2020 Abstracts

Sirrine, Michael; Grose, Julianne (Brigham Young University)
Faculty Advisor: Grose, Julianne (Brigham Young University, Microbiology and Molecular Biology)

PAS kinase is a serine/threonine protein kinase known to regulate the pivotal switch between cellular respiration and lipid biosynthesis. One substrate of PAS kinase is Cbf1, a known transcription factor which regulates lipid biosynthesis in yeast and mammalian cells (human homolog USF1). USF1 is associated with hyperlipidemia and hypercholesterolemia in several GWAS studies. We have recently identified and characterized a role for Cbf1 in the regulation of respiration as well, making it a key player in partitioning cellular resources towards respiration versus lipid metabolism. The goal of this proposal is to use the powerful tools of yeast genetics to identify physical interactors of Cbf1 in order to characterize the molecular mechanisms of its action.

Lemmon, Skyler; Chaston, John (Brigham Young University)
Faculty Advisor: Chaston, John (Life Sciences, Plant and Wildlife Sciences)

Over the course of the last year, I have dedicated most of my time in the lab to learning about CRISPR/Cas9 and practicing the laboratory techniques that are necessary to make genetic changes in Drosophila melanogaster. Here I aim to expand on that expertise by applying CRISPR to study a genetic question: how the microbial composition of the D. melanogaster microbiome is affected by the modification of 4 specifically selected genes in flies from Florida and Maine. For each of the selected genes, the Florida fly allele will be put into the Maine fly genome and the Maine fly allele will be put into the Florida fly genome. The microbiome composition of these two new flies will be compared against the original lines in a factorial design. Embryos will be injected with the necessary plasmids for a double-stranded cut to take place. After injection, homology dependent repair that will incorporate the new allele. Sanger sequencing will be used to screen for successful knock-in of the allele. Finally, the concentrations of each type of bacteria found in the microbiota of the flies will be measured and compared against the flies from which the allele came from.

Marchant, Nathan; Marchant Erik; Elison, Weston; Herring, Jacob; Yang, Haokun; Tessem, Jeffrey; Hancock, Chad (Brigham Young University)
Faculty Advisor: Hancock, Chad (Brigham Young University; Nutrition, Dietetics, and Food Science); Tessem, Jeffrey (Brigham Young University; Nutrition, Dietetics, and Food Science)

Purpose: To analyze the effect of the Nr4a3 gene on respiratory capacity of mitochondria in skeletal muscle of mice on a normal or high fat diet.

Methods: Nr4a3-/- and WT mice were fed a normal chow (NC) or high fat diet (HF) for at least 20 weeks. After euthanasia, soleus muscle was harvested and wet weight was measured and prepared for respirometry. Mitochondrial respiration was evaluated using an Oroboros Oxygraph Respirometer. Respiratory capacity comparisons were made with a two-way ANOVA and Tukey multiple comparison test.

Results: Oxygen consumption is reported as pmol/(s*mg wet tissue) and statistics are represented as mean ± SEM. In the WT male mice there was a decrease in coupled complex I supported respiration in HF vs. NC diet (25.9 ± 7.3 vs. 64.5 ± 5.0, p=0.004). In the HF WT group there was also a decrease in uncoupled respiration (61.4 ± 15.0 vs. 107.8 ± 7.1, p=0.0004) compared to NC WT. In female mice there was also a decrease between HF WT and NC WT in complex I (28.2 ± 3.7 vs. 57.4 ± 5.7, p=0.0005) and uncoupled respiration (87.1 ± 7.1 vs. 119.4 ± 8.9, p=0.0001). However, there was no significant difference between the WT NC mice and either of the Nr4a3-/- groups. Coupled complex I and uncoupled respiration states in both Nr4a3-/- groups were not significantly different from WT.

Conclusion: Feeding mice a high fat diet impairs proper mitochondrial function in muscle when compared to a normal chow diet. The decrease in respiration from the HF diet is dependent upon the function of the Nr4a3 gene, as no decrease was observed in Nr4a3-/- mice.

