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Characterization Of Lipids In Tenebrio Molitor Larvae And Pupae Under Various Extraction Methods, Nariman A. Ktil

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tenebrio molitor, or the yellow mealworm is an edible insect widely recognized and consumed for its rich nutritional value. Mealworms are known for their flexible nature of adapting to various environmental conditions and being able to thrive under harsh conditions and low-value wastes. In this paper, our main goal was to investigate the mealworm’s ability to grow and develop while being reared on apple pomace, the biowaste from apple production, and the effect it would have on its nutritional value specifically its lipid profile. Then these reared insects were used for oil extraction and analyzing their fatty acid profiles. …

Expanding The Vibrating Sharp-Edge Spray Ionization Toolkit For Oligonucleotide Characterization, Sultan Mahmud

Graduate Theses, Dissertations, and Problem Reports (ETD)

A gentle or soft Ionization process is a critical component in native mass spectrometry (MS) to lift the biomolecules from the bulk solution into the gas phase environment of the mass spectrometer preserving their shape, topology and non-covalent interactions. Electrospray ionization (ESI) facilitates structural preservation of proteins, nucleic acids and their complexes and as a result it has been extensively used in native MS. However, in negative ion mode, ESI is somewhat limited in sensitivity due to corona discharge effect resulting from the requirement of a high amount of voltage. This often disrupts the ESI process and may not preserve …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Probing The 10-23 Dnazyme Catalytic Core: Insights From Structural And Mechanistic Studies, Evan Rhyse Cramer

Graduate Theses, Dissertations, and Problem Reports (ETD)

The 10-23 DNAzyme is a catalytically active DNA oligonucleotide capable of cleaving RNA at purine-pyrimidine junctions in the presence of divalent metal ions, most notably magnesium. Despite its promise as a programmable RNA knockdown tool, its clinical and biotechnical utility has been hampered by limited structural characterization, low catalytic efficiency under physiological conditions, and poor understanding of its in-cell activity. This dissertation presents a comprehensive framework for the structural and functional analysis of DNAzymes using the 10-23 DNAzyme as a model system. In the absence of high-resolution structures, we first employed detailed in vitro biochemical assays to map essential residues …

Raman Spectroscopy For Rapid Quantification Of Macronutrients In Heirloom Beans, K. Chandler Williams

Graduate Theses, Dissertations, and Problem Reports (ETD)

Quantification of macronutrients in food requires a large investment in facilities and instrumentation as well as ongoing expenses of labor, reagents, and hazardous waste disposal. These costs pose a significant barrier to determining macronutrient quantities in the thousands of uncharacterized landrace and heirloom crops and discourage traditional crop breeding projects from ensuring that their selected crops maintain desirable macronutrient profiles in addition to target agronomic traits. Our objective was to test whether a hand-held Raman spectrometer—a technology which has found use in plant disease diagnostics but remains largely overlooked in nutrient quantification-- could provide a feasible means for quantifying the …

P23h Rhodopsin Accumulation Disrupts Synaptic Protein Levels In Rod Photoreceptors, Samantha Thompson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Rod photoreceptors are specialized neurons located in the retina, the neural tissue that lines the back of the eye. Rod photoreceptors are necessary for dim light and peripheral vision through the photoactivation rhodopsin (Rho). Rho is synthesized in the inner segment of rods before being unidirectionally trafficked to the outer segment. In diseases such as retinitis pigmentosa (RP), Rho trafficking can be disrupted, leading to progressive rod cell death. In many cases of RP, Rho is mislocalized to the rod photoreceptor synapse (“spherule”). The impact of Rho mislocalization on spherule structure and protein organization is poorly understood. We hypothesize that …

Kinetic Model Of Glycolysis And Glutaminolysis Interplay Developed In Matlab Simbiology, Zohreh Mirveis, Hugh J. Byrne, Nitin Patil

Datasets

This dataset contains a kinetic model developed in MATLAB SimBiology to simulate the metabolic dynamics of glycolysis and glutaminolysis and their interconnection. The model was used in the study ‘Experimental and computational investigation of the kinetic evolution of the glutaminolysis pathway and its interplay with the glycolysis pathway’ (Mirveis et al., 2024). The dataset includes the original SimBiology project file together with the experimental data used for model training. These resources enable reproduction of the simulations reported in the publication and provide a reusable framework for further computational exploration of metabolic pathway kinetics.

Modeling Functional Connectivity With Learning And Memory In A Mouse Model Of Alzheimer’S Disease, Lindsay Fadel, Elizabeth Hipskind, Steen E Pedersen, Jonathan Romero, Caitlyn Ortiz, Eric Shin, Md Abul Hassan Samee, Robia G Pautler

Faculty, Staff and Students Publications

Introduction: Functional connectivity (FC) is a metric of how different brain regions interact with each other. Although there have been some studies correlating learning and memory with FC, there have not yet been, to date, studies that use machine learning (ML) to explain how FC changes can be used to explain behavior not only in healthy mice, but also in mouse models of Alzheimer's Disease (AD). Here, we investigated changes in FC and their relationship to learning and memory in a mouse model of AD across disease progression.

