Life Sciences
High-Fat Diet Induces Nr4a3-Dependent Decrease in Respiratory Capacity of Mouse Soleus Muscle
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.
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.
Human health and economic costs of air pollution in Utah: an expert assessment
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.
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.
Influenza and Cancer: Shared Pathways and the Potential for New/Repurposed Therapeutics.
Edvalson, Logan; Davis, Morgan; Busath, David (Brigham Young University)
Faculty Advisor: Busath, David (Life Sciences, Physiology & Developmental Biology)
A significant research focus in influenza pathogenesis has been directed towards growth factor receptor tyrosine kinases (RTKs) and their respective phosphorylation cascades. Several recent studies have implicated RTK signaling cascades, that are classically associated with cancer, with increased viral titer. A portion of these studies have focused on early segments of the signaling cascade while others' efforts focus in the late segments. Experiments performed in our lab have identified two receptor pathways—PDGF and VEGF—that, when the receptor inhibited, reduces the efficiency of the influenza virus. These data were achieved using compounds, and variants of compounds, already approved for human use in cancer. Although the drug oseltamivir is already approved for influenza treatment, there is concern for the development of viral drug resistance. The introduction of several types of infection blockers similar to the ones identified by our, and others, laboratories can mitigate viral resistance; like the introduction of several types of antibiotics has reduced bacterial resistance. We hypothesize that these pathways work in multiple parts of the infection cycle ranging from viral endocytosis to the budding off of new virions. Experiments are now under way to determine the specific interactions in these pathways that are important in the viral life cycle.
Faculty Advisor: Busath, David (Life Sciences, Physiology & Developmental Biology)
A significant research focus in influenza pathogenesis has been directed towards growth factor receptor tyrosine kinases (RTKs) and their respective phosphorylation cascades. Several recent studies have implicated RTK signaling cascades, that are classically associated with cancer, with increased viral titer. A portion of these studies have focused on early segments of the signaling cascade while others' efforts focus in the late segments. Experiments performed in our lab have identified two receptor pathways—PDGF and VEGF—that, when the receptor inhibited, reduces the efficiency of the influenza virus. These data were achieved using compounds, and variants of compounds, already approved for human use in cancer. Although the drug oseltamivir is already approved for influenza treatment, there is concern for the development of viral drug resistance. The introduction of several types of infection blockers similar to the ones identified by our, and others, laboratories can mitigate viral resistance; like the introduction of several types of antibiotics has reduced bacterial resistance. We hypothesize that these pathways work in multiple parts of the infection cycle ranging from viral endocytosis to the budding off of new virions. Experiments are now under way to determine the specific interactions in these pathways that are important in the viral life cycle.
Mapping the Potential Distribution of an Invasive Plant, Lythrum salicaria, using Crowd-Sourced Survey Data.
Wertz, Parker (Weber State University)
Faculty Advisor: Dorsey, Bryan (Weber State University, Geography)
Prevention and predicting spread is the best method of control against invasive species. Land managers require accurate and reliable methods for containment and eradication to prevent land cover change and loss of biodiversity. Ecological niche models exist and are used by ecologists to map habitat suitability, but many rely on presence-absence samples which are difficult to obtain. Maximum entropy species distribution modeling (Maxent) is a popular model that has been increasingly used since it can make valid predictions using presence-only data. Many studies have used Maxent to model species distributions, but few have done so with crowdsourced data since it is more likely to be bias and unreliable. The purpose of this study is to test the robustness of Maxent using crowdsourced presence-only data on Lyrthum salicaria, a perennial herb that invades wetlands and pushes out native flora. The study is set in northern and central Utah, and uses environmental variables in climate, landcover, and topography, with landcover being the most contributive factor to the model. Model performance was very good, even with species data being bias towards areas of higher population, proving Maxent as a worthy method to use in species distribution modeling with crowdsourced species presence data. This results of this study show promise for use in modeling other invasive plants in the future.
Faculty Advisor: Dorsey, Bryan (Weber State University, Geography)
Prevention and predicting spread is the best method of control against invasive species. Land managers require accurate and reliable methods for containment and eradication to prevent land cover change and loss of biodiversity. Ecological niche models exist and are used by ecologists to map habitat suitability, but many rely on presence-absence samples which are difficult to obtain. Maximum entropy species distribution modeling (Maxent) is a popular model that has been increasingly used since it can make valid predictions using presence-only data. Many studies have used Maxent to model species distributions, but few have done so with crowdsourced data since it is more likely to be bias and unreliable. The purpose of this study is to test the robustness of Maxent using crowdsourced presence-only data on Lyrthum salicaria, a perennial herb that invades wetlands and pushes out native flora. The study is set in northern and central Utah, and uses environmental variables in climate, landcover, and topography, with landcover being the most contributive factor to the model. Model performance was very good, even with species data being bias towards areas of higher population, proving Maxent as a worthy method to use in species distribution modeling with crowdsourced species presence data. This results of this study show promise for use in modeling other invasive plants in the future.
Is behavioral lateralization in the tropical fish Xenophallus umbratilis related to morphological asymmetry?
Johnson, Erik; Johnson, Ellie; Johnson; Jerald (Brigham Young University)
Faculty Advisor: Johnson, Jerald (Brigham Young University, Biology)
It seems counterintuitive that organisms should evolve handedness (or what we might more broadly refer to as "lateralization"). Individuals who can forage equally well with both hands, who can kick equally well with both feet, who can detect stimuli and orient equally well in both directions, and so on—these individuals should be favored relative to those who are either right handed or left handed. Yet in humans, and in several other species, handedness is common, but we still no very little about why. Here we explore this question using a tropical freshwater fish species with an unusual anatomy. Males have a modified fin—the gonopodium—that they use to internally inseminate females. Interestingly, males are either right or left handed for this structure, which terminates with either a dextral or sinistral twist. In this study, we ask a simple question: is there a link between male gonopodium morphology and male behavioral lateralization. We use a detour test approach to determine how males approach different stimuli, turning either to the left or right to more clearly see each type of stimulus. We focus on how males approach potential mates, predators, and novel items. We predict that males with a dextral gonopodium will orient differently than those with a sinistral gonopodium, consistent with the idea that there is link between behavioral lateralization and morphological handedness. If true, it would suggest that reproductive morphology could be linked to brain and behavioral lateralization in vertebrates.
Faculty Advisor: Johnson, Jerald (Brigham Young University, Biology)
It seems counterintuitive that organisms should evolve handedness (or what we might more broadly refer to as "lateralization"). Individuals who can forage equally well with both hands, who can kick equally well with both feet, who can detect stimuli and orient equally well in both directions, and so on—these individuals should be favored relative to those who are either right handed or left handed. Yet in humans, and in several other species, handedness is common, but we still no very little about why. Here we explore this question using a tropical freshwater fish species with an unusual anatomy. Males have a modified fin—the gonopodium—that they use to internally inseminate females. Interestingly, males are either right or left handed for this structure, which terminates with either a dextral or sinistral twist. In this study, we ask a simple question: is there a link between male gonopodium morphology and male behavioral lateralization. We use a detour test approach to determine how males approach different stimuli, turning either to the left or right to more clearly see each type of stimulus. We focus on how males approach potential mates, predators, and novel items. We predict that males with a dextral gonopodium will orient differently than those with a sinistral gonopodium, consistent with the idea that there is link between behavioral lateralization and morphological handedness. If true, it would suggest that reproductive morphology could be linked to brain and behavioral lateralization in vertebrates.
Is Siphlonuridae Monophyletic: Phylogenetic Relationships of Minnow Mayflies (Ephemeroptera)
Backman, Natalia; Ogden, Heath (Utah Valley University)
Faculty Advisor: Ogden, Heath (Utah Valley University, Biology)
Siphlonuridae is a family of mayflies (order Ephemeroptera) that are nicknamed the "Primitive" Minnow Mayfly family. The family traditionally has consisted of four genera; Edmundsius, Parameletus, Siphlonisca, and Siphlonurus, representing twenty six described species. The family Dipteromimidae was described as a sister group to the family Siphlonuridae (Tojo & Matsukawa, 2003), however, past molecular evidence suggests that Dipteromimidae might nest within Siphlonuridae(T. H. Ogden et al., 2009; T. Heath Ogden & Whiting, 2005). This study aims to use more taxa and more molecular data in order to generate more robust phylogeny for these mayflies. Specifically our goals are to (i) test the monophyly of the family Siphlonuridae; and (ii) compare traditional Sanger sequencing loci to newly generated phylogenomic data from a targeted capture sequencing approach.
Faculty Advisor: Ogden, Heath (Utah Valley University, Biology)
Siphlonuridae is a family of mayflies (order Ephemeroptera) that are nicknamed the "Primitive" Minnow Mayfly family. The family traditionally has consisted of four genera; Edmundsius, Parameletus, Siphlonisca, and Siphlonurus, representing twenty six described species. The family Dipteromimidae was described as a sister group to the family Siphlonuridae (Tojo & Matsukawa, 2003), however, past molecular evidence suggests that Dipteromimidae might nest within Siphlonuridae(T. H. Ogden et al., 2009; T. Heath Ogden & Whiting, 2005). This study aims to use more taxa and more molecular data in order to generate more robust phylogeny for these mayflies. Specifically our goals are to (i) test the monophyly of the family Siphlonuridae; and (ii) compare traditional Sanger sequencing loci to newly generated phylogenomic data from a targeted capture sequencing approach.
Identifying Conservation Needs of Dwarf Bear-Claw Poppy Populations
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.
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.
Methylmercury exposure in orb weaver spiders (Neoscona oaxacensis) on Antelope Island State Park
Faulkner, Megan; Stoneham, Lisa; Brasso, Rebecka (Weber State University)
Faculty Advisor: Brasso, Rebecka (College of Science, Zoology)
Mercury is a toxic heavy metal that poses significant health risks to humans and wildlife. The organic form of mercury, methylmercury (MeHg), is converted from its inorganic form via microbial methylation primarily in aquatic systems. Methylmercury is dangerous because it attaches to proteins in blood and muscle and biomagnifies in food webs. The goal of this project, is to determine mercury concentrations in western spotted orb weaver spiders (Neoscona oaxacensis) collected from two sites on Antelope Island State Park. Previous studies have shown orb weavers associated with the Great Salt Lake ecosystem to accumulate significant methylmercury, connecting the aquatic and terrestrial ecosystems through a shared food web. The Great Salt Lake surrounding Antelope Island has historically shown some of the highest levels of Hg in surface waters in the United States and has both an abundance of orb weaver spiders and their preferred prey—brine flies. We tested the hypothesis that mercury concentrations in orb weaver spiders would differ between two sites on the island based on differences in environmental conditions (salinity) in the water where brine flies develop. All spiders were sexed, weighed, and individually analyzed for total mercury concentration using a Nippon MA-3000 Direct Mercury Analyzer.
