Biology Commons^™

Mathematical Modeling Of Color Perception Using Differential Equation, Siavash Pooretemad

Student Research Symposium

Color perception begins in the retina, where three cone types (L, M, S) detect light and initiate neural signals. These signals are processed by horizontal and bipolar cells to form opponent color channels: red-green (RG), yellow-blue (YB), and light-dark (LD). Perception is not solely based on physical input but also shaped by neural adaptation and context.

This project models color perception using a differential equation approach, simulating how color contrast and adaptation emerge from interactions between photoreceptors and lateral inhibition.

We hypothesize that a system of differential equations can model how retinal cone cells respond to and process light intensity, …

A Checklist Of The Bees Of Utah, Joseph S. Wilson, Anthony Hunsaker, Terry L. Griswold, Olivia Messinger Carril

Biology Faculty Publications

Understanding bee distributions is essential to protecting these vital pollinators. Since conservation efforts and policies are often made at the state level, maintaining state-specific bee species lists can aid conservationists and policy makers. While several North American state- and province-level bee species lists have been published, few exist for the arid western states, where bee diversity tends to be higher. Here we provide a bee species list for Utah, compiled from online occurrence records from the Symbiota Collection of Arthropods Network (SCAN) and specimen records housed in the USDA-ARS Pollinating Insect Research Unit (BBSL). In total we document 1167 bee …

Nutrient Limitation And Seasonality Associated With Phytoplankton Communities And Cyanotoxin Production In A Large, Hypereutrophic Lake, Gabriella M. Lawson, Jakob L. Young, Zachary T. Aanderud, Erin F. Jones, Samuel Bratsman, Jonathan Daniels, Madeleine P. Malmfeldt, Michelle A. Baker, Benjamin W. Abbott, Scott Daly, Hans W. Paerl, Greg Carling, Brian Brown, Raymond Lee, Rachel L. Wood

Biology Faculty Publications

Though freshwater harmful algal blooms have been described and studied for decades, several important dynamics remain uncertain, including the relationships among nutrient concentrations, phytoplankton growth, and cyanotoxin production. To identify when and where nutrients limit phytoplankton, cyanobacteria, and cyanotoxins, we conducted in situ bioassay studies. We added nitrogen (N), phosphorus (P), or N + P across various seasons in water collected from three locations across Utah Lake, one of the largest freshwater lakes in the western U.S. This shallow, hypereutrophic lake provides a powerful testbed for quantifying nutrient-growthtoxin interactions. We assessed a range of parameters over time, including photopigment concentrations, …

Plasmids Encode And Can Mobilize Onion Pathogenicity In Pantoea Agglomerans, Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L. Derie, Lindsey J. Du Toit, Stephen Stresow-Cortez, Jean M. Bonasera, Paul Stodghill, Brian Kvitko

Biology Faculty Publications

Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected > 300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe …

Microbiome Metabolic Capacity Is Buffered Against Phylotype Losses By Functional Redundancy, Kayla Cross, Noelle Beckman, Benjamin Jahnes, Zakee L. Sabree

Biology Faculty Publications

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity …

Spatiotemporal Patterns Of Chlorophyll-A Concentration In A Hypersaline Lake Using High Temporal Resolution Remotely Sensed Imagery, R. Douglas Ramsey, Soren M. Brothers, Melissa Cobo, Wayne A. Wurtsbaugh

Wildland Resources Faculty Publications

The Great Salt Lake (GSL) is the largest saline lake in the Western Hemisphere. It supports billion-dollar industries and recreational activities, and is a vital stopping point for migratory birds. However, little is known about the spatiotemporal variation of phytoplankton biomass in the lake that supports these resources. Spectral reflectance provided by three remote sensing products was compared relative to their relationship with field measurements of chlorophyll a (Chl a). The MODIS product MCD43A4 with a 500 m spatial resolution provided the best overall ability to map the daily distribution of Chl a. The imagery indicated significant spatial …

Halogeton And Greasewood Poisoning In Cattle And Sheep In Utah, E. Jane Kelly, Stephen T. Lee, Ammon Brown, Daniel Cook

Poisonous Plant Research (PPR)

Halogeton (Halogeton glomeratus) is a fast-growing annual plant while greasewood (Sarcobatus vermiculatus) is a perennial shrub of the Western States. Oxalates are the toxic principle in halogeton and greasewood. Most losses occur when hungry animals are allowed to graze in heavy stands of halogeton and greasewood. Halogeton and greasewood are always dangerous and become more toxic as the growing season progresses. Here we report on two clinical cases of halogeton and greasewood poisoning in cattle and sheep. Histologically, oxalate crystals were observed in the kidneys of the cow and sheep consistent with oxalate poisoning. Oxalate was …

Career: The Behavioral, Hormonal, And Neural Basis Of Coyote Monogamy, Sara M. Freeman

Funded Research Records

No abstract provided.