Domyan, Eric; Godoy, Daniela; Gardiner, Kylan (Utah Valley University)
Faculty Advisor: Domyan, Eric (Science, Biology)

Pigmentation is one of the main traits we notice when we look at something, whether it be a flower, an animal, or another human. Variation in pigmentation arises when random mutations affect the function of a gene involved in pigmentation production. In this research our goal is to understand a specific mutation that happens in Pigeons which involves the TYRP1 gene.
The TYRP1 gene instructs the making of the tyrosinase-related protein. This enzyme is located in melanocytes, which are cells that produce melanin. Studies suggest that this enzyme may help stabilize tyrosinase, which is responsible for the first step in melanin production.
TYRP1 has a signal peptide which directs the protein to the ER (endoplasmic reticulum) where the signal peptide is removed before the mature protein is trafficked to melanosomes to perform its normal function. The Ash-red mutation, however, prevents removal of the signal peptide, which somehow results in pheomelanin synthesis (red) instead of eumelanin synthesis (dark blue). These findings suggest that the Ash-red mutation is causing the TYRP1 protein to perform a new function. The goal of this project is to better understand the synthesis and trafficking of TYRP1 throughout the cell organelles.
To study this, we plan to use transgenesis to express normal, or Ash-red versions of TYRP1 protein in melanocytes, label the different intracellular compartments using an immunostain, and determine whether normal or Ash-red TYRP1 proteins are being sent to the same, or different compartments of the cell.

Wilson, Seth; Taylor Adam; Bursell, Madeline; Frandsen, Paul; Stewart, Russell; Steeneck, Amy (Brigham Young University)
Faculty Advisor: Frandsen, Paul (Brigham Young University, Plant and Wildlife Sciences)

Caddisflies (Insecta: Trichoptera) have evolved to produce silk with adhesive and elastic properties in aqueous environments. The silk is used in several ways by different species within the order such as case making, retreat making and using the silk as an anchor in the stream. Previous research on caddisfly silk has focused on understanding the evolutionary changes in the H-fibroin gene, the main protein found in caddisfly silk, which underlies the structural transformation behind these phenotypic properties that allow for diverse usage of the silk across the order (Ashton et al. 2013). Understanding the genetic foundation of the silk is crucial to understanding the phenotypic interactions that determine the unique qualities of caddisfly silk. An accurate assembly of the caddisfly genome will allow us to resolve the H-fibroin gene that plays an integral role in the formation of the caddisfly silk. Next-generation sequencing, Oxford Nanopore, and PacBio will allow us to sequence long reads that can span repetitive regions of the genome. These regions have made it difficult to resolve the H-fibroin gene as there are many repetitive motifs found in the gene. We will combine this next-generation sequencing with second-generation sequencing, Illumina and Sanger Sequencing to optimize the assembly. In this study, we used a combination of next-generation sequencing technologies to assemble the complex H-Fibroin gene in order to look at the underlying genetic structure of the silk protein. We identified unique repetitive motifs in the gene that contribute to the silk's adhesive strength and elasticity when in aqueous environments.

Errigo, Isabella; Abbott, Benjamin; Reimer, Jessica; Glenn, Jeff; Chaney, Robert; Freeman, Andrew; Frei, Rebecca; Howe, Peter, Mendoza, Daniel; Kelly, Kerry; Summers, Laura; Johnston, James; Carter, Thom; Bratsman, Samuel; Stacey, Audrey; Wilson, Derrek; Lange, Leslie (Brigham Young University)
Faculty Advisor: Abbott, Benjamin (Life Sciences, Plant and Wildlife Sciences)

Recent medical and economic research has found that air pollution causes much more damage to our health and economy than previously understood. Globally, 16% of all deaths are attributable to air pollution—15 times more than from all wars and other forms of violence. However, translating these research findings into policy and behavior change at local levels remains a major challenge, partially because of mismatch between the spatial scale of the air pollution research (often national or global) and governance frameworks (typically multi-scale from local to regional). Here, we tested the effectiveness of expert assessment as a tool to resolve research-policy mismatch. We distributed a questionnaire to over 80 researchers living in Utah, asking for quantitative estimates of human health and economic costs of air pollution, and recommendations for what policy actions would be most effective at reducing those costs. Expert responses of air pollution costs varied widely, but were consistently higher than recent public health studies, indicating that experts were including a more complete suite of factors, or that they were biased. We discuss the response of Utah policymakers to these results and present a framework of involving local researchers to increase the assimilation of data into decision making.

