Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

Characterization Of Adaptive Quorum Sensing In Pseudomonas Aeruginosa, Kayla Simanek

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is an opportunistic pathogen that is highly antibiotic resistant and causes tens of thousands of infections each year. It persists in hospitals by forming biofilms on medical equipment like ventilators and catheters, making it difficult to eradicate. Biofilm formation, among other virulence factors of P. aeruginosa, is regulated through quorum sensing, a mechanism of bacterial communication. Quorum sensing is primarily coordinated through LuxI-R type systems comprised of an autoinducer synthase and receptor, respectively. Canonically, the first system to be expressed is LasI-R, and LasR upregulates the second arm of the quorum sensing network, the RhlI-R system. Research …

Unleashing Serine Palmitoyltransferase In Test Tubes And Mice, Matthew W. Peart

Theses and Dissertations

Canonically known both for structural contributions to lipid bilayers and roles in cell signaling, the sphingolipids comprise a dynamic, multifaceted class of molecules which are studied to understand homeostatic cell biology as well as pathophysiology. Sphingolipids contribute to tissue-specific structures such as myelin, a multilayer membrane that allows for rapid conduction of action potentials along neuronal axons. All sphingolipids are downstream products of the rate-limiting and initiating enzyme in the de novo sphingolipid synthesis pathway, Serine palmitoyltransferase (SPT). Demonstrative of its status as the enzyme that catalyzes a crucial step in a biochemical pathway, SPT activity is strictly regulated. This …

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 …

Evaluation Of The Dnazyme Gr5 For The Determination Of Lead Speciation In Natural Waters, Gaganprit Gill

Theses and Dissertations (Comprehensive)

This thesis explores the development and application of a DNAzyme-based biosensor designed to detect labile metal species in environmental samples. Real time and on-site monitoring of labile metal fractions would make a valuable contribution to environmental management, as these fractions are the most bioavailable and pose significant toxicity risks to aquatic organisms. Conventional methods for detecting labile metals, while effective, are often burdened by high costs, complexity, and lengthy processing times, making them less ideal for rapid and widespread environmental assessments.

The first manuscript of this thesis (chapter 2) establishes the fundamental capabilities of the Pb²⁺-specific DNAzyme GR5 …

Impact Of Membrane Lipid Composition On The Structure And Function Of Uncoupling Proteins 1 And 2 From Arabidopsis Thaliana (Atucp1 And Atucp2), Elizabeth Silva

Theses and Dissertations (Comprehensive)

A proton gradient across the inner mitochondrial membrane (IMM) is required for the synthesis of adenosine triphosphate (ATP) via ATP synthase. In other words, generation of the proton gradient is coupled to the synthesis of ATP. Interestingly, uncoupling proteins (UCPs), also located in the IMM, dissipate the proton gradient, meaning that the gradient is not efficiently used for the production of ATP.¹ The mechanism of proton transport activity of UCPs has been hypothesized and widely debated for the past 20 years to also reduce oxidative stress by reducing the production of reactive oxygen species (ROS).² The majority of …

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 …

Inductions Of Long-Term Potentiation With Biomimetic Electromagnetic Fields In Primary Neurons, Cooper E. Kansala

Theses and Dissertations (Comprehensive)

Endogenous brain rhythms guide neural communication and plasticity, raising the question of whether weak, temporally structured electromagnetic fields (EMFs) that mimic these rhythms can modulate neuronal activity in a targeted, biomimetic manner. This thesis investigates whether patterned EMFs designed to reflect the temporal structure of hippocampal long-term potentiation (LTP) are more effective at inducing neural plasticity than conventional sinusoidal fields or no stimulation at all. Cortical neurons cultured from postnatal rats were exposed to patterned EMFs for 30 minutes and assessed across three distinct experimental domains. In Chapter 2, microelectrode array (MEA) recordings revealed that the LTP-patterned field significantly increased …

Conserved A-Rich Regions In The 3’ Utr Of Zika Virus Differentially Affect Viral Gene Expression, Kristen Kaytes

Electronic Theses & Dissertations (2024 - present)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until a rapidly spreading epidemic brough the virus to the global stage in 2015. Continuous advances in research have begun to further the understanding of the molecular biology of Zika virus, however much is still unknown. Much of our understanding of the virus comes from cross reference to other viruses within the same family, such as Dengue virus and West Nile virus. A commonality of these viruses is that they resemble cellular mRNAs and have a single-stranded positive-sense RNA genome that contains a 5’-cap but lacks …

