Analytical Chemistry Commons^™

Amyloid Fibril Polymorphism : Structure, Supramolecular Chiraliy And Spontaneous Interconversion, Dzmitry Kurouski

Legacy Theses & Dissertations (2009 - 2024)

Specific protein aggregation has been linked to more than 25 severe human maladies including prion, Alzheimer's, and Parkinson's diseases. These important malfunctions are often referred to as 'conformational' disorders and result from the conversion of a normal isoform of a protein into a specific b-sheet rich polymeric amyloid form. This work elaborates a comprehensive characterization of amyloids and dedicated to the investigation of the fibril polymorphism using advanced microscopic tools, such as Atomic Force and Scanning Electron microcopies, together with several vibrational spectroscopy techniques, such as Raman, Infrared and Vibrational Circular Dichroism. A new type of protein folding-aggregation phenomenon, spontaneous …

Visualizing The Spatial Localization Of Active Matrix Metalloproteinases (Mmps) Using Maldi Imaging Ms, Sasirekha Muruganantham

Graduate Theses and Dissertations

Biomaterial implantation induces the foreign body response (FBR). Development of longer-term implants relies on the thorough understanding of the FBR. The progression of the FBR is regulated by a number of biomolecules including cytokines, chemokines, and matrix metalloproteinases (MMPs). The nature of the FBR requires the spatial and temporal regulation of these mediators. MMPs are an extremely large and diverse group of enzymes that play key roles in regulating the FBR. Precise spatiotemporal regulation of MMPs defines their proteolytic activities. The aim of this project is to develop a new bioanalytical method to visualize the localization of active MMPs at …

Transformation Of Fusarium Verticillioides With A Polyketide Gene Cluster Isolated From A Fungal Endophyte Activates The Biosynthesis Of Fusaric Acid, Yunxuan Xie, Wei Zhang, Yaoyao Li, Mingzi Wang, Ronald Cerny, Yue Shen, Liangcheng Du

Liangcheng Du Publications

A large number of bioactive natural products have been isolated from plant endophytic fungi. However, molecular mechanisms for the biosynthesis of these metabolites have lagged behind because genetic and biochemical studies are difficult to perform within many of the endophytes. In this work, we describe our attempt to express a putative mycoepoxydiene (MED) biosynthetic gene cluster in Fusarium verticillioides, which has a well-developed genetic system for the study fungal polyketide biosynthesis. MED was isolated from Phomopsis sp. A123, a fungal endophyte of the mangrove plant, Kandelia candel. It has several unusual structural features and interesting biological activities. Integration of …

Nmr Solution Structures Of Two Hairpins Of E. Coli 16s Rrna: The Effects Of Mutations And Chemical Modifications On Structure And Function Of Rrna, Yu Liu

Wayne State University Dissertations

The structures of two functional mutants, the UC (G690U, U697C) and the QM mutants (G690A, G693C, A695C, U697A) of the 690 hairpin of E. coli 16S ribosomal RNA were determined by NMR. The UC mutant and the QM mutant with high biological function are able to fold into structures that are isomorphous with the wild-type 690 hairpin sequence. The structural comparisons among the functional mutants and the wild-type provides structural validation for previously identified specific functional groups that are crucial for maintaining function of the 690 hairpin. The key groups for maintaining the structure and function of the 690 loop …

High Resolution Hybrid Mass Spectrometry For The Determination Of Marine Biotoxins, Azaspiracids, And Their Biotransformation Products., Zuzana Skrabakova

Theses

Azaspiracids (AZAs), polyether marine toxins, are produced by marine microalgae and accumulate in filter-feeding bivalve molluscs, such as mussels, clams, oysters and scallops, while grazing on phytoplankton, from which they derive nutrition. Although being discovered quite recently, AZAs have caused several human intoxication events and thus became a problem for health authorities and shellfish industries. The rapid development of highly sensitive liquid chromatography multiple tandem mass spectrometry (LC-MS/MS, LC-MS") methods enabled the identification of numerous AZA analogues and added to the control of shellfish contamination. Tandem mass spectrometry techniques, while being highly selective and sensitive for determination of AZAs in …

