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In this thesis, a breadboard Integrated Microarray Printing and Detection System (IMPDS) was proposed to address key limitations of traditional microarrays. IMPDS integrated two core components of a high-resolution surface plasmon resonance imaging (SPRi) system and a piezoelectric dispensing system that can print ultra-low volume droplets. To avoid evaporation of droplets in the microarray, a 100 μm thick oil layer (dodecane) was used to cover the chip surface. The interaction between BSA (Bovine serum albumin) and Anti-BSA was used to evaluate the capability of IMPDS. The alignment variability of printing, stability of droplets array and quantification of protein-protein interactions based on nanodroplet array were evaluated through a 10 x 10 microarray on SPR sensor chip. Binding kinetic constants obtained from IMPDS are close with results from commercial SPR setup (BI-3000), which indicates that IMPDS is capable to measure kinetic constants accurately. The IMPDS setup has following advantages: 1) nanoliter scale sample consumption, 2) high-throughput detection with real-time kinetic information for biomolecular interactions, 3) real-time information during printing and spot-on-spot detection of biomolecular interactions 4) flexible selection of probes and receptors (M x N interactions). Since IMPDS studies biomolecular interactions with low cost and high flexibility in real-time manner, it has great potential in applications such as drug discovery, food safety and disease diagnostics, etc.
ContributorsXiao, Feng (Author) / Tao, Nongjian (Thesis advisor) / Borges, Chad (Committee member) / Guo, Jia (Committee member) / Arizona State University (Publisher)
Created2017
Description
Cancer is a heterogeneous disease with discrete oncogenic mechanisms. P53 mutation is the most common oncogenic mutation in many cancers including breast cancer. This dissertation focuses on fundamental genetic alterations enforced by p53 mutation as an indirect target. p53 mutation upregulates the mevalonate pathway genes altering cholesterol biosynthesis and prenylation. Prenylation, a lipid modification, is required for small GTPases signaling cascades. Project 1 demonstrates that prenylation inhibition can specifically target cells harboring p53 mutation resulting in reduced tumor proliferation and migration. Mutating p53 is associated with Ras and RhoA activation and statin prevents this activity by inhibiting prenylation. Ras-related pathway genes were selected from the transcriptomic analysis for evaluating correlation to statin sensitivity. A gene signature of seventeen genes and TP53 genotype (referred to as MPR signature) is generated to predict response to statins. MPR signature is validated through two datasets of drug screening in cell lines. As advancements in targeted gene modification are rising, the CRISPR-Cas9 technology has emerged as a new cancer therapeutic strategy. One of the important risk factors in gene therapy is the immune recognition of the exogenous therapeutic tool, resulting in obstruction of treatment and possibly serious health consequences. Project 2 describes a method development that can potentially improve the safety and efficacy of gene-targeting proteins. A cohort of 155 healthy individuals was screened for pre-existing B cell and T cell immune response to the S. pyogenes Cas9 protein. We detected antibodies against Cas9 in more than 10% of the healthy population and identified two immunodominant T cell epitopes of this protein. A de-immunized Cas9 that maintains the wild-type functionality was engineered by mutating the identified T cell epitopes. The gene signature and method described here have the potential to improve strategies for genome-driven tumor targeting.
ContributorsRoshdi Ferdosi, Shayesteh (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Thesis advisor) / Woodbury, Neel (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2017
Description
Quiescin Sulfhydryl Oxidase 1 (QSOX1) generates disulfide bonds in its client substrates via oxidation of free thiols. Localized to the Golgi and secreted, QSOX1 helps to fold proteins into their active form. Early work with QSOX1 in cancer began with the identification of a peptide from the long form of QSOX1 in plasma from patients with pancreatic ductal adenocarcinoma. Subsequent work confirmed the overexpression of QSOX1 in numerous cancers in addition to pancreatic, including those originating in the breast, lung, brain, and kidney. For my work, I decided to answer the question, “How does inhibition of QSOX1 effect the cancer phenotype?” To answer this I sought to fulfill the following goals A) determine the overexpression parameters of QSOX1 in cancer, B) identify QSOX1 small molecule inhibitors and their effect on the cancer phenotype, and C) determine potential biological effects of QSOX1 in cancer. Antibodies raised against rQSOX1 or a peptide from QSOX1-L were used to probe cancer cells of various origins for QSOX1 expression. High-throughput screening was utilized to identify 3-methoxy-n-[4(1pyrrolidinyl)phenyl]benzamide (SBI-183) as a lead inhibitor of QSOX1 enzymatic activity. Characterization of SBI-183 activity on various tumor cell lines revealed inhibition of viability and invasion in vitro, and inhibition of growth, invasion, and metastasis in vivo, a phenotype that was consistent with QSOX1 shKnockdown cells. Subsequent work identified 3,4,5-trimethoxy-N-[4-(1-pyrrolidinyl)phenyl]benzamide (SPX-009) as an SBI-183 analog with stronger inhibition of QSOX1 enzymatic activity, resulting in a more potent reduction in tumor invasion in vitro. Additional work with QSOX1 shKnockdown and Knockout (KO) cell lines confirmed current literature that QSOX1 is biologically active in modulation of the ECM. These results provide evidence for the master regulatory role of QSOX1 in cancer, making it an attractive chemotherapeutic target. Additionally, the small molecules identified here may prove to be useful probes in further elucidation of QSOX1 tumor biology and biomarker discovery.
ContributorsFifield, Amber (Author) / Lake, Douglas (Thesis advisor) / Ho, Thai (Committee member) / Rawls, Jeffery (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2020
Description
Cytometry is a method used to measure and collect the physical and chemical characteristics of a population of cells. In modern medical settings, the trend of precision and personalized medicines has imposed a need for rapid point-of-care diagnostic technologies. A rapid cytometric method, which aims at detecting and analyzing cells in direct patient samples, is therefore desirable. This dissertation presents the development of light-scattering-based imaging methods for detecting and analyzing cells and applies the technology in four applications. The first application is tracking phenotypic features of single particles, thereby differentiating bacterial cells from non-living particles in a label-free manner. The second application is a culture-free antimicrobial susceptibility test that rapidly tracks multiple, antimicrobial-induced phenotypic changes of bacterial cells with results obtained within 30 – 90 minutes. The third application is rapid antimicrobial susceptibility testing (AST) of bacterial cell growth directly in-patient urine samples, without a pre-culture step, within 90 min. This technology demonstrated rapid (90 min) detection of Escherichia coli in 24 clinical urine samples with 100% sensitivity and 83% specificity and rapid (90 min) AST in 12 urine samples with 87.5% categorical agreement with two antibiotics, ampicillin and ciprofloxacin. The fourth application is a multi-dimensional imaging cytometry system that integrates multiple light sources from different angles to simultaneously capture time-lapse, forward scattering and side scattering images of blood cells. The system has demonstrated capacity to detect red blood cell agglutination, assess red blood cell lysis, and differentiate red and white blood cells for potential implementation in clinical hematology analyses. These large-volume, light-scattering cytometric technologies can be used and applied in clinical and research settings to study, detect, and analyze cells. These studies developed rapid point-of-care diagnostic and imaging technologies for collectively advancing modern medicine and global health.
ContributorsMo, Manni (Author) / Borges, Chad (Thesis advisor) / Tao (Deceased), Nongjian (Thesis advisor) / Wang, Shaopeng (Committee member) / Chiu, Po-Lin (Committee member) / Haydel, Shelley (Committee member) / Arizona State University (Publisher)
Created2020
Description
There is increasing interest and demand in biology studies for identifying and characterizing rare cells or bioparticle subtypes. These subpopulations demonstrate special function, as examples, in multipotent proliferation, immune system response, and cancer diagnosis. Current techniques for separation and identification of these targets lack the accuracy and sensitivity needed to interrogate the complex and diverse bioparticle mixtures. High resolution separations of unlabeled and unaltered cells is an emerging capability. In particular, electric field-driven punctuated microgradient separations have shown high resolution separations of bioparticles. These separations are based on biophysical properties of the un-altered bioparticles. Here, the properties of the bioparticles were identified by ratio of electrokinetic (EK) to dielectrophoretic (DEP) mobilities.
As part of this dissertation, high-resolution separations have been applied to neural stem and progenitor cells (NSPCs). The abundance of NSPCs captured with different range of ratio of EK to DEP mobilities are consistent with the final fate trends of the populations. This supports the idea of unbiased and unlabeled high-resolution separation of NSPCs to specific fates is possible. In addition, a new strategy to generate reproducible subpopulations using varied applied potential were employed for studying insulin vesicles from beta cells. The isolated subpopulations demonstrated that the insulin vesicles are heterogenous and showed different distribution of mobility ratios when compared with glucose treated insulin vesicles. This is consistent with existing vesicle density and local concentration data. Furthermore, proteins, which are accepted as challenging small bioparticles to be captured by electrophysical method, were concentrated by this technique. Proteins including IgG, lysozyme, alpha-chymotrypsinogen A were differentiated and characterized with the ratio factor. An extremely narrow bandwidth and high resolution characterization technique, which is experimentally simple and fast, has been developed for proteins. Finally, the native whole cell separation technique has also been applied for Salmonella serotype identification and differentiation for the first time. The technique generated full differentiation of four serotypes of Salmonella. These works may lead to a less expensive and more decentralized new tool and method for transplantation, proteomics, basic research, and microbiologists, working in parallel with other characterization methods.
As part of this dissertation, high-resolution separations have been applied to neural stem and progenitor cells (NSPCs). The abundance of NSPCs captured with different range of ratio of EK to DEP mobilities are consistent with the final fate trends of the populations. This supports the idea of unbiased and unlabeled high-resolution separation of NSPCs to specific fates is possible. In addition, a new strategy to generate reproducible subpopulations using varied applied potential were employed for studying insulin vesicles from beta cells. The isolated subpopulations demonstrated that the insulin vesicles are heterogenous and showed different distribution of mobility ratios when compared with glucose treated insulin vesicles. This is consistent with existing vesicle density and local concentration data. Furthermore, proteins, which are accepted as challenging small bioparticles to be captured by electrophysical method, were concentrated by this technique. Proteins including IgG, lysozyme, alpha-chymotrypsinogen A were differentiated and characterized with the ratio factor. An extremely narrow bandwidth and high resolution characterization technique, which is experimentally simple and fast, has been developed for proteins. Finally, the native whole cell separation technique has also been applied for Salmonella serotype identification and differentiation for the first time. The technique generated full differentiation of four serotypes of Salmonella. These works may lead to a less expensive and more decentralized new tool and method for transplantation, proteomics, basic research, and microbiologists, working in parallel with other characterization methods.
ContributorsLiu, Yameng (Author) / Hayes, Mark A. (Thesis advisor) / Wang, Xu (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2020
Description
Novel electric field-assisted microfluidic platforms were developed to exploit unique migration phenomena, particle manipulation, and enhanced droplet control. The platforms can facilitate various analytical challenges such as size-based separations, and delivery of protein crystals for structural discovery with both high selectivity and sensitivity. The vast complexity of biological analytes requires efficient transport and fractionation approaches to understand variations of biomolecular processes and signatures. Size heterogeneity is one characteristic that is especially important to understand for sub-micron organelles such as mitochondria and lipid droplets. It is crucial to resolve populations of sub-cellular or diagnostically relevant bioparticles when these often cannot be resolved with traditional methods. Herein, novel microfluidic tools were developed for the unique migration mechanism capable of separating sub-micron sized bioparticles by size. This based on a deterministic ratchet effect in a symmetrical post array with dielectrophoresis (DEP) for the fast migration allowing separation of polystyrene beads, mitochondria, and liposomes in tens of seconds. This mechanism was further demonstrated using high throughput DEP-based ratchet devices for versatile, continuous sub-micron size particle separation with large sample volumes. Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) revolutionized protein structure determination. In SFX experiments, a majority of the continuously injected liquid crystal suspension is wasted due to the unique X-ray pulse structure of XFELs, requiring a large amount (up to grams) of crystal sample to determine a protein structure. To reduce the sample consumption in such experiments, 3D printed droplet-based microfluidic platforms were developed for the generation of aqueous droplets in an oil phase. The implemented droplet-based sample delivery method showed 60% less sample volume consumption compared to the continuous injection at the European XFEL. For the enhanced control of aqueous droplet generation, the device allowed dynamic triggering of droplets for further improvement in synchronization between droplets and the X-ray pulses. This innovative technique of triggering droplets can play a crucial role in saving protein crystals in future SFX experiments. The electric field-assisted unique migration and separation phenomena in microfluidic platforms will be the key solution for revolutionizing the field of organelle separation and structural analysis of proteins.
ContributorsKim, Dai Hyun (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2020
Description
Spatial resolved detection and quantification of ribonucleic acid (RNA) molecules in single cell is crucial for the understanding of inherent biological issues, like mechanism of gene regulation or the development and maintenance of cell fate. Conventional methods for single cell RNA profiling, like single-cell RNA sequencing (scRNA-seq) or single-molecule fluorescent in situ hybridization (smFISH), suffer either from the loss of spatial information or the low detection throughput. In order to advance single-cell analysis, new approaches need to be developed with the ability to perform high-throughput detection while preserving spatial information of the subcellular location of target RNA molecules.
Novel approaches for highly multiplexed single cell in situ transcriptomic analysis were developed by our group to enable single-cell comprehensive RNA profiling in their native spatial contexts. Reiterative FISH was demonstrated to be able to detect >100 RNA species in single cell in situ, while more sophisticated approaches, consecutive FISH (C-FISH) and switchable fluorescent oligonucleotide based FISH (SFO-FISH), have the potential for whole transcriptome profiling at the single molecule sensitivity. The introduction of a cleavable fluorescent tyramide even enables sensitive RNA profiling in intact tissues with high throughput. These approaches will have wide applications in studies of systems biology, molecular diagnosis and targeted therapies.
Novel approaches for highly multiplexed single cell in situ transcriptomic analysis were developed by our group to enable single-cell comprehensive RNA profiling in their native spatial contexts. Reiterative FISH was demonstrated to be able to detect >100 RNA species in single cell in situ, while more sophisticated approaches, consecutive FISH (C-FISH) and switchable fluorescent oligonucleotide based FISH (SFO-FISH), have the potential for whole transcriptome profiling at the single molecule sensitivity. The introduction of a cleavable fluorescent tyramide even enables sensitive RNA profiling in intact tissues with high throughput. These approaches will have wide applications in studies of systems biology, molecular diagnosis and targeted therapies.
ContributorsXiao, Lu, Ph.D (Author) / Guo, Jia (Thesis advisor) / Wang, Xu (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2019
Description
Exerting bias on a diverse pool of random short single stranded oligonucleotides (ODNs) by favoring binding to a specific target has led to the identification of countless high affinity aptamers with specificity to a single target. By exerting this same bias without prior knowledge of targets generates libraries to capture the complex network of molecular interactions presented in various biological states such as disease or cancer. Aptamers and enriched libraries have vast applications in bio-sensing, therapeutics, targeted drug delivery, biomarker discovery, and assay development. Here I describe a novel method of computational biophysical characterization of molecular interactions between a single aptamer and its cognate target as well as an alternative to next generation sequencing (NGS) as a readout for a SELEX-based assay. I demonstrate the capability of an artificial neural network (ANN) trained on the results of screening an aptamer against a random sampling of a combinatorial library of short synthetic 11mer peptides to accurately predict the binding intensities of that aptamer to the remainder of the combinatorial space originally sampled. This machine learned comprehensive non-linear relationship between amino acid sequence and aptamer binding to synthetic peptides can also make biologically relevant predictions for probable molecular interactions between the aptamer and its cognate target. Results of SELEX-based assays are determined by quantifying the presence and frequency of informative species after probing patient specimen. Here I show the potential of DNA microarrays to simultaneously monitor a pool of informative sequences within a diverse library with similar variability and reproducibility as NGS.
