Arts and Sciences Undergraduate Research Theses and Honors Research Theses

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Undergraduate Research Theses and Honors Research Theses from the College of Arts and Sciences. More about the College of Arts and Sciences Honors Program can be found at:

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    Detecting Biosignatures in Nearby Rocky Exoplanets Using High-contrast Imaging and Medium-resolution Spectroscopy with the Extremely Large Telescope
    (The Ohio State University, 2024-05) Zhang, Huihao; Wang, Ji
    In the upcoming decades, one of the primary objectives in exoplanet science is to search for habitable planets and signs of extraterrestrial life in the Universe. Signs of life can be indicated by thermal-dynamical imbalance in terrestrial planet atmospheres. O2 and CH4 in the modern Earth's atmosphere are such signs, commonly termed biosignatures. These biosignatures in exoplanetary atmospheres can potentially be detectable through high-contrast imaging instruments on future extremely large telescopes. To quantify the signal-to-noise ratio (S/N) with extremely large telescopes, we select up to 10 nearby rocky planets and simulate medium-resolution (R ∼ 1000) direct imaging of these planets using the Mid-infrared ELT Imager and Spectrograph (ELT/METIS, 3–5.6 μm) and the High Angular Resolution Monolithic Optical and Near-infrared Integral field spectrograph (ELT/HARMONI, 0.5–2.45 μm). We calculate the S/N for the detection of biosignatures including CH4, O2, H2O, and CO2. Our results show that GJ 887 b has the highest detection of S/N for biosignatures, and Proxima Cen b exhibits the only detectable CO2 among the targets for ELT/METIS direct imaging. We also investigate the TRAPPIST-1 system, the archetype of nearby transiting rocky planet systems, and compare the biosignature detection of transit spectroscopy with JWST versus direct spectroscopy with ELT/HARMONI. Our findings indicate JWST is more suitable for detecting and characterizing the atmospheres of transiting planet systems such as TRAPPIST-1 that are relatively further away and have smaller angular separations than more nearby nontransiting planets.
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    MHV-68 Induces the Development of Encephalitogenic Disease in an MBP-Specific TCR Transgenic Mouse Model of Multiple Sclerosis
    (The Ohio State University, 2022-12) Deffenbaugh, Joshua; Lovett-Racke, Amy
    Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system. While the precise etiology of the disease is unknown, several genetic and environmental factors play a role in the disease's development. Several epidemiological studies have indicated that prior infection with Epstein-Barr Virus (EBV), as well as vitamin D insufficiency, smoking, among other factors are significantly associated with the development of MS. Large seroprevalence studies have indicated a significant correlation between EBV seropositivity and the development of MS. Thus, characterizing how viral infections reshape immune profiles may elucidate pathways that potentiate encephalitogenic disease development. We report that latent infection with MHV-68, an EBV analog, exacerbates autoimmune disease development in a MBP-specific transgenic T cell receptor mouse model. Furthermore, we report that these mice present with MS-like signs previously unreported in EAE models. The purpose of this study was to characterize immunological and transcriptional changes that result from latent MHV-68 infection to further characterize pathways that promote autoimmunity.
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    Acute exercise and cognition: An examination of the effect of exercise intensity on episodic memory and executive function performance
    (The Ohio State University, 2022-12) Melville, Michael; Hayes, Scott M.
    Background: Acute aerobic exercise has been linked to improvements in certain types of memory and executive function following exercise cessation, however, the characteristics of exercise (e.g., intensity) that provide maximal cognitive benefits are still debated. Objective: To investigate the dose-response relationship between acute aerobic exercise intensity and performance in multiple cognitive domains (episodic memory and executive function). Methods: 18 young adults (M age = 21.6, SD = 2.6; M education = 15.3, SD = 2.6; 50% female) each completed a control (rest), light intensity, and vigorous intensity aerobic exercise condition across three counterbalanced appointments. Participants then completed a continuous Mnemonic Similarity Task (MST; Stark et al., 2019) to assess pattern separation and a gradual-onset continuous performance task (gradCPT; Esterman et al., 2013) to assess sustained attention and inhibitory control after each condition. Results: For the MST, a hypothesized significant main effect of lure similarity on task performance (p < .001) was revealed; however, there was not a significant main effect of exercise intensity on task performance (or a significant interaction). A significant main effect of exercise intensity on gradCPT performance on task discrimination ability (d') and commission error rate (p's < .05) was observed. Post-hoc comparisons revealed task discrimination ability was significantly higher following the light intensity exercise condition versus the control condition. Commission error rate was significantly lower for both the light and vigorous exercise conditions compared to the control condition. Conclusions: The current study does not replicate previous work demonstrating an improvement in pattern separation following bouts of acute aerobic exercise in young adults. Our results further indicate that vigorous intensity exercise did not detrimentally impact or improve pattern separation performance. The current study indicated that bouts of acute aerobic exercise improve both sustained attention and inhibitory control as measured with the gradCPT. Our results show that light intensity aerobic exercise was sufficient to enhance sustained attention and inhibitory control as assessed with the gradCPT. Keywords: Cognition; Episodic Memory; Executive function; Attention; Aerobic Exercise.
