Digital Commons Network^™

The Water, Ji Kim

Open Educational Resources

Water is everywhere, thus, we tend to take it for granted. However, access to clean water has been inequitable; climate change is threatening the sea water level, causing the acidification of ocean water. In this project, we will investigate the environmental and social issues related to clean water and its impacts on our life by reading articles, watching videos, and exploring activities.

Dinitrogen Emissions Dominate Nitrogen Gas Emissions From Soils With Low Oxygen Availability In A Moist Tropical Forest, Maya Almaraz, Peter M. Groffman, Whendee L. Silver, Steven J. Hall, Yang Lin, Christine S. O'Connell, Stephen Porder

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Lowland tropical forest soils are relatively N rich and are the largest global source of N₂O (a powerful greenhouse gas) to the atmosphere. Despite the importance of tropical N cycling, there have been few direct measurements of N₂ (an inert gas that can serve as an alternate fate for N₂O) in tropical soils, limiting our ability to characterize N budgets, manage soils to reduce N₂O production, or predict the future role that N limitation to primary productivity will play in buffering against climate change. We collected soils from across macro- and micro-topographic gradients …

Three-Stage Conversion Of Chemically Inert N-Heptane To Α-Hydrazino Aldehyde Based On Bioelectrocatalytic C-H Bond Oxyfunctionalization, N. Samali Weliwatte, Hui Chen, Tianhua Tang, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Simple petrochemical feedstocks are often the starting material for the synthesis of complex commodity and fine and specialty chemicals. Designing synthetic pathways for these complex and specific molecular structures with sufficient chemo-, regio-, enantio-, and diastereo-selectivity can expand the existing petrochemicals landscape. the two overarching challenges in designing such pathways are selective activation of chemically inert C-H bonds in hydrocarbons and systematic functionalization to synthesize complex structures. Multienzyme cascades are becoming a growing means of overcoming the first challenge. However, extending multienzyme cascade designs is restricted by the arsenal of enzymes currently at our disposal and the compatibility between specific …

Dual Ionic Liquid-Functionalized Cellulosic Materials: Thermal, Mechanical And Conductive Properties, Elizabeth Mcgrew, Kevin M. Miller Phd

Posters-at-the-Capitol

Cellulose, an inexpensive and renewable biomacromolecule, represents an intriguing synthetic foundation for new materials with task-specific properties. Here, we wish to report a synthetic route for functionalizing cellulose with a side chain containing two ionic liquid functional groups using azide-alkyne ‘click’ cyclization strategy, followed by quaternization of the two resulting heterocycles (1,2,3-triazole and imidazole). Through this functionalization strategy, the resulting cellulosic materials exhibited significant softening, with several glass transition (T_g) values observed below room temperature, indicating the amorphous nature of the materials, with the T_g dependent on both the length of the side chain and the …

Targeting Brd4 And Pi3k Signaling Pathways For The Treatment Of Medulloblastoma, Bharti Sethi, Virender Kumar, Thilina D. Jayasinghe, Yuxiang Dong, Donald R. Ronning, Haizhen Zhong, Donald W. Coulter, Ram I. Mahato

Chemistry Faculty Publications

Medulloblastoma (MB) is a malignant pediatric brain tumor which shows upregulation of MYC and sonic hedgehog (SHH) signaling. SHH inhibitors face acquired resistance, which is a major cause of relapse. Further, direct MYC oncogene inhibition is challenging, inhibition of MYC upstream insulin-like growth factor/ phosphatidylinositol-4,5-bisphosphate 3-kinase (IGF/PI3K) is a promising alternative. While PI3K inhibition activates resistance mechanisms, simultaneous inhibition of bromodomain-containing protein 4 (BRD4) and PI3K can overcome resistance. We synthesized a new molecule 8-(2,3-dihydrobenzo[b] [1, 4] dioxin-6-yl)-2-morpholino-4H-chromen-4-one (MDP5) that targets both BRD4 and PI3K pathways. We used X-ray crystal structures and a molecular modeling approach to confirm the interactions …

Strategies For Identifying Important Residues In The Trna Modification Protein Trm732, Alex K. Mullins, Natalie N. Creech, Holly Funk, Michael Guy

Posters-at-the-Capitol

Post-transcriptional tRNA modifications are required for efficient protein translation. In yeast, the Trm7 methyltransferase forms a complex with Trm732 to modify tRNA at position 32. In humans, lack of the human homolog for Trm7, FTSJ1, causes intellectual disability. Little is known about the function of Trm732, although we have shown that one conserved motif in Trm732 is important for tRNA modification. We have identified other residues important for function using two strategies. First, we compared Trm732 proteins of different organisms using protein alignments to determine conserved regions to mutate for testing. We have generated four new Trm732 variants and have …

