Digital Commons Network^™

Analog Digital Frame: User Centered Design In Arts-Based Neighborhood Resilience Modeling, David Robledo, Sydney F. Walker, Zlatka Rebolledo Sánchez, Richard Nickel

English Faculty Publications

We explicate a mapping of digital documents through computer machinery as an analog frame for Research and Design in neighborhood environmental literacy, within an applied interdisciplinary ecosystem theory. In the arena of communicating localized climate phenomena and solutions, the design of communication frameworks has provided a core methodology to map climate adaptive conclusions as analogs for actionable community interpretive media. In this experience report, we articulate User Centered Design (UCD) in project research and development, while reporting on difficulties and solutions in shaping an analog digital frame to integrate student driven research and design with mentor based interdisciplinary project theorization. …

Systematic Review Of Immunohistochemistry Protocols, Arpitha Parthasarathy

Pitzer Senior Theses

Immunohistochemistry (IHC) is an essential technique in biological research that allows for the visualization and localization of proteins within tissue samples. This systematic review analyzes the most effective, efficient and reproducible protocols for IHC. It focuses on three critical steps: freezing, cryosectioning, and staining of skeletal muscle tissues in mice models. A total of 41, 44, and 48 articles on freezing, cryosectioning, and staining techniques, respectively, were analyzed, from reputable sources in biology like PubMed and Web of Science. Results showed the following. For freezing, the use of isopentane combined with liquid nitrogen appeared to be the best method, minimizing …

The Cognition Of Emotion: How Cognitive Control And Working Memory Underly Emotion Regulation Strategy Differences, Nathan Chabin

Pitzer Senior Theses

Working memory is crucial for comprehensively grasping the dynamics of emotion regulation (ER) and cognitive control, as it serves as a foundational cognitive resource that influences how individuals manage their thoughts, emotions, and behaviors. This research aimed to examine the role working memory capacity (WMC) has on Frontal Midline Theta (FMT), an EEG marker for cognitive control, during two common ER strategies: emotional suppression and cognitive reappraisal. Participants performed both an Operation Span working memory task and an ER task, where they viewed a series of negative and neutral images across three conditions. First, participants were instructed to passively view, …

Impact Of Hiv-2 Rod9 Vpx Mutations On Samhd1 Degradation And Vpx Nuclear Trafficking, Tolulope R. Oladimeji

All Graduate Theses, Dissertations, and Other Capstone Projects

Human Immunodeficiency Virus (HIV) is a leading cause of death in many parts of the world. HIV-2, endemic to West Africa, has infected over 2 million people globally. A key difference between HIV-2 and the more widespread HIV-1 is the HIV-2 protein Vpx, which facilitates infection in non-dividing cells by targeting SAMHD1, a host innate immune protein, for proteasomal degradation. This research aims to identify specific amino acid residues in HIV-2 ROD9 Vpx that are essential for mediating SAMHD1 degradation by the proteosome. I hypothesize that amino acid residues located in the C-terminal region of Vpx play a critical role …

Inquiries Into The Mycobacterial Caseinolytic Protease System, Felipe Badke D'Andrea

Student Theses and Dissertations

Despite progress over the last century, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains the leading cause of death from an infectious disease worldwide. The high global burden of Mtb, alongside its protracted treatment regimen and insidious rise of multi-drug resistance, underscores the need for non-canonical drug targets and pathways to improve antitubercular chemotherapy. Mtb's success as a pathogen is linked to its ability to infect and evade clearance by the human immune system despite a wide range of noxious host stressors. Along with transcriptional responses, the maintenance of protein homeostasis is critical to this adaptability and pathogenicity. …

Serine Metabolism Leverages The Integrated Stress Response To Direct Stem Cell Fate During Tissue Regeneration, Jesse Stephen Swyer Novak

Student Theses and Dissertations

Epidermal stem cells constantly rejuvenate the skin's barrier, which excludes harmful microbes and prevents dehydration. While hair follicle stem cells (HFSCs) normally regenerate hair, they must also reconstruct and thereafter maintain the overlying epidermis upon a barrier breach, such as a wound. How these fate choices are balanced to restore physiologic function to damaged tissue remains poorly understood. Here, I uncover the non-essential amino acid serine as a surprising regulator in this process. Utilizing dietary intervention and HFSC-specific loss-of-function studies, I demonstrate that under serine-depleted conditions HFSCs delay hair growth. Upon injury, serine-restricted HFSCs skew their fate towards epidermal re-epithelialization …

Investigation Of Csld And Pme Genes In Cell Division And Expansion In Physcomitrium Patens, Lia Bozza