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    Determining Pathways of Health: A Study of the Role of Social Factors
    (The Ohio State University, 2022-05) Brown, Madison; Knoester, Chris
    This study examines the extent to which social structural (e.g., socioeconomic status, gender, race/ethnicity) and sports related factors lead to different dimensions of adults' health (e.g., mental, physical), while considering the differential relevance of childhood and adulthood stages of life. Nested multiple regression analyses of the National Sports and Society survey (N = 3,993) tested the implications of social structural factors, childhood sports and physical activities, and adulthood sports and physical activities on U.S. adults' subjective health, life satisfaction, and depressive symptoms. Results show a number of notable associations between the predictor variables and different dimensions of adults' health, which overall suggest more should be done to mitigate the adverse effects of social structure on health outcomes, encourage more inclusive and positive organized sports experiences during childhood, support and encourage very hard physical activities over the life course, and support and encourage sports involvement opportunities among adults.
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    Childhood Sports Participation and Parent-Child Closeness Through the Life Course
    (The Ohio State University, 2022-05) Arens, Adelyn; Knoester, Chris
    In past generations, parents were typically less involved in their children's sporting experience compared to today. With the increasing professionalism and competitiveness of youth sports it is now expected that parents take an active role in their child's sporting experience. Middle-class parents are investing earlier and more heavily in their children's sports participation than ever before. Youth sports are gaining popularity because of their potential to lead to college scholarships as tuition prices continue to rise. Parents concerned about their ability to pay for their child's schooling may have more motivation to push participation in sports. With the current popularity of youth sports, it is becoming increasingly important to understand how sporting involvement affects parent-child closeness. Most previous research in the field of sport sociology has found positive associations between children's involvement in sports and parent-child feelings of closeness. However, previous research is lacking identifications of specific factors that affect feelings of closeness and indicators of their relative impacts. To identify these specific factors that will lead to parent-child closeness when the child plays sports, it is important to first consider the child's background. Organized sport participation has been found to be positively associated with health and whiteness. Secondly, it is necessary to consider the opportunities available to the child. Income level is likely to dictate to some extent the chances for organized sports participation. Finally, the child's actual sporting experience will be considered. Certain factors such as mistreatment (the child was harmed either physically or mentally) during the sport, especially if this mistreatment was inflicted by the parents, can lessen the benefits of increasing parent-child feelings of closeness. Conversely, if the child's parents report being sports fans or athletes themselves, this could lead to above average parent-child closeness as the pair is able to participate in a shared hobby. The goal of this project is to identify the factors related to sports that lead to the increase in parent-child closeness and assess the extent to which they lead to feelings of closeness in both the short and long term as the dependent variables of the study. The main independent variables for this project are duration and time spent playing sports (how long the child was involved in sports and how much time per week they dedicated to sports), level of involvement (recreational, high school, club, etc.), goal alignment (if parents and children wanted to be involved in sports for the same reason, for example, for the child to play in college), if the parent considers themselves to be an athlete or a sports fan, socioeconomic factors (parent's income, race, gender, neighborhood), and if the child ever experienced mistreatment while playing sports.
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    Ecological Correlates of the Morphology of the Auditory Bulla in Rodents: Applications to the Fossil Record
    (The Ohio State University, 2020-12) Scarpitti, Erica; Calede, Jonathan
    For rodents, hearing is essential to survival; it enables predator evasion, prey detection, and conspecific recognition. The hearing system of rodents is likely to be ecology-specific since hearing is constrained by the surrounding physical environment. Previous research on the middle ear of rodents shows this ecomorphological association. The link between tympanic bulla morphology and ecology has never been investigated across a broad array of rodent species before; such link may enable the determination of the ecological affinities of many fossil species only known from partial skulls. In this study, I use geometric morphometrics to quantify the shape of the auditory bulla of 197 specimens of extant rodents representing 91 species from 17 families across four different locomotory modes. I use landmarks and semi-landmarks on the ventral and lateral views of the skull to capture characteristics of bullar inflation and external auditory meatus extension. The results of my principal component analyses and canonical variate analyses demonstrate an association between bullar morphology and locomotion in rodents. The classification phase of my combined analysis of the two views enables the correct classification of 76% of the species in the training set. A phylogenetically-informed flexible discriminant analysis shows a weak phylogenetic effect on tympanic morphology. The application of this approach to select fossil rodents from the Oligo-Miocene shows broad agreements with prior studies and yields new locomotory inferences for 17 fossil species, including the first proposed locomotion for members of the family Florentiamyidae. Such results call for the timing of burrowing diversification in rodents to be reevaluated.