Identification And Biosynthetic Study Of The Siderophore Lysochelin In The Biocontrol Agent Lysobacter Enzymogenes, Amanda Lynn Miller, Shanren Li, Catherine D. Eichhorn, Yongbiao Zheng, Liangcheng Du

Liangcheng Du Publications

Lysobacter is a genus of bacteria emerging as new biocontrol agents in agriculture. Although iron acquisition is essential for the bacteria, no siderophore has been identified from any Lysobacter. Here, we report the identification of the first siderophore, N1,N8-bis(2,3-dihydroxybenzoyl)spermidine (lysochelin), and its biosynthetic gene cluster from Lysobacter enzymogenes. Intriguingly, the deletion of the spermidine biosynthetic gene encoding arginine decarboxylase or SAM decarboxylase eliminated lysochelin and the antifungals, HSAF and its analogues, which are key to the disease control activity and to the survival of Lysobacter under oxidative stresses caused by excess iron. The production of …

Electromechanical Coupling In Collagen Measured Under Increasing Relative Humidity, Arwa Bazaid, Fengyuan Zhang, Qiancheng Zhang, Sabine Neumayer, Denise Denning, Stefan Habelitz, Ana Marina Ferreira, Brian J. Rodriguez

Articles

The functional role of collagen piezoelectricity has been under debate since the discovery of piezoelectricity in bone in 1957. The possibility that piezoelectricity plays a role in bone remodelling has generated interest in the investigation of this effect in relevant physiological conditions; however, there are conflicting reports as to whether collagen is piezoelectric in a humid environment. In macroscale measurements, the piezoelectricity in hydrated tendon has been shown to be insignificant compared to dehydrated tendon, whereas, at the nanoscale, the piezoelectric effect has been observed in both dry and wet bone using piezo response force microscopy (PFM). In this work, …

Phytochemical Screening, Chemical Composition And Antimicrobial Activities Of Ethanol, Methanol And Chloroform Extracts From The Leaves Of Digitaria Sanguinalis, Digitaria Ischaemum And The Bark Of Carapa Guianensis Found In Guyana, South America., Rajendra Kumar Khelawan

Theses and Dissertations

Chloroform, Ethanol and Methanol extracts of the leaves from DIGITARIA SANGUINALIS, DIGITARIA ISCHAEMUM and the bark from CARAPA GUIANENSIS found in Guyana were obtained via maceration and reflux extraction processes. Ethanol extracts obtained from the 25-minute reflux process produced the best percentage yield and the most thin layer chromatographic spots. All further analyses were conducted on the ethanol extracts of all plant materials. The ethanolic extracts showed positive phytochemical testing results for Terpenes, Flavonoids, Steroids, Tannins, Phenolic, Proteins, Cardiac Glycoside, Reducing Sugars, and Carbohydrates. Conversely, Saponins were absent in Smooth Crabgrass and Crabwood’s bark but present in Long Hairy Crabgrass. …

Design, Synthesis And Biological Evaluation Of A Novel Bioactive Indane Scaffold 2-(Diphenylmethylene)C-2,3-Dihydro-1h-Inden-1-One With Potential Anticancer Activity, Tao Zhang, Vilmar Bandero, Claire Corcoran, Ismael Obaidi, Manuel Ruether, John O'Brien, Lorraine O'Driscoll, Neil Frankish, Helen Sheridan

Articles

Over the past decades, designing of privileged structures has emerged as a useful approach to the discovery and optimisation of novel biologically active molecules, and many have been successfully exploited across and within different target families. Examples include indole, quinolone, isoquinoline, benzofuran and chromone, etc. In the current study, we focus on synthesising a novel hybrid scaffold constituting naturally occurring benzophenone (14) and indanone (22) ring systems, leading to a general structure of 2-(diphenylmethylene)-2,3-dihydro-1H-inden-1-one (23). It was hypothesised this new hybrid system would provide enhanced anti-cancer activity owing to the presence of the common features associated with the tubulin binding …

Green Synthesis Of Nanoparticles And Their Utilization In Electrochemical Detection Of Catechol- Or Phenol-Based Substances, Daniel Laurence Myers Iii

