Phytophthora is a group of destructive microscopic plant pathogens found in the Kingdom Protista. This water mold poses a substantial threat in the Pacific Northwest, as it infects rhododendron leaves. More Phytophthora are yet to be found here than are currently documented. Understanding the factors that contribute to the diversity of Phytophthora species found in an area is essential in predicting where the spread of this species is most likely. It is hypothesized greater levels of rainfall increase Phytophthora diversity. The sampling location, Chambers Creek in Pierce County, WA, is situated in an area of comparatively moderate rainfall; therefore, about three species are expected to be found. After baiting Chambers Creek with rhododendron leaves, PARP agar was inoculated, then Phytophthora was isolated. DNA was analyzed and bioinformatics was used to identify species present. By understanding the number of Phytophthora species present in local creeks, patterns in WA can be identified to help control this plant pathogen. Our samples identified three species of Phytophthora present in Chambers Creek. This matches our hypothesis that moderate levels of rainfall correspond to moderate species diversity. Based on the specific species found, we suggest to continue monitoring, but no urgent action is needed.

Phytophthora is a genus of oomycete water molds that harms plants. They are a group of fungi-like microbes responsible for several plant diseases, including blight, canker, dieback, and root rot. Even though approximately 30 species have been identified in Oregon and Alaska, the number of species currently present in Washington is yet to be determined. Our research focuses on the diversity of Phytophthora species. First, in an analysis of previously collected data and US Census data, the Phytophthora species diversity is higher in counties with a higher human population. Based on this analysis, we expected to find more than three species of Phytophthora present in Chambers Creek (our sample site) due to the high human population in Pierce County. Secondly, we sampled Chambers Creek for nine days using Rhododendron leaves, incubated the leaves for two days, then performed a PCR. The PCR product was sequenced using Sanger sequencing and a BLAST was used to identify the species present in our sample. Ultimately, we identified four species of the harmful plant pathogen Phytophthora present in Chambers Creek. From this, we conclude that there is a high diversity of Phytophthora present in this Pierce County water source. Phytophthora can be extremely harmful to trees and crops, and it has caused mass famines in the past. This research is vital because understanding patterns of its diversity allows us to monitor its presence locally; should a particularly harmful species be found, we can work to mitigate its effect on our ecosystems.

Skin is a densely innervated sensory organ, populated with various somatosensory receptors that help us perceive touch stimuli. Frequent injuries to the skin cause axon damage and lead to axon degeneration. Degenerating axons leave behind debris that must be cleared before reinnervation can occur and sensation is restored. We use adult zebrafish as a model to study injury and innervation because they have homologous cells and structures to humans and have transparent skin, allowing for high-resolution microscopy. Previous experiments in our lab revealed that skin-resident immune cells known as Langerhans cells (LCs) use highly motile protrusions to engulf axonal debris in the zebrafish epidermis. How are these dynamic protrusions regulated at a molecular level? Calcium signaling regulates phagocytosis and cell motility in other cell types, but the role of calcium signaling in LCs is unstudied. Through scale pluck assays and fluorescent microscopy, I have established a model for monitoring calcium signaling in LCs. I observed transient calcium flashes in LCs that varied in frequency, intensity, and subcellular location. I perturbed calcium flux using a calcium chelator and observed decreased flash intensity and protrusion length in LCs, suggesting that calcium signaling is required for protrusion dynamics. To investigate how calcium signaling affects engulfment, I imaged calcium flux in LCs during phagocytosis of apoptotic cells after laser injury. In contrast to the transient flux normally observed, LCs exhibited sustained high concentrations of cellular calcium during corpse engulfment. Because of the effects of perturbed calcium flux on intracellular calcium and protrusion motility, I hypothesize that perturbing calcium concentrations will inhibit LC phagocytosis. Identifying the molecular mechanisms underlying debris removal, such as calcium signaling in LCs, is relevant to understanding skin repair and disease states in which axon homeostasis is altered, including diabetic and chemotherapy-induced peripheral neuropathies.

To test questions on the evolutionary history of a species, it is important to consider the drivers of genetic diversification that lead to speciation. Species diversification is often driven by the formation of geographical boundaries, ecological diversity, sexual preference, or a combination of these factors. However, for the Western Banded Gecko (Coleonyx variegatus), a species native to the southwestern region of the United States, few of these factors exist. Despite the lack of clear barriers to gene flow, prior research identified several distinct populations of C. variegatus in this region, though there is some uncertainty with these distinctions as they relied solely on the signal from one mitochondrial DNA (mtDNA) locus. The aim of this project is to instead use genomic data to assess the validity of the C. variegatus populations defined by mtDNA, and to investigate how these populations are distributed across the geographic region they inhabit. Using genomic data allows us to more confidently define population boundaries and assess how they have evolved through time. To explore the aim of this project, we sequenced reduced representation genomic data for 224 individuals across the range of the species to determine how populations of C. variegatus are structured. We then built species trees to assess the relatedness of these populations with respect to each other and the overall evolutionary history of the species. Our findings show that there are consistencies between both the genomic and mitochondrial data population definitions, but distinct differences are also present, with mtDNA overestimating the number of populations. Thus, relying on mtDNA data alone may be insufficient for confidently ascribing population boundaries for C. variegatus. Accurately defining populations can have great implications for the conservation of native biodiversity, but as shown by our study, relying on a single mtDNA locus may mislead this crucial process.

To navigate their surroundings, migratory cells respond constantly to many signals in their environment, including both chemical and electric cues. These signals are produced locally by other cells, pathogens, and in the context of electrical signals, by disruption to the normal ionic balance across cell boundaries. Disruption to this ionic balance will create a local electric field to which immune cells will respond to guide their movement and prevent infection. How cells sense or respond to this electrical cue is not known. To better understand this phenomenon, we are using HL-60 cells that are a migratory neutrophil-like human leukemia cell line, which we have found migrates to the cathodal pole of an applied DC electric field. We have identified a number of gene candidates related to glycosylation, the modification of proteins with the addition of sugar molecules, that reduce the directionality of HL-60 cells in an electric field. Using CRISPR interference to create cell lines with reduced expression (knockdown) for eleven of the gene candidates, we are studying how the loss of these genes alter migration. We used video microscopy to track their migration in 3D at different intensity levels of current to see how the loss of these genes affected cell movement when cells are exposed to an electric field. All of these knockdown lines showed marked change in the cell's response, with less persistence towards the cathode at higher currents than control HL-60 cells. Of these eleven, knockdown of UXS1, a gene that encodes for UDP-xylose that is used in the attachment of long sugar chains (glycosaminoglycans) to certain proteins on the cell surface, showed the greatest effect. Our results suggest that UXS1 is critical for neutrophils' ability to sense or respond to DC electric fields. 

STEM education tends to avoid extensive discussion of ethics on topics such as climate change, treatment of disease, and nutrition. However, as textbooks set the foundation for curricula, it is crucial that they allow students to think critically about the ethics of performing science and societal impacts of biological research. Our work tests the hypothesis that introductory biology textbooks use predictable strategies to humanize science (e.g., inviting the reader to act like a scientist to develop a solution) and that some topics are more likely to have humanizing elements than others (e.g., some topics are better positioned to serve as launching points for instructors who seek to include humanizing elements in their class). Bringing in discussions of ethics into the science classroom is one strategy instructors can use to humanize biology. We define humanization as the act of positioning science in a social context and/or the act of discussing science through the lens of justice and/or injustice. Of the instances of humanization identified in these textbooks, ethics was mentioned in only 4.57% of these quotes. Ethics was discussed in relation to impacts on humans (41.0%), impacts on humans by humans (41.0%), and impact of humans (16.7%). Discussion of ethics was nuanced (43.6%), detailed (30.8%), and rarely included justice (10.3%) and equity/inequity (5.1%). Ethics was most commonly discussed in terms of biotechnology (38.7%), treatment of disease (12.0%), and environment (10.7%). These findings demonstrate that ethics is rarely made reference to in introductory biology textbooks, yet the field of biotechnology is at the forefront of biomedical innovation, thus having nuanced discussions about controversial subjects (e.g., CRISPR, GMOs, and eugenics) rather than only teaching what these subjects are is pertinent to the training of future scientists.

With respiratory diseases, namely COVID, becoming exceedingly present, new diagnostic techniques are important in delivering quick and accurate results to patients. With the broad aim of creating a COVID breath test diagnostic, the project focuses on building a classifier able to detect various volatile organic compounds (VOCs). I applied a panel of VOCs to the antennae of the moth Manduca sexta and recorded the change in voltage across the antenna over time, also known as an electroantennogram (EAG). After recording the voltage response it is essential to extract important features associated with the response to avoid overfitting in the classifier. Each odor will have a unique dose-response curve. By identifying the pattern of intensity-related response for each odor, I have extracted important information that can be useful in classifying EAGs. Going forward, this project will be scaled to include COVID-related VOCs and multichannel experiments to measure electrical response in multiple areas of the antenna simultaneously. Multi-channel recordings will provide an increased number of important features for the classifier to use in learning the unique voltage signature related to each odor in our panel.
Preliminary data has shown that the administration of floral odors to the antenna elicits unique voltage signatures when recorded in single-channel EAGs. I predict that if we record from two sites in the antenna, we will observe a set of unique dose-response curves relative to the differential expression of olfactory sensors in the base and the tip of the antenna. These sets of dose-response curves may provide our classifier with better parameters to categorize and detect the presence of odors associated with COVID, as two dose-response curves must be consistent with an assigned odor’s electrical signature instead of only one. This may improve our chances of creating a classifier able to reliably differentiate between COVID and non-COVID odors.