Investigating Rna Dysfunction Of Inherited Neuromuscular And Neurodevelopmental Disease, Jacob H. Schroader

Electronic Theses & Dissertations (2024 - present)

ITPase deficiency is a rare but fatal, autosomal recessive enzyme deficiency involving encephalopathy, microcephaly, congenital cataracts, hypotonia, developmental delay, and dilated cardiomyopathy. Within a decade since the original description of the severe form in humans, there are huge gaps in the field regarding the underlying molecular mechanisms driving pathogenesis resulting from ITPase deficiency. Past studies have focused on characterization of the organism level ITPase-deficient phenotype, but the molecular and cellular characterization remains to be fully described. Due to the biochemical function and established biological role of the ITPase enzyme, investigation into the consequences of inosine accumulation and misincorporation into RNA …

Characterization Of The Erv41-Erv46 Complex As A Retrograde Receptor For Misfolded Secretory Proteins, John Andrew Fuesler

Dartmouth College Ph.D Dissertations

The Endoplasmic Reticulum (ER), the site of secretory protein biosynthesis

provides a favorable environment to promote polypeptide folding, protein

oligomerization and export. Although the ER contains many chaperones and other

factors that assist in protein folding, this process is error prone. Eukaryotes have

evolved protein quality control checkpoints to maintain homeostasis in the secretory

pathway, however these processes are imperfect and may result in proteotoxicity

when toxic levels or aggregates of proteins arise. Mutations in proteins involved in

trafficking in the early secretory pathway are closely associated with disease states.

Therefore, it is of great interest to further understand how …

Structural Insights Into Peptidoglycan O-Acetylation In Gram-Negative Bacteria, Tyler Malloch

Theses and Dissertations (Comprehensive)

The Centres for Disease Control has acknowledged that we are entering a post-antibiotic era, where increasing numbers of bacterial pathogens are becoming resistant to known antibiotics. One of the most successfully targeted features of bacteria is also the main component of the cell wall, peptidoglycan (PG). PG is a heteropolymer of alternating sugar residues, namely N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) which are joined together by b-(1,4)-glycosidic bonds and crosslinked via stem peptide chains. PG is a target, readily lysed by exogenous and endogenous autolysins, such as lysozyme and lytic transglycosylase, respectively. This event leads to cell death …

Exploring The Interconnections Between Mitochondrial Carrier Proteins Involved In Energy Transfer: The Case Of Uncouplig Proteins 2 And 4, Adenine Nucleotide Translocase, And Phosphate Translocase, Marzieh Tabefam

Theses and Dissertations (Comprehensive)

Mitochondrial carrier (MC) proteins play an essential role in cellular energy metabolism by mediating the transport of solutes and protons across the mitochondrial inner membrane (MIM). This thesis explores the structural and functional characteristics of three groups of MC proteins—Uncoupling Proteins (UCPs), Adenine Nucleotide Translocase (ANT), and Phosphate Translocase (P_iT)—to elucidate their individual and interrelated cooperative roles in mitochondrial proton transport and energy regulation.

The study develops and applies novel methodologies for the overexpression, purification, and reconstitution of MC proteins into model lipid bilayers mimicking the native mitochondrial inner membrane environment. These methods ensure proteins maintain their native-like …

Molecular Interactions Between The Shellfish Pathogen Vibrio Coralliilyticus Re22 And The Probiont Phaeobacter Inhibens S4sm, Jessica Coppersmith

Open Access Dissertations

Oyster larvae aquaculture is an important industry, both economically and environmentally, helping to create sustainable food systems by supplying seed oysters to farms, and also to restoration projects aimed at building coastal resilience and improving water quality by rejuvenating wild populations. However, oyster larvae are highly susceptible to rapid mortality events, crashes, which can seriously impact the industry. One source of these crashes in hatchery systems is vibriosis, caused by pathogenic species of Vibrio bacteria that are ubiquitous in temperate coastal waters, and with rising surface water temperatures their prevalence and virulence are increasing. To prevent these larval crashes from …

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 …