Little is known about how male and female Pieris rapae behave during territorial behaviors, making this project particularly significant. Through our previous experiment, we have uncovered intriguing insights into the unique behaviors exhibited by male P. rapae when interacting with pseudo-females (males in disguise). Our observations suggest a complex interplay between competitive instincts and courtship behaviors. Specifically, male Pieris rapae display distinct responses when encountering pseudo-females, indicating a potential recognition of the sex of the interacting butterfly. This recognition may trigger competitive behaviors like a territorial move if perceived as a rival male or foster a display of courtship if perceived as a potential mate. Additionally, we aim to study how female P. rapae interact with other females to determine if there are any behavioral differences in these interactions. By studying the intricacies of both male and female courtship and/or territorial behaviors in P. rapae, this project seeks a deeper understanding of the factors shaping mating systems and reproductive success in this species and beyond.

Microbial odors are essential for attracting mosquitoes to their hosts, but their role in attraction to other nutrient sources remains unknown. Sugar sources provide nutrients that lengthen the lifespan of both male and female mosquitoes and increase the vectorial capacity in host-seeking female mosquitoes. Microbial odors have been shown to act as proxy signals for the availability and composition of certain nutrients, such as amino acids and mineral ions, found in nectar and fruit sap. As microbes are abundant in flowers and fruits, we hypothesize that Microbial Volatile Organic Compounds (mVOCs) from these nutrient sources play an important role in the feeding behavior of mosquitos. To test this, we analyzed the microbial community of a known attractive fruit, Mangifera indica ‘Keitt.’ Microbial species were identified from our environmental samples through amplicon sequencing of the 16S and 26S regions. Isolates of the most abundant and relevant species were cultured for mVOC collection and chemical analysis via Gas Chromatography and Mass Spectroscopy (GC-MS). Behavioral assays were then performed with Aedes aegypti mosquitoes to observe the effect of microbial odors on the attractiveness of nutrient sources. Through the identification of behaviorally-relevant microbial compounds, we can gain a stronger understanding of the ecological dynamics of mosquito chemoreception and microbial community signaling, which can help inform future mosquito-control measures.

Orientation Patch Count (OPC) is a method of research used by biologists and paleontologists to analyze the complexity of an animal’s feeding surface while inferring their diets; diet and tooth complexity have evolved in concert with one another, which is why this method has been used on reptilian and mammalian (denticular) species. However, it has not been extensively tested on edentulous (toothless) clades. Therefore, my research examines the OPC of an edentulous species - specifically the endangered Madagascar big-headed turtle (Erymnochelys madagascariensis) using  three CT-scanned specimens. Three primary programs were used in order to analyze the quantitative morphometricsof the species: Slicer for processing and editing CT scans from the University of Washington’s Friday Harbor Lab, MeshLab for editing 3D models, and RStudio for data analysis. This research contributes to a broader study on turtle species led by paleontologist Brenlee Shipps, who will apply these findings to extinct beaked clades, specifically dicynodonts.

Circadian clocks have evolved as a powerful adaptation in response to daily environmental changes, allowing optimally timed sleep-wake cycles. The solar light-dark (LD) cycle is the dominant zeitgeber (time-giver) for entrainment (synchronization) of sleep and wake to external cues. While our lab has found that humans sleep less and later the days prior to the full moon phase where moonlight is available in the early night, moonlight was found to be an unreliable cue in determining lunar modulation of sleep for the light-polluted city population. Thus, my project investigates whether lunar cycling on activity patterns remains present without photic moonlight exposure using a diurnal non-human primate model: captive titi monkeys (Plecturocebus). The California National Primate Research Center collected titi monkey data (n=16) between 2022 to 2024 using AX3 from Axivity, a wearable data log that measures acceleration to monitor physical activity. I am using the statistical software R to derive activity onset and sleep onset/offset as phase markers of activity. Additionally, I am fitting different cosine models to a 30/15-day period, respectively lunar and semilunar, to analyze the periodic data for activity across the lunar month. We expect to see phase markers of activity oscillate with the monthly lunar phase, showing how the lunar cycle influences circadian rhythms in diurnal non-human primates, even in the absence of moonlight. This study may reveal a novel finding on lunar rhythms on activity patterns and could incur interest on how endogenous processes have adapted to the lunar cycle. Further molecular work could elucidate the neural mechanism behind lunar modulation of sleep and provide insights on improved treatment of dysregulated sleep.

Fluoride intake is essential for dental health, yet excessive consumption can lead to fluorosis, a condition negatively affecting teeth and bones. Tea, one of the most widely consumed beverages globally, naturally accumulates fluoride, making it a significant but often overlooked dietary source. Black tea is the most popular type of tea consumed in the U.S. In this study we compared fluoride levels across six brands of black tea and investigated how brewing conditions and water sources affect fluoride concentrations in tea. We brewed black tea from six locally popular brands (Lipton, Tazo, Fortnum & Mason, Twinings, Tetly, and Harney & Sons), using two water sources (distilled water and Seattle tap water), with four samples for each brand using both water sources. We brewed 50 mL of water at 100°C, then we let each sample of the tea sit for 5, 10, and 20 minutes. Ion chromatography was used to measure fluoride concentrations at each time interval. We compared these values to the U.S. Environmental Protection Agency's (EPA) recommended fluoride level of 4.0 mg/L. Our results help characterize the variation between brands and the influence of brewing duration on fluoride release. These findings contribute to a better understanding of fluoride exposure from tea consumption, helping consumers make informed choices about their dietary fluoride intake.

Beaver dams can function as natural filters helping decrease pollution in streams, creeks, and rivers. Beaver dams slow down the water flow in a creek or river, forming ponds that help trap excessive nutrients. An excess of nutrients such as phosphate and nitrate can cause eutrophication, leading to increased algal blooms that can produce toxins and ultimately deplete oxygen in the water. This study investigates the ion levels of chloride, fluoride, phosphate, nitrate, sulfate, and bromide upstream and downstream of the major beaver dam at Pipers Creek in North Seattle's Carkeek Park over the course of a year to better understand the long-term impacts of the dam. We collected three water samples at each of eleven sites along the creek, eight upstream from the dam, and three downstream. Ion chromatography was used to measure the concentrations of anions at each site. The results of this study help elucidate the role of beavers in moderating water quality and provide important baseline data documenting seasonal variations in the nutrient load at Pipers Creek. These findings can also be used to better understand the impact of new beaver dams in other freshwater systems.

Low-income communities are often disproportionately exposed to air pollution. High concentrations of pollutants such as particulate matter under 2.5 µm (PM2.5) and human aerosol emissions, including carbon dioxide (CO2), have been linked to various health and cognitive issues. Performance arts, including singing and playing instruments, produce human aerosol emissions and are considered high risk for airborne disease transmission. Our study evaluated the accumulation of CO2 and PM2.5 in high-risk environments (band classrooms) in low-income public schools in King County (WA), to determine whether there is a correlation between accumulation rates and Title 1 designation. Title 1 designation, which provides government funding for schools with a high percentage of students from low-income households, was used to represent low-income communities. We compared four middle schools that qualified for Title 1 designation to one school that did not qualify. Concentrations of CO2 and PM2.5 were measured using the Aranet4 Home CO2 sensor and a PurpleAir Classic sensor for PM2.5. We took a baseline measurement of both concentrations when the classroom was unoccupied. We then analyzed the change in concentration rates when classes were in session, taking into account classroom size and number of students. Our data showed concentrations above recommended levels at 1,370 ppm (parts per million) for CO2 in one of the Title 1 schools suggesting that Title 1 schools may be at greater risk of poor indoor air quality, though additional studies are needed. This additional exposure to pollutants and human aerosol emissions in already high-risk environments like band classrooms may lead to increased airborne disease transmission, highlighting the disparity in healthy learning environments. These classrooms require additional measures to maintain healthy concentrations of CO2 and PM2.5 to reduce the risk of airborne disease transmission particularly in low-income communities. 

Malaria is one of the most prevalent diseases worldwide, with nearly half of the world residing in regions at risk of transmission. It is commonly spread to humans through the bite of a female Anopheles mosquito infected with Plasmodium spp. parasites. When feeding, mosquitoes ingest biogenic amines at concentrations found in the blood of the host. Adult patients with severe malaria have altered concentrations of serotonin and histamine in their blood compared to healthy individuals. Previous work showed the ingestion of serotonin and/or histamine concentrations associated with adult patients with severe malaria influenced key mosquito behaviors, such as the tendency to take a second blood meal, flight behavior, and visual object inspection—traits that are related to the transmission of malaria. However, the mechanisms by which serotonin and histamine modulate mosquito behavior remain unclear. Given the known involvement of these biogenic amines in physiological processes, we hypothesize that the ingestion of varying serotonin and histamine concentrations in Anopheles stephensi mosquitoes will alter their distribution across tissues. Mosquitoes are fed with deuterated serotonin and histamine at levels associated with patients with severe malaria versus healthy individuals. These deuterated compounds serve as tracers to distinguish endogenous (natural) from exogenous (ingested) serotonin and histamine in the tissue. The mosquitoes are dissected to retrieve the head as a proxy for the brain, the midgut, and sensory appendages including maxillary palps, antennae, legs, and proboscis. All tissue samples are extracted and analyzed via liquid chromatography-mass spectrometry (LC-MS) to distinguish and quantify deuterated and non-deuterated serotonin and histamine. By viewing all aforementioned tissue regions and comparing endogenous versus exogenous biogenic amine levels in the samples, we hope to understand the modulation of biogenic amine distribution in An. stephensi tissue and offer insights into possible connections between neuromodulators and behavior in the mosquitoes.

With an estimated billion people impacted by malaria, yellow fever, and zika every year, the mosquito has built its reputation as the "World's Deadliest Animal." Mosquitoes have an exquisite sense of smell, widely studied for its role in locating human hosts for blood meals. However, mosquitoes also use their olfactory systems to locate and access sources of plant sugar- an essential food that contributes to longevity and fecundity. In fact, only female mosquitoes feed on human blood, whereas all mosquitoes rely on plant sugar as a source of energy. Despite plant sugar being an essential nutrient source, relatively little is known about the identity of plants preferred by mosquitoes for their sugar meals. Unlike prior studies, this research utilizes molecular techniques to uncover the mosquito plant diet as found directly within the mosquito gut. In my research, I use wild-caught Aedes aegypti and Aedes albopictus mosquitoes- the vectors for yellow fever, zika, dengue, and chikungunya. I first extract the DNA within its digestive tracks, then use PCR to amplify plant-specific sequences. Following, I use DNA sequencing to identify the plant species consumed based on barcoding markers. Each plant possesses a unique bouquet of scent chemicals that may influence mosquitoes' foraging behavior. To investigate the profile of chemicals emitted by mosquito-attractive plants, I analyze their volatile organic compounds (VOCs) using gas chromatography-mass spectrometry (GC-MS). I first separate the individual VOCs present in the plant species using gas chromatography, then identify and quantify the compounds using mass spectrometry. By linking these chemical profiles to mosquito feeding preferences, this research helps determine which plant volatiles attract mosquitoes, providing insight into how odor-based mosquito traps can be improved. This work contributes to a broader understanding of mosquito feeding ecology, with applications for public health and mosquito population management.

The health risks of particulate matter measuring less than 2.5 micrometers (PM2.5)  include: respiratory disease, cardiovascular issues, and cognitive impairments. Its presence near schools and colleges remains underexplored. This study examines the relationship between PM2.5 exposure levels and academic outcomes in community colleges located in historically redlined neighborhoods across four major West Coast cities: Los Angeles and San Diego in California; Portland, Oregon; and the greater Seattle area in Washington. Using data from the PurpleAir Network, state air quality indices, and community college governing bodies, we analyzed and compared PM2.5 levels near institutions located within historically redlined neighborhoods and institutions located outside those neighborhoods. Leveraging the Python programming language and Google Colab, we examined correlations between an institution’s demographic makeup and transfer rates relative to PM2.5 exposure. Data sets obtained were filtered between the hours of 8 AM and 1 PM during the months of January 2024 through December 2024. Our findings indicate a correlation between higher PM2.5 exposure and lower academic performance for colleges serving predominantly racially marginalized communities located within historically redlined neighborhoods. This research reinforces the role of environmental inequities in shaping educational disparities and highlights the need for targeted policies to address air quality in affected communities.

Safe drinking water in schools is crucial for children's safety and academic performance. While Seattle Public Schools has tested for some contaminants, such as lead, the district's responsibility for ion-specific testing for anions such as phosphate, bromide, nitrite, nitrate, chloride, sulfate, and sulfite is less clear. High concentrations of anions pose potential health risks, including reduced oxygen in red blood cells, higher risks of tumors in children, and diarrhea. This research investigated the anion concentration in water fountains across seven high schools in the Seattle Public Schools. Twenty-one water samples were collected from seven public high schools and analyzed for anion concentration using ion chromatography. Results were compared to the Environmental Protection Agency's (EPA) maximum contaminant level (MCL). All test samples were below the EPA's MCL. These results suggest that the drinking water in these schools does not pose potential risks to students from anion contamination. While regular monitoring and management are still necessary to maintain safe drinking water, Seattle Public Schools have met the safety requirements for anion concentration in their drinking water. 

The Red-legged Honeycreeper, Cyanerpes cyaneus, is a member of the passerine bird family Thraupidae (tanagers) and is part of a group commonly called Neotropical honeycreepers.  Along with other honeycreeper species, C. cyaneus is a nectarivore, meaning that floral nectar is a large component of its diet.  It is expected that C. cyaneus, like other avian nectarivores, exhibits specialized adaptations to the tongue and bill and specialized feeding mechanisms for feeding on nectar, but this remains unexplored.  This study analyzes the kinematics (movements in space) of the bill and tongue during nectar feeding in C. cyaneus to investigate how this species is adapted for nectar feeding.  The feeding kinematics of C. cyaneus are then compared to those of three frugivorous (fruit-eating), but opportunistically nectarivorous, tanager species: the Crimson-backed tanager (Ramphocelus dimidiatus), the Palm tanager (Thraupis palmarum), and the Blue-grey tanager (Thraupis episcopus).  These opportunistic nectar feeders were given access to nectar and their feeding kinematics were characterized and compared to those of C. cyaneus to determine how ancestral patterns of feeding kinematics could be co-opted for specialized nectarivory.  Birds were filmed in Panama using high-speed videography and footage was digitized using the DLTdv8 imaging tool. Data were subsequently processed in Microsoft Excel and RStudio.  By comparing the feeding mechanics of C. cyaneus with those of closely related opportunistic nectarivores, this research aims to not only uncover the nectar extraction mechanisms used by C. cyaneus, but will be the first study to examine the evolutionary trajectory of nectar-feeding biomechanics.  These anticipated findings will contribute to a more comprehensive understanding of the evolution of avian nectarivory.