Circadian rhythms are adaptive biological processes that govern the synchronous timing of biological functions and behaviors with the daily light-dark cycle. These rhythms are crucial for the timed regulation of sleep-wake cycles, metabolism, and hormone release, as well as for maintaining harmonious physiological functioning within the body. Within the mammalian brain, a central pacemaker, the Suprachiasmatic Nucleus (SCN), governs the timing of these circadian rhythms. This area contains a subpopulation of neurons that express and release the neurotransmitter Vasoactive intestinal peptide (VIP). These neurons play a role in synchronizing activity across the entire SCN network. Thus, this project is aimed at better understanding how VIP-neurons change shape throughout the day. Preliminary research in the de la Iglesia lab suggests that these neurons change shape across the day, such that VIP neuron fibers-axons and dendrites- are more branched during the day than the night. These results were obtained through the use of mouse models expressing a red fluorescent protein in the VIP neurons (VIP-TdTomato). The mice were perfused at a range of timepoints, and the samples underwent a tissue clearing protocol so that the entire SCN can be captured in one image. Then the software QuPath was used to train a machine learning algorithm to aid in the identification of VIP neuron fibers based on fluorescence expression. However, the performance of the machine learning algorithm has not been validated. To address this issue, I compared the algorithm-generated segmentations with manual annotations from humans, finding agreement 75.3% of the time in terms of fiber location and 77.4% of the time regarding background. These rather promising results demonstrate the usefulness of the algorithm in aiding the investigation of the entire dataset. This research provides a step towards better understanding the structural organization of the SCN, and thus circadian control of essential physiological processes.

Conjugative plasmids are extrachromosomal genetic elements commonly found in bacteria and are capable of being shuttled between different bacterial cells via a process called conjugation. The Luria-Delbruck Method (LDM) is a stochastic based modeling framework used to estimate the conjugation rate of a particular plasmid between bacterial strains. In my experiment, I am probing the theoretical experimental assumptions made by the LDM; in particular, I am testing that when there is variation in the precision of the selection assay, the application of a theoretical correction can result in accurate quantification of the conjugation rate. In the early phases of the experiment, I performed experimental assays in liquid medium to determine antibiotic concentrations in which donors (strains hosting a conjugative plasmid) and recipients (strains able to receive plasmids from donors via conjugation) die and transconjugants (recipient cells that have received plasmid from donor) grow. To test the theoretical correction, I chose two antibiotic concentrations that differ in the amounts of extinction occurring in the transconjugant population. I executed the LDM conjugation assay with these two conditions which produced equivalent conjugation rate estimates, as would be predicted if the correction factor is effective at mitigating the bias produced from variable amounts of transconjugant extinction in the selective conditions. My experiments demonstrate that the LDM continues to be robust in the face of violations to experimental assumptions which affirms the viability of applying the method to a wider range of bacterial populations with variable selective conditions and thereby broadens our ability to understand the dynamic movement of conjugative plasmids.

Changes within the body that repeat approximately every 24 hours, called circadian rhythms, are controlled by a central pacemaker in the mammalian brain, the suprachiasmatic nucleus (SCN). Circadian rhythms can synchronize to cues like the light-dark (LD) cycle, allowing them to predict the 24-hour environment. SCN neurons are interconnected and connect to other regions within the brain. Our hypothesis is that SCN neurons have the ability to physically change connections throughout the day and that these changes are essential for it to act as a master clock. I explored this plasticity through the study of vasoactive intestinal peptide (VIP) and polysialylated neural cell adhesion molecules (PSA-NCAM). VIP is a neurotransmitter expressed in a subset of SCN neurons and plays a role in the SCN's ability to respond to light. PSA-NCAM is involved in decreasing cell interactions through facilitating events like cell migration and axon guidance; it is only expressed in areas of the adult brain in which neurons display plasticity in their fiber connectivity. Mice house in a 12 hour:12 hour LD cycle were sacrificed at two times, 12 hours apart. I used immunohistochemistry against VIP and PSA-NCAM to determine the levels of these molecules in the SCN. I found that the expression of VIP is higher 9 hours after lights were turned off (ZT 21) compared to 9 hours after lights were turned on (ZT 9). I found that PSA-NCAM has a higher trend of expression levels at ZT 9 than ZT 21. Although these results are preliminary, we find the implication of the results promising. VIP and PSA-NCAM express in anti-phase; as a negative regulator of cell adhesion, higher levels of PSA-NCAM should correlate with lower levels of VIP. Understanding how mammals keep time is important because circadian rhythms are essential for virtually every aspect of an organism's behavior.

The Center for Disease Control estimates that one in three Americans do not regularly get enough sleep per night. This is considering people have access to a bed and a reliable place to sleep, highlighting how arduous it may be for the 500,000 individuals experiencing homelessness in the US to obtain a good night of rest. Seattle is facing a homelessness crisis exasperated by the pandemic and on any given night there may be 11,000 individuals in King County without their own place to stay. This project investigates how sleep differs between individuals living in shelters, tent cities, and tiny homes to determine where the best sleep can be achieved throughout the year. Data was collected using actigraphy watches and sleep diaries for four weeks in September 2022 and four weeks in February 2023. These two time points allow for a seasonal comparison due to the drastic change in light availability and temperature between seasons in Seattle. There were 29 participants across four sites in September and 25 participants across the same sites in February. Interviews were completed to establish a baseline of individuals health and sleep habits. The watch data and interviews were analyzed to compare sleep duration, efficiency, disruptions, and individual consistency, all of which are factors that impact sleep quality which is foundational to mental and physical health. The seasonal comparison is expected to show longer sleep duration in the winter and more efficient sleep for those living in tiny houses or shelters. It is more difficult to control these factors without a home, but it is especially important for people experiencing homelessness who face a disproportionately high incidence of chronic mental and physical health issues. There has been little sleep research in this population and especially for individuals not living in an organized community.

Mytilid mussels are foundation species who serve a vital role in temperate coastal ecosystems. As ecosystem engineers, mussels modify the physical and local chemical environment, which can both inhibit or facilitate other species. Through a mussel’s metabolic process (i.e., respiration and calcification) they have the ability to alter their chemical environment which has been suggested to be influenced by their gaping behavior. The objective of this project is to associate a given gape behavior to a known mussel behavior (e.g. active/passive filter feeding or laying byssal threads). We installed Hall effect sensors – a specialized magnetic sensor– on the posterior end of the mussels to analyze how wide a mussel gapes. A video camera filmed the mussels concurrently with the sensors to verify the gape signal with a known behavior. We recorded and captured mussel behavior for three Mytilus mussel species (M. trossulus, M. galloprovincialis and M. californianus) for 24 hours (n=8 for each species). We hypothesize that behaviors in mussels that are more active (e.g. active filtering or laying byssal threads) may have more variation in gaping behavior than behaviors like passive filtering where mussels could be resting. We also expect that gaping behavior will differ among the three species, with M. californianus spending less time closed compared to M. trossulus and M. galloprovincialis. Our project takes the first step in interpreting how valve gaping and its relationship with a given mussel behavior may determine how a mussel’s behavior plays a role in their ability to modify their local chemical environment.

Climate change has resulted in environmental changes that pose direct and indirect challenges to marine organisms. One such organism that has been widely studied is the common murre (Uria aalge), which has experienced decreased reproductive success and adult survival in response to climate change-induced ocean warming. Because common murres molt flight feathers relatively synchronously, they may be especially vulnerable to environmental stresses, such as the challenge this may pose on obtaining food. In this study, we explore the degree to which shifting environmental conditions impact adult survival of common murres at a physiologically sensitive point: flight feather molt. The data we used for this study include: monthly expert-verified observations of bird carcasses from the Coastal Observation and Seabird Survey Team (COASST) citizen science program collected from the outer coast of Northern Washington south down to Humboldt, California; significant wave height data from the National Data Buoy Center (as a proxy for storminess); spring transition date (from the Columbia Basin Research website) as an indication of annual production potential; and Bakun upwelling index (from the Pacific Fisheries Environmental Laboratory website) as a measure of upwelling strength and production potential. We annualized both the bird and environmental data over the years 2003-2021. For this project, my role was to conduct statistical analyses using the statistical program R. I employed generalized additive mixed models to determine the relationship between the proportion of adult carcasses in molt and the environmental variables. To select models, I used Akaike Information Criterion corrected for small sample size (AICc). Our research will give insights into how the combined effects of physiological and environmental stressors may impact upper trophic seabirds as climate change continues to intensify.

 Reconstructing past environments can help us understand plant community evolution over time. For example, plant silica (phytoliths) can help us reconstruct canopy openness. Phytoliths are formed when plants uptake monosilicic acid from the surrounding soil through their roots and deposit it as opalized silica in and around cells; they have been used as a tool in paleoecology because they are well-preserved in the fossil record. For phytoliths formed in the outermost layers of leaves (epidermis), there is a relationship between morphology and light availability. A previous method established this correlation using modern soils in Costa Rica to apply to sites in the Eocene-Miocene of Argentina. However, it is unclear whether this model can make accurate inferences in other geographic regions. Here, we expand the method using modern phytolith samples from the Southeastern United States to generate a dataset and apply it to fossil phytolith assemblages from the North American Great Plains Region to reconstruct changes in vegetation during Oligocene-Miocene grassland expansion. For this work, we use an optical microscope to observe and count the phytolith assemblages to reflect a range of vegetation types in North America. We focus on phytolith morphotypes representing silicified epidermal pavement cells and measure their size and shape using ImageJ. We expect a linear trend between LAI (Leaf Area Index, the quantified relationship between morphology and light availability) from phytoliths and observed LAI which can be used to form the model for North American environments and applied to the fossil phytolith record of the Great Plains Region. Expanding on this method could make its use more widespread and lead to similar research in other regions of the world. Current models suggest the persistence of closed forests through this entire interval, a result we wish to further test using this updated model.

Hydrogen sulfide (H₂S) impacts biological systems in multiple ways, including the arrest of aerobic respiration, and thus is mechanistically similar to cyanide. Unlike cyanide, however, H₂S can accelerate as well as end cell growth, including in plants, where it drives germination rates when administered in micromolar concentrations. However, the limited research to date leads to a need to better quantify and contextualize chemical composition changes in plant tissue following H₂S-induced plant growth. This study resulted in the ability to quantify the biophysical impacts of H₂S-induced growth in plants. The novel use of δ³⁴S and δ¹⁵N isotope ratios produced at the IsoLab in University of Washington represent the results of this sampling and its subsequent analysis. They may represent a new means to understanding the effects of H₂S on plant growth, including during the crucial phase of plant germination. The effects were observed on hypocotyl tissues from seedlings of Pisum sativum (pea), Phaseolus vulgaris (bean), and Zea mays L. (corn), all grown in hydroponic H₂S solutions, ranging from 0-100μM. These specific isotopic methods may allow comparison between modern and fossil material, because these isotopic species are known to have been preserved across a wide diversity of plant fossils. This novel application of these classic staples in the biochemical toolbox may have further implications for better understanding past events, because many major mass extinctions have now been linked to excess oceanic and atmospheric H₂S (compared to today), and may also, paradoxically, present new paths toward increased crop yields.