Faculty Advisor: Brasso, Rebecka (College of Science, Zoology)
Mercury is a toxic heavy metal that poses significant health risks to humans and wildlife. The organic form of mercury, methylmercury (MeHg), is converted from its inorganic form via microbial methylation primarily in aquatic systems. Methylmercury is dangerous because it attaches to proteins in blood and muscle and biomagnifies in food webs. The goal of this project, is to determine mercury concentrations in western spotted orb weaver spiders (Neoscona oaxacensis) collected from two sites on Antelope Island State Park. Previous studies have shown orb weavers associated with the Great Salt Lake ecosystem to accumulate significant methylmercury, connecting the aquatic and terrestrial ecosystems through a shared food web. The Great Salt Lake surrounding Antelope Island has historically shown some of the highest levels of Hg in surface waters in the United States and has both an abundance of orb weaver spiders and their preferred prey—brine flies. We tested the hypothesis that mercury concentrations in orb weaver spiders would differ between two sites on the island based on differences in environmental conditions (salinity) in the water where brine flies develop. All spiders were sexed, weighed, and individually analyzed for total mercury concentration using a Nippon MA-3000 Direct Mercury Analyzer.
Implications of Testing Sexual Assault Kits: Justice for Suspects and Victims
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.
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.
Lichens as bioindicators for air quality in the Intermountain West - creating a model for large-scale monitoring
Smith, Hayden; Leavitt, Steve (Brigham Young University)
Faculty Advisor: Leavitt, Steve (College of Life Sciences, Biology)
Brigham Young University's Lichen Air Quality Biomonitoring Program (Herbarium of Non-Vascular Cryptogams) represents one of the largest and longest-running lichen biomonitoring programs worldwide, with nearly 500 permanent reference plots distributed across the Intermountain West. At each reference site, sensitive indicator lichens are selected for elemental analyses of 25 potential pollutants, with the aim of subsequent resampling every five to 15 years for ongoing evaluations of ecological health. Using elemental analysis (EA) data from the past 30 years, a model for large-scale monitoring has been developed with the aim to (i) improve interpretation of air quality using lichen bioindicators, (ii) establish a framework to integrate future EA samples for comparison to historical data, and (iii) develop a platform in the future to more effectively share these data with land management agencies, research groups, and the broader public. The model will be field-tested with new EA samples collected along the Wasatch Front.
Faculty Advisor: Leavitt, Steve (College of Life Sciences, Biology)
Brigham Young University's Lichen Air Quality Biomonitoring Program (Herbarium of Non-Vascular Cryptogams) represents one of the largest and longest-running lichen biomonitoring programs worldwide, with nearly 500 permanent reference plots distributed across the Intermountain West. At each reference site, sensitive indicator lichens are selected for elemental analyses of 25 potential pollutants, with the aim of subsequent resampling every five to 15 years for ongoing evaluations of ecological health. Using elemental analysis (EA) data from the past 30 years, a model for large-scale monitoring has been developed with the aim to (i) improve interpretation of air quality using lichen bioindicators, (ii) establish a framework to integrate future EA samples for comparison to historical data, and (iii) develop a platform in the future to more effectively share these data with land management agencies, research groups, and the broader public. The model will be field-tested with new EA samples collected along the Wasatch Front.
Inhibitory Effect of Probiotics on Streptococcus Agalactiae Serotypes
L'Ecuyer, Katia (Utah Valley University)
Faculty Advisor: Gazdik Stofer, Michaela (Utah Valley University, Microbiology)
Streptococcus agalactiae most commonly known as Group B streptococcus (GBS), are encapsulated gram-positive bacteria encountered in approximately 15-40% of pregnant women's urogenital and gastrointestinal tracts. While most women are asymptomatic, GBS colonization of newborns as they pass through the birth canal can lead to sepsis. GBS bloodstream infections are the leading cause of mortality and morbidity amongst infants in the United States. In recent years, several studies have examined the benefits of oral probiotics to promote a healthy vaginal flora and assessed the inhibitory activity of lactobacilli against urogenital pathogens, with mixed results. The purpose of our research is to examine the effect of Lactobacilli on the growth of different GBS serotypes in the vaginal environment using in vitro culture competition experiments. Previously published microbiome studies were used to determine the dominant species found in the vaginal microbiota. We are examining the growth rate of GBS when co-cultured with vaginal microflora species, both individually and as a mixed community. This will provide a baseline regarding what strains of GBS could easily colonize the vagina in high levels when in competition with different normal flora communities. Different species of probiotic Lactobacilli will then be added to the vaginal culture collection to examine if there is an effect on GBS growth. Our goal is to identify probiotic species that prevent or slow the growth of GBS in a vaginal community.
Faculty Advisor: Gazdik Stofer, Michaela (Utah Valley University, Microbiology)
Streptococcus agalactiae most commonly known as Group B streptococcus (GBS), are encapsulated gram-positive bacteria encountered in approximately 15-40% of pregnant women's urogenital and gastrointestinal tracts. While most women are asymptomatic, GBS colonization of newborns as they pass through the birth canal can lead to sepsis. GBS bloodstream infections are the leading cause of mortality and morbidity amongst infants in the United States. In recent years, several studies have examined the benefits of oral probiotics to promote a healthy vaginal flora and assessed the inhibitory activity of lactobacilli against urogenital pathogens, with mixed results. The purpose of our research is to examine the effect of Lactobacilli on the growth of different GBS serotypes in the vaginal environment using in vitro culture competition experiments. Previously published microbiome studies were used to determine the dominant species found in the vaginal microbiota. We are examining the growth rate of GBS when co-cultured with vaginal microflora species, both individually and as a mixed community. This will provide a baseline regarding what strains of GBS could easily colonize the vagina in high levels when in competition with different normal flora communities. Different species of probiotic Lactobacilli will then be added to the vaginal culture collection to examine if there is an effect on GBS growth. Our goal is to identify probiotic species that prevent or slow the growth of GBS in a vaginal community.
Intravenous dopamine enhancement of dopamine release in the nucleus accumbens is peripheral dopamine 2 receptor dependent
Small, Christina; Obray, J Daniel; Steffensen, Scott (Brigham Young University)
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
Recent studies have shown that administration of dopamine in the periphery (outside of the brain) produces a robust enhancement of dopamine release in the nucleus accumbens and alleviates cognitive deficits associated with schizophrenia-like and attention deficit hyperactivity disorder (ADHD)-like phenotypes in rodent models. Despite this, the mechanism whereby peripheral administration of dopamine produces these effects is unknown as dopamine does not cross the blood brain barrier. Activation of dopamine 2 receptors on circulating leukocytes encourages extravasation and can trigger production and release of cytokines such as TNF-_ and IL-10 as well as IL-1_. IL-1_ and IL-10 are both known to enhance dopamine release. In this study we demonstrate that the effects of intravenous dopamine on dopamine release in the NAc are mediated by peripheral dopamine 2 receptors. Additionally, we show that intravenous dopamine is rewarding and that these rewarding effects can be blocked by antagonism of peripheral dopamine 2 receptors. As many drugs of abuse enhance plasma dopamine levels this research elucidates a secondary pathway which may play a role in the development of substance use disorders.
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
Recent studies have shown that administration of dopamine in the periphery (outside of the brain) produces a robust enhancement of dopamine release in the nucleus accumbens and alleviates cognitive deficits associated with schizophrenia-like and attention deficit hyperactivity disorder (ADHD)-like phenotypes in rodent models. Despite this, the mechanism whereby peripheral administration of dopamine produces these effects is unknown as dopamine does not cross the blood brain barrier. Activation of dopamine 2 receptors on circulating leukocytes encourages extravasation and can trigger production and release of cytokines such as TNF-_ and IL-10 as well as IL-1_. IL-1_ and IL-10 are both known to enhance dopamine release. In this study we demonstrate that the effects of intravenous dopamine on dopamine release in the NAc are mediated by peripheral dopamine 2 receptors. Additionally, we show that intravenous dopamine is rewarding and that these rewarding effects can be blocked by antagonism of peripheral dopamine 2 receptors. As many drugs of abuse enhance plasma dopamine levels this research elucidates a secondary pathway which may play a role in the development of substance use disorders.
Loading a Novel Anti-biofilm Compound into Polyurethane Foam for Use in Negative Pressure Wound Therapy
Rawson, Kaden; Nueberger, Travis; Looper, Ryan; Sebahar, Paul; Williams, Dustin (University of Utah)
Faculty Advisor: Williams, Dustin (Engineering, Bioengineering)
Negative pressure wound therapy (NPWT) is commonly used to treat high energy, traumatic battlefield-related injuries, typically caused by an explosion. NPWT may be applied in the field at the time of injury or in the operating room as a therapeutic measure. Wounds are susceptible to contamination from the soil, which contains high amounts of bacteria (>10^9 colony forming units (CFU)/g of material). Greater than 99% of wild-type bacteria favor the biofilm phenotype in the natural world. Biofilms are aggregates of bacteria that are more resistant to traditional antibiotics due to their altered phenotypic and metabolic expressions. Thus, developed biofilms can potentially contaminate these wounds and lead to chronic infection. Furthermore, the lattice structure of polyurethane (PU) foam used in NPWT can potentially harbor and encourage increased biofilm growth. Since the introduction of NPWT as a standard of care for soldiers in 2004, "superficial and deep infections of soft tissue remain a clinical concern after sustaining combat-related trauma [while] using NPWT." To date, GRANUFOAM Silver by KCI is the only variation of PU foam for NPWT that possesses any degree of antimicrobial efficacy. However, silver nanoparticles are minimally effective against biofilms. Thus, the goal of this project is to develop a PU foam that is loaded with a biofilm-specific antimicrobial compound, CZ-01179 in order to decrease the rate of infection when NPWT is utilized in the field of battle.
To date, two prototypes have been developed: One prototype (V1) relies on THF and H2O to coat the Pu foam with CZ-01179 while the second prototype (V2) relies on a hydrogel scaffold to provide a sustained release of CZ-01179 over 24 hours. V1 has been shown to reduce MRSA AND A. baumanii by 7 Log10 CFU during in vitro dilution testing compared to a 1 Log10 reduction produced by GRANUFOAM Silver.
Faculty Advisor: Williams, Dustin (Engineering, Bioengineering)
Negative pressure wound therapy (NPWT) is commonly used to treat high energy, traumatic battlefield-related injuries, typically caused by an explosion. NPWT may be applied in the field at the time of injury or in the operating room as a therapeutic measure. Wounds are susceptible to contamination from the soil, which contains high amounts of bacteria (>10^9 colony forming units (CFU)/g of material). Greater than 99% of wild-type bacteria favor the biofilm phenotype in the natural world. Biofilms are aggregates of bacteria that are more resistant to traditional antibiotics due to their altered phenotypic and metabolic expressions. Thus, developed biofilms can potentially contaminate these wounds and lead to chronic infection. Furthermore, the lattice structure of polyurethane (PU) foam used in NPWT can potentially harbor and encourage increased biofilm growth. Since the introduction of NPWT as a standard of care for soldiers in 2004, "superficial and deep infections of soft tissue remain a clinical concern after sustaining combat-related trauma [while] using NPWT." To date, GRANUFOAM Silver by KCI is the only variation of PU foam for NPWT that possesses any degree of antimicrobial efficacy. However, silver nanoparticles are minimally effective against biofilms. Thus, the goal of this project is to develop a PU foam that is loaded with a biofilm-specific antimicrobial compound, CZ-01179 in order to decrease the rate of infection when NPWT is utilized in the field of battle.
