Biochemistry, Biophysics, and Structural Biology Commons^™

Structural And Functional Consequences Of Pde6 Prenylation In Rod And Cone Photoreceptors, Faezeh Moakedi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Phosphodiesterase-6 (PDE6) serves as a pivotal component in the phototransduction pathways of both cone and rod photoreceptors. In cones, PDE6 consists of tetrameric subunits: inhibitory (γ') and catalytic (α'). The catalytic subunit, PDE6α', contains a C-terminal prenylation motif. Deletion of this motif is associated with achromatopsia (ACHM), a form of color blindness. The mechanisms underlying the disease and the roles of PDE6 lipidation in vision remain elusive. Meanwhile, rod PDE6 is composed of α and β catalytic subunits and γ inhibitory subunits, with alterations in the C-terminal "prenylation motif" of PDE6β linked to retinitis pigmentosa (RP) pathology. In this comprehensive …

Characterizing 4,4’-Methylene Diphenyl Diisocyanate Exposure In Primary Human Epidermal Keratinocytes: A Multi-Omics Approach, Brandon F. Law

Graduate Theses, Dissertations, and Problem Reports (ETD)

Exploring the routes of exposure and biological fate of 4,4’-methylene diphenyl diisocyanate (MDI) has been a challenge for many years. Occupational exposure to MDI can result in the development of occupational asthma (MDI-OA) which results in loss of productivity, large economic costs, and costs to the individual worker. Initially, it was thought that respiratory exposure to MDI was the most likely route leading to MDI-OA. Industries utilizing MDI have been successful at controlling airborne concentrations according to industrial hygiene assessment and newly diagnosed cases of MDI-OA decreased and plateaued. New research suggests that dermal exposures to MDI may explain this …

Evaluating The Efficacy Of The Archaeal Proteasome To Alleviate Protein-Misfolding Retinopathy, Celine Brooks

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nearly all neurodegenerative diseases (NDs) and some eye diseases are characterized by the presence of misfolded and aggregated proteins. The ubiquitin proteasome system (UPS) is responsible for degrading the majority of proteins including misfolded and aggregated proteins. However, in NDs the performance of the UPS is impaired, and this impairment partially comes from these protein aggregates inhibiting the proteasome. This inhibition leads to an accumulation of protein aggregates, more proteasomal inhibition, and fewer chaperones for newly synthesized proteins, triggering a collapse in proteostasis, which is thought to contribute to the pathogenesis of NDs. Consequently, stimulating proteasome function is being investigated …

Hybridization And Duplex Stability Of Peptide Nucleic Acid Containing An Azobenzene Switch, Carmen J. Velasquez

College of Graduate Studies: Theses & Dissertations

Light-driven molecular switches that can be turned on and off on demand have found many biological applications. For DNA, RNA, and synthetic derivatives, the switch can be used to interfere with a hybridization event with a complementary strand. To explore this potential, we have synthesized three light-sensitive PNA which have an azobenzene group (PNA-5azo5 and PNA-4azo4), and two azobenzene groups (PNA-2azo5azo2) as part of the PNA backbone. UV experiments were used to verify the conversion to the cis-isomer from the initial trans state for all of the single-stranded Azo-PNA ( PNA-5azo5, PNA-4azo4, and PNA-2azo5azo2) by irradiating at 365 nm …

Quantitative Raman Analysis Of Human Blood Serum Of Glaucoma Patients Supplemented With Macular Pigment Carotenoids., Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh J. Byrne

Datasets

Carotenoids have been widely studied for their high dietary, antioxidant, and vision protection roles in the human body. Blood contains all major dietary carotenoids and hence presents as a suitable and efficient substrate for the estimation of dietary carotenoids in vivo. Following the 18-month supplementation of open angle glaucoma patients with macula pigment carotenoids (Lutein, Zeaxanthin and Meso-Zeaxanthin) in the European Nutrition in Glaucoma Management (ENIGMA) trial, Raman spectroscopic analysis of the pre-supplementation baseline and 18-month supplemented blood serum carotenoids from participants was carried out, to investigate the systemic impact of supplementation in the blood and explore a more direct …

