2020 Abstracts

Da Silva, Adrik; Greenwald, Michael; Li, Yongtai; Manseau, Julianna; Woods, Ciera (Westminster College)
Faculty Advisor: Conwell, Peter (Westminster College, Physics); Kamenetzky, Julia (Westminster College, Physics)

The long jump is a track and field event that has a history dating back to 656 BC. Understably, much theorizing and experimenting has been done to find the ideal conditions necessary for an athlete to win such an event. This experiment tests the efficacy of such a theory by using an equation derived by Yongtai Li and comparing its calculations to measurements from a force sensor. Based on Newton's Second Law, the force and its respective range produced from a jump were analyzed and Yongtai's equation proved to be similar to the actual force due to the theoretical results overlapping with the measured results, but will be modified in the future to include angle and initial running velocity to provide an accurate measure of the force necessary to travel a certain horizontal distance. This equation and the ease of calculations will prove useful to long jumper's who attempt to defy the limits of the human body by breaking world records in their events

Keyes, E. Dalles; Alvey, Brighton; Smith, T. Andrew; Roberts, Andrew G. (University of Utah)
Faculty Advisor: Roberts, Andrew G. (University of Utah, Chemistry)

Medicinal chemistry has long relied on the development of small molecule therapeutics to treat human disease. Small molecules affect change at the cellular level through specific interactions with biological targets (e.g. proteins), thereby eliciting a desired physiological response. Conversely, small molecules can also interact non-specifically, which can complicate their targeted application. In many cases, the use of peptide-based medicines can address this limitation. Like small molecules, peptide-therapeutics are designed to modulate specific biological processes. They often exhibit desirable activity at low concentrations as a result of high selectivity. Being comprised of natural amino acid building blocks, peptides offer an inherent advantage. Their natural breakdown leads to minimally toxic degradation products. However, premature and rapid degradation can result in failure to reach an established target in vivo. The cyclization of peptides has shown to be a promising strategy to address this problem. Inspired by Nature's wide collection of non-ribosomal peptides, specifically those comprising electron-rich aromatic moieties, we have developed a new chemical strategy for the synthesis of cyclic peptides. Our cyclization method leverages the inherent reactivity of the tyrosine (Tyr) phenol nucleus with electrophilic 1,2,4-triazoline-3,5-dione (TAD) moieties. Using this reaction, we can construct macrocyclic peptidomimetic scaffolds. Upon synthesizing an N4-substituted 1,2,4-triazolidine-3,5-dione (aka urazole) at the N-terminus of a solid-supported peptide, the urazole moiety is chemoselectively oxidized under mild conditions to generate a TAD derivative in situ. The TAD moiety reacts with the sidechain phenol nucleus of internally or terminally located Tyr residues and results in the formation of a macrocyclic peptide. We envision that this method will significantly augment current strategies for constructing macrocyclic peptides by enabling the facile synthesis of complex peptidomimetic scaffolds. Furthermore, this approach is anticipated to expand the repertoire of tools used for developing medicinally relevant peptides and, thus, may be suitable for preparing unique peptide-based therapeutics.

Sevy, Jonathon; Radebaugh, Jani; McDougall, Dylan; Kerber, Laura; Rabinovitch, Jason (Brigham Young University)
Faculty Advisor: Radebaugh, Jani (Brigham Young University, Geology)

Yardangs are wind-carved linear ridges that are found selectively on Earth and extensively on Mars. The history of the morphologic development of yardangs is not well known. In the Puna high plateau of Argentina there are ignimbrite deposits, many of which have been eroded into yardang fields, commonly called fleets. Yarding fleets are evenly spaced forms, facing into the wind, that resemble a fleet of boats sailing. A prominent fleet, known as Campo de las Piedras Pomez (CCP) was studied to more fully understand their formation and morphology, including field research in December 2018 and 2019. Some physical characteristics looked at in the field included: dedos direction and lengths; heights and lengths of yardangs; structural features; wind and gravel ripple direction. In addition, relationships between yardang organization and structural control have been analyzed. The dedos on the fronts of yardangs averaged 4.0cm in length, while the reverse dedos were 3.3cm. From this it was determined that: Two wind directions, with one dominant, are present; Structural features can shape morphology of yardangs.

