Digital Commons Network^™

Converting Hydrazone-Based Photoswitches Into Functional Materials, Sirun Yang

Dartmouth College Ph.D Dissertations

The development of new classes of molecular switches with enhanced performance and brand-new functionalities enables practitioners to push the frontiers of adaptive materials. In the realm of photoswitches, the bistability of hydrazones (i.e., molecules that incorporate the C=N-NH functional group) allows for the kinetic trapping of polymer and supramolecular assemblies resulting in multistate actuation and emergent phenomena that are not tractable with other photoswitches. This property has transformed hydrazone photoswitches into powerful tools that can be used in understanding fundamental molecular interactions and how to apply them in modulating the physicochemical properties of materials.

Progressing from disordered to …

Identification Of Nitrates Within Coldwater Cave, Blake Schany, Joshua Sebree

Fall 2022 - Chemical Analysis Class Projects

Agricultural runoff has the potential to greatly damage the ecosystem of Coldwater Cave. Agricultural runoff includes elements found in herbicides and fertilizers used on crops as well as increased amounts of nitrogen in the water due to runoff from cattle sites. Identification of the presence of water soluble pollutants from cattle feedlot runoff and toxic components found in common herbicides used in maintaining cropland within the cave is needed to address the potential damage that the contaminants can do to the ecosystem of the cave. Identifying contaminants present within the cave systems using UV Vis will allow for more targeted …

Chemical Interactions And Cytotoxicity Of Terpene And Diluent Vaping Ingredients, Yanira Baldovinos, Alexandra Archer, James C. Salamanca, Robert M. Strongin, Christie Sayes

Chemistry Faculty Publications and Presentations

Vaping devices have risen in popularity since their inception in 2007. The practice involves using a variety of commercially available devices. Internal heating systems in devices aerosolize e-liquid formulations of complex mixtures including an active ingredient (e.g., THC, CBD, and nicotine), diluents (or cutting agents), solvents, and flavoring agents (e.g., terpenes and aldehydes). The vaping toxicology literature consists of cytotoxicity studies of individual chemicals and commercial formulas. Because of the variation of e-liquid composition, there is a limited understanding of the toxicity of ingredient combinations. This study analyzed the cytotoxic effects after exposure to individual and binary mixtures of a …

Evaluating The Impact Of Submarine Groundwater Discharge On Nutrients And Trace Elements In Coastal Systems: The Examples Of The Tuckean Swamp (Australia) And The Mississippi Sound (Usa), Amy Moody

Dissertations

Submarine groundwater discharge (SGD) is the advective flow of both fresh terrestrial groundwater and recirculating seawater through aquifer sediments, which is released into the coastal ocean. In this dissertation, I evaluated the impact of SGD on the distributions and input of trace metals and nutrients. In the Tuckean Swamp, an estuary in Australia dominated by coastal acid sulfate soils, I determined the impact of groundwater on Ba and U during the flood season, when the local aquifer is flushed out after a rapid increase in water table elevation. For Ba and U, groundwater contributed up to 18 and 66 % …

Deciphering The Molecular Circuitry That Controls Iron Regulation In Non-Pathogenic Yeast, Debolina Hati

Theses and Dissertations

The trace metal iron is essential for the survival of almost all living organisms. It is a co-factor for many proteins involved in a variety of vital functions such as respiration, nitrogen fixation, and DNA biosynthesis, to name a few. Iron homeostasis in non-pathogenic fungi such as Schizosaccharomyces pombe has been extensively studied over the past few decades to better understand how intracellular iron is regulated under different environmental conditions. Iron regulation in S. pombe is controlled by two Fe-responsive transcriptional repressors known as Php4 and Fep1. Both rely on iron-sulfur (Fe-S) clusters as signals to balance iron acquisition, storage, …

Stemficohort1preinterviewdata, Rebecca L. Sansom, Bryn Stclair, Jamie Jensen, Richard West

ScholarsArchive Data

The science, technology, engineering, and mathematics faculty institute (STEMFI) is a National Science Foundation funded project designed to provide support, measurement, and training to BYU faculty developing their own student-centered curriculum.

This PDF file contains pre-institute participation interview data from the first cohort of faculty involved in the STEM faculty institute (2018).

