Biochemistry, Biophysics, and Structural Biology Commons^™

A Look Into Alzheimer’S Disease—Interventions At The Molecular Level, Priscila Feliciano Nieves

Honors Undergraduate Theses

There are puzzle pieces to the cure for Alzheimer’s Disease (AD), and such can emerge by inspecting the biomolecular interactions and their effects on neuronal cells. The upcoming presented literature review will cover the molecular changes caused by AD pathological progression, explore the relationship between non-AD molecules and AD molecules in the body, and analyze potential contributing factors in AD. In addition, the information to be provided will highlight medicinal alternatives respective to a particular stage in AD.

Investigation Of Dna Hybridization In Localized Systems In Close Proximity, Ashley M. Sewsankar

Honors Undergraduate Theses

Hybridization of two or more DNA or RNA strands is well documented for the process taking place with all strands free in solution or when one strand is immobilized on a substrate. This study contributes to the investigation of the hybridization process when two single DNA strands (ssDNA) are in close proximity. We took advantage of an X sensor in which hybridization of four DNA strands enables the formation of a DNA four-way junction (crossover or X) structure. We immobilized multiple layers of crossover structures to study its hybridization being triggered by short ssDNA coming from solution and further investigate …

Peripheral And Central Glucose Flux In Type I Diabetes, Jelena Anna Juras

Theses and Dissertations--Neuroscience

Diabetes is a complex metabolic disorder, of which high blood glucose concentration is the primary hallmark. Type I diabetes mellitus (T1DM) is characterized by the lack of insulin production, due to a poorly understood autoinflammatory cascade. In the words of historian Barnett “Diabetes may no longer be a death sentence, but for more and more people in the 21st century, it will become a life sentence”, making it the focal point of many research groups. It is estimated that around 20 million individuals worldwide live with T1DM.

Effects of long-term chronically elevated blood glucose are not only seen in micro/macro-vascular …

Building Tools For Improved Modulation Of The Human Gabaa Receptor, A Central Nervous System Target For The Treatment Of Anxiety, Garrett Edward Zinck

Theses and Dissertations--Pharmacy

In the U.S., anxiety is recognized as an increasing range of mentally and physically debilitating psychiatric health disorders with significant economic repercussions. Over the last 20 years, several novel anti-anxiety therapies have entered the drug development pipeline, but none have made it to market.

The work in this dissertation focused on structurally modifying valerenic acid (VA), a structurally unique carboxylated sesquiterpene acid found in Valeriana officinalis. VA is putatively reported to have allosteric modulatory activity of the human GABA_A receptor, a ligand-gated ion channel responsible for attenuating neurotransmissions. Structural modeling of VA’s GABA_A receptor interaction suggests that …

Apoe Genotype And Cerebral Glucose Metabolism: A Multi-Omics Approach, Holden C. Williams

Theses and Dissertations--Physiology

Apolipoprotein E (APOE) is encoded by the APOE gene, present in humans as three main isoforms (E2, E3, and E4). E4 carriers face up to a 15-fold increased risk for developing late-onset Alzheimer’s disease (AD), while E2 carriers are protected. Understanding the risk conferred by E4 has been an extensive research focus for nearly three decades, but the exact mechanism has yet to be proven. Many studies have demonstrated attenuated roles of E4 in classical hallmarks of AD, notably amyloid processing and neurofibrillary formation, which normally present later in disease progression. How APOE influences hallmarks that present much earlier are …

A Study Of Cobalt (Iii) Oxide Nanoparticle Delivery Of Sirna Molecules Directed Against Signaling Intermediates Of The P2y2 Receptor, Rachel Blair Stroud

Graduate Theses/Dissertations

G protein-coupled receptors are evolutionarily ubiquitous sensors of extracellular signals, propagating intracellular signal cascades through heterotrimeric G proteins. P2Y₂ receptors are GPCRs which are activated by extracellular nucleotides to mediate signaling cascades via Gαq coupling. Many GPCRs are subject to a common mechanism for signal termination involving phosphorylation of the C-terminal tail followed by β-arrestin binding and subsequent endocytic internalization of the complex. This effect has been described for the P2Y₂ R in the 1321N1 astrocytoma cell line, and UTP-induced activation and desensitization profiles have been previously defined. There is need to develop molecular vehicles for safe and …