Methods: We assessed the APP/PS1 mouse model of AD and wild-type controls …

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 …

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Characterizing The Targeting Of Toc159 Receptors To The Chloroplast Outer Envelope Membrane And Their Role In The Assembly Of Distinct Toc Complexes, Michael Fish

Theses and Dissertations (Comprehensive)

Global agriculture and food security face challenges from climate change, population growth, and other human-driven pressures. Enhancing our understanding of plant biology, particularly chloroplast function, is critical for improving crop yield and stress resilience. As the sites of photosynthesis and key regulators of plant responses to environmental cues, chloroplasts depend on the precise import of thousands of nuclear-encoded proteins to maintain their biogenesis and function. While much is known about the core translocon components in the chloroplast outer envelope membrane that form the TOC complex, the mechanisms underlying their targeting, assembly, and regulation remain incompletely understood.

Plastids, including chloroplasts, evolved …

The Detection Of Multiple Human Papillomavirus (Hpv) Types Through The Development Of An Isothermal Dna Amplification Assay, Lauren Powell

Doctoral

Human Papillomaviruses (HPV) belong to the Papillomaviridae family, with over 200 known types classified into high-risk (HR-HPV) and low-risk (LR-HPV) groups based on their carcinogenic potential. While most HPV infections are asymptomatic and transient, persistent infection can lead to health issues, including cervical cancer. Given the high prevalence of HPV and its potential for malignant transformation, nucleic acid amplification assays have become a widely implemented tool for routine HPV testing. This study developed a real-time isothermal DNA amplification assay for the detection and differentiation of multiple HPV types. A universal primer set was designed to target a highly conserved region …

Positive Allosteric Modulation Of Glun1/Glun3 Nmda Receptors, Mia Ruth Johns

Graduate Student Theses, Dissertations, & Professional Papers

N-methyl-D-aspartate (NMDA) receptors are ionotropic glutamate receptors that mediate excitatory neurotransmission in the central nervous system (CNS) where they play critical roles in normal and pathological brain functions and neurodevelopment. While the glutamate/glycineactivated GluN2-containing NMDA receptors (GluN1/GluN2) have been extensively studied, the physiological roles and pharmacology of glycine-activated GluN3-containing receptors (GluN1/GluN3) remain less understood. Although GluN1/GluN3 receptors exhibit unique functional properties and play distinct roles in neuronal development and synapse maturation, studies of their precise roles in neurophysiology and circuit function are impeded by limited availability of GluN3-selective pharmacological tools. This study describes UCM-A86, a novel GluN3-selective positive allosteric …

Ocean Acidification Mitigation: Potential Expansion Of Sav Restoration Strategy In The Chesapeake Bay, Cree N. Taylor

Undergraduate Research Posters

Zostera marina is a species of marine macrophyte that has been largely prioritized in past submerged aquatic vegetation (SAV) restoration initiatives within the Chesapeake Bay because of its 1) previous abundance, 2) demonstrated carbon burial abilities, and 3) observed ability for meadows of Z. marina to ameliorate low pH conditions. Due to the temperature variability and poor water quality associated with anthropogenic disturbances in the Chesapeake Bay, Z. Marina beds have experienced several die-off events with limited capacity for regrowth. This systematic review explored the possible benefits of focusing future SAV recovery initiatives on ensuring a diverse variety of SAV …

Analysis Of Differential Gene Expression In Androgen-Independent Clones Derived From The Mycap Pca Cell Line, Jessie L. Tignor, Melanie Sinanian, Richard Inho Joh, David Gewirtz, Jason Reed

Undergraduate Research Posters

Androgen deprivation therapy (ADT) is a primary treatment strategy for prostate cancer (PCa), yet many tumors eventually develop androgen independence, leading to treatment resistance. To investigate the molecular changes underlying this transition, we analyzed differential gene expression in four androgen-independent (AI) clones derived from the Myc-CaP prostate cancer cell line using RNA sequencing. Gene expression profiles were compared to the parental Myc-CaP line, and differentially expressed genes (DEGs) were identified using DESeq2 and edgeR. The AI clones exhibited significant downregulation of senescence-associated genes, including Ezh2 and lamin B1, suggesting a loss of senescence-related chromatin repression. Additionally, upregulation of Wnt pathway …

Addressing Unprofessional Behaviors In The Clinical Learning Environment: Lessons From A Multi-Year Virtual, Intergenerational, Interdisciplinary Workshop, Stacey Rose, Anita Kusnoor, Phuong Huynh, Jocelyn Greely, Yesenia Rojas-Khalil, Doris Kung, Anne Gill, Nadia Ismail, Nital Appelbaum

Faculty, Staff and Students Publications

INTRODUCTION: Optimizing the clinical learning environment (CLE) is a medical education priority nationwide.