To date, two prototypes have been developed: One prototype (V1) relies on THF and H2O to coat the Pu foam with CZ-01179 while the second prototype (V2) relies on a hydrogel scaffold to provide a sustained release of CZ-01179 over 24 hours. V1 has been shown to reduce MRSA AND A. baumanii by 7 Log10 CFU during in vitro dilution testing compared to a 1 Log10 reduction produced by GRANUFOAM Silver.
Micropropagation of Lepidium ostleri, an edaphic endemic plant species
DeNittis, Alyson; Larson, Joseph; Perez, June; Kopp, Olga R. (Utah Valley University)
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology)
Lepidium ostleri (Ostler's peppergrass) is an edaphic endemic plant species restricted to Ordovician limestone outcrops of the San Francisco Mountains in western Utah. L. ostleri is a species of conservation concern due to its restricted range and proximity to modern mining operations. The purpose of this research is to develop a micropropagation protocol to produce mature plants for population augmentation and introduction to support conservation efforts. De novo shoot organogenic response in tissue explants was highest with various concentrations and combinations of 6-Benzylaminopurine (BAP) and indole-3-acetic acid (IAA). In vitro and ex vitro rooting experiments were conducted on micropropagated plantlets supporting adequate number of shoots, with highest success in pulse treatments of indole-3 butyric acid (IBA). Plantlets were then acclimated to external environments for further propagation. Additional effects of different plant growth regulators, media, and growth conditions will be described. Methods for organogenesis for L. ostleri has not been published and this represents the first known instance of successful micropropagation of this rare plant species. Establishing a micropropagation protocol for L. ostleri provides valuable information for potential restoration or relocation efforts.
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology)
Lepidium ostleri (Ostler's peppergrass) is an edaphic endemic plant species restricted to Ordovician limestone outcrops of the San Francisco Mountains in western Utah. L. ostleri is a species of conservation concern due to its restricted range and proximity to modern mining operations. The purpose of this research is to develop a micropropagation protocol to produce mature plants for population augmentation and introduction to support conservation efforts. De novo shoot organogenic response in tissue explants was highest with various concentrations and combinations of 6-Benzylaminopurine (BAP) and indole-3-acetic acid (IAA). In vitro and ex vitro rooting experiments were conducted on micropropagated plantlets supporting adequate number of shoots, with highest success in pulse treatments of indole-3 butyric acid (IBA). Plantlets were then acclimated to external environments for further propagation. Additional effects of different plant growth regulators, media, and growth conditions will be described. Methods for organogenesis for L. ostleri has not been published and this represents the first known instance of successful micropropagation of this rare plant species. Establishing a micropropagation protocol for L. ostleri provides valuable information for potential restoration or relocation efforts.
How long is too long? Developing CODIS eligible profiles from sexual assault evidence collection
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.
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.
Effects of TrkB activation by alcohol withdrawal-mediated secretions of BDNF following chronic alcohol exposure
Murley, Jordan; Stockard, Alyssa; Payne, Andrew; Steffensen, Scott (Brigham Young University)
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
Brain-derived neurotrophic factor (BDNF) is implicated in varied physiological processes. Its main receptor in the central nervous system is tyrosine receptor kinase B (TrkB), and the main ligand for TrkB in the central nervous system is BDNF. It has been shown previously that activating TrkB can cause a downregulation of the chloride-exporting potassium chloride cotransporter 2 (KCC2), presumably resulting in a decreased chloride gradient. It is hypothesized that this down-regulation, caused by an increase in BDNF levels, creates hyperexcitable GABA neurons in the ventral tegmental area (VTA) due to a reduced efficacy of inhibitory currents. Here we investigate this mechanism of adaptation in the context of chronic alcohol exposure. We demonstrate that BDNF levels are elevated in the VTA during withdrawal from chronic alcohol exposure. We also observe that blocking TrkB activity decreases alcohol seeking behavior. Further, we investigate the expression patterns of KCC2 in connection with chronic alcohol administration. Additional work is underway to validate this mechanism and further elucidate its putative role in alcohol dependence.
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
Brain-derived neurotrophic factor (BDNF) is implicated in varied physiological processes. Its main receptor in the central nervous system is tyrosine receptor kinase B (TrkB), and the main ligand for TrkB in the central nervous system is BDNF. It has been shown previously that activating TrkB can cause a downregulation of the chloride-exporting potassium chloride cotransporter 2 (KCC2), presumably resulting in a decreased chloride gradient. It is hypothesized that this down-regulation, caused by an increase in BDNF levels, creates hyperexcitable GABA neurons in the ventral tegmental area (VTA) due to a reduced efficacy of inhibitory currents. Here we investigate this mechanism of adaptation in the context of chronic alcohol exposure. We demonstrate that BDNF levels are elevated in the VTA during withdrawal from chronic alcohol exposure. We also observe that blocking TrkB activity decreases alcohol seeking behavior. Further, we investigate the expression patterns of KCC2 in connection with chronic alcohol administration. Additional work is underway to validate this mechanism and further elucidate its putative role in alcohol dependence.
Ethanol enhancement of dopamine release in the nucleus accumbens and ethanol reward is mediated by peripheral dopamine 2 receptors
Diaz, Paula; Baptista, Gabriella; Obray, J Daniel; Steffensen, Scott (Brigham Young University)
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
The prevailing view is that enhancement of dopamine (DA) transmission in the mesolimbic DA system underlies the rewarding properties of alcohol. The aim of the present study was to help reconcile the relative insensitivity of DA neurons to ethanol in vitro (EC50 = 96 mM) with the sensitivity of DA neurons in vivo (EC50 = 3 mM). To do this we investigated the role of peripheral dopamine 2 receptor (D2R) mediated neuroimmune responses in ethanol enhancement of DA release in the NAc and ethanol reward. We found that systemic administration of ethanol (0.5-4.0 g/kg) markedly enhanced DA release in the NAc while pretreatment with a peripheral-only D2 receptor (D2R) antagonist blocked these effects. A place conditioning paradigm was used to test rats for ethanol preference. Administration of a peripheral D2R antagonist before ethanol conditioning trials was found to prevent acquisition of ethanol conditioned place preference. Finally, ethanol suppression of locomotor activity in rats was attenuated by domperidone pre-administration. Domperidone pre-administration did not affect ethanol impairment of motor coordination. These findings suggest that ethanol enhancement of DA release, intoxication, and ethanol reward are all mediated, at least in part, by a peripheral mechanism involving D2Rs. These results challenge the dogma regarding direct ethanol actions on mesolimbic DA transmission and potentially provides novel pharmacological targets for the treatment of alcohol use disorder.
Faculty Advisor: Steffensen, Scott (Family, Home, and Social Sciences; Psychology)
The prevailing view is that enhancement of dopamine (DA) transmission in the mesolimbic DA system underlies the rewarding properties of alcohol. The aim of the present study was to help reconcile the relative insensitivity of DA neurons to ethanol in vitro (EC50 = 96 mM) with the sensitivity of DA neurons in vivo (EC50 = 3 mM). To do this we investigated the role of peripheral dopamine 2 receptor (D2R) mediated neuroimmune responses in ethanol enhancement of DA release in the NAc and ethanol reward. We found that systemic administration of ethanol (0.5-4.0 g/kg) markedly enhanced DA release in the NAc while pretreatment with a peripheral-only D2 receptor (D2R) antagonist blocked these effects. A place conditioning paradigm was used to test rats for ethanol preference. Administration of a peripheral D2R antagonist before ethanol conditioning trials was found to prevent acquisition of ethanol conditioned place preference. Finally, ethanol suppression of locomotor activity in rats was attenuated by domperidone pre-administration. Domperidone pre-administration did not affect ethanol impairment of motor coordination. These findings suggest that ethanol enhancement of DA release, intoxication, and ethanol reward are all mediated, at least in part, by a peripheral mechanism involving D2Rs. These results challenge the dogma regarding direct ethanol actions on mesolimbic DA transmission and potentially provides novel pharmacological targets for the treatment of alcohol use disorder.
Habitat Preference of Ateles geoffroyi at La Selva Biological Station, Costa Rica
Desdames, Chloe; Smith, Mick (Salt Lake Community College)
Faculty Advisor: Seaboch, Melissa (Salt Lake Community College, Anthropology)
Spider monkeys (genus Ateles) is one of the many endangered species in Costa Rica and they can now only be found in very few places due to deforestation. It is important for conservation reasons to know what forest types spider monkeys prefer. According to prior research in Surinam, Mexico, and Bolivia, Ateles prefers primary forests (undisturbed, high canopy) over secondary forests (degraded, lower canopy). Ateles are frugivores and their habitat preference depends highly on fruit availability. Fruit is more abundant in primary over secondary forests. This goal of this study was to determine whether spider monkeys in Costa Rica have a similar habitat preference. I hypothesize that spider monkeys will be found more often in high canopy primary forests compared to secondary forests. This research was conducted at La Selva Biological Station in northeastern Costa Rica. La Selva is a protected lowland tropical rainforest consisting of both primary forest (55%) and secondary forest in various stages of regeneration. I conducted a census of Ateles geoffroyi by walking established trails, with markers every 50 meters, in May 2019. Whenever a spider monkey was spotted, the trail name, nearest meter marker, and forest type were recorded. On a census of 9 trails, five Ateles groups were located, with four of the sightings being in primary forests. My hypothesis, that Ateles geoffroyi would be found in primary over secondary forests, was supported because 80% of the sightings were in primary forests. This is especially significant because, of the 20.5 kilometers censused, only 4.6 km censused (22%) were in primary forests with the remaining 15.9 km (78%) in secondary forests. This preference for primary forests agrees with prior studies on Ateles in other Neotropical forests. This highlights the importance of conserving primary forest for the well-being of spider monkeys.
Faculty Advisor: Seaboch, Melissa (Salt Lake Community College, Anthropology)
Spider monkeys (genus Ateles) is one of the many endangered species in Costa Rica and they can now only be found in very few places due to deforestation. It is important for conservation reasons to know what forest types spider monkeys prefer. According to prior research in Surinam, Mexico, and Bolivia, Ateles prefers primary forests (undisturbed, high canopy) over secondary forests (degraded, lower canopy). Ateles are frugivores and their habitat preference depends highly on fruit availability. Fruit is more abundant in primary over secondary forests. This goal of this study was to determine whether spider monkeys in Costa Rica have a similar habitat preference. I hypothesize that spider monkeys will be found more often in high canopy primary forests compared to secondary forests. This research was conducted at La Selva Biological Station in northeastern Costa Rica. La Selva is a protected lowland tropical rainforest consisting of both primary forest (55%) and secondary forest in various stages of regeneration. I conducted a census of Ateles geoffroyi by walking established trails, with markers every 50 meters, in May 2019. Whenever a spider monkey was spotted, the trail name, nearest meter marker, and forest type were recorded. On a census of 9 trails, five Ateles groups were located, with four of the sightings being in primary forests. My hypothesis, that Ateles geoffroyi would be found in primary over secondary forests, was supported because 80% of the sightings were in primary forests. This is especially significant because, of the 20.5 kilometers censused, only 4.6 km censused (22%) were in primary forests with the remaining 15.9 km (78%) in secondary forests. This preference for primary forests agrees with prior studies on Ateles in other Neotropical forests. This highlights the importance of conserving primary forest for the well-being of spider monkeys.