Ecological data from the Green River College main campus trails have recently shown a significant increase in fungi observations in recent months compared to previous years. In addition, the diversity of these fungi vary greatly in comparison to previous years, raising concerns of identification errors. This project works to manually sort fungi observed on Green River College into their proper taxonomic groups to observe the species abundance and diversity of September 2023-December 2023 compared to September 2024-December 2024. Results show that, although there were several errors with the initial identification of several species, the abundance, distribution, and variation of fungi had significantly increased in Fall 2024 compared to Fall 2023.

Changing patterns of human land use near coastal zones have increased the abundance of aquatic habitats where mosquito and midge larvae develop. Salt-tolerant species, such as Aedes togoi mosquitoes and Dicrotendipes enteromorphae midges, have evolved distinct anatomical and physiological mechanisms that allow them to thrive in saltwater environments while also being able to develop in freshwater. While much is known about how freshwater-confined species maintain salt and water homeostasis (i.e. osmoregulation) in dilute freshwater, these processes remain largely unexplored in salt-tolerant species. The main goal of this research was to describe and compare the osmoregulatory strategies of Ae. togoi and D. enteromorphae larvae reared in seawater and freshwater, focusing on how they maintain ion and water balance in saline conditions. Based on information from other salt-tolerant insects, I hypothesized that the rectum of these species is the main organ that excretes salts and will have higher expression of ion pumps compared to other osmoregulatory organs of the larvae. This increased expression would support the secretion of hyperosmotic (salty) urine, a critical adaptation for survival in saltwater. Using immunohistochemistry and fluorescence microscopy, I localized key ion-transport pumps within the rectum and other osmoregulatory organs of Ae. togoi and D. enteromorphae larvae. I identified a high expression of Na⁺/K⁺-ATPase (sodium/potassium pump), and V-type H⁺-ATPase (proton pump) enriched in the anal gills, renal tubules, and the rectum. My findings suggest that the coordinated function of many osmoregulatory organs, and not just the rectum, allows for salt-secretion by marine insects, and this establishes an initial framework of cellular mechanisms among marine insects. This research has implications for predicting future species distributions with rising sea levels, as well as the potential to identify novel targets to control salt-tolerant mosquito populations to mitigate disease transmission in coastal regions.

Neotrypaea californiensis, or burrowing shrimp, is a native pest for oyster growers in Washington. The shrimp create networks of interconnected burrows that displace and liquify sediment, suffocating oysters. The pesticide carbaryl was used for decades to effectively control shrimp populations. More recently, the Environmental Protection Agency (EPA) deemed carbaryl an environmental hazard, leading to a vital need for a shrimp control method with minimal non-target effects. Very little is known of the physiology of shrimp that allows them to tolerate environmental extremes. My study aims to understand the tolerance of Netotrypaea californiensis to high concentrations of salts that challenge their ability to regulate internal ions, pH, and metabolic wastes. Using a laboratory-based system whereby shrimp burrow in 6 inch deep sediment in seawater, my research findings revealed that the addition of high concentrations of sodium bicarbonate (NaHCO₃) caused shrimp mortality while high concentrations of regular sea salts did not. This suggested that an ionic imbalance—high levels of sodium and reduced levels of chloride—may be causing shrimp death. To investigate, I collected the gills, a critical organ that regulates systemic ion levels, of shrimp after NaHCO₃ exposure and quantified the abundance and localization of key ion pumps using Western blotting, immunohistochemistry and confocal microscopy. I found a significantly higher expression of Na⁺/K⁺ pumps in the gills with NaHCO₃ exposure, suggesting a major ion-regulatory disturbance caused by NaHCO₃. These data will expand our understanding of how salts that cause ionic imbalance in seawater can disrupt the internal levels of ions that are critical for most biological processes. Findings will be disseminated to Washington oyster growers to aid in the management of their crop.

This research study explores the evolutionary adaptations of the TLR7 protein receptor in primates in relation to Flavivirus (Yellow Fever) recognition. TLR7, an important receptor in the immune system, is essential for recognizing single stranded RNA viruses such as Flavivirus. Given the growing prevalence of Yellow Fever in tropical climates, I hope to understand how environmental factors shape immune response. I hypothesize that ecological niches, particularly wet vs dry climates, play a crucial role in the evolution of the TLR7 receptor among primate species. Since Yellow Fever is transmitted by mosquitoes, which thrive in wet climates, these environments are likely driving the transmission of the virus. As a result, wet climates may exert selective pressure on the evolution of TLR7 to enhance immune responses against Yellow Fever in regions where mosquitoes are prevalent. To conduct comparisons of the TLR7 receptors, I will be running Blast, a bioinformatics software that compares genomic sequences across different species. This tool will allow for identification of both conserved and divergent regions in the TLR7 sequences from primate species, including humans, that inhabit wet and dry climates. These variations could reveal evolutionary adaptations influenced by ecological pressures. Through these sequence comparisons, I aim to explore how differences in TLR7 might affect susceptibility to Yellow Fever and other similar viral infections. Understanding how ecological conditions shape immune receptor evolution could also improve our ability to predict how different populations might respond to emerging infectious diseases.

Dynamic marine environments require long-term spatiotemporal datasets to successfully monitor and understand patterns in ecosystem composition on a decadal scale. High-resolution photography is often used to compensate for the field logistical constraints associated with marine sites, such as personnel availability or weather conditions, and works well to quickly capture data in the field. However, these photos require extensive manual analysis after the fact. As a research mentee, I asked the question: “Can image annotation with machine learning models provide enough clear data to inform community ecology studies of sessile organisms in subtidal habitats?” Using images collected through transect/quadrat sampling by the Sebens Lab’s Salish Sea Long-term Monitoring Project (University of Washington Biology and Friday Harbor Laboratories), a variation of an open-source model (CoralNet) was trained in the identification of relevant sessile flora and fauna. I then used CoralNet to continue the work of the lab by generating sessile assemblage metrics for a single site in the Friday Harbor Laboratories Biological Preserve. This site included images from transects at two different depths, with sampling from 2014 and 2024. After being uploaded, CoralNet identified 200 random points per image to the lowest possible taxon. I then reviewed all annotations for accuracy and corrected them whenever necessary. This technique greatly reduced the time spent per identification, without sacrificing accuracy. Next, I calculated species richness and Simpson’s Diversity for each quadrat and transect, comparing between depth and year. My analysis showed significant increases in both metrics from 2014 to 2024 and no significant differences between depths, demonstrating a successful report on the dynamics of a subtidal marine community. Application of this method to the entire existing dataset (7 sites, 63 transects per year), and others, provides opportunities to streamline analysis of sessile community composition.

Neutrophils are a type of white blood cell in the human immune system that can migrate through tissues to respond to sites of injuries and infections. In the laboratory, we can recapitulate neutrophil migration under controlled experimental conditions by using a cell line, called HL-60, that was originally derived from a person with leukemia. These cells can be cultured to imitate the behavior of neutrophils, and specifically they are able to migrate while we watch them on the microscope. First, I determined how HL-60 cell migration depends on the physical nature of the substrate they are crawling on. I compared cell migration under three different conditions: 1) uncoated plastic, 2) plastic treated to make the surface stickier for cells, and 3) plastic coated with a protein, BSA, to make the surface less sticky. I found that cells moved faster and with straighter paths on the uncoated plastic. Next, I used a drug, CK666, which is known to inhibit a protein that is important in the assembly of the cell’s actin cytoskeleton, the mechanical driver of cell migration. As expected, I found that the cells moved more slowly in the presence of the drug. Also, I found that the drug made the cells move in less straight paths. Finally, I explored how the HL-60 cells responded when I exposed them to an electric field. Electric fields are thought to arise naturally at sites of skin wounds. I observed that the cells moved toward the cathode of the electric field. I am currently analyzing whether the cells also move faster or straighter when there is an electric field present. In future experiments, I plan to determine whether mutating specific proteins thought to be involved in cell motility can change the behavior of the HL-60 cells on the microscope.

Glaciers have long been used as the bellwethers of climate change, given their ability to store gases, dust, microbes, and other environmental materials in their layers; tracking their recession has also been an important visual indicator of climate change. In this research, I examine how anions in newly exposed vary with depth. To do this, I took samples from exposed vertical ice faces on the Coleman glacier, on the north face of Mount Baker. Samples were thawed and analyzed using ion chromatography.  Trace amounts of chloride, nitrate, sulfate, and phosphate were found in each sample. The ion concentrations showed no trend with depth, and the ice itself appeared uniform. This is in contrast from vertical cores taken from solid ice in numerous other surveys, which show distinct annual layers and variation. This suggests that the ice at vertical faces has different properties from that at the top layers, including in its ability to trap environmental markers. Further research is needed to confirm this difference and examine which of these markers is most affected. Increased understanding of these markers could give more insight into how glaciers change over time and interact with their environment.

The widespread use of makeup raises concerns about bacterial contamination, which can lead to acne, rashes, pink eye, and staph infections. Despite these risks, hygiene practices in cosmetic use, especially in public settings, are often overlooked. This study investigates bacterial contamination in both personal makeup products and in-store testers to assess potential health risks. Swab samples were collected from used personal cosmetics and store testers at popular beauty retailers, focusing on mascaras, foundation bottles, lipsticks, and sponges. Samples were transferred to nutrient-rich media plates, incubated at 37°C for 24–48 hours, and analyzed through colony-forming unit (CFU) counts and Gram staining for bacterial classification. Preliminary results suggest that store testers contain higher bacterial loads than personal products, emphasizing the need for improved hygiene practices in retail environments. These findings could encourage cosmetic brands and retailers to implement better sanitation protocols, such as stricter single-use applicator policies or improved packaging designs, to limit bacterial contamination and promote safer cosmetic use.

Manduca sexta is a model lepidopteran insect organism which has been widely used in the field of chemical ecology due to its impressive olfactory senses. Odorant reception plays an important role in locating nectar sources, mating, and ovipositioning. Insects detect volatile chemical compounds (VOCs) present in their complex environment primarily through their sensory organ antenna. Each antenna is made up of thousands of olfactory receptor neurons (ORNs) and each neuron detects specific odor molecules with specific odorant receptor proteins. The whole genome sequencing of Manduca sexta has identified the major chemosensory receptor proteins: odorant (ORs), ionotropic (IRs) and gustatory (GR) but the role of each receptor is still unclear. In this project, we are investigating the role of female-biased odorant receptors OR5 and OR6, which might be involved in detecting VOCs present in their environment and play an important role in mating and oviposition. To investigate the role of these ORs, we have generated mutant strains by using a CRISPR/Cas9 approach and we are checking their effect on odor detection and oviposition behavior by comparing them with wild type strains. We are also performing an RNA-FISH experiment to visualize the ORs and locate the olfactory sensory neurons in the female antennae. In addition to this, we are also working on developing a neurogenetic tool which will allow us to measure the neuronal activity in response to different olfactory stimuli by generating a pan-neuronal BRP-GCaMP6s transgenic line.

Hyalella azteca are freshwater amphipod crustaceans abundantly found throughout North America and are frequently used in toxicology for water and sediment toxicity testing. As freshwater bodies change due to anthropogenic climate change, understanding chronic, sublethal impacts to aquatic life is critical. Amphipods are known to have a higher tolerance to heavy metals (i.e. Cu²⁺) and road salt (i.e. NaCl) compared to other aquatic invertebrates, however, these contaminants may have subtle, sublethal consequences on their ability to smell and detect chemical cues for survival and reproduction. This research identifies the combined impacts of environmentally relevant levels of Cu2+ and NaCl, on the olfactory system and olfactory-related behaviors of H. azteca. H. azteca underwent acute 96 hour exposure to control, Cu2+ (30 µmol/L), and combined Cu2+ (30 µmol/L) and NaCl (5 ppt) contaminated freshwater. I recorded daily measurements of survival, and utilized qPCR to examine changes in the expression of key olfactory genes that we predicted would be modulated in response to these multiple stressors. I assessed the olfactory-associated foraging behavior to determine changes in their detection of an attractive food cue when exposed to Cu2+ and NaCl, which would indicate olfactory impairment. Preliminary results show that amphipod survival is not impacted by Cu2+ and NaCl contamination but changes to their olfactory system occur. Therefore, U.S. Environmental Protection Agency water quality standards for heavy metals and salt may not mitigate long-term, sublethal effects on aquatic animal populations as it relates to this important sensory modality.

The focus of this research was to test the effectiveness of a silicone-based paint in the marking of Pieris rapae in a manner that was non-invasive and durable. Previous studies have tested other marking methods but have faced challenges such as harm to the organism. By using a paint made from red cabbage (Brassica oleracea), I aim to minimize the harm to larvae in current marking methods while retaining durability under moist conditions. This experiment examined both the durability and health effects of cabbage-based paints on P. rapae caterpillars. Preliminary experiments tested a water-based version, which did not appear to affect survival but faded under moist conditions, and a silicone-based version, which withstood moisture but raised concerns about potential effects on health due to the additional ingredients required for the silicone base. My research continued testing the cabbage paint with a cosmetic-grade dimethicone base and aimed to determine the extent that the cabbage paint may have on caterpillar health and survival. Survival experiments were conducted on 4th and 5th instar caterpillars to determine larva mortality rates when exposed to the pigment. Weight change experiments were conducted from the 4th instar to pupation to be used as a metric of the overall health of the larvae. I conclude that the silicone-based cabbage pigment is a promising marking method for larger caterpillars, offering improved durability and minimal impact on overall health compared to many conventional methods. These findings contribute to the development of safe durable marking techniques suitable for ecological research on soft-bodied insects.