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    The Effect of Corporate Mantra Personalization on Newcomer Attitudes
    (The Ohio State University, 2020-05) Mathew, Jordan; Wegener, Duane
    "Corporate mantras" are internally-resonating phrases aimed to perpetuate values and guide decisions at every level of an organization (e.g., Nike's mantra is "authentic athletic performance"). Despite the commonality of these phrases, no scholarly work has examined instantiation and repetition of such mantras from an intraorganizational perspective. When multiple employees are involved in "onboarding" (orienting) a new colleague, those employees might be viewed as multiple independent sources (where multiple sources have a more polarizing effect than a single source delivering the same arguments; Harkins & Petty, 1981a). Yet, if people view the employees as all representing the organization, and therefore not independent, the potential benefit of multiple sources is lost unless the employees are made to seem more independent (cf. Harkins & Petty, 1987). This study aims to assess the extent to which personalized expressions of corporate mantras might capitalize on the multiple source effect, mitigating any perceptions of non-independence across employees, to produce favorable attitudes towards an organization and an increased sense of autonomy amongst group members. Participants imagined going through orientation at a new corporation and hearing from three employees. The canned-mantra condition had each employee stating the exact same mantra and subsequent argument within their description. In preliminary data collection, the "middle" partially-personalized condition (same mantra but varied argument expression) did not significantly differ from the canned or fully-personalized conditions and was removed from the main study. The fully-personalized mantra variation condition maintained the argument variations from the middle condition but synonymized (personalized) the common values in each mantra. Participants were asked a series of questions on their perceptions of the employees, their attitudes toward the company, and their fit with the company's mantra and values. Fully-personalized mantras (vs. canned-mantras) significantly affected the participants' perceived fit and autonomy in the organization and led to a more positive organizational evaluation.
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    Synthesis, Structural, and Electronic Properties of Sr1-xCaxPdAs
    (The Ohio State University, 2020-05) Redemann, Benjamin; Goldberger, Joshua
    Layered honeycomb intermetallic phases have attracted considerable research interest due to the wide array of exciting physical properties inherent in these materials. Here, we follow the evolution in structure and electronic properties of a relatively unexplored material system, Sr1-xCaxPdAs, as the hexagonal PdAs honeycomb layer in SrPdAs distorts into the orthorhombic CaPdAs structure. The Sr-rich compounds (x = 0 to 1/3) form symmetric, hexagonal honeycomb PdAs layers, whereas in the Ca rich region (x = 1/2 to 1) the PdAs layers distort into an orthorhombic structure featuring long and short Pd-Pd distances. This distortion occurs when the average Pd-Pd distance falls below 4.21 Å. All compounds are observed to exhibit metallic temperature-dependent resistivity trends. There are no apparent discontinuities indicative of metal-to-insulator transitions and the room temperature resistivity values range from 18 to 180 mΩ cm. In total, this work maps out the structural and electronic phase diagram of Sr1-xCaxPdAs compounds.
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    Examination of RAL Proteins in C. elegans
    (The Ohio State University, 2020-05) Rizzo, Joseph, Jr.; Chamberlin, Helen
    Introduction: Ras-related proteins (RAL proteins) are part of the Ras superfamily and these proteins are relevant in many cancers such as breast, colorectal, and prostate. In humans, there are two RAL genes, RALA and RALB. While the structures of RALA and RALB proteins are similar, and they compensate for each other in many cases, they have some specific, distinct functions. In particular, RALA is overexpressed in triple-negative/basal-like breast cancer, while RALB is under expressed (Data not yet published). Reasons and mechanisms for the functional differences are currently unknown, and further research is vital to understanding these proteins. Caenorhabditis elegans, the nematode worm, has a single ortholog to the human proteins, RAL-1. Rescuing nematodes that lack RAL-1 with RALA or RALB can be used to observe differences between the two proteins, which could lead to better understanding of these proteins. Methods: The promoter, cDNA, and 3' UTR were cloned from DNA, and cDNA from human were used to generate worm-specific expression constructs for each protein (RAL-1, RALA, and RALB) using PCR. These were added together into a plasmid using a Gibson Assembly. The constructs were then inserted into C. elegans using the MosSCI method; the construct is inserted into a transposable element in the genome, which allows for the expression of a single copy of the gene. This created 3 different strains. The capability of each strain to rescue a C. elegans ral-1 mutant was tested. Production of lateral alae, paraquat resistance, and gonad structure were tested. Chimeric constructs containing the RAL-1 N-terminus and the RALA/RALB strain are being developed using PCR to determine regions of the proteins that lead to functional differences. Results: No significant differences occurred in lifespan or paraquat resistance in RAL-1, RALA, or RALB, suggesting that the human RAL proteins are able to compensate for RAL-1 interactions with reactive oxygen species (ROS).RALB fully rescues lateral alae production, a structure in the cuticle dependent on exosome secretion, whereas RALA rescues incompletely. The gonad structure is similar between RALA and RALB, where egg yolk accumulates, and the animals are sterile. The rachis width is more narrow in RALB, whereas RALA width is more comparable to wild-type (WT). Comparison of RAL-1, RALA, and RALB in C. elegans suggests in vivo differences. Conclusions: RALA and RALB both rescue to viability. RALB is unable to rescue the rachis, whereas RALA rescues the rachis. RALB rescues the lateral alae, but RALA does not. This suggests that this assay can be used to distinguish functions of RALA and RALB. RALA and RALB may also be used to observe the effects of RAL-1 on fertility in C. elegans.