Function And Expression Of Ribonucleotide Reductase-Encoding Genes In Flavobacterium Johnsoniae, Hunter Scott Doheny

All Graduate Theses, Dissertations, and Other Capstone Projects

Ribonucleotide reductases (RNRs) are essential enzymes that are involved in DNA synthesis. While this makes them ideal targets for antiproliferative drugs, most known RNR targeting agents are nonspecific. This poses a problem when considering antimicrobials, but several groups of bacteria have RNRs that utilize unique mechanisms that could be exploited if fully understood. One such bacteria, Flavobacterium johnsoniae, has the gene for a class Id RNR with a novel activation mechanism. Class Id RNRs belong to the aerobic class I RNRs and seem to have a unique metallocofactor and activation mechanism involving superoxide and manganese. The goal of this research …

Antibacterial Activity Of Commiphora Molmol (Myrrha) Against The Yeast, Mohammad Hassan Alshehri

Selected Full-Text Master Theses 2021-

Commiphora molmol (myrrha) is widely used as a traditional medicine around the globe against inflammatory diseases. It is also considered to be effective as anti-fungal, anti-cancer and anti-oxidant agent. The minimum inhibitory concentration, bactericidal activity and heat stability of antibiotic component in myrrha oil extract has been investigated. The MIC was determined in nutrient free buffer and in nutrient rich peptone glucose buffer. The results showed that MIC was 0.6% in nutrient free buffer as no growth was shown by cells, whereas, in peptone glucose media a slight increase in cell count was seen. It can be concluded that it …

Further Investigation Of The Initiating Mechanism Of The Type I Collagen Glomerulopathy, Matthew James Freese

Graduate Theses/Dissertations

The progressive accumulation of collagen and other extracellular matrix proteins in the renal mesangium results in fibrosis, glomerulosclerosis, and eventual renal failure. Mice deficient in integrating α2(I) collagen into the type I collagen structure, termed Col1a2-deficient mice, model kidney fibrosis through the condition Type I Collagen Glomerulopathy, because homotrimeric type I collagen accumulates extracellularly in the mesangium of renal glomeruli. Accumulation of homotrimeric type I collagen compresses blood vessels in glomeruli, which reduces filtration, increases pressure, and results in fibrosis. Picrosirius red (PSR) staining was used on Col1a2 deficient and wildtype mice to evaluate collagen deposition. Histological evaluation and …

Exosomal-Long Non-Coding Rnas Journey In Colorectal Cancer: Evil And Goodness Faces Of Key Players, Nehal I. Rizk, Ahmed I. Abulsoud, Mohamed M. Kamal, Dina H. Kassem, Nadia M. Hamdy

Pharmacy

Exosomes are nano-vesicles (NVs) secreted by cells and take part in cell-cell communications. Lately, these exosomes were proved to have dual faces in cancer. Actually, they can contribute to carcinogenesis through epithelial-mesenchymal transition (EMT), angiogenesis, metastasis and tumor microenvironment (TME) of various cancers, including colorectal cancer (CRC). On the other hand, they can be potential targets for cancer treatment. CRC is one of the most frequent tumors worldwide, with incidence rates rising in the recent decades. In its early stage, CRC is asymptomatic with poor treatment outcomes. Therefore, finding a non-invasive, early diagnostic biomarker tool and/or suitable defender to combat …

Sources And Therapeutic Strategies Of Mesenchymal Stem Cells In Regenerative Medicine, Mohamed M. Kamal, Dina H. Kassem

Pharmacy

During the past decade, mesenchymal stem cells (MSCs) have made their mark as a potential weapon in regenerative medicine. Since their first isolation by Friedenstein in the late 1970s of the last century, MSCs have opened new avenues in the field of regenerative medicine. The main fascination about MSCs lies in their ease of isolation and large ex vivo expansion capacity, as well as demonstrated multipotency and immunomodulatory activities. Basically, several reports have proved that MSCs isolated from different sources possess different characteristics and potentials. In addition, the mechanisms by which these cells can help regenerate tissues and treat several …

Protumorigenic Effects Of Mixed Lineage Kinase Domain-Like Protein In Cholangiocarcinoma Cells, Nattaya Duangthim