Parada, Michelle (Weber State University)
Faculty Advisor: Schramm, Katharina (Weber State University, Botany)

This research focuses on anti-tumor and the biotoxicity of A. millefollium (yarrow).
Yarrow is an interesting plant with a long history of medicinal uses, but very little has been done to research and prove the different beneficial properties claimed. There are two simple bench-top assays performed in this study, the potato disc assay which inoculates potato slices with Agrobacterium tumefaciens as well as different concentrations of yarrow extracts and assesses the resulting tumor formation and the brine shrimp toxicity assay to assess the LD-50 of the extracts. My results will indicate whether or not the native yarrow extracts inhibit or do not inhibit tumor formation and its toxicity level. The results of this research could lead to further studies of the phytochemicals in the plant to be used for cancer treatments.

Asay, Spencer; Graham, Andrew; Burke, Lexady; Barnes, Brad; Oblad, Richard; Kenealey, Jason (Brigham Young University)
Faculty Advisor: Kenealey, Jason (Life Sciences; Nutrition, Dietetics, and Food Science)

Prostate cancer is the second most commonly diagnosed cancer in men, and metastatic prostate cancer is currently incurable. Prostate cancer frequently becomes resistant to standard of care treatments. Moreover, the administration of conventional chemotherapeutic drugs, such as docetaxel (DOC), poses the risk of debilitating toxic side effects. Combination therapy, in which several compounds targeting multiple cellular pathways are administered jointly, is one tool that can be used to combat therapeutic resistance and drug toxicity. Vitamin E (VE) compounds and analogs have been proposed as potential non-toxic chemotherapeutics. We modeled combination therapy using mixture design response surface methodology (MDRSM), a statistical technique designed to optimize mixture compositions, to determine whether combinations of three chemotherapeutic agents (γ-tocotrienol (γ-T3), γ-tocopherol ether acetate (ɑ-TEA), and DOC) would prove more effective than DOC alone in the treatment of PC-3 human prostate cancer cells. A response surface was generated for cell viability, and the optimal treatment combination for reducing cell viability was calculated. We found that a combination of 30 µM ɑ-TEA, 20 µM γ-T3, and 25 nm DOC was most effective in the treatment of PC-3 cells. We also found that combining γ-T3 and ɑ-TEA with DOC decreased the dose of DOC required to significantly reduce cell viability in PC-3 cells. Finally, we found that combining γ-T3 and ɑ-TEA with DOC enhanced treatment efficacy in DOC-resistant PC-3 cells.

Sundstrom, Rebecca; Jensen, Joseph B. (Utah Valley University)
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)

We will measure Surface Brightness Fluctuations (SBF) in three galaxies (ESO137-G006, NGC 3309, and NGC 5128) using images from two cameras: the GeMS Multi-Conjugate Adaptive Optics (MCAO) system and the FLAMINGOS-2 (F-2) near-infrared imaging spectrograph, at the 8-meter Gemini South Telescope in Chile. To make an accurate measurement we need to first determine a photometric calibration for the MCAO system by comparing flux, or captured light, from both detectors. This is necessary because MCAO collects crisp, sharp images but omits some of the total incoming flux from the stars in the galaxies. F-2 takes broader images but includes more measurable flux. By finding the ratio of the flux collected by MCAO to the flux collected by F-2 we can take this "missing" light into account without compromising the crisp, sharp resolution MCAO provides.

Schmidt, Jack; Leonard, Christina; Jukes, Thomas (Utah State University)
Faculty Advisor: Schmidt, Jack (S.J. & Jessie E. Quinney College of Natural Resources, Watershed Sciences Department)

Abstract: Western rivers are impounded by a suite of water resource infrastructure that supports human life and has fueled western development. These rivers also support a unique ecosystem for endemic endangered species, whose habitat has been degraded by water resource development that has disrupted the flow and sediment delivered to the system. Channel morphology, and within-channel habitat are the consequence of sediment deposition and erosion. One way to measure the amount of sediment deposition or erosion is by measuring the amount of sediment transported into and out of a river segment to calculate the mass-sediment budget. Such analyses, however, cannot identify the locations within the river segment where aggradation or degradation has occurred, or predict how habitat has changed. In this study, we aim to correlate field-based measurements of channel and habitat change with flux-based sediment budgets. We propose that in order to predict detailed channel response and habitat change, flux-based sediment budgets must be partitioned by grain size class, because different grain size classes are eroded and deposited in different parts of the channel. As part of this study, we have collected samples and observations throughout the study area to analyze and characterize the grain size distribution of the channel and floodplain in units identified as eroding or aggrading. By obtaining information about where different grain size classes of sediment are deposited and eroded, we are working to link the partitioned mass-sediment budget to channel change to understand where and why channel change occurs.