Escarate, Ashley; Brunetti, Bryce; Conway, Matthew (Utah Valley University)
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology); Slezak, Cyrill (Utah Valley University, Physics)

Medical device-associated infections can lead to serious complications affecting the health of patients. Electrohydraulic shockwave treatments have shown bactericidal activity in some microorganisms. Biofilms are structures formed by microorganisms enclosed in an extracellular matrix. They form on a variety of surfaces protecting the microorganisms from antibiotics and facilitating their growth. This can result in a high rate of drug resistance and in many cases result in chronic bacterial infections.
Previously determined MIC50 concentrations of vancomycin had little effect on biofilms at twelve hours of treatment when not paired with shockwave therapy. This research evaluates the synergistic effect of different concentrations of vancomycin and shockwaves after twelve and twenty four hours of treatment given that vancomycin has shown time-dependent activity. Biofilms were grown in 96 well plates and the corresponding treatments were applied. XTT and Crystal Violet assays were used to quantify and qualify the presence of the biofilm and the antibiosis effect. The results of this experiment will be discussed in detail. A better understanding of the synergistic effects of antibiotics and shockwave therapy may lead to a more effective treatment of biofilm and device-associated infections.

Stoner, David; Clark, Debbie; Bufton, Ali (Utah State University)
Faculty Advisor: Stoner, David (S.J. & Jessie E. Quinney College of Natural Resources, Wildland Resources Department)

A challenge facing Utah mule deer is habitats with older shrubs and little to no regeneration of young plants, or habitats being replaced with cheatgrass (Bromus tectorum)—both in critical winter ranges. Forested habitats provide cover but when there is little understory, there isn't enough forage. Hunting funds the management of big game animals. If there is inadequate funding, there will not be funding for habitat. Thus population objectives will not be met. Mule deer (Odocoileus hemionus) may alter activity schedule during the hunting season by selecting restricted hunter access areas, including agricultural lands. Here we test the hypothesis that deer alter activity schedules in space (accessible and WILD sites) and time in response to human presence. We defined WILD as being further than 100 meters away from a human or OHV trail, or road. Our research question asks if accessible roads have an effect on mule deer activity schedule in response to hunting pressure, as indexed by access differences. We predicted that increased human activity during the hunting season would cause reduced deer activity during daylight. We expect more deer detections in September, less in October (hunting season), and an increase in November during the rut. Spatially we expect higher buck detection rates in remote areas, with no change in activity schedule, or are active in the day. The study area is in the Bear River Range east of Logan, Utah. We are using Before-After-Control-Impact (BACI) Sampling Design. We used camera trap data from October 2017 through December 2017 to measure (1) detection rates of bucks (photos/camera-day), and (2) activity times (diurnal, crepuscular, or nocturnal) by sex-age class. We controlled for habitat type by grouping cameras within common elevation bands and plant communities. Reduced hunter success may result in decreased hunting interest with economic implications for mule deer conservation.

Kelleher, Justin; Costa, Rodrigo; Potts, Wayne (University of Utah)
Faculty Advisor: Potts, Wayne (University of Utah, School of Biological Sciences)

Influenza A Virus (IAV) is a highly adaptable pathogen with the ability to cross over into different host species. Theory predicts that when a pathogen adapts to specific host genotypes, it loses virulence when encountering novel genotypes. This study focuses on whether influenza virulence is lost when infecting novel host genotypes. To test whether influenza adaptation to different genotypes leads to viral fitness and virulence tradeoffs, IAV was adapted to 2 strains of mouse via serial passage and subsequently tested against the host of passage (familiar) and in the novel host (unfamiliar). After 10 rounds of passage, IAV virulence increased in the familiar host. However, when adapted IAV strains were used to infect unfamiliar hosts, influenza virulence effects were mitigated, but not to a statistically significant degree. This study helps elucidate why different barriers to infection, including novel host genotypes, affect IAV virulence and fitness. Studying genotype-dependent virulence tradeoffs focuses can further research on more effective Influenza control in epidemiological, agricultural and conservation settings.