Eelgrass (Zostera marina) is a crucial marine flowering plant that provides intertidal ecosystem services in and outside the Puget Sound. However, eelgrass populations are under threat due to the adverse effects of climate change. Maintaining genetic diversity is essential for their survival. This project aims to enhance our understanding of eelgrass reproduction and how populations will react to climate change by characterizing the molecular mechanisms of flowering in eelgrass. We have identified candidate eelgrass flowering genes that are homologous to genes found in Arabidopsis thaliana, a model organism. These candidate genes were selected based on the clock-regulated model of flowering, in which FLOWERING LOCUS T (FT) encodes for a critical protein that triggers the flowering response pathway. To investigate this model, we created transgenic overexpression lines in Arabidopsis and identified two candidate eelgrass FT genes that exhibit an early flowering phenotype similar to FT overexpression in Arabidopsis. We are also using Yeast 2-Hybrid Assays (Y2H) to confirm the identity of the suspected eelgrass FT. Y2H is a technique for studying protein-protein interactions and allows us to investigate interactions between eelgrass FT and other transcriptional regulators within the flowering response pathway. Based on our data, we expect to see the two candidate eelgrass FT genes result in a simultaneous early flowering phenotype and in interactions with other transcriptional regulators to form a transcription factor complex that enables the expression of a reporter gene. Identifying FT in eelgrass will prompt further study of individual and population-wide flowering patterns, and how these patterns change with shifting ocean conditions.

One of the most striking adaptations in land plant evolution is the specialization of reproductive structures. LEAFY (LFY) is well characterized in flowering plants (angiosperms) as a transcription factor initiating the development of the flower, which contains the reproductive organs. LFY also regulates the first cell division of the zygote (diploid phase) in mosses (a type of non-vascular plant). The fern Ceratopteris richardii is a type of non-flowering plant that is midway phylogenetically between mosses and flowering plants, in the sister clade to seed plants. With a lab-friendly, independent haploid phase (gametophyte), transgenic protocols and a reference genome, C. richardii is ideal for studying LFY’s functional evolution. Previously, targeted silencing of the two fern LFY homologs CrLFY1/2, demonstrated that it maintains the identity of the apical stem cell in gametophytes. To further characterize the function of fern LFY, I study the effects of its over expression on gametophyte development. To that end, I record gametophyte development using bright-field and fluorescent microscopy. Preliminary results suggest that overexpression of CrLFY may affect development of the sperm-producing gametangia (antheridia) in fern gametophytes, with more antheridia found in transgenic plants late in development. Given that antheridia continue to be produced in wild type gametophytes in the absence of fertilization, I test the hypothesis that CrLFY overexpression causes delayed fertilization (by a yet unknown mechanism) and that increased antheridia represent a secondary effect. Here, I experimentally delay fertilization by withholding water needed for sperm release (“flooding”), and compare the number and pattern of antheridia on transgenic and wild type gametophytes with and without flooding. Functional characterization of LEAFY in a fern, and of other master regulators of development more generally, contributes to a better understanding of the evolution of land plants via the potential repurposing of ancestral genetic pathways into novel functions.

The visual system is a critical portion of the sensory arsenal in many animals, since light is a fundamentally important factor that allows animals to assess and navigate their surroundings. Differences in latitude have measured effects on the quality, quantity, and consistency of daylight, and animals have adapted to these varying light levels in different ways. Research has shown that animals with larger eyes, reflected in their bony orbit dimensions, are able to perceive their environments better in more dimly lit settings. Studies have also suggested that animals at higher latitudes exhibit larger eyes for better visual performance. Our group seeks to understand if there is any significant relationship between latitude and orbital size in Canidae (wolves, foxes, and relatives) due to the difference in light levels at different latitudes. I collected several linear measurements using ImageJ and 3D Slicer from skull 3D scans of 29 species of the Canidae family over a latitude range from -104.07° - 99.02°. Additionally, our team collected data on the average tree coverage, diet, and hunting style of species, to test for additional variables that may affect orbital size. We conducted regressions and ANOVAs among the variables collected. The preliminary results show there is no significant relationship between latitude and orbital size. However, we found that both hunting style and skull length have a significant relationship with orbital volume in Canidae. These results potentially impact the field by allowing us to infer the possible evolutionary trajectories of bony orbital dimensions, and how eye size could allow for more complex hunting styles in Canidae. Future research may seek to validate these findings in other carnivore families.

Ascidians are invertebrate chordates, with tadpole larvae that metamorphose into sessile adults. Molgulidae are a clade of ascidians where tailless larvae have evolved several times independently and our lab is interested in understanding the molecular mechanisms underlying the evolution of taillessness. There are two closely related Molgulidae species that are sympatric in Roscoff, France: Molgula oculata, a tailed ascidian and Molgula occulta, a tailless ascidian. The tailless M. occulta, have 20 notochord cells that do not converge and extend, called a "notoball", and have evolved a number of larval pseudogenes. During embryonic development, the Wnt planar cell polarity (PCP) pathway plays an essential role in regulating cell fate determination and other cell processes. Previous experiments have found that the Stolidobranch ascidian, Halocynthia roretzi, has a Wnt5 duplication, where Wnt5a is invovled in the notochord development whereas Wnt5ß is involved in muscle development. Bioinformatic analysis has been done on several developmental genes involved in notochord formation and the Wnt pathway which showed that most genes are highly conserved between M. oculata and M. occulta. We have identified two Wnt5 isoforms that may play a role in tail formation, and we are in the process of subcloning the 3'UTR regions to obtain gene specific RNA probes for in-situ hybridization. We expect to find Wnt5a expressed in the notochord and Wnt5ß to be expressed in the muscle cells. We are also cloning Dsh to examine gene expression. This information will allow insight into how the Wnt5 genes in M. occulta and M. oculata are implicated in notochord convergence and extension as well as whether the Wnt/PCP pathway contributes to the evolution of tailless larvae. 

Phytophthora is a genus of water mold that causes plant disease and spreads quickly. Certain Phytophthora species can wreak havoc among crops and ecosystems. Early detection of the plant pathogen is key to preventing its spread. Based on observed blight on oak trees, we set out to detect Phytophthora in our local watershed, at Clark's Creek Park in Puyallup, Washington. We baited pathogens in the water by placing rhododendron leaves in netted bags, and submerging the bags in one of the park streams for 14 days. We then cultured the infected leaves and extracted deoxyribonucleic acid (DNA) from the cultures. We performed polymerase chain reaction (PCR) to amplify the Phytophthora internal transcribed spacer (ITS) gene, and sent our PCR product out for DNA sequencing. Once we received the results, we used the Basic Local Alignment Search Tool (BLAST), an online tool that matches DNA sequences with available DNA databases. Using BLAST, we identified which species were present in our cultures from Clark’s Creek. We confirmed the presence of two Phytophthora species: P. gonapodyides, P. chlamydospora. These species preferentially infect forest and fruit trees. Scientists and community leaders can use our research to track Phytophthora and focus containment efforts in our local ecosystem.

As part of cellular metabolism, all organisms produce reactive oxygen species (ROS), such as (O₂^– ) and hydrogen peroxide (H₂O₂). ROS can damage multiple cellular organelles and processes, disrupting normal physiology. Proteins, lipids, and nucleic acids can be damaged by ROS molecules, resulting in cell death. Also, several human diseases have been linked to an imbalance between ROS production and antioxidant defenses. Plants' chloroplasts and mitochondria contribute a substantial amount of ROS, as they are responsible for photosynthesis and aerobic respiration. In maize, Whirly ssDNA-binding proteins help to maintain the stability of the plastid genome. We recently demonstrated that maize seedling development is accompanied by increasing oxidative stress to the demise of chloroplasts, mitochondria, and their DNA. We also showed that maize seedlings grown in the light had higher levels of oxidants and lower levels of antioxidants than dark-grown seedlings. Here, our objective is to elucidate the role of Whirly proteins in oxidative damage. We isolated organelles from maize seedlings and performed oxidant and antioxidant assays for both wild-type and whirly-mutant plants. We found a significant difference in oxidation levels between wild-type and mutant plants. Our study should provide a better understanding of the role of ssDNA-binding proteins in oxidative damage to organelles.

Without proper genetic regulation, the creation and maintenance of cells within eukaryotic organisms such as yeast, plants, and humans is doomed to fail before it even begins. Protein corepressors are key to the genetic repression in all eukaryotic organisms and are vital for an organism to be able to properly coordinate their development and respond to environmental stimuli. In Arabidopsis thaliana, a model plant for genetic studies, the corepressor TOPLESS (TPL) is one of the main proteins that is used to repress the auxin pathway, which is essential to development and organ creation. Recently, the active domain of TPL has been pinpointed to an 18-amino acid long region named LIS1 homology (LisH) that is sufficient for activity. Previously, we found that the helix H1 of LisH in a plant corepressor functioned as a transcriptional repression domain in yeast. These observations suggest a broad conservation of mechanisms across kingdoms, suggesting this motif could be engineered to be a potent, short, and adaptable protein domain suitable for synthetic biology and therapeutics. My project aims to test the ability of the LisH protein domain to repress gene transcription in metazoans using mammalian cell culture. We will transfect human cancer cell lines with DNA encoding a dCas9-TPL fusion protein, which can be targeted to promoters of endogenous genes such as the cell surface antigen CD4, or synthetic constructs such as fluorescent reporter genes to detect differences in protein levels. Results of the project are expected to show that TPL and other foreign corepressors can function within the human cell just as efficiently if not more than human corepressors. Research into LisH's abilities will provide knowledge of its active domains and mechanisms in mammalian cells while also having the possibility to aid the scientific community by developing TPL as a rapidly deployable synthetic biology tool.