The timing of flowering in Arabidopsis thaliana is tightly regulated by environmental cues that induce the expression of FLOWERING LOCUS T (FT), a mobile signal responsible for floral induction. Recent studies have identified FPF1-LIKE PROTEIN 1 (FLP1), a gene co-expressed with FT in phloem companion cells, as a potential regulator of flowering. Given FLP1’s genetic similarity to known flowering regulators, we hypothesize that it functions as a mobile flowering-promoting signal. Using predictive protein interaction modeling with AlphaFold 3, followed by Bimolecular Fluorescence Complementation (BiFC) and Yeast-Two Hybrid assays, we confirmed that FLP1 interacts with key proteins in the shoot apical meristem. Overexpression of FLP1 leads to early flowering in Arabidopsis, while loss-of-function mutants exhibit delayed flowering, supporting its role in floral induction. Interestingly, while FLP1 homologs generally promote flowering across species, a contrasting effect in Brachypodium distachyon has been observed, where overexpression of its homolog (BdFLP1/BdFLP7) delays flowering. This unexpected result raises critical questions about the molecular basis of functional divergence among FLP1 homologs. To investigate this, we are introducing BdFLP1 and BdFLP7 into Arabidopsis to assess their effects on flowering time and to determine whether structural differences or distinct protein interactions underlie their divergent functions. Through molecular cloning, transgenic expression analysis, and biochemical assays including western blotting, immunoprecipitation, and mass spectrometry, we aim to elucidate the role of FLP1 and its homologs in flowering regulation. Understanding these mechanisms will provide deeper insights into conserved and species-specific pathways controlling floral induction. This knowledge is essential for improving crop adaptation strategies in the face of climate change, highlighting the broader significance of our research in plant developmental biology.

The Manduca sexta hawkmoth, a proficient pollinator, employs its antennae to efficiently navigate its surroundings. The antennae have highly sensitive olfactory receptor cells, allowing the moths to have an acute olfactory sense and odor recognition ability, making the moth antennae an ideal candidate tissue for developing reliable biosensors. In contrast, commonly used portable artificial sensors are inefficient and inaccurate in chemical detection. To evaluate the moth antenna's effectiveness as a biosensor model, I assessed the longevity in neural activity of the antenna via an electroantennogram over 24-hour durations. To do this, I attached an excised antenna to a circuit board to measure voltage variations across the antennal nerves during odor stimulation to understand the baseline antennal lifespan. To increase the longevity of electrical activity, I formed a hydrogel solution to enclose the antenna to protect it from drying out, and Leibovitz's L-15 Medium so the antenna has access to Amino Acids to build and repair its tissues, serving as an energy source. Preliminary findings show a tradeoff between longevity and electrical activity, where the antenna-only trials had high voltage readings over 4 hours while the hydrogel antenna had less intense electrical readings over 8 to 12 hours. The hydrogel proved to be a quality medium for the diffusion of the L-15 media over long periods of time, preserving the antenna from dying prematurely. These results demonstrate that moth antennae are a suitable model for  highly accurate and efficient long-duration biosensors and support the feasibility of implementing them in devices that detect and identify substances of interest with a longer life span. Future work will apply machine learning methods for enhanced chemical discrimination in disease diagnosis.

Transcriptional repression plays a critical role in the regulation of various biological processes, including developmental pathways and disease progression. Corepressors are proteins recruited by partner proteins to negatively influence the transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and is known to play a pivotal role in transcriptional repression. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single engineered locus. To further understand the function of corepressors, we built a synthetic repressor system, dCas9-TPL, designed to specifically repress the transcription of the RUBY reporter gene. When expressed, the RUBY reporter turns Arabidopsis thaliana pink. In previous phases of this research, we utilized the EMS (ethyl methanesulfonate) mutagenesis protocol to create a population of plants containing many random mutations. Screening these plants for increased RUBY expression, I successfully Identified promising homozygous lines where plants demonstrated bright pink flowers and unique phenotypes such as early flowering, light avoidance, and small stature. Last quarter, I sent five lines to be sequenced and each line displayed distinct mutations that I can further explore to pinpoint the exact TPL interactor responsible for its unique phenotype. I am also investigating known TPL interactors such as SPT4, SPT5, and MED21 by creating transgenic lines within my control dCas9-TPL + RUBY line. Through genetic screening, I have validated the phenotypes among these control experiments. By investigating the intricate network of interactions between these regulatory proteins, I aim to gain a deeper understanding of how gene expression is coordinated across different cell types and how this process controls complex developmental pathways.

One of the most deadly creatures, the Aedes aegypti mosquito, flies under the radar of the everyday person far too often. However, as known carriers of vector-borne diseases such as dengue fever, Zika and yellow fever, these insects pose a significant risk for disease transmission. Our study aims will investigate the role of human-associated odors and colors in mosquito learning. I plan to test hexanoic acid and acetophenone, both odors which are commonly found on human skin. Acetophenone in particular is found in increased levels in patients with dengue fever, so by studying that particular odor more can be learned about the spread of disease. Using aversive training, mosquitoes are exposed to these odors paired with a shaking stimulus that simulates defensive swatting. A human-like color (orange) will additionally be paired with the odor to assess whether visual and olfactory stimuli presented together will strengthen the learning. After training we will place them in a two-way maze to test whether the scent and/or color was learned or not. This research will contribute to understanding how mosquitoes associate human-related  visual and olfactory cues, which may help inform future research on mosquito behavior and control strategies.

Plants' defense mechanism against herbivory is integral to both resistance in nature and the global food supply. Glycine max or soybean, is one of the most widely grown crops in the world, and suffers substantial losses from pests, including many Lepidopteran species. Related legumes, including cowpea, and common bean, can respond to Lepidopteran herbivory by detecting Inceptin-11 (In11), a short peptide found in larval oral secretions. The protein responsible for this ability, Inceptin Receptor (INR), is not found in soybean. The aims of this project are two fold, firstly introducing INR into soybean lines and testing for improved resistance to Lepidopteran herbivory, and secondly studying the effects of INR on defense gene expression in soybean, in order to better understand mechanisms of herbivory resistance. The first step in this project was to create soybean lines which consistently express INR. This was done by sending our INR construct to collaborators, who used it to inoculate multiple soybean lines, then breeding the corresponding lines until response to In11 was seen in all offspring. We will then test larval beet armyworms (Spodoptera exigua) on both INR- and INR+ lines. We expect the INR+ lines to have significantly lower S. exigua growth, indicating an improved immune response. We are also infiltrating INR- and INR+ lines with both In11 and flg22 (a well studied bacterial elicitor) for RNA sequencing of the early immune response. We expect genes involved specifically anti herbivory mechanisms being upregulated when compared to flg22. These two prongs allow us not just to demonstrate the viability of stable transgenic herbivory resistant lines, but to uncover the molecular mechanisms involved in that resistance, allowing for future scientists to better engineer the next wave of pest resistant crops.

The King County Brightwater Treatment Plant includes a marine outfall pipe anchored to the seafloor that discharges highly treated effluent from the Seattle metropolitan area into Puget Sound, Washington. Since 2009, as part of an eelgrass survey study, King County biologists have collected annual video footage of the outfall pipes from which they witnessed the abundance of organisms colonizing the pipe at all depths. Consequently, in 2012, King County biologists launched a ten-year project assessing the effectiveness of the high-density polyethylene (HDPE) outfall pipe at providing habitat for marine organisms and the composition of organisms it houses. Using a  remotely operated vehicle (ROV), they placed thirty plates of HDPE material adjacent to the outfall pipe at 100ft, 300ft and 600ft depths. Sets of replicate plates were then retrieved after 2, 5, and 10 years of deployment, at which time King County staff immediately took photos of each plate for analytical assessment. In this study, we analyzed the photos for percent live cover and composition of marine organisms inhabiting the pipe material, all across depths and time intervals. We hypothesized that the wastewater outfall pipe can function as a habitat; and the extent to which different organisms, their identifications and abundance, likely vary by depths due to the environmental conditions at different levels of depths. We found that percent live cover increased over time but did not vary across depths, and that certain phyla consistently dominated cover on the plates but dominant groups varied across depths. These findings allow experts in the field to consider using outfall pipes to provide additional habitats for marine organisms, and to assess communities of organisms at depths that are less accessible. 

In mammals, the primary mechanism regulating circadian rhythms is the central circadian pacemaker in the suprachiasmatic nucleus (SCN). The 24-hour light-dark (LD) cycle is the primary environmental cue, or zeitgeber, that entrains the SCN and sets its phase by adjusting its timing via phase advancing or delaying. Our laboratory has demonstrated that when mice are foraging outside of their safe nest, cyclic fearful stimuli can act as a nonphotic zeitgeber, entraining circadian rhythms and shifting activity from nocturnal to diurnal. However, the mechanisms of this so-called “fear entrainment” and phase-specific properties of cyclic fear remain unclear. This study examined whether cyclic fear via footshocks differentially entrains activity depending on the circadian phase of exposure. Mice were housed under a 12h:12h LD cycle and divided into three groups based on shock timing: the first six hours of the dark phase, the last six hours of the dark phase, and the middle of the light phase. Both dark phase groups showed delayed activity, with only the early dark phase group exhibiting evidence of entrainment. The mid-light phase group remained nocturnal. To further investigate the interaction between light and nonphotic entrainment, we conducted a follow-up experiment in which mice were placed under constant laboratory conditions (constant darkness) before undergoing cyclic footshock exposure. We hypothesized that, in the absence of light cues, the phase shifts induced by fear would differ from those observed under LD conditions, potentially revealing a distinct mode of nonphotic entrainment. Our findings so far suggest that entrainment to cyclic fear may only be achieved through delays, and that circadian oscillators may use different mechanisms of entrainment in response to photic vs. nonphotic zeitgebers.

In mammals, circadian rhythms are regulated by a hierarchy of oscillators governed by a central circadian pacemaker in the suprachiasmatic nucleus (SCN), which is principally entrained by the light-dark (LD) cycle. Recent experiments in our lab have revealed that cyclic 24-h fearful stimuli can act as a potent nonphotic zeitgeber, entraining circadian rhythms of behavior in mice and rats. This discovery utilized a naturalistic rodent cage with a safe nesting area separated from a foraging area where feeding and drinking occur. While foraging behaviors naturally occur at night, when the foraging area is rendered dangerous by nocturnal aversive stimuli (footshocks), animals entrain behaviors to the shock schedule by shifting activity to the daytime. Under conditions of fear-entrainment, SCN clock gene expression remains loyal to the LD cycle and the SCN is necessary but not sufficient for sustaining diurnal activity. Therefore, we propose the existence of extra-SCN fear-entrained oscillators capable of overriding SCN output and influencing behavioral timing. Here, we subjected 40 mice to either diurnal shocks (DS; control) or nocturnal shocks (NS) under a 12:12 LD cycle. Following confirmation of fear-entrainment, animals were released into constant conditions and sacrificed between 24-36h after the last presentation of footshocks, either CT 1 or CT13. Brains were dissected, sliced, prepared for immunohistochemistry processing, and c-FOS and PER2 protein quantification is currently underway in the SCN, basolateral amygdala, paraventricular nucleus of the thalamus, and dentate gyrus. We hypothesize that c-FOSs and PER2 expression within the SCN will align with the LD cycle, while centers involved in fear processing and memory will exhibit altered levels of c-FOS and PER2 expression in response to time-specific fear. Results from this study may be useful for identifying putative brain regions containing fear-entrainable oscillator(s).

Understanding the ecology of vegetation systems in Earth’s past in response to past warming events helps contextualize how they might respond to current climate events. Ecological succession is an ecosystem dynamic in which plant species with different life strategies replace each other as plants colonize a disturbed habitat. Reconstructing which successional stage a fossil plant represents is an important step in reconstructing this process in the past. However, fossil plants preserve a limited number of traits. Leaf vein density (LVD) is a trait that relates to maximum photosynthetic rates and can be measured from fossil leaves, but there is limited empirical evidence for how it varies across succession in temperate deciduous forests. To address this knowledge gap, our study measures LVD of modern plant communities across a successional gradient in western North Carolina. We hypothesize that plants in younger forests have greater access to sunlight due to a less established canopy and will therefore have higher LVD to support a higher photosynthetic rate. As succession progresses and the canopy closes, we hypothesize that LVD will decrease with reduced light availability. Samples were taken from five sites in western North Carolina that vary in how long forest re-growth occurred following clear-cut timber harvesting, 4, 21, 44, 94, and roughly 200 years. At each site, leaves were collected and sampled at a community scale and were chemically treated to create images that highlight the veins. We then used ImageJ to measure LVD. The community mean and variance of LVD across succession will be analyzed, using both unweighted and weighted approaches, to test our proposed hypothesis of decreasing LVD through succession. Preliminary results suggest a potential LVD decrease as hypothesized but driven more by understory species rather than dominant tree species. Future work will refine interpretations and consider implications for the fossil record.

The Miocene Climatic Optimum (MCO) (17-14 Ma) represents the most recent significant global warming event and provides valuable insights into the future of our planet with higher CO2 levels and warmer temperatures. The Mascall Formation in central Oregon contains a fossil plant assemblage that reflects the vegetation present during the height of the MCO. Despite over 50 years of research in this formation, there is still much to learn about the ancient plant community. For instance, a fossil specimen, consisting of several leaves, that was collected recently exhibits similar trait to bamboo, which represents a new fossil finding in this formation. This project seeks to confidently assign this specimen to the bamboo subfamily Bambusoideae. By analyzing morphological and vein architectural features of the leaves using various microscopic techniques and digital photography. In addition to studying the specimen itself we explore the fossil plant silica bodies (phytoliths) also present in the surrounding substrate to provide independent evidence that bamboo was present in the region. The phytoliths can then be compared to those of current Native American bamboo to find evidence for relatedness or if it was part of some other lineage of bamboo, whether extinct or still present in South America or Eastern Asia. If the specimen turns out to be bamboo, it would have implications for the climate and ecology of eastern Oregon during the MCO as bamboo was not assumed to have previously been present.  