The Southwest Climate Adaptation Science Center (Sw Casc), Michelle Baker

Funded Research Records

No abstract provided.

Extensive Admixture Among Karst-Obligate Salamanders Reveals Evidence Of Recent Divergence And Gene Exchange Through Aquifers, Chris C. Nice, Katherine L. Bell, Zachariah Gompert, Lauren K. Lucas, James R. Ott, Ruben U. Tovar, Paul Crump, Peter H. Diaz

Biology Faculty Publications

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The E. neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture among species …

Factors Influencing The Discovery And Use Of Carrion By Vertebrate Scavengers From Human-Induced Mass-Mortality Events, Samantha J. Leivers, Michael J. Bodenchuk, Tyler A. Campbell, John M. Tomeček

Human–Wildlife Interactions

Scavengers play critical roles in ecosystem health and stability, and both biotic and abiotic factors can influence scavenger guild dynamics. Carrion is often limited both temporally and spatially on the landscape, but mass mortality events (MMEs)—in which there is an influx of carrion biomass on the landscape—may result in different scavenger community dynamics compared to when carrion is scarcely distributed. In this study, we investigated factors affecting the discovery and use of carrion by a natural, unharrassed scavenger guild during wild pig (Sus scrofa) MMEs conducted at East Foundation’s San Antonio Viejo Ranch in South Texas, USA. We …

Quantitative Analysis Of Protective Effect Of Resveratrol Against Nanoplastic-Induced Oxidative Stress, Bryan Gustafson

All Graduate Reports and Creative Projects, Fall 2023 to Present

Nanoplastics and microplastics are a growing ecological and health concern due to their widespread prevalence. The effects of these microscopic particles in biological systems primarily relate to their potential to produce reactive oxygen species and interactive effects with other cytotoxic agents. Of particular interest in this work is the effect on mammalian intestinal cells, due to the regular unintentional ingestion of micro- and nanoplastics in the normal western diet. In this study, Caco-2 cells were cultured and exposed to polystyrene particles in vitro as a simple model of the human digestive endothelium.

Resveratrol, a naturally occurring polyphenolic compound, has been …

Soil Organic Matter Processes From The Treetops To The Clay Particle: The Role Of Climate, Minerals, And Organic Matter Chemistry In Soil Carbon Accumulation And Stability, Jessica G. Murray

All Graduate Theses and Dissertations, Fall 2023 to Present

Soils store more carbon than plants and the atmosphere, yet release ten times more carbon dioxide (CO₂) to the atmosphere than human activities each year. Small shifts in the balance of soil carbon storage and soil carbon emissions could make climate change less severe, by acting as a sink for the carbon plants pull from the atmosphere, or make climate change worse, by releasing even more planet-warming greenhouse gases. The processes governing whether soils store or release carbon depend on tiny soil microorganisms which convert plant carbon to soil organic matter, releasing CO₂ in the process. In …

Immune Variation Across Different Contexts In Non-Model Systems, Kwanho Claudia Ki

All Graduate Theses and Dissertations, Fall 2023 to Present

The immune system is important to an animal’s survival against disease-causing agents and physical injuries. Accordingly, many resources are required to maintain and activate the immune system (such as energy). However, as these resources also need to be shared with other important systems of the body, the portion of resources that can be allotted to the immune system is variable. Thus, many different factors may alter how well the immune system operates. My dissertation sought to understand what sorts of factors can lead to changes in the immune system. Reptiles are known to have a very robust immune system. Therefore, …

Analysis Of An Outdoor Pilot-Scale Rotating Algae Biofilm Reactor For Power Optimization, Ash-Enhanced Productivity, And Nutrient Uptake, Peter F. Jeppesen

