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  The Cold Hard Truth: Cryopreserved Tissue is Superior to FFPE Tissue in Molecular Analysis

  DeLaney Anderson, Jeffrey Okojie, Mackenzie Burr, Peyton Worley, Isaac Parker, Jack Davis, Bridger Kearns, and Jared Barrott

  Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for all testing of tumor tissue in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). Specific to genomics assays, numerous studies have shown significant discordance in genetic information obtained from FFPE samples and cryopreserved or flash frozen samples. To explain the discordance between FFPE samples and cryopreserved samples, a head-to-head comparison between FFPE and cryopreserved tissues was performed to analyze the DNA yield, DNA purity and DNA quality in terms of DNA length.

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  Variation in Vital Rates Among Least Chub (Iotichthy phlegethontis)

  Lauren Applebee, Mark C. Belk, and Nathan St. Andre

  Conservation plans for a species often requires knowledge of population trends. These trends can be difficult to acquire, but one piece of information that can be attained from populations is the catch per unit effort (CPUE). We are trying to use CPUE in a new way to determine population demography for populations of Iotichthys phlegethontis, Least Chub.

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  The Effect of Percussive Massage on Collagen Gene Expression in Skeletal Muscle

  James Bartling, Robert D. Hyldahl, Emma Schaugaard, and Mohadeseh Ahmadi

  INTRODUCTION

  • Exercise is a critical aspect of healthy living due in part to its effects of muscle adaptation, which are largely regulated by alterations in gene expression

  • Sedentary behavior can be required by diverse life circumstances, suggesting a need to reproduce the beneficial effects of exercise by an alternative means

  • Like exercise, percussive massage introduces a mechanical strain on the muscle, which could potentially replicate a similar remodeling response of the extracellular matrix (ECM). However, this has not yet been studied

  • Collagen 1,3,&4 are major components of the ECM that adapt in response to exercise, and we hypothesized that the Percussive Massage would result in increased muscle mRNA expression compared to the control group

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  Tree Damage Patterning in Alaskan Forests

  Emma Barton, Richard Gill, and Haden Penrod

  • Tree defoliation (from insect parasites) is not abnormal in the densely forested areas of Alaska, but large outbreak events in recent years have led to cause for alarm.

  • To better understand the factors affecting defoliation, we used remote sensing and GIS (geospatial information system) technologies to look at mortality spatial patterns across Hemlock and Spruce forests in southeast Alaska.

  • Elevation and proximity to water as well as other factors were considered in determining the impacts of outbreak events due to evidence that changes in landscape can alter parasitism behaviors (Roland & Taylor, 1997).

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  The Effect of Epicatechin and its Microbial Metabolites on Differing Pathways of Beta-Cell Death in Type I and Type II Diabetes

  Aubree Bench and Jeffery S. Tessem

  The pathogenesis of type 1 (T1D) and type 2 diabetes (T2D) is associated with progressive beta-cell death and loss of insulin secretion, making functional betacell mass preservation a priority in the treatment of diabetes. T1D beta-cell death is primarily mediated by autoimmune exposure of beta-cells to proinflammatory cytokines such as IL-1b, TNFa, and IFNg (1, 2). Beta-cell loss in T2D, however, is characterized by damage caused by a destructive metabolic state of persistent hyperglycemia and elevated free fatty acid (FFA) levels (2, 3). Our lab has shown that the monomeric flavonoid epicatechin and its metabolites hippuric acid, homovanillic acid, and 5-phenylvaleric acid enact diverse beneficial effects on beta-cell viability, including reduction of oxidative stress and increased mitochondrial respiration, both important sites of intervention in the prevention of beta-cell death (5). This study aims to explore potential protective effects of epicatechin and its gut bacteria derived metabolites against cytokine or glucolipotoxic (GLT) mediated beta-cell death. This study’s findings will have important implications for differing therapeutic approaches to T1D and T2D, as well as insight regarding potential areas of intervention against both major antagonists of beta-cell death.