The Campanian stage of the Late Cretaceous (~84–72 million years [Ma]) was a dynamic interval for North American ecosystems including the evolution of angiosperm plants and the regression and transgression of the Western Interior Seaway (WIS). These dynamics likely impacted terrestrial fauna across the continent. Most studies investigating biodiversity in western North America during the Campanian focus on a single group (e.g., dinosaurs or herpetofauna), whereas few investigate diversity patterns of multiple taxa. This approach is imperative because comparing diversity patterns among taxa can provide rare insight into the synecology of animal communities. Vertebrate microfossil sites are ideal for such a study because they preserve large sample sizes, multiple taxonomic groups that likely coexisted, information about environmental conditions, and they sample multiple stratigraphic intervals. The Judith River Formation (JRF) of north central Montana preserves ~4 Ma of the Campanian (~79–74 Ma) and large regressive and transgressive cycles of the WIS. This formation, which is contemporaneous with the Dinosaur Park and Two Medicine formations, is also rich in vertebrate microfossil sites. To examine vertebrate diversity patterns through this critical interval, we compared taxonomic richness and relative abundances of Dinosauria, Squamata, and Lissamphibia from the JRF from three temporally distinct microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (~76.5 Ma), and Clamfetti (~75.2 Ma). Over four years, we collected and screenwashed fossiliferous, bulk-sediment samples from these sites. Thus far, we have recovered 998 and aim to recover 1,200 specimens total. We use our data and knowledge from the literature to evaluate the extrinsic factors (e.g., seaway regressions) that drove diversity changes in the JRF fauna.  Our preliminary results suggest a connection between diversity patterns and WIS cycles. We observe shifts in relative abundances and richness near the onset of the WIS transgressive cycle. 

Chloroplasts are central to plant immunity and act as a hub for immune signalling and defence-related hormone synthesis. The essential chloroplast-localized protein FtsHi1 is a component of the FtsHi import motor and is vital to translocating proteins across the chloroplastic membrane. Viral-induced gene silencing (VIGS) of FtsHi1 in Nicotiana benthamiana results in a bleached phenotype, indicative of decreased translocation of essential chloroplastic proteins and decreased chlorophyll synthesis. Previous work identified herbivore-induced kinase 1 (HIK1) as a potential interactor of FtsHi1. HIK1 is a receptor-like cytoplasmic kinase (RLCK) implicated in the immune response to caterpillars. FtsHi1 contains a predicted RLCK phosphorylation site, indicating possible phosphorylation of FtsHi1 by HIK1, which could promote defence signalling over photosynthesis. This project aims to test the impact of phosphorylation on FtsHi1 function and its role in protein translocation across the chloroplastic membrane. This work utilises engineered FtsHi1 variants, which mutate the serine phosphosite to either mimic FtsHi1 phosphorylation (Ser→Asp), prevent it (Ser→Ala), or recapitulate the wild-type protein sequence. To test the phosphosite mutation effects, FtsHi1 VIGS knockdown of N. benthamiana leaves will be transiently modified using Agrobacterium tumefaciens bacteria to express WT or phosphorylation-modified FtsHi1 constructs. The resulting colour phenotype for each construct will then be compared to the bleached phenotype of TRV2:FtsHi1 plants and the phenotype of wild-type plants. I hypothesise that the FtsHi1 phospho-null mutant will result in a rescue phenotype similar to wild-type FtsHi1, whereas FtsHi1(phospho-mimic) will retain the bleached phenotype.Examining FtsHi1 phosphorylation enhances our understanding of its potential interaction with HIK1 in herbivory-induced plant defences. Future studies will explore FtsHi1's role in defence mechanisms, with implications for engineering herbivory-resistant crops. 

Plants defend themselves against invading pathogens and herbivores using immune receptors that detect molecular signals associated with danger. Two types of plant immune receptors are the leucine-rich repeat (LRR) receptor, receptor-like kinases (RLKs), and receptor-like proteins (RLPs) through which signal transduction may proceed through the cell. Coreceptors like SERK3/BAK1 and SOBIR1 pair with LRRs to facilitate intercellular communication. We studied a specific LRR receptor, the inceptin receptor (INR) that recognizes an eleven amino acid-long peptide chain known as inceptin-11 (in11). Given the close interaction of LRR and its coreceptors, and considering that we still don’t fully understand how INR recognizes in11, we investigated its three-dimensional structure to analyze the mechanism of ligand binding and signal activation. Through predictive modeling in Alphafold of homolog RXEG1, a carboxy-terminal loop out domain was identified as a facilitator in the binding interaction between INR and the BAK1 coreceptor. To explore this mechanism, we introduced targeted mutations in the domain’s K-X5-Y motif to potentially change its ability to recruit BAK1. When a ligand attaches to a receptor, its conformation change allows signals to pass through the cell membrane. We constructed a library of 36 single and double mutants in the K-X5-Y motif and coexpressed them with a luminescence-based reporter construct in Nicotiana benthamiana to screen their activity. We expect that a mutation at K or Y or both will affect BAK1 recruitment, leading to phenotypes that are hypersensitive or inactive. Insight into LRR-RLP coreceptor interactions could open doors to further INR-immunology research alongside better modeling of BAK1 protein binding. Targeting immune-related peptides in this screen could significantly advance cultivation programs for INR expressing organisms.

Grasses (family Poaceae) are highly diverse (~11,800 species), cover nearly 40% of Earth’s ice-free land surface, and play critical ecological and economic roles. Grasses have evolved a variety of unique traits, including an exceptionally high accumulation of silicon in the form of biological silica bodies (phytoliths) in some lineages. Silicon accumulation confers resistance to both abiotic and biotic stresses, including drought and salinity resistance, herbivore defense, and structural support. Despite the role of silicon in the enormous success of grasses, a clear picture of the exact drivers of silicon accumulation in grasses across species and environments has not yet emerged. I hypothesize that elevated silicon concentrations are primarily driven by environmental stress, most notably high temperatures and low precipitation. To test this hypothesis, I used X-ray fluorescence to analyze the leaf silicon concentration of 482 grass leaf samples, encompassing approximately 200 species across all 12 grass subfamilies. Using occurrence records from online databases, I identified the realized climate niche and its environmental conditions (e.g., temperature, precipitation) for each sampled species. The next step is to collect geolocation data from each individual sample, which will be combined with the climate niche data of its species. By comparing the relationship between a plant’s climate niche, its individual growing conditions, and its silicon concentration, a better understanding of environmental drivers of silicon will begin to emerge. Preliminary results taking into account only climate niche and silicon concentration showed no relevant correlations, illustrating the need for individual growing condition data. Because many of the stresses that silicon helps to alleviate are also those that will worsen under climate change (high temperature, drought, insect herbivory), an improved understanding of the environmental drivers of silicon accumulation will allow us to better prepare for the impacts of climate change on our agricultural and ecological systems.

The Campanian stage of the Late Cretaceous (84–72 million years [Ma]) was a dynamic interval for North American ecosystems and included the zenith of dinosaur diversity and the regression and transgression of the Western Interior Seaway (WIS). Most studies that investigate vertebrate biodiversity during this interval focus on dinosaurs, whereas few focus on changes in herpetofauna (lizards, frogs, and salamanders). Herpetofauna are important indicator species of ecosystem dynamics, because they are fragile to ecosystem change. Vertebrate microfossil sites are ideal for studying herpetofauna diversity dynamics through time because they can produce large sample sizes, sample aquatic environments, and are plentiful through stratigraphic intervals. The Judith River Formation (JRF) of north central Montana is rich in vertebrate microfossil sites, preserving ~4 Ma of the Campanian (~79–74 Ma). Here we aim to document patterns of herpetofauna diversity change in the JRF by quantifying herptile taxonomic richness and relative abundances using specimens from three temporally separated microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (76.5 Ma), and Clamfetti (~75.2 Ma). We collected sediment samples from these sites over four years and processed them via underwater screen-washing techniques. Presently we have studied 470 herptile microfossils (600 planned). Our preliminary results show changes in the taxonomic diversity across the sampled sites. Taxonomic richness of herptiles varies through the formation, first increasing and then decreasing. Salamanders have the highest relative abundance, lizards decrease in relative abundance, and frogs fluctuate. We hypothesize that taxonomic patterns are influenced by the impact of WIS cycles on water supply in ecosystems: amphibians thrive in wetter environments, whereas lizards are more terrestrial. These preliminary results reflect a connection between diversity patterns and extrinsic drivers not observable through the analysis of dinosaur fossils. Our continued analysis will provide more fine-scale resolution of herptile diversity during the Campanian.

Plants utilize molecular patterns in order to detect threats to the plant. Through the recognition of molecular patterns by their associated receptor, plants are able to initiate an appropriate immune response, measurable by the increased production of reactive oxygen species (ROS). In the model organism Arabidopsis thaliana, the pathogen associated molecular pattern flg22 is detected by the pattern recognition receptor Flagellin Sensitive 2 (FLS2) to initiate intracellular signaling. The immune signaling kinase Botrytis-Induced Kinase 1 (BIK1) is then phosphorylated by FLS2 to transduce the immune signal, initiating ROS production. However, A. thaliana lacks a group of immune signaling kinases related to BIK1 called Herbivory-Induced Kinase Like Kinases (HLKs), which are present in multiple species including tobacco (Nicotiana benthamiana) and common bean (Phaseolus vulgaris). The goal of this project is to determine the role of HLKs in immune signaling. To investigate the role of HLKs in immune signaling, A. thaliana were transformed with transgenes to express HLKs or overexpress BIK1. Stably transformed A. thaliana lines were then bred to produce progeny that are homozygous for the transgenes. These lines are treated with flg22 in order to initiate an immune response. ROS is used to measure the immune response of each transgenic line, where HLK expressing individuals are compared with BIK1 overexpressing individuals as a control group. I anticipate that HLKs will increase the ROS production when compared with the controls, signifying an increased immune response, since HLKs are related to the native BIK1. An understanding of the role of HLKs in FLS2 immune signaling in the model organism A. thaliana can be applied to crop species that employ HLK mediated immune signaling.

Carpels are invaluable floral organs that have undergone myriad innovations in flowering plant evolution, providing fruits and seeds. Carpels consist of a pollination site (stigma), pollen growth area (style), and a region containing ovules (ovary) which become the fruit after fertilization. Understanding carpel development and evolution is fundamental for efforts to increase food production. A decreased abundance of insect pollinators due to anthropogenic climate change has made this pursuit all the more urgent. The plant genus Thalictrum comprises perennial herbs in temperate regions that have repeatedly transitioned from insect to wind-pollination in their evolutionary history. Hence, they are ideal to investigate the adaptations and genetics that decrease reliance on insects for reproduction. A key feature of wind pollination is a longer stigmatic surface that increases pollen capture. I am taking a candidate gene approach, examining homologs of the stigma development gene families STYLISH (STY) and NGATHA (NGA). I am characterizing the role of NGA and two STYLISH gene copies in our model species, Thalictrum thalictroides. Previous work has found that silencing one of the STY gene copies results in the loss of stigma development, while the function of the other copy remains unknown. In other genera, altered NGA expression has been shown to alter stigma development. To characterize the function of both NGA and STY, I am implementing Virus-Induced gene Overexpression (VOX) by infiltrating tubers with Agrobacterium transformed with Tobacco Rattle Virus (TRV) carrying an overexpression construct. STY genes will be overexpressed, and NGA will be both overexpressed and silenced using Virus-Induced Gene Silencing (VIGS). I will characterize the phenotypes resulting from these treatments to determine the functionalization of STY and NGA. By dissecting the genetic basis of floral adaptations to wind-pollination in this system, I hope to contribute solutions to enhance crop production in the face of pollinator decline. 

It is estimated that ~15% of all cancers are caused by oncogenic virus infections. Two of the top seven cancer-causing human viruses are members of the gammaherpesvirus family: Epstein Barr Virus (EBV) and Kaposi’s Sarcoma Herpesvirus (KSHV). Our lab uses Murine Herpesvirus 68 (MHV-68), a mouse gammaherpesvirus with shares significant genetic homology to KSHV and EBV, as a model system to understand how gammaherpesviruses alter the metabolism of their host during lytic infection to promote their replication. We recently metabolically profiled MHV-68 infected host cells at various time points during the lytic infectious cycle. Our data showed nucleotide metabolism is significantly induced in MHV-68 infected NIH/3T3 cells, revealing a potential antiviral target. This study investigates the antiviral efficacy of Methotrexate (MTX), an FDA-approved nucleotide biosynthesis inhibitor currently used to treat cancer, rheumatoid arthritis, and psoriasis. MTX inhibits dihydrofolate reductase (DHFR), an enzyme crucial for producing thymidylate and purine nucleotides, which are essential for de novo nucleotide synthesis. We hypothesized that MTX can block MHV-68 production and be repurposed as an antiviral drug. To test our hypothesis, we first determined a safe concentration of MTX in NIH/3T3 cells using both qualitative (microscopy) and quantitative (trypan blue exclusion) cell viability assays. Next, we infected NIH/3T3 cells with MHV-68 and treated them with a safe level of MTX or solvent control. After 48 hours, we assessed viral production in control vs MTX treated cellular supernatants via viral plaque assays. Our results revealed that MTX significantly suppressed MHV-68 virion production by ~50-fold. These findings suggest that targeting host metabolic pathways could be an effective antiviral strategy against gammaherpesviruses in humans. Further research is needed to explore the use of MTX as a broad viral therapy against other viruses.

Flowering plants are important sources of agricultural crops and are diverse in flower and fruit structures. To study how this diversity has evolved, I am developing a new plant model system in the order Ranunculales, an underrepresented clade that will help bridge the knowledge gap within dicotyledonous plants, where most of the angiosperm diversity is found. A key tool in model system development is the ability to transform plants to study gene function, therefore, I aim to develop a method for genetic transformation. Specifically, I am implementing the tried and true  “floral dip” transformation method of Arabidopsis using Agrobacterium tumefaciens in Myosurus minimus, tiny mousetails. This is a small, fast-growing plant that produces many seeds, making it feasible to generate and propagate stable transformants. As proof of principle, I am expressing fluorescent proteins (GFP and YFP) and a visual reporter called RUBY, which causes transformed plants to produce red pigment. I found red color on the petals of treated plants, suggesting that transformation is working in Myosurus. I am currently validating this phenotype by planting the seeds on antibiotic selective media. I expect to see that certain individuals are resistant to antibiotics, while others die, which will allow me to identify the genetically transformed plants. By developing this transformation method, I will be able to test the function of candidate genes of interest in this new model plant species, which will further enable the investigation of gene network evolution in flowering plants. Increased understanding of gene function provides opportunities for engineering crop species to have beneficial traits for agricultural purposes. 