All Graduate Theses and Dissertations, Fall 2023 to Present

Outdoor testing of a rotating algae biofilm reactor (RABR) was performed to see how well it could remove nutrients from water and produce algae. By adjusting the operation settings, we found the lowest power needed to remove nitrogen and phosphorus. The lowest power values needed were 1.36 kWh per kilogram of nitrogen and 20.1 kWh per kilogram of phosphorus. The algae production rate reached a maximum of 7.09 grams per square meter per day. Detailed analysis showed that the reactor worked like a continuous flow system, and the performance was influenced by factors including light and temperature. The results also …

Multidecadal Data Demonstrate The Role Of Climate And Natural History Traits In Shaping Butterfly Phenology, Gbolahan Anthony Reis

All Graduate Theses and Dissertations, Fall 2023 to Present

Climate change is transforming the natural world, altering the timing of key events in the lives of plants and animals, such as when flowers bloom or when butterflies take flight. These timing changes, known as phenology shifts, can disrupt ecosystems and species interactions, creating ripple effects through food webs and biodiversity. While scientists have studied these shifts for decades, much of the focus has been on simple metrics, like the first or last day a butterfly is seen flying each year. However, these measures do not tell the whole story of how climate change is impacting the entire flight season …

Evaluating The Stress System Of The Grieving Brain: Corticotropin-Releasing Factors And Partner Loss In Female Coyotes, Rachel Tong Xin Ning

Undergraduate Honors Capstone Projects

Forming social bonds is fundamental in helping us foster connections with others. The loss of a loved one often results in grief, stress, and loneliness, and the stress response system of the body has been implicated in the physiological symptoms associated with grieving. Corticotropin releasing factor (CRF) is the hormone that initiates the stress response in the body and acts at two different receptor subtypes CRF receptor (CRFR)1 and CRFF2. Many studies on CRF and social loss have been conducted in monogamous prairie voles, but studies in longer-lived monogamous mammals could improve understanding of the effects of losing pair bonds. …

Chasing A Little-Known Fairy Bee (Perdita Meconis) In A Dynamic Desert Landscape, Sarit Chanprame, Colleen Meidt, Terry Griswold, Joseph S. Wilson, Kelsey K. Graham

Biology Student Research

The Mojave poppy bee, Perdita meconis Griswold, is a small fairy bee endemic to the eastern Mojave Desert, known to be associated with the Las Vegas Bearpoppy, Arctomecon californica. Because of the reported decline in populations of P. meconis, it has been targeted for protection under the Endangered Species Act. Here, we present the results of a 3-year study investigating the current distribution and floral preferences of P. meconis in Clark County, Nevada. We found that populations of P. meconis fluctuated dramatically from 2020 to 2022. This area experienced extreme drought conditions during these years, which consequentially affected …

Cannabinoid-Inspired Inhibitors Of The Sars-Cov-2 Coronavirus 2′ -O-Methyltransferase (2′ -O-Mtase) Non-Structural Protein (Nsp10–16), Menny M. Benjamin, George S. Hanna, Cody F. Dickinson, Yeun-Mun Choo, Xiaojuan Wang, Jessica A. Downs-Bowen, Ramyani De, Tamara R. Mcbrayer, Raymond F. Schinazi, Sarah E. Nielson, Joan M. Hevel, Pankaj Pandey, Robert J. Doerksen, Danyelle M. Townsend, Jie Zhang, Zhiwei Ye, Scott Wyer, Lucas Bialousow, Mark T. Hamann

Chemistry and Biochemistry Student Research

The design and synthesis of antiviral compounds were guided by computationally predicted data against highly conserved non-structural proteins (Nsps) of the SARS-CoV-2 coronavirus. Chromenephenylmethanone-1 (CPM-1), a novel biphenylpyran (BPP), was selected from a unique natural product library based on in silico docking scores to coronavirus Nsps with high specificity to the methyltransferase protein (2′ -O-MTase, Nsp10–16), which is responsible for viral mRNA maturation and host innate immune response evasion. To target the 2′ -O-MTase, CPM-1, along with intermediate BPP regioisomers, tetrahydrophenylmethanones (TPMs), were synthesized and structurally validated via nuclear magnetic resonance (NMR) data and DP4+ structure …

