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- All Subjects: Biochemistry
- Creators: Borges, Chad
- Status: Published
Description
Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.
ContributorsRai, Samita (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Borges, Chad (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Microbial fuel cells (MFCs) promote the sustainable conversion of organic matter in black water to electrical current, enabling the production of hydrogen peroxide (H2O2) while making waste water treatment energy neutral or positive. H2O2 is useful in remote locations such as U.S. military forward operating bases (FOBs) for on-site tertiary water treatment or as a medical disinfectant, among many other uses. Various carbon-based catalysts and binders for use at the cathode of a an MFC for H2O2 production are explored using linear sweep voltammetry (LSV) and rotating ring-disk electrode (RRDE) techniques. The oxygen reduction reaction (ORR) at the cathode has slow kinetics at conditions present in the MFC, making it important to find a catalyst type and loading which promote a 2e- (rather than 4e-) reaction to maximize H2O2 formation. Using LSV methods, I compared the cathodic overpotentials associated with graphite and Vulcan carbon catalysts as well as Nafion and AS-4 binders. Vulcan carbon catalyst with Nafion binder produced the lowest overpotentials of any binder/catalyst combinations. Additionally, I determined that pH control may be required at the cathode due to large potential losses caused by hydroxide (OH-) concentration gradients. Furthermore, RRDE tests indicate that Vulcan carbon catalyst with a Nafion binder has a higher H2O2 production efficiency at lower catalyst loadings, but the trade-off is a greater potential loss due to higher activation energy. Therefore, an intermediate catalyst loading of 0.5 mg/cm2 Vulcan carbon with Nafion binder is recommended for the final MFC design. The chosen catalyst, binder, and loading will maximize H2O2 production, optimize MFC performance, and minimize the need for additional energy input into the system.
ContributorsStadie, Mikaela Johanna (Author) / Torres, Cesar (Thesis director) / Popat, Sudeep (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2015-05
Description
Protein AMPylation is a recently discovered and relatively unstudied post-translational modification (PTM). AMPylation has previously been shown to play an important role in metabolic regulation and host pathogenesis in bacteria, but the recent identification of potential AMPylators across many species in every domain of life has supported the possibility that AMPylation could be a more fundamental and physiologically significant regulatory PTM. For the first time, we characterized the auto-AMPylation capability of the human protein SOS1 through in vitro AMPylation experiments using full-length protein and whole-domain truncation mutants. We found that SOS1 can become AMPylated at a tyrosine residue possibly within the Cdc25 domain of the protein, the Dbl homology domain is vital for efficient auto-AMPylation activity, and the C-terminal proline-rich domain exhibits a complex regulatory function. The proline-rich domain alone also appears to be capable of catalyzing a separate, unidentified covalent self-modification using a fluorescent ATP analogue. Finally, SOS1 was shown to be capable of catalyzing the AMPylation of two endogenous human protein substrates: a ubiquitous, unidentified protein of ~49kDa and another breast-cancer specific, unidentified protein of ~28kDa.
ContributorsOber-Reynolds, Benjamin John (Author) / LaBaer, Joshua (Thesis director) / Borges, Chad (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
In this thesis, glycan nodes, the basic subunits of complex biological sugars, were studied to determine the reproducibility of gas chromatography-mass spectrometry (GC/MS) based methylation analysis of whole blood plasma by normalization using an internal standard of heavy permethylated glycans. Glycans are complex biological sugars that have a variety of applications in the human body and will display aberrant compositions when produced by cancerous cells. Thus an assay to determine their composition can be used as a diagnostic tool. It was shown that the assay may have potential use, but needs further refinement to become an improvement over current methods by analyzing the results of ratio-determination and replicate experiments.
ContributorsMiyasaki, Tyler Takeo (Author) / Borges, Chad (Thesis director) / Van Horn, Wade (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Chemical Engineering Program (Contributor)
Created2015-05
Description
In our modern world the source of for many chemicals is to acquire and refine oil. This process is becoming an expensive to the environment and to human health. Alternative processes for acquiring the final product have been developed but still need work. One product that is valuable is butanol. The normal process for butanol production is very intensive but there is a method to produce butanol from bacteria. This process is better because it is more environmentally safe than using oil. One problem however is that when the bacteria produce too much butanol it reaches the toxicity limit and stops the production of butanol. In order to keep butanol from reaching the toxicity limit an adsorbent is used to remove the butanol without harming the bacteria. The adsorbent is a mesoporous carbon powder that allows the butanol to be adsorbed on it. This thesis explores different designs for a magnetic separation process to extract the carbon powder from the culture.
ContributorsChabra, Rohin (Author) / Nielsen, David (Thesis director) / Torres, Cesar (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2015-05
Description
Dielectrophoresis is a separations strategy that has the potential to separate small amounts of different proteins from each other. The forces at play in the channel used for dielectrophoresis are electroosmotic flow (EOF), electrophoresis (EP), and dielectrophoresis (DEP). EOF is the force exerted on liquid from an applied potential (1). EP is the force exerted on charged particles in a uniform electric field (2). DEP is the force exerted on particles (charged and uncharged) in a non-uniform electric field (3). This experiment was focused on the testing of a new microfluidic device to see if it could improve the focusing of proteins in dielectrophoresis. It was predicted that the addition of a salt bridge would improve focusing by preventing the ions created by the electrolysis of water around the electrodes from interacting with the proteins and causing aggregation, among other problems. Control trials using the old device showed that electrolysis was likely occurring and was the causal agent for poor outcomes. After applying the electric potential for some time a pH front traveled through the channel causing aggregation of proteins and the current in the channel decreased rapidly, even while the voltage was held constant. The resistance in the channels of the control trials also slightly decreased over time, until the pH shift occurred, at which time it increased rapidly. Experimental trials with a new device that included salt bridges eliminated this pH front and had a roughly linear increase of current in the channel with the voltage applied. This device can now be used in future research with protein dielectrophoresis, including in the potential differentiation of different proteins. References: 1) Electroosmosis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006. 2) Electrophoresis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006. 3) Dielectrophoresis. Oxford Dictionary of Biochemistry and Molecular Biology. 2. Oxford University Press: Oxford, England. 2006.
ContributorsHayes, Katelyn Donna (Author) / Hayes, Mark (Thesis director) / Borges, Chad (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Anaerobic digestion (AD), a common process in wastewater treatment plants, is traditionally assessed with Biochemical Methane Potential (BMP) tests. Hydrolysis is considered its rate-limiting step. During my research, I assessed the impact of pretreatment on BMPs and microbial electrochemical cells (MECs). In the first set of experiments, BMP tests were performed using alkaline and thermal pretreated waste activated sludge (WAS), a control group, and a negative control group as samples and AD sludge (ADS) as inoculum. The data obtained suggested that BMPs do not necessarily require ADS, since samples without inoculum produced 5-20% more CH4. However, ADS appears to reduce the initial methanogenesis lag in BMPs, as no pH inhibition and immediate CH4 production were observed. Consumption rate constants, which are related to hydrolysis, were calculated using three methods based on CH4 production, SSCOD concentration, and the sum of both, called the lumped parameter. All the values observed were within literature values, yet each provide a different picture of what is happening in the system. For the second set of experiments, the current production of 3 H-type MECs were compared to the CH4 production of BMPs to assess WAS solids' biodegradability and consumption rates relative to the pretreatment methods employed for their substrate. BMPs fed with pretreated and control WAS solids were performed at 0.42 and 1.42 WAS-to-ADS ratios. An initial CH4 production lag of about 12 days was observed in the BMP assays, but MECs immediately began producing current. When compared in terms of COD, MECs produced more current than the BMPs produced CH4, indicating that the MEC may be capable of consuming different types of substrate and potentially overestimating CH4 production in anaerobic digesters. I also observed 2 to 3 different consumption events in MECs versus 3 for BMP assays, but these had similar magnitudes, durations, and starting times in the control and thermal pretreated WAS-fed assays and not in alkaline assays. This might indicate that MECs identified the differences of alkaline pretreatment, but not between control WAS and thermal pretreated WAS. Furthermore, HPLC results suggest at least one hydrolysis event, as valerate, butyrate, and traces of acetate are observed in the reactors' effluents. Moreover, a possible inhibition of valerate-fixing microbial communities due to pretreatment and the impossibility of valerate consumption by ARB might explain its presence in the reactors' effluents.
ContributorsBrown Munoz, Francisco (Author) / Torres, Cesar (Thesis director) / Rittmann, Bruce E. (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The dopamine 2 receptor (D2R) is a Class A GPCR which is essential for signaling in the nervous system, and has been implicated in numerous illnesses. While there are over 50 currently approved drugs which act on D2R, the structure has never been determined in detail. Although crystallography has historically been difficult with GPCRs, in recent years many structures have been solved using lipidic cubic phase (LCP) crystallization techniques. Sample preparation for LCP crystallization typically requires optimization of genetic constructs, recombinant expression, and purification techniques in order to produce a sample with sufficient stability and homogeneity. This study compares several genetic constructs utilizing different promoters, fusion proteins, fusion positions, and truncations in order to determine a high quality construct for LCP crystallization of
D2R. All constructs were expressed using the Bac-to-bac baculovirus expression system, then extracted with n-Dodecyl-β-D-Maltoside (DDM) and purified using metal affinity chromatography. Samples were then tested for quantity, purity, and homogeneity using SDS-PAGE, western blot, and size-exclusion chromatography. High quality samples were chosen based on insect cell expression levels, purification yield, and stability estimated by the levels of homomeric protein relative to aggregated protein. A final construct was chosen with which to continue future studies in optimization of thermal stability and crystallization conditions. Future work on this project is required to produce a sample amenable to crystallization. Screening of ligands for co-crystallization,
thermostabilizing point mutations, and potentially optimization of extraction and purification techniques prior to crystallization trials. Solving the D2R structure will lead to an increased understanding of its signaling mechanism and the mechanisms of currently approved drugs, while also providing a basis for more effective structure-based drug design.
D2R. All constructs were expressed using the Bac-to-bac baculovirus expression system, then extracted with n-Dodecyl-β-D-Maltoside (DDM) and purified using metal affinity chromatography. Samples were then tested for quantity, purity, and homogeneity using SDS-PAGE, western blot, and size-exclusion chromatography. High quality samples were chosen based on insect cell expression levels, purification yield, and stability estimated by the levels of homomeric protein relative to aggregated protein. A final construct was chosen with which to continue future studies in optimization of thermal stability and crystallization conditions. Future work on this project is required to produce a sample amenable to crystallization. Screening of ligands for co-crystallization,
thermostabilizing point mutations, and potentially optimization of extraction and purification techniques prior to crystallization trials. Solving the D2R structure will lead to an increased understanding of its signaling mechanism and the mechanisms of currently approved drugs, while also providing a basis for more effective structure-based drug design.
ContributorsErler, Maya Marie (Author) / Liu, Wei (Thesis director) / He, Ximin (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Alternative ion exchange membranes for implementation in a peroxide production microbial electrochemical cel (PP-MEC) are explored through membrane stability tests with NaCl electrolyte and stabilizer EDTA at varying operational pHs. PP-MEC performance parameters \u2014 H2O2 concentration, current density, coulombic efficiency and power input required \u2014 are optimized over a 7 month continuous operation period based on their response to changes in HRT, EDTA concentration, air flow rate and electrolyte. I found that EDTA was compatible for use with the membranes. I also determined that AMI membranes were preferable to CMI and FAA because it was consistently stable and maintained its structural integrity. Still, I suggest testing more membranes because the AMI degraded in continuous operation. The PP-MEC produced up to 0.38 wt% H2O2, enough to perform water treatment through the Fenton process and significantly greater than the 0.13 wt% batch PP-MEC tests by previous researchers. It ran at > 0.20 W-hr/g H2O2 power input, ~ three orders of magnitude less than what is required for the anthraquinone process. I recommend high HRT and EDTA concentration while running the PP- MEC to increase H2O2 concentration, but low HRT and low EDTA concentration to decrease power input required. I recommend NaCl electrolyte but suggest testing new electrolytes that may control pH without degrading H2O2. I determined that air flow rate has no effect on PP-MEC operation. These recommendations should optimize PP-MEC operation based on its application.
ContributorsChowdhury, Nadratun Naeem (Author) / Torres, Cesar (Thesis director) / Popat, Sudeep (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
G protein-coupled receptors, or GPCRs, are receptors located within the membrane of cells that elicit a wide array of cellular responses through their interactions with G proteins. Recent advances in the use of lipid cubic phase (LCP) for the crystallization of GPCRs, as well as increased knowledge of techniques to improve receptor stability, have led to a large increase in the number of available GPCR structures, despite historic difficulties. This project is focused on the histamine family of receptors, which are Class A GPCRs that are involved in the body’s allergic and inflammatory responses. In particular, the goal of this project was to design, express, and purify histamine receptors with the ultimate goal of crystallization. Successive rounds of optimization included the use of recombinant DNA techniques in E.coli to truncate sections of the proteins and the insertion of several fusion partner proteins to improve receptor expression and stability. All constructs were expressed in a Bac-to-Bac baculovirus expression system using Sf9 insect cells, solubilized using n-Dodecyl-β-D-Maltoside (DDM), and purified using immobilized metal affinity chromatography. Constructs were then analyzed by SDS-Page, Western blot, and size-exclusion chromatography to determine their presence, purity, and homogeneity. Along with their expression data from insect cells, the most stable and homogeneous construct from each round was used to design successive optimizations. After 3 rounds of construct design for each receptor, much work remains to produce a stable sample that has the potential to crystallize. Future work includes further optimization of the insertion site of the fusion proteins, ligand screening for co-crystallization, optimization of purification conditions, and screening of potential thermostabilizing point mutations. Success in solving a structure will allow for a more detailed understanding of the receptor function in addition to its vital use in rational drug discovery.
ContributorsCosgrove, Steven Andrew (Author) / Liu, Wei (Thesis director) / Mills, Jeremy (Committee member) / Mazor, Yuval (Committee member) / W. P. Carey School of Business (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12