Open Access Master's Theses

Cellulose Synthase-Like Ds (CSLDs) are cellulose synthase known to participate in cell plate formation and cell wall remodeling. In the moss model, Physcomitrium patens, double csld2/6 knockout (KO) mutants were previously shown to have gametophore leaf phenotypes that are consistent with defects in cytokinesis, including irregular cell shape, cell separations, and incomplete midrib formation (Wu et al., 2023a). When these mutants were grown on ammonium-free medium to promote gametophore development, the severity of the phenotype was more extreme, including incompletely formed cell plates and multinucleated cells (A. Roberts, personal communication). It was also reported that expression of several enzymes …

Investigating Regulation And The Regulome Of The Nucleic Acid Binding Protein Spovg Within Borrelia Burgdorferi, Timothy C. Saylor

Theses and Dissertations--Medical Sciences

Prior studies indicated Borrelia burgdorferi SpoVG protein was regulated, SpoVG binds specifically to a number of nucleic acids, and SpoVG binds to the non-variable section of the major virulence factor vlsE. Although a direct transcriptional activator or inhibitor was not elucidated, it is shown that SpoVG is regulated based on cell culture density independent of the growth rate of B. burgdorferi, indicating that SpoVG regulation is outside the scope of the alternative sigma factor RpoS. Using a dCas9 CRISPRi construct to target SpoVG resulted in protein expression trending towards upregulation of the BosR-RpoS regulon, and a marked decrease …

Bed Bugs: Health Risks And Control, Simona Principato

Theses and Dissertations--Entomology

Bed bugs are blood-feeding hemipterans strongly associated with humans. Their detection in indoor environments, such as homes, hotels, trains, and public facilities, has increased gradually over the past 20 years. The exact cause of their resurgence is still unclear, but the increase of international travel and insecticide resistance are thought to have contributed to it.

Although bed bugs are not known to transmit diseases, the EPA, CDC, and USDA have classified them as a pest of significant public health concern, mainly due to the dermatitis that they can cause. Beyond the dermatological burden of the bites, other health implications often …

The Role Of Nutrition In Managing Honey Bee Viral Pathogen, Caroline Wylie Kane

Theses and Dissertations--Entomology

This study evaluated the impact of nutritional supplements on viral infections in honey bee colonies, focusing on Lake Sinai Virus 2 (LSV2), Deformed Wing Virus A (DWVA), and Deformed Wing Virus B (DWVB). I partnered with 32 hobbyist beekeepers across Kentucky, who volunteered 138 colonies for a month-long field study. Half of the colonies received weekly commercial supplements, while the other half served as controls. Viral titers were measured before and after the supplementation period using qPCR. Supplements did not significantly reduce viral titers for any of the three viruses, suggesting that short-term supplementation may not be effective in lowering …

Impacts Of Utilizing Reverse Osmosis Concentrate On Mashing, Fermentation, And Water Use In Bourbon Whiskey Production, Ryan C. Sarhan

Theses and Dissertations--Biosystems and Agricultural Engineering

This thesis addresses the feasibility of reusing reverse osmosis concentrate (ROC) in the bourbon whiskey fermentation processes. Initial work compared laboratory-scale mashing and fermentation methods, demonstrating that simultaneous saccharification and fermentation reliably reflects industrial-scale processes, with lower complexity and process time. Building upon this, laboratory and distillery-scale experiments demonstrated that reusing ROC in the mashing and fermentation steps does not negatively impact ethanol yields. ROC produced by systems with a water softener was found to significantly increase mash rheology, suggesting a need for potential process adjustments. Softened ROC also altered the production of flavor-influencing volatile congeners. Under worst case conditions, …

The Impact Of Solvent Extraction And Enzyme-Assisted Extraction On The Yield And Quality Of Black Soldier Fly Larvae (Hermetia Illucens) Oil, Achini Madushani Mannawa Arachchige, Mark Williams, W. M.A.D.Binosha Fernando, Weeraya Karnpanit, Jane Lumanlan, Vijay Jayasena

Research outputs 2022 to 2026

The increased interest in black soldier fly larvae (BSFL) oil is driven by its beneficial fatty acid composition, leading to the development of effective extraction methods. This study evaluated the impact of solvent extraction (SE) and enzyme-assisted extraction (EAE) on the yield and quality of BSFL oil. SE using hexane, petroleum ether, isopropanol, and ethanol after 6 hr of extraction resulted in higher yields compared to EAE using alcalase, papain, and trypsin after 24 hr, with the highest yield recorded for petroleum ether (33%), followed by isopropanol (30%). Isopropanol extraction demonstrated the highest antioxidant activity (77%). The results indicated a …

