Biochemistry Commons^™

An Approach To An Agave Problem: The Bioremediation Of Agricultural Waste By Yeast Fermentations, Joshua Michael Jarodsky

Theses and Dissertations

The agricultural waste products created by industries, such as the Tequila manufacturing industry, create thousands of tons of waste material every year. This agricultural waste often becomes an environmental and ecological problem for fields and surrounding areas. The purpose of this study is to determine the potential of using the yeast Kluyveromyces marxianus 7-1 and Kluyveromyces marxianus 8-1 to ferment the leaf waste from the harvesting of the Agave tequilana as a form of bioremediation. Fermentations (anaerobic, under constant shaking, and at room temperature) were monitored for colony forming units, pH of fermentation broth, concentration of reducing sugars, and protein …

Expression, Localization, And Kinetic Characterization Of The Phospholipid Biosynthesis Enzyme Ctp: Phosphocholine Cytidylyltransferase From The Protozoan Parasite Leishmania Major, Justin Daniel Theodore Lange

Theses and Dissertations

The eukaryotic parasite Leishmania is the causative agent of the disease leishmaniasis. L. major is the most common of 21 species that causes visceral leishmaniasis in humans, and 30 that cause the same disease in other mammals. Visceral leishmaniasis causes fever, weight loss, and over a short amount of time, multiple organ failure, and has a 100% mortality rate within 2 years. This makes it the second largest parasitic killer in the world behind malaria. Over 90% of the worldâ??s cases of visceral leishmaniasis have been reported in underdeveloped countries of India, Bangladesh, Nepal, Sudan, Ethiopia and Brazil, with 500,000 …

A Study Of Allylic Aminations As Catalyzed By Heterobimetallic Pd-Ti Complexes, Diana Lauren Ellis

Theses and Dissertations

Heterobimetallic complexes present a unique approach to catalyzing challenging reactions. By having two metals in close proximity to each other, the metals are able to interact and alter their electronics in a way that simple organic ligands (carbon, nitrogen, sulfur etc.) cannot. Our studies of heterobimetallic complexes focus on a Pd–Ti complex. The complex features a dative interaction between the palladium and the titanium held together by a phosphonamide scaffold. This interaction increases the electrophilicity of the palladium and makes it a very suitable catalyst for allylic amination reactions. We have conducted extensive studies of this catalyst in allylic aminations, …

Synthesis And Characterization Of Carbonized Poly (Divinylbenzene) Microspheres For Carbon/Nanodiamond/Polymer-Based Core-Shell Materials And Applications Of This Mixed-Mode Phase To High-Performance Liquid Chromatography, Chuan-Hsi Hung

Theses and Dissertations

This work focuses on improving the quality of carbon-based core-shell materials for high performance liquid chromatography (HPLC) via the characterization of the core materials, and also the development of chromatographic methods (separations) for them. In the early part of this work, I applied organic synthesis to make uniform, spherical poly(divinylbenzene) (PDVB) microspheres, and then carbonized them to prepare carbon core materials for core-shell particle synthesis. Here, I studied in detail the surface and material properties of these particles with multiple instruments, which allowed me to describe the physical and chemical changes that took place during each treatment. The uniform, spherical …

Investigating The Initial Detection Stage Of Meiotic Silencing By Unpaired Dna In The Model Organism Neurospora Crassa, Pegan A. Sauls

Theses and Dissertations

In an attempt to neutralize transposable elements or retrovirus invasions Neurospora crassa will rely on one of its many genome defense mechanism, Meiotic Silencing by Unpaired DNA (MSUD). MSUD works in a two-step process that first detects unpaired sequences between homologous chromosomes followed by downstream silenced expression of the sequence. The ultimate silencing stage of MSUD is widely accepted to operate through an RNAi-like system. However, the mechanics of the detection step of MSUD remains elusive. The research presented attempts to elaborate on how the initial stage of MSUD occurs and its specifics. First, a genetic approach is utilized to …

Immunoassays Of Potential Cancer Biomarkers In Microfluidic Devices, Jayson Virola Pagaduan