Browse all Theses and Dissertations

PART A: GREEN SYNTHESIS OF COPPER NANOPARTICLES AND THEIR UTILIZATION IN THE DETECTION OF NEUROTRANSMITTERS Neurotransmitters, such as dopamine and epinephrine, are chemicals frequently found in the brain and are responsible for a number of human moods, needs, and emotions.1, 2 Detection of such neurotransmitters allows for a better judgement of a person’s physical and mental state, a utility that is vital in determining the presence of disease and mental illnesses.2 Electrochemical detectors used for such detections are often modified by materials such as metal nanoparticles.3 However, synthesizing nanoparticles can involve or produce chemicals, ammonium hydroxide among them, that are …

Molecular Organic Photovoltaic Cells And Applications, Julie Liu

Theses and Dissertations

The absorption, light scattering, and anti-Stoke’s fluorescence of chlorophyll and closely related sodium copper chlorophyllin were examined in various solutions with a wide range of refractive index and permittivity. It was evident that radiative photo electron decay corresponded to low permittivity solvents, but not to solvent refractive index. Additionally, non-radiative decay was dominant in high permittivity solvents. The properties suggest evolution has provided plants with an ability to redirect light to the chlorophyll in the high permittivity (water) photosynthesis center. Exploratory solar cells exploiting lifetime switching were developed and tested, wherein strong photovoltaic response was exhibited, along with the unique …

Mechanistic Insights Into Mftr-Dependent Regulation Of The Redox Cofactor Mycofactocin, Aigera Mendauletova

Electronic Theses and Dissertations

Organic redox cofactors are essential for life. While classic flavins and nicotinamides are widely distributed across all domains of life, nature has also evolved niche cofactors in subsets of life domains. For example, in Actinobacteria, coenzyme F420 is commonly used in place of flavin mononucleotide in enzymes associated with carbon fixation and oxidation of secondary alcohols. The importance of niche cofactors has long been recognized however, detailed understanding about their biosynthesis and physiological uses has been lagging. One class of niche cofactors is derived from ribosomally synthesized and posttranslationally modified peptides (RiPPs). To achieve their mature form, the genetically …

Temperature Dependency Of Ion Channel Opennings, Loren Haarsma, Sebastian Grabill, Dylan Mount

Summer Research

Alamethicin is a 20 amino-acid peptide produced by fungus. When added to a lipid bilayer they self-assemble into voltage-dependent ion channels which open for brief periods called dwell times, usually on order of a few milliseconds. See poster by Dylan Mount regarding electrical properties of lipid bilayers without Ion channels. Our goal is to measure the electrical current through a single Alamethicin ion channel as it opens and closes and see how its gating behavior is affected by lipid temperature and lipid composition. Since lipid bilayers and ion channels are critical for almost all living cells, studying them can prove …

Enhancement Of Metal Nanostructure Deposition On Silicon Laser-Induced Periodic Surface Structures By Galvanic Replacement, Nicholas Simpson, Eric J. Broadhead, Addison Casto, Katharine M. Tibbetts

Chemistry Publications

We report a chemically motivated, single-step method to enhance metal deposition onto silicon laser-induced periodic surface structures (LIPSSs) using reactive laser ablation in liquid (RLAL). Galvanic replacement (GR) reactions were used in conjunction with RLAL (GR-RLAL) to promote the deposition of Au and Cu nanostructures onto a Si LIPSS. To increase the deposition of Au, sacrificial metals Cu, Fe, and Zn were used; Fe and Zn also enhanced the deposition of Cu. We show that the deposited metal content, surface morphology, and metal crystallite size can be tuned based on the difference in electrochemical potentials of the deposited and sacrificial …

Modification Of Hyaluronic Acid To Enable Click Chemistry Photo-Crosslinking Of Hydrogels With Tailorable Degradation Profiles, Ciara Buckley

Articles

Hyaluronic acid (HA) is a naturally occurring mucopolysaccharide that, due to its inherent bioactivity and extracellular matrix-like structure, has the potential to be utilised extensively in tissue engineering. However, this glycosaminoglycan lacks the properties required for cellular adhesion and photo-crosslinking by UV light, which significantly hinders this polymers applicability. This research presents a method for modifying hyaluronic acid via thiolation and methacrylation to generate a novel photo-crosslinkable polymer with improved physicochemical properties, biocompatibility and the potential to customize biodegradability according to the ratio of monomers used. A decrease in stiffness proportional to increasing thiol concentration was observed when testing the …