Single Cell Analysis For The Characterization Of Cell Populations Using A Live Cell Array, Maureen Ann Walling

Legacy Theses & Dissertations (2009 - 2024)

In the past decade, the shift from whole cell population analyses towards single cell measurement methods and techniques is based on experimental results that reveal significant levels of non-genetic heterogeneity in clonal cell populations. This heterogeneity manifests in multiple aspects of cell activity and is, in part, a result of stochastic noise in processes leading to gene expression, namely transcription and translation. The growing understanding of this occurrence has led to the development of methods to monitor and analyze heterogeneity for a more thorough description of cell populations and overall activity.

Advanced Statistical Methods For Biochemical And Forensic Applications Of Raman Spectroscopy, Vitali Sikirzhytski

Legacy Theses & Dissertations (2009 - 2024)

This work is dedicated to the development and application of advanced statistical methods for biochemical and forensic applications of Raman spectroscopy. We developed a new concept of multidimensional Raman signatures for forensic identification of body fluid traces, which was successfully applied to the study of dried blood, semen, saliva, sweat and vaginal fluid stains. Several alternative advanced chemometric techniques were also successfully tested for the problems of pure body fluids discrimination and mixture analysis. Studies of body fluid mixtures with low blood and semen concentrations indicated that the detection limit of a minor contributor was as low as a few …

Development And Validation Of A Rapid Multi-Class Method For The Confirmation Of Fourteen Prohibited Medicinal Additives In Pig And Poultry Compound Feed By Liquid Chromatography Tandem Mass Spectrometry, Mark Cronly, Patrice Behan, Barry Foley, Liam Regan, Marella Gallagher, Sean Earley, Paula Shearan, Edward Malone

Articles

A confirmatory method has been developed to allow for the analysis of fourteen prohibited medicinal additives in pig and poultry compound feed. These compounds are prohibited for use as feed additives although some are still authorised for use in medicated feed. Feed samples are extracted by acetonitrile with addition of sodium sulphate. The extracts undergo a hexane wash to aid with sample purification. The extracts are then evaporated to dryness and reconstituted in initial mobile phase. The samples undergo an ultracentrifugation step prior to injection onto the LC-MS/MS system and are analysed in a run time of 26 minutes. The …

Using Photoactive Vitamin Nanoparticles As Photodynamic Antimicrobial Chemotherapeutic (Pact) Agents To Treat Chronic Wounds, Rahul A. Khanke

All Capstone Projects

The objective of the proposed study is to develop new materials and methods to manage microbial growth in chronic wounds using phototherapy. Chronic wounds are considered as a worldwide health problem. The most common chronic wounds can be classified into three categories: venous ulcers, diabetic ulcers, and pressure ulcers. Venous ulcers, which usually occur in the legs, account for about 70% to 90% of chronic wounds and can become infected easily. Venous ulcers are sores that develop after veins in the legs have been damaged. These ulcers can penetrate deeply into the skin. Occasionally, if a venous ulcer persists for …

Ruthenium Complexes As Dna Photonucleases In Treatment Of Malignant Skin Carcinoma, Devi Kalyan Karumanchi

All Capstone Projects

A variety of Ruthenium complexes possessing terpyridine complexes as ligands in their coordination sphere have been investigated extensively as DNA photo nucleases in vitro. This work has led to the realization that compounds of Ruthenium bind to DNA purines and that the interactions are of an unprecedented bridging variety. Owing to the molar absorptivity of these complexes in the visible region, direct cleavage of duplex DNA by these complexes requires irradiation in the range of 400-500 nm.