Exploring the Ability of 6 Novel Phages in Reducing and Inhibiting MRSA Biofilms
MacLachlan, Aileen; Berges, Bradford (Brigham Young University)
Faculty Advisor: Berges, Bradford (Life Sciences, Microbiology and Molecular Biology)
Staphylococcus Aureus (SA) is a well-known human pathogen causing infection in hospital settings world-wide. Given that SA is becoming increasingly resistant to antibiotics, the need to discover alternative treatments is urgent. One path that SA uses to combat antibiotics is by forming biofilms. Biofilms are microbial cell communities that form on surfaces and employ a complex extracellular polysaccharide matrix to protect the bacteria. In the past, bacteriophage (phage) has been investigated as a potential alternative to treat methicillin-resistant SA (MRSA) and break down its biofilm. Recently, students from Dr. Berges' laboratory isolated 6 novel strains of phage. In a recently published paper from Dr. Berges' lab, these phages demonstrated significant reduction of planktonic strains of SA and MRSA.
In this project, we further explore the ability of these 6 phages in breaking down biofilms from hospital associated SA strains. We plan to measure the reduction of SA biofilms caused by these novel phages against a control. The reduction results will be analyzed with previous research results to detect the presence of a polysaccharide degrading enzyme for the purpose of future research. In addition, we also plan on measuring the ability of the phage in preventing biofilm formation.
Faculty Advisor: Berges, Bradford (Life Sciences, Microbiology and Molecular Biology)
Staphylococcus Aureus (SA) is a well-known human pathogen causing infection in hospital settings world-wide. Given that SA is becoming increasingly resistant to antibiotics, the need to discover alternative treatments is urgent. One path that SA uses to combat antibiotics is by forming biofilms. Biofilms are microbial cell communities that form on surfaces and employ a complex extracellular polysaccharide matrix to protect the bacteria. In the past, bacteriophage (phage) has been investigated as a potential alternative to treat methicillin-resistant SA (MRSA) and break down its biofilm. Recently, students from Dr. Berges' laboratory isolated 6 novel strains of phage. In a recently published paper from Dr. Berges' lab, these phages demonstrated significant reduction of planktonic strains of SA and MRSA.
In this project, we further explore the ability of these 6 phages in breaking down biofilms from hospital associated SA strains. We plan to measure the reduction of SA biofilms caused by these novel phages against a control. The reduction results will be analyzed with previous research results to detect the presence of a polysaccharide degrading enzyme for the purpose of future research. In addition, we also plan on measuring the ability of the phage in preventing biofilm formation.
Genomic Analyses Between Neofelis nebulosa and Neofelis diardi Aid in Conservation Efforts for Clouded Leopards
Bursell, Madeline; Dikow, Rebecca; Johnson, Warren; Koepfli, Klaus-Peter; Frandsen, Paul (Brigham Young University)
Faculty Advisor: Frandsen, Paul (Life Sciences, Plant and Wildlife Sciences)
Due to decreasing costs in genome sequencing, conservation genomics is a field that has experienced immense growth over the last few years. By comparing whole genome data within threatened and endangered populations, we can estimate important elements in conservation such as levels of homozygosity and demographic histories that reveal the level of endangerment of a species. This information informs conservation priorities and captive breeding programs. In the present study, we focus on two species of clouded leopards: Neofelis nebulosa and Neofelis diardi. N. nebulosa is a species of clouded leopard that lives in mainland southeast Asia. N.diardi inhabits the islands of Sumatra and Borneo in Indonesia. While these two species were initially thought to be a single species, evidence, such as differences in fur color and sizes of cloud markings, hint that they have diverged into two species. To shed more light on the genomic differences between them, we sequenced, assembled, and annotated whole genomes from both species. With genomes, we will explore differences in demographic histories, variation in blocks of homozygosity, and generate a whole genome phylogeny with other large cat species. Using these analyses, we share insights that will inform the conservation status of the two species.
Faculty Advisor: Frandsen, Paul (Life Sciences, Plant and Wildlife Sciences)
Due to decreasing costs in genome sequencing, conservation genomics is a field that has experienced immense growth over the last few years. By comparing whole genome data within threatened and endangered populations, we can estimate important elements in conservation such as levels of homozygosity and demographic histories that reveal the level of endangerment of a species. This information informs conservation priorities and captive breeding programs. In the present study, we focus on two species of clouded leopards: Neofelis nebulosa and Neofelis diardi. N. nebulosa is a species of clouded leopard that lives in mainland southeast Asia. N.diardi inhabits the islands of Sumatra and Borneo in Indonesia. While these two species were initially thought to be a single species, evidence, such as differences in fur color and sizes of cloud markings, hint that they have diverged into two species. To shed more light on the genomic differences between them, we sequenced, assembled, and annotated whole genomes from both species. With genomes, we will explore differences in demographic histories, variation in blocks of homozygosity, and generate a whole genome phylogeny with other large cat species. Using these analyses, we share insights that will inform the conservation status of the two species.
Great Salt Lake Halophilic Archaea: A model for mineral-entrapment of life
Bonnie K. Baxter (Westminster College)
Faculty Advisor: Baxter, Bonnie (Westminster College, Biology)
Gypsum is a calcium sulfate mineral in a hydrated form. NASA's Mars Exploration Rover, Opportunity, found veins of gypsum deposited by water in 2011(Figure 7), and gypsum has been detected on Mars as early as 2005 by the ESA's Mars Express Orbiter. On Earth, gypsum is formed in hypersaline environments, in minerals left behind when water evaporates and it can trap microorganisms in fluid inclusions. Gypsum obtained from Great Salt Lake was used to develop a method to extract halophilic archaea and culture it in the lab. Our studies show that the mineral was difficult to dissolve in aqueous microbiological media. We tested various methods of dissolution involving mechanical crushing and tested solvents including microbiological media. We also employed a variety of cultivation methods. We will present data on best practices for obtaining halophilic microorganisms from gypsum samples. The method obtained could be used to isolate potential microorganisms present in gypsum samples from Mars.
Faculty Advisor: Baxter, Bonnie (Westminster College, Biology)
Gypsum is a calcium sulfate mineral in a hydrated form. NASA's Mars Exploration Rover, Opportunity, found veins of gypsum deposited by water in 2011(Figure 7), and gypsum has been detected on Mars as early as 2005 by the ESA's Mars Express Orbiter. On Earth, gypsum is formed in hypersaline environments, in minerals left behind when water evaporates and it can trap microorganisms in fluid inclusions. Gypsum obtained from Great Salt Lake was used to develop a method to extract halophilic archaea and culture it in the lab. Our studies show that the mineral was difficult to dissolve in aqueous microbiological media. We tested various methods of dissolution involving mechanical crushing and tested solvents including microbiological media. We also employed a variety of cultivation methods. We will present data on best practices for obtaining halophilic microorganisms from gypsum samples. The method obtained could be used to isolate potential microorganisms present in gypsum samples from Mars.
Electrohydraulic Shockwaves as a Possible Treatment for Bacterial Biofilms
Brunetti, Bryce; Escarate, Ashley; Conway, Matthew; Slezak, Cyrill; Kopp, Olga (Utah Valley University)
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology); Slezak, Cyrill (Utah Valley University, Physics)
Purpose:
This study evaluates the effect of electrohydraulic shockwaves on Staphylococcus aureus biofilms. This system could be a great alternative to the use of antibiotics, and potentially life-saving technology that could save billions of dollars.
Background:
The rise of antibiotic-resistant bacteria is a global threat. Staphylococcus aureus is typically harmless, but this gram-positive species has become highly resistant and extremely pathogenic. Strains like MRSA and VRSA have the highest rate of drug resistance and are the leading cause of chronic bacterial infections via bacterial biofilms on medical devices. Biofilms are an aggregation of microbes that excrete an extracellular matrix providing an ideal environment for gene exchange and quorum sensing. Their complexity hinders the diffusion of antimicrobials. A proposed method to prevent device-associated infection is shockwave sterilization and therapy. A shockwave is a high-energy wave causing a sudden change in temperature, pressure and density in the medium. This study investigates the potential disruption of bacterial biofilms by electrohydraulic shockwaves.
Methods:
E. coli and S. aureus biofilms were grown on polystyrene plates. Biofilms were treated with shockwaves (0.19mJ/mm2, 300 pulses, 3 Hz) in a water bath and compared with those treated with Vancomycin. Cell viability was determined through XTT/menadione absorbance and specific biofilm formation through crystal violet absorbance.
Results:
Current testing has shown that electrohydraulic shockwaves have a bacteriostatic effect on biofilms. Other finding show potential for shockwaves to increase bacterial susceptibility to lower levels of antibiotics.
Conclusions:
Device-associated infections are a serious threat to patients' health. The diminishing effectiveness of antibiotics in treating and preventing infections along with evolution of mass resistance in bacteria have given rise to the term "post-antibiotic era." The better understanding of electrohydraulic shockwaves bacteriostatic effect could lead to more effective treatments for antibiotic resistant bacteria such as S. aureus.
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology); Slezak, Cyrill (Utah Valley University, Physics)
Purpose:
This study evaluates the effect of electrohydraulic shockwaves on Staphylococcus aureus biofilms. This system could be a great alternative to the use of antibiotics, and potentially life-saving technology that could save billions of dollars.
Background:
The rise of antibiotic-resistant bacteria is a global threat. Staphylococcus aureus is typically harmless, but this gram-positive species has become highly resistant and extremely pathogenic. Strains like MRSA and VRSA have the highest rate of drug resistance and are the leading cause of chronic bacterial infections via bacterial biofilms on medical devices. Biofilms are an aggregation of microbes that excrete an extracellular matrix providing an ideal environment for gene exchange and quorum sensing. Their complexity hinders the diffusion of antimicrobials. A proposed method to prevent device-associated infection is shockwave sterilization and therapy. A shockwave is a high-energy wave causing a sudden change in temperature, pressure and density in the medium. This study investigates the potential disruption of bacterial biofilms by electrohydraulic shockwaves.
Methods:
E. coli and S. aureus biofilms were grown on polystyrene plates. Biofilms were treated with shockwaves (0.19mJ/mm2, 300 pulses, 3 Hz) in a water bath and compared with those treated with Vancomycin. Cell viability was determined through XTT/menadione absorbance and specific biofilm formation through crystal violet absorbance.