Post-Translational Modification Of Proteins Via Ambient Air Pollutants And Endogenous Reactive Species, Rachel Lauren Davey

Electronic Theses and Dissertations

Proteins can react with reactive oxygen species (ROS) and reactive nitrogen species (RNS) to form post-translational modifications (PTMs), which can affect protein structure and function. The formation of 3-nitrotyrosine (NTyr) and dityrosine (DiTyr) upon reaction of proteins with ROS/RNS are two common PTMs studied due to their stability and irreversibility, as well as their ability to enhance the allergenicity of pollen allergens upon formation. Many common techniques used to study the formation of these PTMs can reliably detect the PTMs but can only provide semi-quantitative information due to many assumptions and limitations. In Chapter 2 we present an analysis of …

Glutathione And Glutaredoxin—Key Players In Cellular Redox Homeostasis And Signaling, Yuh-Cherng Chai, John J. Mieyal

2023 Faculty Bibliography

This Special Issue of Antioxidants on Glutathione (GSH) and Glutaredoxin (Grx) was designed to collect review articles and original research studies focused on advancing the current understanding of the roles of the GSH/Grx system in cellular homeostasis and disease processes. The tripeptide glutathione (GSH) is the most abundant non-enzymatic antioxidant/nucleophilic molecule in cells. In addition to various metabolic reactions involving GSH and its oxidized counterpart GSSG, oxidative post-translational modification (PTM) of proteins has been a focal point of keen interest in the redox field over the last few decades. In particular, the S-glutathionylation of proteins (protein-SSG formation), i.e., mixed disulfides …

Trichloroethylene (Tce) Metabolite S-(1,2-Dichlorovinyl)-L-Cysteine (Dcvc) Inhibits Lps-Stimulated Cxcl-2 Production In Thp-1 Cells, Karena Moleakunnel, Audrey Luce, Lyric Johnson, Erica Boldenow, Sean Harris

Summer Research

• TCE is a volatile industrial solvent commonly found in the environment is known to be a "human carcinogen". However, its effects on gestational tissues and inflammatory pathways remain unknown. 1
• TCE inhibits various cytokines like IL-1b, IL-6, IL-8, and TNF-a.
• CXCL2 is a cytokine involved in the recruitment of neutrophils which serve as a key immune defense against infection. 3
• In past research, mice with the reduction of CXCL-2 showed reduced survival rates.
• Goal:• Analyze CXCL-2 production in THP-1 cells treated with DCVC • Understand how DCVC affects the cytokine pathway

Use Of Inner/Outer Sphere Terminology In Electrochemistry—A Hexacyanoferrate Ii/Iii Case Study, John Cassidy, Rafaela Cristina De Carvalho, Tony Betts

Articles

Salts of hexacyanoferrate II/III anions have been widely used as redox couple probe molecules to determine the characteristics of electrode surfaces. Examples include the assessment of electrocatalysts for energy applications and electrocatalysts for the detection of biological or chemical species, as well as the determination of electrochemically active surface areas. An examination of the electrochemical literature, based largely on cyclic voltammetric investigations, reveals a wide range of peak separation and/or heterogeneous electron transfer rate constants, classified sometimes as inner or outer sphere electron transfer processes. Originally developed for the mechanistic interpretation of inorganic transition metal compounds in solution, this terminology …

Novel Application Of Graphene Oxide In Conjunction With Dna Binding Dcas9 For Detecting Antibiotic Resistance Genes, Langley Williams

Mahurin Honors College Capstone Experience/Thesis Projects

The frequent emergence of antibiotic resistance genes poses a stumbling block to prompt treatment of pathogen-originating diseases and therefore spurs the demand for a simple, rapid diagnostic device that can outcompete the time and cost of traditional methods such as PCR and cell culturing. The proposed method for detecting pathogenic DNA utilizes the binding properties of deactivated CRISPR-associated protein9 (dCas9) complexed with fluorescein-labeled single-guide RNA (sgRNA) and the fluorescence quenching properties previously demonstrated in graphene oxide (GO). For our assay, we designed sgRNAs to target specific 20 nucleotide sequences extracted from the tetracycline resistance (tetM) gene sequence and covalently modified …

Chemistry And Public Policy: Equipping Advocates, Herbert R. Fynewever, I. Bos, C. Demlow, G. Fulkerson

Summer Research

No abstract provided.