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  A Survey of Molecular Diagnostics Education

  Kristina Berman, Ryan Cordner, and Mary Davis

  Medical Laboratory Science (MLS) is vital for healthcare, involving the analysis of clinical samples to diagnose and monitor diseases. However, there's a scarcity of courses focused on molecular diagnostics, which could greatly benefit medical laboratory scientists.

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  A Rare Plant in Peril: Conservation Concerns for an Endemic Alpine Plant, Ipomopsis spicata ssp tridactyla

  Kainoa Bolinder, Loreen Allphin, Madison Huie, and Steven Flinders

  Ipomopsis spicata ssp. tridactyla, (I. tridactyla or IPTR; Fig. 2 & 12), is a rare alpine plant species endemic to the Tushar Mountains and Markagunt Plateau of southern Utah. There is limited knowledge available about population dynamics and community composition. Due to difficult abiotic conditions, alpine environments are more vulnerable to lasting damage from disturbance (Scherrer & Pickering, 2005). Ipomopsis tridactyla is listed as high-priority for conservation (Alexander, 2016). As conservation concerns for alpine plant communities increase due to climate change (Kopp & Cleland, 2013), so does the need for long-term monitoring of plant populations. Thus, we set up long-term monitoring transects (LT) and camera traps to determine plant community characteristics, dynamics, and conservation concerns.

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  Making Sense of Messy Data: Classifying Metadata Variables in Public Transcriptomic (RNA) Data

  Grace S. Brown, Tolulope Akinbo, and Stephen Piccolo

  US researchers are required to deposit data in public repositories so other researchers can validate their findings and reuse their data for new studies. There are > 100,000 transcriptomic (RNA) datasets in the public domain. However, it is of little use without metadata (details about individual samples e.g. sex, race). Having quality metadata provides many benefits including

  • controlling for confounding factors.
  • improving precision medicine.

  Research has suggested

  • males are studied more than females.
  • people of European descent are studied most.

  We need to make representation more equitable so genetic research will be relevant to all people. The first step is characterizing current subgroup representation in more detail. But classifying datasets by their metadata is time intensive and requires manual curation because metadata are described inconsistently across studies.
  
  

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  Using Arbuscular Mycorrhizal Fungi to Help Establish and Increase Vigor of Plants in Mineland Soils

  Melissa Burrell, Brad Geary, Shannon Nelson, Josh Moroni De Santiago Lazalde, Scott Kent, and Matthew Madsen

  • Vegetation establishment in areas impacted by mining can be difficult due to a lack of beneficial soil microbes.
  • The introduction of soil mutualists, such as arbuscular mycorrhizal fungi (AMF), may improve mineland revegetation efforts. AMF forms a mutually beneficial relationship with plants to aid in nutrient absorption and improve water uptake.
  • Practitioners commonly need to decide where to source their AMF. Locally collected AMF requires effort to collect and process, but this source should be adapted to the restoration site. Commercial products are easy to obtain, but their strains may not be suitable for the environment they are being placed in.

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  Theranostic Approaches to Treat Synovial Sarcoma

  Machenzie Burr, Jared Barrott, Jeffrey Okojie, DeLaney Anderson, Peyton Worley, Jack Davis, Bridger Kearns, and Melanie I'anson-Holton

  Synovial sarcomas (SS) are rare soft tissue cancers that are found beside bone in children and adolescents. Currently, the prognosis for these diseases are low, as diagnostic and treatment options are limited due to the rarity of the disease. With high rates of metastasis, treatment options for these diseases become further limited to primarily radiation and chemotherapies. These therapies have limited specificity in their mechanisms, causing severe side effects in patients. This work examined alternative options for synovial sarcoma theranostic approaches, specifically using immunoconjugates for Oncostatin M Receptors (OSMR). This receptor was chosen due to the high rate of expression of Oncostatin M in many cancers, including synovial sarcoma. It is involved in cancer proliferation and metastasis, making it a good target for treatment.