Results:
Current testing has shown that electrohydraulic shockwaves have a bacteriostatic effect on biofilms. Other finding show potential for shockwaves to increase bacterial susceptibility to lower levels of antibiotics.
Conclusions:
Device-associated infections are a serious threat to patients' health. The diminishing effectiveness of antibiotics in treating and preventing infections along with evolution of mass resistance in bacteria have given rise to the term "post-antibiotic era." The better understanding of electrohydraulic shockwaves bacteriostatic effect could lead to more effective treatments for antibiotic resistant bacteria such as S. aureus.
Finding the interactors of Cbf1 and its role in the regulation of respiration and lipid biosynthesis
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.
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.
Genetic influences on the microbiome of Drosophila melanogaster using CRISPR/Cas9
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.
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.
Evaluating the Knock Out Effects of Nr4a1 and Nr4a3 on Delta cells of the Pancreas
Hess, Kavan; Herring, Jacob; Yang, Haokun; Tessem, Jeff (Brigham Young University)
Faculty Advisor: Tessem, Jeff (Brigham Young University; Department of Nutrition, Dietetics, and Food Science)
Diabetes is the seventh leading cause of death in the United States, and often accompanies other life-threating complications. There are two main types of diabetes that are both characterized by disfunction or destruction of insulin producing beta cells found in the islets of Langerhans. Islets of Langerhans are composed of endocrine hormone secreting cells, including alpha cells (glucagon), beta cells (insulin) delta cells (somatostatin), epsilon cells (ghrelin) and PP cells (pancreatic polypeptide). While alpha and beta cells make up ~90% of all the cells in the islet, delta cells comprise only ~10% and are responsible for cross talk in the islet. Delta cells regulate intra-islet cross talk through the secretion of somatostatin-14. It has been shown that Nr4a1 and Nr4a3 overexpression induces beta cell proliferation, while Nr4a1 or Nr4a3 deletion inhibits insulin secretion when challenged with glucose. Delta cells contain three times the amount of Nr4a1 mRNA than beta cells. However, no research has been done on the role of either of these transcription factors in the cross talk between the different cell types of the islet. Here we aim to show how a lack of Nr4a1 and Nr4a3 affects delta cell somatostatin release when challenged with glucose.
Faculty Advisor: Tessem, Jeff (Brigham Young University; Department of Nutrition, Dietetics, and Food Science)
Diabetes is the seventh leading cause of death in the United States, and often accompanies other life-threating complications. There are two main types of diabetes that are both characterized by disfunction or destruction of insulin producing beta cells found in the islets of Langerhans. Islets of Langerhans are composed of endocrine hormone secreting cells, including alpha cells (glucagon), beta cells (insulin) delta cells (somatostatin), epsilon cells (ghrelin) and PP cells (pancreatic polypeptide). While alpha and beta cells make up ~90% of all the cells in the islet, delta cells comprise only ~10% and are responsible for cross talk in the islet. Delta cells regulate intra-islet cross talk through the secretion of somatostatin-14. It has been shown that Nr4a1 and Nr4a3 overexpression induces beta cell proliferation, while Nr4a1 or Nr4a3 deletion inhibits insulin secretion when challenged with glucose. Delta cells contain three times the amount of Nr4a1 mRNA than beta cells. However, no research has been done on the role of either of these transcription factors in the cross talk between the different cell types of the islet. Here we aim to show how a lack of Nr4a1 and Nr4a3 affects delta cell somatostatin release when challenged with glucose.
Examining the Trafficking of Normal and TYRP1 Ash-Red Proteins' in Melanocytes
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.
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.
Genomic Assembly Targeting Repetitive Regions in the Caddisfly Genome
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.
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.
Exploring the Synergies Between Vancomycin and Electrohydraulic Shockwave in Treating Staphylococcus Aureus Biofilms
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.
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.
Habitat Accessibility May Alter Mule Deer Activity Schedule in Response to Hunting Pressure
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.
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.
Experimental adaptation of Influenza A Virus to specific host genotypes
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.
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.
Genomic Analysis Between Trichoptera and Lepidoptera Show Evolutionary Innovations Allowing Trichoptera to Adapt to an Aquatic Environment
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
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
Engineered bacterial tight junctions: a high-throughput method to characterize claudins and identify epithelial modulators
Rollins, Jay; Whitney, Jordan; Hope, Sandra; Mizrachi, Dario (Brigham Young University)
Faculty Advisor: Mizrachi, Dario (Brigham Young University, Physiology and Developmental Biology)
Epithelial and endothelial tissues form selectively permeable barriers, with the permeability largely controlled by intercellular tight junctions. Claudin (CLDN) proteins are critical components of these tight junctions, making them the gatekeepers that control the paracellular space in multicellular organisms. CLDN proteins are thus targets for studies on epithelial and endothelial absorption, to therefore learn how to regulate them for potential drug delivery or therapeutics. CLDN characterization is still in progress. Previously, the relative strength of each member of the CLDN family was unknown. Additionally, no high-throughput method to study absorption enhancers or inhibitors had been found.
Through CLDN expression in Escherichia coli, we determined the relative strength of each CLDN protein and confirmed the effects of various absorption enhancers from previous studies. Therefore, we propose that CLDN expression in Escherichia coli is a valid model for the study of tight junctions and that, through flow cytometry, it is a high-throughput method for interrogating large libraries of potential drug delivery compounds. Using CLDN 2 because of its role in cancer-metastasis prevention and its measured sensitivity towards epithelial modulators, we studied a fifty thousand compound library (DIVERSet-CL Library) to identify absorption moderators, drug delivery compounds, and possible cancer-metastasis prevention.
Faculty Advisor: Mizrachi, Dario (Brigham Young University, Physiology and Developmental Biology)
Epithelial and endothelial tissues form selectively permeable barriers, with the permeability largely controlled by intercellular tight junctions. Claudin (CLDN) proteins are critical components of these tight junctions, making them the gatekeepers that control the paracellular space in multicellular organisms. CLDN proteins are thus targets for studies on epithelial and endothelial absorption, to therefore learn how to regulate them for potential drug delivery or therapeutics. CLDN characterization is still in progress. Previously, the relative strength of each member of the CLDN family was unknown. Additionally, no high-throughput method to study absorption enhancers or inhibitors had been found.
Through CLDN expression in Escherichia coli, we determined the relative strength of each CLDN protein and confirmed the effects of various absorption enhancers from previous studies. Therefore, we propose that CLDN expression in Escherichia coli is a valid model for the study of tight junctions and that, through flow cytometry, it is a high-throughput method for interrogating large libraries of potential drug delivery compounds. Using CLDN 2 because of its role in cancer-metastasis prevention and its measured sensitivity towards epithelial modulators, we studied a fifty thousand compound library (DIVERSet-CL Library) to identify absorption moderators, drug delivery compounds, and possible cancer-metastasis prevention.
Evaluating the use of Drones for Yield Estimates, Disease Detection, and Other Problems in Agriculture
Nischwitz, Claudia; Compton, Tyson (Utah State University)
Faculty Advisor: Nischwitz, Claudia (College of Science, Biology Department)
This research evaluates the use of Unmanned Aerial Vehicles (UAVs) in agricultural applications. We center our research on early disease detection and yield estimation in vegetable crops using aerial imagery and computer software. Previous research on UAV use in agriculture has addressed topics such as soil and field analysis (Long, 2017), Precision Viticulture in Italy (Matese, et al., 2015), and other areas pertinent to agriculturists. Our research builds on previous studies and aims to provide Utah farmers with knowledge and tools to increase agricultural productivity. A DJI Inspire drone is used with both a traditional light camera and a Near-Infrared (NIR) camera. Normal and NIR images are taken at the USU Research Farm in Kaysville Utah, and over local farm fields in Utah throughout the growing season. Unhealthy plants, identified from the aerial images, are tested at the USU Plant Pathology lab to identify diseases. Computer software (ImageJ, Microsoft ICE, and MATLAB) is used to process the images and collect crop health and yield estimate data. At the end of the growing season, the yield for each crop is measured and correlated to the aerial image data to create a predictive model for yield. Some plant diseases including Beet curly top virus in tomato and powdery mildew in squash are readily identified. We find that yield estimation with aerial imagery works well for specific crops. Potato yield was correlated with plant size at different numbers of days after planting. Further tests in coming years will provide validation for these results. Our current data show that the use of an UAV can be a valuable tool for early disease detection and yield estimation in vegetable crops.
Faculty Advisor: Nischwitz, Claudia (College of Science, Biology Department)
This research evaluates the use of Unmanned Aerial Vehicles (UAVs) in agricultural applications. We center our research on early disease detection and yield estimation in vegetable crops using aerial imagery and computer software. Previous research on UAV use in agriculture has addressed topics such as soil and field analysis (Long, 2017), Precision Viticulture in Italy (Matese, et al., 2015), and other areas pertinent to agriculturists. Our research builds on previous studies and aims to provide Utah farmers with knowledge and tools to increase agricultural productivity. A DJI Inspire drone is used with both a traditional light camera and a Near-Infrared (NIR) camera. Normal and NIR images are taken at the USU Research Farm in Kaysville Utah, and over local farm fields in Utah throughout the growing season. Unhealthy plants, identified from the aerial images, are tested at the USU Plant Pathology lab to identify diseases. Computer software (ImageJ, Microsoft ICE, and MATLAB) is used to process the images and collect crop health and yield estimate data. At the end of the growing season, the yield for each crop is measured and correlated to the aerial image data to create a predictive model for yield. Some plant diseases including Beet curly top virus in tomato and powdery mildew in squash are readily identified. We find that yield estimation with aerial imagery works well for specific crops. Potato yield was correlated with plant size at different numbers of days after planting. Further tests in coming years will provide validation for these results. Our current data show that the use of an UAV can be a valuable tool for early disease detection and yield estimation in vegetable crops.
Genome-wide CRISPR-Cas9 Screen Identifies Genes Required for Ꞵ-cell Survival of Metabolic Stressors.
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.
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.
Field based real time sequencing of microbial samples via nanopore technology
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.
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.
A Proposal to Investigate Protein Expression of Rhizopus oryzae Biofilms Upon Treatment with Extracorporeal Shockwaves and Amphotericin B
Nanasi Sekona, Ashley Balderrama, Carlos Nunez, Kyle Hendricks, Tyson Hillock, and Dr. Olga Kopp (Utah Valley University)
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology)
Over the last 30 years, the incidence of fungal infections has gradually increased. Mucormycosis is a fungal infection primarily caused by Rhizopus Oryzae. The majority of patients who develop invasive mucormycosis die within 12 weeks of diagnosis. Mucormycosis is commonly treated with an antifungal agent called Amphotericin B (AMB). When used in high concentrations, AMB causes severe side effects such as nephrotoxicity. It has been reported that 99% of microbes exist as biofilm: thus, there is a direct association between mucormycosis and biofilms. Shockwave has been shown to inhibit living bacteria in biofilm, but few studies have focused on the effects of shockwave on fungal biofilm. Previous work in our lab showed that shockwaves were effective in damaging biofilms of R. oryzae; but at the same time helped promote the metabolism of surviving R. oryzae. This study aims to investigate the proteins expressed in fungal biofilms when introduced to different intensities of shockwave coupled with the treatment of AMB. This will be accomplished by culturing sporangiospores and propagating R. oryzae biofilms. Standardized biofilm will be treated with 0.5 µg/mL AMB in 1% DMSO, and/or shockwave treatment of 300 pulses at 0.19 mJ/mm2 energy density to be measured against a control group. The proteins will be extracted, determined by 2D gel electrophoresis, and identified by mass spectrometry. Studying protein expression resulting from combination therapy of extracorporeal shockwave and AMB on R. oryzae biofilm could progress research surrounding the difficulties of mucormycosis treatments. Particularly, research aimed at counteracting the antifungal and antimicrobial resistance contributed by proteins in the fungi's biofilm.