Behavioral Observations And Analysis Of Twix: The Cape Porcupine At The Lake Superior Zoo, Erin Davidson

Scripps Senior Theses

The three main goals of zoos are outlined as: education, conservation, and research. In our modern world, the focus of zoos has shifted away from simply housing animals, and towards how we can best promote proper animal welfare for individuals in human care. Animal welfare can be defined as the “mental health” of non-human species of fauna, and is greatly influenced by the stressors within the environment, as well as the option of choosing how to interact with and respond to the environment. Animals housed in zoos are presented with unique stressors that they often do not choose to experience, …

A Transferable Approach For Quantifying Benthic Fish Sizes And Densities In Annotated Underwater Images, Peter C. Esselman, Shadi Moradi, Joseph K. Geisz, Christopher Roussi

Michigan Tech Publications

Benthic fishes are a common target of scientific monitoring but are difficult to quantify because of their close association to bottom habitats that are hard to access. Advances in image-acquisition technologies, machine vision and deep learning have made capturing and quantifying fishes with cameras increasingly feasible. We present a method and open-source software called ‘FishScale’ to estimate benthic fish lengths, numeric abundance and biomass density in underwater environments assessed with down-looking monocular images. ‘FishScale’ estimates fish abundances and size frequencies from near-nadir monocular images where fish have already been semantically segmented. The software accounts for lens distortion, underwater magnification effects …

Characterization Of Actin Capping Protein Beta Isoform Specific Dynamics In Metastatic Cells, Etinosa Osamudiamen

All Graduate Theses, Dissertations, and Other Capstone Projects

To gain insight into the mechanism of cancer progression, we examined the isoform-specific roles of actin capping protein (CPβ1 and CPβ2) related to actin cytoskeletal dynamics and metastatic progression in human uterine epithelial cells (HeLa). We employed qPCR to determine the relative expression levels of CPβ1 and CPβ2 in actively growing HeLa cells. Our findings confirmed that CPβ1 and CPβ2 are differentially expressed, with CPβ2 being the predominant isoform, two-fold higher, consistent with its expression in other non-muscle tissues. To extend our expression studies, the localization and spatial distribution of the isoforms were visualized via immunolocalization studies using isoform-specific monoclonal …

Comparative Evaluation Of Fungal Strains For The Bioprocessing Of Soybean Hulls Using Cheese Whey As Fermentation Medium, Ruchita Bhattarai

Electronic Theses and Dissertations

Globally, soybean is the most widely cultivated oilseed crops, and serve as the primary source of cooking oil, contributing to around 50% of global oilseed production. During the industrial processing of soybean oil, a significant amount of soybean hull (SH) is produced, which makes up about 8% of the grain yield, resulting in approximately 18–20 million tons of hulls, one of the largest by-products in the soybean industry. The hulls have limited commercial value and are primarily used as fiber additives in dairy cattle feed, but a large portion is still discarded as agricultural waste. Similarly, cheese whey (CW), a …

Isolation And Characterization Of Rhizobia Bacteria From Midwest Soils, Jr Loya

Electronic Theses and Dissertations

Symbiotic bacteria, known as rhizobia, can colonize the roots of legume plants and then convert atmospheric nitrogen into a usable form by the host through the process called biological nitrogen fixation (BNF). Many of these bacteria produce other plant-growth-promoting benefits, such as nutrient acquisition, phytohormone production, and the modification of plant stress responses. Agricultural inoculants made from these bacteria have helped reduce the need for man-made nitrogenous fertilizers, known causes of pollution and eutrophication. There are additional benefits in developing bacteria inoculants local to regional soils. The ability to survive and compete in Midwest soil and climates present an opportunity …

Investigating Antimicrobial Efficacy Of Turmeric And Rosemary Oil Against Staphylococcus Aureus, Aishwarya Tripathi

Selected Full-Text Master Theses 2021-

This study investigates the antimicrobial efficacy of turmeric (Curcuma longa) and rosemary essential oil (Rosmarinus officinalis) against Streptococcus aureus, with a comparative analysis to phenoxyethanol, a widely used synthetic preservative. The growing consumer demand for natural cosmetic formulations have intensified the search for plant-derived alternatives to synthetic preservatives. Turmeric and rosemary oil were selected based on their documented antimicrobial, antioxidant, and anti-inflammatory properties. The objective of this research was to evaluate whether these natural agents can serve as effective preservatives in topical gel formulations, either individually or in combination, and how their efficacy compares to phenoxyethanol.