Olsen, Lindsey; Frandsen, Paul (Brigham Young University)
Faculty Advisor: Frandsen, Paul (Life Science, Plant and Wildlife)

Trichoptera (caddisflies) have evolved to become the most diverse, exclusively aquatic insects, yet many of the genomic changes that contribute to Trichoptera's the success of this order of insects are still unknown. Trichoptera and Lepidoptera (moths and butterflies) are reciprocally monophyletic meaning that they both share their most recent common ancestor. Despite being closely related, Trichoptera have evolved into the most diverse, exclusively aquatic insects, whereas, Lepidoptera have evolved to become a diverse, almost exclusively terrestrial insect (Holzenthal et al. 2007). Trichoptera and Lepidoptera are the subjects of scientific inquiry because they are both capable of spinning silk. Trichoptera produce silk as larvae and use it to make cases or fixed retreats. Trichoptera silk is of particular interest because its properties allow for it to be an underwater adhesive. While other research has focused primarily on the evolution of Trichoptera silk, little research has been done to identify the evolutionary innovations that allowed Trichoptera to adapt and diversify in an aquatic environment. Our research focuses on identifying the genomic basis of their evolutionary innovations. We report the genome annotation of four newly sequenced Trichoptera species Hesperophylax magnus, Parapsyche elsis, Philanisus plebeius, and Rhyacophila brunnea. These annotations will reveal levels of homozygosity, conserved elements, and gene duplications. We then conducted a genome-wide search for gene family expansions and retractions using CAFE, in order to identify genomic regions that could contribute to Trichoptera's unique qualities and evolutionary history.

Holzenthal R. W., R. J. Blahnik, A. L. Prather, and K. M. Kjer, 2007 Order Trichoptera Kirby, 1813 (Insecta), Caddisflies*. Zootaxa 1668: 639—698. https://doi.org/10.11646/zootaxa.1668.1.29

Thatcher, Spencer; Eyere, Gloria (Dixie State University)
Faculty Advisor: O'Brien, Erin (College of Science, Engineering, and Sciences; Biological Sciences Department)

Dwarf bear-claw poppies (Arctomecon humilis Coville) are an endemic species of wildflower in Washington county Utah. These poppies only flower for about a month during the summer. There are currently seven known locations where these poppies are found. Conservation efforts to protect these populations includes research to understand the reproductive success of each site. Populations with low reproductive success may indicate the need for additional efforts or interventions to save this unique species. Four specific locations were monitored over a three-year period. Poppies in these areas were tagged and studied during their flowering seasons and individual inflorescences were bagged and collected to determine struggling locations and their correlating issues related to population decline. Seeds were split into two groups: immature and mature and were weighed and counted. A large percentage of immature seeds may indicate a resource or pollinator issue for the population. A low overall seed production may indicate that a resource limitation or other stressor is reducing the population viability.

Ekpo, Idongesit; Yates, Joshua; Tessem, Jeffery; Hill, Jonathan (Brigham Young University)
Faculty Advisor: Tessem, Jeffery (Life Sciences; Nutrition, Dietetics, and Food Science); Hill, Jonathan (Life Sciences, Physiology and Developmental Biology)

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity and oxidative stress induced by reactive oxygen and nitrogen species. Current treatment methods for diabetes are not curative and do not help us understand its pathogenesis. A more effective method involves exploring the pathogenesis of diabetes by probing the genetic variation involved in diabetes so that we can understand the disease better and develop curative methods to combat it. Gene therapy is a method for determining genetic variation in disease and CRISPR-Cas9 is a gene-editing tool that can be used. Because of its convenience, CRISPR-Cas9 has been used to create many forward genetic screens. We use the CRISPR-Cas9 tool to create a knockout forward genetic screen of all the genes in the INS-1 Ꞵ-cell line that are required for _-cell survival of metabolic stressors. We hypothesize that the gene knockouts generated by the CRISPR-Cas9 system will help us identify genes that are involved in the mechanistic pathways of these metabolic stressors. Here we present the results of our forward genetic screen.

Caten, Reilly; Valentine, Julie; Miles, Leslie (Brigham Young University)
Faculty Advisor: Valentine, Julie (Brigham Young University, Nursing); Leslie, Miles (Brigham Young University, Nursing)

In the United States, there is a push to mandate submission and testing of all sexual assault kits. A typically-overlooked benefit of testing sexual assault kits is the exoneration of wrongfully accused suspects. Sexual assault kits include DNA samples from the victim of sexual assault, and occasionally are submitted with DNA samples collected from the identified suspect for comparison. Inclusion of suspect samples is beneficial because it can lead to a DNA match with samples collected from the victim or exclude the suspect as the source of DNA. For a sexual assault kit to meet the criteria for "excluded the suspect" a DNA profile had to be developed from analysis of the sexual assault kit evidence which excluded the named suspect with submitted DNA sample.

