2020 Abstracts

Lake, Alexander; Soboleva, Tatiana; Berreau, Lisa (Utah State University)
Faculty Advisor: Berreau, Lisa (College of Science, Chemistry and Biochemistry)

Carbon Monoxide (CO) has been found to have a wide range of potential therapeutic effects. For example, low concentrations of CO have been shown to produce anti-inflammatory, anti-hypoxia, anti-proliferative, and anti-apoptotic effects, as well as vasodilation. CO-releasing molecules (CORMs), particularly those which release CO upon triggering with light in the visible range (photoCORMs), are of significant current interest for targeted CO delivery. Our laboratory is developing extended flavonols as highly tunable tunable photoCORMs. In this presentation, the synthesis, characterization, and CO release reactivity studies exploring the use of flavonol esters as CO delivery molecules will be presented.

Lange, Christian; Shen, T.-C. (Utah State University)
Faculty Advisor: Shen, T.-C. (College of Science, Physics Department)

An ideal black surface should have low reflectance uniformly across the spectrum of electromagnetic radiation. Black paints are not ideal because they have specific reflection peaks and bands. Vertically aligned nanopillars of proper shapes and physical properties are good candidates, but the fabrication and oxidation in air are challenging. Carbon nanotube (CNT) forests could be a cheap alternative but the optical properties are sensitive to the density, length, and alignment of the CNTs in a forest. A model to understand the correlation between the morphology and optical reflectance of CNT forests and strategies to achieve extremely low reflectance in the infrared region will be presented.

Perdue, Perdue; Burke, Joshua; Bylund, Kevin; Stephen, Daniel (Utah Valley University)
Faculty Advisor: Stephen, Daniel (Utah Valley University, Earth Science)

The Sundance Sea covered much of western North America during the Middle to Late Jurassic Period. Deposits from this vast epeiric sea are now widely exposed across the region, including the Stump Formation in northeastern Utah, which consists of sandstones and shales reflecting shallow marine deposition. Well-preserved belemnites (Pachyteuthis densus, Oxfordian Stage, ~156 Ma) collected from this unit preserve stable isotope data (_18O and _13C ) that can be used to better understand the paleoceanography and paleoclimatology of the area, as well as possibly some paleobiologic characteristics such as migration patterns through the life cycle and age at sexual maturity and death. Incremental growth of belemnites created growth bands that record isotopic values through various life stages, thus potentially providing information about the life history traits of these organisms, in addition to seasonal temperature variations. Preliminary results suggest our material is consistent with previous reports from other locations in the region, with paleotemperatures in the 17 to 20° C range. In addition, there is some indication of seasonal variations. However, analyses of more samples and further evaluation of potential diagenetic alteration is necessary before more robust conclusions can be drawn.

Hedelius, Bryce; Millecam, Todd; Wingate, David; Della Corte, Dennis (Brigham Young University)
Faculty Advisor: Della Corte, Dennis (BYU College of Physical and Mathematical Sciences, Physics); Wingate, David (BYU College of Physical and Mathematical Sciences, Computer Science)

Substantial progress has been made in the past several years towards the accurate prediction of protein tertiary structures from primary sequence, aided greatly by the integration of machine learning. Current success is based on two-stage protocols: first, the training of a deep convolutional neural network (CNN) to predict macromolecular structure restraints, and second, the use of these restraints to construct a folded three-dimensional structure of the target protein. Such a two-stage folding protocol was used by DeepMind in the recent Critical Assessment of Structure Prediction (CASP13), which outperformed all established groups. However, DeepMind has not expressed a plan to publish the code of their AlphaFold protocol. Here we present ProSPr, a network representing the first part of the AlphaFold pipeline for predicting interatomic distances, and demonstrate its abilities in the contact prediction task relative to other state-of-the-art methods. We also investigate and report on the roles of certain input features in prediction quality. ProSPr is made freely available to the scientific community both as source code and a Docker container, which we anticipate will encourage the development of better techniques for assembling protein structures from restraints.

