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  Comparative Whole Genome Sequencing of Cryopreserved and FFPE Cancer Tissue

  DeLaney Anderson, Ken Dixon, Ryan Miller, Sangmoon Lee, Jeffrey Okojie, and Jared Barrott

  Whole genome sequencing (WGS) determines the DNA sequence of an organism’s entire genome & plays a key role in cancer precision medicine

  • Currently, the main preservation method of cancer tissue for WGS is formalin-fixed, paraffin-embedded (FFPE) tissue; cryopreserved (CP) tissue is not routinely used in clinical settings
  • Previous studies have determined CP tissue yields higher quality & quantity of DNA
  • This study aimed to compare the outcomes of WGS in CP & FFPE samples.

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  Invasive Species and Water Loss: Automating the Study of Phragmites in Utah Wetlands

  Alexander Atkinson and Dr. Rachel Wood

  Phragmites australis is an invasive reed threatening Utah wetlands by not only outcompeting native flora and disrupting ecological system but also potentially increasing evapotranspiration (ET), the combined process of evaporation and plant transpiration. Increased ET may accelerate water loss in the already shrinking Great Salt Lake (GSL), exacerbating ecological and economic consequences.

  To address this, we are developing an automated R-based data analysis pipeline to analyze Utah Geological Survey (UGS) data at the GSL Phragmites site, and to validate evapotranspiration measurements with satellite estimates from OpenET. By making the data and analyses easily accessible, we can better understand and mitigate the negative effects of this invasive plant, and also examine whether Phragmites actually increases ET, by how much, and identify the mechanisms driving this increase.

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  Chilling Insights: A Comparative Study of Cancer Tissue Preservation

  Rebecca Bascom, Paige Nelson, Jacob Harris, Jack Davis, Mackenzie BUrr, Jeffrey Okojie, David Booker, Ken Dixon, and Jared Barrott

  It is a fact that personalized cancer treatment leads to better patient outcomes. But what if the current treatments aren't as personalized as they could be?

  Clinical cancer tissue samples are typically sent to labs as formalin-fixed and paraffin-embedded (FFPE) tissues. A recent study4 indicates that cryo-preserved (CP) tissues offer significantly better DNA quality and quantity than FFPE samples, suggesting a need to reevaluate preservation methods. We aim to expand this research by comparing protein expression in FFPE and CP samples.

  Specifically, we will focus on PD-L1, a protein that inhibits T-cells and is overexpressed in all cancer cells. The quantity of PD-L1 is crucial for identifying cancer in tissue, making it an ideal candidate for our comparison.

  Hypothesis: CP tissue samples will yield higher amounts of PD-L1 compared to FFPE preserved tissue samples.

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  Engineering Chromoprotein Variants With New Colors

  Anna Bowman, Joel S. Griffitts, and Kyler Fullmer

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  For dust thou art, and unto dust shalt thou return — Testing soil-derived plant-beneficial bacteria for potential as biofertilizers

  Johnathon Brim, Blake Oler, Jacob Hardy, Joseph Richardson, Ryan Bjazevich, Kate Whalen, Emmelia Wevers, Foxx Naylor, Ethan Shreeve, Alex Cherry, Ethan Cherry, Tanner Gunnell, Jayden Longhurst, Andrew Burrows, Mailon Odell, Jacob Sy, and Jeffrey Schacterle

  • The results of plant testing have shown that bacteria treated seeds outperform the control seeds on a consistent basis
  • We will continue to receive more data from out own experiments as well as crowdsourcing methods.
  • Our next step is to begin comparing results of our soil/seed treatment against commercially available fertilizers that use beneficial bacteria.

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  Where the Green-to-Red Neurexin Grows: Analyzing Neurexin-3a Expressing Neurons Through Dendra2 Knock-Ins and Full Locus Deletion

  Dillon J. Brown, Isaac E. Greenwood, Annalie Martin, and Arminda Suli Ph.D.

  The optic tectum (OT) is a zebrafish midbrain structure homologous to the mammalian superior colliculus (SC). The OT facilitates integration of multisensory input and coordinates a corresponding involuntary response. Single-cell RNA sequencing data from our lab indicates the differential expression of the presynaptic cell adhesion protein - neurexin3a - within two cell populations (OT5 and OT8) of the zebrafish OT. The SC and neurexin3a have both been implicated in autism spectrum disorder (ASD), warranting, therefore, a further investigation. To visualize neurexin3a positive neurons in the OT, we are generating a transgenic zebrafish line that expresses the green-to-red photoconvertible protein Dendra2 wherever and whenever the neurexin3a gene is transcribed. We will then photoconvert Dendra2 in individual neurons to determine the morphology of the neurons expressing neurexin3a in the OT. To better comprehend neurexin3a function in the OT, we will generate a transgenic zebrafish line in which the full locus of neurexin3a is deleted. We will then determine how this deletion affects zebrafish larval behavior and OT activity using behavioral assays and in vivo calcium imaging.