Eight gel-based formulations were …

Near-Infrared Hemicyanine And Bodipy Sensors For Monitoring Mitochondrial Viscosity In Live Cancer Cells, Drosophila Melanogaster Larvae, And Adpkd Kidney Tissue, Joseph Peters

Dissertations, Master's Theses and Master's Reports

Two near-infrared fluorescent sensors, sensor A and sensor B, were synthesized and characterized. Sensor A was a hemicyanine derived structure, and sensor B was a BODIPY derived sensor. The sensors were tested to measure their ability to monitor viscosity, and sensor A was used to monitor viscosity in live cells. Both sensors were found to be effective in monitoring the viscosity level through optical measurements with glycerol. Sensor A was found to be successful in monitoring mitochondrial viscosity in HeLa MBA-MD-453 and MDA-MB-231 cell lines. It was also successful in monitoring viscosity in Drosophila melanogaster larvae as well as …

Caspases Protect Against Hyperglycemia Induced Necroptosis-Like Cell Death In Brain Endothelial Cells, Aleena S. Mathew

Theses and Dissertations

Acute diabetes characterized by high spikes in blood glucose levels in association with severe hyperglycemia can lead to an increased risk of ischemic stroke in the brain. To better understand high blood glucose levels, hyperglycemia, in the brain we explored its effects on endothelial cells. Endothelial cells line the inner walls of blood vessels and are directly impacted in hyperglycemia. Brain endothelial cells are a major component of the blood brain barrier (BBB) which tightly regulates the brain’s microenvironment. The type of cell death such as apoptosis, caspase dependent, or necroptosis, caspase independent, can exacerbate diabetes associated complications. There is …

Distinct Odorant Receptor Response Patterns To Aliphatic Odorants In Freely Behaving Mice, Claire A. De March, Patrick Breheny, William B. Titlow, Hiroaki Matsunami, Timothy S. Mcclintock

Physiology Faculty Publications

In mammals, odors are encoded by a combinatorial code determined by the pattern of responses across hundreds of odorant receptors expressed monogenically and monoallelically in olfactory sensory neurons. The compositions of these receptor response patterns are largely unknown and overlap between them has yet to be explored. Activity-dependent reporter gene expression in freely behaving S100a5-tauGFP mice allowed capture of activated olfactory sensory neurons and identified 168 receptors responsive to moderate concentrations of 1 or more of 12 aliphatic (5 to 8 carbons) ketones, alcohols, and carboxylic acids. These 12 response patterns are remarkably different, with only 19% of the receptors …

Targeting Als: A Multi-Cellular Study On The Potential Therapeutic Role Of Azole-Based Compounds, Alisha R. Kennedy

Theses and Dissertations

Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig’s disease, is a progressive neurodegenerative disorder that leads to the degeneration of motor neurons, which control voluntary muscle movements such as eating, speaking, and breathing. As these neurons are damaged, voluntary movement ceases, leading to a fatal outcome. The survival time of ALS patients varies, ranging from a few months to up to 10 years. Chapter 1 of this thesis provides an overview of ALS, highlighting the role of transactive response DNA-binding protein 43 (TDP-43), a key feature in ALS and other neurodegenerative diseases. The aggregation of TDP-43, particularly due to …

Valorizing Municipal Solid Waste For Sustainable Aviation Fuel And Polyhydroxyalkanoate Bioplastics: Pyrolysis And Microbial Pathways, Emon Das

Theses and Dissertations--Biosystems and Agricultural Engineering

The escalating global burden of municipal solid waste (MSW), projected to reach 3.88 billion tons annually by 2050, calls for innovative valorization strategies to mitigate environmental impacts and promote a circular bioeconomy. This thesis investigates the conversion of MSW into two high-value products: sustainable aviation fuel (SAF) and polyhydroxyalkanoate (PHA) bioplastics. Chapter one presents comprehensive physicochemical characterization and pyrolysis-GC/MS analysis of MSW feedstocks. The physicochemical results reveal that densification enhances handling and storage properties, while pyrolysis-GC/MS analysis indicates that plastic-rich MSW streams produce bio-oils with favorable hydrocarbon profiles suitable for SAF production, potentially contributing to decarbonization efforts in the aviation …

Confronting Indecision, Lane Allison Murray

ENGS 15.11: Design and Education

This course aims to increase students' understanding of indecision and how to confront it. The class provides insight into how the fear of the unknown holds people back from making decisions and about understanding one's values as a means to combat indecision. Students and teachers alike explore instances of indecision and evaluate their own impulses & thought processes by reflecting on the deeper reasons for their choices. Students will increase their comfort level of asking themselves and their peers questions about the values that guide them and, in doing so, strengthen their relationships with themselves and others.