Theses and Dissertations

Laboratory test results are important in making decisions regarding a patient's diagnosis and response to treatment. These tests often measure the biomarkers found in biological fluids such blood, urine, and saliva. Immunoassay is one type of laboratory test used to measure the level of biomarkers using specific antibodies. Microfluidics offer several advantages such as speed, small sample volume requirement, portability, integration, and automation. These advantages are motivating to develop microfluidic platforms of conventional laboratory tests. I have fabricated polymer microfluidic devices and developed immunoassays on-chip for potential cancer markers. Silicon template devices were fabricated using standard photolithographic techniques. The template …

Functional Expression And Characterization Of A Truncated Candida Antarctica Lipase B In Yeast, Samantha Robinson

Theses and Dissertations

Candida antarctica lipase B is an enzyme capable of hydrolyzing ester bonds in a lipid-water interface with potential to become a useful biocatalyst for production of biodiesel fuel. Enzymatically catalyzing the transesterification of triacylglycerides to produce fatty acid alkyl esters (biodiesel) is an environmentally cleaner alternative to the current process which utilizes chemical reagents as catalysts. Optimization and development of strains to express highly active, stable, large quantities of these biocatalysts is essential for inexpensive production of biodiesel. Additionally, lipase enzymes can be immobilized onto a resin, eliminating the need to recover the catalyst from the product and allowing multiple …

Elucidation Of A Novel Pathway In Staphylococcus Aureus: The Essential Site-Specific Processing Of Ribosomal Protein L27, Erin A. Wall

Theses and Dissertations

Ribosomal protein L27 is a component of the eubacterial large ribosomal subunit that has been shown to play a critical role in substrate stabilization during protein synthesis. This function is mediated by the L27 N-terminus, which protrudes into the peptidyl transferase center where it interacts with both A-site and P-site tRNAs as well as with 23S rRNA. We observed that L27 in S. aureus and other Firmicutes is encoded with a short N-terminal extension that is not present in most Gram-negative organisms, and is absent from mature ribosomes. The extension contains a conserved cleavage motif; nine N-terminal amino acids are …

Regulation Of Tie2 Extracellular Complex Formation In Angiogenesis, Annamarie Dalton

Theses and Dissertations

Pathological angiogenesis is an essential component of tumor growth, development, and metastasis for which few effective therapeutic options exist. Though many cancer therapies target the function of cell surface receptors, mechanisms regulating membrane receptor crosstalk remain unclear. Two important families of receptors in angiogenesis, the Ties and Integrins, respond to the extracellular environment via outside-in and, in the case of Integrins, also inside- out signaling. Recent reports showed that the endothelial specific tyrosine kinase receptor, Tie2, forms complexes with two of the endothelial Integrin heterodimers, α₅β₁ and α_Vβ₃, providing a convenient mechanism for …

Characterization Of A Novel Protease In Staphylococcus Aureus, Adam L. Johnson

Theses and Dissertations

A newly discovered cysteine protease, Prp, has been shown to perform an essential, site-specific cleavage of ribosomal protein L27 in Staphylococcus aureus. In Firmicutes and related bacteria, ribosomal protein L27 is encoded with a conserved N-terminal extension that must be removed to expose residues critical for ribosome function. Uncleavable and pre-cleaved variants were unable to complement an L27 deletion in S. aureus, indicating that this N-terminal processing event is essential and likely plays an important regulatory role. The gene encoding the responsible protease (prp) has been shown to be essential, and is found in all organisms …

Fluorescence Imaging Of Analyte Profiles In An Inductively Coupled Plasma With Laser Ablation As A Sample Introduction Source, Lance Moses

Theses and Dissertations

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has risen to among the top tier techniques for the direct analysis of solid samples. However, significant problems remain that must be solved to achieve the full analytical potential of LA-ICP-MS. Inefficient conversion of aerosol to ions within the ICP or transmission through the MS interface may decrease precision, sensitivity, and/or accuracy. Although fundamental mechanisms that govern ion production and transmission have been studied extensively in solution-nebulization (SN) ICP-MS instruments, significant gaps in our understanding remain. Furthermore, it is unclear to what extent differences between the aerosols generated during SN and LA …

Dysregulation Of Micrornas In Blood As Biomarkers For Diagnosing Prostate Cancer, Rhonda W. Daniel

Theses and Dissertations

Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers.

Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such …

Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas

Theses and Dissertations

The gram-negative bacterium E. coli encodes the Suf pathway to assemble iron-sulfur (Fe-S) clusters under iron starvation and oxidative stress conditions. The ATPase activity of SufC is critical for in vivo Fe-S cluster assembly by the Suf pathway. SufC shares homology with the nucleotide binding domain (NBD) of ATP-binding cassette (ABC) transporters and belongs to the AAA+ (ATPases Associated with diverse cellular Activities) ATPase superfamily, a family of proteins that utilizes energy from ATP hydrolysis to perform a variety of cellular functions. SufC forms a stable SufBC2D complex with partner proteins SufB and SufD. The SufBC2D complex serves as a …

The Role Of Srsf3 In Control Of Alternative Splicing Of Cpeb2 In Triple Negative Breast Cancer, Brian P. Griffin

Theses and Dissertations

In the presented study, we identified that SRSF3 controls the alternative splicing of CPEB2 and consequently promotes a metastatic phenotype in triple negative breast cancer (TNBC). TNBC causes thousands of deaths annually, frequently due to a lack of effective treatments and a high rate of metastasis in patients. Alternative splicing has been found to be dysregulated in numerous cancers, while splicing factors such as SRSF3 are variably expressed. In this study we performed a siRNA panel to screen potential splicing factors, then used specific siRNA to study the effect of its knockdown on cellular function. These results showed that SRSF3 …

Pemetrexed, A Modulator Of Amp-Activated Kinase Signaling And An Inhibitor Of Wild Type And Mutant P53, Stuti Agarwal

Theses and Dissertations

New drug discoveries and new approaches towards diagnosis and treatment have improved cancer therapeutics remarkably. One of the most influential and effective discoveries in the field of cancer therapeutics was antimetabolites, such as the antifolates. The interest in antifolates increased as some of the antifolates showed responses in cancers, such as mesothelioma, leukemia, and breast cancers. When pemetrexed (PTX) was discovered, our laboratory had established that the primary mechanism of action of pemetrexed is to inhibit thymidylate 22 synthase (TS) (E. Taylor et al., 1992). Preclinical studies have shown that PTX has a broad range of antitumor activity in human …

Interaction Between Atm Kinase And P53 In Determining Glioma Radiosensitivity, Syed F. Ahmad

Theses and Dissertations

Glioblastoma multiforme (GBM) is the most common primary brain tumor. Studies have shown that targeting the DNA damage response can sensitize cancer cells to DNA damaging agents. Ataxia telangiectasia mutated (ATM) is involved in signaling DNA double strand breaks. Our group has previously shown that ATM inhibitors (ATMi) sensitize GBM cells and tumors to ionizing radiation. This effect is greater when the tumor suppressor p53 is mutated.

The goals of this work include validation of a new ATM inhibitor, AZ32, and elucidation of how ATMi and p53 status interact to promote cell death after radiation. We propose that ATMi and …

Nitric Oxide Synthase Activity And Its Modulation In The Treatment Of Colorectal Cancer, Asim Alam

Theses and Dissertations

The American Cancer Society estimates more than 141,000 new cases of and about 50,000 deaths from colorectal cancer every year. Treatment options include surgery, radiation therapy and targeted therapies such as anti-angiogenics. However, no therapies address the key driving factor of colorectal cancer: inflammation. It is well known that chronic inflammatory conditions such as Crohn’s Disease, ulcerative colitis, diabetes, obesity and cigarette smoking all elevate the risk of developing colorectal cancer. One of the hallmarks of chronic inflammation is the elevated levels of reactive oxygen/nitrogen species (ROS/RNS). A primary source of these ROS/RNS is uncoupled Nitric Oxide Synthase (NOS). Under …

Microchip Thermal Gradient Gas Chromatography, Anzi Wang

Theses and Dissertations

Although the airbath oven is a reliable heating method for gas chromatography (GC), resistive heating is needed for higher analytical throughput and on-site chemical analysis because of size, heating rate and power requirements. In the last thirty years, a variety of resistive heating methods were developed and implemented for both benchtop and portable GC systems. Although fast heating rates and low power consumption have been achieved, losses in column efficiency and resolution, complex construction processes and difficulties experienced in recovering damaged columns have also become problematic for routine use of resistively heated columns. To solve these problems, a new resistively …

Fabrication, Characterization, Optimization And Application Development Of Novel Thin-Layer Chromatography Plates, Supriya Singh Kanyal

Theses and Dissertations

This dissertation describes advances in the microfabrication of thin layer chromatography (TLC) plates. These plates are prepared by the patterning of carbon nanotube (CNT) forests on substrates, followed by their infiltration with an inorganic material. This document is divided into ten sections or chapters. Chapter 1 reviews the basics of conventional TLC technology. This technology has not changed substantially in decades. This chapter also mentions some of the downsides of the conventional approach, which include unwanted interactions of the binder in the plates with the analytes, relatively slow development times, and only moderately high efficiencies. Chapter 2 focuses primarily on …

Synthesis And Characterization Of Complex Molecular Assemblies On Surfaces, Nitesh Madaan

Theses and Dissertations

The research presented in this dissertation is focused on the construction of complex molecular structures on planar gold and silicon dioxide surfaces using a variety of surface modification techniques, along with thorough surface characterization at each modification step. The dissertation is structured into six separate chapters. In Chapter 1, an introduction to the importance and implications of molecular level surface modification, commonly employed surface modification methods, and available surface characterization techniques is presented. Chapter 2 shows applications of novel methodologies for the functionalization of gold surfaces using alkane dithiol self-assembled monolayers and thiol-ene click chemistry. The resulting functionalized gold substrates …

Chaperone-Mediated Folding And Assembly Of Β-Propeller Proteins Into Cellular Signaling Complexes, Rebecca L. Plimpton

Theses and Dissertations

G protein signaling depends on the ability of the individual subunits of the G protein heterotrimer to assemble into a functional complex. Formation of the G protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings the Gβ and Gγ subunits together. This system includes the cytosolic chaperonin containing TCP-1 (CCT) and a co-chaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and their structures …

Ion Structure And Energetics In The Gas Phase Characterized Using Fourier Transfom Ion Cyclotron Resonance Mass Spectrometry, Chad A. Jones

Theses and Dissertations

In this dissertation, I use Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to study the structure and energetics of gas phase ions. Infrared multiphoton dissociation spectroscopy (IRMPD) is a technique for measuring the IR spectrum of gas phase ions in a Penning trap. I use this technique to investigate the conformation of cucurbituril complexes, terminal diamines, and protonated amino acids. Cross sectional areas by Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) is a technique developed by the Dearden lab to measure the cross section of gas phase ions. In this work, I further develop a fundamental understanding of …

Simple, Label-Free And Non-Instrumented Analyte Quantitation By Flow Distance Measurement In Microfluidic Devices, Debolina Chatterjee

Theses and Dissertations

Rapid determination of the concentrations of molecules related to diseases can provide timely information for treatment options. However, most biomarker quantitation methods require costly and complex equipment. On the other hand, point-of-care systems have less complex instrumentation needs than laboratory-based equipment, but often provide less information; for example, biomarker presence or absence instead of concentration. A complete analysis setup addressing key limitations of both laboratory-based and portable systems is highly desirable. I developed microfluidic devices with visual inspection readout of a target’s concentration from microliter volumes of solution flowed into a microchannel. Microchannels are formed within polydimethylsiloxane (PDMS), and the …

Synthesis Of 4'-Ester Resveratrol Analogues, Chromium Trioxide Oxidation Of Terpenes, And Synthesis Of Mimics Of (-)-Englerin A, Mark Jeffrey Acerson

Theses and Dissertations

4’ -ester analogues of resveratrol were synthesized using reaction conditions developed to produce mono-ester products in the presence of two other unprotected phenols. Basic conditions were employed to deprotonate the most acidic 4’ phenol followed by addition of anhydrides or acid chlorides to give the ester product. The reaction favored 4’-ester formation in polar aprotic solvents with DMSO being the optimal solvent.

