFN-I) has potent anti-tumor effects against urothelial carcinoma (UC) and may be an alternative treatment option for patients who do not respond to BCG standard of care. However, the mechanisms that mediate the IFN-I-stimulated immune responses against UC are not fully elucidated. Herein, we evaluated the anti-tumor mechanisms of IFN-I in UC by use of adenoviral interferon-α (Ad-IFNα/Syn3) in human patients, and poly(I:C) or lentiviral IFNa …

Space Use And Nesting Ecology Of Common Ravens (Corvus Corax) In Central Washignton State, Brandon A. Rossi

Master of Biology Theses

The ecology and space use of Common ravens (Corvus corax; hereafter ravens) is not well understood in the shrub-steppe of central Washington State. Raven populations have increased by more than 254% since 1990 in Washington State (North American Breeding Bird Survey; www.mbr-pwrc.usgs.gov/bbs/). Ravens in central Washington are implicated as top predators of a small endemic population of greater sage-grouse (Centrocercus urophasianus). Researchers have related increased raven populations to anthropogenic subsidies such as landfills, agriculture, and livestock operations. Analyzing movement can help researchers understand the characteristics of habitat that are important and potentially drive population fluctuations. We found that daily and …

International Ocean Discovery Program Expedition 382 Preliminary Report: Iceberg Alley And Subantarctic Ice And Ocean Dynamics, Michael E. Weber, Maureen E. Raymo, Trevor Williams, Linda Armbrecht, Ian Bailey, Stefanie Brachfeld, Zhiheng Du, Gerson Fauth, Marga Garcia, Anna Glüder, Michelle Guitard, Marcus Gutjahr, Sidney Hemming, Ivan Hernandez-Almeid, Frida S. Hoem, Ji Hwan Hwang, Mutsumi Iizuka, Yuji Kato, Bridget K. Lee, Yasmina M. Martos, Suzanne O'Connell, Victoria L. Peck, Lara F. Perez, Brendan Reilly, Thomas A. Ronge, Osamu Seki, Lisa Tauxe, Shubham Tripathi, Jonathan Warnock, Xufeng Zheng, Fabricio G. Cardillo, Anthony D. Mello

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

International Ocean Discovery Program (IODP) Expedition 382, Iceberg Alley and Subantarctic Ice and Ocean Dynamics, investigated the long-term climate history of Antarctica, seeking to understand how polar ice sheets responded to changes in insolation and atmospheric CO2in the past and how ice sheet evolution influenced global sea level and vice versa. Five sites (U1534-U1538) were drilled east of the Drake Passage: two sites at 53.2°S at the northern edge of the Scotia Sea and three sites at 57.4°-59.4°S in the southern Scotia Sea. We recovered continuously deposited late Neogene sediment to reconstruct the past history and variability in Antarctic Ice …

The Utility Of Music-Based Interventions In Dementia Care, Adriana C. Doerr

Dissertations

While research has investigated the impact of music-based interventions on management of behavioral and psychological symptoms of dementia (BPSD), there is limited discussion of which music-based interventions are most effective for various levels of dementia severity, or of how to determine which music-based interventions are both accessible and feasible for caregivers and nursing staff. This review sought to identify the benefits of music-based interventions in dementia care within various domains of functioning and determine whether music-based interventions are effective for various levels of dementia severity. Peer-reviewed articles and studies that evaluated the effectiveness of various music interventions or demonstrated music's …

Understanding The Molecular And Cellular Functions Of Odd-Skipped Related 1 In Outflow Tract Development, Menglan Xiang

Theses and Dissertations

The cardiac outflow tract (OFT) is a transient conduit that connects the embryonic heart chambers to the vascular network. Transcription factor Osr1 promotes the proliferation and cell cycle progression of second heart field (SHF), an essential cell population that contribute to the developing OFT. In this study, we investigated the role of Osr1 in OFT development on cellular and molecular levels using a systems biology approach. We observed OFT rotation and elongation defects, as well as double-outlet right ventricle and overriding aorta as a result of SHF-specific deletion of Osr1. Using genetic inducible fate mapping, we showed that Osr1-expressing SHF …