A Retrospective Analysis Of Sheep Generated By Somatic Cell Nuclear Transfer, Ying Liu, Rusty Stott, Misha Regouski, Zhiqiang Fan, Iuri Viotti Perisse, Tayler Patrick, Jacob Keim, Qinggang Meng, Irina A. Polejaeva

Animal, Dairy, and Veterinary Science Faculty Publications

Somatic cell nuclear transfer (SCNT) is one of the primary methods for production of genetically engineered sheep, which allows for gene editing or transgene introduction in somatic cells. The use of SCNT eliminates the risk of genetic mosaicism in embryos and animals that is commonly observed after zygote micromanipulations. This retrospective analysis of SCNT in sheep performed at Utah State University, spanning from 2016 to 2021, examined parameters that may impact pregnancy and full-term development, including donor oocytes (donor age), donor cell lines, SCNT parameters (time of oocyte activation following SCNT, number of transferred embryos, in vitro maturation and culture …

From Inbreeding To Admixture: How The Diverse Consequences Of Gene Flow Shape Evolutionary Dynamics And Population Viability, Amy L. Springer

All Graduate Theses and Dissertations, Fall 2023 to Present

When Homo sapiens traveled out of Africa and interbred with the Neanderthals of Europe, human genes spread into the Neanderthal population. Likewise, genes from Neanderthals spread into the human genome—genes humans still carry to this day. The process whereby genetic material from one population is spread to another is known as gene flow. Gene flow—or the absence thereof—can have critical consequences for a population’s health and survival. On one hand, if no gene flow occurs, mating among close relatives can lead to high levels of inbreeding. Inbreeding can have devastating consequences for the health of populations, in some cases even …

Shifting Paradigms In Recreation Management: Applying Social-Ecological System Frameworks To Parks And Protected Areas, Noah Creany

All Graduate Theses and Dissertations, Fall 2023 to Present

Park and protected area (PPA) recreation management is often characterized by social, ecological, and managerial dimensions. These dimensions have increasingly been conceptualized as social-ecological systems (SESs) to understand the complex interrelationships between them. Contemporary trends of increased visitation on public lands in the United States, including US National Parks, have accentuated the complex interactions between the amount of recreation use, the capacity of the setting, the quality of the visitor experience, and ecological resource conditions. These challenges of managing recreation use and understanding these interactions will be further compounded by climate change and its effects on ecosystem composition and dynamics. …

Using Wasp Specimens In Taxonomic, Biogeographic, Evolution, And Informal Education Studies, Brenna Lynn Decker

All Graduate Theses and Dissertations, Fall 2023 to Present

Entomology collections hold an untapped wealth of information, from insect morphology, genetics, locality and association data, and potential for use in education. Especially with insects that generate initial fears, such as wasps, seeing insect specimens provides a safe environment to learn about their behaviors. Wasps are insects in the order Hymenoptera, along with ants and bees. The public may hold fears against wasps, due to their negative portrayal in various media, but they serve as integral components of a functional ecosystem. Even with their importance, many groups of wasps are still highly understudies. This dissertation aims to tackle this fear …

Evidence For Partitioning? A Comparison Of Thermal Niche In Three Species Of Sympatric Lizards In Northeastern Utah, Kristopher B. Pedersen

All Graduate Theses and Dissertations, Fall 2023 to Present

Lizards actively maintain a narrow range of body temperatures through behavioral thermoregulation and microhabitat selection. Body temperature plays a critical role in many physiological processes. As a result, there is a range of body temperatures at which a lizard’s reproductive success (fitness) is maximized, known as the lizard’s thermal niche. There is strong evidence linking the available temperatures, or thermal properties of a microhabitat, to success in maintaining body temperatures within a preferred set range. Microhabitats have differing thermal properties, and so have different relative quality. Because thermal properties are limited in space and time, competition for high quality microhabitat …

Impacts Of Anthropogenic Disturbances And Urbanization On The Behavior And Morphology Of Two Free-Living Lizard Species (Uta Stansburiana And Aspidoscelis Neotesselatus), Layne O. Sermersheim