ContributorsLevenberg, Symon (Author) / Woodbury, Neal (Thesis advisor) / Borges, Chad (Committee member) / Ghirlanda, Giovanna (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2021
Description
Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two facets of the field: (1) introducing functionality through the incorporation of peptides to create DNA-peptide hybrid materials, and (2) the development of self-assembling DNA crystal lattices for scaffolding biomolecules. DNA nanostructures have long been proposed as drug delivery vehicles; however, they are not biocompatible because of their low stability in low salt environments and entrapment within the endosome. To address these issues, a functionalized peptide coating was designed to act as a counterion to a six-helix bundle, while simultaneously displaying numerous copies of an endosomal escape peptide to enable cytosolic delivery. This functionalized peptide coating creates a DNA-peptide hybrid material, but does not allow specific positioning or orientation of the peptides. The ability to control those aspects required the synthesis of DNA-peptide or DNA-peptide-DNA conjugates that can be incorporated into the nanostructure. The approach was utilized to produce a synbody where three peptides that bind transferrin with micromolar affinity, which were presented for multivalent binding to optimize affinity. Additionally, two DNA handle was attached to an enzymatically cleavable peptide to link two unique nanostructures. The second DNA handle was also used to constrain the peptide in a cyclic fashion to mimic the cell-adhesive conformations of RGD and PHSRN in fibronectin.
The original goal of DNA nanotechnology was to use a crystalline lattice made of DNA to host proteins for their structural determination using X-ray crystallography. The work presented here takes significant steps towards achieving this goal, including elucidating design rules to control cavity size within the scaffold for accommodating guest molecules of unique sizes, approaches to improve the atomic detail of the scaffold, and strategies to modulate the symmetry of each unique lattice. Finally, this work surveys methodologies towards the incorporation of several guest molecules, with promising preliminary results that constitute a significant advancement towards the ultimate goal of the field.
ContributorsMacCulloch, Tara Lynn (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021
Description
S-cysteinylated albumin and methionine-oxidized apolipoprotein A-I (apoA-I) have been posed as candidate markers of diseases associated with oxidative stress. Here, a dilute-and-shoot form of LC–electrospray ionization–MS requiring half a microliter of blood plasma was employed to simultaneously quantify the relative abundance of these oxidized proteoforms in samples stored at −80 °C, −20 °C, and room temperature and exposed to multiple freeze-thaw cycles and other adverse conditions in order to assess the possibility that protein oxidation may occur as a result of poor sample storage or handling. Samples from a healthy donor and a participant with poorly controlled type 2 diabetes started at the same low level of protein oxidation and behaved similarly; significant increases in albumin oxidation via S-cysteinylation were found to occur within hours at room temperature and days at −20 °C. Methionine oxidation of apoA-I took place on a longer time scale, setting in after albumin oxidation reached a plateau. Freeze–thaw cycles had a minimal effect on protein oxidation. In matched collections, protein oxidation in serum was the same as that in plasma. Albumin and apoA-I oxidation were not affected by sample headspace or the degree to which vials were sealed. ApoA-I, however, was unexpectedly found to oxidize faster in samples with lower surface-area-to-volume ratios. An initial survey of samples from patients with inflammatory conditions normally associated with elevated oxidative stress-including acute myocardial infarction and prostate cancer—demonstrated a lack of detectable apoA-I oxidation. Albumin S-cysteinylation in these samples was consistent with known but relatively brief exposures to temperatures above −30 °C (the freezing point of blood plasma). Given their properties and ease of analysis, these oxidized proteoforms, once fully validated, may represent the first markers of blood plasma specimen integrity based on direct measurement of oxidative molecular damage that can occur under suboptimal storage conditions.
ContributorsBorges, Chad (Author) / Rehder, Douglas (Author) / Jensen, Sally (Author) / Schaab, Matthew (Author) / Sherma, Nisha (Author) / Yassine, Hussein (Author) / Nikolova, Boriana (Author) / Breburda, Christian (Author) / Department of Chemistry and Biochemistry (Contributor)
Created2014-07-01