Optimal Control Strategies For Complex Biological Systems, Afroza Shirin

Mechanical Engineering ETDs

To better understand and to improve therapies for complex diseases such as cancer or diabetes, it is not sufficient to identify and characterize the interactions between molecules and pathways in complex biological systems, such as cells, tissues, and the human body. It also is necessary to characterize the response of a biological system to externally supplied agents (e.g., drugs, insulin), including a proper scheduling of these drugs, and drug combinations in multi drugs therapies. This obviously becomes important in applications which involve control of physiological processes, such as controlling the number of autophagosome vesicles in a cell, or regulating the …

Investigating Parental Effects On End-Use Quality In Hard Winter Wheat (Triticum Aestivum L.) Hybrids, Anthony Delaney

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

To optimize the performance and marketing of hybrid wheat, breeders need to understand the impact parents have on end-use quality. The goal of this study was to investigate the inheritance of end-use quality traits of hard winter wheat reciprocal hybrids produced by Easterly (2017). The 2016 analysis included 71 reciprocal hybrid combinations from 13 parents and the 2017 analysis included 79 reciprocal hybrid combinations from 14 parents. The reciprocals were composed of crosses between the top performing and bottom performing parents with respect to end-use quality as quantified by a Mixograph, a SDS sedimentation assay, and a SDS-SRC hybrid assay. …

Rust And Viral Mosaic Diseases In Biofuel Switchgrass, Anthony A. Muhle

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Switchgrass (Panicum virgatum L.) is a perennial warm-season monocot that is indigenous to locations in North America east of the Rocky Mountains, and is considered a model grass for biofuel feedstock production. As switchgrass production increases, diseases pose a potential threat to biomass production and ethanol extraction. The two predominant switchgrass diseases in Nebraska are rust caused by Puccinia spp. and a viral mosaic disease caused by Panicum mosaic virus (PMV) and its associated Satellite panicum mosaic virus (SPMV). In this thesis, one study determined how SPMV affects PMV infection and systemic spread in two populations of switchgrass at different …

Hormonal Signaling Induced In Soybean By Lysobacter Enzymogenes Strain C3, Jessica C. Walnut

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The biological control bacterium Lysobacter enzymogenes strain C3 has been shown to suppress fungal diseases by producing a suite of lytic enzymes and antimicrobial secondary metabolites. Previous studies have found that C3, when applied to grass and cereal plants, also is capable of inducing local and systemic resistance against fungal pathogens. It is unknown, however, whether the bacterium has the ability to induce resistance in dicots and what signaling pathways are involved. This study assessed the ability of C3 to trigger local and systemic induced resistance responses in soybean (Glycine max ‘Williams82’) by analyzing relative expression of salicylic acid …

Dual Biological Control: Characterization Of Fungi And Bacteria To Control Granary Weevil And Fungal Pathogens Of Stored Grain, Gülçin Ercan

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Cereals are main food sources for humans and animals. However, during storage, cereal grains can be infested by insects and fungi. One of the most important insect storage pests is Sitophilus granarius (L., Coleoptera: Curculionidae). Adults and larvae can cause serious grain losses. In addition to insect pests, fungal pathogens may also invade the grain and cause economic loss, including contamination with mycotoxins, which threaten mammal health by causing serious disease. The most common mycotoxigenic grain fungi are species that belong to the genera Fusarium, Aspergillus and Penicillium. Currently, the most commonly used management strategies for insect and …

Preparation, Functionalization, And/Or Characterization By X-Ray Photoelectron Spectroscopy Of Carbon Surfaces For Biosensors And Other Materials, Varun Jain

Theses and Dissertations

My dissertation is primarily divided into two parts. The first deals with the preparation, functionalization, and characterization of carbon surfaces prepared by direct current magnetron sputtering (DCMS) and high power impulse magnetron sputtering (HiPIMS) as substrates for bioarrays. Part two discusses applications of XPS peak fitting in surface chemical analysis. Chapter 1, the introduction, includes (i) a discussion of the construction of bioarrays and the preparation of sputtered surfaces, e.g., by DCMS and HiPIMS, and also functionalization (bioconjugate) chemistry with special emphasis on the importance of covalent functionalization of surfaces, and (ii) a discussion of the surface characterization techniques and …