Variations in floral structures influence how plants are pollinated, showier flowers are more attractive to pollinators, while wind-pollinated plants benefit from having smaller, inconspicuous flowers that produce increased amounts of pollen, and have the appropriate morphology to receive pollen from the wind. The genus Thalictrum contains species that range from insect-pollinated to wind-pollinated. Certain transcription factors are known to affect the stigma, the area of pollen reception that consists of papillae, and to increase stigmatic papillae length. By better understanding the genes that influence stigma morphology, this gene could be used in economically important crops to increase their stigmatic surfaces and consequently the likelihood of pollination. In this study, we use in situ hybridization to analyze gene expression of candidate genes for stigma development in the genus Thalictrum, which has had multiple transitions from insect to wind pollination in its evolutionary history. We selected three species representing the range of stigma morphologies found in Thalictrum. I will test the hypothesis that expression of my candidate genes will correlate with stigma morphology, such that the short (capitate) stigmas characteristic of insect-pollinated species will exhibit restricted areas of gene expression just prior to stigma development, while the more elongated stigmas of the wind-pollinated species will show an extended temporal and spatial domain of expression, with mixed-pollinated species lying in between. Thus, this work will provide a connection between developmental genetics and morphology to improve understanding of the wind pollination syndrome.

Our sense of touch plays an important role in how we perceive the world. Touch sensation is the result of an intricate interplay between the nervous system and specialized sensory cells in the skin, one such example being the Merkel cell-neurite complex. Within the Merkel cell-neurite complex, Merkel cells (MCs) detect gentle touch signals in the skin and relay them to innervating neurites via synapse-like connections. Many aspects of the MC-neurite complex, including the molecules required for its formation and structure, remain poorly understood. Our lab recently discovered the presence of MCs in the transparent zebrafish skin, making the organism well-suited for study of MC-neurite complexes. Here, we show that Protocadherin-9 (pcdh9), a cell adhesion molecule important in synaptic structure and nervous system organization, is highly expressed in both zebrafish and mammalian MCs. Using a loss-of-function mutation in zebrafish pcdh9, we find a reduction in the number of MC-neurite complexes, but not in the number of MCs, compared to controls. This suggests a role for Pcdh9 in either the formation or maintenance of MC-neurite synapses. Additionally, we observe a higher rate of MCs contacting one another in pcdh9 mutant skin, consistent with a difference in MC spatial organization. In summary, our data indicate that Pcdh9 may regulate one or more aspects of MC-neurite complex formation. We are now in the process of developing tools to further investigate and quantify MC spatial arrangement, and to uncover the ways in which Pcdh9 may affect MC maturation and behavior.

The transcription factor LEAFY (LFY) controls the development of flowers in angiosperms, but it is found in all lineages of land plants, including those that do not flower. In the non-vascular plants like moss, LFY promotes the first cell division in the zygote, and in early vascular plant representatives like ferns, LFY controls stem cell activity. Ferns are the sister lineage of seed plants, making them an ideal model to study the evolution of LFY. The model fern Ceratopteris richardii has two copies of the LFY gene, while most angiosperms have one, and the two genes are expressed at different levels across development, suggesting the possibility of sub- or neo-functionalization. In this study, we use transgenic C. richardii plants overexpressing one or both LFY genes to determine their function across development. Since LFY is expressed in sperm cells, I set up assays to observe C. richardii sperm cells during fertilization and determine the role that LFY may be playing in fern sperm development and reproduction. To test whether the two fern LFY proteins interact with each other, I perform yeast two-hybrid assays, which will provide insight into whether the genes play independent roles or share overlapping functions. Determining the function(s) of LFY in ferns will help uncover the evolutionary history of this important plant transcription factor and how it came to control the crucial role of initiating flower development.

Chronic stress has been associated with maladaptive behaviors in both human and animal research models, but the underlying mechanisms are unclear. In this research study, we sought to define whether stress induces neural inflammation in the ventral tegmental area, the brain region primarily responsible for regulating reward consumption, learning, memory, and addictive behaviors through moderating dopamine release in other brain areas. To do this, male Sprague-Dawley rats were subjected to a chronic intermittent stress paradigm that included stressors such as wet bedding, delayed feedings, social isolation, strobe lights, and forced swims. Following the chronic stress intervention, brain sections were collected from control and experimental groups. Subsequently, immunohistological analysis was performed of microglia and astrocytes, cell types known to mediate inflammatory responses within the brain. By assessing inflammation in the ventral tegmental area through fluorescent microscopy and quantitative morphological analysis of these glial cell types, we will establish whether inflammation in this key brain region regulating motivation may be involved in the harmful behavioral outcomes often associated with chronic stress.

Rotated orientation patch count (OPCr) is a measurement used to quantify the complexity of a 3D surface. OPCr has previously been used to analyze tooth complexity, showing a correlation between complexity and diet in lizards, crocodilians, and mammals. We applied this technique to toothless taxa, with the goal of determining if there is a correlation between the complexity of the occlusal surface of a given species of turtle and its diet category. OPCr is determined by analyzing a 3D mesh of the occlusal surface of turtle specimens, with meshes based on both photogrammetry and CT scans of turtle skulls. Photogrammetry and CT scans are fundamentally different. Photogrammetry is a 3D mesh created from a series of surface images of an object, where the lighting and shadows cast on the object potentially distort its complexity. CT scans are not subject to these errors, and are typically more consistent provided the scan is made properly. However, there is little research analyzing the impact of different scanning techniques on the surface complexity of the resulting mesh. This project is therefore a comparison of photogrammetry and CT scans: do models made from these different methods produce significantly different OPCr scores? Nineteen specimens previously digitized using photogrammetry have been CT scanned. I created 3D models from the CT scan data and analyzed their surfaces using OPCr. I then compared the OPCr values produced by the CT scan models to the photogrammetry counterpart of each specimen. We hypothesize that statistical analyses will show no significant difference between the two methods of digitizing specimens.

Underground storage organs (USO) allow plants to retreat underground during periods of resource scarcity and/or abiotic stress. These adaptations help plants survive seasonal climates and have evolved repeatedly across the vascular plant tree of life. USOs develop as modifications of various plant tissues, including root, leaf, and stem tissues. The non-model plant Bomarea multiflora (Alstroemeriaceae) offers a unique opportunity to study the development and evolution of USOs as it has two types of USOs (rhizomes and root tubers), allowing for direct comparison. B. multiflora’s dual USOs and its phylogenetic position within the monocots makes it a good candidate for future development as a model species for USO development. Here we analyze a transcriptomic dataset of four distinct tissue types in B. multiflora: aerial shoot, rhizome, fibrous root, and root tuber tissues. We use ZigZag, a recently developed hierarchical Baysian model that determines the probability of active expression for each gene in each tissue type. We found 56 genes differentially expressed between individual tissues and 29 between root vs. shoot tissue. We review these genes and describe avenues for future investigation of USO developmental pathways within monocots.

Skin serves two key functions: hardened cells at the surface of the skin form a superficial layer to protect against the environment, while the inner layers of the skin are packed with diverse sensory machinery which allow us to perceive and navigate the world. Incredibly, the basal most layer of the epidermis houses stem cells which allow the skin to constantly renew itself, fortifying its protective function and maintaining somatosensation by replenishing all these diverse cell types. Perhaps unsurprisingly, these multipotent and highly active skin stem cells are emerging as an effective way to treat genetic skin conditions, promote wound healing, and rejuvenate ageing skin. To understand how skin stem cells contribute to these different functions, investigators are studying the many niches within the skin which may house diverse skin stem cells. Zebrafish are an excellent model to dissect this topic due to their translucent skin and the many genetic tools available. However, the anatomy and molecular characteristics of zebrafish skin is poorly described. Recently, we performed single cell RNA-sequencing of zebrafish skin and identified seven presumptive skin stem cell subpopulations. Informed by this data, I performed whole-mount hybridization chain reaction, a form of in-situ hybridization, to investigate molecular and spatial heterogeneity in zebrafish skin stem cells. My results have identified three novel skin stem cell subpopulations which occupy distinct spatial domains along the anterior-posterior axis. I found that the appearance of each subpopulation and the establishment of their spatial domain is dynamic throughout skin development. Finally, we have constructed a tool to interrogate their behavioral and functional differences. Moving forward, I aim to determine each subpopulation’s role in skin development, homeostasis, and regeneration, as well as whether they serve as specific progenitors for certain cell types.

Somatosensory neurons innervate the skin, where their peripheral axons detect signals like touch and pain. The neurons relay stimuli to the brain via peripheral axons in the skin and spinal cord axons in the spinal cord. Given their superficial location, somatosensory axons are susceptible to damage. Axon damage can cause tingling, increased pain, or sensory inhibition, and reinnervation in mammals is often slow or incomplete. I use injury models in zebrafish to study the mechanisms of successful axon regeneration in an adult vertebrate with optically accessible skin. I aim to reveal conserved regeneration patterns of somatosensory neurons. Furthermore, I seek to understand the extent of reinnervation success and observe the prevalence of hyperinnervation post-injury. Using in vivo confocal microscopy and adult zebrafish skin models, I created a methodology to capture somatosensory reinnervation over a three-week span following a scale pluck injury. Zebrafish scales separate epidermal and dermal layers of skin, and scale removal induces regeneration of epidermal skin and surrounding dermal tissue. I use transgenic zebrafish with fluorescent labels for dorsal root ganglion DRG neurons and osteoblast cells Tg(p2rx3a:mCherry);Tg(sp7:EGFP). DRG neurons are the primary somatosensory neuron in adult zebrafish, and osteoblasts allow me to view the scale alongside axon reinnervation. For image acquisition, I designed a 3d-printed chamber for zebrafish mounting and intubation within our confocal microscope. For analysis, I developed Image J macros which use threshold analysis to quantify changes in axon density of specific regions of regenerating axons. Dermal axons tend to regenerate first while superficial axons in the epidermis regenerate secondarily in conjunction with the novel scale. To examine skin layer differences, I separate epidermal and dermal layers to compare the reinnervation trends between superficial and dermal axons. With this data, I can gain insight in the regeneration potential of somatosensory neurons.

Lagomorphs (hares, rabbits and pikas) exhibit a range of specialized locomotory modes and predator avoidance strategies while maintaining similar herbivorous diets. Their close evolutionary relationship and similar trophic role makes lagomorphs an ideal group for examining the effects of habitat and locomotory modes on skeletal morphology. This project examines two aspects of lagomorph morphology to further understand its relationship to the habitat in which those lagomorphs live. The first aspect, limb anatomy, is quantified through caliper measurements and robusticity calculations of the appendicular skeleton. We previously hypothesized a relationship between limb anatomy and digging behavior in rabbits and hares. As an extension of this previous research, we have classified the extent to which each species burrows to further explore the relationships between limb morphology, evolutionary relatedness, and current burrowing behavior. The second aspect is body shape, which is quantified through caliper measurements of the vertebral column and calculated as the ratio between body length and body depth. We previously found no relationship between body shape and locomotory mode. This year, we plan to examine the third lagomorph group (pikas) and increase our hare and rabbit sample sizes to determine whether the patterns that we previously found to be insignificant remain. Further, we plan to compare these different groups using a phylogenetic ANCOVA to correct for evolutionary relationships that may cause bias in our analysis. We predict lagomorphs that burrow will have the most robust forelimbs to allow for greater force to be applied while digging. Additionally, we predict that while greater size will be associated with lower elongation, there will be no significant difference in elongation between groups of lagomorphs, based on our results last year. This project will describe the effect of habitat on skeletal morphology, which could allow for better understanding of extinct groups.

Previous studies suggest that tooth morphology (shape, size, and other features of teeth) strongly correlates with an organism’s dietary patterns, and analyzing dentition is common practice in the field of Biology. Orientation patch count rotated (OPCr), a technique used in establishing dentition-diet correlations, has recently been demonstrated as applicable to turtle triturating surfaces to understand their dietary adaptations. The aim of this study is to add to an ongoing project characterizing the relationship between diet and the cutting/grinding surface in the jaw (triturating surface) in edentulous (toothless) organisms using techniques used in traditional dental topographic analysis. Turtles are a diverse group of edentulous organisms with beaks of keratin to process their food — making them ideal for this study. Specimens of the omnivorous Forest-Hinge Back Tortoise (Kinixys erosa) were micro-computed tomographically (CT) scanned. We reconstructed the CT scans into photogrammetric 3D models using Slicer software. Then, we isolated the triturating surface using MeshLab software. Finally, we read the triturating surface into the R package molaR — resulting in OPCr values that estimate the complexity of their specimen’s triturating surface. Ideally, the OPCr values showcase extreme high triturating surface complexity, as previous research suggests tortoises (Testudinidae) have highly complex triturating surfaces compared with other clades of turtles. Our research hopes to contribute to a new technique for analyzing extinct beaked or edentulous taxa.

Human activity continues to significantly affect nature, expanding its area of influence via multiple sources. Artificial light at night (ALAN) is a major source of this human interference, originating from urban areas, roadways, and streetlights. Its influence is widespread, disrupting not only ecosystems but also the development, population size, life expectancy, and reproduction of plants and animals. We worked with house crickets (Acheta domesticus) to test whether and how exposure to ALAN throughout juvenile development altered behavior, development, and reproductive investment in the form of maternal hormone provisioning compared to crickets that experienced no light pollution. Here we report that lifelong exposure to ALAN affects cricket development and may influence the hormone provisioning to eggs by female crickets. However, ALAN had no effect on the behavior or movements of crickets. While our result is consistent with some previous findings in animal systems, it contradicts others: we conclude that the influence of light pollution on animal physiology and behavior is likely nuanced, and its effects are dependent on life history, development stage, and ecology.

Assessing one’s circadian phase is important to both clinicians and researchers. The gold standard method of estimating circadian phase involves identifying the clock time when melatonin levels increase when under dim light (<5 lux), called Dim Light Melatonin Onset (DLMO). This method involves collecting 8 hourly saliva samples, starting in the afternoon and finishing one hour after habitual bedtime. As external conditions can mask markers of circadian phase, such as bright evening lights inhibiting melatonin production, this method requires strictly controlled conditions (i.e. no eating, drinking, standing 30 minutes before each sample). This increases money and time cost of studies assessing circadian phase, and it reduces the accuracy and accessibility of DLMO assessments. The current study (n=17) attempts to validate a new method of estimating circadian phase, developed by Dr. Achim Kramer at Charité University, based on a one-time collection of hair follicles (HFs). Participants collected their own HFs in the morning before arriving at the lab to complete an evening DLMO assessment. I verified dim light levels via lux meter, ensured participants did not stand, eat, or drink 30 minutes before providing each saliva sample, and recorded the exact time of individual participants’ sample collection. I assayed saliva samples for melatonin levels to estimate DLMO. HF samples are processed at Charité University using the RNA levels of different relevant genes. We predict the circadian phases calculated by this method will significantly correlate with those of the DLMO assessment. If validated, this method would reduce the time burden on participants from ~8 hours to a matter of minutes. Reducing the cost of circadian phase studies will benefit researchers and clinicians alike, including for those living in remote areas or in areas with less healthcare access.