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  Signal Integration: How it changes across cell types in the Vestibulo-Ocular Reflex

  Alisa Burt and Trace Stay

  The Vestibulo-ocular reflex (VOR) is a reflex that controls eye movements in order to keep images stable on the retina. The precise circuitry behind the VOR is not well understood. Using awake in-vivo recording and high-density neural probes, this study aims to identify how signal integration varies across cell types.

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  Relationship Between the Gut Microbiome and Immune Responses in Drosophila Melanogaster

  Killian Bynum and John M. Chaston

  Flies possess several immune pathways, including the Toll pathway for defending against Gram-positive bacteria (which have thick cell walls) and the IMD pathway for targeting Gram-negative bacteria (which have thinner cell walls).

  Previous studies have shown that antimicrobial peptides (AMPs) interact with these immune pathways and play a role in modulating the gut microbiome.

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  Effect of Isostatic Rebound on Soil Biodiversity

  Robert Candland, Blake Harrison, Solinus Farrer, Kyle Lake, and Byron Adams

  Purpose: Understand the effect of shifting tide lines on organism diversity and abundance

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  Fishing for Neurocircuitry: Identifying Multi-Sensory Integrating Neurons in the Optic Tectum of Zebrafish

  Logan Carson, Arminda Suli, Adeline Hamilton, Logan Carson, KariAnne Jex, Erika C. Marks, Jordan T. Yorgason, and Tracianne B. Neilsen

  The superior colliculus (SC) is a mammalian midbrain structure involved in multimodal sensory integration and is implicated to have a role in neurodevelopmental disorders. Although the presence of multisensory integrating neurons (MINs) in the SC has been well documented by electrophysiology techniques, little is known about their morphological or molecular characterization. To identify and study MINs, we utilized SC’s non-mammalian homologous structure–the optic tectum (OT)–in the genetically tractable model organism zebrafish. In this process, we generated transgenic lines that allowed for fluorescent detection of neuronal activity by expressing the genetically engineered calcium indicators: cytoRGECO and H2B-jRGECO1a, respectively in mechanosensory hair cells of the ear and OT. To activate the vestibular sensory pads in 7 days-post-fertilization (dpf) larvae, we used a piezoelectric actuator probe. We found that upon the application of this vestibular stimulus in the posterior cristae (PC), some OT neurons showed time-locked activation. This indicates that OT circuitry in 7dpf larvae is mature enough to receive vestibular stimuli. Furthermore, when 7dpf larvae were sequentially and simultaneously exposed to vestibular and visual stimulations (1 second pulse of 488nm light), we found OT neurons that responded to concurrent stimuli and showed characteristics of multisensory integration. Identification of MINs in the zebrafish OT sets up the stage for better morphological and molecular characterization and their role in neurodevelopmental disorders using a genetically tractable model.

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  Taking Out The Taxonomic Trash: Refining Skink Classification in the Genus Sphenomorphus

  Phillip Cockrell, Leah Stimpson, and Alison Whiting Ph.D

  Distributed in New Guinea, Wallacea, Indonesia, and SE Asia (see figure 2), Sphenomorphus is often called a “Waste Bin” genus because species that don’t fit elsewhere are “dumped” there.

  These cryptic skinks (see figure 1) have been problematic for traditional taxonomy due to a lack of discrete morphological characters.

  Recent molecular studies of Sphenomorphus in the Philippines find the genus to be paraphyletic.

  New Guinea has one of the largest concentrations of Sphenomorphus, has been poorly studied (figure 4), and is known for its extreme biodiversity¹,².

  We seek to test the monophyly of Sphenomorphus in New Guinea, and the currently described species.

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  Research Process toward the Creation of Transgenic Beetles

  Taylor Coffman, Christian McCombs, Jonah Jex, Chris Daley, Brian D. Jensen, and Sandra Hope Ph.D

  Create a generalized efficient procedure for the reliable creation of transgenic insects.

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  Optimizing Carbon Nanotube Diameter and Copper Coating to Inhibit Pseudomonas aeruginosa Biofilm Growth

  Owen Cramer, Jenny Finlinson, Lucy C. Bowden, and Bradford K. Berges Ph.D.

  • ~30% of surgical implant failure is caused by infection¹
  • 10-23% of all implant-associated bone and joint infections are caused by gram-negative bacteria²
  • Pseudomonas aeruginosa, a gram-negative bacterium, forms biofilms (bacterial communities encased in a matrix) that are extremely difficult to treat
  • Carbon-Infiltrated Carbon Nanotubes (CICNT) have a surface structure that prevents the formation of biofilms³
  • The mechanism of biofilm disruption on CICNT is still unknown.
  • Our current research is focused on creating the optimal CICNT conditions that result in the greatest reduction of adherent P. aeruginosa.

