In Silico And In Vitro Screening Of Newly Designed Compounds Against Coxsackivirus A16 And Enterovirus A71, Amita Sripattaraphan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Outbreaks of hand, foot, and mouth disease (HFMD) occur around the world. It is caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71) that belong to the Enterovirus genus. Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir, one of the drug candidates for HFMD treatment, has been attractive for the development of its analogs with broad biological activities. This drug is an inhibitor for 3C protease of CV-A16 and EV-A71, an enzyme that plays a crucial role in the viral replication process. ). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 …

In Silico And In Vitro Studies On Inclusion Complexation Of Anthraquinone Derivatives With Beta-Cyclodextrin Derivatives, Amy Oo

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this study, we investigated the cytotoxicity of 6 anthraquinones (ventilanone K, emodin, chrysophanol, aurantio-obtusin, 1-O-methyl-2-methyoxychrysophanol, and questin) toward A549 lung cancer cells and emodin (ED) exerted the most potent cytotoxicity with IC50 value of 34.27 ± 1.27 µM. The anti-cancer activity of ED has been well reported but its usage in practical applications has been restricted due to its poor solubility. To address this issue, we performed inclusion complexation of ED with βCD, hydroxypropyl-β-cyclodextrin (HPβCD), 2,6-di-O-methyl-β-cyclodextrin (DMβCD), and sulfobutylether-β-cyclodextrin (SBEβCD) theoretically using molecular dynamics simulations and experimentally using phase solubility study and cytotoxicity screening toward cholangiocarcinoma cell lines (KKU-213A …

Mechanistic Insights Of Mitochondrial Reactive Oxygen Species In Alzheimer's Disease Models, Jakob C. Green

Theses and Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disease that results in impaired cognition, disorientation, confusion, poor judgement, and behavioral changes. The mitochondrial cascade hypothesis (MCH), which postulates that accumulating oxidative stress and mitochondrial dysfunction plays an integral role in the development of the disease, potentially upstream, in conjunction with or independent of Aβ and tau. The literature supports the critical role of mitochondrial dysfunction in the progression and development of AD, but is inconclusive about what precise role, as initiator or delegate, it performs. Regardless, the impact that oxidative stress and mitochondrial dysfunction have on AD deserves further study and investigation. …

Cryogenic Electron-Microscopy (Cryo-Em) Analysis Of Mscs, Ynai, Connexin 26 And Bioinformatic Analysis Of Cysteine And Serine In Experimental Protein Structures, Claudio Catalano

Theses and Dissertations

Functional insights into macromolecules lie in the arrangement of their molecular structures. Investigating the atomic framework of a biomolecule could unwind its biochemical mechanism, providing aid to many relevant biological questions, thus facilitating drug discovery processes. Two approaches have been used to gain knowledge at the atomic level of a protein function: experimental and computational methodologies.

From an experimental perspective, membrane proteins (MPs) were investigated. Such proteins represent ~20% of the human proteome, and ~60% of them are drug targets since they are exposed to the surface of cells and are responsible for a wide range of fundamental functions like …

Characterization Of Cytochrome P450 3a4 Structure And Ligand Binding Mechanism In Anionic Nanodiscs, David T. Sweeney

Theses and Dissertations

The Cytochromes P450 superfamily are ubiquitous throughout life and are present in some viruses. Humans encode for 57 of these enzymes that are involved in the metabolism of ~90% of all chemicals. These membrane-bound monooxygenase enzymes utilize a heme protoporphyrin at their active site to activate molecular oxygen and oxidize their substrates through an intermediate deemed nature's most powerful oxidizer. They are a powerful system at our disposal yet understanding of their structure and ligand binding mechanisms in the presence of a lipid bilayer remains poorly understood. The focus of this work is on Cytochrome P450 3A4 (CYP3A4). We set …

Development Of Unnatural Amino Acid Mutagenesis Technologies To Control Enzyme Activity And Synthesis Of Chemically Reactive Ubiquitin Probes, Jenny Cheung

Theses and Dissertations

Most of the work vital for the survival of the cell are performed by proteins. The primary sequence of proteins is composed of 20 canonical amino acids. However, these 20 amino acids do not offer the full range of functionalities needed for proteins to do their job. Often times, post-translational modifications (PTM’s) occur to add the required functional group. This interaction between all the different proteins in the proteome in addition to PTM’s create a complex system that scientists are still trying to unravel to this day. Many different tools had been developed for this purpose, and one such tool …

Interclass Gpcr Heteromerization Affects Localization And Trafficking, Rudy Toneatti

Theses and Dissertations

Class A serotonin (5-hydroxytryptamine) 2A (5-HT_2AR) and class C metabotropic glutamate 2 receptors (mGluR2) are seven transmembrane receptors (7TMRs or G protein-coupled receptors – GPCRs) involved in multiple neuropsychiatric disorders including schizophrenia. Previous findings from our laboratory reported that 5-HT_2AR and mGluR2 are dysregulated in the prefrontal cortex of patients suffering from this psychiatric condition, although 5-HT_2AR’s expression was recovered in antipsychotic-medicated patients. Genome-wide association studies on schizophrenia reported that endosomal trafficking that regulates cell surface abundance of another 7TMR implicated in this disease (dopamine D2 receptor) can be altered. Ligand-activated receptors, including the …

Development And Evaluation Of A Combinatorial Rt-Qpcr Multiplex For Forensic Body Fluid Identification, Carolyn A. Lewis

Theses and Dissertations

Body fluid identification is essential in the forensic biology workflow that assists DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the sensitivity and specificity molecular techniques can achieve; therefore, molecular methods, such as microRNA and microbial signatures, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance. A disadvantage of RNA analysis in forensic …

Detrimental Role Of Irf1 In Myeloid Cells During Influenza Infection, Bianca L. Baum

Theses and Dissertations

The influenza virus is constantly evolving new ways to overcome both innate and vaccine-induced host defenses, making the innate immune response a critical therapeutic target for minimizing morbidity and mortality caused by infection. Here we examined the role that interferon regulatory factor 1 (IRF1) plays in regulating host innate immune responses in myeloid cells. We found that knocking out IRF1 from myeloid cells in mice (IRF1^DMy) led to a partial protection during IAV infection. Interestingly, recruitment of bone marrow derived myeloid cells as well as NLRP3 inflammasome expression were decreased in the lungs of IRF1^DMy mice, whereas …

Virtual Reality Tool For Visualizing The Oral Microbiome, Alexus M. Harris

Theses and Dissertations

There are limited teaching tools for helping both students and patients understand the oral microbiome. It is important to understand the oral microbiome as it heavily influences the health of your oral cavity and the dysbiosis of disease. The oral microbiome influences other aspects of health and serves as an indicator for health. With a greater understanding of the oral microbiome, patients can make healthier lifestyle changes and dentists can better educate their patients. For that reason, the goal of this project was to create a virtual reality tool for visualizing the oral microbiome. The assets for the VR tool …

Conformational Modulation Of Α-Helical N-Acetylated Α-Synuclein, Ricardo Fernandez

Theses and Dissertations

Human N-acetylated α-synuclein (^NAcαSyn) has long been accepted as an intrinsically disordered protein (IDP) predominantly found in terminal nerve regions in healthy subjects. ^NAcαSyn structural fluidity enables the formation of transient or dynamic assemblies. Some of these assemblies may serve functional, yet undefined purposes. ^NAcαSyn is highly susceptible to the surrounding environment, leading to misfolding under high cytosolic oxidative stress conditions, which in turn assemble in the form of toxic oligomers or amyloid fibrils. These ^NAcαSyn inclusions along with their accretion and migration within neurons, are pathological hallmarks of Parkinson’s disease (PD), dementia, and multiple …

A Mechanism Behind The Mechanotransduction Of Surface Characteristics In Osteoblasts, Otto J. Juhl Iv

Theses and Dissertations

Biomaterials for use in bone regeneration and healing range from metal and metal alloy implants to hydrogel-based solutions. These materials can be optimized to increase bone healing and integration by improving the mechanical and biological properties. Regardless of the material itself, the cell-substrate interaction is key to the success of the biomaterial once implanted. Substrate surface characteristics such as roughness, wettability, and particle density are well-known contributors to a substrate’s overall osteogenic potential, and therefore the substrate's overall success. Unfortunately, it is still unknown how these substrate surface characteristics are transduced into intracellular signals by cells, preventing specific tailoring of …

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Data from screen of TP-5801 against in vitro kinases

Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

ScholarsArchive Data

The 14-3-3 family of phospho-binding proteins regulate a variety of major cellular processes through interaction with a network of dynamic proteins. Deregulation of the 14-3-3 interaction network contributes to a variety of degenerative disorders and cancers. Our lab focuses on identifying novel 14-3-3 interactions and understanding how 14-3-3 binding regulates protein function. A major gap in this process is that identifying the phospho-site where 14-3-3 docks on a given protein is time- and resource-consuming. Prediction algorithms have been developed to predict canonical 14-3-3 binding sites, however, there are many non-canonical sites that existing software is unable to predict. To fill …

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

Stomatal Conductance And Reed Canary Grass Suppression Of Native Michigan Trees, David E. Martinez Vasquez, Martin L. Vanderschoot, David Warners

Faculty and Professional Research

Reed canary grass (Phalaris arundinacea), a prominent invasive understory species, threatens native Michigan biodiversity statewide. A notable affected area includes a stretch of agricultural land along Schooley Drain in Caledonia, MI, located in the headwaters of the Plaster Creek watershed. Our study pursues the following questions: “Do native trees provide enough shade to reduce the growth of Reed canary grass?” and “Which native trees best transpire water from a floodplain?”: To answer these questions, we initiated a long-term evaluation of seven different species of native Michigan trees to investigate which species best inhibits the growth of reed canary grass and …

Plaster Creek Floodplain And Adjacent Ravines Near Stanaback Park: Botanical Inventory Highlights And Management Considerations, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the summer of 2021, the research team visited this area of ravines and floodplain a total of twenty-one times to conduct our field research. During the visits, they carefully walked throughout different sections of the study site, identifying each vascular plant species they saw growing there and observing how the flora developed throughout the season. In addition to keeping detailed field notes, they documented permanent records of the findings of our inventory by collecting voucher specimens that have been deposited in the Calvin University Herbarium. Additionally, they sent duplicate specimens to the Michigan State University Herbarium and/or University of …

Botanical Inventory Highlights And Management Considerations For Covenant Park, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the spring and summer of 2021, Calvin University students and faculty conducted a botanical inventory and assessment of the natural areas in Covenant Park, located at 3724 Shaffer Avenue SE, Kentwood, MI 49512. Given that the property was recently acquired by the City of Kentwood Parks & Recreation, the purpose of this inventory is to inform Kentwood Parks and Recreation staff about the site’s floristic quality, diversity, and ecological significance. The specific objectives of this study are to 1) provide a comprehensive inventory of the species of plants occurring on the property, 2) identify particular areas that would benefit …

On The Structure And Function Of Mitochondrial Uncoupling Proteins: The Case Of Ucp2, Afshan Ardalan

Theses and Dissertations (Comprehensive)

Uncoupling proteins (UCPs) are regulated proton transporters of the mitochondrial inner membrane. UCP-mediated proton leak negatively impacts the rate of ATP synthesis. Despite the importance of their physiological role(s) in certain tissues, molecular aspects of UCPs’ structure-function relationships are not fully understood. The current study explores the tertiary and quaternary structure of UCP2, as well as its proton transport mechanism in lipid membranes. The proteins were expressed in the E. coli inner membrane, purified and reconstituted into liposomes. Proteins were characterized by semi-native SDS-PAGE. Circular dichroism spectroscopy (CD) and fluorescence quenching assays were utilized to study the conformation of proteins …

Physiological Impacts Of Lampricides On Invasive Sea Lamprey (Petromyzon Marinus) And Non-Target Fishes, Razvan, Adrian Ionescu

Theses and Dissertations (Comprehensive)

Parasitic sea lamprey (Petromyzon marinus) ingest large quantities of blood from fishes using their oral disc and rasping tongue, most often killing the host. In the early 1900s, sea lamprey invaded the Laurentian Great Lakes, decimating sport, commercial and culturally significant fisheries. Since the early 1960s, chemical control using the lampricides 3- trifluoromethyl-4-nitrophenol (TFM) and niclosamide have helped to reduce sea lamprey populations by 90%. Lampricides are applied to larval lamprey nursery streams targeting many generations of lamprey at once. However, there is concern about the potential adverse effects of lampricides on other fishes, particularly vulnerable lake sturgeon (Acipenser fulvescens) …

A Bioinformatic Analysis Of The Biosynthesis Of Carotenoids In The Copepod Tigriopus Californicus, Anchalya Balasubramaniam

Theses and Dissertations (Comprehensive)

Abstract

Biological pigments, also called biochromes, are coloured compounds which are displayed by a variety of life forms, including animals, due to selective colour absorption. The combination of light absorption and reflection enables each pigment to portray a distinct colour which results in the broad spectrum of colours we observe in our surroundings. Carotenoids are a large group of yellow, orange, and red biological pigments found in living organisms. Our current biomolecular knowledge of carotenoids is heavily derived from studying the pathway in photosynthetic prokaryotes, bacteria, fungi, and plants. Carotenoid pigments are exceptionally multifunctional as they act as photo-protectors against …

Geometric Morphometric Analyses Define Riverine And Lacustrine Species Flocks Of Himalayan Snowtrout (Cyprinidae: Schizothorax) In Nepal, Binod Regmi, Marlis R. Douglas, David R. Edds, Michael E. Douglas

Biological Sciences Faculty Publications and Presentations

Freshwater fishes in the river and lake systems in the Himalayas and Tibetan Plateau are morphologically diverged but the evolutionary relationship of putative subspecies separated in these freshwater systems has not been explored. Snowtrout (Schizothorax spp.) are minnows (Cyprinidae) broadly distributed in Asia. Body shapes of 3 Lake Rara (northwest Nepal) endemics (S. macrophthalmus, S. nepalensis, S. raraensis) and 2 widely distributed riverine species (S. progastus, S. richardsonii) across 3 drainages in Nepal (i.e. Karnali, Gandaki, and Koshi Rivers) were studied using geometric morphometry. Data were derived from museum voucher specimens/tissues collected …