As a diverse mammalian clade defined by encephalization and an increased reliance on learned behaviors, primates serve as a uniquely well-suited subject for the study of how environmental factors may influence the diversity of brain morphology. Endocasts, which are 3D models of the cranial cavity, have been proven to be reliable proxies for brain shape and size and provide an accessible method for studying brain morphology. While it has been demonstrated that environment has caused convergent cranial morphology in lemur species, more investigation is necessary to uncover the exact causal variables of these changes and how they affect primates more broadly. In this study, we test the hypothesis that climatic factors contribute to morphological differences in the neocortex, olfactory bulbs, and cerebellum among primate species. For example, food scarcity caused by greater variability in rainfall and temperature may be correlated with investment in regions associated with learning and processing as described by the cognitive buffer hypothesis. Thus, we predict that increased rainfall leads to increased food availability and an increase in neocortex size which is responsible for higher order functions. To test our hypothesis, we obtained CT scans of primate skulls from the Natural History Museum, London, United Kingdom. We then used 3D Slicer to create endocasts from the cranial cavity and quantify endocranial morphology using landmark-based geometric morphometrics. We used phylogenetic comparative methods in R to test whether climate variables like temperature, rainfall, and altitude have induced changes in endocast morphology across species. Our findings will enhance the understanding of the evolutionary mechanisms particular to our own lineage and may help us better predict how Anthropogenic changes to climate will affect the evolution of organisms moving forward.

The mandible plays a central role in the mammalian skull as it is responsible for feeding. Various selective pressures, such as diet, habitat, and climate shape mandibular morphology across mammals, and in this study, we investigated their impact on mandibular evolution of primates and carnivores. This relationship will allow us to understand how environmental factors collectively impact the evolution of various species. In our previous research, we found that diet accounts for only 21% of the variation in mandibular morphology of primates. In this study, we extended our investigation to additional factors such as climate and habitat. We hypothesized that habitat and climate will affect mandibular morphology by driving adaptations in jaw structures to meet various functional demands of different environmental conditions. We tested these hypotheses by analyzing a database of 3D scans of primate and carnivoran mandibles from natural history museums. Mandibular shape and size were quantified using geometric morphometrics of the digitized 3D models. Habitat and dietary data were sourced from the carnivoran and primate literature, and climate data was obtained from WorldClim for species with matching habitat and diet information.  We used regressions and ANOVAs to evaluate the relationships between mandibular morphology, diet, habitat, and climate. Our research may be helpful for future primate and mammal studies focusing on the selective pressures on the evolution of the mandible.

Previous studies have found a correlation between the complexity of an animal’s teeth and its diet. However, not all vertebrates have teeth, such as turtles, which is problematic because dental topographical analysis has not been completed on toothless—or, edentulous—animals. Regardless of whether a species has teeth, we can use the measurement OPCr (orientation patch count rotated) to quantify the complexity of a surface, and subsequently use that value to analyze species’ diet. OPCr calculates the number of separately oriented patches on a 3D surface. A higher OPCr value indicates a more complex topography. To obtain OPCr values, we edited CT scans of the turtle species Malaclemys terrapin in Slicer and MeshLab, then analyzed the resulting model using the R package molaR. From this, we obtained OPCr values. However, R struggles to analyze meshes at a higher resolution, so we use various downsampling filters in MeshLab to make the models usable in R. One such filter is Quadratic Edge Collapse Decimation (QECD). The algorithm behind QECD is QSLIM, which reduces the complexity of polygonal meshes by eliminating edges based on error metrics from quadratic formulations, but still preserves the original shape as much as possible. Currently, we downsample all meshes to just 10,000 faces before reading them into R. My role in this project is to determine whether we can reliably use higher resolution scans by altering the number of faces to be slightly higher at 15,000 and slightly lower at 5,000, then examining the impact of these resolutions on OPCr values. So far, our analysis shows that importing a higher resolution mesh tends to give higher OPCr values, and a lower resolution gives a lower OPCr value.

Gaze tracking is a fundamental technology in human-computer interaction (HCI) and is integrated into interactive gaze devices, which serve as essential tools for enabling communication among nonverbal users. Gaze estimation reconstructs the line of sight in a single image by leveraging different kinds of information, such as head pose, face geometry, facial expressions, scene contents, eye model and localization, human-object relationships, and camera parameters. When performed continuously, gaze estimation evolves into gaze tracking, enabling the analysis of visual exploration patterns and fixation points. Through infrared lights, the eye gaze device calibrates by way of tracking the eye’s cornea through planes. Subsequently, users have increased accuracy to interact with pre-established icons manually. However, navigating through different pages on the device can be tedious, adding to the overall challenge of usability. Hence, I outline a framework for integrating predictive modeling into gaze-based interfaces, where convolutional neural networks (CNNs) analyze gaze patterns to infer intended actions, and large language models (LLMs) process contextual cues to refine predictions (i.e., input from auditory interface). Through an initial simulation and qualitative analysis, I explore the feasibility of these models in streamlining navigation and improving response accuracy. Preliminary findings indicate that predictive automation reduces cognitive load and interaction time by 90%, though challenges regarding model precision and adaptability to individual users remain. Future work will focus on refining predictive models to enhance personalization and trust in the modulated eye gaze device in order to reduce cognitive overload while safekeeping ethics.

Assessing how organisms respond to shifting climatic conditions is crucial in the era of climate change to predict species' resilience to environmental changes. This study aimed to explore the effects of heatwaves on grasshopper development and fitness. Specifically, I investigated the reproductive potential of two grasshopper species within the framework of a common garden heatwave experiment. In Spring 2023, we reared the grasshoppers under three heatwave intensity treatments, exposing each treatment group to three heatwaves during set developmental stages. Afterward, I dissected the preserved females frozen for analysis, quantifying the number of primary and secondary oocytes in their ovaries. Oocytes develop into eggs and as such are a metric of reproductive potential. I hypothesized that increased heat stress would result in a decline in fecundity. However, we did not find a significant effect of the heatwave treatment on oocyte count, suggesting any fecundity effects of heatwaves are via a different mechanism. Understanding how organisms respond to changing environmental conditions is key to understanding how ecosystems will change in the coming years, and is important for informing conservation efforts.

Diet is one of the most significant contributors to an organism’s morphology, as without morphological features to acquire food the organism will cease to live. Previous studies have quantified these morphological features in toothed taxa using Rotated Orientation Patch Count (OPCr) but not in edentulous taxa. Previously, we obtained OPCr from several turtle species using photogrammetry, created 3D models with Slicer, edited them down to just the triturating surface in MeshLab, and ran statistical analysis in R. Specifically, I worked on the unique, endangered turtle species Carettochelys insculpta (n=6) using CT scans obtained from MorphoSource to add to our photogrammetry data. However, the OPCr values obtained from these meshes discarded more surface area and were significantly lower than the meshes made from photogrammetry. To increase the surface area counted in the OPCr and potentially get results more comparable to the photogrammetry meshes we experimented with decreasing the percentage of patches discarded during analysis in R from 1% to 0.1% and tried smoothing the meshes in Slicer using a factors of 0.3, 0.5, and 0.7. A simple T-test was used to determine significant differences. To increase the number of available specimens and compare turtle species with different diets – durophagous and omnivorous respectively – Malaclemys terrapin specimens (n=5) were used in addition to the Carettochelys insculpta specimens. We expect to find increased surface area and higher OPCr values when increasing the percentage of patches discarded from 1% to 0.1%. We also expect that smoothing will increase the amount of surface area counted at both 1% and 0.1%. As a result of this study, we hope to create a better method for processing CT scans for morphological analysis of the triturating surfaces of turtles, and to develop a methodology for determining diet in any edentulous organism.

Previous studies have shown that the diet of an organism can provide valuable insight into a variety of characteristics including habitat, behavior, and ecological role. Analyzing dentition is one method used to determine an organism’s diet, but this becomes complicated for edentulous taxa. In this study, we investigated the dietary ecology of Caretta caretta, or the loggerhead sea turtle, through the 3D morphometrics of several CT-scanned skull specimens. We are particularly interested in studying a notable feature on the occlusal surface: the accessory triturating ridge. This structure functions as a way to process food and thus provides important insight into what kinds of nutritional sources Caretta caretta may be drawing from. To analyze and interpret the morphology of the ridge, we took a series of computed tomography (CT) scans and processed them into 3D models using Slicer. We then isolated the occlusal surface in MeshLab and used R to assess variations in morphology. This results in a rotated orientation patch count (OPCr), which we can use to analyze the complexity of the occlusal surface. This acts as a topographic map, with a higher OPCr value likely indicating an omnivorous or herbivorous diet, and a lower OPCr value predicting a carnivorous diet. Because Caretta caretta are known to be omnivorous, we expect to see a higher OPCr value, suggesting that their occlusal surface is more complex than that of other turtles. Analysis of this species contributes to our project's overarching goal of applying morphological analyses to edentulous species and can offer insights into conservation efforts for this ecologically vulnerable turtle.

Lepidosauria is a clade of reptiles including Rhyncocephalia and Squamata, constituting much of the diversity of living reptiles. Squamates include lizards and snakes, and are the most species-rich group of lepidosaurs. Rhyncocephalians were more diverse and widespread in the Mesozoic Era, but today are represented by a single living species, the tuatara of New Zealand. Lepidosaurs first evolve in the Triassic Period, making their fossil record from this interval critical to understanding the evolutionary origins this group. New lepidosaur fossil material from Petrified Forest National Park has been recovered from screenwashing sediment from the Kaye Quarry, a fossil bearing locality within the Sonsela Member of the Upper Triassic Chinle Formation. Three mandibles of unknown taxonomic affinity from the Kaye Quarry have been selected for anatomical description and phylogenetic analysis. All three mandibles display labiolingually compressed, recurved teeth, along the majority of the dentary. Two dentaries display a larger conical tooth, protruding dorsally from the anterior end of the mandible. Other mandibles recovered from the Chinle Formation display similar dental anatomy, indicating these specimens belong to the clade Rhynchocephalia. There are currently no lepidosaur fossils known from the Sonsela Member of the Chinle Formation. Sectioning and computed tomography (CT) scanning will be used to create detailed three-dimensional images of the mandibles for the basis of anatomical description and phylogenetic analysis. CT scanning hosts the potential for internal morphology including tooth implantation and neurovasculature.

The rapid evolution of antimicrobial resistance (AMR) in bacteria poses a critical global health challenge, predicted to cause 10 million deaths annually by 2050 if left unaddressed. AMR genes frequently reside on plasmids– small, circular DNA separate from bacterial chromosomes. These plasmids spread between bacteria through horizontal gene transfer (HGT), where genetic material moves directly from one cell to another, rapidly disseminating resistance genes across populations and species. In contrast, vertical gene transfer (VGT) occurs during bacterial reproduction, passing genes from parent to daughter cells. The machinery plasmids use for HGT imposes a fitness cost on the host, slowing its growth and reproduction (VGT). This means plasmids typically face a trade-off: investing resources in HGT limits the host’s ability to reproduce efficiently through VGT. My research uncovered a “trade-off-breaking mutation” that simultaneously enhances both HGT and VGT, accelerating the spread of AMR genes. Such mutations have significant public health implications, potentially leading to highly virulent, drug-resistant bacterial strains. I am creating a genotype-to-phenotype map to link specific plasmid mutations to their effects on HGT and VGT rates, aiming to understand the dynamics of resistance spread. This work involves verifying mutations in our mutant plasmid library using targeted sequencing techniques and applying the Luria-Delbrück method, a specialized approach developed by my mentor, Dr. Olivia Kosterlitz, to measure gene transfer rates. By analyzing these mutations, I seek to uncover how some plasmids avoid the typical trade-offs, enabling them to reproduce quickly while spreading resistance efficiently. Understanding the relationship between HGT and VGT is critical for predicting how antibiotic resistance evolves and for developing strategies to slow its spread. This research reveals the importance of trade-off-breaking mutations in resistance management, providing new insights into how we might combat one of our time's greatest public health challenges.

Bacteria can shuttle pieces of DNA between unrelated cells via a process called horizontal gene transfer (HGT). Genes that undergo HGT (i.e. mobile genes) evolve in different host bacteria with different genomic backgrounds, which can influence the types of mutations the mobile gene acquires. Studying the effect of HGT on mobile gene evolution is important as many clinically relevant antibiotic resistance genes are mobile. In a prior study, we used a simple model to simulate mobile gene evolution as they engage in HGT. Under the simple model, the mobile gene evolves in only one species at a time. With this model, we found that fitness landscape similarity between two host species engaging in HGT is highly indicative of the effect HGT has on mobile gene fitness outcomes (i.e. whether performing HGT has a positive, negative, or neutral effect on fitness). We expanded the simple model into a more ecologically realistic consumer-resource model (CRM), in which the mobile gene continuously transfers between species. We observed similar outcomes between the two models; however, in the CRM there was an increase in cases in which performing HGT had a positive fitness effect. We hypothesize that the CRM highlights features like the continuous existence of host species, resulting in constant gene flow between the two species. To further probe how gene flow influences the effect HGT has on mobile gene evolution, I tested how varying the HGT rate with the CRM (effectively allowing us to control the amount of gene flow) affects mobile gene fitness outcomes. I used the same host landscape pairs used in our pilot study while varying the HGT rate along a biologically relevant range. I expect to find a positive correlation between HGT rate and the magnitude of positive fitness effects conferred by a mobile gene that has undergone HGT.