Backman, Natalia; Bell, Mckenzie; Gostick, Anthony; Kiggins, Kendrick; Koller, Christopher; Naylor, Emily; Porter, Tyrel; Rawlings, Bree; Domyan, Eric, Ph.D (Utah Valley University)
Faculty Advisor: Domyan, Eric (Utah Valley University, Biology/Biotechnology)

The domesticated rock pigeon has been the subject of selective breeding for hounds of years and so displays an immense variety of phenotypes. This variety provides opportunities to further understand the genetic basis of phenotypic evolution. Pigmentation of pigeon feathers is controlled by multiple alleles at different loci, which influences the type and amount of melanin deposited in the feathers. A specific phenotype, known as "recessive red", consists of distinctly red plumage and is caused by a mutation that greatly reduces the expression of the gene Sox10. This gene encodes a transcription factor, known to play a key role in melanocyte maturation and proliferation. Sox10 likely regulates the transcription of multiple downstream genes but the identities of these genes are largely unknown. To identify downstream targets of Sox10, we compared the transcriptomes of regenerating feathers from wild-type and recessive red birds to identify genes that had different expression levels between the two groups. We identified 46 genes that are expressed at different levels between wild-type and recessive red birds, and thus are potential targets of Sox101.
While several of the target genes have known roles in pigmentation, the role that many of the targets play in pigmentation has not been studied, making them interesting candidates for further investigation. Using CRISPR-Cas9, we introduced mutations in candidate genes that were chosen because of their unusually low expression in recessive red birds due to the mutation of Sox10. By observing the effects of the mutated genes, we can determine their roles in pigmentation. The genes that we are mutagenizing in our research is Tbx2, Arsg, and Abcb5 to see if they play a role in the melanin synthesis pathway.

Backman, Natalia; Ogden, Heath (Utah Valley University)
Faculty Advisor: Ogden, Heath (Utah Valley University, Biology)

The Family Baetidae, is in the order Ephemeroptera, also commonly known as Mayflies. The first baetids were described around 1815 by Leach, and since there are more than 900 species have been described. The family Baetidae is an important group of mayflies because of their position on the mayfly tree of life in that they are a key to understanding evolutionary trends, such as the origin of wings and flight. Taxon sampling for this study consisted of over 100 taxa, representing ??? genera, from lineages distributed geographically worldwide, except Antarctica. Two main datasets were constructed. The genes 12s, 16s, H3, 18s, 28s and CO1 were used as part of a traditional dataset. Targeted capture sequencing was used to generate a phylogenomic dataset, consisting of over 400 loci. Trees were reconstructed from the aligned datasets, and the results were compared. The phylogenomic data resulted in a much more resolved topology.

Durrant, Bianca; Bennion, Sean; Shipp, Dustin (Utah Valley University)
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)

determine bacteria is growing the bacteria on agar and then identify the bacteria via the API system (analytical profile index). In some medical cases, 24 hours is too long to wait, especially if a patient needs antibiotics. Raman spectroscopy uses laser light to excite a spectrum specific to each molecule. This molecular specificity enables Raman spectroscopy to identify the species of bacteria without a lengthy growth period. Raman spectroscopy is non invasive and only needs one bacterium for detection. It is therefore faster than growing bacteria and identifying via the API system.

From other research groups we know that Raman spectroscopy is able to classify bacteria, albeit with limited breadth of bacterial types. The next step is to implement imaging techniques to make the identification even faster, so that those techniques can be used in hospitals to determine pathological bacteria, so that the treatment can be given faster. Furthermore, when a hospital is unsure whether the patient has a disease caused by bacteria usually they start treating the patient with antibiotics in case they are infected. If identification only take a few hours instead of two to three days, doctors would only prescribe antibiotics when necessary, thus decrease the risk of multiresistant bacteria.