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    A new diagnostic assay for classical galactosemia
    (The Ohio State University, 2020-05) Bashian, Eleanor; Gopalan, Venkat
    Classical galactosemia is a potentially lethal disorder of the Leloir metabolic pathway that affects approximately 1 out of 53,000 newborns in the United States each year. In the Leloir pathway, galactokinase converts galactose to galactose 1-phosphate, which then reacts with uridine diphosphate (UDP)-glucose to produce glucose 1-phosphate in a reaction catalyzed by galactose 1-phosphate uridylyltransferase (GalT). Glucose 1-phosphate is subsequently converted to glucose 6-phosphate, which enters glycolysis and generates energy. Since lactose, a disaccharide comprised of galactose and glucose, is the first sugar metabolized by breast-fed infants, diagnosis of classical galactosemia is a high priority in newborn screening. GalT is deficient in classical galactosemia. Therefore, the current method for diagnosing this inborn disorder involves adding to a blood sample the two substrates for GalT [galactose 1-phosphate and UDP-glucose] and measuring the production of glucose 1-phosphate. Since glucose 1-phosphate cannot be measured directly by spectro-photometric/-fluorometric methods, available methods entail the use of a coupled assay involving two or three additional enzymes. A simpler, less expensive, and more accurate diagnostic method is desirable. To this end, we explored the utility of an easier assay based on a phosphatase that cleaves glucose 1-phosphate into glucose and orthophosphate; we reasoned that the orthophosphate in turn can be detected colorimetrically by using malachite green-based phosphate detection. Before implementing this method, however, it is necessary to identify a phosphatase that exhibits a significant bias for glucose 1-phosphate over galactose 1-phosphate in order to ensure a readout from the GalT product and not the substrate. Here, I present results from kinetic studies on two haloacid dehalogenase (HAD)-like phosphatases from Salmonella enterica subspecies enterica serovar Typhimurium that indicate such a strong preference for glucose 1-phosphate. I also describe approaches that I have initiated to improve the yield of these phosphatases in recombinant form. Another key requisite prior to translating this phosphatase-based assay for routine clinical use is the removal of endogenous phosphate in the blood samples. Since GalT activity will be determined by measuring the concentration of glucose 1-phosphate produced, which in turn is determined by measuring the concentration of phosphate produced by the Salmonella phosphatase, phosphate in blood samples would interfere with an accurate measurement of GalT activity. I will summarize findings from ongoing studies that demonstrate the challenges associated with phosphate removal, and conclude with the prospects of implementing this new assay for classical galactosemia.
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    Parameters of DNA Fingerloop Structured Antisense Probes that Discriminate Against Mismatched Pairing Partners
    (The Ohio State University, 2020-05) Traverse, Elizabeth; Lease, Richard; Jackman, Jane
    Nanotechnology is a rapidly expanding field of study due to its potential use in several fields, including medicine and industry. Many RNA nanotechnology objects are designed for proof–in–principle, but a few are derived from natural RNAs (1-3). One such natural RNA is the E. coli native antisense regulatory small RNA, DsrA, which can translationally regulate gene expression by antisense RNA interactions with mRNA targets. DsrA contains atypical structured antisense domains in stem-loops called fingerloops, which behave similarly to toehold sequences (4) to initiate seed sequence pairing and form a base–paired complex with a target mRNA. The fingerloop contains antisense sequence in the loop and one side of the stem that can form base pairs with a specific nucleotide sequence. Additionally, the fingerloop has the interesting quality of being able to discriminate against even single base mismatches between the fingerloop loop sequence and the target sequence. It was previously observed that DNA fingerloops function similarly to RNA in single-base mismatch exclusion. With DNA as with RNA, if a mutation between the nucleic acid pairing target and fingerloop probe falls within the loop portions of the fingerloop, some degree of discrimination is seen against pairing with a mismatched target. To better understand this fundamental property, we delineated certain parameters and limitations of the fingerloop. In this study, we evaluated mismatch location, loop size and sequence content contributions to the mismatch exclusion function of fingerloop DNAs. Strikingly, by forcing the entire 18-nt antisense sequence into the loop portion, exclusion of mismatched targets is enhanced.