(—)-Englerin A is a guaiane-type sesquiterpene containing two ester side chains. Mimics of (—)-englerin A were proposed that retained the ester side chains while replacing the non-polar core with less complicated structures. These proposed mimic cores would maintain …

High-Performance Polymer Monoliths For Capillary Liquid Chromatography, Pankaj Aggarwal

Theses and Dissertations

This dissertation focuses on improving the chromatographic efficiency of polymeric organic monoliths by characterizing and optimizing the bed morphology. In-situ characterization techniques such as capillary flow porometry (CFP), 3-dimensional scanning electron microscopy (3D SEM) and conductivity measurements were developed and implemented to quantitatively characterize the morphology of poly(ethylene glycol) diacrylate (PEGDA) monoliths. The CFP measurements for monoliths prepared by the same procedure in capillaries with different diameters (i.e., 75, 150, and 250 μm) clearly showed a change in average through-pore size with capillary diameter, thus, certifying the need for in-situ measurement techniques. Serial sectioning and imaging of PEGDA monoliths using …

Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor

Theses and Dissertations

Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …

Laser-Induced Fluorescence Imaging Of Calcium And Barium Ion Beams In The Second Vacuum Stage Of A Commercial Inductively Coupled Plasma Mass Spectrometer, Alisa Jane Edmund

Theses and Dissertations

Inductively coupled plasma-mass spectrometers (ICP-MS) have become the workhorses of many analytical labs over the past few decades. Despite the instruments' high sensitivities and low detection limits there is still a demand for improvements in several aspects of their performance. One area of improvement is in the understanding of "space charge effects" Space charge effects are classified as problems associated with the ion beam. Problems are created when the mutual repulsions of the ions make consistent focusing of the ion beam difficult. This is particularly problematic with samples containing a low concentration analyte contained within a high salt solution matrix, …

Desorption Electrospray Ionization Mass Spectrometry Imaging: Instrumentation, Optimization And Capabilities, Manan Dhunna

Theses and Dissertations

Desorption Electrospray Ionization Mass spectrometry Imaging (DESI-MSI) is an area of great interest and a promising tool in the field of chemical imaging. It is a powerful, label-free technique, which can determine, map and visualize different molecular compounds on a sample surface. The amount of information acquired in a single DESI-MSI experiment is enormous compared to other techniques, as it can simultaneously detect different compounds with their spatial distribution on the surface. The experiment can be used to produce two-dimensional and three-dimensional images. Chapter 2 focuses on the design and optimization of the setup for performing DESI-MS imaging on various …

Facile Synthesis And Characterization Of A Thermally Stable Silica-Doped Alumina With Tunable Surface Area, Porosity, And Acidity, Maryam Khosravi Mardkhe

Theses and Dissertations

Mesoporous γ-Al2O3 is one of the most widely used catalyst supports for commercial catalytic applications. The performance of a catalyst strongly depends on the combination of textural, chemical and physical properties of the support. Pore size is essential since each catalytic system requires a unique pore size for optimal catalyst loading, diffusion and selectivity. In addition, high surface area and large pore volume usually result in higher catalyst loading, which increases the number of catalytic reaction sites and decreases reaction time. Therefore, determination of surface area and porosity of porous supports is critical for the successful design and optimization of …

On Chip Preconcentration And Labeling Of Protein Biomarkers Using Monolithic Columns, Device Fabrication, Optimization, And Automation, Rui Yang

Theses and Dissertations

Detection of disease specific biomarkers is of great importance in diagnosis and treatment of diseases. Modern bioanalytical techniques, such as liquid chromatography with mass spectrometry (LC-MS), have the ability to identify biomarkers, but their cost and scalability are two main drawbacks. Enzyme-linked immunosorbent assay (ELISA) is another potential tool, but it works best for proteins, rather than peptide biomarkers. Recently, microfluidics has emerged as a promising technique due to its small fluid volume consumption, rapidness, low fabrication cost, portability and versatility. Therefore, it shows prominent potential in the analysis of disease specific biomarkers. In this thesis, microfluidic systems that integrate …