The Role Of Chronic Activity-Based-Anorexia In Drug-Paired Environmental Preference, Abby Bendixen

Behavioral Neuroscience Honors Papers

Anorexia nervosa (AN) has one of the highest mortality rates among psychiatric disorders. This disorder, and other eating disorders, have features that overlap with substance use disorder (SUD), including reward sensitivity, impulsivity, and emotional dysregulation. The purpose of this study was to investigate the role of chronic, restrictive eating disorders on the development of cocaine-paired environmental preference. Seven-week-old female rats were induced to a model of chronic activity-based-anorexia (ABA) and underwent conditioned place preference (CPP) testing to examine cocaine-paired environmental conditioning. The activity patterns of rats that underwent chronic ABA were not consistent with previous studies inducing chronic ABA in …

Exploring The Role Of Transcription Factor Nrf1 In Autophagy And Inhibiting The Nrf1 Bounce-Back Response, Madison A. Ward

Theses and Dissertations

Cells exposed to proteotoxic stress invoke adaptive responses aimed at restoring proteostasis. Our previous studies have established a firm role for the transcription factor Nuclear factor-erythroid derived-2-related factor-1 (Nrf1) in responding to proteotoxic stress elicited by inhibition of cellular proteasome. Following proteasome inhibition, Nrf1 mediates the synthesis of new proteasomes, thus enabling cells to mitigate proteotoxic stress. Here, we report that under similar circumstances, multiple components of the autophagy-lysosomal pathway (ALP) were transcriptionally upregulated in an Nrf1-dependent fashion, thus providing the cells with an additional route to cope with proteasome insufficiency. In response to proteasome inhibitors, Nrf1-deficient cells exhibited profound …

Toxin-Like Proteins In The Venom Of Drosophila Parasitoids, Lady V. Cardenas

Dissertations and Theses

The figitid parasitoid wasps of Drosophila are gaining importance in agriculture due to their ability to kill the resilient soft-fruit pest Drosophila suzukii. Their success and infection strategies vary, and the mechanisms underlying these differences are largely unknown. Some of their venom proteins have been shown to be important in suppressing host defense. Here, we report that Ganaspis brasiliensis, a parasitoid of D. suzukii survives well on Drosophila yakuba, a host species with a strong cellular immunity, and infected flies are unable to mount a strong immune response. To predict possible toxin-like proteins in Ganaspis venoms that might suppress cellular …

How To Approach Medical Education Research, Stefanie Attardi, Jeff Cross, Sarah Lerchenfeldt

Books and Book Chapters

Medical education research blends two of the core functions of academic medicine: teaching and scholarship. Its value is increasingly recognized in promotion and tenure decisions, and in the number of funding sources available. Similar to other types of research, it starts with a well-crafted question and a thorough review of the literature. For a successful project, it is critical to select the research design that can best answer the research question, keeping in mind its advantages and limitations. Because the research design must also adhere to ethical principles, working closely with the local Institutional Review Board prior to starting the …

“What’S Supp” Developing An In Vitro Model For Healthy Oral Biofilms, Alex Labossiere

Open Access Dissertations

The study of oral plaque has largely been influenced by the study of pathogens. Here in Chapter 1, I will discuss how this pathogenic focus has been dominant until the onset of microbiome research and begin to explain microbiomes in the context of supragingival plaque in homeostatic communities. From there we will then discuss the possible roots where dysbiosis may arise from plaque to cause disease and ways in which we can study healthy supragingival plaque by in vitro models.

In chapter 2, I will discuss molecular commensalism and how it can be viewed as a tool to further understand …

Nanotube Spectral Fingerprinting And Machine Learning For Optimized Bioimaging/Sensing And Disease Detection Applications In Als, Rodrigo Monroy Lopez

Open Access Master's Theses

Single-walled carbon nanotubes (SWCNTs) possess unique physicochemical and optical properties that make them ideal candidates for biomedical imaging, biosensing, and disease diagnostics. This thesis explores the potential of SWCNT-based spectral fingerprinting combined with ML (Machine Learning) algorithms to optimize bioimaging, disease detection and prediction, with a specific focus on differentiating between healthy and amyotrophic lateral sclerosis (ALS) lymphoblastic patient samples. By functionalizing SWCNTs with single-stranded DNA, we enhance their stability and target specificity, enabling their application in serum patient samples.

A comprehensive spectral analysis of DNA-SWCNTs was conducted using near-infrared fluorescence spectroscopy and other characterization techniques, including UV-Vis-absorption spectroscopy. The …