Faculty Advisor: Kopp, Olga (Utah Valley University, Biology)
Over the last 30 years, the incidence of fungal infections has gradually increased. Mucormycosis is a fungal infection primarily caused by Rhizopus Oryzae. The majority of patients who develop invasive mucormycosis die within 12 weeks of diagnosis. Mucormycosis is commonly treated with an antifungal agent called Amphotericin B (AMB). When used in high concentrations, AMB causes severe side effects such as nephrotoxicity. It has been reported that 99% of microbes exist as biofilm: thus, there is a direct association between mucormycosis and biofilms. Shockwave has been shown to inhibit living bacteria in biofilm, but few studies have focused on the effects of shockwave on fungal biofilm. Previous work in our lab showed that shockwaves were effective in damaging biofilms of R. oryzae; but at the same time helped promote the metabolism of surviving R. oryzae. This study aims to investigate the proteins expressed in fungal biofilms when introduced to different intensities of shockwave coupled with the treatment of AMB. This will be accomplished by culturing sporangiospores and propagating R. oryzae biofilms. Standardized biofilm will be treated with 0.5 µg/mL AMB in 1% DMSO, and/or shockwave treatment of 300 pulses at 0.19 mJ/mm2 energy density to be measured against a control group. The proteins will be extracted, determined by 2D gel electrophoresis, and identified by mass spectrometry. Studying protein expression resulting from combination therapy of extracorporeal shockwave and AMB on R. oryzae biofilm could progress research surrounding the difficulties of mucormycosis treatments. Particularly, research aimed at counteracting the antifungal and antimicrobial resistance contributed by proteins in the fungi's biofilm.
Transcriptomics of Ephemeroptera (Mayflies): Generation of New Data and Bioinformatics Workflow
Vilela, Ernie; Seal, Isaac; Ogden, Heath T. (Utah Valley University)
Faculty Advisor: Ogden, Thomas (College of Science, Biology Deapartment)
We are interested in using transcriptome data, generated with next generation sequencing technology, to investigate the evolutionary trends of specific genes and their associated expression in mayflies. We generated an additional transcriptome for mayflies. RNA was extracted from a freshly frozen specimen preserved in RNAlater® (Ambion) using TRIzol® Reagent (Ambion) and cDNA libraries were prepared from mRNA. RNA-seq data was generated using a paired-end protocol (PE100) on Illumina HiSeq2000 with an expected 60 million reads. In order to effectively investigate the large amount of sequences, we created a bioinformatics workflow to analyze the newly generated transcriptome data along with previous data for mayflies. The workflow consists of these main steps: Trinity (Assemblying the transcripts), Transdecoder (Identifying candidate coding regions), HMMER (Searching biological sequence databases for homologous sequences). We tested the workflow looking at opsin genes.
Faculty Advisor: Ogden, Thomas (College of Science, Biology Deapartment)
We are interested in using transcriptome data, generated with next generation sequencing technology, to investigate the evolutionary trends of specific genes and their associated expression in mayflies. We generated an additional transcriptome for mayflies. RNA was extracted from a freshly frozen specimen preserved in RNAlater® (Ambion) using TRIzol® Reagent (Ambion) and cDNA libraries were prepared from mRNA. RNA-seq data was generated using a paired-end protocol (PE100) on Illumina HiSeq2000 with an expected 60 million reads. In order to effectively investigate the large amount of sequences, we created a bioinformatics workflow to analyze the newly generated transcriptome data along with previous data for mayflies. The workflow consists of these main steps: Trinity (Assemblying the transcripts), Transdecoder (Identifying candidate coding regions), HMMER (Searching biological sequence databases for homologous sequences). We tested the workflow looking at opsin genes.
A Study of the Changes in the Oral Microbiome of Horses by Age Group
Forbush, Micah; Gold, Roger (Southern Utah University)
Faculty Advisor: Gold, Roger (Southern Utah University, Biology)
The health of a horse's teeth and oral cavity is strongly correlated with the horse's overall health and well-being. As a horse ages the oral cavity undergoes many distinct physical changes, which may lead to changes in the composition of the oral microbiome as well. While there has been extensive research performed on the oral microbiomes of healthy horses compared to horses with various oral diseases, very little is known about normal changes to the horse oral microbiome as they age. The aim of this study was to use high-throughput sequencing to compare the oral microbiomes of horses in different age categories. Total genomic DNA was isolated from oral swabs taken from horses in the 7 day-old, 1-7 years old, 8-15 years old and 16+ years old age categories. The V3-V4- region of the 16S rRNA gene was amplified by PCR and amplicons were submitted for paired-end sequencing on the Illumina HiSeq system. Sample reads were analyzed using the QIIME 2.0 microbiome bioinformatics platform and overall bacterial diversity was compared among age classes.
Faculty Advisor: Gold, Roger (Southern Utah University, Biology)
The health of a horse's teeth and oral cavity is strongly correlated with the horse's overall health and well-being. As a horse ages the oral cavity undergoes many distinct physical changes, which may lead to changes in the composition of the oral microbiome as well. While there has been extensive research performed on the oral microbiomes of healthy horses compared to horses with various oral diseases, very little is known about normal changes to the horse oral microbiome as they age. The aim of this study was to use high-throughput sequencing to compare the oral microbiomes of horses in different age categories. Total genomic DNA was isolated from oral swabs taken from horses in the 7 day-old, 1-7 years old, 8-15 years old and 16+ years old age categories. The V3-V4- region of the 16S rRNA gene was amplified by PCR and amplicons were submitted for paired-end sequencing on the Illumina HiSeq system. Sample reads were analyzed using the QIIME 2.0 microbiome bioinformatics platform and overall bacterial diversity was compared among age classes.
A Novel Natural Product PIM3 Inhibitor with Anti-Cancer Activity
Fazio, Nicholas; Russell, Michael; Krapohl, John; Andrus, Brayden; Hansen, Marc (Brigham Young University)
Faculty Advisor: Hansen, Marc (Brigham Young University, Physiology and Developmental Biology)
PIM 3 is a proto-oncogene with serine/threonine kinase activity that can prevent apoptosis, promote cell survival and protein translation. Abnormal PIM3 activity contributes to tumorigenesis by phosphorylation of targets that release anti-apoptotic proteins. Pathological PIM3 expression is common in pancreatic and prostate cancer. Inhibiting this kinase activity can be used to therapeutically suppress uncontrolled cell growth in cancerous tissues. Synthetic inhibitors are being developed as therapeutics to treat PIM3 related disorders. Compounds derived from plants and natural sources have therapeutically-relevant biological activity. Additionally, they often well tolerated, making them important starting points for drug discovery efforts. A less widely used approach to discover the biological activity of molecules is built around using a large scale in-silico molecular screening, which has emerged as a critical drug discovery tool. Here, we screen a large (>100,000 compound) virtual library of natural product compounds for binding in the PIM3 ATP binding site, then validate compounds with using cell-based and immuno-based assays. This approach reveals PIM3 inhibition by a saponin scaffold, which suggests potential utility as a therapeutic or as a lead for further optimization.
Faculty Advisor: Hansen, Marc (Brigham Young University, Physiology and Developmental Biology)
PIM 3 is a proto-oncogene with serine/threonine kinase activity that can prevent apoptosis, promote cell survival and protein translation. Abnormal PIM3 activity contributes to tumorigenesis by phosphorylation of targets that release anti-apoptotic proteins. Pathological PIM3 expression is common in pancreatic and prostate cancer. Inhibiting this kinase activity can be used to therapeutically suppress uncontrolled cell growth in cancerous tissues. Synthetic inhibitors are being developed as therapeutics to treat PIM3 related disorders. Compounds derived from plants and natural sources have therapeutically-relevant biological activity. Additionally, they often well tolerated, making them important starting points for drug discovery efforts. A less widely used approach to discover the biological activity of molecules is built around using a large scale in-silico molecular screening, which has emerged as a critical drug discovery tool. Here, we screen a large (>100,000 compound) virtual library of natural product compounds for binding in the PIM3 ATP binding site, then validate compounds with using cell-based and immuno-based assays. This approach reveals PIM3 inhibition by a saponin scaffold, which suggests potential utility as a therapeutic or as a lead for further optimization.
Deep learning for image segmentation
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.
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.
Development of a New Molecular Predictor for Risk of Melanoma Brain Metastases
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.
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.
Effect of Mercury Chloride and Methyl Mercury
Villanueva,Xitlalli; Berthelemy Nicole (Weber State University)
Faculty Advisor: Berthelemy, Nicole (Weber State University, Zoology)
Introduction: Mercury, originating from mining and industrial activity, has been accumulating in the Great Salt Lake water and has contaminated its food web. Some of the mercury chloride (HgCl) is transformed by benthic bacteria to the more toxic monomethyl mercury (MeHg). While the effect of HgCl on the brine shrimp Artemia franciscana has been described, little is known about the effects of MeHG on this shrimp, except that it is more toxic. We correlated the tissue mercury concentrations to the amount of mercury present in the sea-water (SW). We also tested the ability of the shrimp to depurate mercury accumulated in the tissues.
Results: - Adult Artemia survived at least one week when exposed to concentrations ranging from 10-9 to 10-5g/L HgCl or MeHg. Shrimp exposed to 10-4g/L HgCl or MeHg died within two days.
Fertility was influenced by mercury exposure. The number of offspring per brood produced by females exposed to 10-6g/L or less HgCl was around 150, significantly higher than the average 80 offspring per brood produced by females exposed to 10-6g/L MeHg. When exposed to 10-5g/l HgCl and MeHg, the females brood size was 47 and 24, respectively.
- Artemia is able to maintain low level of tissue mercury, up to exposure to 10-6g/L HgCl and 10-7 g/L for MeHg. Exposure to higher mercury concentrations leads to much higher mercury levels, about 35 ppm HgCl for SW reaching 10-5g/L and 300 ppm with exposure to 10-4 MeHg.
Discussion: While both HgCl and MeHg are lethal to the shrimp, after a few days exposure, at concentration higher than 10-6 g/L, MeHg has a stronger effect on fertility, with brood size near half the size. Also, MeHg, the organic form of mercury, is accumulated in much higher level than the inorganic form. The organic form has a better ability to cross cell membranes. Since the mercury levels in the Great Salt Lake reach 55 ng/L (= 0.055 10-6g/L) and 30 ng/L (0.03 10-6 g/L) for HgCl and MeHG, respectively, the brine shrimp population is likely not affected by this pollutant.