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  Valproic Acid Alters Larval Behavior and Neuronal Composition Within the Optic Tectum of Zebrafish

  Bailey J. Calder, Jacquelyne C. Howell, Michael J. Zeyer, Annalie Martin, Sierra C. Dixon, Shane M. Lilya, Jason M. Hansen, and Arminda Suli

  The mammalian superior colliculus (SC) and its non-mammalian homolog–the optic tectum (OT)–are midbrain structures that integrate multimodal sensory inputs and guide involuntary movements in response to relevant environmental cues. Recent work has drawn strong connections between the functions of the SC/OT and behavioral deficits observed in autism spectrum disorder (ASD), thus implicating this structure as a possible site affected in ASD. Since fetal exposure to valproic acid (VPA) has been associated with increased prevalence of ASD in humans, and ASD-like phenotypes in animal models, we exposed embryonic zebrafish to VPA to investigate the connection between ASD and OT development. In this process, we confirmed that VPA exposure alters larval behavior in a manner consistent with increased anxiety and an increased preference for a dark background. Additionally, through the use of scRNA-seq, we determined that VPA alters genes associated with ASD and increases the proportion of immature neurons within the OT. In summary, our work provides insight into the dynamics of OT development and begins to shed light on the relationship between the OT, VPA, and ASD.

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  MMAPPR2: An improved bioinformatics approach to find novel genes

  Aiden Cardall, Jonathon T. Hill, Kyle Johnsen, Connor Ward, Maliha Tasnim, and Jared Taylor

  Introduction

  • New genes are commonly found by randomly inducing mutations in model organisms.

  • Mapping the mutations to the genome to find novel genes is difficult, time-consuming, and expensive.

  • We created a bioinformatics program, MMAPPR, to automate this process.

  • Here, we introduce a new algorithm, MMAPPR2, which requires little to no bioinformatics knowledge to use.

  • MMAPPR2 makes several improvements that allow it to identify genes more rapidly and precisely.

  • MMAPPR2 will aid the rapid identification of genes in a wide range of species and developmental systems.

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  Increasing student capability to confront difficult topics through structured conversations

  Parker R. Carlquist, Lexi Brady, Seth Dotson, and Jeff Glenn Dr.

  • Health is shaped by numerous determinants including race, socioeconomic status, education, and personal behaviors
  • Addressing determinants often requires the formation and implementation of comprehensive policy
  • Public health issues and efforts are intrinsically controversial and can be polarizing
  • If individuals are unable to discuss public health issues, long-term viable solutions will not be found
  • A dramatic increase in political polarization has occurred since the 1980s leading to less common ground and agreement between political parties on contentious issues4-6
  • Research shows reflective structured dialogue improves:
  • Polarization attitudes towards openness, tribal identity, and moral disdain
  • Knowledge, trust in others, and tolerance of differences
  • Social and interpersonal skills are critical to success in education and the workplace

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  Cell Death, Inflammation, and Extracellular Vpr in the R77Q Mutation of Vpr in HIV-1

  Amanda Carlson, Brad K. Berges, and J. Brandon Lopez

  One potential target for therapeutic treatment of HIV-1 is Viral Protein R (Vpr), an accessory protein encoded by the HIV-1 genome. Vpr plays an important role in pathogenesis and replication for HIV and is involved in transcription, the pre-integration complex, cell cycle arrest, and cell death via apoptosis. Mutations in this protein dramatically impact the rate of AIDS progression compared to the wild type (WT) version of Vpr. The Vpr polymorphism R77Q is associated with the Long Term Non Progressor (LTNP) phenotype. Regular AIDS onset is 5-7 years for WT virus and 10 or more years for R77Q. These differences in AIDS progression have been observed in vivo by following people with HIV over time.

