Matching Items (101)
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Description
Exposure of liquid biospecimens like plasma and serum (P/S) to improper handling and storage can impact the integrity of biomolecules, potentially leading to apparent quantitative changes of important clinical proteins. An accurate and quick estimate of the quality of biospecimens employed in biomarker discovery and validation studies is essential to

Exposure of liquid biospecimens like plasma and serum (P/S) to improper handling and storage can impact the integrity of biomolecules, potentially leading to apparent quantitative changes of important clinical proteins. An accurate and quick estimate of the quality of biospecimens employed in biomarker discovery and validation studies is essential to facilitating accurate conclusions. ΔS-Cys-Albumin is a marker of blood P/S exposure to thawed conditions that can quantitatively track the exposure of P/S to temperatures greater than their freezing point of -30 C. Reported here are studies carried out to evaluate the potential of ΔS-Cys-Albumin to track the stability of clinically important analytes present in P/S upon their exposure to thawed conditions. P/S samples obtained from both cancer-free donors and cancer patients were exposed to 23 C (room temperature), 4 C and -20 C degrees, and the degree to which the apparent concentrations of clinically relevant biomolecules present in P/S were impacted during the time it took ΔS-Cys-Albumin to reach zero was measured. Analyte concentrations measured by molecular interaction-based assays were significantly impacted when samples were exposed to the point where average ΔS-Cys-Albumin fell below 12% at each temperature. Furthermore, the percentage of proteins that became unstable with time under thawed conditions exhibited a strong inverse linear relationship to ΔS-Cys-Albumin, indicating that ΔS-Cys-Albumin can serve as an effective surrogate marker to track the stability of other clinically relevant proteins in plasma as well as to estimate the fraction of proteins that have been destabilized by exposure to thawed conditions, regardless of what the exposure temperature(s) may have been. These results indicated that P/S exposure to thawed conditions disrupts epitopes required for clinical protein quantification via molecular interaction-based assays. In continuation of this theme, a spurious binding event between two clinically important proteins, Apolipoprotein E (ApoE) and Interferon-  (IFN) present in human plasma under in vitro experimental conditions is also reported. The interaction was confirmed to be evident only when ApoE was expressed in vitro with a Glutathione-S-Transferase (GST) fusion tag. Future steps required to find the exact manner in which the GST fusion tag facilitated the association between ApoE and IFNγ are discussed with emphasis on the possible pitfalls associated with using fusion proteins for studying novel protein-protein interactions.
ContributorsKapuruge, Erandi Prasadini (Author) / Borges, Chad R (Thesis advisor) / LaBaer, Joshua (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Osteocalcin (Oc) is the most abundant non-collagen protein found in the bone, but its precise function is still not completely understood. Three glutamic acid (Glu) residues within its sequence are sites for vitamin K-dependent post-translational modification, replacing a hydrogen with a carboxylate located at the γ-carbon position, converting these to

Osteocalcin (Oc) is the most abundant non-collagen protein found in the bone, but its precise function is still not completely understood. Three glutamic acid (Glu) residues within its sequence are sites for vitamin K-dependent post-translational modification, replacing a hydrogen with a carboxylate located at the γ-carbon position, converting these to γ-carboxyglutamic acid (Gla) residues. This modification confers increased binding of Oc to Ca2+ and hydroxyapatite matrix. Presented here, novel metal binding partners Mn2+, Fe3+, and Cr3+ of human Oc were determined, while the previously identified binders to (generally) non-human Oc, Ca2+, Mg2+, Pb2+ and Al3+ were validated as binders to human Oc by direct infusion mass spectrometry with all metals binding with higher affinity to the post-translationally modified form (Gla-Oc) compared to the unmodified form (Glu-Oc). Oc was also found to form pentamer (Gla-Oc) and pentamer and tetramer (Glu-Oc) homomeric self-assemblies in the absence of NaCl, which disassembled to monomers in the presence of near physiological Na+ concentrations. Additionally, Oc was found to form filamentous structures in vitro by negative stain TEM in the presence of increased Ca2+ titrations in a Gla- and pH-dependent manner. Finally, by combining circular dichroism spectroscopy to determine the fraction of Gla-Oc bound, and inductively-coupled plasma mass spectrometry to quantify total Al concentrations, the data were fit to a single-site binding model and the equilibrium dissociation constant for Al3+ binding to human Gla-Oc was determined (Kd = 1.0 ± 0.12 nM). Including citrate, a known competitive binder of Al3+, maintained Al in solution and enabled calculation of free Al3+ concentrations using a Matlab script to solve the complex set of linear equations. To further improve Al solubility limits, the pH of the system was lowered to 4.5, the pH during bone resorption. Complementary binding experiments with Glu-Oc were not possible due to the observed precipitation of Glu-Oc at pH 4.5, although qualitatively if Glu-Oc binds Al3+, it is with much lower affinity compared to Gla-Oc. Taken together, the results presented here further support the importance of post-translational modification, and thus adequate nutritional intake of vitamin K, on the binding and self-assembly properties of human Oc.
ContributorsThibert, Stephanie (Author) / Borges, Chad R (Thesis advisor) / LaBaer, Joshua (Committee member) / Chiu, Po-Lin (Committee member) / Arizona State University (Publisher)
Created2021
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Description