Conclusion: Mercury has a strong effect on Artemia metabolism. We will study, next, the shrimp response to the oxidative stress induced by the mercury exposure.
Faculty Advisor: Berthelemy, Nicole (Weber State University, Zoology)
Introduction: Mercury, originating from mining and industrial activity, has been accumulating in the Great Salt Lake water and has contaminated its food web. Some of the mercury chloride (HgCl) is transformed by benthic bacteria to the more toxic monomethyl mercury (MeHg). While the effect of HgCl on the brine shrimp Artemia franciscana has been described, little is known about the effects of MeHG on this shrimp, except that it is more toxic. We correlated the tissue mercury concentrations to the amount of mercury present in the sea-water (SW). We also tested the ability of the shrimp to depurate mercury accumulated in the tissues.
Results: - Adult Artemia survived at least one week when exposed to concentrations ranging from 10-9 to 10-5g/L HgCl or MeHg. Shrimp exposed to 10-4g/L HgCl or MeHg died within two days.
Fertility was influenced by mercury exposure. The number of offspring per brood produced by females exposed to 10-6g/L or less HgCl was around 150, significantly higher than the average 80 offspring per brood produced by females exposed to 10-6g/L MeHg. When exposed to 10-5g/l HgCl and MeHg, the females brood size was 47 and 24, respectively.
- Artemia is able to maintain low level of tissue mercury, up to exposure to 10-6g/L HgCl and 10-7 g/L for MeHg. Exposure to higher mercury concentrations leads to much higher mercury levels, about 35 ppm HgCl for SW reaching 10-5g/L and 300 ppm with exposure to 10-4 MeHg.
Discussion: While both HgCl and MeHg are lethal to the shrimp, after a few days exposure, at concentration higher than 10-6 g/L, MeHg has a stronger effect on fertility, with brood size near half the size. Also, MeHg, the organic form of mercury, is accumulated in much higher level than the inorganic form. The organic form has a better ability to cross cell membranes. Since the mercury levels in the Great Salt Lake reach 55 ng/L (= 0.055 10-6g/L) and 30 ng/L (0.03 10-6 g/L) for HgCl and MeHG, respectively, the brine shrimp population is likely not affected by this pollutant.
Conclusion: Mercury has a strong effect on Artemia metabolism. We will study, next, the shrimp response to the oxidative stress induced by the mercury exposure.
Effects of Exercise on Subjective Feelings of Vitality: A Randomized Crossover Study
Stevens, Andrew; Hicks, Joseph; Savage, Ryland; Bailey, Bruce (Brigham Young University)
Faculty Advisor: Bailey, Bruce (Life Sciences, Exercise Science)
Purpose: This study examined the effect that differing exercise intensities have on subjective ratings of vitality both immediately following the condition and after 60 minutes of intense cognitive testing.
Methods: These findings come as a secondary analysis of a larger randomized crossover study that examined the effects of differing exercise intensities on cognitive performance. We recruited 228 men and women in roughly equal numbers to participate in the study. Each participant reported to the study lab four times one week apart. During the first day the participants ran a VO2 max test to establish pacing and baseline values. During the next three visits the participant completed a subjective vitality questionnaire before exercise, after 40 minutes of exercise or watching a video, and after 60 minutes of cognitive testing. The exercise conditions of vigorous (70% VO2 Max), moderate (35% VO2 Max) and sedentary activity (watching a video) were randomly assigned each week.
Results: The vitality rating before exercise was not significantly different between the three conditions with a mean rating of 19.9 ± 8.6 cm. After the sedentary condition, subjective ratings of vitality decreased from 19.9 cm to 12.5 cm after the condition and increased to 15.0 cm after the cognitive testing, remaining below pre-exercise values. After the moderate exercise condition, vitality did not change significantly after exercise (20.2 cm to 21.0 cm) but was lower following the cognitive tasks (15.9 cm). Vitality was slightly elevated following the vigorous exercise condition (19.8 cm to 21.3 cm) but went down after the cognitive tasks (17.1 cm). Vitality ratings did not differ significantly between exercise conditions at any time. The sedentary condition was lower than both exercise conditions after the 40-min intervention (p<0.001) and was lower than the vigorous exercise condition after the cognitive tasks (p<0.001).
Conclusion: Sedentary tasks may reduce subjective feelings of energy and vitality and this subjective evaluation remains suppressed after a period of cognitive exertion. Feelings of vitality and energy remain similar before and after exercise (vigorous or moderate) but then reduce after cognitive exertion. Vigorous exercise may be slightly beneficial for subjective feeling of vitality after exercise and following extended cognitive exertion.
Faculty Advisor: Bailey, Bruce (Life Sciences, Exercise Science)
Purpose: This study examined the effect that differing exercise intensities have on subjective ratings of vitality both immediately following the condition and after 60 minutes of intense cognitive testing.
Methods: These findings come as a secondary analysis of a larger randomized crossover study that examined the effects of differing exercise intensities on cognitive performance. We recruited 228 men and women in roughly equal numbers to participate in the study. Each participant reported to the study lab four times one week apart. During the first day the participants ran a VO2 max test to establish pacing and baseline values. During the next three visits the participant completed a subjective vitality questionnaire before exercise, after 40 minutes of exercise or watching a video, and after 60 minutes of cognitive testing. The exercise conditions of vigorous (70% VO2 Max), moderate (35% VO2 Max) and sedentary activity (watching a video) were randomly assigned each week.
Results: The vitality rating before exercise was not significantly different between the three conditions with a mean rating of 19.9 ± 8.6 cm. After the sedentary condition, subjective ratings of vitality decreased from 19.9 cm to 12.5 cm after the condition and increased to 15.0 cm after the cognitive testing, remaining below pre-exercise values. After the moderate exercise condition, vitality did not change significantly after exercise (20.2 cm to 21.0 cm) but was lower following the cognitive tasks (15.9 cm). Vitality was slightly elevated following the vigorous exercise condition (19.8 cm to 21.3 cm) but went down after the cognitive tasks (17.1 cm). Vitality ratings did not differ significantly between exercise conditions at any time. The sedentary condition was lower than both exercise conditions after the 40-min intervention (p<0.001) and was lower than the vigorous exercise condition after the cognitive tasks (p<0.001).
Conclusion: Sedentary tasks may reduce subjective feelings of energy and vitality and this subjective evaluation remains suppressed after a period of cognitive exertion. Feelings of vitality and energy remain similar before and after exercise (vigorous or moderate) but then reduce after cognitive exertion. Vigorous exercise may be slightly beneficial for subjective feeling of vitality after exercise and following extended cognitive exertion.
Ecology of Male Mating in Alfaro cultratus: Is morphology a response to the environment?
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.
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.
Comparative anatomy and connectivity of the Aii amacrine cell in mouse and rabbit retina
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.
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.
Does phylogenetic relatedness influence response to heterospecific alarm cues in Brachyrhaphis rhabdophora?
Chou, Audrey; Duffy, Alexandra; Johnson, Jerald (Brigham Young University)
Faculty Advisor: Johnson, Jerald (Brigham Young University, Biology)
Upon injury, fish release chemicals that cause fear and a dramatic change in behavior in nearby members of the species. Chemical alarm cues are released from injured epidermal tissue and provide an early warning signal for individuals to detect the presence of an active predator, and potentially increase the chances of individual survival. This research project investigates the conservation of alarm cue recognition and response across species boundaries by measuring the behavioral response of Brachyrhaphis rhabdophora to the alarm cues from five different species. Since these species will be of known phylogenetic relatedness, we will determine conservation of alarm cue response as a function of phylogenetic distance. I will also discuss the method of quantifying behavioral response through the use of a two-choice flume tank to measure both changes in activity and spatial avoidance upon alarm cue exposure.
Faculty Advisor: Johnson, Jerald (Brigham Young University, Biology)
Upon injury, fish release chemicals that cause fear and a dramatic change in behavior in nearby members of the species. Chemical alarm cues are released from injured epidermal tissue and provide an early warning signal for individuals to detect the presence of an active predator, and potentially increase the chances of individual survival. This research project investigates the conservation of alarm cue recognition and response across species boundaries by measuring the behavioral response of Brachyrhaphis rhabdophora to the alarm cues from five different species. Since these species will be of known phylogenetic relatedness, we will determine conservation of alarm cue response as a function of phylogenetic distance. I will also discuss the method of quantifying behavioral response through the use of a two-choice flume tank to measure both changes in activity and spatial avoidance upon alarm cue exposure.
Effects of Mycorrhizal Associations on Tomato Defensive Compounds
Jones, Dalton (Weber State University)
Faculty Advisor: Schramm, Katharina (Science, Botany)
Tomatoes (Solanum lycopersicum) are an important agricultural crop around the world. In order to produce food with less impact on the environment, many researchers are looking to utilize natural systems to maximize production with minimal inputs. Maximizing tomato defenses is one possible way to increase productivity. Tomatoes produce both physical and chemical defenses in response to the stress. Increasing the number of trichomes on the plant is a physical means of deterring insects from eating the plant. Trichomes come in two forms glandular trichomes and non-glandular trichomes. The non-glandular trichomes are strictly a physical defense while the glandular trichomes produce chemical defensive compounds against a wide variety of insects. Most land plants can form a symbiosis with arbuscular mycorrhizal fungi (AMF). This symbiosis has been shown to increase nutrient supply, decrease drought stress, and prime plant defenses, all increasing a plant's ability to withstand herbivory stress better. This study examines the response of trichomes and the number of chemical defenses after insect herbivory has occurred with the additional support of the AMF symbiosis. Treatments were exposed to Manduca sexta to stimulate trichome and chemical production. The extracted leaves were analyzed via gas chromatography to examine the make-up of the tomato's chemical defenses. The growth rates of M. sexta were recorded to examine the effects of tomato's chemical defenses after feeding the insects the induced tomato leaves. Measuring trichome density quantifies the change in physical defenses. The addition of the AMF increased the plant defenses, both the number of trichomes present on the plants and the quantity of the chemical defenses. Insects feeding on plants with increased defenses were also shown to have decreased growth. This study shows an alternative strategy for the use of commercial pesticides, lessening the impact of tomato crops on the ecosystem.