Taylor, Madison; Ault, Alexis; Newell, Dennis (Utah State University)
Faculty Advisor: Ault, Alexis (College of Science, Geosciences Department)

Hematite-coated fault surfaces offer the potential to characterize and understand the mechanisms and timing of past deformation in exhumed fault zones. We apply integrated micro- to nanoscale microscopy and geochemistry with hematite (U—Th)/He (He) thermochronometry dates to document hematite textural evolution and timing of fault slip on the seismically-active Hurricane fault in southwestern Utah. Hematite is preserved on this bedrock fault scarp that cuts the Triassic Moenkopi Formation. It occurs in elongate, striated, mm- to cm-scale lenses on the slip surface, and we target this material for thermochronometry. Scanning electron microscopy (SEM) shows hematite within ~100—200 μm of the fault surface comprises rounded hematite particles ~100 nm to 2 μm in diameter that lack grain boundaries. Away from the surface and beneath these nanoparticles are randomly-oriented, ~70—150 nm-thick hematite plates. Plate and rounded, "fused" particle morphologies likely reflect initial hematite crystallization from fluids and deformation, respectively. SEM imaging and energy dispersive X-ray spectroscopy also reveal a featureless, ~3 μm-thick, Al-rich silica film enveloping the hematite nanoparticles at the fault surface, suggesting it is amorphous silica. This layer is exclusively found in contact with deformed hematite, implying association with fault slip. A preliminary mean hematite He thermochronometric date is 375 ± 54 ka (±1σ std. dev.; n = 11). This date is appreciably younger than previously-reported, regional apatite He thermochronometry data. This suggests hematite He data may record hematite formation or thermal resetting from friction-generated heat during fault slip. Ongoing hematite He analyses targeting the distinct textural domains will discriminate between these possibilities, and scanning/transmission electron microscopy will evaluate the crystallinity of the surface silica and hematite nanoparticles. Collectively, these data will allow us to decipher the timing and mechanisms of past deformation of the Hurricane fault and understand analogous relationships in other hematite-bearing fault zones.

Johnston, Olivia; Preston, Kolten; Hoyt, Tyson; Owens May, April; Bentley, Kaden; Gunnerson, Shane; Johnson, Alex; Parr, McKenna; Reeves, Duncan; Parry, Whitney; Rawson, Clayton; Hart, Vern (Utah Valley University)
Faculty Advisor: Hart, Vern (Science, Physics)

Recent efforts in early cancer detection require identifying the disease at a cellular level, by distinguishing cancer cells from healthy cells at low concentrations (<0.1%). Cancerous cells typically have larger nuclei than healthy cells and can be distinguished using a variety of optical techniques, however, this process is complicated when the fraction of malignant cells is extremely low. As such, high-precision detection requires highly accurate measurements of cell confluence and the ratio of healthy to cancerous cells. Techniques such as machine learning and Fourier analysis have been used to auto-segment cells in microscopy images. However, these techniques often lack a ground truth standard to validate the segmentation results. We present a methodology for producing agarose tissue phantoms embedded with mixed polystyrene microbeads of varying diameters. These phantoms were imaged using a 2D translational stage and a microscope camera, collecting hundreds of images that were input to an artificially intelligent neural network for training and classification. The ability of this binary classifier to identify and quantify micro-beads in the images was assessed by comparing the automated results to manual counts, producing accuracies above 90% for bead sizes ranging from 50-200 microns. Auto-segmentation results will also be presented for mixtures of micro-beads and U-87 (glioblastoma) cancer cells, which differ in shape and morphology from the beads but whose boundaries are significantly less defined. The ability to accurately segment two different cell types in vitro would be highly beneficial for future cellular imaging studies.

Ballantyne, Eliza; Buck, Lance; Cox, Zach; Adams, Brittney; Trappett, Matthew; Shipp, Dustin (Utah Valley University)
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)

Understanding how cells metabolize the chemicals around them on a single cellular level is paramount to analyzing the effectiveness of pharmaceutical drugs. Discrepancies between pharmaceutical drug results during lab testing versus in actual patients are an expensive and time consuming obstacle. These differences could be alleviated using Raman spectroscopy by testing based on an overall chemical map instead of individual factors. Raman spectroscopy has great potential to aid this process because of its ability to present a chemical fingerprint of an entire cell without interfering with the cell's natural responses to chemical changes.