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    Muscle degeneration in zebrafish dmd mutants is reduced upon Tgfβ inhibition
    (The Ohio State University, 2020-05) Beljan, Joseph; Amacher, Sharon
    Duchenne muscular dystrophy (DMD) is a degenerative neuromuscular disease affecting 1 in 3,500 to 5,000 human males. DMD is caused by a loss-of-function mutation in the DMD gene. DMD encodes for dystrophin, a structural protein crucial to muscle cell membrane (sarcolemma) integrity. In patients with DMD, chronic tearing of the skeletal muscle sarcolemma causes perpetual muscle degeneration and regeneration. Transforming Growth Factor Beta (TGFβ) is a super-family of multifunctional cytokines responsible for a wide variety of cellular responses and processes. TGFβ1 is a member of the TGFβ super-family and is activated during muscle tissue injury. The continuous cycle of muscle cell death and replacement in DMD results in hyperactive TGFβ1 signaling. Recent human genome-wide association studies (GWAS) correlated the age at loss of ambulation (LoA) in DMD patients with specific alleles of Latent TGFβ1 Binding Protein 4 (LTBP4) and Thrombospondin 1 (THBS1). LTBP4 and THBS1 both function in the TGFβ1 signaling pathway. Protective alleles of LTBP4 and THBS1 result in lowered expression of their respective proteins. Lowered expression of either LTBP4 or THBS1 confers decreased TGFβ1 signaling and correlates with an increased age at LoA. An additional protective allele of LTBP4, causing greater binding affinity between LTBP4 and TGFβ1, also confers lowered levels of TGFβ1 signaling and an increased age at LoA. Utilizing the zebrafish dmd model (dmdta222a, originally isolated as the sapje mutant), I have tested whether lowering TGFβ1 (Tgfβ1 in zebrafish) signaling ameliorates muscle degeneration in dmd mutant embryos. I treated wild-type and dmd mutant embryos with Tgfβ1 signaling antagonists and assayed the resulting phenotypes. Using birefringence and confocal microscopy, I studied overall muscle structure and muscle cell morphology. After testing two Tgfβ1 signaling antagonists, my results show that antagonist treatment reduces phospho-Smad3 (pSmad3) expression, a Tgfβ1 signaling readout. I found that overall birefringence intensity, an indicator of healthy muscle structure, is significantly increased with antagonist treatment in dmd mutants (p<0.001). The number of healthy muscle segments (somites) are also dramatically increased in inhibitor-treated dmd mutants compared to their untreated dmd mutant siblings. These results conclude that treating dmd mutant zebrafish embryos with known Tgfβ1 signaling antagonists leads to partial rescue of the dmd mutant phenotype. My work encourages further investigation into TGFβ1 signaling manipulation to slow DMD disease progression.
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    Historicizing Change in 20th Century Belizean Political Economy
    (The Ohio State University, 2020-05) Ferrell, Jake; Wainwright, Joel
    This thesis explores why the Belizean state was unable to form a developmental state in the period following the emergence of the nationalist movement in the 1950s. In the period following World War II, successful developmental states, like those those formed in Botswana and Korea for example, were able to discipline capital, coordinate and plan effectively, and bring the goods of development to the poor and marginalized communities in their countries. A quick historical accounting of economic development and poverty confirms this did not occur in Belize. Why not? I traveled to and lived in Belize for this project. I examined developmental plans, meeting minutes, and other documents in the Belize Archives in addition to conducting interviews with ten Belizeans familiar with the period. I argue that the Belizean nationalist movement lacked the capacity to form a developmental state and guide the country down a developmental path like that of Botswana or Korea. The anticolonial People's United Party (PUP), and its leader George Price, did not achieve the necessary intrinsic and extrinsic state capacity to coordinate development plans effectively and to discipline capital. I attribute this in largely part to the legacies of Belize's colonial political economy and its status on the periphery of global capitalism. On a concluding note, I also explore a late attempt to form a developmental state by the PUP government of 1998-2003. This attempt failed. I argue that it did so because of the persisting colonial-historical limitations as well as the crystallization of neoliberalism's global hegemonic power to prevent the formation of any new developmental states.