Mechanistic Insights Into An Iron-Responsive Repressor, Fep1, From Schizosaccharomyces Pombe, Allison Nicole Kimsey

Theses and Dissertations

Iron is an essential metal cofactor required for a variety of biochemical pathways in most living organisms. In recent years, the nonpathogenic fungi Schizosaccharomyces pombe has been used to study iron regulation and uncover the molecular mechanisms for controlling intracellular iron levels. Some of these regulation pathways are conserved with those of pathogenic fungi, making these studies applicable for the future development of antifungals that target iron homeostasis. In S. pombe, the GATA-type transcriptional repressor Fep1 is responsible for repressing iron uptake genes during times of iron abundance. Previous reports have proposed that the binding of an iron-sulfur (Fe-S) …

Characterization Of The Interaction Between Grx4-Bol2 And The Iron-Responsive Transcription Factor Aft1 In Candida Glabrata, Evan A. Talib

Theses and Dissertations

Iron is an indispensable protein cofactor that plays a critical role in biological functions such as cellular respiration. However, excess iron causes cellular damage via the generation of reactive oxygen species. To obtain optimal intracellular iron levels, eukaryotic cells have developed mechanisms to tightly regulate iron levels. The molecular mechanism for iron regulation in the pathogenic yeast Candida glabrata has not yet been explored, although this yeast bears iron regulation pathways that are very similar to the model yeast Saccharomyces cerevisiae. Understanding how C. glabrata regulates iron levels is critical for the treatment of infections caused by this opportunistic …

Redefining The Catalytic Hect Domain Boundaries For The Hect E3 Ubiquitin Ligase Family, Emma I. Kane, Steven A. Beasley, Johanna M. Schafer, Justine E. Bohl, Young Sun Lee, Kayla J. Rich, Elizabeth F. Bosia, Donald E. Spratt

Chemistry

There are 28 unique human members of the homologous to E6AP C-terminus (HECT) E3 ubiquitin ligase family. Each member of the HECT E3 ubiquitin ligases contains a conserved bilobal HECT domain of approximately 350 residues found near their C-termini that is responsible for their respective ubiquitylation activities. Recent studies have begun to elucidate specific roles that each HECT E3 ubiquitin ligase has in various cancers, age-induced neurodegeneration, and neurological disorders. New structural models have been recently released for some of the HECT E3 ubiquitin ligases, but many HECT domain structures have yet to be examined due to chronic insolubility and/or …

Reversible Dioxygen Binding To Co(Ii) Complexes With Noninnocent Ligands, Praveen Kumar, Laxmi Devkota, Maximilian C. Casey, Anne A. Fischer, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

A series of mononuclear Co(II) complexes with noninnocent (redox-active) ligands are prepared that exhibit metal–ligand cooperativity during the reversible binding of O₂. The complexes have the general formula, [Co^II(L^S,N)(Tp^R2)] (R = Me, Ph), where L^S,N is a bidentate o-aminothiophenolate and Tp^R2 is a hydrotris(pyrazol-1-yl)borate scorpionate with R-substituents at the 3- and 5-positions. Exposure to O₂ at room temperature results in one-electron oxidation and deprotonation of L^S,N. The oxidized derivatives possess substantial “singlet diradical” character arising from antiferromagnetic coupling between an iminothiosemiquinonate (ITSQ^•–) …

Advances Of Biowaste-Derived Porous Carbon And Carbon–Manganese Dioxide Composite In Supercapacitors: A Review, A. Zekenova, M. Nazhipkyzy, Wanlu Li, A. Kalybayeva, G. Zhumanova, O. Zubova

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

One of the global problems is environmental pollution by different biowaste. To solve the problem, biowaste must be recycled. Waste-free technology is also a way of saving exhaustible raw materials. Research on electrochemical energy sources is currently the most dynamically developing area of off-grid energy. Electrochemical capacitors can operate for a long time without changing performance, they have smaller dimensions, high mechanical strength, and a wide operating temperature range. These properties are effective energy-saving devices. Therefore, supercapacitors are widely used in various industries. This review discussed the methods of obtaining and the characteristics of biowaste-derived activated carbon and carbon–manganese oxide …

Structural And Functional Studies Of Mtr4 And The Tramp Rna Surveillance Complex, Sean Johnson

Funded Research Records

No abstract provided.