All Graduate Theses and Dissertations, Fall 2023 to Present

Urbanization can alter wildlife, requiring species to adjust to anthropogenic changes via life history strategies. Reptiles are particularly vulnerable to these changes, as ectotherms directly rely on their environment to maintain their optimal homeostatic state. As urbanization changes the landscape, reptiles will have to adapt to anthropogenic change, but it is unclear what behaviors may be aiding in this adaptation and whether there are morphological tradeoffs existing to support this change. To analyze the impact of urbanization and anthropogenic disturbances on reptile behavior and morphology, I conducted three research studies on two different species – the common side-blotched lizard and …

The Interactions Between Drought Tolerant Corn Hybrids And Plant Water-Stress On Weeds And Their Host Capability For Spider Mites, Mercy Adhiambo Odemba

All Graduate Theses and Dissertations, Fall 2023 to Present

With climate change, it is predicted that more frequent high temperatures and drought severity will lead to an increase in damage caused by pests that thrive under these conditions. Spider mite outbreaks, for example, are associated with plant waterstress and there is evidence that some weeds are more resilient and adapted to drought than some crops, leading to major concerns for the management of these two pest types. Weeds directly compete with crops for limited resources, but what is unclear is which weeds harbor spider mites and whether they exacerbate the impact of spider mites on corn crops under water-stressed …

Comparative Morphology And Development Of The Trigeminally Innervated Infrared-Imaging System In Boas And Pythons, Helen Bond Plylar

All Graduate Theses and Dissertations, Fall 2023 to Present

Boas and pythons use specialized sense organs called pit organs to detect radiant heat. Pit organs in these lineages occur in paired arrays along the upper and lower jaws and are served by the trigeminal nerve (the fifth cranial nerve and one of the largest). Information from the pit organs travels via branches of the trigeminal to the brain and ultimately is processed in the optic tectum, along with information from the visual system. That means these snakes effectively “see” heat. While studies of the pitviper infrared-imaging system are numerous, very few studies of this system in pythons or boas …

Microbiome Assembly And Function In The Solitary Mason Bee, Osmia Lignaria (Megachilidae), Bailey Crowley

All Graduate Theses and Dissertations, Fall 2023 to Present

Animal-microbe interactions can influence host biology, ecology, and evolution. The assembly and function of microbes found within animal hosts oftentimes depends on which species are involved. Advances in sequencing technologies have permitted the exploration of host-microbe interactions in a variety of animals, including bees. Early research aimed at understanding the microbiomes of social bees, such as honey bees and bumble bees, found that microbes prevent the spoilage of stored pollen, breakdown indigestible nutrients into smaller molecules available for uptake by the host, and also protect the host from pathogens. When environmental stressors, such as increased temperatures, disrupt the microbiome, the …

Please Don’T Break: Best Practices For Digitizing And Archiving Glass Plate Photographs, Ariel Hammond, Noelle Zocco, Alejandra Tomeo, Diego Jimenez

Journal of Western Archives

Glass plate photographs, taken primarily between 1860-1930, were meant to document and preserve imagery, however, these photographs developed directly on glass are increasingly prone to destruction. With recent advances in imaging techniques, metadata, and collections care, the preservation of glass photography has evolved. This paper is a snapshot of the current best practices for preserving, digitizing, and storing glass plate and lantern slide photographs. It also features a case study from the San Diego Natural History Museum Library & Archives, which digitized a collection of 2,000+ glass photographs depicting the earliest images of flora and fauna in San Diego County, …

High Sugar Diet Alters Immune Function And The Gut Microbiome In Juvenile Green Iguanas (Iguana Iguana), Kwanho C. Ki, Erin L. Lewis, Elizabeth Wu, Francis J. Oliaro, Lise M. Aubry, Charles R. Knapp, Karen M. Kapheim, Dale Denardo, Susannah S. French

Biology Faculty Publications

The present work aimed to study whether a high sugar diet can alter immune responses and the gut microbiome in green iguanas. Thirty-six iguanas were split into four treatment groups using a 2x2 design. Iguanas received either a sugar-supplemented diet or a control diet, and either a lipopolysaccharide (LPS) injection or a phosphate-buffered saline (PBS) injection. Iguanas were given their respective diet treatment through the entire study (~3 months) and received a primary immune challenge 1 and 2 months into the experiment. Blood samples and cloacal swabs were taken at various points in the experiment and used to measure changes …