Breitenbach, Makenzie; Lyman, Seth; Tran, Huy (Utah State University)
Faculty Advisor: Lyman, Seth (College of Science, Chemistry and Biochemistry Department); Tran, Huy (College of Science, Chemistry and Biochemistry Department)

The Uintah Basin is a rural area in Northeast Utah where the oil and gas industry is prominent. During multi-day temperature inversions that occur during some winters, locally-emitted air pollutants, particularly from the oil and gas industry, react in the atmosphere to produce ozone. While it is well known that oxides of nitrogen and organic compounds are the main precursors to ozone formation, significant gaps exist in understanding of the sources and composition of organics emitted from various oil and gas-related sources. Better understanding of organic compound emissions will allow regulators and industry to make better decisions to reduce ozone-forming pollution to protect the health of residents and workers in the Uintah Basin.

During the winter of 2018-2019, we are deploying 14 remote measurement stations that collect air samples in silonite-coated canisters (for non-methane hydrocarbons and light alcohols) and on 2,4-dinitrophenylhydrazine-coated sorbent cartridges (for carbonyls). We are analyzing the canister and cartridge samples in our laboratory via gas and liquid chromatography, respectively, to determine concentrations of a suite of 76 organic compounds, all of which are known to be involved in the formation of wintertime ozone in the Uintah Basin. We position these stations in different configurations around the Basin to characterize certain facility types and to characterize organic compound concentrations across the entire Basin. For this presentation, we will use meteorological data and trajectory modeling to determine how facilities in the vicinity of our measurement stations impacted ambient organic compound concentrations and speciation. Later in 2019-20, we will use the 2014 Utah Air Agencies Oil and Gas Emissions Inventory with a three-dimensional photochemical model (WRF-CMAQ) to simulate air concentrations of the measured compounds. We will compare modeled and measured results to determine how well the inventory and model simulate actual ozone precursor concentrations.

Craig, Michael W. ; Valle, Hugo E. (Weber State University)
Faculty Advisor: Valle, Hugo (Weber State University, Computer Science)

Project atmosniffer has provided me a unique opportunity to work with existing code, updating and maintaining both software and hardware.

Project atmosniffer's purpose is to develop a scientific and comercial air-quality monitoring and recording tool. This project has undergone many transformations over the years since its birth and is continuing to be improved during the period of my contributions.

Most of the learning and developing was self-driven with guidance and learning tools provided by Dr. Valle and the university (pluralsight). The atmosniffer has changed much of its hardware, using a new microprocesser, a new gas board, a new OLED screen, and new drivers. Learning to code to hardware, update legacy code, and reading/coding how each module communicates with each other has been very fascinating.

More details covering the development of Project Atmosniffer will be presented.

Smith, Mick; Desdames, Chloe (University of Utah)
Faculty Advisor: Seaboch, Melissa (University of Utah, Anthropology)

Census and sampling work are important because they provide critical information on population size, distribution, and habitat preference — all important factors in conservation. La Selva Biological station is located on the north eastern side of Costa Rica and is a protected biological reserve. It is home to three species of primates including Alouatta palliata, commonly known as the mantled howler monkey. It is comprised of primary forest that has been undisturbed by human forces and secondary forest that is regenerating from past disturbances, such as deforestation. Past research conducted on howler monkeys shows they prefer primary forest over secondary because primary forests have higher species richness and a wider range of trees which provides food for howler monkey's selective diet. I predict that the majority of A. palliata in Costa Rica will be located in primary forest because it offers more resources. I censused 11 established trails at La Selva (two trails in primary forest, seven trails in secondary forest, and two trails crossing both forest types). For each howler monkey encountered, I recorded the location, forest type, and group size. I identified four different groups of A. palliata with group size ranging between 6-10 individuals. One group was located in primary forest and three groups in secondary forest; thus, my hypothesis that A. palliata would prefer primary forests was not supported. Anecdotally, A. palliata were observed more frequently around rivers or streams. This could indicate that rather than being concerned with primary versus secondary forest, they prefer riparian habitats found along the banks of rivers or other actively moving sources of water. A study conducted by Stoner found howler monkeys in riparian habits supporting this hypothesis. This type of research continues to provide critical information for understanding primate's habitats which helps with conservation of species.

