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Aloe Barbadensis Rinds Employ Physical And Chemical Defense Mechanisms Against Insect Herbivores With Varying Success, Zachary Johnson, Ishveen Kaur, Fernando Castillo, Rupesh R. Kariyat, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences Faculty Publications

Plants deter herbivory through a suite of physical and chemical defenses. While most studies have focused on understanding one or the other, efficient plant defense against herbivory is often cumulative. To examine this, we used Aloe barbadensis (Asphodelaceae) as a model, since in natural settings, the species is found to be well-defended against insect herbivores. To start with, we hypothesized that the epicuticular wax potentially plays an important role in herbivore defense as the major physical defense. To test our hypothesis, we conducted bioactivity-guided extraction and polarity-based fractionation of A. barbadensis rinds. We then mixed them into an artificial diet, …

Exploring Protein Conformations And Functions Through Molecular Dynamics Simulations And Machine Learning, Hao Tian

Chemistry Theses and Dissertations

Proteins are essential biomacromolecules that perform a variety of critical functions in living organisms. The tertiary structure of a protein plays a crucial role in its biological activity as it determines how the protein interacts with other molecules. Consequently, understanding protein conformation and function is an important area of research with implications in medicine, biotechnology, and other fields.

The first part of this dissertation focuses on protein allostery, a process by which proteins transmit perturbations caused by binding at one site to a distal site, thereby regulating activity. With the development of computational methods like molecular dynamics simulations and machine …

Evaluation Of A Radium-Thorium Disequilibrium Sediment Method Used To Model And Assess Porewater And Submarine Groundwater Exchange In The Coastal Marsh, Madeline R. Bodine

Theses and Dissertations

Ground, pore, and surface water exchange has been extensively studied in beach and near shore environments but has been long neglected in saltmarsh systems due to their complexity. Saltmarsh systems are of particular importance as they are the interface between fresh and saltwater. Saltmarshes impact carbon exchange, release and sequestration, and they process particulate matter. Understanding the characteristics of a marsh system such as the nutrient and particulate loads in conjunction with the flux of water exchange through the marsh provides a deeper understanding of these systems and can impact our understanding of the global water and carbon cycles, as …

Phenotypic And Target-Based Drug Discovery, Angelica Veronica Carmona

Theses & Dissertations

Batten Disease or Neuronal Ceroid Lipofuscinosis (NCL) is a group of rare, fatal, inherited pediatric neurodegenerative lysosomal storage disorders. NCLs are characterized by intracellular accumulation of an auto-fluorescent lipopigment called ceroid lipofuscin and neurodegeneration. Several forms of NCLs exist, some of which share some of the same features and symptoms but vary in severity and onset of symptoms with respect to age. Some common symptoms include progressive loss of vision, mental and motor deterioration, epileptic seizures, premature death, and in the rare adult-onset, dementia. Subtypes of NCLs occur when one of 13 different genes are mutated, and only two subtypes …

Toward The Yeast Surface Display Of Microviridin B, Jillian Leigh Stafford

Chemistry and Chemical Biology ETDs

Humans have turned to natural products for medicinal therapeutics for millennia. In recent years, the ribosomally synthesized and post-translationally modified peptide (RiPP) class of natural products have garnered a lot of attention due to their ability for heterologous expression, relative ease of mutation, and vast biological activates. Microviridins are a family of RiPPs that contain a tricyclic cage-like structure through the formation of two lactone rings and one lactam ring catalyzed by two ATP-grasp ligase family enzymes. Microviridins are potent inhibitors of serine proteases and mutational studies of a small number of residues indicates the potential of peptide engineering protease …

Simulating A Flexible Water Model As Rigid: Best Practices And Lessons Learned, Raymond Weldon, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models …

Biophysical And Structural Characterization Of Non-Canonical Dna Structures, Paul C. Seth , '23

Senior Theses, Projects, and Awards

G-quadruplex (GQ) and i-motif (iM) non-canonical DNA structures can be formed by G- and C-rich sequences within the genome, respectively. GQ and iM DNA play important roles in different biological processes and are promising therapeutic targets. Recently, the first left-handed GQ (LHGQ) was discovered and much remains to be learned about the structure and function of LHGQ DNA.