Drosophila Parasitoids Go To Space: Unexpected Effects Of Spaceflight On Hosts And Their Parasitoids, Jennifer Chou, Johnny R. Ramroop, Amanda M. Saravia-Butler, Brian Wey, Matthew P. Lera, Medaya L. Torres, Mary Ellen Heavner, Janani Iyer, Siddhita D. Mhatre, Sharmila Bhattacharya, Shubha Govind

Publications and Research

While fruit flies (Drosophila melanogaster) and humans exhibit immune system dysfunction in space, studies examining their immune systems’ interactions with natural parasites in space are lacking. Drosophila parasitoid wasps modify blood cell function to suppress host immunity. In this study, naive and parasitized ground and space flies from a tumor-free control and a blood tumor-bearing mutant strain were examined. Inflammation-related genes were activated in space in both fly strains. Whereas control flies did not develop tumors, tumor burden increased in the space-returned tumor-bearing mutants. Surprisingly, control flies were more sensitive to spaceflight than mutant flies; many of their …

Alopecia As An Early Clinical Marker For Azathioprine Induced Myelosuppression: A Case Report, Nilanjana Dutta , Final Year Mbbs, Dr. M Suresh Babu , Professor, Dr. Subramanian Ramaswamy , Professor, Dr. Mahabaleshwar Mamadapur , Assistant Professor

Digital Journal of Clinical Medicine

Azathioprine is a pro-drug and is metabolized by the TPMT enzyme in the body. In South Asians, Azathioprine is known to cause alopecia and bone marrow suppression in patients with TPMT enzyme deficiency. In India, the prevalence of TPMT mutation varies from 1.2- 10%. A new mutation was detected in 2014, NUDT15 whose incidence varies from 8.5-16%. Patients with mutation in both TPMT and NUDT15 develop myelosuppression faster. In our case, alopecia manifested as the first clinical feature of Azathioprine myelosuppression. Physicians need to recognize early clinical clues (alopecia) to avoid the impending development of myelosuppression and to look for …

Investigations Of A Nox2 Activator, P47phox, Px Domain Membrane Anchoring Interactions And Inhibition, Angela Develin

Theses and Dissertations

The regulation of cellular signaling across plasma membranes is a well-organized process through cross-talk of biomolecules such as proteins and membranes. Peripheral membrane proteins (PMPs) are a class of water soluble, membrane associated, proteins that play a critical role in transducing such signals. Due to the dynamic nature of their membrane interactions, relatively smooth surfaces, and general lack of deep ligand binding pockets, PMPs are commonly associated with an approximate 85% of the human proteome that is classified as ‘undruggable’ by current drug discovery methodologies. One such PMP, p47^phox, contains a PX domain which is essential in activation …

Single-Molecule Pulldown (Simpull) For Detection Of Gpcr Complexes In Mammalian Cells, Julie M. Kraft

Theses and Dissertations

G protein-coupled receptors (GPCRs) constitute the most numerous and diverse superfamily of cell membrane receptors. While GPCRs can perform signal transduction as monomers, evidence suggests they also function as homo- and hetero- dimers and oligomers. These diverse quaternary structures can affect GPCRs’ downstream cellular signaling, pharmacological properties, and regulation of internalization.

The single-molecule pulldown (SiMPull) assay combines a co-immunoprecipitation assay with single-molecule total internal reflection fluorescence (TIRF) microscopy and can be used to probe the stoichiometry of GPCR oligomers in mammalian cells.

This project replicates the SiMPull assay by confirming the quaternary structure of mGluR2 homodimers. Plasmid constructs SNAP-mGluR2-HA and …

Mechanistic Analysis Of Four-Way Dna Junctions And Cytokine-Binding Aptamers For Therapeutic Interventions, Roaa S. Mahmoud

Theses and Dissertations

DNA is inherently dynamic and topologically diverse and can fold into many different structures. Besides the canonical Watson-Crick structure, other higher-order structures such as G-quadruplexes (G4), i-motifs (iM), and four-way DNA junctions are possible. Although these high-order DNA structures are known to form transiently, they are important due to the crucial roles they play in many cellular processes including DNA replication, recombination, and repair. Among these DNA structures, 4-way junctions (also known as Holliday junctions, HJ) which are formed during the repair of double-strand DNA breaks (DSBs) and interact with proteins have garnered significant attention due to their central role …

Synthesis And Biophysical Analysis Of Modified Cell-Penetrating Peptides, Joel Mitchell