MATERIALS AND METHODS: We developed a virtual, one-hour workshop engaging students, housestaff and faculty in small-group discussions of five case scenarios adapted from reported unprofessional behaviors in the CLE, plus didactics regarding mistreatment, microaggressions and bystander interventions.

RESULTS: Over two sessions (2021-2022), we engaged 340 students and 73 faculty/housestaff facilitators. Post-session surveys showed significant improvement in participants' ability to recognize and respond to challenges in the CLE.

DISCUSSION: Our innovative workshop, including scenarios derived from institutional reports of unprofessional behaviors, advanced participants' knowledge and commitment to improve …

Determination Of The Kinetic Parameters Of Cholesterol Oxidation Using Cholesterol Oxidase From Streptomyces Sp., Meka Saima Perdani, Heri Hermansyah, Muhamad Sahlan, Dwini Normayulisa Putri, Teguh Pambudi, Anggi Khairina Hanum Hasibuan

Makara Journal of Technology

Cholesterol oxidase (CO) was successfully produced from Streptomyces sp. via the submerged fermentation method, and 69 U/mL enzyme activity was obtained. This study aimed to determine cholesterol oxidation kinetics and the production of CO as a catalyst. The enzyme was diluted to 0.15, 0.075, and 0.00375 U/mL for the oxidation reaction. The substrate was also prepared in three concentrations: 3.23, 6.46, and 12.93 mM. The optimization of conditions for enzymatic cholesterol oxidation was investigated through measurement of the effect of initial cholesterol and enzyme concentrations. Cholesterol concentration was rapidly measured via high-performance liquid chromatography (HPLC). The kinetics of CO were …

Regulation And Function Of Mec-2 Alternative Splicing In Single Cells, Canyon Calovich-Benne

Biological Sciences Theses and Dissertations

One mechanism for generating diversity at the single cell level is selective expression of a unique set of transcription factors (TFs) and RNA binding proteins (RBPs). These regulatory factors contribute to functions of cells by controlling cell fate, turning genes on and off, and processing of transcripts either co- or post-transcriptionally. Many genes, especially neuronal genes, have multiple different splicing events, promoters, and/or polyadenylation sites. Post-transcriptional coordination is in the infancy of being studied and the functional consequences of this coupling at the single cell level has yet to be explored. Here we show, mec-2 coordination of alternative transcription start …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Molten Flux Synthesis Of Plutonium (Iv) Silicates K2Pusi2O7 And Rb2Pusi6O15, Travis K. Deason, Gregory Morrison, Amir Mofrad, Jake Amoroso, David Diprete, Theodore M. Besmann, Shanna L. Estes, Hans Conrad Zur Loye

Faculty Publications

Few plutonium containing silicates have been reported in the literature and only one other tetravalent plutonium silicate structure has been reported using the flux growth method. With the goal of understanding actinide incorporation into silicates, we describe herein two new plutonium (IV) silicates, Rb2PuSi6O15 and K2PuSi2O7, synthesized using a mixed alkali chloride/alkali fluoride flux growth. Both structures crystallize in the C2/c space group with lattice parameters a=24.2980(10) Å, b=7.1466(3) Å, c=17.2025(8) Å and 96.6560(10)° for Rb2PuSi6O15, and a=9.9478(2) Å, b=5.59820 (10) Å, c=13.1848(2) Å, and 105.7400(10)° for K2PuSi2O7. Comparisons to the synthesis of other reported alkali actinide silicates (Ce, U, …

Vimentin Inside And Outside The Cell: From Cell Spreading To Nuclear Mechanics To Covid-19, Maxx Swoger

Dissertations - ALL

Cells are constantly subjected to both external forces encountered from the extracellular environment and internal stresses generated by the cell necessary to migrate and undergo healthy cellular function. Central to the ability of cells to both generate and mediate forces is the cell cytoskeleton, which forms the muscles and bones for cells. There are three main components of the cell cytoskeleton: microtubules, actin, and intermediate filaments. The role of actin and microtubules in cell function, particularly force generation and mediation have been well studied; however, the role of intermediate filaments is less understood. Intermediate filaments represent a broad and diverse …

P85Α Degradation Mediated By Ubiquitin E3 Ligase Fbxo21 Offers Therapeutic Potential In Leukemia, Kasidy K. Weber