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cholangiocarcinoma (CCA), a heterogeneous malignancy of bile duct system, has the highest incidence in Thailand. CCA is one of the leading causes of death which has low 5-year survival rate from 5% to 10% in advanced stages due to the difficulty of diagnosis in early stage and lack of effective therapies. Therefore, understanding the molecular mechanisms and pathogenesis of CCA development and progression is urgently needs and will lead to the development of novel therapeutic targets and strategies. Mixed lineage kinase domain-like (MLKL) was identified as a key effector in a novel regulated necrosis or necroptosis pathway. Recently studies have …

Characterizing The Relationship Of Lgl1 And Akt In Migration Of Murine Neural Stem And Progenitor Cells, Natalie Pedicino

Cal Poly Humboldt theses and projects

Asymmetric cell division and migration are critical for neural stem cell differentiation and brain development. When these processes are dysregulated in neural progenitor cells (NPCs), developmental defects and diseases like glioma can result. Lgl1 is a tumor suppressor gene that was first characterized in Drosophila neuroblasts (Strand et al., 1994). It is best known for its regulation of asymmetric cell division through its association with the Par complex. The PI3K/AKT signaling cascade is involved in cellular migration and is also regulated by Par signaling. Unpublished data from the Sprowles laboratory suggests a potential role of Lgl1 in migration and other …

Investigating The Main Protease (Mpro) Of Sars-Cov-2 As A Potential Drug Target, Valerie Giovina Pascetta

Honors Theses and Capstones

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 19 (COVID-19) pandemic has claimed the lives of roughly 6.2 million people worldwide as of May 2022. The virus’s main protease (M^pro ) has been identified as an attractive drug target due to the critical role it plays in the viral life cycle. The roughly 34 kDa M^pro cleaves functional viral polypeptides out of two long polyproteins at conserved cut sites, allowing them to fulfill their role in processes like transcription and replication. Here, we have studied the enzymatic activity …

Production And Biological Activities Of Oligo Pectin From Early Immature Fruit Of Durio Zibethinus L., Aunchiya Pitaksa

Chulalongkorn University Theses and Dissertations (Chula ETD)

Early immature durian (EID) fruits, 30-45 days after anthesis with 6-12 cm in length, are considered agricultural waste from cultivation. It is known that durian rinds of mature fruits contain pectin, but there have been no reports on the pectin content of early immature durian (EID) fruits. Therefore, the objective of this study was to determine the pectin content in EID fruits. We extracted pectin from EID fruits using distilled water at different temperatures (25°C, 50°C, and 75°C) for 1 h to investigate pectin content. Instrumental analyses, including X-ray diffraction (XRD) and Fourier Transform Infrared Spectrometer (FT-IR), confirmed the presence …

Anti-Neuroinflammatory Effects Of Auricularia Polytricha Extracts On Bisphenol A (Bpa)-Induced Microglial Cell Activation And Reduction Of Hippocampal Cell Damage, Chanin Sillapachaiyaporn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Bisphenol A (BPA) is widely used in the production of polycarbonate plastics, it has been reported that BPA can activate neuroinflammation. Neuroinflammation is a brain pathology that involves the high levels of pro-inflammatory mediators, including tumor necrosis factor-alpha (TNF-α). An excessive TNF-α expression could result in neuronal cell death and subsequently lead to neurodegeneration. Auricularia polytricha (AP) is an edible mushroom with several medicinal properties. Herein, the anti-neuroinflammatory effects of AP extracts against BPA-induced BV2 microglial inflammation were investigated. Hexane (APH) and ethanol (APE) extracts of AP inhibited BPA-induced neuroinflammation in BV2 cells by reducing the expression of pro-inflammatory cytokines. …

Purification And Activity Assay Optimization Of Bacterial Catalase From Psychrobacter Koprana, Sydney Willis

Honors Program Theses

To date, catalase protein from bacterial species is not the most widely used commercial catalase. Catalase, the enzyme that breaks down hydrogen peroxide in most living organisms, is an invaluable enzyme in the food, agriculture, and pharmaceutical industries. In 2019, a novel species of a psychrotolerant bacterium was discovered in Cold Harbor, NY. This species, Psychrobacter koprana, exhibits highly active catalase. Preliminary data from activity assays demonstrates that P. koprana catalase has the same activity as commercially available catalase. After purification and activity assay optimization, the activity of this catalase has the potential to be more active than other easily …

Identifying The Role Of Cholesterol And The Cholesterol Transfer Protein, Ysp1-2, In Cell-Cell Fusion In Tetrahymena Thermophila, Natasha D. Kusibab