Documenting plant-animal interactions allows for a better understanding of biodiversity, the behavioral ecology of frugivores, and the coevolution between plants and animals. Bats are important seed dispersers on hundreds of plant species in the tropics, but their patterns of plant use across habitats is still relatively unknown. The overarching goal of my research project is to characterize the interactions between mutualistic fruit bats and plants across different habitats at a site in Costa Rica (La Selva). My hypothesis is that bats will exhibit frequent interactions with Piper plants overall, with more variable interactions across forest Piper species over time because these species have intermittent fruiting peaks. Existing field data consist of 24h camera trap videos and nightly acoustic ultrasonic recordings taken at dozens of forest and gap Piper plants at La Selva during both rainy and dry seasons between 2019-2021. The acoustic data collected is heavy in background noise from organisms and weather conditions; therefore I developed a program in MATLAB to streamline this analysis. I am using RavenPro to identify relevant parameters of bat calls within the filtered files using focal calls as a guide to later identify the species participating in these visitations. I am comparing the number of calls across 10 P. sanctifelicis plants (open habitat) to the number of calls found across 8 P. generalense plants (closed habitat) to observe the frequency of possible fruit-bat interactions across habitats. This project is significant in the field of ecology because of its focus on plant-animal mutualistic interactions: by understanding the frequency of bat visitations to plants across habitats, we can gain a better understanding of the importance of these frugivores for seed dispersal and survival of plants.

The dynamic expression of genes in an organism creates the biological complexity of life. Many are unique to a given lineage, while other genes are conserved and carry out the essential functions of life. Unsurprisingly, these essential genes are complicated to study, as interfering with their function often leads to death. One critical component of transcription is the multi-protein Mediator complex, which is found at every eukaryotic promoter where it helps coordinate the activation of gene expression. My project focuses on a core component of the Mediator complex, Mediator 21 (MED21). While MED21 is required for gene activation, my lab found that it also plays a role in the repression of gene expression, suggesting a complicated interplay between these two states. This can be challenging as many mutations in MED21 lead to lethal phenotypes. As an alternative, I hypothesize that using an integrase-based molecular switch to create a switchable MED21 will then allow me to differientate the role that MED21 plays in activation through the Mediator complex versus repression through the corepressor protein (TPL) in the model plant Arabidopsis. Integrases are capable of inverting DNA sequences flanked by unique sites, and I am engineering a switch that will turn off MED21 in certain tissues or in response to the addition of a chemical. By expressing an integrase protein from a lateral root-specific promoter, we can engineer a MED21 loss of function only in those specific cells while the rest of the plant is wild type and healthy. Future experiments include a switch from wild-type MED21 to a mutant form incapable of binding to corepessor TPL. This study will help us better understand the role MED21 has in repression versus activation, and also how state switching contributes to organogenesis.

Rensch’s rule suggests that sexual dimorphism increases as body size increases in species where males are larger than females. One hypothesis explaining this pattern is that through sexual selection, male-male competition for food, mating partners, and territory increases with body size. Here, we examine whether mandibular sexual dimorphism follows Rensch’s rule in the feliforms, a clade consisting of Nandiniidae (African palm civets), Felidae, Viverridae (civets and genets), Hyaenidae (hyenas), and Herpestidae (mongooses and meerkats). Although previous work found that few carnivoran families exhibit Rensch’s rule trends for their body size, whether a more consistent signal can be found in a trophic morphology such as the mandible has yet to be investigated. To test the hypothesis that carnivoran mandibles follow Rensch’s rule, we 3D scanned 349 mandibles across 73 species from museum collections and performed geometric morphometrics to quantify shape and size differences between male and female mandibles. We then used ANOVAs to test for mandibular dimorphism in each species, and linear regressions to test for Rensch’s rule. Preliminary analyses have revealed that viverrids, herpestids, and felids all do not follow Rensch’s rule, and that the degree of mandibular sexual dimorphism varies among families. We predict that mandibular sexual dimorphism will be highest in feliform clades with a high degree of dietary specialization because the specialized diet of carnivorous species may lead to greater competition between males and females for food. However, we predict that we will find little support for Rensch’s rule, as mandibular dimorphism may vary more with social system or diet than with body size. Overall, our research will add to the growing body of research on Rensch's rule and help elucidate the effects of niche divergence and sexual selection on the evolution of sexual dimorphism in mammals.

Corepressors are proteins recruited by partner proteins to negatively influence transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and while we understand a lot about how TPL works, there are still many mysteries remaining. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single-engineered promoter site. First, we created a synthetic repressor called dCas9-TPL that binds and represses the transcription of the RUBY reporter. The RUBY reporter is a visual marker designed to express throughout the entire plant, turning the green plant a bright purple. Our engineered RUBY line also carries two guide RNAs in its promoter with sequences not found anywhere else in the Arabidopsis genome. This allows dCas9-TPL to bind to and repress this particular gene and not affect the transcription of other genes. Visual screening of the repressed RUBY line showed these plants turn a faint whitish-pink instead of bright purple, signifying that the repression by TPL is working. I have identified the promising repressed RUBY homozygous line and have generated three mutagenized populations of 40,000 individuals using the chemical Ethyl methanesulfonate (EMS). The EMS protocol creates new point mutations allowing us to identify genes involved in repression that we can map through DNA sequencing. I will use visual screening to search for plants with bright purple organs, meaning that the repression by TPL is broken and that a putative TPL interactor may be mutated. By identifying regulators of corepressor function in plant biology, I hope to learn principles that can inform cellular engineering across many organisms and better understand why certain mutations associated with transcriptional repression cause developmental defects or diseases like cancer in humans. 

Synthetic promoters are increasingly being used to control and fine-tune gene expression in multicellular organisms as part of engineering novel traits. For this genetic engineering project, we aim to build and activator system that when engaged leads to a statistically significant increase in gene expression compared to the unengaged system. Previously, our lab screened for promoters that are constitutively and ubiquitously expressed in Arabidopsis Thaliana. From this screen, multiple viable promoters were found, and a subset was selected for modification by adding sequences not found anywhere else in the genome (target sites). Our first experiments used the CRISPR-mediated gene regulation system to recruit repressors to create NOR logic gates (where a reporter is only expressed when two different inputs are absent) through the use of guide RNAs (gRNAs) complimentary the engineered target site. Currently, we are working to expand the capabilities of these synthetic promoters by swapping the repressor with an activator to see if we can boost expression from these promoters. Our activator construct has an enzymatically disabled Cas9 connected to an activation domain called EDLL, and an aptamer in the gRNA that attracts a second activation domain, VPR. We are currently generating transgenic plants carrying our synthetic promoters and activator constructs. I will quantify gene expression by measuring the levels of a fluorescent reporter under the control of our synthetic promoter. The use of both activator and repressor approaches will allow for the construction of increasingly complex genetic circuits. These circuits have wide potential applications across the fields of synthetic biology and metabolic engineering.

The protozoan parasite Giardia lamblia infects hosts via the ingestion of cyst-contaminated water. We recently identified EncystR, a 7-trans membrane protein at the cell surface that acts as a negative regulator of encystation and responds to encystation cues by internalizing. By following the localization of EncystR through an encystation timecourse we discovered a novel compartment of unknown function. The Giardia endocytic pathway was only believed to include hybrid endosome/lysosome compartments statically positioned beneath the plasma membrane. We suspect this newly identified compartment may be a lysosome-like compartment. Using EncystR as a marker for this compartment we found that the compartment is highly acidified based on the florescent reporter pHluoren2. Canonically endomembrane compartments are marked by specific phosphatidylinositol phosphates (PIP). Relevant to endomembrane compartments, PI(3)P marks endosomes and PI(3,5)P2 marks multi-vesicular bodies and lysosomes. To test if this newly identified compartment is evolutionarily related to lysosomes, we will generate reporters for these phosphoinositides. Namely, we utilized the FYVE protein’s PIP binding domain as a sensor for PI(3)P which is located on endocytic membranes, the pH domain of PLC delta as a sensor for PI(4,5)P2 or PIP2 which is necessary for endocytosis and membrane-based cytoskeletal protein regulation, and ML1N for PI(3,5)P2 which is localized to lysosomes. Additionally, a mutant variant of the ML1N protein which is incapable of binding to PIPs is utilized as a negative control. These protein sensors were fused to the fluorescent protein mNeonGreen and imaged via fluorescent microscopy. While the experiment is currently in progress, we hypothesize that the localization of PIPs to the novel compartment will likely feature PI(3,5)P2 due to the previously found acidic nature of the compartment, implying a lysosome-like functionality. This possibly novel or conserved compartment could give insight into the evolution of eukaryotic cellular organisms and could potentially offer treatment routes for Giardia.

Mosasaurs are extinct, enormous lizards that dominated the oceans in the Late Cretaceous, from 90 to 66 million years ago. They were important members of Late Cretaceous marine ecosystems, with some species being the top predators. However, there remain many uncertainties about mosasaur diets, which likely varied considerably among species. Therefore, I aim to investigate mosasaur diets to provide more information on lizard evolution and Cretaceous marine ecosystems. To infer the diets of mosasaurs, I examine the lower jaws and teeth of their closest living relatives, modern lizards, and test for correlations between craniodental morphology and diet. For example, a lizard that eats primarily hard-shelled foods will likely have more robust jaws and teeth than a lizard that primarily consumes insects. To quantify the morphologies of the lower jaw and teeth, I measured the width and height of the jaws at three points, and the height, width, length, curvatures, root length, and cusp numbers of the teeth at the same three points (n = 43 species). I then used the jaw measurements to calculate cross sectional shape values that represent the amount of stress the jaws experience during feeding. Finally, I used phylogenetic regressions and multivariate analyses to test the relationship between jaw/tooth shapes and diets. I find evidence that jawbone heights increase among diets in the following order: insectivores, carnivores, herbivores, and durophagous taxa. Further, bone width is greater in herbivores than in non-herbivorous taxa, and durophagous lizards have the most diverse tooth morphologies. These results provide a foundation for future studies to examine the relationship of jaw/tooth shapes and diet more robustly, with the goal of using modern lizards as analogs for inferring diets of mosasaurs.