Theses & Dissertations

Acute myeloid leukemia (AML) is a complex and heterogeneous disease characterized by the clonal expansion of myeloid blasts in the bone marrow. Despite significant therapeutic advances over the years, the prognosis for AML patients remains dismal, with high relapse rates and poor overall survival. The ubiquitin-proteasome system (UPS) plays a critical role in maintaining cellular homeostasis by regulating the degradation of proteins involved in essential processes such as cell cycle control, DNA repair, apoptosis, and various signaling pathways. Given this vital function, targeting ubiquitin E3 ligases within the UPS presents a promising strategy for developing more effective and targeted therapies …

Quantitative Approaches To Dissect Bivalent Antibody Binding And Detect Viruses From Aerosolized Samples, Ananya Benegal

McKelvey School of Engineering Graduate Student Theses & Dissertations

Influenza A virus (IAV) poses substantial epidemiological burdens around the world, with an estimated annual global mortality rate in the hundreds of thousands. Its rapid rate of mutation gives it a propensity for causing seasonal epidemics and occasional pandemics. As an airborne virus, IAV is most commonly transmitted through droplets and aerosols. Antibodies play a crucial role in the immune defense against IAV infection. By understanding the mechanisms of antibody-mediated defense and the transmission dynamics of IAV, we can better inform strategies for prevention, vaccination, and treatment, ultimately mitigating its impact on public health. The work encompassed in this dissertation …

Chilling- And Dark-Regulated Photoprotection In Miscanthus, An Economically Important C4 Grass, Jared Haupt, Katarzyna Glowacka

Department of Biochemistry: Faculty Publications

Tolerance of chilling dictates the geographical distribution, establishment, and productivity of C4 crops. Chilling reduces enzyme rate, limiting the sink for the absorbed light energy leading to the need for quick energy dissipation via non-photochemical quenching (NPQ). Here, we characterize NPQ upon chilling in three Miscanthus accessions representing diverse chilling tolerance in C4 grasses. High chilling tolerant accessions accumulate substantial amounts of zeaxanthin during chilling nights in both field and growth chamber settings. Chilling-induced zeaxanthin accumulation in the dark enhances rate of NPQ induction by 66% in the following morning. Based on our data, the emerging ways for the unique …

Capacity-Weighted Figures-Of-Merit For Battery Transport Metrics, Cj Sturgill, Christopher Sutton, Julian Schwenzel, Morgan Stefik

Faculty Publications

New battery materials with improved transport are needed. Typical measurements yield widely varying voltage-dependent diffusivities and reporting practices are diverse. Some materials (e.g. first-order phase change) have most redox occur at a specific voltage and may be sufficiently represented by singular transport metrics. Many rapid intercalation materials, however, exhibit second-order phase transitions with redox over a broad voltage range. How should such cases be compared? The use of capacity-weighted average values is suggested where voltage-dependent metrics are consolidated into representative descriptors as figures-of-merit. Examples are elaborated where differential capacity (dQ/dV) is used to derive a …

Investigating The Expression Of C-Myc And Birc5 In Trail And Pbox-15 Treated Metastatic Prostate Cancer Cells, Corinne Kai Leng Chew, Hannah O'Toole, Daniela M. Zisterer, Seema M. Nathwani, Jade K. Pollock

SURE Journal: Science Undergraduate Research Experience Journal

Purpose Metastatic prostate cancer is associated with poor survival rate and limited treatment options. Overexpression of c-Myc and BIRC5 has been reported in prostate cancer cells which contribute to the development of the tumour environment. The specific tumour receptor mechanism of the death ligand TRAIL (tumour necrosis factor related apoptosis inducing ligand) has attracted remarkable therapeutic interest. However, many cancer cells are resistant to TRAIL monotherapy. A novel microtubule-targeting agent, PBOX-15 is known to exhibit anti-tumour activity in cancer cell lines including those with multi-drug resistance. Previous studies demonstrated that PBOX-15 is capable in sensitising cancer cells to TRAIL-mediated cell …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Design And Evaluation Of A Novel Binder Protein For Sars-Cov-2 Using The Online Game Foldit, Searre H. Abebe

The Journal of Purdue Undergraduate Research

No abstract provided.

Investigating Tumor Growth And Regulation In Supratentorial Ependymomas; The Impact Of Dlk1 And Egr1 Knockout, Om Sinojia

Honors Scholar Theses

Ependymomas (EPNs) are primary brain tumors that often arise from radial glial cells lining the ventricular system. Supratentorial ependymomas (ST-EPNs) are particularly aggressive, and understanding the molecular factors driving their growth is critical for developing targeted therapies. This study investigates the roles of DLK1 and EGR1, key regulators in cellular differentiation and tumorigenesis, in the development of ST-EPNs. We utilized genetically engineered mouse models to induce postnatal knockouts of DLK1 and EGR1 and evaluated tumor growth using histological and imaging techniques. Tumor area was quantified across multiple brain sections from both male and female mice. DLK1 knockout brains exhibited consistent …