Theses and Dissertations (Comprehensive)

Cell-penetrating peptides (CPPs) are a family of peptides that have the ability to penetrate biological membranes. They were discovered in the late 1980s and have been the topic of many studies. Much of the interest in CPPs has been due to their ability to translocate biological membranes, and the possibility that they could offer a novel drug delivery method by conjugation to biologically active molecules. Linear CPPs can be modified to form cyclic structures. This change in structure has been observed to enhance the stability and penetrative ability of the CPPs which have been studied. The current thesis focuses on …

Structural And Functional Analysis Of The Putatively Virulent Gene Products Tde1414, Tde1511, And Tde2714 From The Oral Pathogen Treponema Denticola, Brock W. Corbett

Theses and Dissertations (Comprehensive)

Periodontitis is a destructive polymicrobial disease of the teeth and gums characterized by dental plaque biofilms on the tooth surface, severe inflammation of surrounding gum tissues, and the resorption of alveolar bone. Discussed as one of the most prevalent conditions plaguing humankind, increased clinical parameters of periodontitis is associated with the increased presence of three bacteria known as the “red complex”: Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Various transcriptomic and proteomic studies of T. denticola when incorporated into mature biofilms have illuminated key gene targets the bacterium may use as virulence factors to aid in pathogenesis. …

Characterizing The Targeting Pathway Of Chloroplast Outer Membrane Protein Oep18 In Arabidopsis Thaliana And Other Targeting Signals Utilized By Outer Envelope Membrane Proteins, Ceaira Hiemstra

Theses and Dissertations (Comprehensive)

Approximately 95% of chloroplast proteins are encoded by nuclear DNA and are post-translationally targeted to the chloroplast. Over half of the 138 known or predicted chloroplast outer membrane (OM) proteins are predicted to utilize four non-canonical targeting pathways. The first two pathways are characterized by containing a single α-helical transmembrane domain (TMD) within the first or last 50 amino acids (AAs), the third pathway is utilized by β-barrels, and the last requires an N-terminal cleavable transit peptide (TP). Recently, a fifth novel pathway called Toc159-like (TOC159L) has been characterized by the presence of a C-terminal reverse TP in Toc159. Subsequent …

Inactive Metallopeptidase Homologs: The Secret Lives Of Pseudopeptidases, Peter Lyons

Faculty Publications

Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. …

Investigating The Roles Of Dapk, P53/Cep-1, And Mitochondrial Damage In Necrotic Neurodegeneration In C. Elegans, Anil Singh

Dissertations and Theses

Stroke is one of the leading causes of death in the U.S., with minority groups, suffering higher fatality rates. Stroke is caused by ischemia, where occlusion of blood supply to the brain results in neurodegeneration. Most of the damage is attributed to excitotoxicity, where an accumulation of the neurotransmitter glutamate in the synapse overstimulates postsynaptic neurons and ultimately leads to cell death (largely by necrosis). Stroke treatments are often ineffective, due to the delay between the onset of stroke and the delivery of effective treatment. To address this, we focus our study on putative later-acting mediators of excitotoxicity such as …

A Phytochemical Analysis Of Secondary Metabolites In Eupatorium Serotinum, Elise Snow

Theses and Dissertations

Phytochemistry, a subset of Natural Products Chemistry, studies chemically derived products from natural substances. Advances in this field have important applications in medicinal research due to the distinctive and unique properties of natural compounds. All metabolites are produced from the metabolic cycle, which is a pathway that provides energy for the organism. These metabolic compounds vary greatly and are classified based on their function within the organism. Primary metabolites are abundant and contribute to organism growth, development, and maintenance of energy. Secondary metabolites are found in lesser quantity and correlate to natural defense mechanisms. For example, salicylic acid is a …

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …

The Study Of Ribosome-Amplified Metabolism, Rambo, Effect In Vitro And In Live Cells, Jianchao Yu

Electronic Theses & Dissertations (2024 - present)

Quinary interactions arise due to the extreme macromolecular crowding inside live cells. Quinary interactions affect intracellular protein stability, activity, and homeostasis. Ribosomes, traditionally known for their role in protein synthesis, have been found to engage in quinary interactions with metabolic enzymes, modulating their activity and thereby revealing a potential regulatory role for ribosomes in cellular metabolism. This phenomenon, termed the Ribosome-Amplified MetaBOlism (RAMBO) effect, was investigated in this dissertation through a series of in vitro and in vivo studies using primarily Nuclear Magnetic Resonance (NMR) spectroscopy.