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    Determination of the Elution Kinetics of Antibiotic-Loaded Calcium Sulfate Beads and Powdered Antibiotic Bolus for Surgical Site Infections
    (The Ohio State University, 2020-05) Moore, Kelly; Stoodley, Paul
    Antibiotic tolerant bacterial biofilms are notorious in causing surgical site infections (SSI). Stimulan rapid cure antibiotic-loaded calcium sulfate has shown promising results for eradication of biofilms in vitro. Antibiotic-loaded calcium sulfate beads (CSBv+t) and PMMA bone cement spacers (Spacerv+t or Spaceru), and powdered antibiotic sprinkled in the surgical site as a bolus (VP) are used to achieve high local concentrations of antibiotics. However, antibiotic concentrations in the joint using these different release methods is poorly understood. Conventional release testing relies on elution into a fixed liquid volume and is not compatible with a bolus application. Also, in periprosthetic joint infections there is liquid exchange from joint fluid and exudate. We describe an artificial draining knee model which can provide controlled drainage to better determine the predicted antibiotic concentration profile. An in vitro flow reactor model was designed which consisted of a reservoir and a pump to pump Ringers solution at flow rates taken from clinical drainage rates measured after knee revision surgery. Stimulan calcium sulfate beads were loaded with vancomycin (VAN) at 1000 mg and 240 mg tobramycin (TOB) per 10cc pack. PMMA bone cement spacers were loaded with 2g VAN and 2g TOB. These beads were added to the reactor containing 75mL Ringer's solution and the flow was initiated. In the vancomycin bolus, 1000 mg was directly added to the reactor immediately prior to initiating flow. Effluent samples were collected, and zones of inhibition (ZOI) were measured using the Kirby-Bauer method against Staphylococcus aureus UAMS-1 and Pseudomonas aeruginosa PAO1 to confirm the efficacy of antibiotic release over time. Experiments were performed in independent triplicates. The concentration of vancomycin into the reactor effluent was initially greater from the VP method as compared to the CSBv+t plus Spacerv+t method, however within 2 hours, vancomycin concentration had dropped below inhibitory levels. The CSBv+t plus Spacerv+t method provided higher concentrations of VAN and TOB than other release methods in this study suggesting a combination between VP and CSBv+t plus Spacerv+t might present an optimal combination for killing bacteria entering the surgical site and provide long term protection against subsequent biofilm formation. The in vitro elution kinetics of antibiotics is highly dependent on the specifics of the system. This continuous reactor model shows potential to more accurately predict how antibiotic released from CSB may be optimized to treat biofilms associated with SSIs.
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    Insights into Iron-Sulfur Cluster Delivery and Coordination
    (The Ohio State University, 2020-05) Fries, Brian; Cowan, James
    Metal cofactors are used throughout biology and are vital for life, being involved in nitrogen fixation, cellular metabolism and DNA repair. Iron-sulfur clusters are one of the most ancient and important cofactors necessary for life. Iron-sulfur clusters are first synthesized in the mitochondria in the eukaryotic system and then trafficked to proteins that utilize the iron sulfur cluster in the mitochondria, cytoplasm or nucleus. Lipoic acid synthase (LIAS) is a [4Fe-4S] containing protein that catalyzes the final double sulfur insertion into octanoic acid to synthesize lipoic acid. Lipoic acid is molecule that is used in the pyruvate dehydrogenase complex and the glycine cleavage system. The mechanism of how LIAS obtains its two [4Fe-4S] clusters is not well understood and the specific [2Fe-2S] donor proteins are not well identified. Mutations in LIAS have been known to cause non-ketotichyperglycinemia and infant death. Mutations in potential [2Fe-2S] donors have also shown lowered levels of lipoic acid in patients. A recently discovered [2Fe-2S] protein, mitoNEET, has been under intense investigation due to its very rare and unique 3Cys-1His type coordination. It is hypothesized to have varying roles in the cell, such as protection from reactive oxygen species, [2Fe-2S] donation to apo-acceptor proteins and interactions with a voltage depended anion channel found in the mitochondria. It is the hope of this this work to understand [4Fe-4S] cluster maturation into LIAS and to identify potential physiological donors of a [2Fe-2S] cluster to the enzyme. It also under investigation to determine the importance of the unique coordination site in mitoNEET and to understand how altering this coordination alters the properties of the [2Fe-2S] cluster.
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    Nucleosome Accessibility to Multiple Transcription and Pioneer Factors
    (The Ohio State University, 2020-05) Jipa, Caroline; Poirier, Michael
    DNA contains vital information for a cell to function including genes that must be transcribed into functioning proteins. Due to the limited size of a cell and to provide protection from damage, DNA is packaged into chromatin. Additionally, Chromatin serves as a regulator of gene expression, with more densely packed regions being less accessible to transcription factors and less dense regions being more transcribed. The base unit of chromatin is the Nucleosome, 147 bp of DNA wrapped around a histone octamer. Merely packaging into Nucleosomes reduces Transcription Factor binding around 100 fold. So the question arises, how do transcription factors access more dense regions of chromatin? Enter a class of transcription factors called Pioneer Factors who can bind to DNA and Nucleosomes with the same affinity. These are believed to be the first to bind dense regions of chromatin and open them up to Transcription factors. However their mechanism is currently unknown as one pioneer factor on its own cannot evict a nucleosome. Previous studies have looked at cooperativity in protein binding between Transcription Factors as a way to make nucleosomes more accessible. However a comprehensive look a Transcription Factor and Pioneer Factor cobinding has not been done and may hint at a mechanism through which Pioneer factors increase accessibility. We used two Transcription Factors from S. Cerevisiae, Gal4 and Pho4 along with two Pioneer Factors, Reb1 and CBF1 to test the change in accessibility of multiple proteins binding to a nucleosome, both with sites across the nucleosome and with sites adjacent to one another. Binding affinity is measured through ensemble Fluorescence Resonance Energy Transfer (FRET). We found that binding across the nucleosomes tends to decrease accessibility two-fold regardless of whether the transcription factor has pioneering abilities. The only exception is two pioneer factors, where binding seems unaffected. For adjacent binding, accessibility to an internal site in the nucleosome increases by 10-fold regardless of whether it is a Pioneer Factor or transcription factor. The exception again is the case of two pioneer factors where the effect is smaller, only a 3.5 fold increase. Overall, the decrease in accessibility across the nucleosome and the increase in accessibly of an adjacent site seem to be a universal property of nucleosomes and may reflect a structural change caused by binding. Pioneer factors only seem to act differently when in contact with another pioneer factor, in which case the effect on accessibility is reduced. However the mechanism by which they would be able to detect another pioneer factor's presence requires further study.