Although the observation of DNA photo cleavage in vitro makes these systems good candidates for further investigation, it does not provide any information …

Total Protein Determination Using Micro Plate Assay, Julie Ruffatti

All Capstone Projects

One of the largest challenges that food manufactures are facing today is the management of food allergens. Allergenic protein in trace amounts, part per million concentrations, will trigger a reaction in some individuals. Food manufacturers need to prevent allergen cross-contamination by performing adequate sanitation after production of an allergenic containing food. Allergen detection kits are used to determine if sufficient protein was removed from the equipment surfaces during sanitation. One kit on the market is the 3M™ Clean- Trace™ Surface Protein (Allergen) swab tests. The test qualitatively detects the presence of protein based on the biuret reaction and will yield …

Rapid Multi-Class Multi-Residue Method For The Confirmation Of Chloramphenicol And Eleven Nitroimidazoles In Milk And Honey By Liquid Chromatography Tandem Mass Spectrometry, Mark Cronly, Patrice Behan, Barry Foley, Liam Regan, Sheila Martin, Michael Doyle, Edward Malone

Articles

A confirmatory method has been developed to allow for the analysis of eleven nitroimidazoles and also chloramphenicol in milk and honey samples. These compounds are classified as A6 compounds in annex IV of council regulation 2377/90 and therefore prohibited for the use in animal husbandry. Milk samples are extracted by acetonitrile with addition of NaCl, while honey samples are first dissolved in water before a similar extraction. Honey extracts undergo a hexane wash to remove impurities. Both milk and honey extracts are evaporated to dryness and reconstituted in initial mobile phase. These are then injected onto an LC-MS/MS system and …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Characterization Of Glycation Sites On Human Serum Albumin Using Mass Spectrometry, Omar S. Barnaby

Department of Chemistry: Dissertations, Theses, and Student Research

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that  explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation …

Toxicodynamics And Biotransformation Of Azaspiracids Incorporating Liquid Chromatography-Tandem-Mass Spectrometry (Lc-Ms/Ms) Techniques., Daniel O'Driscoll

Theses

Azaspiracids (AZAs) are a family of lipophilic polyether marine biotoxins, that have caused a number of human intoxication incidents in Europe since 1995, which was the first incident reported following the consumption by consumers of intoxicated shellfish {Mytilus edulis). This class of phycotoxins has been responsible for extended closures of shellfisheries in various locations around Europe, where levels of AZAl-3 are regulated in shellfish. Since their discovery in 1995, AZAs have become the focus of extensive research, resulting in the discovery of numerous analogues. Only AZAl and AZA2 have been found in phytoplankton and all the other analogues are believed …

Determination Of Lead, Cadmium, Zinc And Nickel Inedible Oil Products By Stripping Voltammetry., Ng Khan Loon

Student Works (2010-2019)

Edible oil products had become an everyday food that been consumed by most of the people either for dressing or for cooking purpose. Metal has become a common contamination to the food product, which it found the way into the edible oil through environment and processing contamination such as crushing, distillation, and hydrogenation. In this Study, the main focuses of metal analysis are only confined to 4 common metals which are the Cadmium, Lead, Zinc and Nickel. These elements are selected in this study due to reason that Cadmium and Lead are commonly known for their contamination from environment and …

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

Arsenic Speciation Analysis Of Biological Fluids : A Study Of Liquid Chromatography Coupled To Analytical Atomic Spectrometric Instrumentation, Kanna Ito

Legacy Theses & Dissertations (2009 - 2024)

Arsenic exists as many different chemical forms including inorganic, methylated and dietary species. The toxicity of these species varies: some are highly toxic and can cause adverse health effects in many parts of the body; others are considered relatively non-toxic. Monitoring arsenic exposure is usually accomplished by its direct measurement in biological fluids. Urine is the specimen of choice for assessing arsenic exposure, because of its short biological half-life in blood. There have been very few studies of arsenic species in blood, yet such research can provide valuable information on arsenic distribution and its metabolism in the body.

Application Of Solid-Phase Microextraction For The Analysis Of Polycyclic Aromatic Hydrocarbons In Hyophila Involuta As A Natural Biosensor., Elizabeth Fong Yew Mei

Student Works (2010-2019)

This work describes a simple and rapid extraction method by using solid-phase microextraction (SPME) technique for the determination of polycyclic aromatic hydrocarbons (PAHs) from mosses of Hyophila involuta which is found commonly and abundantly throughout Peninsular Malaysia. Mosses have been chosen in our study since they are effective bioindicators as they take up nutrients and pollutants directly from the atmosphere and they have no root system. These properties make them ideal for evaluating pollutant levels in the air over a monitored period of time. This study has been developed and optimized based on the extraction of the analytes of interest …

Studies Of Antioxidant Activity Of Bioactive Compounds Derived From Ardisia Crispa., Hassan Mahmood Kzar Jindal

Student Works (2010-2019)

In recent times, researches have focused on medicinal plants in order to extract natural and low cost antioxidants that can help protect the human body against oxidative stress, and replace the synthetic additives that might be carcinogenic. In present study, the crude extracts of leaves and fruits from Ardisia crispa were investigated for their chemical constituents and antioxidant activity. Preliminary phytochemical screening of the crude extracts via TLC analysis revealed the presence of several secondary compounds mainly, terpenoids and phenolic compounds in addition to alkaloids and saponins. HPLC analysis showed the possibility of presence of gallic acid in the fruits …

Optimization Of Solid-Phase Microextraction For The Determination Of Organo-Phosphorus And Organo-Chlorine Pesticide Residues In Natural Water Near Aquaculture Farms., Chan Chun Foong

Student Works (2010-2019)

The global shrimp farming industry had a rapid growth in the 1980s due to the high demand for shrimp. Apart from the destruction of mangroves and wetlands, the intensive operation of shrimp aquaculture deteriorated the water quality in the region. Variety of chemicals and biological products were used to prevent the outbreaks of diseases in the intensively managed shrimp ponds. Pesticides were used as disinfectands to kill unwanted organisms in the pond. SPME-GC-ECD method was developed for the determination of azinphos-ethyl, chlorphyrifos-methyl, diazinon, dichlorvos, endosulfan-I, endosulfan-II, endosulfan sulfate and malathion from water samples of shrimp aquaculture area in Manjung district, …

Explorations In Homeoviscous Adaptation And Mass Spectral Analysis Of Membrane Lipids, Michael Douglas Timmons

University of Kentucky Doctoral Dissertations

The focus of this dissertation is centered on the mass spectral analysis of lipids and changes occurring in keeping with the concept of homeoviscous adaptation [1]. Homeoviscous adaptation is the process of modification of membrane lipids in response to environmental stimuli [1]. Dissertation investigations applied this concept to prokaryotic and eukaryotic organisms, and expanded the perception of environmental factors from exogenous organic solvents to intracellular environment.

The field of lipidomics deals with the analysis of phospholipid and fatty acid components of membranes the changes that occur due to environmental stimuli and their biological significance [2-6]. The high sensitivity of mass …

Identification And Quantification Of Pesticides Residue In Vegetables By Liquid Chromatography Quadrupole-Time-Of Flight Mass Spectrometry (Lc-Q-Tof Ms)., Tin Ae Ru

Student Works (2010-2019)

A liquid chromatography tandem mass spectrometry (LC-Q-TOF MS) technique was used to simultaneously determine six types of carbamates and organophosphorus pesticides residue in vegetables. The pesticides were extracted by ultrasonic solvent extraction method using ethyl acetate as the extraction solvent followed by Florisil column clean up. Four types of common consumed vegetables from local hypermarket were used to study the recovery. The accurate mass measurement and retention time were used to identify and determine the empirical formula of the pesticides. The mass accuracy errors were less than 7 ppm for all the investigated pesticides. The limit of detection (LOD) were …

Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson

School of Computing: Conference and Workshop Papers

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSN- PSSM), which uses all the information in the entire ToF- SIMS …

Application Of Multiple Mass Spectrometric Techniques In The Isolation, Determination And Characterisation Of The Marine Toxins; Azaspiracid, Keith O'Callaghan

Theses

The Azaspiracids are a class of polyether marine biotoxins that present a significant health risk to consumers of shellfish. Since their discovery in the late 1990s several human intoxications have been reported, and traced to Irish shellfish farms resulting in closures or harvest rejections. As such incidents involving azaspiracid shellfish poisoning have a major socio-economic impact on communities that rely on shellfish farming revenues.