Generation Of Geochemical Exploration Targets From Regional Stream Sediment Data Using Principal Component And Factor Analysis: A Case Study Of Kibaya-Kiteto, Manyara-Tanzania, Yusto J. Shine, Charles D. Moye, Godfrey J. Mallya, Ambaliche L. Tamambele

Tanzania Journal of Science

A regional-scale stream sediment geochemical sampling was carried out with an average sampling density of one sample per nine square-kilometre in Kiteto District, Manyara Region. A total of 358 stream sediment samples were collected and analysed for major and trace elements by X-ray fluorescence (XRF) and fire assay with atomic absorption spectrometry (AAS) finish methods. In this study, Factor and Principal Component Multivariate (FPCM) analyses have been used to the stream geochemical data to delineate potential mineralization zones by plotting correlated factors as geochemical anomaly maps. Four factors that account for 73.7% of the total variance of the stream sediment …

Mineralogy And Geochemistry Of The Asanje Iron Ore Deposit Within The Mayamaya-Hombolo Belt, Dodoma Region, Central Tanzania, Yusto J. Shine, Michael M. Msabi, Jagarlamudi Seetharamaiah

Tanzania Journal of Science

This paper presents the mineralogy and chemical composition including iron ore impurities to ascertain its suitability for industrial applications. The Asanje iron ore deposit is hosted in Precambrian volcano-sedimentary rocks in the Mayamaya-Hombolo Belt in Dodoma region, within the Lake Nyanza Superterrane. Iron ores are found in two parallel ridges trending NW-SE. Ridge I occurs as vein and banded hematite-type ore and Ridge II as massive-type ore. A total of 24 ore samples were analysed for major and trace elements by XRF and petrographic studies by optical microscopy and XRD. The XRD results revealed that hematite and goethite are the …

Evaluation Of Natural Antifungal Compounds From Artemisia Afra And Its Effectiveness On Prevention Of Aflatoxins, Noela G. Kilenga, Daniel Maeda, Oscar Kibazohi, Lilian D. Kaale

Tanzania Journal of Science

Artemisia afra is a medicinal plant with antimicrobial activities, known to treat tuberculosis, measles, cough, and influenza. In consequence, its applications have increasingly become pivotal to control various microbes which cause different diseases. This study therefore, evaluated the chemical composition and the antifungal activity of A. afra essential oil. The extraction of essential oil was done using steam distillation. The essential oil chemical composition was analysed by GC-MS. The analysis revealed 19 compounds from A. afra. The main compounds were borneol (71.529%), terpinen-4-ol (8.582%), β-thujone (3.283%), β-terpineol (2.590%), α-terpineol (1.791%), chrysanthenone (1.507%), myrtenal (1.393%), eucalyptol (1,8-cineole) (1.263%), cis-sabinene hydrate (1.172%) …

Leveraging The Structure Of Dnaja1 To Discover Novel Potential Pancreatic Cancer Therapies, Heidi E. Roth, Aline De Lima Leite, Nicolas Y. Palermo, Robert Powers

Department of Chemistry: Faculty Publications

Pancreatic cancer remains one of the deadliest forms of cancer with a 5-year survival rate of only 11%. Difficult diagnosis and limited treatment options are the major causes of the poor outcome for pancreatic cancer. The human protein DNAJA1 has been proposed as a potential therapeutic target for pancreatic cancer, but its cellular and biological functions remain unclear. Previous studies have suggested that DNAJA10s cellular activity may be dependent upon its protein binding partners. To further investigate this assertion, the first 107 amino acid structures of DNAJA1 were solved by NMR, which includes the classical J-domain and its associated linker …

Recent Development Of Low Iridium Electrocatalysts Toward Efficient Water Oxidation, Jing Ni, Zhao-Ping Shi, Xian Wang, Yi-Bo Wang, Hong-Xiang Wu, Chang-Peng Liu, Jun-Jie Ge, Wei Xing

Journal of Electrochemistry

Developing high-performance and low-cost electrocatalysts for oxygen evolution reaction (OER) is the key to implementing polymer electrolyte membrane water electrolyzer (PEMWE) for hydrogen production. To date, iridium (Ir) is the state-of-the-art OER catalyst, but still suffers from the insufficient activity and scarce earth abundance, which results in high cost both in stack and electricity. Design low-Ir catalysts with enhanced activity and stability that can match the requirements of high current and long-term operation in PEMWE is thus highly desired, which necessitate a deep understanding of acidic OER mechanisms, unique insights of material design strategies, and reliable performance evaluation norm, especially …

Interpretable Machine Learning Models For Molecular Design Of Tyrosine Kinase Inhibitors Using Variational Autoencoders And Perturbation-Based Approach Of Chemical Space Exploration, Keerthi Krishnan, Ryan Kassab, Steve Agajanian, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In the current study, we introduce an integrative machine learning strategy for the autonomous molecular design of protein kinase inhibitors using variational autoencoders and a novel cluster-based perturbation approach for exploration of the chemical latent space. The proposed strategy combines autoencoder-based embedding of small molecules with a cluster-based perturbation approach for efficient navigation of the latent space and a feature-based kinase inhibition likelihood classifier that guides optimization of the molecular properties and targeted molecular design. In the proposed generative approach, molecules sharing similar structures tend to cluster in the latent space, and interpolating between two molecules in the latent space …

Electrospun Poly(3-Hydroxybutyrate-Co-3-Hydroxyvalerate)/Olive Leaf Extract Fiber Mesh As Prospective Bio-Based Scaffold For Wound Healing, Jose Gustavo De La Ossa, Serena Danti, Jasmine Esposito Salsano, Bahareh Azimi, Veronika Tempesti, Niccoletta Barbani, Maria Digiacomo, Marco Macchia, Mohammed Jasim Uddin, Caterina Cristallini

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Polyhydroxyalkanoates (PHAs) are a family of biopolyesters synthesized by various microorganisms. Due to their biocompatibility and biodegradation, PHAs have been proposed for biomedical applications, including tissue engineering scaffolds. Olive leaf extract (OLE) can be obtained from agri-food biowaste and is a source of polyphenols with remarkable antioxidant properties. This study aimed at incorporating OLE inside poly(hydroxybutyrate-co-hydroxyvalerate) (PHBHV) fibers via electrospinning to obtain bioactive bio-based blends that are useful in wound healing. PHBHV/OLE electrospun fibers with a size of 1.29 ± 0.34 µm were obtained. Fourier transform infrared chemical analysis showed a uniform surface distribution of hydrophilic -OH groups, confirming the …

Reactivity Of Aminophenols In Forming Nitrogen-Containing Brown Carbon From Iron-Catalyzed Reactions, Hind A. Al-Abadleh, Fatemeh Motaghedi, Wisam Mohammed, Md Sohel Rana, Kotiba A. Malek, Dewansh Rastogi, Akua A. Asa-Awuku, Marcelo I. Guzman

Chemistry Faculty Publications

Nitrogen-containing organic carbon (NOC) in atmospheric particles is an important class of brown carbon (BrC). Redox active NOC like aminophenols received little attention in their ability to form BrC. Here we show that iron can catalyze dark oxidative oligomerization of o- and p-aminophenols under simulated aerosol and cloud conditions (pH 1–7, and ionic strength 0.01–1 M). Homogeneous aqueous phase reactions were conducted using soluble Fe(III), where particle growth/agglomeration were monitored using dynamic light scattering. Mass yield experiments of insoluble soot-like dark brown to black particles were as high as 40%. Hygroscopicity growth factors (κ) of these …

Ligand-Based Virtual Screening And Molecular Docking Of Benzimidazoles As Potential Inhibitors Of Triosephosphate Isomerase Identified New Trypanocidal Agents, Lenci K. Vazquez-Jimenez, Alfredo Juarez-Saldivar, Rogelio Gomez-Escobedo, Timoteo Delgado-Maldonado, Domingo Mendez-Alvarez, Isidro Palos, Debasish Bandyopadhyay, Carlos Gaona-Lopez, Eyra Ortiz-Perez, Benjamin Nogueda-Torres, Esther Ramirez-Moreno, Gildardo Rivera

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Trypanosoma cruzi (T. cruzi) is a parasite that affects humans and other mammals. T. cruzi depends on glycolysis as a source of adenosine triphosphate (ATP) supply, and triosephosphate isomerase (TIM) plays a key role in this metabolic pathway. This enzyme is an attractive target for the design of new trypanocidal drugs. In this study, a ligand-based virtual screening (LBVS) from the ZINC15 database using benzimidazole as a scaffold was accomplished. Later, a molecular docking on the interface of T. cruzi TIM (TcTIM) was performed and the compounds were grouped by interaction profiles. Subsequently, a selection of compounds was made based …

A Blind Benchmark Of Analysis Tools To Infer Kinetic Rate Constants From Single-Molecule Fret Trajectories, Dorothy A. Erie, Lydia Kisley, Dushani Dunukara

Faculty Scholarship

Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise …

Chemical Investigation And Drug Discovery Potential Of Terpenoid Secondary Metabolites From Three Deep-Sea Irish Soft Corals, Joshua Thomas Welsch

