Matching Items (116)
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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
People with disabilities are underrepresented in the Science, Technology, Engineering, and Math (STEM) workforce (NSF, 2016). One way to increase representation of people with disabilities in STEM fields is by supporting students with disabilities (SWDs) at the undergraduate level. In undergraduate education in the United States, SWDs represent approximately 19%

People with disabilities are underrepresented in the Science, Technology, Engineering, and Math (STEM) workforce (NSF, 2016). One way to increase representation of people with disabilities in STEM fields is by supporting students with disabilities (SWDs) at the undergraduate level. In undergraduate education in the United States, SWDs represent approximately 19% of the undergraduate community (U.S. Census Bureau, 2021). However, SWDs have lower graduation and retention rates. This is particularly true for STEM majors, where SWDs make up about 9% of the STEM community in higher education. The AAC&U has defined a list of High-Impact Practices (HIPs), which are active learning practices and experiences that encourage deep learning by promoting student engagement, and could ultimately support student retention (AAC&U). To date, student-centered disability research has not explored the extent to which SWDs participate in HIPs. We hypothesized that SWDs are less likely than students without disabilities to be involved in HIPs and that students who identify as having severe disabilities would participate in HIPs at lower rates. In this study, we conducted a national survey to examine involvement in HIPs for students with disabilities in STEM. We found that disability status significantly affects the probability of participation in undergraduate research, but is not a significant factor for participation in most other HIPs. We also found that self-reported severity of disability did not significantly impact participation in HIPs, though we observed trends that students reporting higher severity generally reported lower participation in HIPs. Our open-ended responses did indicate that SWDs still faced barriers to participation in HIPs.
ContributorsPais, Danielle (Author) / Brownell, Sara (Thesis director) / Cooper, Katelyn (Committee member) / Barrett, The Honors College (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor)
Created2022-05
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Description

There is increasing interest in understanding how active learning affects students’ mental health as science courses transition from traditional lecture to active learning. Prior research has found that active learning can both alleviate and exacerbate undergraduate mental health problems. Existing studies have only examined the relationship between active learning and

There is increasing interest in understanding how active learning affects students’ mental health as science courses transition from traditional lecture to active learning. Prior research has found that active learning can both alleviate and exacerbate undergraduate mental health problems. Existing studies have only examined the relationship between active learning and anxiety. No studies have examined the relationship between active learning and undergraduate depression. To address this gap in the literature, we conducted hour-long exploratory interviews with 29 students with depression who had taken active learning science courses across six U.S. institutions. We probed what aspects of active learning practices exacerbate or alleviate depressive symptoms and how students’ depression affects their experiences in active learning. We found that aspects of active learning practices exacerbate and alleviate students’ depressive symptoms, and depression negatively impacts students’ experiences in active learning. The underlying aspects of active learning practices that impact students’ depression fall into four overarching categories: inherently social, inherently engaging, opportunities to compare selves to others, and opportunities to validate or invalidate intelligence. We hope that by better understanding the experiences of undergraduates with depression in active learning courses we can create more inclusive learning environments for these students.

ContributorsAraghi, Tala (Author) / Cooper, Katelyn (Thesis director) / Brownell, Sara (Committee member) / Busch, Carly (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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Description
Mounting evidence suggests that gender biases favoring men and racial biases favoring whites and Asians contribute to the underrepresentation of women and underrepresented minorities (URM) in science, technology, engineering, and mathematics (STEM). Systemic issues caused by gender and racial biases create barriers that prevent women and URM from entering STEM

Mounting evidence suggests that gender biases favoring men and racial biases favoring whites and Asians contribute to the underrepresentation of women and underrepresented minorities (URM) in science, technology, engineering, and mathematics (STEM). Systemic issues caused by gender and racial biases create barriers that prevent women and URM from entering STEM from the structure of education to admission or promotions to higher-level positions. One of these barriers is unconscious biases that impact the quality of letters of recommendation for women and URM and their success in application processes to higher education. Though letters of recommendation provide a qualitative aspect to an application and can reveal the typical performance of the applicant, research has found that the unstructured nature of the traditional recommendation letter allows for gender and racial bias to impact the quality of letters of recommendation. Standardized letters of recommendation have been implemented in various fields and have been found to reduce the presence of bias in recommendation letters. This paper reviews the trends seen across the literature regarding equity in the use of letters of recommendation for undergraduates.
ContributorsKolath, Nina (Author) / Brownell, Sara (Thesis director) / Goodwin, Emma (Committee member) / Barrett, The Honors College (Contributor) / School of Criminology and Criminal Justice (Contributor) / School of Life Sciences (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
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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
Description