In the developing brain of a fruit fly (Drosophila melanogaster), neural stem cells, called neuroblasts, divide to produce new cells that will become neurons. These divisions follow strict biological rules, but because many factors influence how and when neuroblasts divide, predicting their behavior is challenging. While lab experiments provide crucial insights, they are often limited in how many conditions can be tested at once (genetic, physical, or otherwise). To address these limitations, we developed an agent-based computer model that simulates neuroblast divisions and their interactions with neighboring cells. Our model allows exploration of different conditions to predict how neuroblasts behave in complex environments. This work focuses on three key hypotheses about neuroblast behavior: (1) post stem cell division, the larger cells are more likely to remain as stem cells, (2) the cell positioned on top during division will keep its stem cell identity, and (3) clustering of differentiated neural cells on the membrane of a neuroblast suppresses their division. To investigate these hypotheses, we examine emergent behaviors in our model through size-based, location-based, and clustering-based differentiation rules. By adjusting parameters such as cell placement, division timing, and proximity to other neuroblasts, we analyze how these factors influence neuroblast fate. We validate model predictions against experimental data by comparing division patterns observed in simulations to those seen in Drosophila brains through live imaging. By combining computational modeling with experimental data, this work provides a framework for understanding the factors responsible for neural development. Our findings will refine existing models of neural stem cell behavior and help guide future experiments, making it easier to uncover the fundamental rules of brain development.

The San Juan Archipelago is situated in the state of Washington, south of the Strait of Georgia and east of Vancouver Island. An abundance of marine mammal species, including harbor porpoises, harbor seals, and Steller sea lions rely on this biodiverse ecosystem. Since these animals are near the top of the trophic food chain, they rely on fish for prey while avoiding the predator at the very top: the transient killer whale. Pinnipeds and cetaceans act as ecosystem sentinels; their behaviors provide obvious, visible responses to environmental stressors and serve as warnings for underlying problems in the ecosystem. Marine mammal surveys were conducted aboard a research vessel over the course of 17 years, from 2008 to 2024. Species of mammal and number present were recorded. Sea surface temperatures, zooplankton samples, and catch per unit effort of Pacific sand lance were obtained, as well as a dataset from the Whale Museum on transient orca sightings and Pacific herring spawn counts from Fisheries and Oceans Canada herring stock. Our results imply that rising sea surface temperatures are related to decreases in marine mammal density. While prey abundance could also be a factor, the data so far indicates it is unlikely. To understand if rising sea surface temperature is impacting lower trophic levels and causing marine mammals to redistribute would entail further study. This research aims to address whether climatic factors, particularly sea surface temperature and the 2014-2015 marine heat wave, and prey abundances affect marine mammal density in the San Juan Archipelago. The report also examines the presence of transient killer whales in relation to pinnipeds over the years 2012 to 2019.

Disruption of the Wnt signaling pathway is critical in the emergence of some of the most difficult cancers to treat. Transducin β-like protein 1 (TBL1) forms a complex with β-catenin, a transcription factor that switches ON Wnt target genes (Li & Wang, 2008). The Nemhauser Lab engineered a synthetic repressor circuit, dCas9-TBL1, that targets a constructed constitutive promoter driving GFP expression in human cells. I hypothesize that levels of TBL1 activity will correlate strongly with expression of Wnt target genes. My research uses time course qPCR to test Wnt-induced gene expression in both HEK293 and HCT15 cell lines. HEK293 have normal levels of Wnt signaling, whereas the HCT15 colon cancer cell line is known to have high Wnt activity which contributes to uncontrolled cell growth. Specifically, I will extract RNA from both cell types at 6, 24, and 48 hours after treatment with a control chemical and test for expression levels of  Wnt-target genes such as AXIN2. These experiments will test whether the elevation of downstream Wnt-target gene expression is correlated negatively or positively with TBL1 activity, and will enable further understanding of this route to oncogenesis and future optimization of chemotherapy targets.

Corepressors are an essential element of gene repression – complexes of proteins that keep genes off, yet poised to turn on when needed. Clarifying the mechanism of this repression is key to understanding gene regulation in all eukaryotes in diseased and non-diseased states. My project is implementing a forward genetic screen in Arabidopsis thaliana to identify and characterize proteins that bind to and regulate the conserved plant corepressor TPL. TPL is fully essential to plant development, so to visualize TPL inhibition in living plants, we created an Arabidopsis line containing a synthetic repressor, TPL fused to dCas9(dCas9-TPL), that represses RUBY, a genetic reporter that turns Arabidopsis plants dark pink. Plants with both constructs appear light pink as dCas9-TPL represses RUBY expression. Mutations in proteins needed to maintain TPL-based repression lead to dark pink plants, allowing us to identify mutants to study. Using ethyl methanesulfonate (EMS), we created a pool of seeds with random point mutations and the repressed RUBY construct. My team and I visually screened the mutated pool for pink plants showing inhibited RUBY repression and successfully identified promising homozygous mutants with unique phenotypes including infertility, shade avoidance, and irregular growth patterns. Using whole genome sequencing and computational analysis, I selected specific loci to further investigate. We are currently testing our candidate mutants' sensitivity to the plant hormone auxin, one of the best-understood TPL-regulated pathways. My next steps will be to identify the causal mutation through the following: (1) characterizing additional mutations in the same gene to compare phenotypes using available mutant libraries, (2) testing whether the candidate gene interacts with TPL using assays like yeast two-hybrid, and (3) complementing my mutants with wild-type versions of candidate genes. By uncovering new proteins, I aim to piece together more of TPL's conserved mechanism of repression. 

Sexual dimorphism, the difference in structural features between males and females, is observed in many species across vertebrates. However, even between closely related species, the differences in sexual dimorphism can be extreme. In this study, I examine the functional implications of sexual dimorphism in two mustelids, the American marten (Martes americana) and the fisher (Pekania pennanti). Martens and fishers are prime targets for comparison because despite inhabiting similar geographic ranges and consuming similar diets, fishers exhibit significant sexual dimorphism in cranial size and shape while martens do not. Thus, my goal is to assess if these characteristics exhibited by male fishers result in enhanced biting performance compared to female fishers and American martens of both sexes. My first hypothesis is that size-corrected male fisher skulls, with their more robust morphology, exhibit lower stress than female fisher skulls. In martens, I test the second hypothesis that there is no difference in stress between size-corrected male and female martens due to the lack of size and shape sexual dimorphism observed. I quantified the stress on the mandible and cranium as a proxy for biting performance. Higher stress indicates areas likely to fracture with increasing forces or continuous use, signifying lower biting performance. To model the stress caused by jaw adductor muscles, I employ finite element analysis (FEA). FEA allows me to input scans of the skulls sourced from the Burke Museum and simulate forces on the models. I then conduct t-tests on the stress of shared regions between the species and sexes. My preliminary results in fishers show males having lower cranial stress but similar mandibular stress compared to females, suggesting males and females exhibit stress in different areas of the skull when biting. This research adds to existing literature by proposing a mechanical explanation for the evolution of sexual dimorphism.

Alzheimer's disease (AD) affected approximately 6.9 million Americans aged 65 and older in 2024, and it is projected to rise to 13 million by 2050 (Alzheimer’s Association, 2024). AD is characterized by progressive cognitive decline, but sleep disruption is an often overlooked symptom that emerges early in the disease's progression. Evidence suggests that AD-related sleep disturbance may originate from dysfunction in the circadian system, particularly in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN regulates sleep-wake cycles, and recent findings from de la Iglesia lab have shown that specific SCN neurons exhibit a daily rhythm of fiber expansion and retraction. This study aims to investigate how aging and AD affect SCN structural plasticity; this could help explain circadian disturbances in AD patients. I aim to identify the age at which abnormal circadian phenotypes emerge in a mouse model of AD which shows circadian disruptions. We are currently comparing activity patterns of AD mice ages 6 to 16-months old with their wild-type littermate controls using behavioral running wheel data. We hypothesize that the AD mice will exhibit a decreased mean total sleep and shorter circadian period in constant darkness. While these symptoms are common with aging in healthy mice, we expect that they will appear earlier in AD mice than in their wild-type littermates, as disrupted sleep is an early-onset symptom of AD. Future studies will assess whether these symptoms are associated with deficits in daily structural plasticity of the SCN. By elucidating the relationship between AD, SCN neuronal structure, and circadian rhythm disruptions, this research aims to provide insights into the mechanisms underlying sleep disturbances in AD patients. Understanding these processes could potentially lead to the development of targeted interventions to mitigate sleep disruptions and slow disease progression in AD patients.

The King County Brightwater Treatment Plant includes two twin outfall pipes that were installed in 2012, and discharge approximately 36 million gallons of highly treated effluent into Puget Sound daily. After observing colonization of the pipes by marine organisms, King County biologists launched a ten-year study examining the impact of effluent discharge on motile and sessile species on and near the outfall over time. They placed plates of the pipe material, high-density polyethylene (HDPE), on the seafloor, with replicates near the effluent discharge diffusers and approximately 300 ft away. King County retrieved the replicate plates after 2, 5, and 10 years and, photographed each plate for subsequent image analysis. In this study, we analyzed the photos to investigate whether there was a measurable effect of effluent discharge on the abundance, identity, and size of organisms colonizing the plates. We concluded that effluent discharge likely does not affect percent live cover, number of taxa, or the identities of taxa present. However, some motile species may be more abundant in the absence of effluent discharge, and there may be some effect of effluent on the size of some species. These abundance and size differences are worth further investigation as they may indicate that, although highly treated, effluent discharge from the Brightwater Treatment Plant impacts some species' demographic rates, like survival and growth rates, and the water quality of the Puget Sound. Our results indicate that even highly treated effluent impacts the surrounding water and the species that depend on it and that further research is needed to fully investigate the impacts of wastewater discharge in the Puget Sound ecosystem.

The relationship between morphology and behavior reflects evolutionary pressures leading to adaptation and anatomical diversity. We investigated how locomotive behavior influences scapular morphology in Old World monkeys and Great Apes, and how these adaptations may be mediated by body mass, to better understand the morphological evolution of Primates. To do so, we compared scapular length-to-width ratios (LWR), scapular spine depths (SSD), and scapular shapes across 67 specimens (18 species) grouped by locomotion strategy and body mass. We determined scapular shape using landmark-based geometric morphometrics and traditional linear measurements. Seven anatomical landmarks were digitized and analyzed via Generalized Procrustes Analysis (GPA) and Principal Component Analysis to examine shape differences. Maximum LWR was measured using ImageJ, while SSD was measured with calipers. Statistical tests, including Procrustes-based Linear Models (PLM), Analysis of Variance (ANOVA), and phylogenetic ANOVA were used to assess the influence of locomotion strategy and body mass on scapular morphology. We specifically tested the hypothesis that scapular morphology is primarily shaped by locomotion strategy (H1), body mass (H2), or neither (null hypothesis). We found that: (1) scapular shape variation is influenced by factors beyond species and size, with body mass showing a small effect, indicating an allometric relationship; (2) there were significant differences in scapular LWRs and SSDs across locomotion categories, with arboreal species having narrower scapulae and deeper spines compared to terrestrial species; and (3) SSD did not vary significantly between body mass groups while LWR did. The amount of morphological variation was greater in smaller primates than in larger ones, contradicting H2. These results suggest that locomotor habits play a dominant role in shaping scapular morphology, with limited influence from body mass. Our study highlights the interplay between ecological pressures, body size, and skeletal adaptations, offering insights into the evolutionary mechanisms driving morphological variation in primates across diverse habitats.

Self-splicing domains, called inteins, are part of a class of selfish genetic elements that are present in highly conserved regions of unicellular eukaryotes and prokaryotes. Our research investigates the self-splicing behavior of two different algal inteins in Saccharomyces cerevisiae and the competitive advantages they may confer. We have found that inteins can affect cell viability and plasmid retention in their yeast host over time, and the intein with an enzymatic domain causes different effects than the one without. To identify whether these inteins undergo cleavage, we will construct Leu2 proteins with a 3’ 6xHis tag to be assessed by Western blots. Our set of plasmids contain the LEU2 gene, with or without an intein, and the URA3 gene for double selection. Using PCR and cloning, we are adding the 6xHis tag to the 3’ end of the LEU2 gene in these plasmids. Future research will provide deeper insights into the evolution of inteins as selfish genetic elements and their impacts on protein biology.

Clathrin mediated endocytosis (CME) is a cellular process that is critical for internalizing nutrients, molecules, and involved in drug delivery and viral infection. During CME, individual actin proteins assemble into filaments that produce force to help internalize clathrin coated pits against membrane tension. It has previously been shown that in vivo actin networks assemble non-uniformly around an endocytic vesicle. However, there is little understanding of how the cell leverages this non-uniformity and the variables that influence the degree of non-uniformity. Due to the small scale of the molecules involved in endocytosis, we used a stochastic, agent-based simulation to test what conditions impact actin network formation at a high resolution. We studied how varying the distribution of the actin branch nucleator Arp2/3 complex affects CME progression. We hypothesized that non-uniform localization of the Arp2/3 complex around sites of CME would drive the formation of a non-uniform actin network. To test this idea, we analyzed data from simulations with varied distributions of Arp2/3 around the endocytic vesicle (n=50 runs for each condition). We utilized the Wasserstein Distance between distributions as a quantitative metric of the non-uniformity in actin networks, studied the change in uniformity over time, and correlated this property with internalization amount. We found that median internalization was robust to varying the distribution of Arp2/3, but that with smaller regions of Arp2/3, non-uniform networks were able to internalize more. While our findings provide a deeper understanding of the conditions under which non-uniform networks assemble in CME, they also prompt further exploration of the underlying mechanisms of non-uniform networks.

Pseudomonas aeruginosa PA14 and Escherichia coli K12 are gram-negative bacilli that produce outer membrane vesicles (OMVs). Gram-negative bacteria have a cell wall composed of an inner and outer membrane with a layer of peptidoglycan. OMVs are spherical buds that bleb and detach from the outer membrane of bacteria, and contain material that was previously within the periplasmic space, such as proteins, nucleic acids, and virulence factors. OMVs are produced for various reasons, including nutrient acquisition, signaling, protection, and horizontal gene transfer. Other work has aimed at identifying the structure and function of these vesicles, as well as mechanisms of their production. This study concentrates on the creation of methods to produce and isolate OMVs, with a particular focus on ensuring separation from extracellular substances that inhibit direct quantification. To test how biogenesis could be increased, growth conditions were changed. Results indicated that media had a larger influence than temperature or incubation period on OMV biogenesis. In addition, a direct quantification method of OMVs was developed using spectrophotometry, whereas previous studies relied on indirect quantification methods, like protein or lipid assays, or incredibly expensive equipment for direct quantification assays. Gel electrophoresis was used to optimize and identify biological molecules by being able to separate them based on size and charge throughout the gel. Our work will contribute to the research methods of OMVs, and support the potential for them to be used biomedically for mechanisms of drug delivery.