Honors Program Theses

A cell’s shape directly affects how it behaves as one’s structure directly correlates to its function. The shape of cells and organelles is driven in part by the lipid bilayer that makes up their membranes. The process by which cells systematically adjust the types of lipids in membranes to facilitate changes in membrane shape remain uncertain. In our research, we aimed to address this issue by studying the role of lipid transfer proteins in the ciliate, Tetrahymena thermophilia. Specifically, we focus on the process of cell-cell fusion during mating in Tetrahymena as this requires a drastic change in membrane shape …

Effects Of Azadirachta Indica Extract On Inhibition Of Glutamate-Induced Neuronal Cell Apoptosis Via Preventing Excessive Mitophagy Activation And Inhibiting Endoplasmic Reticulum Stress In Ht-22 Cells, Kuljira Mongkolpobsin

Chulalongkorn University Theses and Dissertations (Chula ETD)

Neurodegenerative diseases (NDs) are the age-related diseases which represent a major cause of mortality in aging population nowadays. Previous studies have shown that glutamate, the most abundant excitatory neurotransmitter, significantly increases in extracellular fluid of the patient’s brain and is the cause of neurodegeneration in NDs. The increase of extracellular glutamate elevates reactive oxygen species (ROS) accumulation and calcium (Ca2+) which exacerbate mitochondrial function, followed by inducing MAPK pathway and endoplasmic reticulum (ER) stress, respectively. In addition, Ca2+ overload also triggers calpain, a Ca2+ dependent protease, activity which further stimulates Cdk5/p35/p25 signaling leading to neuronal apoptosis. Azadirachta indica A. Juss. …

Type-B Energetic Processes And Their Associated Scientific Implications, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Recently, our work has identified two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type-A energy processes such as the classical heat engines, ATP hydrolysis, and many of the known chemical, electrical, and mechanical processes apparently follow well the second law of thermodynamics; Type-B energy processes, for example, the newly discovered thermotropic function that isothermally utilizes environmental heat energy to do useful work in driving ATP synthesis, follow the first law of thermodynamics (conservation of mass and energy) but do not have to be constrained by the second law, owing to its special asymmetric functions. …

Optimization And Standardization Of Dms Chemical Mapping Experiments For Probing Rna 3d Structure, Sarah Brady

Honors Program: Senior Projects (Public)

RNA plays a significant and crucial role in biological processes. The properties of RNA are ultimately responsible for each molecule’s unique function. The configuration and structural integrity of RNA is important for its functionality. Chemical mapping detailed in this thesis can be used to analyze the 3D structure of an RNA sequence. RNA is modified via methylation of adenine and cytosine bases using dimethyl sulfate, then reverse transcribed to DNA, then sequenced. The sites where the bases were methylated become mutations in the DNA sequence, allowing for identification of these locations when analyzing sequencing data. Conditions for modification can be …

Here, There, And Everywhere: Probing Ubiquitin-Cavitand Binding Via 15n-1h Hsqc, Julia Didziulis

Scripps Senior Theses

Ubiquitination and other post-translational modifications play a major role in the proliferation of many neurodegenerative diseases, developmental disorders, and cancers, and as such are subjects of recently increased biochemical interest. Expanding upon such research, this study confirmed a robust method of ubiquitin expression and purification, then used 15N-1H HSQC to analyze ubiquitin samples containing varying concentrations of a deep cavitand with affinity for lysine and arginine side chains. In the pure ubiquitin spectrum, arginine side chain chemical shifts were detected in the nitrogen 80-85 ppm range and lysine side chain signals were undetected. However, upon introduction of the cavitand, collection …

Simulation Of An Inflammatory Model Using Schwann Cells, Caitlyn E. Henry, Peyton Kimmel, Mackenzie Wilcox, Angela Asirvatham

SURF Posters 2022

Schwann cells are a type of glial cell in the peripheral nervous system that produce the myelin sheath surrounding neuronal axons. This myelin insulates the neurons and promotes the rapid conduction of electrical impulses throughout the body. Schwann cells have also been found to play a critical role in neuron repair following nerve injury. During nerve injury, the myelin sheath is damaged, stimulating Schwann cells to release cytokines, or inflammatory mediators, that recruit immune cells to the site of injury so that the myelin debris can be cleared, and repair can take place.1 Then neuronal growth is facilitated by heregulin …