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  Using Chimeric autoantigen receptor (CAAR) T cells to eliminate autoreactive B cells in autoimmune diseases

  Abigail Cheever, Chloe Kang, Hunter Lindsey, Mackenzie Hansen, Kim O'Neill, and Scott Weber

  • Graves’ disease (GD) is an antibody-mediated autoimmune disease affecting the thyroid and causes hyperthyroidism
  • 4th most common autoimmune disease in the US
  • Autoreactive B cells produce anti-TSHR antibodies (TRAbs) which mimic thyroid stimulating hormone (TSH) and chronically stimulate thyroid cells causing hyperthyroidism
  • There currently is no treatment which addresses the root cause of the disease

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  Determining if Optic Tecti of Larval Zebrafish Receive Input from Deep Brain Photoreceptors

  Emalie A. Christensen, Allison G. Pickens, Colby Odom, Griffin Sauer, Sarah Y. Jarrett, Maurice Hunt, Annalie Martin, and Arminda Suli

  Deep brain photoreceptors (DBPs) are light-responsive sensory cells present in mammals and non-mammalian vertebrates. In non-mammalian vertebrates, studies have shown DBP involvement in various time and light dependent behaviors including circadian rhythm, phototaxis, and seasonal reproduction. In adult telosts, DBPs are present throughout the brain, including the optic tectum (OT), a midbrain structure that receives and integrates input from multiple sensory modalities. In this study, we aimed to determine if DBPs are part of or send input to the OT of larval zebrafish. Single-cell RNA sequencing of the larval zebrafish OT showed the presence of several opsins. We focused on opsins that respond to the violet- blue light range - one typical of optogenetic studies. To identify OT neurons with similar activation patterns following light stimulation, we used live calcium imaging to detect brain activity, followed by watershed segmentation and k-means clustering. Data comparing neuronal activity patterns following presentation of 450nm or 488nm light stimuli to control (eyes intact) and larvae whose eyes have been removed (mono-enucleated and bi-enucleated) indicate the presence of two different groups of opsin responding neurons: one that activates independently of retinal innervation consistent with DBP input, and another that activates more frequently when the visual system is intact suggesting they receive both retinal and DBP inputs. Subsequent studies will include 1) morphological studies to determine the different subclasses of OT neurons responding with different activity patterns to DBP activation, 2) ISH studies for candidate opsins to determine their localization, and 3) CRISPR-Cas9 knockouts of select opsins to determine their necessity in OT micro-circuitry and behavior.

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  Jaspine B and the Sea Sponge That Fights Cancer

  Jack Davis, Jared Barrott, Adriene Pavek, Farjana Afrin, Sameena Mateen, Brendon Meldrum, Rocio Rojas, Pamela Diaz, Megan Condie, Ali Aghazadeh-Habashi, and Srinath Pashikanti

  Jaspine B is a natural marine product, derived from the sea sponge, Jaspis, found in some tropical climates. Jaspine B has been shown to be an effective treatment in some cancers with an upregulation of sphingomyelin synthase. This research aimed to understand the effects of Jaspine B on synovial sarcoma, and investigate its potential to be used as targeted treatment in other cancers that have an upregulation of sphingomyelin synthase

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  Myofiber necrosis to electrical stimulation-induced damage: Influence of menstrual cycle phase

  Collin Deshler, Brandon Pfeifer, Mohadeseh Ahmadi, Werner N. Hunter, Madeline N. Nielsen, Krista S. Shimizu, and Robert D. Hyldahl

  • Estrogen plays important roles in women's overall health, including cardiovascular health, metabolism, bone, connective tissue, and skeletal muscle.
  • Existing evidence, mostly based on studies with ovariectomized rodents or post-menopausal women suggests that estrogen is essential for normal muscle recovery, growth, and function.
  • Evidence indicates that estrogen plays a role in facilitating skeletal muscle regeneration by activating satellite cells.
  • There is a lack of research on the impact of estrogen levels on skeletal muscle damage and recovery in premenopausal populations who have fluctuating levels of estrogen throughout their menstrual cycle.
  • The purpose of this study was to determine how menstrual cycle phase affects muscle fiber damage and regeneration after electrical stimulation.