Jenkins, Abigail; Baugh, Makinnon; Frandsen, Paul; White, Alexander; Dikow, Rebecca (Brigham Young University)
Faculty Advisor: Frandsen, Paul (Life Sciences, Plant and Wildlife Sciences)

Historically, physical plant specimens have been preserved and mounted on paper sheets and stored in plant collections, or herbaria. Herbarium collections are used for a wide variety of research purposes, including plant taxonomy, ecology, and evolutionary biology. The process of digitizing the herbarium sheets is simple and involves taking high resolution photos of each sheet and recording the corresponding metadata and attributes of the particular sample. Digitized herbarium sheets can be useful for a variety of purposes, and, by making images freely available online, they become immediately accessible to the scientific community, facilitating remote analysis. In addition, in a digital format, the images become computable and usable for purposes such as training deep learning models for classification or analysis of morphology.

While the process of digitizing is simple, herbarium sheets contain other features not directly representative of the plant, such as annotations, labels, museum stamps, color palettes, and rulers. There are additional inconsistencies in the herbarium sheets that are introduced through staining, record keeping, and natural degradation. Taken together, this information can contribute a substantial amount of noise if one is to use the image for downstream research analysis concerning the pattern, shape, or color of the specimen. We have developed a pipeline to filter this extraneous information, using image segmentation (whereby the specimen material is partitioned from the background) and deep learning.

We present this pipeline for generating training data for image segmentation tasks along with a novel dataset of highly resolved image masks segmenting plant material from background noise. We used this dataset to train a neural network to segment plant material in herbarium sheets more generally, and our method is applicable to other museum data sources where masking may be useful for quantitative analysis of patterns and shapes.

Lin, Jade; Park, Yeram; Ross, Micah; Stark, Michael; Hansen, Marc (Brigham Young University)
Faculty Advisor: Stark, Michael (Brigham Young University, Physiology and Developmental Biology); Hansen, Marc (Brigham Young University, Physiology and Developmental Biology)

Neural Tube Defects (NTDs) such as spina bifida and anencephaly are due to incomplete closure of neural tubes in developing embryos. While the etiology is still unknown, environmental and genetic factors, toxicants, and maternal health are implicated as potential causes. Previous research shows that NTDs are associated with increased levels of ceramide (C2) and possible exposure to fumonisin (FB1), and valproic acid (VPA). We hypothesize that these molecules may interfere with cell-to-cell interactions which are important for neural tube formation. To investigate the potential mechanisms by which these toxicants can induce NTDs, I will use a well-characterized MDCK cell model treated with C2, FB1, and VPA to assess their impact on cell adhesion.

Stehn, Christopher; Colman, Howard; Boucher, Kenneth; Grossman, Allie H; Holmen, Sheri L (University of Utah)
Faculty Advisor: Holmen, Sheri (University of Utah, Surgery)

Despite therapeutic advances in the treatment of melanoma, development of brain metastases continues to be a major cause of treatment failure. Prognosis for patients with brain metastases is exceedingly poor, therefore the development of sensitive and specific biomarkers to predict which melanoma patients are at highest risk for disease progression are needed. To accomplish this goal, we developed a novel combined molecular/clinical/pathologic predictor of brain metastasis risk. We first analyzed multiple gene expression datasets including The Cancer Genome Atlas (TCGA; n = 437) and an independent series from the European Genome-Phenome Archive (n = 183) and identified a list of 60 consensus genes that is robustly predictive of development of melanoma brain metastases (p < 0.05; FDR 5%). Next, we performed a similar analysis of association of miRNAs and melanoma brain metastasis risk which identified a set of miRNAs with significant predictive power. An optimized combined set of 15 mRNA and miRNA markers was a better predictor of brain metastasis risk than either mRNA or miRNA list alone when applied to the TCGA data set. The combined predictor was most sensitive in separating patients with no metastases from those with either brain metastases or systemic metastases. Current efforts are focused on optimizing miRNA and mRNA separation of patients specifically with brain metastases from those with other metastases using a machine learning linear classifier, and with integrating the expression classifier with other clinical and pathologic predictive factors including: age, stage, thickness, location, histology, ulceration, and gender. The sensitivity and specificity of the resulting clinical/molecular predictor will be validated in an independent retrospective patient dataset, and subsequently implemented in a prospective brain metastasis screening trial to determine real-world utility of this approach in preparation for prospective brain metastasis adjuvant/chemoprevention trials utilizing both immunotherapy and targeted therapy approaches.