Firstly, an NMR-based direct enzyme assay compatible with ribosome was developed and validated using …

Novel Photobase Generators For Photoinduced Polymerization And Ph Regulation, Shupei Yu

Dissertations

Photochemistry encompasses the investigation of chemical processes instigated by light absorption. As important branches of photochemistry, photosensitive and optical materials have attracted extensive research interests in both academia and industry. Photosensitive and optical materials are composed of polymers / small molecules with photo-responsive properties. These materials not only can absorb light in the desired energy spectrum, but also exhibit chemical / physical reactions, which can be applied to different fields such as photoredox, photo-heat, phototherapy, solar cells, diodes, etc. Among them, photobase generators (PBGs) are a series of photosensitive compounds, which absorb the incident light, then release the basic species …

The Effect Of Walnut Shell Ash On The Properties Of Cement Paste And Mortar: A Study On Partial Replacement Of Cement, Ali Shebli, Jamal Khatib, Adel Elkordi

BAU Journal - Science and Technology

In the pursuit of a more sustainable future, the utilization of agricultural waste in cementitious products has emerged as a popular and effective solution. The current study explores the feasibility of incorporating ash derived from walnut nutshells, considered agro residues, into eco-friendly blended cement paste and mortars to examine its impact on their properties. A range of blended cement mixtures was formulated by incorporating walnut shell ash (WSA) in three varying proportions of 5%, 10%, and 15% relative to the weight of the cement. Tests were conducted to investigate the properties of the blended cement paste and mortar incorporating WSA, …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Comparative Histological Study On The Algerian Thymus Ciliatus At Different Phenological Stages, Nina Sadou, Ratiba Seridi, Hamdi Bendif

Journal of Bioresource Management

The aim of the current study was to compare the histological observations of stems, leaves, and different secretory structures of Thymus ciliatus at three phenological stages. The anatomical observations of stems, leaves, and glandular trichomes were carried out by light microscopy. The results showed that phenological stages do not affect significantly the anatomical, whereas there was a significant increase in secretory trichomes. The glandular trichomes are distributed on the surface of the stems and the leaves. There are only two distinct types of secretory trichomes, Peltate consisting of a basal cell, a stalk cell, and an 8-celled head type, which …

Structural Basis For Dna Proofreading, Gina Buchel, Ashok Nayak, Karl Herbine, Azadeh Sarfallah, Viktoriia Sokolova, Angelica Zamudio-Ochoa, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement …

The Mechanobiology Of Cell Plasticity, Yuan Hong

McKelvey School of Engineering Graduate Student Theses & Dissertations

The cell is a sophisticated machine, integrating chemical and physical inputs to decide upon the mechanobiological outputs that the body requires every second, in cardiomyocytes that make heartbeats, in fibroblasts that heal wounds, and in sarcomeres that contract muscles. Malfunction of mechanotransduction or mechanical inputs is implicated in diseases such as fibrosis, cancers, and cardiomyopathies, and a pressing quest is underway to unravel the intricacies of how mechanical force orchestrates the activation of cells. This dissertation explores these fundamental mechanisms of cell activation using integrated mathematical and engineered cell culture models. The work begins with the discovery that the directionality …

The Potential Of Stem Cell Therapy In Multiple Sclerosis Treatment: A Review, Sorina Amarculesei, Ava O'Meara Cushen, Cathy Brougham

SURE Journal: Science Undergraduate Research Experience Journal

Multiple Sclerosis is an autoimmune and neurodegenerative disease of the central nervous system. There are currently 2.8 million people living with Multiple Sclerosis worldwide, including 9000 people in Ireland, with a prevalence of 193 per 100,000 people. Symptoms of Multiple Sclerosis include sensory loss, fatigue, cognitive dysfunction, spasticity, depression, optic neuritis, gait ataxia, diplopia, and loss of bladder control. Currently, there is no standardised treatment or cure for Multiple Sclerosis with many strategies focusing on symptoms. Stem cells have emerged as promising approaches for Multiple Sclerosis therapeutics. Clinical trials primarily focus on mesenchymal stem cell-based therapies for Multiple Sclerosis. Furthermore, …