The 5-year survival rate for late-stage metastatic melanoma is only ~30%. A major reason for this low survival rate is that one of the most commonly mutated genes in melanoma, NRAS, has no FDA-approved targeted therapies. Because the RAS protein does not have any targeted therapies, patients with RAS mutant

The 5-year survival rate for late-stage metastatic melanoma is only ~30%. A major reason for this low survival rate is that one of the most commonly mutated genes in melanoma, NRAS, has no FDA-approved targeted therapies. Because the RAS protein does not have any targeted therapies, patients with RAS mutant tumors have an ongoing need for treatments that indirectly target RAS. This thesis project aims to identify expression and phosphorylation levels of proteins downstream of RAS in melanoma cell lines with the most common driver mutations. By analyzing the protein-level differences between these genetic mutants, we hope to identify additional indirect RAS protein targets for the treatment of NRAS mutant melanoma. RAS has several downstream effector proteins involved in oncogenic signaling pathways including FAK, Paxillin, AKT, and ERK. 5 melanoma cell lines (2 BRAF mutant, 2 NRAS mutant, and 1 designated wildtype) were analyzed using western bloting for FAK, Paxillin, AKT, and ERK phosphorylation and total expression levels. The results of western blot analysis showed that NRAS mutant cell lines had increased expression of phosphorylated Paxillin. Increased Paxillin phosphorylation corresponds to increased Paxillin binding at the FAT domain of FAK. Therefore, cell lines with increased FAK FAT – Paxillin interaction would be more sensitive to FAK FAT domain inhibition. The data presented provide an an explanation for the reduction in cell viability in NRAS mutant cell lines infected with Ad-FRNK. This information also has significant clinical relevance as researchers work to develop synthetic FAK FAT domain inhibitors, such as cyclic peptides. Additionally, cell lines with high levels of phosphorylated AKT showed a significant reduction in the amount of phosphorylated ERK. The identification of this inverse relationship may help to explain why BRAF and NRAS mutations are mutually exclusive. To conclude, NRAS mutant cell lines have increased expression of phosphorylated Paxillin and AKT which may explain why NRAS mutant cell lines are more sensitive to FAK FAT domain inhibition.

ContributorsSherwood, Nicole (Author) / Gould, Ian (Thesis director) / LaBaer, Joshua (Committee member) / Marlowe, Timothy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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Description

Heart disease is the leading cause of death in the developed world and often occurs following myocardial infarction. Apelin is an endogenous prepropeptide that has been studied for its role in improving cardiac contractility and vasodilation but suffers from a short half-life in the body. By encasing apelin in a

Heart disease is the leading cause of death in the developed world and often occurs following myocardial infarction. Apelin is an endogenous prepropeptide that has been studied for its role in improving cardiac contractility and vasodilation but suffers from a short half-life in the body. By encasing apelin in a nanoparticle patch, we were able to slowly release apelin to cardiac tissue and observe its effects for one month following induced myocardial infarction surgery in mice. This study demonstrates that the apelin nanoparticles can protect the heart from myocardial-induced heart failure, observing overall improved cardiac function and reduction of fibrotic scarring associated with post-myocardial infarction compared to a nontreated group.

ContributorsHenderson, Adam (Author) / Chen, Qiang (Thesis director) / Zhu, Wuqiang (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor)
Created2022-05
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Description
Emerging pathogens present several challenges to medical diagnostics. Primarily, the exponential spread of a novel pathogen through naïve populations require a rapid and overwhelming diagnostic response at the site of outbreak. While point-of-care (PoC) platforms have been developed for detection of antigens, serologic responses, and pathogenic genomes, only nucleic acid