Faculty Advisor: Schramm, Katharina (Science, Botany)
Tomatoes (Solanum lycopersicum) are an important agricultural crop around the world. In order to produce food with less impact on the environment, many researchers are looking to utilize natural systems to maximize production with minimal inputs. Maximizing tomato defenses is one possible way to increase productivity. Tomatoes produce both physical and chemical defenses in response to the stress. Increasing the number of trichomes on the plant is a physical means of deterring insects from eating the plant. Trichomes come in two forms glandular trichomes and non-glandular trichomes. The non-glandular trichomes are strictly a physical defense while the glandular trichomes produce chemical defensive compounds against a wide variety of insects. Most land plants can form a symbiosis with arbuscular mycorrhizal fungi (AMF). This symbiosis has been shown to increase nutrient supply, decrease drought stress, and prime plant defenses, all increasing a plant's ability to withstand herbivory stress better. This study examines the response of trichomes and the number of chemical defenses after insect herbivory has occurred with the additional support of the AMF symbiosis. Treatments were exposed to Manduca sexta to stimulate trichome and chemical production. The extracted leaves were analyzed via gas chromatography to examine the make-up of the tomato's chemical defenses. The growth rates of M. sexta were recorded to examine the effects of tomato's chemical defenses after feeding the insects the induced tomato leaves. Measuring trichome density quantifies the change in physical defenses. The addition of the AMF increased the plant defenses, both the number of trichomes present on the plants and the quantity of the chemical defenses. Insects feeding on plants with increased defenses were also shown to have decreased growth. This study shows an alternative strategy for the use of commercial pesticides, lessening the impact of tomato crops on the ecosystem.
Cocoa Epicatechin Metabolites' affect on β Cell Proliferation and Cell Cycle
Ross, Mimi; Tessem, Jeffery; Orton, Emily; Ekpo, Idongesit; Beales, Joseph (Brigham Young University)
Faculty Advisor: Tessem, Jeffery (Life Sciences; Nutrition, Dietetics, & Food Science)
In 2015 there were over 30 million Americans with diabetes and over 84 million Americans ages 18 and older had pre-diabetes. With diabetes being the seventh leading cause of death in the United States and becoming more prevalent the race is on to find a cure. One of the main problems with this disease is the decrease in functional β-cell mass. β-cells produce insulin to maintain blood glucose levels at healthy levels. Thus, if we can increase β-cell proliferation we are one step closer to curing diabetes. Cocoa epicatechins have been shown to be beneficial in blocking diabetes progression. Studies have shown that oligomeric and polymeric cocoa epicatechin extracts improve diabetes onset in a mouse model of Type 2 diabetes. We have demonstrated that the oligomeric fraction of cocoa epicatechins enhances β-cell proliferation in an in vitro model. Absorption studies have shown that while the oligomeric and polymeric forms are not readily absorbed in the gut, they are metabolized by gut bacteria and that these metabolites can be observed in circulation. Using flow cytometry we have studied how these phytochemicals: epicatechin, 5-phenylvaleric acid, Homovanilic acid, and Hippuric acid. Here we present the data regarding the effect of microbial cocoa flavanol metabolites on β-cell cell cycle during proliferation.
Faculty Advisor: Tessem, Jeffery (Life Sciences; Nutrition, Dietetics, & Food Science)
In 2015 there were over 30 million Americans with diabetes and over 84 million Americans ages 18 and older had pre-diabetes. With diabetes being the seventh leading cause of death in the United States and becoming more prevalent the race is on to find a cure. One of the main problems with this disease is the decrease in functional β-cell mass. β-cells produce insulin to maintain blood glucose levels at healthy levels. Thus, if we can increase β-cell proliferation we are one step closer to curing diabetes. Cocoa epicatechins have been shown to be beneficial in blocking diabetes progression. Studies have shown that oligomeric and polymeric cocoa epicatechin extracts improve diabetes onset in a mouse model of Type 2 diabetes. We have demonstrated that the oligomeric fraction of cocoa epicatechins enhances β-cell proliferation in an in vitro model. Absorption studies have shown that while the oligomeric and polymeric forms are not readily absorbed in the gut, they are metabolized by gut bacteria and that these metabolites can be observed in circulation. Using flow cytometry we have studied how these phytochemicals: epicatechin, 5-phenylvaleric acid, Homovanilic acid, and Hippuric acid. Here we present the data regarding the effect of microbial cocoa flavanol metabolites on β-cell cell cycle during proliferation.
Collared Peccary (Pecari tajucu) Group Size at La Selva Biological Station, Costa Rica
Shin, Seungwon (Salt Lake Community College)
Faculty Advisor: Seaboch, Melissa (Salt Lake Community College, Anthropology)
The abundance of collared peccaries (Pecari tajucu) is crucial to study because they are a keystone species that plays a large role in their ecosystems. They consume fallen fruits and nuts, disperse seeds, and provide food for predators. Additionally, they are ecosystem engineers altering the landscape for other species. Previous studies have shown that collared peccaries at La Selva Biological Station travel in smaller groups (averaging 10 individuals per group) compared to peccaries at other Neotropical sites. La Selva Biological Station is located in northeastern Costa Rica and it consists of both primary and secondary (i.e. degraded) forests surrounded on three sides by farmland. Due to the general decline of mammals in degraded habitats, I predicted that the average group size of collared peccaries at La Selva will be even smaller than previously reported. I collected data at La Selva Biological Station for two weeks in May 2019. I used three census methods: total count sampling (counting all the species in a certain area), line transect sampling (counting all the species I see when I walk through a trail), and point sampling (standing at selected viewpoints and recording the species visible from that location). I observed 39 peccaries in 17 separate sightings. Group size ranged from 1 to 7 peccaries with an average of 2.3 peccaries per group. Eight sightings (20%) were of single peccaries. My hypothesis that peccary group size would be smaller than 10 individuals was supported. Some limitations of the study were low visibility due to the dense forest and the dispersed social organization of peccary individuals within the group. Both of these factors would underestimate the actual group size of collared peccaries. Nevertheless, the results support previous findings that peccary group size at La Selva are smaller than at other Neotropical sites.
Faculty Advisor: Seaboch, Melissa (Salt Lake Community College, Anthropology)
The abundance of collared peccaries (Pecari tajucu) is crucial to study because they are a keystone species that plays a large role in their ecosystems. They consume fallen fruits and nuts, disperse seeds, and provide food for predators. Additionally, they are ecosystem engineers altering the landscape for other species. Previous studies have shown that collared peccaries at La Selva Biological Station travel in smaller groups (averaging 10 individuals per group) compared to peccaries at other Neotropical sites. La Selva Biological Station is located in northeastern Costa Rica and it consists of both primary and secondary (i.e. degraded) forests surrounded on three sides by farmland. Due to the general decline of mammals in degraded habitats, I predicted that the average group size of collared peccaries at La Selva will be even smaller than previously reported. I collected data at La Selva Biological Station for two weeks in May 2019. I used three census methods: total count sampling (counting all the species in a certain area), line transect sampling (counting all the species I see when I walk through a trail), and point sampling (standing at selected viewpoints and recording the species visible from that location). I observed 39 peccaries in 17 separate sightings. Group size ranged from 1 to 7 peccaries with an average of 2.3 peccaries per group. Eight sightings (20%) were of single peccaries. My hypothesis that peccary group size would be smaller than 10 individuals was supported. Some limitations of the study were low visibility due to the dense forest and the dispersed social organization of peccary individuals within the group. Both of these factors would underestimate the actual group size of collared peccaries. Nevertheless, the results support previous findings that peccary group size at La Selva are smaller than at other Neotropical sites.
Effects of Exercise on Subjective Feelings of Fatigue: A Randomized Crossover Study
Savage, Ryland; Stevens, Andrew; Hicks, Joseph (Brigham Young University)
Faculty Advisor: Bailey, Bruce (Brigham Young University, Exercise Science)
Purpose: This study examined the effect of different intensities of exercise on subjective feelings of fatigue both immediately following exercise and after 60 minutes of intense cognitive testing in men and woman.
Methods: These results come from a secondary analysis of a larger randomized crossover study examining the different levels of exercise intensity on cognitive performance. We recruited 228 men and woman to participate in the study. Each participant was tested after three exercise conditions: moderate (35% VO2 max), vigorous (70% VO2 max), and sedentary (no exercise). Each exercise condition was randomized and each test was separated by one week. After each 40-minute exercise condition, we administered a visual analog scale to evaluate subjective feelings of fatigue. This assessment of fatigue was delivered before treatment, immediately after treatment and then again after a variety of cognitive tasks were performed for the duration of one hour.
Results: For the sedentary condition, feelings of fatigue increased after the 40-minute intervention (p<0.001) and decreased after 60 minutes of cognitive work but remaining elevated compared to baseline (p<0.01). For the moderate condition, feelings of fatigue did not change immediately after exercise (p=0.063) but then increased after 60 minutes of cognitive work (p<0.001). For vigorous condition, feelings of fatigue increased after exercise(p<0.001) and remained elevated after performing the cognitive tasks (p=0.163). Following the 40-minute intervention, fatigue was highest after the sedentary condition, followed by the vigorous condition and did not change after completion of the moderate condition. Following 60 minutes of cognitive work, fatigue was highest in the vigorous condition (p<0.001) and did not differ between the sedentary and moderate conditions (p=0.063).
Conclusion: The results of this study show that moderate exercise has no significant impact on feelings of fatigue but exercise at a higher intensity and being sedentary increase fatigue. Doing cognitive work increases fatigue if exercise precedes the tasks but being sedentary beforehand decreases feelings of fatigue during cognitive tasks. This suggests cognitive work is usually draining, but if performed after sedentary or low activity states such as watching TV, cognitive work will be invigorating and help feel more alert.
Faculty Advisor: Bailey, Bruce (Brigham Young University, Exercise Science)
Purpose: This study examined the effect of different intensities of exercise on subjective feelings of fatigue both immediately following exercise and after 60 minutes of intense cognitive testing in men and woman.
Methods: These results come from a secondary analysis of a larger randomized crossover study examining the different levels of exercise intensity on cognitive performance. We recruited 228 men and woman to participate in the study. Each participant was tested after three exercise conditions: moderate (35% VO2 max), vigorous (70% VO2 max), and sedentary (no exercise). Each exercise condition was randomized and each test was separated by one week. After each 40-minute exercise condition, we administered a visual analog scale to evaluate subjective feelings of fatigue. This assessment of fatigue was delivered before treatment, immediately after treatment and then again after a variety of cognitive tasks were performed for the duration of one hour.
Results: For the sedentary condition, feelings of fatigue increased after the 40-minute intervention (p<0.001) and decreased after 60 minutes of cognitive work but remaining elevated compared to baseline (p<0.01). For the moderate condition, feelings of fatigue did not change immediately after exercise (p=0.063) but then increased after 60 minutes of cognitive work (p<0.001). For vigorous condition, feelings of fatigue increased after exercise(p<0.001) and remained elevated after performing the cognitive tasks (p=0.163). Following the 40-minute intervention, fatigue was highest after the sedentary condition, followed by the vigorous condition and did not change after completion of the moderate condition. Following 60 minutes of cognitive work, fatigue was highest in the vigorous condition (p<0.001) and did not differ between the sedentary and moderate conditions (p=0.063).
Conclusion: The results of this study show that moderate exercise has no significant impact on feelings of fatigue but exercise at a higher intensity and being sedentary increase fatigue. Doing cognitive work increases fatigue if exercise precedes the tasks but being sedentary beforehand decreases feelings of fatigue during cognitive tasks. This suggests cognitive work is usually draining, but if performed after sedentary or low activity states such as watching TV, cognitive work will be invigorating and help feel more alert.