In comparison to the abundance of research focusing on early Paleocene mammalian recovery from the K-Pg mass extinction, the mid-Paleocene (63–58 Ma) is an understudied period of mammalian evolution, particularly at the Mehling Site near Ekalaka, Montana. Previous work suggests this site dates to the mid-Paleocene, but its absolute age is not well established due to limited ash beds for radiometric dating. An isolated mammalian molar tooth specimen from the Mehling Site had been tentatively identified as Microsyopinae, a subfamily of an extinct clade of stem primates called Microsyopidae. However, the first appearance of Microsyopidae in the fossil record is during the late Paleocene (58–55 Ma). The purpose of this study is to investigate the incongruity between the taxonomic identification of this specimen and the age of the locality it was found in. I conducted a comparative analysis of the molar tooth specimen using fossil specimens, casts, and digital 3D models of the dentition of microsyopid mammals and their relatives in order to identify the specimen down to the finest taxonomic level possible. My preliminary results show that this specimen shares some features with Navajovius and Arctodontomys, two of the earliest possible genera of the Microsyopidae. The findings of this study will enhance our understanding of the origin of Microsyopidae and of this stage of mammalian evolution during the mid-Paleocene. If the specimen is confirmed to belong to the Microsyopidae and the geological age of the site is correct, then this fossil would push back the earliest occurrence of Microsyopidae in the fossil record to the mid-Paleocene, extending the temporal range of this clade by several million years. Ultimately, this knowledge informs our understanding of the origin and evolutionary history of stem primates.

Giardia Lamblia is an intestinal parasite known for causing the diarrheal disease giardiasis in host organisms. It commonly infects humans and companion animals such as cats and dogs. Giardia’s life cycle is defined by its infectious cyst stage and proliferative trophozoite stage. GlRac is a small Rho-family GTPase which we recently determined to play a role in regulating encystation in Giardia, the process of transition from a trophozoite to a cyst. Guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) are key regulatory proteins of GTPase activity. The GEFs and GAPs that regulate GlRac activity are currently unknown, but four candidates for GAPs and three candidates for GEFs have been identified. We are testing these GAP and GEF candidates in Giardia with a two-phase approach. First, we are using the protein-protein interaction reporter NanoBit to determine if the candidate GAPs and GEFs interact with GlRac. We are verifying results for NanoBit assays, a split NanoLuciferase reporter that indicates protein-protein interaction. Nanobit can reveal interaction but not the localization of the interaction, so we are performing co-localization with deconvolution microscopy. Candidate GAP and GEF proteins are being visualized using a mNeonGreen fluorescent tag while GlRac is being followed using the halogenase (HALO) tag labeled with Janeliafluor 646. The microscope assays allow us to determine if and where GlRac co-localizes with candidate proteins. Subsequently we will test the role of the identified GAP and GEF proteins in encystation through transcriptional repression using CRISPRi and translational repression using morpholino-modified antisense oligonucleotides (MOs.) If the candidate proteins are truly GAPs and GEFs, the knockdown cells should not progress through encystation as normal. GAPs and GEFs are potential drug targets for treatment of Giardiasis, as well as important in understanding the process of encystation in Giardia.

Giardia lamblia is a gastrointestinal parasite which causes diarrheal disease and hinders nutrient absorption. G. lamblia colonizes the small intestine by a two-phase life cycle: the reproducing trophozoite stage and the transmissive, infective cyst stage via a fecal-oral route. How G. lamblia detects encystation signals in the encystation process is unknown. Our laboratory discovered EncystR, a seven transmembrane protein which compartmentalizes after perceiving cholesterol depletion and increased pH. Knockdown of EncystR promoted encystation, indicating negative regulation. We hypothesize that EncystR is responsible for perceiving encystation stimuli and de-repressing cAMP signaling to promote encystation. However, the mechanism responsible for triggering cAMP signaling is uncharacterized. This project hopes to identify EncystR transient interactions using proximity labeling and mass spectroscopy (LC-MS/MS). Proximity labeling of EncystR over an early encystation time course will identify proteins involved in downstream signaling. To determine time points of interest, EncystR was endogenously labeled with mNeonGreen (mNG), and imaging of non-encysting cells displayed EncystR-mNG at the plasma membrane. To delineate the EncystR trafficking pattern, we induced encystation and followed EnystR localization for several hours using fluorescent microscopy. Individual cells were categorized by localization to peripheral vesicles, a novel acidic compartment, or non-responsive cells where localization remained on the plasma membrane. Percent peripheral vesicle localization peaked at 1h and percent compartmentalization stabilized after 3 hours. Proximity labeling proteomics at these time points can identify connections to cell trafficking to the novel acidic compartment. While EncystR does not tolerate TurboID proximity labeling, miniTurbo produced significant biotin labeling after 30 minutes in 50 mM biotin. Biotin-tagged proteins are sequestered using Streptavidin-coated columns through liquid chromatography, then cataloged using mass spectroscopy (LC/MS-MS). Proximity-tagged proteins using miniTurbo can inspire drug inhibition candidates of Giardiasis. Due to Giardia’s model nature to other parasites, such as reliance on cholesterol, parallel drugs may be found as well.

The Hell Creek Formation (HCF) of northeastern Montana is known globally for preserving some of the last non-avian dinosaurs, including Tyrannosaurus rex. In addition to T. rex, several other species of theropod dinosaur lived in the HCF. These theropods differ morphologically from each other in a variety of ways; however, given that many of these taxa are represented primarily from dental remains (i.e., teeth), the best diagnostic feature available is dental morphology, with the exception of toothless theropods such as Anzu. In this project, I am utilizing imaging processing software in order to collect diagnostic linear measurements of key aspects of tooth morphology from tooth-bearing theropods of the HCF and plot this data against time to ascertain if changes occurred in the dentition of individual taxa through the approximately 2-million-year time span recorded in the formation, utilizing specimens from the upper, middle, and lower portions of the HCF. My current dataset of 20 teeth is insufficient for statistical analysis, but already possesses great potential for future use tracking the various observed dental morphologies. The amount and precision of this morphometric data will only increase as I continue to grow the dataset through the imaging and measurement of at least 40 additional theropod specimens. Once complete, the morphological data I produce will assist in testing my current taxonomic identifications through the establishment of ranges of individual variation. Additionally, quantifying observed morphological variation relative to time can provide insight into the continuing evolution of HCF theropods due either to speciation or extinction. Through these measurements, I hope to gain clarity on both the community composition and dental evolution in the HCF theropods, which is vital to understanding the evolutionary history of those dinosaurs that are closest to birds and their ecological standing as a group immediately prior to the Cretaceous/Paleogene mass extinction.

This paper describes the expression of a non receptor tyrosine kinase, cymric (Uro-1), a HTK16-like (HydraTyrosineKinase-16) gene in Molgula oculata, an ascidian species with a tadpole larva and proposes that it plays a role in muscle development during the development of the tadpole phase. Cymric is also a member of the SHARK (Src-homology ankyrin-repeat containing tyrosine kinase) family of non-receptor TKs, a group of similar tyrosine kinases that can be found across many invertebrate species, but whose function is not yet known. The role of cymric in the development of the tail in tadpole ascidians was suspected after a subtractive hybridization showed cymric is expressed in M. oculata, a species with a tail and not in Molgula occulta a closely related ascidian whose tadpole is missing a tail. In Situ hybridization shows that in M. oculata embryos, cymric localizes to primordial muscle cells. Through transcriptome and genome analysis using both ANISEED and NCIB we show that the tyrosine kinase of the cymric gene in the M.occulta is disrupted by a large retrotransposon insertion. This indicates that, although the mechanism is still not known, cymric is involved in determination of muscle cells. A better understanding of the role cymric plays in development in ascidian species could provide insight into its importance in the many other invertebrate species which also express SHARK proteins.

What type of future manufacturing system would satisfy both the economic and environmental needs of the planet? A circular economy could be the answer. A circular economy operates much like a solitary spaceship that must regenerate water, organic nutrients, and technical materials in a constant process to sustain life. We are privileged to live on a much larger, regenerative spaceship, however, running out of resources is still a risk. Opposed to the current linear economy where end-of-life products such as toasters will be disposed of without extraction of the metals, ceramics, and plastic parts, a circular economy would realize the economic and environmental potential of keeping the parts of toasters in circulation. The purpose of this research is to discern the possible advantages and disadvantages of a widely adopted circular economy through critically evaluating peer-reviewed sources on a multitude of circular industrial sectors and applications. Much of the current research focuses on emerging technologies such as the hydrometallurgy process for lithium-ion batteries. These emerging technologies require heavy investment to become activated before the returns may be realized. It is anticipated that further research will describe natural plastic alternatives such as vegetable cellulose, but there will likely be a gap in research covering the amount of arable land required to grow crops to meet demand. Predictions detail larger corporations likely have more capability for designing circular products and a probable lack of small businesses with circular potential. Additionally, public support would be lacking due to the esoteric nature of the system and a lack of real-world circular business models currently. That is why the motivation behind this literature review is to spotlight the circular economies that are already thriving.

The drug rapamycin can increase lifespan in a variety of model organisms by repressing the activity of the mTOR complex, a cellular component required for growth and development. Other than one small study that looked at genetic variation in the effect of rapamycin on lifespan in fruit flies (Rohde et al., 2021), little is known about how natural genetic variation affects the response to rapamycin. Previous work by the Promislow lab, utilizing developmental time to indicate rapamycin’s affect, has shown that some strains of fruit flies are completely resistant to rapamycin while others are sensitive. These genotypic differences are also reflected in the metabolome, the complete set of small molecules and metabolites present within cells. Metabolome analysis of these strains revealed significant differences in metabolite concentrations between resistant and sensitive lines. Interestingly, when we treated sensitive strains with rapamycin, their metabolome profiles were like those of starved larvae. I hypothesize that rapamycin is affecting larval ability to take up nutrients and that the starved metabolome is a result of actual starvation. To test my hypothesis, I am designing a starvation assay to compare the death rate of sensitive and resistant larvae. Measurement of resistance to starvation is taken two days after rapamycin treatment by transferring larvae to nutrient deficient food. The duration of time for individual larvae to die is recorded, and the death rates between the two populations are compared. If my hypothesis is true, the sensitive larvae will have a higher death rate than the resistant larva. If death rates are similar however, that could mean that rapamycin does not cause a nutrient deficit and there is another explanation for its effects on the metabolome. This study will provide insights to the underlying mechanisms of sensitivity to rapamycin, and why it might differ between individuals.