Emerging pathogens present several challenges to medical diagnostics. Primarily, the exponential spread of a novel pathogen through naïve populations require a rapid and overwhelming diagnostic response at the site of outbreak. While point-of-care (PoC) platforms have been developed for detection of antigens, serologic responses, and pathogenic genomes, only nucleic acid diagnostics currently have the potential to be developed and manufactured within weeks of an outbreak owing to the speed of next-generation sequencing and custom DNA synthesis. Among nucleic acid diagnostics, isothermal amplification strategies are uniquely suited for PoC implementation due to their simple instrumentation and lack of thermocycling requirement. Unfortunately, isothermal strategies are currently prone to spurious nonspecific amplification, hindering their specificity and necessitating extensive empirical design pipelines that are both time and resource intensive. In this work, isothermal amplification strategies are extensively compared for their feasibility of implementation in outbreak response scenarios. One such technology, Loop-mediated Amplification (LAMP), is identified as having high-potential for rapid development and PoC deployment. Various approaches to abrogating nonspecific amplification are described including a novel in silico design tool based on coarse-grained simulation of interactions between thermophilic DNA polymerase and DNA strands in isothermal reaction conditions. Nonspecific amplification is shown to be due to stabilization of primer secondary structures by high concentrations of Bst DNA polymerase and a mechanism of micro-complement-mediated cross-priming is demonstrated as causal via nanopore sequencing of nonspecific reaction products. The resulting computational model predicts primer set background in 64% of 67 test assays and its usefulness is illustrated further by determining problematic primers in a West Nile Virus-specific LAMP primer set and optimizing primer 3’ nucleotides to eliminate micro-complements within the reaction, resulting in inhibition of background accumulation. Finally, the emergence of Orthopox monkeypox (MPXV) as a recurring threat is discussed and SimCycle is utilized to develop a novel technique for clade-specific discrimination of MPXV based on bridging viral genomic rearrangements (Bridging LAMP). Bridging LAMP is implemented in a 4-plex microfluidic format and demonstrates 100% sensitivity in detection of 100 copies of viral lysates and 45 crude MPXV-positive patient samples collected during the 2022 Clade IIb outbreak.
ContributorsKnappenberger, Mark Daniel (Author) / Anderson, Karen S (Thesis advisor) / LaBaer, Joshua (Committee member) / Roberson, Robert (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2023
Description
Weight stigma is present in many aspects of society, and especially in medicine. Weight stigma has detrimental effects on individuals physical and mental health, as well as patient-physician interactions. Application of weight-neutral healthcare ideologies such as Health at Every Size (HAES) are promising ways of decreasing weight stigma within the

Weight stigma is present in many aspects of society, and especially in medicine. Weight stigma has detrimental effects on individuals physical and mental health, as well as patient-physician interactions. Application of weight-neutral healthcare ideologies such as Health at Every Size (HAES) are promising ways of decreasing weight stigma within the medical field without reducing the focus on improving patient health. Most widely applicable interventions include changing the focus of interactions from weight to health-promoting behaviors and lab values, improving provider education, and improving the general population's awareness of the problem.
ContributorsBrouhard, Mya (Author) / Chen, Qiang (Thesis director) / Parker, Lynn (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor)
Created2024-05
Description

Platelet Rich Plasma (PRP) is an emerging procedure in regenerative medicine that offers a non-surgical minimally invasive way for tissue repair and regeneration. PRP has many different bioactive molecules that are able to influence and help achieve greater recovery and regenerative outcomes. Diet has many effects on platelets and looking

Platelet Rich Plasma (PRP) is an emerging procedure in regenerative medicine that offers a non-surgical minimally invasive way for tissue repair and regeneration. PRP has many different bioactive molecules that are able to influence and help achieve greater recovery and regenerative outcomes. Diet has many effects on platelets and looking at the mechanism in which platelet function and aggregation are affected with different diets shows how they are able to affect PRP therapy. Looking at these mechanisms allows for better physician recommendations for preprocedural diets to optimize efficacy. This paper conducts a systematic review to investigate the influence that diet can have on PRP outcomes. It was shown that high fat diets lower the efficacy of treatment while the Mediterranean diet helps promote platelet function and help efficacy. The future is to look at more diets while also integrating lifestyle choice before treatment for optimal outcomes.

ContributorsLaguna, Sebastian (Author) / Chen, Qiang (Thesis director) / Goyle, Ashu (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Dean, W.P. Carey School of Business (Contributor)
Created2024-05
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Description
MicroRNAs (miRNAs) are 17-22 nucleotide non-coding RNAs that regulate gene expression by targeting non-complementary elements in the 3’ untranslated regions (3’UTRs) of mRNAs. miRNAs, which form complex networks of interaction that differ by tissue and developmental stage, display conservation in their function across metazoan species. Yet much remains unknown regarding