An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont

Graduate Student Theses, Dissertations, & Professional Papers

Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …

Genomic Instability At A Polypurine/Polypyrimidine Repeat Sequence, Nathen S. Zavada

Browse all Theses and Dissertations

Microsatellite repeat sequences have been shown to induce replication stalling, fork collapse, double-strand breaks (DSBs), and possibly stimulate break-induced replication. In this study we use a dual-fluorescent HeLa model that is designed to monitor recombination at an ectopic site through use of flow cytometry and inverse PCR with a microsatellite in the lagging strand for DNA synthesis. To test the stability of the 78 bp polypurine/pyrimidine repeat from the PDK1 locus, we subjected cells to replication stress drugs designed to induce DSBs and measure break-induced replication (BIR). The study revealed that polypurine repeat cells undergo endogenous stress contributing to instability …

Sequential Block Copolymers Of Polyisobutylene And Polyolefins, Manwel Labib

Williams Honors College, Honors Research Projects

A two-step approach will be utilized to synthesize random polyolefin multiblock-copolymers. This strategy takes advantage of a,w-terminated telechelic polyolefins. Polypropylene (iPP)/polyethylene (PE) are picked because of their strength, and polyisobutylene (PIB) because of its hemocompatibility. This copolymer is theorized to make for robust bio-inert plastic, which can be used for surgical mesh implants.

Mimicking The Namib Desert Beetle With Hydrophilic And Hydrophobic Surfaces, Tyler Bracewell

Williams Honors College, Honors Research Projects

The Namib Desert beetle, Stenocara gracilipes, condenses fog that rolls in off the west coast of Namibia to provide itself with the water it needs for the day. By lifting its abdomen into the air to collect the water vapor, it condenses on hydrophilic bumps that are about 500μm in diameter and are spaced apart about 500-1500μm. Once the water reaches a critical size, the droplet rolls off the hydrophilic bump and onto the flat hydrophobic surface of the elytra. Since the beetle is angled with its abdomen in the air, the water rolls down to its mouth. A …

Characterizing The Post-Translational Modifications Of The Pro-Oncogenic Type Ii Transmembrane Serine Protease Tmprss13, Carly Elizabeth Martin

Wayne State University Dissertations

TMPRSS13, a type II transmembrane serine protease discovered at the turn of the century, has recently been shown to be significantly overexpressed in both breast cancer (BCa) and colorectal cancer (CRC), and to mediate chemoresistance in cell lines from both cancer types. Furthermore, loss of TMPRSS13 in a genetic model of mouse mammary carcinoma significantly reduced tumor burden and growth rate, and increased overall tumor-free survival. Its location on the cell surface as well as its low expression in normal breast and colon make TMPRSS13 an attractive candidate as an oncogenic biomarker and therapeutic target in cancer. However, little is …

Deconstructing Brown Adipocyte Neogenesis In Brown And White Adipose Tissue, Rayanne Burl

Wayne State University Dissertations

Global incidence of Type 2 Diabetes (T2D) has reached epidemic proportions, and increasing evidence indicates that dysfunctional adipose tissue is an important contributor to the pathogenesis of T2D. Expanding brown adipocyte (BA) populations within adipose tissues through adrenergic activation improves energy balance and insulin sensitivity. In order to exploit this remodeling of adipose tissue for therapeutic benefit, we need to understand the mechanisms by which adrenergic signaling expand populations of BAs in vivo. These studies utilized single-cell RNA-sequencing and transgenic mouse models, in combination with single-molecule fluorescence in situ hybridization (smFISH) and immunoistochemical analysis, to study BA neogenesis in vivo. …

Fluorescent Cellular Assays For Kinase Inhibitors, Myar Mohamed

Graduate Research Theses & Dissertations

One of the most successful and fastest growing groups of kinase inhibitors are small molecules that compete with ATP binding. Kinase function is closely related to many diseases, specifically cancer. Kinases within living cells are essential elements in signaling cascades and post-translational modifications. However, actual kinase activity and the efficacy of its inhibitors in living systems are hard to evaluate. A way to assess inhibitor activity is through cellular assays that directly report the inhibitor’s engagement in native environments. Our goal is to develop a simple near-infrared (NIR) fluorescent HTS-compatible cellular assay for kinase inhibitor profiling in native cellular environments. …