The Pacific Northwest is home to a lush lowland forest that continually changes. Quantitative monitoring is essential in understanding forest health and climate change. The primary task was to help create a comprehensive, multi-year, dataset of floral phenology for Green River College’s learning forest; botany and ecology classes participated together in this endeavor. This quantitative data set allowed us to establish baselines for our forest so we could ask questions about how our forest changed over time. How do the native species compare to the invasive species? How many species are there, and which is most abundant? Using the ArcGIS Survey123 app, we measured floral species, abundance, GPS location, and phenology stages (buds, flower, seed/fruit, and leaves). The data was then analyzed using Qlik, an online visualization software. In 2022 alone, we compiled ~13,000 observations, estimating ~3.2 million inflorescences across ~140 species and are currently curating data from 3+ years. When looking at the floral expression in our forest from the last two dry summers, one native species (Wild Ginger) has disappeared, while many non-native and invasive plants were able to thrive. With our data set we can quantitatively look at entire plant families and monitor ecological change. A secondary benefit of this endeavor was to improve the educational capacity of our classes. Students were fully immersed in the forest and floral details. Photographs from students also helped create a repository for plant images of floral phenology stages which strongly aids in identification and higher level data quality. Our project helped undergraduates contribute scientifically while learning about their world. These contributions can help inform decisions on issues such as mitigating climate change or ecosystem preservation. Future directions include expansion of this to city parks and popular hiking trails to broaden our quantitative understanding of our ecosystems.

The migratory songbird Gambel's White-Crowned Sparrow (Zonotrichia leucophrys gambelli) experiences drastic seasonal shifts in its song production and stereotypy, driven by changes in distinct song circuit nuclei, namely increased neurogenesis in the forebrain nucleus HVC and increased electrical excitability in nucleus RA. Manipulating the photoperiod and hormone levels of these sparrows in a laboratory setting results in changes very similar to the seasonally-induced behavioral and neurophysiological changes they experience in the wild. We are interested in reducing the number of birds necessary for our studies by developing a protocol to produce seasonal effects in vitro via organotypic slice culture. Organotypic slice cultures preserve the neural connections and functions involved in the seasonal changes we are interested in, so they can be more directly observed and manipulated. We maintained slices of neural tissue from white crowned sparrows, including HVC and RA, on a membrane that allowed for exchange with the media, a technique initially developed by Stoppini et al., in 1991. After the tissue was cultured, it was fixed and resectioned into thinner slices so it could be Nissl stained and imaged to test for the presence of healthy cells. Organotypic culture is an established technique for neural tissue from juvenile animals; we are attempting to use it on tissue from adult, wild caught, white crowned sparrows. There is currently no protocol for organotypic cultures of this tissue, and the nature of the tissue itself poses a challenge. Adult tissue is less plastic than the juvenile or neonatal tissue that is usually used with this technique, so it has more difficulty surviving the shift to culture. Once the protocol is developed, we plan to manipulate the hormonal environment to try to mimic changes that occur during their breeding season.

Many genes involved in different cell differentiation processes are known, however it is more challenging to know the history of transcription in each individual cell within a new organ. To fill that gap, I am building and testing a genetically-encoded recorder that uses two serine integrases to follow expression in developing roots of the model plant Arabidopsis thaliana. An integrase is a protein that binds to unique DNA regions, called integrase sites. Once bound, the integrase can perform an inversion or excision of the DNA between the integrase sites, depending on how the sites are oriented relative to one another. In a one-integrase design, we put a constitutive promoter between two fluorescent reporter genes, flanked by integrase sites. When the integrase is expressed under the control of a promoter for a developmental gene, there is a switch between the reporters only in the cells that are undergoing that developmental program. I am now using molecular cloning techniques to build a recorder that can track the expression of two different genes, using two different integrases. My integrase-based recorder will provide insights into when and where genes are “switched” on and off to promote cell specification. In the future, reporter genes can be replaced by genes that control development, and, in this way, we can engineer plants with different root structures. Control over root architecture could lead to plants that are more resilient to heat and drought.

In flowering plants, LEAFY (LFY) is a key floral developmental gene; homologes of LFY exist in nonflowering plants, where this developmental regulatory role cannot exist. In an effort to understand what role LFY serves in a nonflowering plant I am studying the model fern Ceratopteris Richardii, as ferns produce spores not flowers. My goal is to determine if the two fern LFY homologues, CrLFY1/2, play a role in the reproductive or vegetative development of ferns. To investigate this function, I am characterizing the phenotypes of transgenic plants that overexpress one or both of the fern copies. To that end, I record data on key developmental markers across the diploid generation of the fern, or sporophyte. Given that LFY overexpression has been associated with early flowering and leaf compounding in flowering plants, I anticipate early reproductive development and/or abnormal leaf development in my transgenic ferns sporophytes. Preliminary results suggest that transgenic ferns are producing spores earlier than controls, and are not displaying all expected markers of vegetative development. Here, I present data on the vegetative development and appearance of reproductive structures of C. richardii ferns overexpressing one or both of two gene duplicates, CrLFY1 and CrLFY2 to help elucidate the functional evolution of the this important developmental regulator of flowering.

It is well-established that mutations have impacts on an organism’s fitness; however, the fitness effects of mutations are not static, and can vary depending on environmental contexts, such as the species in which a mutation is found. Evolution of the same gene in different species could thus lead to the evolution of different phenotypes, as different species would favour different sets of mutations. If that gene could be exchanged between species, it could lead to increased evolutionary possibilities, as high-fitness genotypes that require a prerequisite deleterious mutation in one species could become accessible if the mutation is not deleterious in another. Our research examines how the presence of two bacterial hosts, Escherichia coli and Klebsiella pneumoniae, could affect the evolution of an antibiotic resistance-conferring TEM-1 β-lactamase gene located on a conjugative plasmid. If different hosts confer different mutational effects to TEM-1, the process of horizontal gene transfer (HGT) that allows mutations to be shared between species could open up more mutational possibilities than those accessible in either single-species population alone. We tested this hypothesis through three rounds of experimental evolution in the presence of the antibiotic cefotaxime, where we evolved two single-species E. coli and K. pneumoniae populations and one multi-species population where HGT was simulated with a shared plasmid pool. We are now reconstructing the genotypes found in all three populations after each round to assess how much antibiotic resistance they confer in both species, and hope to see if the genotypes acquired under HGT treatment provide higher resistance compared to the single-species populations. Our results have practical implications for the predictability and nature of antibiotic resistance development in the real world, a current global health crisis, and potentially motivate further study in predicting resistance emergence in clinically encountered multi-species populations.

Phytoliths, silica bodies formed within and around plant cells, are a key part of a plant's physiological structure that can vary in shape between species. These phytolith shapes (so-called morphotypes) can be found abundantly within grasses and vary between taxa within a subfamily either in shape or in their relative abundances and could therefore provide important evolutionary data on how specific grass subfamilies may be related. Previous work has been done on certain grass subfamilies, including Bambusoideae, to identify similarities and differences in shape within a grass subfamily. This study aims to investigate the distribution of phytolith morphotypes among three closely related grass subfamilies (Arundinoideae, Danthonioideae, and Micrairoideae). To collect this data, we conducted a morphological study on over 300 phytoliths in samples from many species within our three subfamilies. The samples were taken from leaf clearings wherein the phytoliths were isolated through chemical treatment and centrifuging to remove other organic material before staining. Samples are imaged using a confocal microscope and then patched together with computer processing to form three-dimensional phytolith images. These sample objects were compared based on phytolith morphotype three-dimensional shape, their relative abundance, location in plant tissues, and size. In addition to the morphological study of individual phytoliths, we studied cleared leaves to obtain a greater sense of the composition of morphotypes within the tissue of the grasses. The results are expected to show an overlap in similar phytolith morphotypes across clades that have similar ecological niches such as photosynthetic systems. Overall, this research aims to find a link between these three close modern subfamilies that could be compared to fossil phytoliths in order to document their evolutionary history and past distribution.

In the 400 million years since they first emerged on land, plants have acquired numerous adaptations to the terrestrial environment. One of these adaptations is modification of the photosynthetic pathway, from C3 to C4. The C3 pathway, the ancestral form of photosynthesis found in most plants, has limited efficiency under high temperatures and light intensities, whereas the C4 pathway offers improved productivity. C4 photosynthesis has evolved numerous times in flowering plants in the last 66 million years, with C4 grasses being the most diverse and ecologically dominant. Despite their current importance, we still do not understand exactly when and where the evolution of C4 photosynthesis in grasses occurred because the fossil record of grasses is sparse. Phytoliths (hardened silica structures precipitated within plant cells) offer a novel tool for tracking C4 evolution. We will use phytoliths as a comparative tool to examine morphological changes associated with C4 evolution. All C4 grasses are contained within the PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae) clade of grasses. Panicoideae, one of the largest and most diverse subfamilies within PACMAD, containing both C3 and C4 species, is an ideal group to study the ecological and evolutionary factors that drive the distribution of C4 photosynthesis. Through analysis of phytolith morphology, as well as overall density and distribution of phytoliths within leaf tissue using leaf clearings, we will examine a broad sampling of Panicoideae, looking for common trends amongst C4 photosynthesizing groups as compared to their C3 counterparts. To extend the scope of these conclusions beyond Panicoideae, we will seek to confirm these trends by comparison to Aristidoideae, another clade that evolved C4 photosynthesis. Preliminary data indicate that the majority of phytolith morphotypes will be bilobates, crenates, and rondels. We expect these results to correspond between observed leaf clearings and the 3D models.