Mueller, Kaeli; Kaitlyn, Golden; Johnson, J.B. (Brigham Young University)
Faculty Advisor: Johnson, Jerry (Brigham Young University, College of Life Sciences);

Human-induced changes to the environment are causing declines in many of the world's species. Studying model organisms, such as Poeciilidae fishes, can provide crucial information about a variety of other species (Johnson & Bagley, 2011). Alfaro, a monophyletic genus within the family Poeciilidae (Bagley & Johnson, 2014), has the potential to become an exemplary model species. There is currently much scientific knowledge about the two distinct reproductive tactics of Poeciliid males. However, studies about the presence of this trait are lacking for Alfaro. Therefore, I propose adding to the current knowledge about Alfaro cultratus by researching the presence of two distinct sets of traits that accompany different male reproductive tactics. The hypothesis is that male Alfaro will show similar physical characteristics to other Poeciliids, but that these traits will not differ across varying habitats. Measurements of deceased Alfaro specimens will be analyzed to identify differences in physical traits. This will be followed by a live experiment, in which the male size differential is expected to mirror that of the deceased specimens. This research will produce novel information about Alfaro cultratus because its life history strategies have yet to be described. Many intriguing evolution questions could follow.

References:

Bagley, J. C., & Johnson, J. B. (2014). Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: Concerted, independent, or multiple evolutionary responses? Ecology and Evolution, 4(9), 1686—1705.

Johnson, J. B., & Bagley, J. C. (2011). Ecology and Evolution of Poeciliid Fishes, Chapter 4, Ecological drivers of life-history divergence.

Sigulinsky, Crystal; Anderson, James; Emrich, Daniel; Rapp, Christopher; Dahal, Jeebika; Pfeiffer, Rebecca; Rapp, Kevin; Yang, Jia-Hui; Watt, Carl; Marc, Robert; Jones, Bryan (University of Utah)
Faculty Advisor: Jones, Bryan (University of Utah, Ophthalmology/Visual Sciences)

Purpose: Mouse retina differs structurally from rabbit retina, as it is thicker and vascular, while rabbit retina is thinner and avascular. The implications of these differences on neuronal morphology and connectivity is unclear. We compare the morphology and connectivity of the Aii amacrine cell (AC) at ultrastructural precision in connectomes of mouse (RC2) and rabbit (RC1) retina.

Methods: RC1 and RC2 are 0.25 mm diameter volumes built by automated transmission electron microscopy at 2 nm/pixel resolution. RC1 is from a 13 month old, female Dutch Belted rabbit. RC2 is from a 5 month old female C57BL/6J mouse. The Viking application was used to annotate Aii ACs.

Results: Mouse Aii ACs are elongated with a prominent neck region. Lobular appendages in both species extend from the soma, neck and proximal arboreal dendrites in the OFF sublamina, forming reciprocal synapses with OFF cone bipolar cells (BCs). In rabbits, multiple arboreal dendrites emerge from the base of the neck, branch and travel obliquely through the ON sublamina, forming gap junctions with ON cone BCs, neighboring Aii ACs, and itself. They extend laterally at the base of the IPL, collecting ribbon input from rod BCs. In contrast, mouse arboreal dendrites branch from a single primary dendrite, travel vertically through the IPL with limited self-interaction, and terminate at variable depths that align with the more broadly ramified axon terminals of mouse rod BCs. Synaptology reveals greater output in the OFF vs ON layer in mouse versus rabbit. Uniquely, descending axons of mouse ON cone BCs form gap junctions with Aii AC somas.

Conclusions: Lateral expansion of rabbit Aii ACs may be attributable to eccentricity. However, morphological differences correlate with connectivity differences. Comparative anatomy connectomics is essential for understanding implications of retinal structure on neuronal morphology and connectivity underlying network differences between the mouse and rabbit.