Using Raman spectroscopy to develop an additional method for observing cell metabolism will enhance understanding of cell function and advance studies focused on the results of chemical effects on cells in vivo. As a step toward this goal, this project is currently focused on obtaining time-lapsed Raman images of glucose uptake. Using glucose metabolism, we are able to model a system for more complicated pharmaceuticals. This study has explored methods for collecting Raman spectra in vivo, balancing time-dependent data collection with the time-constraint of working with living and changing cells. Raman spectra describing the chemical makeup of glioblastoma cancer cells as they metabolize glucose were analyzed and used to create time-lapsed images during uptake.

Our process presents a new lens for understanding cell metabolism and a potential tool for analyzing an additive's effect on a single-cellular level. We developed a platform and method for measuring chemical changes in cells over time. Next stages for this research include observing how metabolism varies depending on what additives are used for uptake and quantifying metabolic differences between types of cells.

Watts, Austin; Crook, M. B. (Weber State University)
Faculty Advisor: Crook, Matthew (College of Science, Microbiology)

Auxin is a known growth hormone for plants and many plant-beneficial bacteria are known to produce it. It has previously been shown that Rhizobium sp. IRBG74 promotes growth of rice, but the mechanism is unknown. We hypothesized that Rhizobium sp. IRBG74 accomplishes this by production and secretion of auxin. To address this hypothesis, we first performed a bioinformatic analysis to identify putative auxin biosynthesis genes in the genome of IRBG74 using BLAST with known auxin biosynthesis genes as queries. To test whether the genes identified by BLAST play a role in promoting growth of rice, we are making in-frame deletions of each one. Briefly, we use overlap-extension PCR to create and stitch together deletion fragments and then we clone these fragments into the sacB deletion vector pJQ200SK. The target genes are then disrupted by homologous recombination and then deintegration is selected for with sucrose. After this is done we test the mutant to verify the deletion occurred by PCR. Once the deletion mutants are verified, each one is tested on rice seedlings and compared to wild-type IRBG74. Rice growth is quantified by shoot dry weight and by root branching, as measured using ImageJ.

Timothy P. McFadden; Chideraa I. Nwachukwu; Andrew G. Roberts (University of Utah)
Faculty Advisor: Roberts, Andrew (College of Science, Chemistry)

Carbon—nitrogen (C—N) bonds are easy to form relative to carbon—carbon (C—C) bonds due to reliable and predictable reactions. Previous methods to form a C—C bond from a C—N bond require four independent chemical reactions. We report a new method to achieve the desired transformation in one flask. Optimization of this method is ongoing; ultimately, we hope to define a new strategy for accessing future C—C bonds with C—N bonds.

Morris, Nathaniel; Jensen, Joseph (Utah Valley University)
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)

We measured the brightness of Milky Way stars to determine if they have an effect on extragalactic surface brightness fluctuation (SBF) distance measurements. When SBF measurements are made on background galaxies near the Galactic plane, we observe a large number of stars in the foreground. With most SBF measurements, we can mask out the brightest stars, and make measure SBF with a relatively uncontaminated background. This becomes more difficult with galaxies that are close to the Galactic plane because there are many more foreground stars, and undetected fainter stars that escape the masking process can bias the distance measurement. My research will determine if these unmasked foreground stars have a significant effect on the SBF measurements on these galaxies near the Galactic plane.

Stokes, Jessica; Burnett, Brandon (Weber State University)
Faculty Advisor: Burnett, Brandon (Weber State University, Chemistry)

Mechanochemistry has become a growing avenue for materials synthesis, as it typically requires little to no solvent, and often creates different crystalline phases compared to traditional synthetic methods. Liquid-assisted grinding, a form of mechanochemistry, was used to synthesize porphyrin paddle-wheel frameworks (PPFs). Three different crystalline phases were targeted in order to test the viability of this method on this class of materials and observe any difference compared to traditional solvothermal synthesis. X-ray diffraction was used to confirm the formation of each PPF phase. We found that mechanochemistry was indeed successful to sustainably synthesize PPFs. Additionally, we observed a significant difference in phase preference between the traditional solvothermal synthesis and liquid assisted grinding methods.