When managing our natural resources and assessing human impacts on ecosystems, it is important to understand how plant communities respond to disturbance events. The geologic record has the potential to provide an important source of information for scientists to observe how plant communities of the past have responded to disturbances. Currently, there is a limited ability to recognize disturbance as the primary driver of change because there is limited evidence of how functional traits - plant traits that relate directly with plant function and ecological strategy that are measurable in fossil leaves - vary across succession. To improve this ability, I am measuring the carbon stable isotopic composition (δ¹³C) of bulk organic matter in leaves sampled across a successional gradient. This functional trait is often preserved during leaf fossilization and is representative of a plant's water use efficiency (WUE), an important ecological strategy representing the carbon assimilated per water lost in a plant during photosynthesis. The extent to which carbon isotopes measured at the community scale reflect the successional stage of a plant community is not currently known. To improve this knowledge, I am testing the hypothesis that the WUE of plant species within a community will become more conservative in later successional stages. In support of this hypothesis, I predict that the abundance-weighted community average of leaf δ¹³C will increase through succession. In addition, I hypothesize that δ¹³C as a proxy for WUE will be most confounded in early succession, before a tree canopy forms, due to seedling utilizing water resources more rapidly without having established root systems and thus predict a higher variance of δ¹³C values in this earliest stage of succession. This research is helping develop a method of identifying disturbances within geologic records which can give guidance on management decisions regarding modern ecosystems

The geologic record provides opportunity to provide actual examples of how plant communities have responded to climatic changes, providing important perspective for modern anthropogenic-driven climate change. Two important climatic events in the Miocene offer such an opportunity, including a global warming event, the Miocene Climatic Optimum (MCO; 17-14 million years ago), and a global cooling event, the Middle Miocene Climatic Transition (MMCT; 14-12 million years ago). This study is assessing how the diversity and prevalence of ecological strategies within Pacific Northwest (PNW) plant communities changed in response to these events, by analyzing ~6 PNW fossil plant sites that span these events in time. At each site I characterize ecological strategies of taxa comprising these ancient communities by measuring leaf vein density (LVD) of fossil angiosperm leaves, which relates strongly to the maximum photosynthetic rates of the plant. Photosynthetic rates influence ecological strategy by placing plants along a spectrum with fast growth but low tolerance to resource scarcity at one end, and slow growth and high tolerance at the other. I am digitally measuring leaf vein density using microscope images of fossil leaves previously taken at several museums where these fossils are housed. I expect that during the MCO, evergreen plants with slower growth rates become more dominant and the diversity of ecological strategies increased (lower mean and higher variance of LVD). Across the MMCT, I expect that deciduous plants with high growth rates became more dominant and stronger abiotic filtering caused a decrease in the diversity of ecological strategies present (higher mean and lower variance of LVD). This study provides a real-life example of how climatic events reshaped the assembly of plant communities and provide an important perspective for present and future climate change.

The Miocene Climatic Optimum (MCO) was a period of global warming 17-14 million years ago, where temperatures increased 2-4°C and CO₂ levels increased to ~400-600 ppm. Overlapping with the MCO were the Columbia River Basalt eruptions (CRB: 6.6-15.9 Ma), where extensive lava flows spread across the Pacific Northwest, resulting in primary succession. My study is focused on reconstructing the vegetation across the MCO and during CRB eruptions using epidermal phytoliths (i.e., Microscopic Biosilica) to understand how these conditions impacted plant communities. Epidermal phytoliths are formed within living plant matter reflecting the current environmental conditions in their size and undulation. The plant matter then falls to the forest floor and decays leaving behind the resilient Microscopic Biosilica, which is preserved within that sediment. Leaves formed in ecosystems with an abundance of sunlight reflect open-canopy vegetation, with small circular phytoliths; while large-undulated phytoliths come from closed-canopy, shady environments. Previous work has shown a correlation between the average size and undulation of epidermal phytoliths with leaf area index (LAI; i.e., a measure of canopy openness). I am using this process with sediment samples collected across four sites in Central Oregon to calculate ancient reconstructed LAI (rLAI), and thus reconstruct the canopy cover. Each site was chosen due to the time period it represents, with different exposure to increasing variations of CO₂ and CRB impacts. I hypothesize increased temperature and atmospheric CO₂ concentrations during the MCO created favorable conditions for plant communities, which promoted a productive closed-canopy forest structure. Additionally I hypothesize, the primary succession induced by CRB volcanism prevented the re-establishment of forests, leading to open-canopy vegetation structure. As modern day anthropogenic-driven climate change invokes alterations in our planet's ecosystems, we need to better predict and anticipate future responses of plant communities to these environmental perturbations. 

The grass family, Poaceae, dominates over 40% of land ecosystems and is found in every biome except areas covered by ice sheets. Within Poaceae are two major clades, one being the PACMAD clade, named for the six subfamilies: Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonoideae. The PACMAD clade is the only lineage of grasses that evolved C₄ photosynthesis. This derived trait allows plants to efficiently photosynthesize under low CO₂ concentrations and in hot, arid climates. Chloridoideae is the largest subfamily within the PACMAD clade with over 1,500 species across five tribes. Most Chloridoideae species use C₄ photosynthesis and it is likely that some of the first transitions from C₃ to C₄ occurred in this subfamily; however, fossil evidence for this deep history is currently lacking. Phytoliths, which are silica bodies that form in living grass tissues and can be preserved in soils for millions of years, have great potential for filling this gap. We are studying the three-dimensional shape of phytoliths from modern Chloridoideae grasses to better recognize them in the fossil record. By linking modern Chloridoid phytolith shapes to their respective climatic conditions, we will be able to create a robust reference database to be used for future research to identify past Chloridoids and their past growing environments. To do this, we are processing 3D Chloridoid phytolith models from 2D confocal microscope images to analyze and characterize the morphology, abundance, distribution, and diversity of Chloridoid phytoliths. Thus far, preliminary data suggests our findings will be especially useful in making comparisons between past and present bilobate or saddle-shaped phytoliths, though we expect to conduct further analysis on current phytolith shapes. Future studies will be able to compare our 3D modern renderings to fossil phytoliths to infer periods of climatic warming through deep time.

Morphology of leaves informs plant functions from structure to growth rate, all summing to diverse strategies that plant communities employ to thrive. By analyzing strategy changes over time, morphology can describe the strategic response to disturbance events - particularly those precipitated by human activity. My study aims to develop a framework for characterizing those strategies on a temporal scale during ecological succession based on leaf vein density (LVD), which is the length of vein tissue within a given leaf area. I am accomplishing this through the chemical isolation of vein tissues, analytic microscopy, and image analysis, examining temperate deciduous leaves from 5 sites in North Carolina with varying amounts of time since the plot was clear-cut for timber harvest. Once I prepared slides of 4 cm2 of leaf matter, I began imaging the leaves under 8x magnification and following this, I plan on using image analysis software to measure LVD over 2-3 mm2. Based on correlations between early successional species - species populating a cleared area before slow-growth taxa regenerate - and high vein density organisms demonstrating faster growth, I hypothesize that taxa prioritize growth via resource allocation during initial phases of recovery post-disruption due to the increased availability of sunlight due to altered canopy openness, increasing photosynthetic rate. This would be characterized by higher LVD observed in early successional species. Should this prediction bear out, it indicates that LVD can be used to better understand varying ecological strategies in a community over time. Specifically, we will be able to use it to analyze how that spectrum changes based on environmental changes and determine which strategies are prioritized in which stages of community change. By garnering a clearer grasp on the diversity in early versus late successional strategies, I plan on connecting the prevalence of certain functional traits and environmental changes across time.

The Middle Miocene (23-5 Ma) represents a period of rapidly changing climate and active volcanism, particularly in the Pacific Northwest. Our understanding of the structure and composition of plant communities during this timeframe is complicated by a limited or degraded leaf fossil record. Plant fossil assemblages are also often time averaged, representing accumulation of plant material over an extended period. A plant community that was preserved because of a single, short-lived event can provide insight into the composition and structure of that community in life. The Watersnake locality of the Sucker Creek Formation in southwestern Idaho contains two thick (8-14 m) ignimbrite tuffs (volcanic ash layers) that preserve charcoal fragments, reflecting plants that were burned when the tuffs were deposited. In order to identify the woody taxa that made up this community, thin section microscopy is used to examine the preserved cellular detail of the fossil charcoal fragments from the lower tuff. Since ignimbrites are deposited as a part of a single event, the impacts of time-averaging are minimized. Although these deposits reflect a short time, they are likely to integrate across space, providing a view of the broader landscape. The results of this study will reveal the structure of this plant community immediately prior to the eruption that caused the ash flow. I hypothesize that the taxa identified within the ash will be very similar to those of the leaf fossil record found in the shale beds below. A lowland community consisting primarily of wetland Glyptostrobus oregonensis, and Quercus simulata found near flowing water will likely be represented. Upland vegetation consisting of conifers (Pinus, Tsuga) were also likely incorporated into the ash flow as it moved downhill. This study will provide insight into the dynamics of plant community change during the Miocene in relation to volcanic disturbance.

Fire is a fundamental disturbance that drives changes in biome structure. Knowledge of ancient fire regimes may help predict future fire regimes resulting from anthropogenic climate change. Charcoal morphometry (quantified shape of charcoal), particularly charcoal aspect ratio (length:width), is an emerging proxy of ancient fuel type wherein higher mean aspect ratios are associated with grassy fuels. This study aims to experimentally validate this proxy method. Thirty-four modern plant species were sampled from UW Herbarium collections, separating leaf, stem, and reproductive body tissues for each species. Each sample was burned at 500°C for 20 minutes, crushed in a water slurry, and imaged under a binocular microscope. Charcoal particles were enumerated and morphometrics were measured using ImageJ with charcoal particles 125-250 μm and >250 μm analyzed separately to account for differences due to differential particle breakage. Strong evidence was found in the 125-250 μm size fraction through an analysis of variance test (F = 2.66, p = 0.03), that aspect ratio varies as a function of taxonomic group. The strongest evidence for a difference in aspect ratio is found, through Tukey's Honestly Significant Differences to be between graminoid and conifer charcoal (p = 0.03). Evidence is even stronger for a taxonomic effect on aspect ratio in the >250 μm size fraction (F = 3.64, p= 0.007). This variation seems to also be driven by a difference between graminoid and conifer charcoal (p = 0.002), corroborating earlier findings. Future validation of this methodology will be focused on the potential effects of burn temperature and charcoal transport in charcoal morphometric records. Rigorous verification of charcoal morphometry as a proxy of fuel type will help increase confidence in paleo reconstructions of fuel type. 