Mental health conditions can impact college students’ social and academic achievements. As such, students may disclose mental illnesses on medical school applications. Yet, no study has investigated to what extent disclosure of a mental health condition impacts medical school acceptance. We designed an audit study to address this gap. We

Mental health conditions can impact college students’ social and academic achievements. As such, students may disclose mental illnesses on medical school applications. Yet, no study has investigated to what extent disclosure of a mental health condition impacts medical school acceptance. We designed an audit study to address this gap. We surveyed 99 potential admissions committee members from at least 43 unique M.D.-granting schools in the U.S. Participants rated a fictitious portion of a medical school application on acceptability, competence, and likeability. They were randomly assigned to a condition: an application that explained a low semester GPA due to a mental health condition, an application that explained a low semester GPA due to a physical health condition, or an application that had a low semester GPA but did not describe any health condition. Using ANOVAs, multinomial regression, and open-coding, we found that committee members do not rate applications lower when a mental health condition is revealed. When asked about their concerns regarding the application, 27.0% of participants who received an application that revealed a mental health condition mentioned it as a concern; 14.7% of participants who received an application that revealed a physical health condition mentioned it as a concern. Committee members were also asked about when revealing a mental health condition would be beneficial and when it would be detrimental. This work indicates that medical school admissions committee members do not exhibit a bias towards mental health conditions and provides recommendations on how to discuss mental illness on medical school applications.

ContributorsAbraham, Anna (Author) / Brownell, Sara (Thesis director) / Cooper, Katelyn (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2022-05
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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
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Description
Similar-identity role models, including instructors, can benefit science undergraduates by enhancing their self-efficacy and sense of belonging. However, for students to have similar-identity role models based on identities that can be hidden, instructors need to disclose their identities. For concealable stigmatized identities (CSIs) – identities that can be hidden and

Similar-identity role models, including instructors, can benefit science undergraduates by enhancing their self-efficacy and sense of belonging. However, for students to have similar-identity role models based on identities that can be hidden, instructors need to disclose their identities. For concealable stigmatized identities (CSIs) – identities that can be hidden and carry negative stereotypes – the impersonal and apolitical culture cultivated in many science disciplines likely makes instructor CSI disclosure unlikely. This dissertation comprises five studies I conducted to assess the presence of instructor role models with CSIs in undergraduate science classrooms and evaluate the impact on undergraduates of instructor CSI disclosure. I find that science instructors report CSIs at lower rates than undergraduates and typically keep these identities concealed. Additionally, I find that women instructors are more likely to disclose their CSIs to students compared to men. To assess the impact of instructor CSI disclosure on undergraduates, I report on findings from a descriptive exploratory study and a controlled field experiment in which an instructor reveals an LGBTQ+ identity. Undergraduates, especially those who also identify as LGBTQ+, benefit from instructor LGBTQ+ disclosure. Additionally, the majority of undergraduate participants agree that an instructor revealing an LGBTQ+ identity during class is appropriate. Together, the results presented in this dissertation highlight the current lack of instructor role models with CSIs and provide evidence of student benefits that may encourage instructors to reveal CSIs to undergraduates and subsequently provide much-needed role models. I hope this work can spark self-reflection among instructors to consider revealing CSIs to students and challenge the assumption that science environments should be devoid of personal identities.
ContributorsBusch, Carly Anne (Author) / Cooper, Katelyn (Thesis advisor) / Brownell, Sara (Thesis advisor) / Collins, James (Committee member) / Zheng, Yi (Committee member) / Arizona State University (Publisher)
Created2024