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  The Possible Role of Cysteine Synthesis in E. Coli Mastitis

  Caz Cullimore and David Erickson

  Clinical mastitis is an infection of the udders of dairy cows

  Mastitis is the leading cause of economic losses to the dairy industry

  E. coli is the most common cause of clinical mastitis (Gonçalves)

  Genetic factors may affect the ability for E. coli to establish an infection

  Genome-wide association studies (GWAS) can detect genetic variants correlating with disease. However, most GWASes aren’t validated experimentally

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  A different dimension: a comparison between 2D cell lines and 3D organoids in cancer drug screening cell viability​

  Payton Curran, Isaac Packer, DeLaney Anderson, VIctoria Johnson, Jeffery Okojie, and Jared Barrott

  Cancer drug screening is commonly performed on two-dimensional (2D) cancer cell lines. Recent innovations in cell line development and methods of incubation has led to further interest in the development of three-dimensional (3D) organoids from standard cancer cell lines and patient-derived tissue. Our research intends to test the relationship between cell viability of 2D cancer cell lines and the viability of 3D organoids during cancer drug screening.

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  Examining Purkinje Cell Modulation of the VOR: An Optogenetic Study

  Ben Davis, D Garcia, B Haack, J Lewis, J Jackson, C Worthington, and Trace Stay

  The vestibulo-ocular reflex (VOR) is coordinated eye movement to maintain a stable gaze during head rotation. This reflex can be adapted in behavioral training by using repeated head movements and shifting visual stimuli.

  Previous research (Kimpo et al., 2014) implicates cerebellar output as critical to VOR adaptation, but it is unclear whether Purkinje cell (PC) output paired with a vestibular or visual stimulus is sufficient for driving reflex adaptation.

  We hypothesize that PC output is sufficient for driving gain up behavioral VOR adaptation when paired with peak ipsiversive head movement in mice. Stimuli include a rotating vestibular environment or visual motion cues such as a rotating drum around the mouse. If PC stimulation when combined with one of these two stimuli is sufficient for changing VOR gain, we would see increased long term gain during optogenetic stimulation.

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  Engineering Chimeric Autoantibody Receptor T cells (CAAR): a potential cure for Graves' Disease

  Kimbal Demars, Abigail Cheever, Chloe Kang, Hunter Lindsay, Mackenzie Hansen, Kim O'Neill, and Scott Weber

  • Graves’ Disease (GD) is the 4th most common autoimmune disease in the United States.
  • GD is characterized by autoreactive B cells releasing anti-thyroid stimulating hormone receptor (TSHR) Ab that bind to TSHR, causing an overexpression of hormones.
  • Excessive hormonal release leads to hyperthyroidism, causing a variety of metabolic issues.
  • No cure exists, only limited effectiveness of treatments, including chemotherapy, radiation, or thyroidectomy.
  • Chimeric antigen receptors (CAR) T cell therapy has been effective in treating blood cancers.
  • Modifying this therapy by engineering T cells that replace the antigen as the T cell receptor will selectively target autoreactive B cells, namely chimeric autoantibody receptor (CAAR) T cell therapy.
  • By using TSHR as the binding domain, we believe that our CAAR T cell that will be able to eliminate anti-TSHR B cells in GD.

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  Mitigating Herbivory Impacts on Aspen Forest Regeneration Through Fire and Mechanical Thinning in High-Grazing Landscapes

  Chloe Denham and Sam St. Clair

  • Monroe Mountain in Fishlake National Forest has experienced rising herbivory pressure from elk, deer, and cattle in its stable aspen forest.
  • Stable aspen stands have minimal conifers, low stand turnover, and rare disturbances.
  • We looked at how herbivory patterns change over time under different treatments on Monroe Mountain.

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  Frequency-Specific Training of VOR Generalization in Mice

  Natalie Dietrich; J, Mckeon; I. Phillips; and Trace Stay

  The Vestibulo-Ocular Reflex (VOR) is a critical neural mechanism allowing the eye to stabilize vision during head movements by generating compensatory eye movements. The VOR can be adapted to make larger or smaller eye movements for the same amount of head movement by associating head movement with rotation of a visual field at a specific frequency The change in Serial = Sum of Sines Serial ≠ Sum of Sines Training frequencies change but no generalization occurs eye movement at one frequency of head rotation also induces smaller magnitude changes in eye movement at closely-related frequencies, a process termed generalization. It is not clear whether serial training at different rotation frequencies would produce the same generalization effects as combined training with multiple frequencies simultaneously. We hypothesize that generalization will be more effective for frequencies close to the training frequency most recently experienced, and less effective for training frequencies that were experienced more distantly, when presented in series. In contrast, we hypothesize that generalization will be equally effective across frequencies when training stimuli are presented simultaneously.