 The diversification of many vertebrate groups was spurred by the use of novel food resources, and jaw functional morphology provides clues about the adaptations associated with dietary diversification. The external dimensions along the mandible reflect strength to resist bite forces, which are in turn associated with physical properties of the diet. Variation in these dimensions along the jaw and between different species therefore may reflect adaptations of the jaw to specific diets. We applied this biomechanical framework to investigate the relationship between jaw robustness and diverse diet types in bats. Using mandibles of more than 60 species, we quantified the external dimensions at interdental gaps to generate mandibular strength profiles. The strength profiles of frugivorous, insectivorous, and omnivorous bats showed similar patterns, with a trend of increasing jaw depth toward posterior teeth. All diet types showed a high level of variation in jaw shape along the toothrow, suggesting differences in the functional roles of different teeth. Insectivores showed the greatest within-guild variation in jaw shape, while nectarivores had noticeably gracile symphyses. Further, insectivorous bats showed relatively deep jaws at the canine and premolars, which may be associated with the use for prey capture, while frugivores have relatively deep jaws at the posterior molars, possibly linked to adaptations for crushing seeds and pulp. These results suggest that mandible strength profiles reflect dietary adaptations in bats.

 Dravet syndrome (DS) is a genetic form of epilepsy characterized by febrile seizures in infancy, developmental delays, and sudden unexpected death in epilepsy (SUDEP) as a result of being drug-resistant. Finding new and innovative treatments is essential to reducing the risk of SUDEP and other symptoms in DS patients. Using a mouse model of DS (SCN1a+/- mouse), I showed that a machine learning-based detection algorithm could be used to detect interictal spikes (IS), which are abnormal neuronal discharges typical of epilepsy. The goal of the current experiment is to see whether the prior findings can be generalized to a larger dataset and whether the detected IS can be used to predict seizures before their onset. Data is collected by implanting two electrocorticographic electrodes and one electromyography electrode, as well as a wireless body temperature sensor in DS mice. Ambient temperature is controlled so that the animal’s core body temperature is initially maintained at 37°C and then is gradually increased by 0.5 °C every 2 min until a seizure is observed or the core body temperature reaches 42.5 °C. A machine learning model previously trained using manually scored data from the de la Iglesia lab is used to autonomously detect IS in the collected data. My results so far showed a moderate yet significant positive correlation between ambient temperature increases and IS frequency and points to a positive correlation between IS frequency and seizure onset. However, these results did not include the continuous recordings of body temperature. In the current experiment, I test if these correlations hold using a larger sample size and including continuously recorded body temperature, which may have more predictive power than ambient temperature. Our long-term plan is to design a closed-loop experiment that uses the algorithm to predict and stop seizures before their onset.

The modern education system has the opportunity to raise students with a well-rounded, interdisciplinary knowledge base, but that does not begin until textbooks (the backbone of many science curricula) include such topics. We wondered to what extent Multiple Ways of Knowing (MWoK), particularly in the topics of religion, culture, traditional medicine, and philosophy, are represented in introductory biology textbooks. The term MWoK describes these topics and recognizes that there is more than one way to learn and understand, crediting different cultures for their scientific contributions. This study is a spin-off from a greater project in which our team scored and evaluated six introductory biology textbooks on how much and how well they included a variety of social justice topics. Using the data gathered from the aforementioned study, we categorized the instances of MWoK by frequently occuring themes - religion, culture, traditional medicine, and other. We found that across over 9670 pages, these textbooks lack adequate discussion of MWoK, with only 32 mentions. Within these few instances, only one showed themes of justice or injustice, and one demonstrated themes of equity and inequity. Textbooks alone are insufficient for implementing the diversity of science in American classrooms. We envision this research as a starting point for instructors to integrate these topics into their classes. Incorporating more involved conversations about MWoK within the context of science can act as a way to foster a more inclusive learning environment wherein all students are able to engage more meaningfully with the material. Including MWoK in biology textbooks, and thus, biology curricula, would bring the STEM classroom one step closer towards increased diversity. 

Mutations in the genetic sequences of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) has played a major part of the pandemic. This is evidenced by the increasing number of distinct strains that have appeared. Evaluating these mutations and their frequency within genetic sequences offers the opportunity to identify patterns that aid in increased virility for SARS CoV-2. We identified prevalent SARS CoV-2 strains in GISAID and downloaded genetic sequences from the NCBI nucleotide database. We used MAFFT (Multiple Alignment using Fast Fourier Transform) in Seaview to align SARS CoV-2 strains to the reference genome. We also built a custom python script to identify locations of mutations, and their potential effect on the proteins’ amino acid sequence. Preliminary work identified a mutation in the ORF1ab gene of the omicron strain. Part of this gene codes the typically conserved NSP-16, associated with the product 2’-O-ribose methyltransferase, an enzyme that catalyzes the transfer of a methyl group from a methyl donor molecule. The modification could affect the stability, localization, and function of RNA such as RNA splicing and post-transcriptional modification. We then generated a phylogenetic tree using BEAST/BEAuti to estimate the frequency and history of mutation across different strains. Our analysis identifies mutations accumulated over the course of the pandemic. Studying the effects of these mutations offers insights into SARS CoV-2 virology. These insights can be used to build a predictive model to aid in effective and efficient vaccine development.

Science and biology are intextricably linked to policymaking and thus interconnected to justice and injustice in our society. Yet, STEM education fails to emphasize this perspective. Our purpose in this research was to find ways undergraduate biology students can apply their scientific knowledge in the pursuit of justice, such that they can go beyond reading the text, thinking critically and answering questions applying science to the policymaking process. Accordingly, we asked, to what level of humanization do undergraduate biology textbooks frame scientific influence on policy as a tool for achieving justice? To investigate this, we, along with a larger team, analyzed six popular introductory biology textbooks searching for excerpts that contextualized science in society through ideas such as government policy or the judicial system. If an excerpt was found to contain these topics, it was coded based on topic and degree of humanization (in increasing order of humanization: none/scarce, detail, nuance, equity/inequity, or justice). For this project, we defined humanization as discussing or positioning science within the context of society or justice and/or injustice. We found that textbooks' contextualization of science within society is underdeveloped and does not foster critical thinking about the applications of science in policy and justice. Additionally, where this is addressed, there is limited depth in the text and breadth of examples. While our data suggests that these textbooks rarely contain humanizing concepts related to policy, our intent is not to suggest edits to the textbooks. Rather, we have identified trends in humanizing biology content that instructors can add to their curricula to contextualize the role of science in policymaking and justice in their classrooms. Additionally, these changes can encourage students to acknowledge the applications of their biology knowledge to policy in the pursuit of justice in society outside the classroom. 

The drug rapamycin has been shown to extend lifespan in model organisms ranging from mice to fruit flies, but little is known about how genetic variation affects the response to rapamycin. It is possible that some individuals might not respond to the drug, or may even respond negatively. To study the impact of genetic variation on rapamycin sensitivity, the Promislow lab has been using the fruit fly, Drosophila melanogaster, to test the ability of rapamycin to slow early development in different strains. They found a range of responses, from strains that were completely resistant to those that were highly sensitive. To better understand why resistant and sensitive strains differ, the Promislow lab analyzed their metabolome profiles. The metabolome consists of diverse small molecules, metabolites, that are fundamental to sustaining life in cells, and the relative abundance of metabolites is referred to as a metabolome profile. By comparing metabolome profiles, the Promislow lab found that the metabolome of sensitive larvae treated with rapamycin was similar to those of larvae starved of nutrients. One possible explanation for this observation is that sensitive larvae on rapamycin-treated food eat less food than resistant larvae. To test my hypothesis, I am measuring how much food they ingest, using dyed food, and scoring how much dye each larva ingests over time. If sensitive larvae eat less rapamycin-treated food than resistant larvae, then we can investigate why rapamycin affects feeding. If no significant difference is found between scores for sensitive and resistant larvae, then we can investigate why rapamycin affects early development in sensitive strains when their food consumption is not limited. By determining if sensitivity to rapamycin is accompanied by differences in feeding, then we could potentially manipulate feeding to sensitize flies, and possibly humans, to this beneficial drug.

It is important for us humans to take responsibility for how our actions have exacerbated climate change and the disproportionate effects that climate change has had and continues to have on various minority groups. Through educating students about climate change in a humanizing manner, we can hope that students will view science as a discipline willing to confront inequities to seek change. However, the textbooks commonly used in introductory biology classes fail to accurately communicate the full scope of the inequities behind who is intensifying climate change and who is the most impacted. My research serves to determine if the humanization of climate change is communicated to undergraduate students taking introductory biology through aiming to answer two important questions: To what extent are textbooks acknowledging humans’ responsibilities in the severity of climate change today and to what degree is equity/inequity discussed? In order to investigate these questions, my team and I evaluated six popular introductory biology textbooks in the United States by pulling passages that discussed the connection between climate change and society. Coded passages were evaluated on where their level of humanization of science fell on the following scale: none/scarce, detail, nuance, equity/inequity, and finally justice. Out of the 1351 total “humanizing” passages pulled from the text, only 7.8% of the quotes were categorized as relating to climate change. Of these quotes, 19% were coded as none/scarce, 60% had detail, 6.7% contained nuance, 11% discussed equity/inequity, and 4.8% included justice (sum total > 100% due to two quotes falling under multiple categories of humanization). As climate change will continue to negatively impact humans, it is important to teach students the specific inequities connected to climate change in order to spread awareness and help solve issues of justice in the living world.