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    Carbon Export at Shatsky Rise During Maastrichtian from 67.776 to 67.704 Million years ago Using Marine Barite Accumulation Rate as Proxy
    (The Ohio State University, 2018-12) Ahmad Zulkifli, Siti Faizura; Griffith, Elizabeth
    The ocean regulates CO2 concentrations in the atmosphere through physical, biological and carbonate pumps. The biological pump sequesters CO2 in the form of organic carbon (organic carbon export) while the carbonate pump sequesters the CO2 in the form of inorganic carbon in marine sediments. In this study, carbonate content and barite accumulation rate (BAR) were used as carbon export proxies to reconstruct ocean conditions at Shatsky Rise in the Pacific Ocean over a ~70 kyr time interval during the Maastrichtian at ~67 million years ago (Ma). Since carbonate accumulation in deep sea sediments can be affected by temperature, pH, depth and productivity of phytoplankton, BAR was used to eliminate the possibility of low primary productivity and constrain interpretations of the carbonate proxy. Barite is a refractory mineral with high preservation rate (~30%) in deep sea sediments that are not sulfate reducing. Marine barite forms in the water column when the organic matter degrades. Eight consecutive samples (67.776 Ma to 67.704 Ma) from Ocean Drilling Program (ODP) Expedition 198 Site 1210B were processed through a sequential leaching method to obtain barite residue. BAR is the highest (5.0 mg/cm2.kyr) starting from 232.78 mbsf until 232.83 mbsf (10kyr) suggesting carbon export and primary production during this interval is the highest. The BAR results show negative correlation to the color reflectance used to estimate carbonate content in the core. The drop in carbonate content might be caused by decreasing bottom water temperature and more corrosive water dissolving carbonate resulting in the short term shoaling of the carbonate compensation depth (CCD). Based on previous work, the bottom water temperature and chemistry was changing due to variations in ocean circulation at this time.
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    Use of noble gas and hydrocarbon geochemistry to determine the source of hydrocarbons in Gulf of Mexico gas hydrates
    (The Ohio State University, 2018-05) Lary, Brent; Darrah, Thomas
    Global gas hydrate deposits along continental slopes and below permafrost are estimated to contain between 1,000 and 22,000 gigatonnes of carbon. However, their role in the energy sector and the global carbon cycle remains uncertain. Integration of noble gas geochemistry with conventional hydrocarbon molecular and isotopic composition approaches offers an insight into how natural gas contained in hydrates was generated (e.g., biogenic, thermogenic, mixed) and/or the manner in which hydrocarbons contained in clathrates migrated. By integrating the above techniques, one can also help to improve exploration techniques for natural gas in clathrates and help better estimate their economic hydrocarbon extraction potential. Furthermore, the accumulation of 4He can be used to estimate the residence time of fluids associated with clathrate formation in gas hydrate reservoirs. Because the original noble gas composition of a fluid is preserved independent of microbial activity, chemical reactions, or changes in oxygen fugacity, the integration of noble gas data can provide both a geochemical fingerprint for the sources of fluids and an additional insight as to the uncertainty between effects of mixing versus post-genetic modification. Fluids from pressurized cores acquired from the UT-GOM2-01 drilling project in the GC955 block of the Green Canyon within the Gulf of Mexico were analyzed for hydrocarbon molecular composition (e.g., C1-C6), major gas abundances (e.g., H2, N2, CO2), and noble gas elemental and isotopic abundances (e.g., He, Ne, Ar). Clathrates acquired during this cruise were dominantly biogenic in origin and contained evidence of 2-phase migration with a range of residence times of 37,300 years to 575,000 years. The data collected in this study were compared with previously published data from 3 additional locations within the Gulf of Mexico. The additional data displayed gases from regions in the Gulf of Mexico that exhibited a purely biogenic endmember and a region that exhibited a mixture of biogenic and thermogenic sources.