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  Discovering Diet-Dependent Changes in Amino Acid Metabolism

  Benjamin Driggs, Coleman Nielsen, and J. C. Price

  The Price Lab ran a mouse diet experiment to see if we could detect changes in amino acid metabolism according to diet. The diets used were low protein ad libitum (LP AL), low protein CR (LP CR), high protein ad libitum (HP AL), and high protein CR (HP CR). Multiple individuals were randomly assigned to each diet. Extracting D2O labelled samples across several time points allows us to use mass spectrometry to measure both protein concentration and turnover (figure 1) (1). These are measured by analyzing the shift in isotopic peaks (2). Using these changes in isotopic peaks we can also calculate n-values (see figure 2 below), which are metabolic indicators for the associated molecule.

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  Walking in Super Shoes: Reduced Ankle Power, Decreased Stability?

  Bethany Esplin, Thomas Anderson, Nate Jacobsen, Luke VanKeersbilck, Dustin A. Bruening, and Iain Hunter

  Super shoes improve running economy by reducing gastrocsoleus work [1]

  Could the same benefit apply to walking to benefit clinical populations?

  Is there a trade-off for balance?

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  Laying Framework for a Novel System to Test Effects of Histone Modifications

  Taryn Evans, Luke Ramirez M.S, Aaron Bohn, Jacob Hunter, Sarah Hodson, Sarah Ricks, David Bates Ph.D, and Steven M. Johnson Ph.D.

  Chromatin structure and composition play a significant role in regulating gene expression within eukaryotic cells. The fundamental organizational unit of chromatin is the nucleosome, which is composed of ~147 base pairs of DNA wrapped around a histone protein core. Post-translational modifications (PTM’s) to the protruding tails of histone proteins are known to regulate nucleosome occupancy and positioning, which influence chromatin architecture and thus gene expression. However, relatively little is known about the residual effects of histone PTM’s on transcription rate, especially in nucleosomes along the gene body. Here, we demonstrate a method for measuring transcription rate in real-time with a common qPCR machine. This lays the framework for a novel in vivo system in which we will use C. elegans transcriptional machinery to directly study the effects of histone PTM’s on transcription rate, independent of changes to chromatin architecture.

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  Tight Junction Protein Impact on Sonic Hedgehog Pathway

  Josh Freeman, Hudson Christensen, and Dario Mizrachi

  The Sonic Hedgehog Pathway is critical for cell division and proliferation, and when disrupted, can be a major contributor to the overproliferation of cells and complications in the organism from the resultant cancers. Experimentation upon the organism Planaria Torva and A549 cells using chimera Occludin (COC)–a traditionally isolated tight junction protein having no role in the SHH pathway–has shown dramatic changes within the organism/cell signaling system, suggesting that tight-junction proteins may play a role in–or can be used to manipulate–this specific cell signaling pathway by inhibiting or activating key proteins. The possibility of a “mechanotransduction” effect by COC on SHH pathway has major implications regarding our understanding of the physiological pathways related to cancer, as well as its research and treatment.

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  Effects of Ethanol on G-CSF Sensitivity in the Ventral Striatum

  Kaleb Gardner, Rachel Campbell, Camryn Holt, Zachary Valentine, Chase Seiter, and Jordan T. Yorgason

  Granulocyte-colony stimulating factor (G-CSF) is a known neuromodulator for dopamine (DA) release in the ventral striatum • Increased peripheral G-CSF levels enhances abused substance effects • The G-CSF mechanism for enhancing release remains unknown • How ethanol affects G-CSF neuromodulation also remains unknown • The present studies examined G-CSF effects on striatal and mesolimbic circuitry and chronic ethanol effects on this system

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  Mechanism of Copper-Coated CICNT Inhibition of Staphylococcus aureus Biofilm Formation

  Emilia Gregory, Lucy Bowden, and Bradford Berges

  Staphylococcus aureus is a leading cause of healthcare-associated infections, particularly through biofilm formation on medical devices, leading to severe and recurrent complications¹. The resistance of S. aureus biofilms to traditional antibiotics requires new strategies to mitigate these infections. Our previous findings indicate that the anti-biofilm properties of carbon-infiltrated carbon nanotubes (CICNT) significantly inhibit the growth of S. aureus biofilms². We will further explore if copper, an innately antimicrobial material, will enhance this effect.

  To determine the impact that copper would have on bacterial growth, we coated the CICNT with a thin layer of copper and used colony-forming unit analysis to determine the difference. Our prediction was that the structure of CICNT combined with the copper coating would inhibit the formation of S. aureus biofilms.