MicroRNAs (miRNAs) are 17-22 nucleotide non-coding RNAs that regulate gene expression by targeting non-complementary elements in the 3’ untranslated regions (3’UTRs) of mRNAs. miRNAs, which form complex networks of interaction that differ by tissue and developmental stage, display conservation in their function across metazoan species. Yet much remains unknown regarding their biogenesis, localization, strand selection, and their absolute abundance due to the difficulty of detecting and amplifying such small molecules. Here, I used an updated HT qPCR-based methodology to follow miRNA expression of 5p and 3p strands for all 190 C. elegans miRNAs described in miRBase throughout all six developmental stages in triplicates (total of 9,708 experiments), and studied their expression levels, tissue localization, and the rules underlying miRNA strand selection. My study validated previous findings and identified novel, conserved patterns of miRNA strand expression throughout C. elegans development, which at times correlate with previously observed developmental phenotypes. Additionally, my results highlighted novel structural principles underlying strand selection, which can be applied to higher metazoans. Though optimized for use in C. elegans, this method can be easily adapted to other eukaryotic systems, allowing for more scalable quantitative investigation of miRNA biology and/or miRNA diagnostics.
ContributorsMeadows, Dalton Alexander (Author) / Mangone, Marco (Thesis advisor) / LaBaer, Joshua (Committee member) / Murugan, Vel (Committee member) / Wilson-Rawls, Jeanne (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Coccidioidomycosis, or valley fever (VF), is a fungal infection caused by Coccidioides that is highly endemic in southern Arizona and central California. The antibody response to infection in combination with clinical presentation and radiographic findings are often used to diagnose disease, as a highly sensitive and specific antigen-based assay has

Coccidioidomycosis, or valley fever (VF), is a fungal infection caused by Coccidioides that is highly endemic in southern Arizona and central California. The antibody response to infection in combination with clinical presentation and radiographic findings are often used to diagnose disease, as a highly sensitive and specific antigen-based assay has yet to be developed and commercialized. In this dissertation, a panel of monoclonal antibodies (mAbs) was generated in an attempt to identify circulating antigen in VF-positive patients. Despite utilizing a mixture of antigens, almost all mAbs obtained were against chitinase 1 (CTS1), a protein previously identified as a main component in serodiagnostic reagents. While CTS1 was undoubtedly a dominant seroreactive antigen, it was not successfully detected in circulation in patient samples prompting a shift toward further understanding the importance of CTS1 in antibody-based diagnostic assays. Interestingly, depletion of this antigen from diagnostic antigen preparations resulted in complete loss of patient IgG reactivity by immunodiffusion. This finding encouraged the development of a rapid, 10-minute point-of-care test in lateral flow assay (LFA) format to exclusively detect anti-CTS1 antibodies from human and non-human animal patients with coccidioidal infection. A CTS1 LFA was developed that demonstrated 92.9% sensitivity and 97.7% specificity when compared to current quantitative serologic assays (complement fixation and immunodiffusion). A commercially available LFA that utilizes a proprietary mixture of antigens was shown to be less sensitive (64.3%) and less specific (79.1%). This result provides evidence that a single antigen can be used to detect antibodies consistently and accurately from patients with VF. The LFA presented here shows promise as a helpful tool to rule-in or rule-out a diagnosis of VF such that patients may avoid unnecessary antibacterial treatments, improving healthcare efficiency.
ContributorsGrill, Francisca J (Author) / Lake, Douglas F (Thesis advisor) / Magee, D Mitch (Committee member) / Grys, Thomas (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2023
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Description

Under the direction of Dr. Carolyn Compton, a group of seven Barrett honors students have embarked on a truly unique team thesis project to create a documentary on the process of creating a COVID-19 testing laboratory. This documentary tells the story of the ASU Biodesign Clinical Testing Laboratory (ABCTL), the

Under the direction of Dr. Carolyn Compton, a group of seven Barrett honors students have embarked on a truly unique team thesis project to create a documentary on the process of creating a COVID-19 testing laboratory. This documentary tells the story of the ASU Biodesign Clinical Testing Laboratory (ABCTL), the first lab in the western United States to offer public saliva testing to identify the presence of COVID-19.

ContributorsCura, Joriel (Director, Photographer) / Foote, Hannah (Producer, Sound designer) / Raymond, Julia (Production personnel) / Bardfeld, Sierra (Narrator, Editor) / Dholaria, Nikhil (Writer of added commentary) / Liu, Tara (Writer of added commentary) / Varghese, Mahima (Writer of added commentary) / Compton, Carolyn C. (Interviewee, Project director) / Harris, Valerie (Interviewee) / LaBaer, Joshua (Interviewee) / Miceli, Joseph (Interviewee) / Nelson, Megan (Interviewee) / Ungaro, Brianna (Interviewee)
Created2021