Creating Meaningful Connections With The Electron Transport Chain Beyond A Virtual Classroom, Lesley-Ann Giddings

Feminist Pedagogy

At the center of feminist pedagogy is community. Creating community within the classroom and between the class and local communities increases student engagement and access to knowledge. Communities can be a source of solidarity and further decenter authority in the classroom, empowering students, teachers, and the surrounding community to be co-learners. Amid the COVID-19 pandemic, remote teaching posed challenges to student engagement. Here, I describe an assignment used to build an inclusive community of co-learners within a virtual biochemistry class and our local communities. Oxidative phosphorylation is a cellular process used to create energy that depends on the electron transport …

Physically And Chemically‑Crosslinked L‑Arginine‑Loaded Polyvinyl Alcohol‑ Hyaluronic Acid‑ Cellulose Nanocrystals Hydrogel Membranes For Wound Healing: Influence Of Crosslinking Methods On Biological Performance Of Membranes In‑Vitro, Elbadawy A. Kamoun, Elbadawy A. Kamoun

Nanotechnology Research Centre

Two types of polyvinyl alcohol-blended hyaluronic acid and cellulose nanocrystals (PVA/HA/CNCs) hydrogels membranes were developed as delivery agents for L-arginine using chemical/and/physical crosslinking methods for exploring biological performance of the obtained membranes. Chemically and physically/crosslinked membranes were fabricated by solution-casting and freeze-thawing techniques, respectively. The characterization of the crosslinked PVA/HA/CNCs/Larginine membranes were conducted by SEM, FTIR, TGA, swelling ratio, and in—vitro L-arginine release. Furthermore, applying two types of crosslinked membranes in vitro were investigated in terms of cytotoxicity, hemocompatibility, and cell adhesion affinity of HFB-4 cell line. Chemical and physical-crosslinked membranes were verified through the esterification and hydrogen bonds interactions, …

Air-Jet Bioprinting Of Stem Cell-Encapsulated Alginate Micro-Droplets For Organoid Biomanufacturing, Mirabella B. Stump

Electronic Theses and Dissertations

Biomanufactured 3D-organoids show promise for modeling and treating various conditions, particularly insulin-dependent diabetes mellitus (type-1 diabetes). Pancreatic islet organoids serve as sustainable sources of insulin-producing β-cells, potentially restoring insulin regulation in patients and providing a long-term solution for diabetes. Hydrogel droplet printing is an emerging technique in regenerative medicine due to its advantageous tunability and biocompatibility; however, challenges of consistency, quality control, and scalability persist. To address these issues, we developed a novel air-jetting based droplet bioprinting system for the generation of monodispersed alginate micro-droplets. The objective of this project was to incorporate human induced pluripotent stem cells (hiPSCs) into …

Targeting Metabolic Switches And Dna Damage Repair For The Treatment Of Human Diseases, Rasangi Chathurika Kankanam Pathirage

Theses & Dissertations

Tuberculosis and Cancer treatments share common challenges due to prolonged therapy, the necessity of combination therapy and severe side effects. Characterization of novel drug targets and identification of new drugs modulating such targets within the context of multidrug treatments will contribute to overcoming current therapeutic challenges.

Tuberculosis (TB) is one of the challenging diseases to treat due to the persistence of Mycobacterium tuberculosis (Mtb) in the dormant phase. Current TB drugs are more effective toward actively dividing bacteria and less effective toward dormant bacteria. The metabolic transition between actively dividing bacteria and dormant bacteria is driven by pivotal metabolic enzymes …

Characterization Of Trafficking And Metabolic Functions Of The Endocytic Regulator Ehd1 In Ewing Sarcoma, Sukanya Chakraborty

Theses & Dissertations

Ewing sarcoma (EWS) is the second most common bone malignancy in children and adolescents. Despite improvement in survival due to advances in multimodality treatment strategies, patients with metastatic or recurrent disease have very poor outcomes. Overexpression of the EPS15 Homology Domain containing 1 (EHD1) protein has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown.

Studies presented in this dissertation establish that EHD1 overexpression is a feature of nearly 90% EWS patient tumors with high EHD1 expression specifying shorter patient survival. ShRNA-knockdown and …