Recent evidence suggests that azaspiracid poisoning events may become more commonplace. With this increased risk the understanding of azaspiracids mode of action and biological targets becomes crucial. To support these endeavours effective analytical methods need to …

Genetically Engineered Repetitive Polypeptides : Design, Synthesis, Characterization, And Applications, Natalya I. Topilina

Legacy Theses & Dissertations (2009 - 2024)

This work is dedicated to the investigation of protein folding with the emphasis on the aggregation and amyloid fibrils formation. The focus of the research is to elucidate the relationship between polypeptide chain sequence and folding/aggregation properties. For this purpose, i) libraries of the de novo macromolecular repetitive β-sheet forming polypeptides were designed, and ii) the strategy for their rapid creation was developed. The strategy enables retention of a basic polypeptide core, yet allowing variations in the repetitive sequence, degree of polymerization and distribution of specific amino acids. The polypeptides were expressed in E. coli, purified, and characterized by various …

The Biophysical Analysis Of The Human Telomeric Repeat (Ttaggg)4 And Characterization Of Porphyrin Binding In Potassium Solutions, Cosimo Antonacci

Seton Hall University Dissertations and Theses (ETDs)

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In Vivo Imaging Of Transport And Biocompatibility Of Single Silver Nanoparticles In Early Development Of Zebrafish Embryos, Kerry J. Lee, Prakash D. Nallathamby, Lauren M. Browning, Christopher J. Osgood, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Real-time study of the transport and biocompatibility of nanomaterials in early embryonic development at single-nanoparticle resolution can offer new knowledge about the delivery and effects of nanomaterials in vivo, and provide new insights into molecular transport mechanisms in developing embryos. In this study, we directly characterized the transport of single silver nanoparticles into an in vivo model system (zebrafish embryos) and investigated their effects on early embryonic development at single-nanoparticle resolution in real time. We designed highly purified and stable (not aggregated and no photodecomposition) nanoparticles and developed single-nanoparticle optics and in vivo assays to enable the study. We …

The Application Of Electrospray Ionization Coupled To Ultrahigh Resolution Mass Spectrometry For The Molecular Characterization Of Natural Organic Matter, Rachel L. Sleighter, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Mass spectrometry has recently played a key role in the understanding of natural organic matter (NOM) by providing molecular-level details about its composition. NOM, a complex assemblage of organic molecules present in natural waters and soils/sediments, has the ability to bind and transport anthropogenic materials. An improved understanding of its composition is crucial in order to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. In the past, low-resolution (> 3000) mass analyzers have offered some insights into the structure of NOM, but emerging ultrahigh resolution (> 200000) techniques such as electrospray ionization (ESI) coupled …

Determination Of Cholesterol In Foods By Flow Injection Analysis With Perroxyoxalate Chemiluminescence., Abisake Feleke

Electronic Theses and Dissertations

Cholesterol is an important biological molecule with many important functions. However, high serum cholesterol is a health hazard. Thus analysis of cholesterol is important and many analytical techniques have been developed. The objectives of the proposed research are to develop an economical, rapid method for the determination of total cholesterol with good selectivity and enhanced sensitivity. For evaluation of proposed flow injection analysis with peroxyoxalate chemiluminescence (FIA-POCL) method, figures of merit such as accuracy, precision, and linear dynamic range will be assessed. The proposed procedure was then applied to the determination of total cholesterol in foods. The procedure was linear …