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  The Biomechanics of Ursine Predation: Investigating the Force Generation and Mechanical Properties of Bear Claws and Teeth in Predatory Behavior

  Katie Dooley, Megan Doxey, Josh Jewell, and Tom Smith

  • Studied over 2,200 human-bear conflicts in North America and witnessed the shear force that bears can exert to access food and eliminate any threats.
  • Polar bears at the Hogle Zoo in Salt Lake City punctured and bent high density polyurethane (HDPE) objects when playing with them.
  • This prompted research into the force it takes bears to puncture objects with their canines and claws.

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  In search of super-scents for carnivore attraction

  Megan Doxey

  Find chemical scents that are more effective at alluring North American predators than what is commercially available, then isolate the scent’s chemical structure to create better trapping lures.

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  Investigating the Correlations Between Medicaid and SNAP Benefit Levels and Health Outcomes

  Will Evans, Michael Barnes, and Richard Evans

  • Socioeconomic factors, such as poverty, have statistically significant impacts on health.
  • SNAP (formerly known as food stamps) and Medicaid are major government programs that exist to reduce these health-detrimental effects for impoverished households.
  • Problem: Determining optimal welfare benefit levels is difficult. Despite vastly different costs-of-living between counties, states offer a standard welfare amount to all counties in the state. Simulating benefits based on geographic living expenses can address the political debate about one-size-fits-all benefits found in most states. Simulating optimal benefits based on achieving optimal health effects is needed to improve SNAP and Medicaid.

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  Determining the Role of Noncoding Insertion and Deletion Mutations in Lung Cancer

  Zachary Everton and Matthew H. Bailey

  Background

  ● Cancer is a disease in which cells grow and divide at an uncontrolled rate and cause damage to surrounding tissue and is caused by mutations in the cells’ DNA.

  ● Though some cancer-causing mutations are inherited from parents, most cancer-causing mutations emerge over the course of a person’s life and are localized to the tumor. These localized mutations are also known as somatic mutations.

  ● The human genome is over 6.27 billion base pairs long and cannot be read from end to end; instead it is read in small pieces that are aligned to best-matching sequences in the human reference genome. Many mutation-calling algorithms will use these alignments to find mutations, but this method is less effective for larger insertion/deletion mutations. Because of complications like this, mid-sized insertion/deletion mutations are often ignored in other studies.

  ● To detect these mutations, I built a pipeline incorporating three tools (Pindel, ABRA, and Platypus) that use methods designed to capture them. Not only is this pipeline useful in analyzing tumor-normal data, it can also provide a more complete

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  Vulnerabilities of Gender Non-Conforming Children Within the ABCD Study

  Mitchell D. Felix and Erik J. Nelson

  • In the broad field of childhood health and development, understanding and caring for society’s most vulnerable populations is vital. One such at-risk population is gender non-conforming children, individuals whose gender expression does not conform to conventional societal norms.1

  • Gender non-conforming individuals are likely to be subject to increased discrimination and violence,2 with non-conforming youths specifically seeing elevated rates of harassment by peers and childhood abuse.3,4

  • The intersection between gender identity and health outcomes is an emerging field with important applications for policy, practice and societal attitudes.

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  Carbon-infiltrated carbon nanotube surfaces affect Pseudomonas aeruginosa biofilm development

  Jenny Finlinson, Lucy C. Bowden, and Bradford K. Berges

  • ~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

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  ADHD medication is more potent and effective during ovulation

  Laurenf@byu.edu Ford

  • Women escalate psychostimulant abuse more quickly than men. Women who are prescribed psychostimulants for ADHD report fluctuations in drug efficacy that correspond to their menstrual cycle.

  • In rodents, females acquire psychostimulant addiction more readily and release more dopamine (DA) in the dorsal striatum, an effect mediated by estrogen.

  • However, the impact of the estrous cycle in the nucleus accumbens (NAc), a core region for learning and addiction in the ventral striatum, is underexplored.

  • Here, we examine cocaine, methylphenidate (Ritalin), and methamphetamine (Desoxyn) effects on DA transmission in male and naturally-cycling female mice.