Progress In 7sk Ribonucleoprotein Structural Biology, Momodou B. Camara, Amr M. Sobeh, Catherine D. Eichhorn

Department of Chemistry: Faculty Publications

The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the noncoding 7SK RNA, core proteins, and numerous accessory proteins, the most wellknown 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK …

Exploration Of Electron Dynamics In A Strong Field By Time Dependent Configuration Interaction With A Complex Absorbing Potential, Paul Hoerner

Wayne State University Dissertations

Strong field electron dynamics are a quickly developing field of study in physical chemistry. In order to better understand experimental observations, there is a need for computational tools to simulate electron dynamics in a strong field. Due to the nature of strong electric fields, this requires the solving of the time dependent Schrödinger equation (TDSE). Various methods have been used to solve the TDSE in a strong field. In order to look at molecular systems while accurately treating the underlying physics, a method that balances computational affordability with theoretical rigor is necessary. The chosen method that matches these criteria is …

Synthesis Of Putative Microcystin-Lr Degradation Products And Full Macrocyclic Cyanopeptide, Mahesh Kumar Yadab

Wayne State University Dissertations

This thesis primarily focuses on synthesizing fragments of microcystin-LR, which is a natural product, with the aim of establishing them as analytical standards for investigating the biodegradation pathways of MC-LR. Despite of the substantial interest in synthesizing, isolating, and degrading Microcystins over the past few decades, the availability of high-purity microcystin standards at known concentration for quantitative analysis of using LC-MS/MS remains limited. The synthesis of the proposed MC-LR fragments employs the Fmoc/t-Bu protecting group strategy to prevent isomerization. Additionally, novel methods for the total synthesis of N-Boc-Adda are explored, incorporating atom-economic approaches, cross-metathesis, and oxidative boron Heck reactions. The …

High Order Structures Formed By The Natural Aromatic Amino Acids, Gabriel Alexander Kupovics, Zeina Alraawi

Inquiry: The University of Arkansas Undergraduate Research Journal

Excessive concentrations of the natural aromatic amino acids phenylalanine and tyrosine are characteristic of the severe genetic abnormalities known as phenylketonuria (PKU) and tyrosinemia, respectively. Within this context, this feature article authenticates claims that tryptophan can form amyloid-like supramolecular structures in vitro and is the first to propose potential mechanisms of tryptophan self-assembly, including hydrophobic and electrostatic interactions. Thioflavin T (ThT) fluorescence kinetics and transmission electron microscopy (TEM) data suggest the formation of amyloid-like fibrillar structures by natural aromatic amino acids in vitro. Additionally, the propensity of amino acid aggregation increases in the presence of sodium dodecyl sulfate (SDS). The …

Selective Melt Recrystallization Of Acetaminophen Polymorphs Through Environmental Control, Eleanor Lowe

Honors Theses

Polymorphism is the ability for a molecule to crystallize into multiple different structures in the solid state. The preparation of one polymorph over another is practically important to pharmaceutical development, as properties of polymorphs can vary and impact the drug delivery method. Polymorph outcomes depend heavily on the environment in which the crystal is nucleated, or initially formed. Acetaminophen, the active ingredient in Tylenol, is one example of a polymorphic compound. Here we use acetaminophen as a model system to better understand primary factors controlling polymorph selection and interconversion. We hypothesize a specific atmospheric environmental factor plays large role in …

Chemical Approach To Tire Mark Analysis, John Lucchi

Graduate Thesis and Dissertation 2023-2024

Fatal accidents on the road are an unfortunate daily occurrence, with almost 30,000 deaths resulting from hit-and-runs in the USA between 2006 and 2021. The identification of the driver responsible for this road crime can become a challenge. Nonetheless, the accident scene provides a large amount of trace evidence that can prove critical to this matter, one of them being the tire marks. While traditional tire mark analysis is full of physical information helping the reconstruction of the event, additional information can be extracted from the rubber left during the braking event. Each tire model is manufactured with a specific …

Lanthanide-Based Responsive Contrast Agents For Magnetic Resonance Imaging, Md Mamunur Rashid

Wayne State University Dissertations

This thesis is a collection of seven chapters that discuss the contributions to the field oflanthanide-based contrast agents for magnetic resonance imaging (MRI), particularly in the context of imaging hypoxia and extracellular pH. These physiological changes play a significant role in life-threatening conditions such as cancer, making it essential to develop effective imaging tools to aid in diagnosis and treatment. The thesis provides insights for the rational development of lanthanide-based contrast agents for MRI. A comprehensive review of divalent europium as a tool for imaging hypoxia using magnetic resonance imaging and how coordination chemistry can be used to tune the …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …