Analytical Chemistry Commons^™

Optimized Peptide Nanomaterials As Delivery Vehicles For Hydrophobic Metal-Based Anticancer Agents, Yaron Marciano

Dissertations, Theses, and Capstone Projects

Enzyme-responsive materials have been well explored, particularly as therapeutic and diagnostic agents. In this thesis we demonstrate that anionic self-assembling peptides can be utilized as delivery vehicles for metal-based hydrophobic payloads. The tunability of the system is highlighted as well as the increase in cytotoxicity and selectivity in vitro. The rapid degradation of peptides in cell media may lead to the formation of new peptide-drug bioconjugates with increased activity and selectivity. The physiological stability of these peptide delivery vehicles has been optimized by capping the N-terminus with an acetyl group. This simple backbone modification was shown to not prevent self-assembly, …

Ultra-Fast Bioorthogonal Spin-Labeling And Distance Measurements In Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids, Subhashis Jana, Eric G. B. Evans, Hyo Sang Jang, Shuyang Zhang, Hui Zhang, Andrzej Rajca, Sharona E. Gordon, William N. Zagotta, Stefan Stoll, Ryan A. Mehl

Chemistry Department: Faculty Publications

Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)—in combination with double electron–electron resonance (DEER) spectroscopy—has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be …

In-Vial Detection Of Protein Denaturation Using Intrinsic Fluorescence Anisotropy, Krishnakumar Chullipalliyalil, Khaled Elkassas, Michael Mcauliffe, Sonja Vucen, Abina Crean

Cappa Publications

The conventional quality control techniques for identifying the denaturation of biopharmaceuticals includes sodium dodecyl sulfate-polyacrylamide gel electrophoresis for identifying fragmentation, ion exchange chromatography and isoelectric focusing for identifying deamidation, reverse-phase high-performance liquid chromatography (HPLC) for identifying oxidation, and size-exclusion HPLC for identifying aggregation. These stability assessments require essential processes that are destructive to the product tested. All these techniques are lab based and require sample removal from a sealed storage vial, which can breach the sterility. In this work, we investigate the heat- and surfactant-induced denaturation of an in-vial-stored model protein, bovine serum albumin (BSA), by analyzing its intrinsic fluorescence …

The Boozi Device’S Effect On Aroma Compounds In Distilled Spirits, Drew Budner, Lindsey Bell, Katherine Thompson-Witrick

Journal of the South Carolina Academy of Science

The BooZi is a commercially available flavor-modifying device that claims to remove the negative flavor agents (congeners) from a number of different types of distilled spirits and wines. SPME was utilized for the extraction of the volatile and semi-volatile compounds within each sample. The analysis of the compounds found in the samples following exposure to the BooZi device were analyzed using a GC-MS. The most significant changes regarding the aroma profile of the distilled spirits were noticeable following 96 hours of exposure. The BooZi device was shown to be effective in reducing the concentration of a number of compounds, including …

Exploring The Complementarity Of Measures Of Instructional Practices, Lu Shi, Robert M. Erdmann, Anthony Pellegrini, Victoria Johnson, Binh Le, Trina Popple, Zachary Nelson, Molly Undersander Gaston, Marilyne Stains

Chemistry Department: Faculty Publications

The assessment of instructional quality has been and continues to be a desirable, yet difficult endeavor in higher education. The development of new teaching evaluation frameworks along with instruments to measure various aspects of teaching practices holds promise. The challenge rests in the implementation of these frameworks and measures in authentic settings. Part of this challenge is for instructors, researchers, and administrators to parse through and select a meaningful set of tools from the plethora of existing instruments. In this study, we aim to start clarifying the landscape of measures of instructional practice by exploring the complementarity of two existing …

Investigating The Interactions Of The Iron-Sulfur Mitochondrial Protein, Mitoneet With Its Binding Partners, Ebenezer Osei Newton

Graduate Theses, Dissertations, and Problem Reports

MitoNEET belongs to the CDGSH Iron-Sulfur Domain (CISD)-gene family of proteins and is a [2Fe-2S] cluster-containing protein found on the outer membrane of mitochondria. The specific functions of mitoNEET/CISD1 remain to be fully elucidated, but the protein is involved in regulating mitochondrial bioenergetics in several metabolic diseases. Unfortunately, drug discovery efforts targeting mitoNEET to improve metabolic disorders are hampered by the lack of ligand-binding assays for this mitochondrial protein. We have developed a protocol amenable for high-throughput screening (HTS) assay, by modifying an ATP fluorescence polarization method to facilitate drug discovery targeting mitoNEET. Based on our observation that adenosine triphosphate …

Investigation Of Early Complex Formation Of Huntingtin Protein With And Without Lipids, Alyssa R. Stonebraker

Graduate Theses, Dissertations, and Problem Reports

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by the expansion of the polyglutamine (polyQ) domain of the huntingtin protein (htt). The expansion of the polyQ domain beyond a threshold of approximately 35 repeats triggers complex toxic aggregation mechanisms and results in altered interactions between htt and lipid membranes. Many factors modulate these processes. One such modulator includes sequences flanking the polyQ domain, most notably the first 17 amino acids at the N-terminus of the protein (Nt17), and environmental factors including the presence of membranous structures. Nt17 has the propensity to form an amphipathic a-helix in the presence of …

Spatial And Temporal Varitations In Dissolved Calcium In The Kentucky Lake Watershed In Relation To Zebra Mussel Colonization, Kelsie Meystedt

Murray State Theses and Dissertations

Calcium is the fifth most abundant element on earth’s crust. Plants and animals require calcium for structure and intracellular metabolism. Recent studies have shown that dissolved calcium (Ca2+) freshwater ecosystems is of growing concern as the increasing concentrations of this element are implicated in altering the natural environment and biota. Elevated levels of dissolved calcium and sporadic re-emergence of an invasive species, namely zebra mussels (Dreissena polymorpha) in Kentucky Lake in the recent years served as a motivation for this study. The objective of this study was to determine spatial and temporal variations in dissolved calcium in selected streams, Kentucky …

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

Uhplc/Ft-Ms Non-Targeted Screening Approach For Biomass Burning Organic Aerosol And Liquid Smoke As Biomass Burning Organic Aerosol Surrogate, D.M.R. Thusitha Dinusha Kumarihami Divisekara

Dissertations, Master's Theses and Master's Reports

Biomass combustion contributes a large amount of aerosol particles to the atmosphere impacting the climate system and human health. Identifying the molecular composition of biomass burning organic aerosol (BBOA) is challenging because of its complex nature. Liquid chromatography mass spectrometric non-targeted screening (NTS) methods provide a comprehensive analysis. However, the instrumentation and data analysis are challenging due to the extreme complexity of environmental samples. In the first part of this study, we implemented a new LC/FT-MS data processing approach by combining existing open-source data processing tools, MZmine2.53 and MFAssignR. The method's validity was checked using the standard polyacrylic acid (PAA) …

Reducing Disposable Plastic Waste From Protein Quantitative Assays, Justin Buiter

All Capstone Projects

Protein concentration quantification is important for many areas of biology and biochemistry. This quantification happens in large quantities in laboratories and needs to be done accurately and quickly. The Bradford assay is one of the most common ways of accomplishing this task (1). This assay relies on the binding of the protein and the Coomassie Blue G250 dye. The anionic blue form binds to the protein and has a maximum at 595 nm. This allows for accurate quantification by reading how much of the sample absorbs at 595 nm (2).

In 2014, it was estimated that 5.5 million tons of …

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

Chemistry Department: 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 …

Food Waste Storage Gaseous Emissions Detection And Quantification Using Infrared Spectroscopy, Ryley A. Burton-Tauzer

Cal Poly Humboldt theses and projects

A growing interest in sustainable waste management and the implementation of new policies have prompted a shift towards alternative resource recovery methods for organic waste, including food waste. To effectively assess alternative food waste treatment scenarios, it is important to evaluate the life cycle impacts associated with each scenario. The storage phase of food waste, encompassing its accumulation in kitchens, and storage in bins for collection and transportation, has been overlooked as a source of greenhouse gases in previous studies. This investigation aimed to identify the greenhouse gases emitted during the initial five-day period of low-oxygen storage. An open dynamic …

Application Of Mass Spectrometry For The Characterization Of Synthetic Oligomers And Natural Lignin, Poorya Kamali

Theses and Dissertations--Chemistry

As part of the ongoing effort to substitute finite fuel and chemical resources with renewable ones, biomass is emerging as one of the most promising sources. Biomass consists of three main components of cellulose, hemicellulose, and lignin. Traditionally, cellulose has been used extensively in pulping industry, while lignin has been considered waste and is burned to generate heat. Lignin, a complex aromatic polymer component of biomass, has the potential to be used as a source of aromatic chemicals and pharmaceutical synthons. The recalcitrant nature of lignin, the lack of effective lignin breakdown methods and analytical techniques to analyze it are …

Comprehensive Analysis And Forensic Investigation Of Cyanide, Thiocyanate, And 2-Amino-2-Thiazoline-4-Carboxylic Acid In-Ante- And Postmortem Blood Utilizing Advanced Analytical Techniques, Abdullah Hamad Alluhayb

Electronic Theses and Dissertations

Cyanide (CN), present as cyanide anion (CN-) or hydrogen cyanide (HCN), is a deadly poison. The main mechanism of CN toxicity is blocking terminal electron transfer, leading to cellular hypoxia, cytotoxic anoxia, and potential death. Determining blood CN concen-trations along with its major metabolite, thiocyanate (SCN-), is crucial. A sensitive method for concurrent detection of CN and SCN- from human ante- and post-mortem blood via liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis was devel-oped. The method involved active microdiffusion with chemical modification using naph-thalene-2,3-dicarboxaldehyde (NDA) and taurine, while monobromobimane (MBB) mod-ification was used for SCN-. The method showed good sensitivity for …

Enhancing The Forensic Comparison Process Of Common Trace Materials Through The Development Of Practical And Systematic Methods, Meghan Nicole Prusinowski

Graduate Theses, Dissertations, and Problem Reports

An ongoing advancement in forensic trace evidence has driven the development of new and objective methods for comparing various materials. While many standard guides have been published for use in trace laboratories, different areas require a more comprehensive understanding of error rates and an urgent need for harmonizing methods of examination and interpretation. Two critical areas are the forensic examination of physical fits and the comparison of spectral data, which depend highly on the examiner’s judgment.

The long-term goal of this study is to advance and modernize the comparative process of physical fit examinations and spectral interpretation. This goal is …

The Influence Of Instrumental Sources Of Variance On Mass Spectral Comparison Algorithms, Isabel Cristina Galvez Valencia

Graduate Theses, Dissertations, and Problem Reports

Current search algorithms for the identification of substances based only on their electron ionization mass spectra provide the correct compound as their top result approximately 80% of the time. One contributing factor to the ~20% deviation in the first-hit recognition rate is that traditional algorithms work by comparing the unknown spectrum to an ‘ideal’ or consensus spectrum of each reference compound. The inclusion of replicate reference spectra in a database has been shown to improve the probability of ranking the correct identity in the number one position, but the variance in ion abundances caused by different conditions or different instruments …

Multiomics Approach Captures Hepatic Metabolic Network Altered By Chronic Ethanol Administration, Isin Tuna Sakallioglu, Bridget Tripp, Jacy Kubik, Carol A. Casey, Paul G. Thomes, Robert Powers

Chemistry Department: Faculty Publications

Using a multiplatform and multiomics approach, we identified metabolites, lipids, proteins, and metabolic pathways that were altered in the liver after chronic ethanol administration. A functional enrichment analysis of the multiomics dataset revealed that rats treated with ethanol experienced an increase in hepatic fatty acyl content, which is consistent with an initial development of steatosis. The nuclear magnetic resonance spectroscopy (NMR) and liquid chromatography–mass spectrometry (LC-MS) metabolomics data revealed that the chronic ethanol exposure selectively modified toxic substances such as an increase in glucuronidation tyramine and benzoyl; and a depletion in cholesterol-conjugated glucuronides. Similarly, the lipidomics results revealed that ethanol …

Determination Of Total Ammonia Nitrogen By Gas-Diffusion Flow Injection Analysis (Gd-Fia)-Spectrophotometry Using Minnieroot Flower (Ruellia Tuberosa) As Natural Reagent, Lani Artana Putri, Puspita Mufidah Sari, Hermin Sulistyarti, Akhmad Sabarudin, Erwin Sulistyo

Makara Journal of Science

Total ammonia nitrogen (TAN) is a pollutant agent found in water and generated from the metabolisms of living organisms and the decomposition of organic matter. This research aims to develop an efficient, low-cost, and environmentally friendly TAN analysis method. The principle of this method is based on the reaction of TAN injected in the donor stream with NaOH to form alkaline gaseous ammonia. The gaseous ammonia diffuses through a hydrophobic membrane into an acceptor stream containing Ruellia tuberosa extract. The presence of NH₃ gas in the acceptor stream changes the extract color from pinkish to green, which is monitored …

Speciated Isotope Dilution Mass Spectrometry In Combination With Thor’S Hammer Metaspike Technology For The Assessment Of Low-Level Biomarkers For Human Health Evaluation, Ashley Ebert

Electronic Theses and Dissertations

Our research team has been focused on quantifying important biological analytes in human blood samples to delineate the biochemical processes underlying certain states of dysfunction and evaluate treatment efficacy. These efforts have been guided by laboratory measurements with the input of medical experts. Speciated isotope dilution mass spectrometry (SIDMS) explained in detail in EPA Method 6800 has been successfully applied in the quantification of an important biomarker analyte for immune function and detoxification processes: glutathione. Past research has proven the molecule a biomarker for autism spectrum disorder (ASD) in the form of the reduced/oxidized glutathione (GSH/GSSG) ratio, and literature has …