Gray, Daniel; Durfee, Dallin (Utah Valley University)
Faculty Advisor: Durfee, Dallin (College of Science, Physics)

IPSII is a fully lensless single pixel imaging technique using mechanically scanned interference patterns. The method uses only simple, flat optics; no lenses, curved mirrors, or acousto-optics are used in pattern formation or detection. The resolution is limited by the numerical aperture of the angular access to the object, with a fundamental limit of a quarter wavelength, which is twice the Abbe limit. ISPII also has no fundamental limit on working distance as well as a depth of field and field of view independent of resolution. Normally, an interference pattern is projected across the target object to obtain information. Currently this uses interfering plane waves which produce sinusoidal interference patterns allowing us to measure in the Fourier basis. Mechanically scanning the laser angles to change the interference pattern is slow. Image times usually require hours or days as regular scan times produce approximately one pixel per second. We intend to improve the time to scan an object by utilizing a micromirror array to modify the interference patterns, such that multiple measurements can be made at one angle. Updating the micromirror array is much faster than changing the angles at which the target is scanned. This will greatly reduce the time required as we will not need to measure with as many angles to obtain an image. With the micromirror array we will be able to generate a wider range of basis functions. In addition to increasing the speed this may allow us to better utilize compressive sensing techniques where an n-pixel image may be obtained by scanning only a fraction of n-points on the object.

Covey, Tracy; Alsup, Garrett; Kreinbrink, Alexia (Weber State University)
Faculty Advisor: Covey, Tracy (College of Science, Department of Chemistry and Biochemistry)

Certain over-the-counter medications, such as acetaminophen and ibuprofen, are known to have an effect on the bioavailability of warfarin, enhancing its anticoagulant properties. The goal of this project is to study how varying the concentration of ibuprofen or acetaminophen affects the amount of warfarin bound to blood plasma proteins. To better understand how strong these drug-drug interactions are with warfarin, we proposed capillary electrophoresis (CE) as an analytical method to separate and detect these compounds. Acetaminophen, ibuprofen, and warfarin have all been analyzed using CE in the literature, so we sought to develop a CE method to separate and detect all three drugs together. We are currently optimizing this method and will use this method to investigate warfarin displacement from plasma proteins by ibuprofen and acetaminophen.

McDowell, Trevor; Durfee Dallin (Utah Valley University)
Faculty Advisor: Durfee, Dallin (College of Science, Physics)

Interference Pattern Structured Illumination Imaging (IPSII) utilizing Mach-Zehnder Interferometry, allows us to surpass the Abbe Limit of traditional imaging techniques. To aid in this endeavor, my primary objective is to utilize a Michelson-Morley Interferometer with one of the arms being a long-distance, 300mm or greater, linear translation stage. Using the long-distance linear translation stage (LDLTS) to test both the repeatability and as well as angular stability of various LDLTS units so we may take measurements of fringe lines at arcseconds approaching a zero degree of angle. Though many designs currently available for consumer use have the linear repeatability needed, most if not all lack the angular stability needed. As such we are currently experimenting with current designs to see where the variances are and work in improvements so we may design our own LDLTS so we may be able to take such extreme angle measurements. In addition to improving the repeatability and angular stability of LDLTS's, the automation of the kinematic mirror mounts utilizing stepper motors is another primary concern. Our current issue is that we need to be able to adjust the reflecting mirrors on both the x-axis and y-axis and to do this the stepper motors need a travel distance of 27mm along the z-axis. The issue we have is we need a stable mount that addresses any torque lash while keeping them still and allowing movement on the z-axis. Through materials research for what to be used with the LDLTS as well as the stepper motor mounts, we will be able to take data points and processes data at a much greater and more accurate rate than we have in the past. Resulting in more time to conduct experiments and less time waiting for results.

Meyr, Katherine (Weber State University)
Faculty Advisor: Matyjasik, Marek (Science, Earth and Environmental Sciences)

The impacts of water quality is among the most highly contested aspects of mining projects. Despite the protection of the majority of land in British Columbia, evidence of the negative environmental impacts of past and present mining activities may be found on the most sacred of lands. Evaluated water samples taken from multiple sites in First Nation territory show evidence of mining contamination, with streams following the sacred Tlingit trail showing the highest percentage of heavy metals. Though British Columbia's regulations have been extensive, mines abandoned before these regulations were put into place may be a source of pollution among current wildlife and vegetation. Abandoned mining sites in British Columbia must be thoroughly evaluated in order to understand the damage that has been done both culturally and environmentally.

Phan, Anh; Jensen, Joseph (Utah Valley University)
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)

We have measured the Surface Brightness Fluctuation (SBF) distances to 12 galaxies. SBF is usually used to measure distances to giant elliptical galaxies that have uniform ages and composition. On the other hand, galaxies that are more disk-shaped potentially have a range of ages, they may have an SBF and color gradient. Elliptical masks that match the shapes of disk galaxies can give a more accurate SBF and color gradient than circular masks. The purpose of this study is to measure the discrepancies between the SBF distances using the two types of masks. For giant elliptical galaxies, the two methods give similar results ($\leq$ 2\%). For disk galaxies, the discrepancies are bigger (up to 6\% difference).

Boatright, Greggory; Medrano, Braxton; Goeckeritz, Joel (Brigham Young University)
Faculty Advisor: Roeder, Beverly (Brigham Young University, Life Sciences)

Schwann cells play a major role in helping heal injured nerves. They help clear debris, produce neurotrophins, upregulate neurotrophin receptors, and form bands of Büngner to guide the healing nerve. But nerves do not always produce enough neurotrophins and neurotrophin receptors to repair themselves. Nerve growth factor (NGF) is an important neurotrophin for promoting nerve healing and lysophosphatidylcholine (LPC) has been shown to stimulate NGF receptors (NGFR). This study tested the administration of a single intraneural injection of LPC (1 mg/mL for single LPC injection and 10 mg/mL for multiple LPC injections) at day 0 and one (day 7), two (days 5 and 7), or three (days 5, 7, and 9) injections of NGF (160 ng/mL for single injections and 80 ng/mL for multiple injections) to determine baseline effects on crushed sciatic nerves in rats. The rats were randomly divided into four groups: control, crush, crush-NGF, and crush-LPC-NGF. The healing of the nerves was measured weekly by monitoring gait; electrophysiological parameters: compound muscle action potential (CMAP) amplitudes; and morphological parameters: total fascicle areas, myelinated fiber counts, fiber densities, fiber packing, and mean g-ratio values at weeks 3 and 6. The crush, crush-NGF, and crush-LPC-NGF groups statistically differed from the control group for all six weeks for the electrophysiological parameters but only differed from the control group at week 3 for the morphological parameters. The crush, crush-NGF, and crush LPC-NGF groups did not differ from each other over the course of the study. Single injections of LPC and NGF one week apart or multiple treatments of NGF at 5, 7 and 9 days post-injury did not alter the healing rate of the sciatic nerves during weeks 1-6 of the study. These findings are important to define the baseline effects of NGF and LPC injections, as part of a larger effort to determine the minimal dose regimen of NGF to regenerate peripheral nerves.

Hyman, Rachel; Light, Tim; Montague, Angela; Lucero, Jessica (Utah State University)
Faculty Advisor: Lucero, Jessica (College of Humanities and Social Sciences; Sociology, Social Work and Anthropology Department)

Refugees are recognized as having unique and complex health needs which demand attention upon arrival and throughout the resettlement process (Agrawal & Venkatesh, 2016). Refugee populations are particularly vulnerable to health disparities due to push factors influencing forced migration (Tempany, 2009). These factors include exposure to political violence, natural disasters, and other forms of anthropogenic conflict (UNHCR, 2014). Refugees may arrive in the host country with undiagnosed and untreated health issues, such as infectious diseases, mental distress due to prior traumas, undiagnosed chronic illness, and nutritional deficiencies (Deen & Bridges, 2011). Refugee populations represent high rates of mental and physical health problems compared with the host population (Kirmayer, Gomez-Carrillo, & Veissi�re, 2017). Additional dynamics compound health disparities facing refugees. These include: language barriers, unfamiliarity with a complex health care system, limited health literacy, and inadequate alignment of medical treatments with religious and cultural beliefs (Bowen, 2001; Brown, Carroll, Fogarty, & Holt, 2010). Though there is robust scholarship in the literature and analysis of prevalent health disparities and needs of refugees post-resettlement, few studies address the specific health care concerns of refugees resettled in northern Utah. This study seeks to expand previous findings related to the most salient health care issues facing the refugee community and develop community response to address health disparity. A secondary aim of the research is to determine best practices for the provision of appropriate and effective health services.