In this thesis, we investigate the biophysical and structural behavior of two LHGQ-forming sequences from the human genome, from the Human Solute Carrier 1 (SLC) and nuclear receptor binding SET domain (NSD) genes. We found that flanking bases play an important role …

Engineering Of Bio-Based And Synthetic Polymers: Synthesis And Application In Superabsorbent Materials And Antibacterial Agents, Jihyeon Hwang

Theses and Dissertations

A polymer consists of a large number of monomer units, which can be obtained naturally or via a chemical process called polymerization. Polymers are important materials that are used in our daily life. Life would not be possible without these polymers, either from plant biomass or petroleum-derived synthetic polymers. The substitution of petroleum-derived to biomass-based polymers has been highlighted to mitigate adverse environmental impact. However, the use of bio-based polymers is still a significant challenge for more demanding applications. In this dissertation work, the engineering of both bio-based and synthetic polymers and their properties are investigated.

In Chapter 1, the …

Coordination Environment And Thermodynamics Of Colloidal Quantum Dots In Polar Solvents, Nuwanthaka Prasad Jayaweera Millaniyage

Theses and Dissertations

Colloidal semiconductor quantum dots (QDs) have been extensively investigated due to their attractive properties such as size-tunable absorption and emission spectra, large molar extinction coefficients, and significant photostability. These properties make them promising candidates for optoelectronic, photocatalytic, and biomedical applications. Common synthetic procedures of QDs produce nanocrystals capped with long-chain fatty acid derivatives which are stabilized in high boiling point solvents. Especially for bioimaging applications, the exchange of these native hydrophobic ligands with hydrophilic ligands should be performed, while preserving the smaller hydrodynamic radius. The coordination environment and thermodynamic parameters of the ligand exchanges should be carefully investigated to engineer …

Molecular Devices For Measuring Weak Solvophobic Interactions And The Development Of Pedagogical Tools For Organic Chemistry Students, Alexander N. Manzewitsch

Theses and Dissertations

The main topics of this dissertation are: 1) the development and discussion of a new molecular balance for measuring alkyl-alkyl interactions in a wide array of organic solvents, 2) the development of linear solvation energy relationships between solvent interaction parameters and solvent accessible surface area (SASA) in CH-arene interactions, and 3) the development of online resources for helping undergraduate students perform organic chemistry mechanisms problems well.

The solvophobic effect, that is the forced association between two solutes due to intermolecular attraction of the solvent molecules, is ubiquitous in organic chemistry and responsible for many significant phenomena thereof. However, there is …

Mapping Per- And Polyfluoroalkyl Substances (Pfas) In South Carolina Surface Waters: Are There Hotspots?, Thomas C. Geiger

Senior Theses

Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals used in consumer products for their unique chemical properties. PFAS compounds are resistant to water, oil, heat, and grease, making them useful for a wide variety of everyday items such as non-stick cooking pans, food packaging, electronics, carpets, upholstery, paints, adhesives, and personal care products.¹ The resilient nature of PFAS has made these compounds immensely popular with consumers but has since been considered a potential environmental and public health hazard for their ability to bioaccumulate and for their stability in the environment. More than 6000 PFAS have been discovered in the …

Development Of Innovative Multi-Drug Approaches To Counteract Illicit Drug Abuse In The Uae Population, Manal Ali Alhefeiti

Dissertations

The abuse of addictive substances is on the rise in the United Arab Emirates (UAE) population. Consequently, the UAE government spends about Dhs 5.5 billion annually on the rehabilitation of drug addicts. Blood, urine, and hair tests can reveal signs of sporadic or chronic drug use. Given the list of banned chemicals in the UAE, our main objective in this work was to develop a novel analytical method to identify and measure banned substances, especially prescription and over-the-counter drugs in the UAE. We developed and validated a rapid, sensitive and reliable liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) approach for the targeted …

Nano-Supported Biocatalysts For Efficient Wastewater Remediation, Khadega Abobaker Al-Maqdi

Dissertations

The existence of various bioactive organic pollutants in wastewater and municipal water sources has raised concerns regarding their potential effects on human health. As a result, different techniques are being explored to effectively break down these persistent organic pollutants. Peroxidases have recently emerged as a new approach to remediation that may have advantages over traditional methods. However, evaluating the effectiveness of different peroxidases in breaking down various emerging pollutants can be time-consuming and difficult. In this study, a quick and reliable method was developed to test the degradability of 21 emerging pollutants by five different peroxidases (soybean peroxidase, chloroperoxidase, lactoperoxidase, …

Sustainable Approaches To Photo-, Thermo-, And Electro-Chemical Reactions Of Amines, James David Sitter

Theses and Dissertations

In recent years, sustainable routes for chemical synthesis have garnered renewed interest. As the world continues to fight pollution and rising costs, it is imperative that new routes of synthesis that continuously fight the issues of pollution and waste are discovered, defined and explored. While traditional synthesis routes that require energy input typically require the burning of fossil fuels to produce heat, the amount of resources that go into the production of these fossil fuels and the sequestration of its waste to minimize its impact on the carbon footprint is enormous. Furthermore, sustainable chemistry research aims to decrease and minimize …

Vaccinia Virus And Measles Virus As Oncolytic Vaccines: The Modulation Of The Viral Infectivity Via Surface Conjugations, Monchupa Kingsak

Theses and Dissertations

Oncolytic virus (OV) therapy has been shown to be an effective targeted cancer therapy treatment in recent years, providing an avenue of treatment that poses no damage to surrounding healthy tissues. Not only do OVs cause direct oncolysis, but they also amplify both innate and adaptive immune responses generating long-term antitumor immunity. However, a key challenge facing oncolytic virotherapy is neutralizing antibodies in vaccinated patients, leading to the viral clearance after systemic administration and failure in the treatment. The encapsulation of OVs using biocompatible polymers is one of the promising methods to prevent the viral clearance from antiviral immune responses. …

Biochemical, Structural, And Immunological Characterization Of Selected Panallergens, Andrea Leigh O'Malley

Theses and Dissertations

Allergies throughout the world are increasing in prevalence and severity. Although the direct causes of the development of allergies are not confirmed, study of proteins that cause reactions will lead to a deeper understanding of allergy. This work focuses on three panallergen families, profilins, parvalbumins, and arginine kinases, to further elucidate the background of allergy from the point of view of the allergens themselves. In Chapter 1, we evaluate pollen, fruit, and mite profilins in the context of allergy, showing the relevance of conserved cysteine residues in stability and oligomerization as well as the first data on cross-reactivity between plant …

Using Caulobacter Crescentus As A Model To Probe The Environmental Reactivity Of Silver Nanoparticles, Madeline M. Farber , '23

Senior Theses, Projects, and Awards

Silver nanoparticles (AgNPs) are an increasingly common environmental pollutant with antimicrobial and antibacterial properties. The elucidation of their interaction with cellular membranes and subsequent mechanisms of toxicity are critical areas of research that need to be better understood in order to manage potential adverse environmental effects. This work investigates the interaction of AgNPs with large unilamellar vesicles (LUVs) as a model membrane system. Similar studies conducted by others in this field have largely been conducted with uncoated AgNPs, ignoring the effect of environmental conditions on the formation of an eco-corona on AgNPs. Thus, in this study, the spent medium (SM) …

Method Design For Separation Of Non-Canonical Dna Structures Via Capillary Electrophoresis, Erin V. Chen , '23

Senior Theses, Projects, and Awards

G-quadruplex DNA structures are highly relevant subjects of biochemical study, implicated in human diseases and cancer. Conventional methods for G-quadruplex DNA structure separation are time-consuming, environmentally unfriendly, and low throughput. Thus, there is a pressing need for alternative methods of separation to be developed for G-quadruplex DNAs. Here we present work in designing a separation method using the capillary electrophoresis instrument. Capillary electrophoresis is a highly automated, reusable, and quantitative technique that separates analytes based on their size and charge. A capillary method for G-quadruplex separation would be a valuable analytical tool to supplement the biophysical methods available by addressing …

Dipole Cooperativity And Polarization Frustration Determine The Secondary Structure Distribution Of Short Alanine Peptides In Water, Ying Yuan, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar …

Pc-01 Synthesis Of Zinc Glycoconjugated Phthalocyanines As A Potential Phototherapeutic, Jessica A. Silva-Conejo, Katrina Mccarter, Tessa Greene, Joshua V. Ruppel

SC Upstate Research Symposium

Photodynamic Therapy (PDT) uses photosensitizers that are activated by light to produce singlet oxygen that can cause cell damage and potential cell death. Phthalocyanines are promising photosensitizers due to their absorption at clinically relevant wavelengths, meaning that they absorb at a wavelength that can penetrate deeper into tissues.

One challenge with using Phthalocyanines is that they have very low solubility in biological media. One potential approach to increase solubility is through glycoconjugation. Glycoconjugation can also be used as a strategy to increase selectivity toward targeted tissues. Glycoconjugated phthalocyanines can be synthesized using a copper catalyzed azide-alkyne cycloaddition reaction, otherwise known …

Considerations For Curricular Reform In Undergraduate Chemistry: Cooperative Adoption Factors, Modeling Social Influence, And Focusing On Specific Populations, Jacob D. Mcalpin

USF Tampa Graduate Theses and Dissertations

This dissertation will go through the details of three projects highlighting considerations for curricular reforms in undergraduate chemistry. Improving the teaching of chemistry is facilitated by considering the problem from multiple directions, namely, faculty and students. In addition to the multiple perspectives, this dissertation also seeks to bring new methodologies into the spotlight to improve the toolbox for other chemistry or discipline-based education researchers. Additionally, this dissertation has shown in several locations how focusing in on subgroups within populations can reveal findings that would not have been apparent from a global average of the population. The three project describes in …

Potential Of Kaolin Clay On Formulation Of Water Based Drilling Mud Reinforced With Biopolymer, Surfactant, And Limestone, Paul M. Omary, Emanuel X. Ricky, Naswibu A. Kasimu, Makungu M. Madirisha, Kessy F. Kilulya, Esther H. J. Lugwisha

Tanzania Journal of Science

Drilling the wellbore into subsurface formations is the earliest stage in the life of a well that requires a suitable drilling fluid with good rheological and filtration control characteristics to achieve a successful drilling operation. This paper reports on the formulation of water-based drilling mud using kaolin clay reinforced with biopolymer, surfactant, and limestone from Tanzania. The raw materials used for the formulation were characterized using XRD, XRF, FTIR, and TGA techniques. The rheological properties, filtration loss, pH, and density of the formulated mud were measured using a viscometer, filter press, pH meter, and mud balance, respectively. The XRD results …

Interdisciplinary Diffusion Lab, Sable Rosana Canales, Chloe Gaban

Andrews University Teaching and Learning Conference

Diffusion is a principle in Physics, Chemistry, and Biology. Students can model the rate of diffusion based on particle size by contrasting blue and yellow dyes. Two petri dishes containing agar-agar receive a drop of dye at the center. The radius of expansion is recorded over time and variance increases linearly with time. Diffusion constants vary by particle size, allowing for a size ratio comparison between blue and yellow dyes. Relating the data to cells, students predict that smaller molecules diffuse into living cells, whereas larger molecules need some assistance from protein channels as in facilitated diffusion.

Traffic Lights For Catalysis: Stimuli-Responsive Molecular And Extended Catalytic Systems, Grace C. Thaggard, Johanna Haimeri, Roland A. Fischer Prof. Dr., Kyoung Chul Park, Natalia B. Shustova Prof. Dr.

Faculty Publications

The advances made in the field of stimuli-responsive catalysis during the last five years with a focus on the novel recently-emerged directions and applications have been surveyed. Metal-free catalysts and organometallic complexes, as well as biomimetic systems and extended structures, which display switchable catalytic activity for a variety of organic transformations, are discussed. Light-activated systems comprised of photochromic molecules capable of modulating reaction rate, yield, or enantioselectivity based on geometric and electronic changes associated with photoisomerization are the focus of the detailed discussion. Alternative stimuli, including pH and temperature, which could be applied either alone or in combination with light, …

Using Augmented Reality For Geometry Learning: Indonesian Elementary School Teachers' Experiences, Asep Nuryadin, Karlimah Karlimah, Dindin Abdul Muiz Lidinillah, Ika Fitri Apriani, Ikairn Rachmawati Putri, Lilis Susilawati, Ginna Islamiati, Dede Nurhidayah

Jurnal Pendidikan Sains

This study aims to discover Indonesian elementary school teachers' experiences (n = 257) of using Augmented Reality (AR) for learning, especially related to one of the topics in mathematics learning, namely, geometry. AR is considered to be an alternative instructional media that can be utilized for teaching geometry, including the topic of three-dimensional shapes. A questionnaire consisting of both close-ended and open-ended questions was used to collect data in this study. This study has successfully revealed teachers' use of digital instructional media during the COVID-19 pandemic, their familiarity with AR, frequency of AR use for geometry learning, and challenges in …

Application Of The Recitation Method To Improve The Competence Of Medical Laboratory Technology Students In The Immunology Field, Patricia Gita Naully, Perdina Nursidika

Jurnal Pendidikan Sains

An accredited mid-level MLT (Medical Laboratory Technology) must have the competence to perform medical laboratory examinations from pre-analytic, analytic, and post-analytic stages in several fields, one of which is immunology. Many D3 MLT students are facing obstacles to passed the immunology course. This obstacle is not only experienced by students of D3 MLT but also by medical students, pharmacy students, and similar majors. The purpose of this research is to determine the effect of recitation method in the form of animation video making and immunology based device on the competence of Diploma 3 (D3) MLT students. This research is a …

The Influence Of The 5e Learning Cycle Strategy With A Link Map On Students' Mastery Of Physics Concepts And Science Process Skills, Dian Farida Rosanti, Markus Diantoro, Sentot Kusairi, Erni Yulianti

Jurnal Pendidikan Sains

Link maps help students correlate interconcepts in order to facilitate students mastery of the concept learned. The researcher accompanied the link map in learning to find out its effect on concept mastery and students science process skills. This study used a quasi-experimental research design by providing a posttest only for the control group. The sample consisted of two classes, divided into an experimental class and a control class. The experimental class was taught using the 5E learning cycle strategy accompanied by a link map, and the control class was taught using the 5E learning cycle strategy only. The results of …

Epistemological Obstacles Of Students In Accomplishing Hots Tests According To Field-Dependent Cognitive Style, Widi Candika Pakaya, Fattah Hanurawan

Jurnal Pendidikan Sains

The main goal of this study is to describe the epistemological obstacles faced by students with field-dependent cognitive styles when attempting to solve HOTS questions. This study uses a qualitative-descriptive methodology. The instruments used are cognitive style tests and HOTS questions. Data is collected through interviews and student work. The research subjects were two participants in third-semester PGSD students at Universitas Negeri Gorontalo. In this study, the data were analyzed by identifying the answers of two respondents to the indicators of epistemological barriers that had been done by the students and then interviewing the respondents. The results of this study …

Ecoliteracy Analysis And Science Teaching Materials: A Survey In Junior High Schools, Ghina Nisrina Ramadhanti, Indarini Dwi Pursitasari, Indriyani Rachman

Jurnal Pendidikan Sains

The study aims to analyze ecoliteracy and the teaching materials required for 21st century learning these days. The study employs the survey method by involving population of 104 junior high school students in grade VIII in Bogor City. The data are collected using ecoliteracy tests and interviews and analyzed using descriptive statistics techniques. The results showed that 48 students (46.15%) fall into the category of lacking ecoliteracy cognitive competence. The results of the questionnaire on the competence of attitudes, skills, and human relations with nature fall into the medium category. Therefore, in order to support the improvement of students’ ecoliteracy, …

Increased Efficiency Of A Functional Sod Mimic Achieved With Pyridine Modification On A Pyclen-Based Copper(Ii) Complex, Magy A. Mekhail, Katherine J. Smith, David M. Freire, Kristof Pota, Nam Nguyen, Marianne E. Burnett, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of Cu(II) complexes with the formula [Cu^RPyN₃]²⁺ varying in substitution on the pyridine ring were investigated as superoxide dismutase (SOD) mimics to identify the most efficient reaction rates produced by a synthetic, water-soluble copper-based SOD mimic reported to date. The resulting Cu(II) complexes were characterized by X-ray diffraction analysis, UV–visible spectroscopy, cyclic voltammetry, and metal-binding (log β) affinities. Unique to this approach, the modifications to the pyridine ring of the PyN₃ parent system tune the redox potential while exhibiting high binding stabilities without changing the coordination environment of the metal complex within …