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    Identification of Rbfox-regulated transcripts important for muscle function
    (The Ohio State University, 2018-12) Zhao, Jinghan; Amacher, Sharon
    Rbfox RNA-binding proteins are important regulators of muscle-specific splicing. Rbfox proteins contain an RNA recognition motif that is conserved from flies to human and binds to (U)GCAUG motifs that are enriched in introns next to muscle-specific alternative exons. Many muscle-specific splicing events are conserved among vertebrates, and we use the zebrafish model to understand how Rbfox-mediated splicing regulates muscle development and function. In zebrafish, Rbfox1l and Rbfox2 are both expressed in muscle. Double knockdown of rbfox1l and rbfox2 using antisense morpholinos leads to splicing changes of muscle-specific alternative exons, coupled with skeletal muscle paralysis and reduced heart rate. To confirm whether splicing changes in morphants are indeed due to Rbfox depletion and not morpholino-induced side effects, I compared alternative splicing changes in rbfox genetic mutants versus morphants. Using our unpublished RNA-seq data, I identified candidate Rbfox-regulated exons with substantial splicing changes between wild-type versus double morphant embryos. To enrich for direct targets, I selected those candidates flanked by intronic (U)GCAUG motifs for further analysis. Seven out of ten tested candidates were similarly affected in double mutants and double morphants. These results indicate that splicing is similarly affected in morphants and mutants, consistent with the observation that rbfox double mutants and double morphants have the same morphological phenotypes. To identify Rbfox-regulated transcript(s) that are sufficient to rescue muscle function in Rbfox-deficient larvae, I set out to clone these seven validated Rbfox-regulated transcripts for mRNA synthesis and injection into double morphant embryos. Thus far, I have found that an Rbfox-regulated tpm3 isoform is not sufficient to rescue contractility in 3 rbfox double morphants. Because it is unlikely that a single Rbfox-regulated transcript is sufficient to restore muscle function in Rbfox-depleted larvae, future rescue experiments with pooled Rbfox-regulated mRNAs will be conducted. Our long-term goal is to identify Rbfox-regulated splicing events that are required for muscle function. The insight gained from this work will improve our understanding of Rbfox-regulated muscle splicing and may provide clues for the development of therapies for human muscle diseases.
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    Elucidating functions of Tyrosine 705 and Serine 727 residues of Stat3 in vivo
    (The Ohio State University, 2018-05) Kim, Hee Kyung; Ramaswamy, Bhuvaneswari; Majumder, Sarmila
    The signal transducer and activator of transcription 3 (Stat3) gene mediates vital processes such as involution, maintenance of pluripotent stem cells, and inflammation. Stat3 is activated by phosphorylation at Tyr705(Y705) and Ser727(S727) residues, that has independent and overlapping functions when studied in overexpressing cells in vitro. In this study, we sought to characterize the roles of Y705 and S727 residues in vivo, using transgenic mice which harbor the inactivating mutants Stat3-Y705F (tyrosine to phenylalanine), Stat3-S727A (serine to alanine) and activation mutant Stat3-S727E (serine to glutamic acid). The Stat3-S727E mimics constitutively phosphorylated Stat3 at S727, while the other two mutants cannot be phosphorylated. We, for the first time, have generated transgenic mice with the Knock-In (KI) mutants of Stat3 at Y705 and S727, alone or in combination. Because previous studies have shown that Stat3 knockout mice are embryonic lethal, we determined the independent roles of the two phosphorylation sites, and their interactions during embryonic development of KI-mice. We have further analyzed if stability of the Stat3 protein is affected by these mutations to support our key observations. Our studies show that Y705F homozygous mutation is embryonic lethal at weaning, only wildtype and heterozygous Stat3Y705F-KI mice survived. Similar observation was made with Stat3Y705F/S727E –KI mice (Stat3Y-SE), where homozygous mutation was also embryonic lethal. However, the KI-mice with Stat3S727E homozygous mutation were viable suggesting that constitutive phosphorylation of 727 had no detrimental effect on embryonic development, but could not rescue the loss of Stat3 function due to Y705F mutation in the double mutant. We analyzed stability of Stat3 protein in mouse embryonic fibroblasts (MEFs) isolated from KI-mice. Stat3Y-SE/- had a significantly decreased level of Stat3 mRNA. Stat3 protein was undetectable in Stat3Y705F/- and Stat3Y-SE/- MEFs, suggesting that phosphorylation at Y705 is critical for stability of Stat3 protein and that phosphomimetic at S727 could not rescue Stat3 from degradation. It is also apparent that Stat3Y705F/- and Stat3Y-SE/- KI-mice phenocopies Stat3-/- mice as both are embryonic lethal. Studies are underway to characterize the Stat3S727A and Stat3Y705F/S727A (Stat3Y-SA) KI-mice and the mutant proteins. Our characterization of Y705 and S727 will result in better understanding of their key roles in activation of Stat3 in a physiological context.