This study investigates the sensory adaptations of nocturnal and diurnal rodent species, focusing on the relationship between orbital structures and whisker morphology. We hypothesized that nocturnal rodents would exhibit larger orbital dimensions, including maximum orbit length (MOL), due to their need for enhanced light-gathering capabilities in low-light environments. Our analysis of various rodent species, including Peromyscus maniculatus, Rattus norvegicus, and Sciurus carolinensis, revealed significant differences in orbital measurements, with nocturnal species consistently displaying larger orbits (p < 0.001). Our data collection involved taking six linear measurements from skulls (four related to orbit size using ImageJ software and two cranial size proxies using digital calipers) and analyzing whisker morphology, followed by statistical analyses including histograms, boxplots, Pearson correlation test, and phylogenetic analysis to explore relationships among traits in diurnal and nocturnal species. Additionally, while whisker length showed a stronger correlation with body size in diurnal species compared to nocturnal ones, the differences in whisker morphology were less pronounced and not statistically significant. Phylogenetic analyses indicated that certain traits, such as interorbital width, are influenced by evolutionary relationships rather than solely by activity patterns. These findings suggest that while visual adaptations in nocturnal rodents are prominent and likely enhance their survival in dim conditions, the role of tactile sensory structures is more complex and may be shaped by a variety of ecological pressures. Overall, this research contributes to our understanding of how different lifestyles influence sensory system evolution in rodents and has implications for fields such as evolutionary biology and biomimetics.

Cryptic diversity, the existence of genetically distinct but morphologically similar taxa that thus were previously classified as a single entity, is a fascinating subject in evolutionary biology and alpha taxonomy, but can be challenging to assess in practice. Genetic analyses have proven successful in identifying cryptic taxa, but are often impractical to employ as a starting point. Morphology thus can play an important role in cases of possible cryptic diversity, especially in determining if further study is warranted. Here, we use statistical analyses on morphological data to assess a possible case of cryptic diversity within Allium acuminatum, a species of wild onion native to western North America. Specimens collected primarily from several counties in Washington State (Kittitas, Yakima, and Klickitat) have been noted to differ morphologically from formal descriptions of the species. Morphological data was recorded for 165 specimens from the University of Washington Herbarium, Burke Museum collection. The data was then analyzed using a Factor Analysis with Mixed Data (FAMD) algorithm, and the results of the FAMD were then analyzed with a k-means clustering algorithm. The k-means clustering results were then plotted on a geospatial map using the original locality data from the herbarium specimens, and geospatial patterns for the clusters were assessed visually. Finally, t-tests and chi-squared tests were performed for the continuous and categorical traits, respectively, between the k-means cluster groups. The k-means clustering algorithm generated 3 clusters from the FAMD data, one of which was strongly centered around the area of interest (Kittitas, Yakima, and Klickitat counties), according to the geospatial map. Further, the statistical tests showed that, for 10 of the 14 traits analyzed, there were notable differences between the k-means cluster groups with a high level of statistical significance (p ≤ 0.0001).  Most of these differences were reflected in the cluster centered around the area of interest. These results indicate there is detectable morphological variation within A. acuminatum, and this variation is centered around the geographical area of interest. Additionally, we believe these results indicate further study is warranted to determine if the morphologically different populations are worthy of taxonomic recognition using more sophisticated methods, such as molecular techniques.

Social insects not only take care of their nestmates in life but also in death. Research has shown that ants, honey bees, and termites demonstrate a variety of corpse managing behaviors, such as corpse removal, burial, avoidance, and even cannibalism. These behaviors, collectively known as undertaking behaviors, help to maintain the fitness of the colony, keeping the nest hygienic and promoting nutrient recycling. However, how undertaking behaviors arose in the evolution of sociality is unknown. To address this gap in knowledge, we performed experiments that exposed bumblebees, Bombus impatiens, to dead adult nestmates or larvae to identify key undertaking behaviors. Unlike ants, honey bees, and termites, bumblebees are described as “annually eusocial” and lack the strict age-based division of labor seen in other highly eusocial insects. Instead, bumblebees exhibit smaller colony sizes, flexible division of labor, and annual life cycles. Their unique position on the spectrum of sociality makes investigating their corpse management behaviors impactful for understanding the evolution and diversity of behaviors that enable social living. Using deep learning methods, we identified key behaviors like corpse removal, antennation, and mandible contact, and even less frequent behaviors like aggression. Our results characterize the intricacies of this important set of social behaviors and help construct the evolutionary history of this behavioral adaptation. Our future work will explore the plasticity and specialization of bumblebee undertaking and the neural mechanisms behind the behaviors.

All cells have a stochastic component to their gene expression, such that even when in the same environment, there will be cell-to-cell differences in gene expression. Studies of this variability in gene expression dynamics have been limited by technological capabilities for measuring gene expression history with single-cell resolution. We have built a history-dependent integrase recorder of gene expression with single-cell resolution in the model plant Arabidopsis thaliana to study the impact of cell-to-cell gene expression variation in two contexts: development of side or lateral roots (LRD) and root regeneration (RR). The recorder uses integrases, proteins from bacteriophages that mediate permanent, heritable DNA changes based on the presence and orientation of a pair of integrase sites. Fluorescent reporter genes within the target construct allows for expression of fluorescent proteins associated with sequential expression of developmental genes. The recorder allows us to tie the switching to expression of developmental genes by expressing integrases with developmental promoters for genes that guide root differentiation. Utilizing our recorder, we are able to illuminate and evaluate variation in the recorder output among roots growing in different contexts. We hypothesize that regeneration leads to more heterogeneity in gene expression than lateral root development, as the latter has more standardized initial conditions and consistent local cues to constrain transcriptional dynamics. We aim to investigate connections between larger scale anatomical variation and underlying cell-to-cell gene expression heterogeneity. This technology will allow us to further understand the dynamics of gene expression during root development and could unlock new avenues for agricultural research and engineering.

The triturating surface of a beaked animal is the part of the beak that contacts food. Previous work has been conducted on determining a value for the complexity of beaked turtles’ triturating surface by creating a 3D mesh of it. We analyzed these meshes using  the R package molaR which then determined an OPCr (orientation patch count rotated) number that could be compared to the known diet of the turtle. My role in this study is  to examine the effect that manipulation of thresholding the skull has on the OPCr output using five different skulls from the species Malaclemys terrapin, which are known to be durophagous. Thresholding is conducted in the first half of mesh construction, when the CT scan is run through Slicer. At this step, we input both a higher and lower threshold value, as well as a standard value. A higher threshold value will lead to higher density material being excluded from the data set. The skull that is constructed in Slicer is then put into MeshLab to be further trimmed into only the triturating surface, and then it is run through molaR. We suspect that a higher threshold value will lead to a higher OPCr value than a lower thresholding value would. The implication of these results will determine what effect thresholding has on the scan, and estimate what value will be most optimal for preserving the integrity of the scan. 

Mutations, which arise spontaneously, are the foundation of genetic variation and play a key role in evolution. Understanding mutation dynamics has relevance for public health, as antibiotic resistance in bacteria often results from genetic mutations that allow them to thrive in the presence of drugs that would typically inhibit their growth. Our research builds on the Luria-Delbrück method, originally designed to estimate mutation rates phenotypically, by using Next-Generation Sequencing (NGS) to measure base-level mutation rates in Escherichia coli that confer resistance to rifampicin. Rifampicin targets the β-subunit of RNA polymerase, and resistance arises from single nucleotide mutations in the rpoB gene. My team and I conducted experiments by inoculating E. coli populations, exposing them to rifampicin at specific times, and sequencing resistant mutants to calculate mutation rates for each base change. Interestingly, our data revealed that identical base changes at different genomic positions can have significantly different mutation rates. However, our mutation rate estimation does assume that every mutant cell has the same probability of establishing a lineage in the presence of rifampicin. If a certain mutant has a lower probability of lineage survival, its mutation rate will be underestimated. Thus, to determine whether the mutation rate variability we found is due to actual differences and not survival differences, I developed an assay to measure the probability that a mutant fails to establish a lineage. To date, I have isolated nine distinct rifampicin-resistant mutants and tested the extinction rates of two, finding no observable extinction, supporting the accuracy of our mutation rate estimates for these mutants. This research refines mutation rate calculations and enhances our understanding of bacterial adaptation, with implications for developing strategies to predict and mitigate antibiotic resistance. Additionally, it contributes to evolutionary biology by revealing the complexities of mutation and survival in microbial populations

In the face of global climate change, there is growing interest in growing seaweed and sinking it to depths to remove carbon dioxide. However, quantifying the carbon sequestration potential of such ventures is challenging. One key consideration is that rising seawater temperatures may increase the rate of kelp decomposition, thereby reducing the export of carbon-containing tissue to the seafloor. To assess whether blades of the bull kelp Nereocystis luetkeana decompose more rapidly in warmer water, twelve 35 mm-diameter tissue disks were allowed to decay at 10-12 °C (ambient temperature treatment) and another 12 tissue disks were allowed to decay at 17-19 °C (elevated temperature treatment). After 7 days, the mean change in disk mass for the ambient temperature treatment was compared to the mean change in mass for the elevated temperature treatment. Samples at elevated temperatures were visibly flimsier and more diaphanous, which was correlated with a significantly greater decrease in weight. In tandem with other studies, this finding suggests that brown algae may decompose more rapidly at elevated temperatures, which has important implications for how to maximize future macroalgal carbon sequestration as ocean temperatures rise.

The auxin hormone is necessary for many essential plant functions. Corepressors from the TPX family hold auxin response genes (ARGs) OFF unless auxin levels are high. TPX proteins are brought to ARGs through interaction with Aux/IAA adaptor proteins, which can bind to auxin-regulated transcription factors. Plant pathogens interfere with the auxin transcriptional pathway, making a plant more susceptible to infection. Oomycetes, for example, are a common plant pathogen commonly found as a mold growing on ripe tomatoes and strawberries. Oomycetes inject RxLR effector proteins into plant cells to reprogram the immune response. RxL21 is one of these effectors, and it contains a binding site for TPX proteins that is very similar to what is found in the Aux/IAA proteins. We hypothesize that RxL21 competes with Aux/IAA for recruitment of TPX proteins and keeps auxin genes on during an infection. I tested this hypothesis by performing a cytoplasmic split ubiquitin assay (Cyto-SUS), which is a protein-protein interaction assay done in yeast. Through this assay, we detected weaker TPX-Aux/IAA interaction when RxL21 was present, suggesting that competition for TPX protein interaction is occurring. I also tested whether the RxL21 competition would alter transcription of an ARG using a fluorescence-based assay in yeast. I observed much greater fluorescence when RxL21 was present, suggesting that RxL21 competition with Aux/IAA for recruitment of TPX results in increased transcription of ARG. In future experiments, I will further test our hypothesis by expressing RxL21 and other effector proteins in specific cell types in the model plant Arabidopsis thaliana. These experiments will allow me to quantify the impact of the competition for TPX corepressors on a developmental process. The results of this work could guide the design of new, broad-spectrum strategies to protect plants from pathogens.

All organisms regulate genes for proper cell development, healthy environmental response, and prevention of disease. One way to regulate genes is through transcriptional repression, specifically through corepressors that bind to repressors to inhibit expression of genes. The TPL/TPR corepressor family is crucial in Arabidopsis thaliana for regulating auxin-dependent genes during embryogenesis, root and shoot axis formation, differentiation, and environmental responses. Due to functional redundancy among the TPL/TPR gene family, partial mutations in the family do not create full loss of function. However, knocking out multiple family members is lethal. My research aims to induce loss of function for TPL in specific tissue. To achieve this, I started with a plant strain that is mutated for three of the five family members through insertional mutagenesis by T-DNA, leading to a partial loss of function, with two remaining genes remaining functional. Then I constructed a single TPL copy under the control of an integrase-based molecular switch, which when expressed, inverts the promoter of the TPL gene, turning it off. This construct, assembled through Golden Gate cloning, includes a YFP-tagged TPL gene and an mScarlet reporter that allows me to confirm TPL expression (YFP) or its absence (mScarlet) through fluorescence microscopy. I have integrated this construct with the controllable TPL switch into Arabidopsis, and my next goal is to use a CRISPR/Cas9 system to mutate the remaining two TPL genes for full loss of function. I will then utilize the integrase control switch system for specific TPL repression in the lateral roots. Such a study helps synthetic biologists understand the necessity of TPL in specific tissues, avoiding full knockout lethality. With corepressors existing among different eukaryotes, this study has broader implications in understanding human repressors, such as TBL-1 that are linked to dysregulation of gene expression in diseases like cancer.

The Aedes aegypti mosquito is the primary transmission vector for dangerous diseases, such as yellow fever and dengue viruses. Emerging vector control efforts use strategies based on mass release of sterile and transgenic male mosquitoes to suppress local populations. These strategies rely on modified males outcompeting wild-type males in securing mates. However, our knowledge of mosquito mating remains limited. Male mosquitoes locate mates by identifying the distinct flight tone (WBF) females produce by beating their wings, which ranges from 450-600 Hz. But auditory neurons in male antennae are tuned to lower frequencies (200-400 Hz). It is hypothesized that as males fly and encounter a female, nonlinear interactions between male and female WBFs occur in the antennae, producing additional tones called distortion products. These distortion products are what male auditory neurons believed to be tuned to. Distortion-based hearing predicts that only flying males can detect a female flight tone. We tested this prediction by conducting behavioral phono-taxis experiments to compare the acoustically-mediated behaviors of flying and walking wild-type Ae. aegypti. Fifteen to twenty male mosquitoes that were either free to fly or had their wings removed were placed in a cage that had a speaker on either side. Pure tones, ranging from 100-1000 Hz, were played randomly from one of the speakers. Positive phono-taxis responses were quantified by recording the number of male mosquitoes that moved towards the speaker while a sound played. In contrast to the prediction of distortion-based hearing in mosquitoes, we found that non-flying, walking mosquitoes responded to similar female-specific WBFs that free-flying mosquitoes did. This challenges current theories on distortion products being the main way male mosquitoes hear and locate mates and suggests there are more complexities to the mosquito hearing process than initially believed. Future work will focus on further characterization of mosquito hearing processes.