A large retrospective study of 2,727 sexual assault kits with completed DNA analysis found 66 cases in which DNA findings excluded the suspect. Findings will be presented on descriptive data on cases in which the named suspect was excluded: relationship between victim and suspect, victim loss of consciousness/awareness at time of assault, alcohol/drug use during the assault, suspected drug-facilitated sexual assault, and multiple perpetrator sexual assault. Each of these cases excluding a suspect represents an individual who was erroneously identified, but DNA analysis findings excluded the identified suspect.

Testing sexual assault kits uses science to aid in the establishment of justice. Sexual assault kit testing transcends accusations and labeling to provide factual evidence supporting the claims of the innocent, whether they are identified as victim or suspect. Additionally, the liberation of an unjustly accused suspect promotes the correct identification and conviction of the responsible perpetrator. Thus, mandated testing of sexual assault kit promotes justice for victims of sexual assault and innocent suspects alike.

Jackson, Ryan; Miller, Charles (Utah State University)
Faculty Advisor: Jackson, Ryan (College of Science, Chemistry and Biochemistry Department); Miller, Charles (College of Engineering, Biological Engineering Department)

The concept of real time species identification in situ is a long time researchers dream. This dream now lies within reach due to the recent innovation of nanopore sequencing technology. These machines, with their small size and powerful computing capability, have made it possible to preform 16s and whole genome sequencing, with a setup that can fit in a backpack. Not only will this increase convenience of sampling for researchers, but a recent study in Wales has shown that sampling on site may help to identify closely related organisms at a greater level of accuracy (Parker, 2017). If sampling in the field really can give more accurate results, field sequencing may help to identify an extraordinarily large amount of biodiversity and genetic pathways.
One obstacle that stands in the way of this technology becoming more accessible across the globe is the lack of scientific literature on how to build the infrastructure necessary to sample on site. This study aims to construct a complete, self-contained kit with which you could field sequence. I have, currently at my disposal, a portable thermocycler, a nanopore sequencer, and computer designed with a workflow to do real time sequencing analysis. Using this technology already available, we aim to round out the kit with the necessary reagents, and structure to house the equipment. We will provide in depth analysis of the equipment, reagents, and all other materials provided to sequence a sample in any given location.

Lauren Schagel; Julie Valentine; Leslie Miles (Brigham Young University)
Faculty Advisor: Valentine, Julie (Brigham Young University, Nursing); Miles, Leslie (Brigham Young University, Nursing)

Question: What is the impact of time between assault and evidence collection on the development of CODIS eligible DNA profiles?

Learning Overview/Synopsis: After attending this presentation, attendees will understand the length of time between sexual assault and evidence collection can be extended to five to six days post-assault and develop an eligible STR DNA profile.

Impact on the Forensic Science Community: This presentation will impact the forensic community by providing individuals with knowledge about the length of time in which victims can receive a sexual assault forensic examination (SAFE) to obtain a DNA profile of their perpetrator.

Synopsis/Abstract: The methodology of the study is an exploratory, retrospective design of over 2,700 submitted and analyzed sexual assault kits from a Mountain West state in the United States. Review of the current literature on time between assault and evidence collection indicate male DNA (Y-STR DNA) can be recovered up to 7 days post-coitus from a cervico-vaginal swab and develop a Y-STR profile.

Findings: In our large-scale, retrospective study of 2,727 sexual assault kits, probative STR DNA CODIS eligible profiles were developed in 39% of kits. Generalized estimating equation (GEE) logistic regression analysis found that for every 24 hours that passes between assault and SAFE, there is a 10% reduction in the development of a CODIS eligible DNA profile. The longest length of time between assault and exam and development of CODIS eligible profile in our study was 122.5 hours, over 5 days. This finding supports the testing of DNA samples collected five to six days post sexual assault due to the possibility of developing a CODIS eligible profile.

Conclusion: This retrospective study is impactful due to large-scale of the sample size. The 2,727 sexual assault kits used in this study are representative of what sexual assault looks like in modern society.

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.