USF Tampa Graduate Theses and Dissertations

Secondary metabolites produced primarily by terrestrial plants and animals have provided the basis for treatments and cures of human diseases as far back as historians have been able to probe. However, recent technological advances including the self-contained underwater breathing apparatus, and even further remotely operated vehicles, have allowed researchers a unique opportunity for targeted collection of marine organisms at depths previously thought to possess conditions unsustainable for life as was understood. This has afforded a glimpse into the potential for not only life, but the potential for new biochemical adaptations developed over billions of years that have been evolutionarily developed …

In Silico Evaluation Of The Antimalarial Potential Of The Phytoconstituents Of The Azadirachta Indica Plant, Areh E.T., Atolani O., Kambizi L

Al-Bahir

Background and Objectives: Malaria, a parasitic protozoan disease caused primarily by Plasmodium falciparum, has killed millions of people in Africa, particularly those with meager or no access to orthodox medical facilities and therapies. Extracts from the Azadirachta indica (neem) plant is believed to possess antimalaria properties among the locals that rely on herbs. Numerous in - vivo studies have suggested the antimalarial properties of neem extract and phytochemicals. This study employs an in - silico method through molecular docking techniques to provide insight while adding credence to the antimalarial potential of phytochemicals of neem plants as claimed …

Multimodal Cotranslational Interactions Direct Assembly Of The Human Multi-Trna Synthetase Complex, Krishnendu Khan, Briana Long, Valentin Gogonea, Gauravi M. Deshpande, Kommireddy Vasu, Paul L. Fox

Chemistry Faculty Publications

Amino acid ligation to cognate transfer RNAs (tRNAs) is catalyzed by aminoacyl-tRNA synthetases (aaRSs)-essential interpreters of the genetic code during translation. Mammalian cells harbor 20 cytoplasmic aaRSs, out of which 9 (in 8 proteins), with 3 non-aaRS proteins, AIMPs 1 to 3, form the similar to 1.25-MDa multi-tRNA synthetase complex (MSC). The function of MSC remains uncertain, as does its mechanism of assembly. Constituents of multiprotein complexes encounter obstacles during assembly, including inappropriate interactions, topological constraints, premature degradation of unassembled subunits, and suboptimal stoichiometry. To facilitate orderly and efficient complex formation, some complexes are assembled cotranslationally by a mechanism in …

Chemical Composition Of Kombucha, Peyton Bishop, Eric R. Pitts, Drew Budner, Katherine A. Thompson-Witrick

Chemistry

Kombucha is a fermented sweetened tea with a mixed fermenting culture of yeast and acetic acid bacteria. While the history of kombucha is not completely clear, it is now available around the world and has shown an increase in availability and demand in the United States market. The proponents of kombucha consumption tout the varied health benefits it can provide. The final kombucha flavor and composition is a function of both the initial tea used and the fermentation process. While the ascribed benefits are varied and numerous, the number of direct studies has been limited. This review focuses on the …

Visible Light Photocatalysis Of Organic Reactions In H2o, Sankarsan Biswas

Dissertations, Theses, and Capstone Projects

Visible-light photocatalysis in H₂O provides an attractive, green alternative to typical organic synthesis, which often involves toxic solvents, metal catalysts, and large energy demands. Hence, there is a growing need for an efficient photocatalytic methods that use either aqueous media as a solvent or can proceed solvent-free. However, commercially available photocatalysts do not work well for aqueous photocatalysis. Supramolecular systems in particular have been explored recently to address these issues associated with aqueous photocatalysis. Chapter 1 will review recent advances in aqueous supramolecular photocatalysis with examples of different supramolecular systems and how they have addressed some of the …

Application Of Peo-Ppo-Peo Triblock Copolymers In Synthesis Of Silica And Organosilica Nanomaterials, Shu Zhang

Dissertations, Theses, and Capstone Projects

In this dissertation, the research work focused on the application of Pluronic triblock copolymers, poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO), in the synthesis of mesoporous material, such as double-helical silica nanotube structures as well as bridged organosilica nanotubes by using swollen micelles of Pluronic surfactants and their mixtures. Chapter 1 introduced the background and several important mesoporous structures, and the relevant topics in this dissertation, such as, silica nanotubes, helical silica nanotubes, silica vesicles and organosilica nanotubes. Chapter 2, continued research works from earlier published paper (ACS Nano 2021, 15, 1016-1029), discussed static treatment and stirring effect on the formation of …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …