Plants, like other multicellular organisms, possess a complex set of defensive measures deployed upon stimulation of the immune system. In the case of insect herbivory, these defensive measures depend upon specific pattern recognition receptors (PRRs). These PRRs enable the plant to detect herbivore associated molecular patterns (HAMPs). The Inceptin Receptor (INR) is a known herbivore receptor found in legumes, which detects Inceptin 11 (In11), a peptide fragment unique to the oral secretion of Spodoptera exigua. Beyond the plasma membrane much of the pathway from In11 detection to immune response is unknown. This research investigates possible signaling kinases downstream from INR. Receptor-Like Cytoplasmic Kinases (RLCKs) are known to mediate both specific immune and developmental signaling cascades in Arabidopsis thaliana. This suggests that they may play a role in the signaling network of herbivore induced immune responses. In this work we systematically investigate seven RLCKs of interest from three clades within the legume RLCK protein family which are upregulated by In11 treatment in the common bean (Phaseolus vulgaris). To better understand their effects, selected RLCK’s are transformed into the plant model organism Arabidopsis thaliana via Agrobacterium tumefaciens, and homozygous transgenic lines overexpressing the RLCKs are isolated. To examine the effects of over-expressing RLCKs on immunity, classic immune assays will measure their effects on Reactive Oxygen Species (ROS) and the phytohormone Ethylene production during immune activation. This research provides insights into plant immune signaling specific to caterpillar herbivory. In the future, this research may enable the intentional amplification or modulation of plant immune response to reduce losses in crops susceptible to herbivore infestation, a growing concern for food security in the near future.

Plants' defense mechanism against herbivory and disease is integral to both natural ecological balance as well as global food supply. Induced plant responses to these threats are often triggered by specific molecules such as Herbivore Associated Molecular Patterns (HAMPS) and Pathogen Associated Molecular Patterns (PAMPS). In this project, we are refining a Luciferase Reporter Assay (LRA) and then using that assay to categorize novel HAMPS and PAMPS. This assay’s first main part is the HAMP/PAMP Receptor (HPR). By inoculating a Nicotiana benthamiana (NB) leaf with an Agrobacterium containing a Plasmid with an HPR, we are expressing specific HPRs. We are then using the second part of the LRA, a Luciferase Reporter, whose promoter is tied to an immune response related gene to measure levels of immune activity without the need for Transcriptomic Analysis. After we have infiltrated the NB leaf with the vector containing Agrobacterium and induced a response by adding a HAMP/PAMP, we are measuring Luminescence as a proxy for immune response via an imaging machine, then using R to run an analysis on the levels of immune response, helping us characterize an HPR and its signal pathway. We recently optimized time points for HPR and Luciferase imaging and have found that infiltration by Agrobacterium only takes 24 hours for sufficient plasmid integration. As such we are using this assay to run an experiment on the molecular mechanisms of an HPR in only a few days. Refining this LRA and the information we have gathered has helped shed light on the underlying mechanisms used in induced plant defense. In the future, we are planning on expressing genes of interest using this technique to seek novel activators and suppressors helping us further understand mechanisms of plant defense.

Plants recognize herbivore-associated molecular patterns (HAMPs) during herbivory that activates signaling to induce immune defenses. Caterpillar oral secretions contain Inceptin 11 (In11) which is a HAMP recognized by legumes such cowpea via Inceptin Receptor (INR). Thus, In11 and INR are a model system to study proteins involved in HAMP induced defenses, including Kunitz trypsin inhibitors (KTIs). It is known that KTIs are serine protease inhibitors with anti-herbivore activity; however, the precise role of In11 induced KTIs and the effect of cysteine content variation in cowpea KTIs remains unknown. Here, we show that selective removal of cysteines has a negative effect on KTI function in cowpea experiencing herbivory from the fall armyworm (Spodoptera frugiperda). We found that cowpea KTIs act as antiherbivore proteins against the fall armyworm when expressed in Nicotiana benthamiana, as we saw reduced weight gain on larvae feeding on leaves expressing wildtype KTI. Furthermore, we found that KTI function was negatively affected by the removal of cysteines, and larvae fed leaves expressing any of the mutant gained more weight than those feeding on wildtype. We hypothesize that these findings are due to reduced protein stability because we did not detect mutant KTIs in frass samples by westernblot. Understanding KTI protein structure and how it influences protein function is important for designing and selecting antiherbivore proteins to be used for plant defense in agriculture.

Evidence-based changes to instruction can lead to better student outcomes and performance. For this reason, instructors are interested in collecting data about student experience and outcomes. However, the process of data collection and analysis can be time-intensive for instructors, making it challenging to gather data necessary to improve their classes. Moreover, when data collection does happen, it often centers quantitative data, but this systematically devalues students' experiences. Therefore, we sought to develop a tool that aids instructors in processing and analyzing qualitative data pertaining to students’ class experiences. As part of our research project, we have developed an R-shiny based data processing app that integrates Artificial Intelligence to summarize findings from open response questions on student surveys. This tool is intended to alleviate the time-intensive nature of analyzing student responses to open-ended survey questions. In order to validate the accuracy of AI-generated summaries, we compared them to manual summaries generated using in vivo qualitative coding methods. We find that our app generates responses that are comparable to the manually generated summaries. The summaries include prominent themes along with details about student experiences within those themes. With this tool, instructors can gather real-time data, even in large classes, eliminating the concern of the time-intensive process of manually reviewing responses. By developing this tool, we hope to empower instructors to explore diverse questions that provide them with valuable insights on how to optimize the structure of their classes to improve student experience and outcomes.

The emergence and spread of antimicrobial resistance (AMR) in bacterial populations pose a significant threat to global health. A key factor in this process is the horizontal gene transfer (HGT) of resistance genes carried by mobile genetic elements (MGEs). This study focuses on understanding how mutations in plasmids influence the rate of HGT and its implications for the spread of AMR. Plasmids are small, extrachromosomal DNA elements that can transfer between different bacterial cells, a process crucial in spreading antibiotic resistance genes. These plasmids often use a mechanism known as conjugation for transfer, a process encoded by approximately 30 genes in the transfer (tra) operon. This research aims to understand how changes in the tra operon affect the plasmid's ability to move between bacteria. This movement can be either horizontal (between different cells) or vertical (from parent to offspring during cell division). Our project is divided into two main aims. The first is creating a library of mutated plasmids. I modified a large, well-studied conjugative plasmid, the F plasmid, and introduced specific mutations into the tra gene. This step is achieved using a method called Lambda Red recombination, a technique suitable for large plasmids where standard cloning methods fall short. The second aim is to measure the rates of vertical and horizontal gene transfer (VGT and HGT) in these mutated plasmids. We employed the Luria-Delbrück method for precise estimation of these transfer rates. Understanding the trade-off between VGT and HGT is crucial in predicting and controlling the spread of AMR. By mapping the relationship between specific mutations in the tra operon and their impact on gene transfer rates, our study contributes to a broader understanding of how antibiotic resistance spreads through bacterial populations. This knowledge is vital for developing strategies to combat the increasing threat of antibiotic-resistant bacteria.

Investigating the mechanisms behind asymmetric cell division (ACD) not only provides insight into an integral aspect of development in organisms such as C. elegans, D. melanogaster, and in human stem cells, but it also has the potential to elucidate the cellular functions that result in disease processes like cancer. ACD describes the cellular activity that results in a singular parent cell dividing into two daughter cells with two distinctive molecular compositions, and, in turn, fates. Drosophila melanogaster neural stem cells, called neuroblasts, are intrinsically polarized and divide asymmetrically. This process involves an uneven distribution of cell-fate-determining proteins that eventually designate the function of the daughter cell. Because of this polarity establishment and orientation, these daughter cells can have highly specialized functions. My work uses Drosophila melanogaster neuroblasts to screen for novel mutations responsible for compromising ACD. I'm specifically interested in finding genes that are involved in the generation of cell size asymmetry. Finding these mutations is imperative because, by doing so, we can identify critical genes involved in this process of interest. To that end, I knocked-down candidate genes with RNAi in neuroblasts and assayed the localization dynamics of myosin and microtubules– two critical components of the ACD and symmetric division process. Through confocal, live-cell imaging, I then examined the dynamics of these cellular proteins as they relate to wild-type ACD to see if my chosen candidates were responsible for this process. I anticipate finding novel cytoskeleton regulators that are important for establishing cell size asymmetry. In the future, finding the genes behind ACD will provide great insights into the mechanisms behind both development and disease in addition to the field of stem cell biology overall.

Plants are generally unable to move reasonable distances as single adult organisms. This lack of mobility necessitates robust pathways that allow for response to environmental stimuli which can cause changes in the plant’s morphology to adapt to their changing environment. One such trait is flowering, and it is crucial for plant survival because it allows for plants to reproduce. The vast majority of agricultural plants are flowering plants, and robust growth and reproduction of these plants is especially important for the growing human population. This experiment aims to understand the interaction between an Arabidopsis thaliana nitrogen response gene named NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1), and an Arabidopsis gene which controls flowering called FLOWERING LOCUS T (FT). NIGT1 is known to modulate plant flowering despite being a nitrogen response gene. Here, I used a Dual-Luciferase Reporter System to test whether NIGT1 proteins directly interact with the FT promoter to regulate FT gene expression. In this system, the FT promoter is used to drive expression of Firefly Luciferase rather than FT. Separately, the NIGT1 gene coding region will be highly expressed under a constitutive 35S promoter. It will also be fused to the transactivation domain of the viral protein VP16 which converts transcriptional repression into transcriptional activation, as NIGT1 is known to be a transcriptional repressor. The VP16 transactivation domain will be repeated as four tandem repeats, forming the construct called VP64. The gene constructs of interest will be inserted into Nicotiana benthamiana using agrobacterium infiltration, then the leaf material from N. benthamiana will be used for the Luciferase assay. I hypothesize that the binding of NIGT-VP64 to the FT promoter will cause increased in Firefly Luciferase production compared to the absence of NIGT1-VP64. Higher amounts of Firefly Luciferase will result in greater luminescence, which we will quantify with a luminometer.

Including undergraduate peer facilitators (UPFs) in lectures can support students in large and often challenging introductory science courses. Our team decided to increase UPF involvement by creating BIOL113, an undergraduate-led companion course to BIOL180, the largest introductory Biology course at the University of Washington. This study is part of a larger project that assessed the overall experience of both UPFs and students, and this particular work focuses on the former. I investigated how BIOL113 contributed to the experience and development of UPFs.This study incorporated qualitative data from graduated and enrolled UPFs alongside UPF applicants. Through surveys, I explored personal, professional, and academic growth, leadership skills, program expectations, and a sense of belonging. My findings underscore the distinctive role of undergraduate-led programs in enhancing UPF experiences. UPFs’ expectations for the program aligned with their experience and enriched their sense of belonging within the biology department, STEM, and the broader University of Washington community. Furthermore, engaging in UPF roles developed individual leadership skills while also contributing to their personal, professional, and academic development. In addition, the survey highlighted an important area for improvement: tailored professional development for UPFs should focus on marketing the skills gained in teaching and leadership as particularly valuable in the job market, graduate school, or professional school. Understanding the impact of BIOL113 on UPF experience can inform instructional approaches, with the possibility of expanding such initiatives university-wide.

Plants utilize cell surface protein receptors to recognize insect herbivory through the detection of Herbivore Associated Molecular Patterns (HAMPs) Following the detection of HAMPs, plants initiate specific immune responses, often measured by the increased production of the hormone ethylene gas and by Reactive Oxygen Species (ROS). The Inceptin Receptor (INR), which is specific to legume plants, recognizes the HAMP Inceptin11 (In11). The binding of In11 to INR initiates a signaling cascade, leading to an immune response. However, the signaling mechanism activated by INR is unknown. The Receptor-Like Cytoplasmic Kinase (RLCK) gene Herbivore Induced Kinase 1 (HIK1) is upregulated by In11 treatment in the bean species Phaseolus vulgaris. The goal of this research is to determine if HIK1 and other RLCKs are downstream proteins required for INR signaling. Because of the genetic intractability of P. vulgaris, I transform Arabidopsis thaliana with RLCK genes using Agrobacterium tumefaciens infiltration. Isolated genetic lines are then used to analyze the effect each RLCK has on immune signaling. Transgenic plants are treated with bacterial associated molecular patterns to trigger an immune response, then tissue samples of the leaves are measured for ROS and ethylene gas production. Results are then compared with ROS and ethylene gas production of wildtype plants. If the studied RLCKs are involved in downstream INR signaling, the transgenic plants will have increased ROS and ethylene gas production. I anticipate HIK1 to have the strongest increase in ROS and ethylene gas production due to the upregulation of HIK1 after In11 treatment in P. vulgaris. Understanding the INR signaling pathway is vital for engineering of plants that are resistant to insect herbivory without the use of pesticides.

Plants grow in designated areas known as meristems that contain stem cells. The gene LEAFY (LFY) is a flower meristem identity gene that initiates flower development in flowering plants and its homologs are also found in plants that do not produce flowers. Ferns are a lineage of land plants phylogenetically midway between the non-vascular bryophytes (such as mosses) and the seed plants. The model fern Ceratopteris richardii (Ceratopteris) contains two LFY homologs (CrLFY1/2). Given the described meristematic function of LFY in flowering plants, I am investigating whether CrLFY overexpression affects the development of the multicellular lateral meristem known as the “notch meristem”, the main site of cell division for the heart-shaped Ceratopteris gametophytes (the haploid stage of a plant’s life cycle). It has previously been established that CrLFY maintains cellular division in the apical cell of Ceratopteris gametophytes (a unicellular meristem that initiates development), but it is unknown if CrLFY also plays a role in notch meristem division once the apical cell terminates early in development. Consistent with our hypothesis, qualitative observations suggested that plants over-expressing CrLFY have larger and more U-shaped meristems, whereas wild type meristems appear more V-shaped. I am working to quantify the meristematic region within the notch in wild type compared to CrLFY over-expressing gametophytes using scanning electron microscopy and cell hand-tracing. I measure each traced cell and identify meristematic cells as those thinner and longer than the surrounding cells, with a length-to-width ratio of 3 or above. Additionally, I analyze the meristem angle to determine if there is a correlation between CrLFY expression and notch meristem shape. Understanding the role of LFY in plant meristems has important implications for the overall evolution of land plants, as master regulator genes such as LFY emerged in early plant lineages and evolved their functions over time.

The seeds and fruits of all flowering plants derive from female reproductive structures called pistils. At the tip of a pistil is an area called the stigma that is the site of pollen reception, making the structure of stigmas critical for ensuring plants are pollinated and produce seeds. In the genus Thalictrum, stigmas vary widely: short stigmas are present in insect-pollinated Thalictrum species to facilitate closer contact with visiting insects and ensure successful pollen deposition, while longer, more feathery stigmas have evolved from these to take advantage of wind for pollination. However, the evolutionary and genetic basis for this transition is not known. I aim to explore the genetic mechanisms that facilitate the transition from insect-mediated to wind-mediated pollination using Thalictrum thalictroides as a model species. Specifically, I am testing the function of two candidate genes in T. thalictroides stigma development, STYLISH1 and STYLISH2 (STY1/2), which are known to be necessary for stigma development in other plant species. To do so, STY1/2 genes have been silenced and overexpressed by virus-induced gene silencing and virus-mediated overexpression. I collected and imaged floral tissue from transgenic plants and validated them by qPCR. The effects of silencing and overexpressing STY1/2 are then determined using scanning electron microscopy to visualize cellular changes to the pistil and stigma. I predict shortened or loss of stigmas in silenced flowers and elongated stigmas in overexpressed flowers, which would support my hypothesis that STY1/2 are necessary for stigma formation in T. thalictroides. Not only do these findings enhance our knowledge of plant adaptation to environmental changes, but they also create implications for efforts toward conservation and sustainable agriculture, offering potential insights into the prospect of engineering wind-pollinated plants in a changing climate with dwindling pollinator populations.

Marine heatwaves have altered ecosystems globally, including changing community composition and facilitating the spread of invasive species. In south Puget Sound, Washington (USA), non-native Pacific oysters (Magallana gigas) have been farmed extensively for almost a century and grown in enhancement sites, however, they have only recently recruited in the wild. This study explores how the appearance of Pacific oysters was related to spatially (eight sites) and temporally (decade) warmer summer water temperatures in south Puget Sound and compares oyster persistence across five sites where recruitment occurred. The largest recruitment event from 2012-2020 was in the summer of 2015, in the middle of the east Pacific Blob marine heatwave which led to warm water temperatures off the west coast of North America. Throughout the study period, the number of oyster recruits each year was positively correlated with warmer water temperatures. Oyster population densities differed across the five sites where recruitment occurred and generally declined after 2015, but showed no site by year interactions, which is consistent with spatially-variable recruitment and similar post-recrutiment survival. Mean oyster shell heights also differed among sites, which could reflect different growth trajectories or recreational harvest patterns. This study supports the claim that warming sea surface temperatures may interact with species introductions to change modern biogeography. 

Eelgrass (Zostera marina) is a marine flowering plant that provides important ecological, environmental, and economic services in the Puget Sound. Z. marina reproduces both asexually and sexually; however, the cellular regulation behind each mode of reproduction is poorly understood. Establishing Z. marina’s regulation behind sexual reproduction will improve predictions of Z. marina’s resilience to anthropogenic pressures. FLOWERING LOCUS (FT) is a highly conserved gene that promotes floral development in flowering plants and is well-characterized in the model organism A. thaliana. As a marine flowering plant, we hypothesized that a homologous, functionall FT exists within Z. marina. We identified 13 candidate Z. marina FT homologs (ZmFT), and from analysis of relative flowering time, 5 homologs of interest emerged: 2 that promote flowering, 2 that inhibit flowering, and 1 that has striking sequence conservation to A. thaliana FT, yet has no observable impact on flowering. To determine how intracellular distinctions alter the function of these respective Z. marina FT homologs, I am currently investigating putative protein-protein interactions of the ZmFT homologs with components of the A. thaliana floral activating complex, such floral promoting transcription factors, and scaffold proteins . I can characterize these protein-protein interactions using Yeast Two-Hybrid assays (Y2H) and BiFC fluorescent microscopy In which protein-protein interactions between ZmFT and A.thaliana floral complex proteins yields either yeast strains with conferred prototrophy, in Y2H, or a fluorescent signal, in BiFC. From my Y2H and BiFC work, I will characterize interactions of the ZmFT homolog proteins, with known components of the A. thaliana flowering pathway. The results of this study will help define how Z. marina regulates flowering onset and sexual reproduction. 

Corepressors are proteins recruited by partner proteins to negatively influence the transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and while we understand a lot about how TPL works, many mysteries still remain. 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 RNA binding sites in its promoter with sequences not found anywhere else in the Arabidopsis genome. This allows dCas9-TPL to bind to and repress this synthetic gene and not affect the transcription of other genes. Many of these plants have morphological phenotypes, and visual screening of the repressed RUBY line showed the plants turn a faint whitish-pink instead of bright purple, signifying that the repression by TPL is working. I have screened mutagenized populations of 40,000 individuals from the validated repressed RUBY plant strains using the Ethyl methanesulfonate (EMS) protocol, which creates new point mutations. I identified 257 individuals from 129 mutagenized families with bright purple organs, which signifies that the RUBY reporter is no longer repressing due to a putative TPL interactor being mutated. I will then proceed to form complementation groups and subsequent DNA sequencing to map the mutations. By identifying regulators of corepressor function in plant biology through downstream whole genome sequencing, 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.

As anthropogenic causes of species declines (i.e. habitat loss, climate change) worsen, many carnivoran species are threatened with extinction. These extinctions could also decrease the overall diversity of carnivorans, which have evolved diets as disparate as herbivorous pandas and carnivorous lions, and body shapes as different as elongate mustelids and robust bears. Because phylogeny and dietary ecology influence the evolution of skull shape, we used skull shape to quantify diversity in carnivorans. In this study, I will investigate whether carnivoran species at high risk of extinction have similar skull shapes to one another and whether their average skull shapes are distinct from the average skull shapes of species with other conservation statuses (i.e., least concern). If this is true, specific skull shapes could eventually cease to exist, decreasing skull diversity in carnivorans. I used 3D geometric morphometrics and phylogenetic principal component analysis to quantify skull shape diversity, and I used the International Union for Conservation of Nature (IUCN) Red List of Threatened Species to determine each species’ conservation status. In preliminary analyses, a phylogenetic ANOVA and pairwise comparisons of skull shape against conservation status indicated that there are significant differences in average skull shape among conservation statuses, specifically between vulnerable species and both least concern and near threatened species. This study will reveal new insights into the conservation of carnivorans and carnivoran morphological diversity.

Sambucus newtoni is a type of elderberry (Adoxaceae, Angiospermae) from the late Eocene epoch. It has not received much research attention since its discovery in the early 20th century. Researchers identify it based on its leaflets (parts of compound leaves), with other traits inferred from more modern Sambucus species. As a result, its flower morphology has remained unknown. Here, I contribute to our understanding of S. newtoni by describing an excellently preserved compression fossil of a floret (small flower) from a S. newtoni cluster of florets, a so-called cyme. The fossil was collected from lake deposits in the Florissant Formation, Colorado. I described and analyzed the specimen with a microscope and observed extremely well-preserved petals and anthers (male flower parts). The flower sits next to a fossilized fly specimen on the adjacent sedimentary rock layer. The close similarities of the flower of S. newtoni to that of the extant species S. javanica (Chinese elder) may help confirm recent common ancestry as originally suggested through comparisons of the leaflets. Further, improved understanding of S. newtoni through study of the new specimen may open the door to greater understanding of Sambucus evolutionary history as a whole.

3D measurements made with digital tools are increasingly useful for studying morphology, but methods that capture sub-millimetric detail are rarely portable, inexpensive, or usable on live animals. These issues are especially troublesome when studying bird bills, which are often small, complex, and delicate to handle. I strove to develop a method that could cheaply, accurately, and quickly generate models of live hummingbird bills in the field. Using photogrammetry, I scanned Burke Museum specimens of several hummingbird species modifying aspects such as light, number of cameras, and number of photographs, to determine the ideal conditions for generating bill models. After developing a methodology, I scanned Green Hermit (Phaethornis guy) specimens from the Burke to establish the efficacy of the system in determining sexual dimorphisms in bill curvature and bill surface area. I then applied the methodology developed in the museum at a replicated setup in the San Juan Islands to study live Rufous Hummingbirds (Selasphorus rufus). This system is capable of quickly capturing and posterior rendering high-resolution 3D models, is field-amenable, allows color analyses, is adaptable to subjects of a variety of sizes, and is easy to update. In hummingbirds, fine-scale details like sharpness, curvature, and minute variations in bill-tip shape can have large behavioral implications. They can tell us more about how bills are used for feeding, fighting, and preening. However, bill tips are delicate, and fine details are difficult to preserve and easily lost in museum specimens due to wear and tear. A complete picture of bill morphology requires individuals that cover a wider range of life history than those commonly available in a museum collection. The 3D imaging of these traits in the field represents a powerful new way to learn about bird bills and other fine-scale features in live animals.

In place of an adaptive immune system, pattern recognition receptors (PRRs) that perceive host-derived herbivore-associated molecular patterns (HAMPs) induce immune signaling cascades in plants. Inceptins are a class of proteolytic peptides that originate from chloroplastic ATP synthase that are produced in the oral secretions of all studied species of caterpillars in the order Lepidoptera. Upon introduction to the plant, inceptin-11 (+ICDINGVCVDA−) binds to Inceptin Receptor (INR), triggering a signaling cascade to up-regulate defensive hormones, specialized metabolite toxins, and other direct resistance mechanisms against herbivores. However, the full ecological extent of the effects of the INR signaling cascade is poorly understood. Here, we show that inceptin-11 signaling in common bean (Phaseolus vulgaris) can mediate the attraction of predatory wasps (Polybia sp., Polistes sp.) as an added, indirect line of defense against herbivore threats. Using a near-isogenic line of P. vulgaris containing a 103 base pair deletion in the INR locus, we found that Polybia and Polistes preferentially forage on sibling lines with wild-type INR that respond to herbivore threats. Siblings with fully functioning INR produce nearly three-fold more (E)-4,8-Dimethyl-1,3,7-nonatriene (DMNT), an established volatile wasp attractant, than the deletion line. Our results demonstrate that INR can leverage cross-kingdom predator-prey relationships to aid in defense of the plant. Moreover, our near-isogenic line of P. vulgaris provides a genetic resource for studying the role of pattern-triggered immunity in indirect defenses.

Chemical communication is the oldest and most widespread form of communication across the tree of life, and markedly present among lizards. However, the drivers of chemical profile variations in this group remain for the most part uninvestigated. In South American lizards of the Tropiduridae family, semiochemicals are produced by epidermal gland organs called α-glands, exclusively found on the ventral side of male individuals of at least 40 species from four genera. The chemicals produced by these glands are hypothesized to interact with their environments in different ways since chemical species are naturally reactive and tend towards their lowest energetic state. Thus, the intrinsic properties of a semiochemical impact its survival and efficacy for communication. Given the diverse ecology and broad geographical distribution of tropidurids, we investigated whether variation in the chemical composition of α-gland secretions correlates with temperature, humidity, and habitat openness. We performed liquid chromatography-mass spectrometry (LCMS) to obtain the metabolomes of three different sample types. We sampled male skin containing the α-glands, undifferentiated male skin, and female skin. Environmental and chemical property data were extracted from online databases, literature, and field observations. Preliminary tests were done by making Venn diagrams comparing the metabolomes of each sample type. These revealed differences in metabolite compositions, notably between males and females as well as between glandular and undifferentiated skin. From the metabolomes of α-glands, we expect to see chemical species with properties that confer greater survival given the specificities of the environment. For example, given a lizard from a hot and humid environment, we expect the metabolome of the α-glands to contain higher molecular weight species with less functional group complexity. Understanding how environmental parameters drive the chemical composition of α-glands is expected to provide a deeper understanding of the evolutionary history of chemical signaling in terrestrial vertebrates.

The mandible is a functionally important part of the mammalian skull. Various selective pressures shape mandibular morphology, with the impact of diet on mandibular evolution across mammals intriguing evolutionary biologists. In this study, we investigate whether diet influences mandibular evolution across a variety of primate species. The diets of primates vary greatly (e.g., omnivory, insectivory, frugivory, folivory, and gummivory) that are characterized by a range of different physical properties that include toughness, nutrient accessibility, and size. Therefore, we hypothesize that primates with different diets will have distinct mandibular morphologies, particularly traits associated with the relative length and width of the whole primate mandible as they may impact the speed and force transmission during biting. To test these hypotheses, we utilized a database of 3D scans of primate mandibles from natural history museums. We quantified the mandibular shape and size by placing landmarks and semilandmarks on digitized 3D models of primate mandibles. We then quantified primate diets by ranking the relative importance of food items found in primate species based on a literature review. We then used phylogenetic comparative methods to test the effect of dietary ranks on primate mandibular size and shape. We predict that different dietary categories and ranking of food items will influence mandibular evolution. For instance, primates feeding on gums by gouging or scraping would require a higher mechanical advantage, resulting in a relatively shorter and more robust mandible. Our research could be helpful for future primate and mammal studies focusing on the selective pressures on the evolution of the mandible.

Sickle cell disease (SCD) is an autosomal recessive disorder caused by the inheritance of two abnormal hemoglobin genes and can present numerous health complications due to the sickling of red blood cells. It can lead to multiple comorbidities, and can have adverse effects on pregnancy. SCD is very common in Sub Saharan Africa in mainly developing countries, but it can pose risks to pregnant women even in developed countries. There has been conflicting information about whether or not the presence of SCD poses a significant risk to pregnancy outcomes. To analyze this, I systematically reviewed previously published evidence on the effects of SCD on maternal pregnancy outcomes in women from multiple hospitals in different countries from 1973 to 2021. I did a matched comparison of the outcomes between mothers with SCD (HbSS genotype) and mothers without SCD (HbAA genotype) using data from 11 studies. For binary variables, I used log risk ratio as the effect size metric, and for continuous variables, I used standardized mean difference. I hypothesized that the presence of SCD would pose a significant risk to pregnancy and lead to higher occurrences of adverse pregnancy outcomes. I found that there was a significantly higher risk of adverse pregnancy outcomes in mothers with SCD and their offspring, compared to mothers without SCD and their offspring. Perinatal mortality and stillbirths increased significantly with SCD, as well as intrauterine growth restriction, urinary tract infection, eclampsia, and occurrences of preterm delivery and c-section. I found that there was not a significantly higher risk of maternal death and premature rupture of membranes in mothers with SCD, although their risk was higher overall. Proper knowledge of the risks of pregnancy with SCD as well as proper management and treatment of the complications associated with it can improve maternal and fetal outcomes.

Carnivorans display a wide array of adaptations in their mandibular morphology, potentially influenced by various evolutionary factors like sexual selection and niche divergence. The Mustelidae family encompasses a diverse range of carnivorous mammals such as otters, badgers, and ferrets. Although mustelids are predominantly carnivorous, there is significant variability in dietary habits, with weasels exhibiting strictly carnivorous behaviors, badgers tending towards omnivory, and otters adopting piscivorous diets. This study explores the relationship between ecomorphological differences in mandibular shape and different dietary groups within the Mustelidae family. We will investigate variations in the breadth and length of the coronoid process, a mandibular element associated with biting performance. We hypothesize that carnivorous mustelids will exhibit shorter mandibles and larger coronoid processes compared to their omnivorous and insectivorous counterparts within the family. We predict these morphological adaptations aid carnivorous species by enhancing bite force and optimizing prey processing efficiency. We will use geometric morphometrics on mandible scans from various mustelid species with different dietary habits using 3D Slicer. Additionally, shape variation and allometry will be assessed using phylogenetic regression and phylogenetic ANOVAs to determine the effectiveness of diet as a predictor of mandibular feature variation within the Mustelidae family. This study will reveal new insights on how diet influences mandibular shape and size in mustelids, which can be applied to all carnivoran families. 

Phytophthora belongs to a group of plant pathogens found in the Kingdom Protista and is known to be highly destructive to plants. The water mold has been found all over the U.S. but just in Washington and Oregon, there are over 30 different species. This water mold is a significant problem in the Pacific Northwest because it infects Pacific Rhododendron leaves. Comprehending the factors that contribute most to the diversification of the Phytophthora species is essential in sourcing and minimizing its spread. We anticipate that the presence of Phytophthora species in residential areas, influenced by human activities, will procure a higher diversity rate of at least 3 or more species. This expectation is rooted in the understanding that the human influence on these environments contribute to an increase in landscaping that works for the proliferation of diverse Phytophthora species. Our location sampling of choice for the bacteria was Chambers Creek located in Pierce County, WA. Chambers Creek has mostly residentially areas surrounding. We gathered four leaves from a rhododendron plant on the Pierce College Fort Steilacoom. We placed the collected rhododendron leaves into bags which were then submerged in the water and left undisturbed for a duration of approximately nine days for observation and analysis. We plan to inoculate the necrotic tissue into V8 agar. We plan to isolate DNA of the Cox-1 subunit protein and sequence it to then use bioinformatics to identify species of Phytophthora. We will use class data to determine if residential areas have an effect on Phytophthora diversity.

Primates are known to have relatively larger brains for their body sizes (i.e., encephalization) when compared to other mammals. Previous studies have examined the relationship between food scarcity and endocast volumes in Old World Monkeys, specifically looking at the Cognitive Buffer Hypothesis –which states that greater rates of encephalization are correlated to living in more variable environments. In this study, we examine whether and how the cognitive requirements of social interactions (Social Brain Hypothesis, SBH) and investment from parents (Parental Investment Hypothesis, PIH) influence the evolution of encephalization in primates at the macroevolutionary scale. Social interactions stimulate the brain, causing it to produce more neural connections and as a result, greater encephalization. A higher degree of parental investment renders a safer space for infants to mature and their brain to develop, providing the capability of reaching larger sizes. To test these hypotheses, we first quantified encephalization as the ratio of endocranial volume to estimated body mass. Our data was collected using CT scans of primate crania from the Natural History Museum, London, United Kingdom. We quantified endocranial volume in 3D Slicer. We then used phylogenetic comparative methods to test how encephalization relates to social factors such as group size, social complexity, gestation length, and litter size across various primate species. Group size and social complexity serves to quantify the social interaction variable stipulated in the SBH, while gestation length and litter size correspond to determining the scale of parental investment per offspring. If the SBH and PIH are supported, then each of the four factors will exhibit a positive relationship with encephalization. Our findings will elucidate how social interactions and parental investment influence the evolution of brain sizes in primates.

The Cretaceous-Paleogene (K-Pg) mass extinction (66.052 Ma) is one of the most important events in mammalian evolution as it was the catalyst for mammals to diversify and fill the ecological holes left by the extinction of the non-avian dinosaurs. This extinction event impacted all groups of mammals, including the multituberculates, one of the longest-lived and most successful clades of Mesozoic and early Cenozoic mammals. The Constenius vertebrate fossil locality is in the lowermost Tullock Member of the Fort Union Formation in Garfield County, northeastern Montana, deposited within the first 28,000 years after the K-Pg mass extinction (66.052-66.028 Ma). Constenius is a very rich but understudied fossil locality that provides a snapshot of the immediate aftermath of the mass extinction. In this study, we used qualitative descriptions partnered with linear measurements to identify 44 lower fourth premolars (p4s) to the lowest possible multituberculate taxon. We recognize three genera of multituberculates from Constenius: Cimexomys, Mesodma, and Stygimys. The presence of these multituberculates supports the previous assignment of Constenius to the Pu1 interval zone of the Puercan North American Land Mammal Age (early Paleocene, 66.052-65.820 Ma). Further work on this project will include expanding the dataset to include other multituberculate dental specimens, such as upper premolars, and conducting a geometric morphometric analysis with the lower fourth premolar specimens to further confirm taxonomic identifications.

The Pacific Northwest (PNW) saw an unprecedented heatwave between June 25 to July 3 of 2021, with temperatures reaching up to 15℃ above the climatological mean. Previous research has examined the impact of this event on plants in Western Washington and Oregon through observational studies, and has focused on the economic implications for poor crop turnout. We used remote sensing data to take a top-down approach and examined how all plants throughout the PNW fared during and after this historical heatwave. Solar induced fluorescence (SIF) and Near-Infrared Reflectance of vegetation (NIRv) are two remotely sensed products that have been used to estimate plant health and gross primary productivity (GPP). SIF is more closely connected to plant processes like photosynthesis but has a short record (2018-2021) compared to VIIRS NIRv (2012-2021). We compared the responses of SIF to NIRv and found that both vegetation indices increased in trees and woody savannas, but decreased in grasslands and crops. However, SIF showed more intense and geographically larger increases in areas covered by trees. We then compared these vegetation indices to in-situ flux tower measurements of carbon fluxes, which did not always agree with SIF during the heatwave in woody areas. This study shows how remote sensing can further our understanding of how extreme events impact plant health, which is increasingly important as heatwaves become more intense and frequent in the future.

Body shape provides useful insight into the diversity and evolution of vertebrate body plans. Previous research revealed that body shape scales with body size in carnivoran mammals, but whether this trend occurs in other mammals remains unknown. Our goal is to examine the relationship between body shape and body size in Leporidae, which consists of rabbits and hares. Leporids exhibit a unique gradient of locomotion types between the smallest rabbits that are primarily saltatorial and the larger hares that are primarily cursorial. We quantified body shape using the head-body elongation ratio and body size using the geometric mean of all measured traits from osteological specimens held at the Burke Museum and other natural history museums. We tested the allometric relationship between body shape and size using a phylogenetic regression and also tested if these allometric relationships differed between saltatorial rabbits and cursorial hares using phylogenetic ANCOVAs. We predict that the differences in locomotory modes within the family could influence the correlation between body shape and allometry, possibly leading to different amounts of correlation in rabbits and hares. Specifically, we predict that larger body size corresponds with more elongate body shape. Elongate body shape would facilitate cursorial locomotion more common in larger leporids. More elongate and flexible bodies would allow the forelimbs to reach farther forward, enabling longer strides while running. This study informs allometric relationships of body shape and size of saltatorial and cursorial members of leporids and can lead to future research into the relationship between locomotion and body shape in other mammalian clades.

Sexual dimorphism describes the distinct characteristics between males and females of the same species. These different traits can be traced back to many external and internal factors. Here, we investigated how temperature and habitat influenced the evolution of sexual dimorphism in the mandible of mustelids. Mustelids are a great clade to study sexual dimorphism because of their mandibular diversity that is associated with their diverse diets, behavior, and ecological niches. We test two hypotheses: first, we examined if mustelids in high temperature environments exhibit higher degrees of dimorphism in their mandibles compared to those in lower temperature environments. Second, we test how the degree in dimorphism varies among mustelids inhabiting different habitats. To test our hypotheses, we quantified sexual dimorphism of mandibular size and shape using 3D geometric morphometrics. We then used phylogenetic ANOVAs to test how habitats influenced the degree of mandibular dimorphism and phylogenetic regressions to test how temperature influences the degree of mandibular dimorphism. We predict that mustelids in high temperature environments will exhibit a higher degree of sexual dimorphism than those in low temperature environments. Higher temperatures could correspond to a limited amount of resources which could lead to interspecies competition for food resources. As males and females use different strategies to survive, sexual dimorphism in mandibles size may occur. In our habitat analyses, we predict that mustelids in deserts will exhibit a higher degree of sexual dimorphism compared to those found in other habitats due to the same factors of resource availability and competition. Deserts tend to have scarce resources compared to forests and we believe that sexual dimorphism will reduce this competition. This research is impactful because as climate change is increasing temperatures all over the world, we should be aware of how that is directly affecting species.

Our undergraduate research project is on Phytophthora. Phytophthora translates to “plant destroyer”. The purpose of our research is to use watershed studies and bioinformatics to find patterns in the diversity of Phytophthora species found in local streams in Washington State. We assessed prior studies to estimate the probability of discovering Phytophthora in Chambers Creek, a local stream. Our hypothesis is, in comparison to freshwater, water sources closer to the ocean will have a higher diversity of Phytophthora species because they have more sources of contamination and higher saltwater concentrations. We chose the stream location based on previous watershed information we had. Additionally, we baited Chambers Creek with Rhododendron leaves in an attempt to grow Phytophthora. We then cultured the lesions on the leaves onto a V8 agar to grow Phytophthora. After that we isolated the DNA and “cleaned” it by using reagents to remove unused primers and deoxynucleoside triphosphates, then sent it off for sequencing. At this time, we used gel electrophoresis to determine the quality and quantity of our DNA. Lastly, we used bioinformatics to become familiar with sequence analysis using the National Center for Biotechnology Information Basic Local Alignment Search Tool. Three out of the four samples we obtained had no sequence matches but one sample was 100% positive for Phytophthora bilorbang. In conclusion our hypothesis was correct. Since our water source was subject to higher saltwater concentrations, it was more contaminated and had a higher diversity of Phytophthora species. Doing this research and discovering this information will help add to the knowledge of Phytophthora in Washington State. This can lead to where Phytophthora treatment is needed to protect our environment.

Quadrupedal locomotion in leporids (rabbits and hares) relies on a unique appendicular skeleton that facilitates a propulsive gait. Long hindlimbs compared to forelimbs supports the pushing followed by a tucking motion that is characteristic of a rabbit hop. Leporids inhabit a range of habitats leading to a variety of specified anatomical needs to support propulsive gaits on different terrains. In this study, we investigated how habitat type influences the morphological diversity of the appendicular skeleton in rabbits and hares. We quantified the appendicular skeleton of different species using caliper measurements from osteological specimens held at the Burke Museum and other natural history museums. We then used phylogenetic comparative methods to test three predictions on how different habitats influenced the evolution of these skeletal traits . First, leporids inhabiting deserts or wetlands will exhibit adaptations in the limb bones that facilitate greater muscle attachment because jumping on softer ground requires more propulsive force than jumping on solid ground. Second, leporids inhabiting open grassile environments will have longer legs to support quickly escaping predators in search of limited vegetation for hiding. Third, more closely related leporids will exhibit more similar hind limb morphologies due to having a more recent common ancestor. Overall, this study elucidates the evolution of appendicular skeleton of leporids and informs us of a possible method to predict how the morphology of limbs evolve based on habitat type and close ancestry in mammals.

Lizards in the family Tropiduridae have ventral epidermal gland organs that are involved in chemical signaling and whose secretory mechanism is entirely unknown. This is because, like other epidermal generation glands, 'alpha-glands' lack a pore through which their secretion can be exerted. Chemical signaling is a valuable aspect of tropidurid lizards' social and ecological interactions, and some have been observed territorially scraping their alpha-glands against the substrate. This process has been hypothesized to facilitate the release of chemical signals via abrasion. To investigate this abrasion hypothesis, we analyzed 74 skin samples from 27 tropidurid species, using light microscopy and scanning electron microscopy (SEM). The SEM revealed incredible surface variability in epidermal glands, providing morphological insight. We found that the exposed glandular mass of each gland scale rests atop the oberhautchen layer of the skin's subjacent generation, which indicates that the secretion of chemicals involves exposing a mostly solid glandular material on the outside of the scales. Histological sectioning of gland scales revealed morphological consistency, indicating that the same secretory mechanism is shared across the tropidurid phylogeny. Imaging of histology samples also revealed that the shedding process which exposes the glandular material may be facilitated by the clear layer, found directly above the glandular mass during development. Characterization of morphological patterns in the formatted SEM images and comparison with histological data should provide evidence for or against taxon-specific or ecology-specific alpha-gland structures, and further support the idea of chemical secretion requiring epidermal exposal of glandular material. Investigations of the morphology and functional mechanism of this unique organ provide insight into the behavior and evolution of tropidurid lizards and shed light on factors influencing the evolution of chemical signaling in terrestrial organisms. 

Skin is a densely innervated sensory organ that protects us every day from environmental trauma. As a barrier organ, skin is susceptible to frequent damage that must be promptly and properly healed to prevent infection and restore sensory function. Our lab uses adult zebrafish as a model to study skin injury and repair. Adult zebrafish skin is similar in composition to human skin and transparent, lending itself to high-resolution microscopy. Previous experiments in our lab revealed that dynamic, skin-resident immune cells known as Langerhans cells (LCs) rapidly engulf cellular and axonal debris after injury in the zebrafish skin. Calcium signaling regulates phagocytosis and cell motility in other immune cells, but the role of calcium signaling in LCs is unstudied. Through skin explant assays, various injury paradigms, and confocal fluorescence microscopy, I have established a model for monitoring calcium signaling in LCs. I found that LCs exhibit rapid, transient calcium flashes under homeostatic conditions. However, upon engulfment of large cellular debris generated by precise laser-ablation of skin cells, LCs exhibit an atypical sustained calcium signal lasting an hour on average. To test the requirement of calcium during engulfment by LCs, I treated skin with the drug Thapsigargin to perturb calcium flux. I confirmed that Thapsigargin increases intracellular calcium in LCs and keeps intracellular calcium concentrations elevated for hours after drug addition. During Thapsigargin treatment, I showed that LCs formed phagocytic cups around cellular debris but engulfed fewer laser-ablated corpses compared to controls. Thapsigargin-treated LCs also experienced normal migration to a wound site. My results indicate that calcium flux regulates LC engulfment of large debris, but not through migration. Identifying the molecular mechanisms underlying LC motility and debris removal is ultimately relevant to understanding skin repair and disease states in which the wound healing response is attenuated, such as in chronic wounds.

The variation in traits associated with fitness often results in selective pressures, thereby influencing the phenotypic traits observed in populations across diverse environments. The exploration of differences among individuals within and between populations has consistently been a key emphasis in evolutionary biology, seeking to understand how organisms adapt to a range of environments. In this research, I analyzed pelage color variation in the least chipmunk (Tamias minimus). Focusing on intraspecific variation—differences observed within a species—I conducted a quantitative analysis of pelage brightness across populations distributed throughout the range of the least chipmunk. This species is well-suited for this study because of its extensive geographic range, encompassing a variety of environments that span from semi-arid shrub steppe to high-elevation forests. I investigated the relationship between chipmunk habitat, utilizing various environmental variables, and pelage brightness. I predicted that precipitation and temperature would influence the brightness of the pelage, which often corresponds to the ability of an individual to camouflage or thermoregulate in their environment. To test this hypothesis, I photographed 334 museum specimens and measured the mean and standard deviation luminosity (two measurements of brightness) along four dorsal stripes and the head. I then extracted environmental variables using the GPS coordinates for each individual, these included 19 bioclimatic variables, elevation, latitude, net primary productivity and other variables related to geographic location. To examine the influence of environmental factors on the pelage color, I conducted generalized least squares analyses and principal component analyses in R. The initial results of my research indicate that the pelage color of a population is influenced the environment. Most notably, there is a significant correlation between pelage color and precipitation. In habitats with increased precipitation, such as forests, chipmunks tend to exhibit darker colors, whereas in regions with low precipitation, like deserts, individuals often display brighter pelage.

Science is rapidly evolving, yet its advances do not enter classrooms at the same rate. Systems Education Experiences (SEE) is a program in the Baliga Lab at the Institute for Systems Biology (ISB) that accelerates the transfer of scientific knowledge and practices to classrooms. One active area of Baliga Lab research is elucidating the level of resilience organisms have, when faced with complex environmental changes. My role is to design laboratory experiments that investigate this with the model organism Halobacterium salinarum (Halo) and to connect this to broader rules governing natural systems for use in high school classrooms. My first experiment probes the resiliency of Halo with the introduction of a combination of stressors (salt and hydrogen peroxide) and its recovery after population collapse. The second measures the long term phenotypic changes in the population. I wanted to see if after being exposed to a new environment if there was an advantage to having gas vesicles and if it is an irreversible trait that allows Halo to be resilient across a variety of environmental conditions. This relates to broadly applicable rules governing resilience across many systems. This project serves as a model for how all organisms respond to stress. Combinations of stressors in human lives can make us less resilient. However, strategies to quickly prepare, respond, and react can improve outcomes for individuals and the overall population. This project connects to a goal of K-12 science education which is to not just teach academic concepts but to equip students with knowledge that can be applied to all parts of life. Our knowledge on the mechanisms that control how organisms respond to stress is extremely limited. By understanding the biological stress response we can promote resilience in the earth's most vulnerable systems in the wake of climate change.

The diversification of many vertebrates was spurred by the use of novel food resources, and jaw morphology provides clues about the adaptations associated with dietary diversification. The external dimensions along the mandible reflect the strength to resist bite forces, which are associated with the diet's physical properties. Variations between different species may reflect adaptations of the jaw to specific diets. Using the mandibles of 60 Chiroptera species, we quantified the external dimensions at interdental gaps to generate mandibular strength profiles. Insectivores showed the greatest within-guild variation in jaw shape, while nectarivores had noticeably gracile symphyses. Further, insectivorous bats showed deep jaws at the canine, which may be associated with the use for prey capture. At the same time, frugivores have deep jaws at the posterior molars, possibly linked to adaptations for crushing seeds and pulp. When compared to measurements of bite force collected in the field, there was a remarkable and significant correlation between field-gathered and inferred bite force profiles. These results show that mandible strength profiles reflect dietary adaptations in bats, and demonstrate the reliability of this method in inferring the mandibular force profiles from preserved (non-living) specimens. These results indicate that this method can be used to further our understanding of the dietary behavior of species with few living specimens or that are extinct.

Countershading is defined as the difference in color between an animal’s dorsal and ventral surfaces, and can serve one of two purposes: to aid in background matching or to create a self-cast shadow, causing the animal to appear less three-dimensional to potential predators. Studies on primates show that species with more frequent horizontal postures and smaller body sizes exhibit higher levels of countershading, however, these links between locomotion behavior and coloration have not been explored in the vast majority of mammals. The Sciuridae family encompasses over 280 species, including squirrels, chipmunks, marmots, and beavers, which are characterized by a wide array of coat colors and use of different locomotion strata. Here, I analyze the correlation between Sciuridae countershading and locomotion strata using specimens from the Burke Museum. To test this hypothesis, I am collecting standardized photographs of specimens from the Burke Museum spanning 73 species, along with data on natural history from the literature to categorize species based on locomotion strata and nesting location. I expect to find that primarily terrestrial Sciuridae species will exhibit low levels of countershading, whereas arboreal species will exhibit high levels of countershading. I expect species with intermediate locomotion strata to rely on a combination of patterns and varying countershading levels, as their locomotion is more variable. This research sheds light on countershading trends in small mammals in relation to their locomotion strata, while also taking into account nesting behaviors and phylogenetic relationships. By using specimens from the Burke Museum, my data collection also aids in the digitization of specimens. In the future, I hope to use the results of this study to inform research on predator-prey relationships with respect to coloration and visual distractions, along with how these relationships are affected by the environment.

Nectar feeding is an impressive ecological niche for a species to fill as it provides a high energy resource for the species, however, obtaining nectar efficiently and without damaging the flower, which will refill the reward, often requires unique specialized mechanisms that can vary among species. Both Anna’s hummingbirds (Calypte anna), from the United States, and White-naped honeyeaters (Melithreptus lunatus), from Australia, are species of birds that are considered primarily nectivorous and have developed morphology that is apt for nectivorous feeding mechanisms independently of each other. One common morphological feature between both species is their long tongue which has a bristled tip that has important nuanced similarities and differences between them. This research looks to analyze the morphological differences between these independently evolved mechanisms through comparing and contrasting the internal and external morphological features present in the tongues of Calypte anna and Melithreptus lunatus. These morphological comparisons are made from two methods; 1) comparing and contrasting external features through 3D models of the specimens tongues from CT scans compiled by using the program 3D slicer and 2) through using paraffin wax histology with hematoxylin and eosin staining to analyze internal cross sectional differences of tongue morphology between species. Understanding comparative differences like location of structures and which structures are present between these species, belonging to unrelated clades, provides insights into how this nectarivorous niche and associated feeding methods can be addressed in different species of birds that are in turn the main pollinators of coevolved plant species. Understanding these comparisons can add to the larger picture of how nectivorous species feed and what features are important enough for allocating energy towards development, as well as understanding plant-pollinator coevolution among continents.

Historically, the field of healthcare and broadly STEM has been slow to match the diversity of our communities. This is in part due to attrition in college of key underrepresented groups (Flynn, 2016). One-time events that invite new students with every workshop, also known as touch-point events, allow for broader outreach and accessibility but it is unknown how impactful they can be on students’ self-efficacy. The aim of this study was to analyze how a touch-point event such as Anatomy for Change (AFC) workshops could impact a student’s learning abilities and academic confidence. We partnered with undergraduate student groups at the University of Washington (UW) from historically underrepresented backgrounds in medicine to host each workshop. Within our events, we invited UW School of Medicine students to guide undergraduates in completing various medical case studies. Our study measured the effects of our workshops with pre and post-event surveys given to undergraduate student attendees. These contained open-ended questions as well as scaled questions based on a 5-point Likert scale. For undergraduate students from a variety of racial, ethnic, and gender backgrounds we saw an increased confidence in their ability to learn anatomy, problem-solve in a medical context, and pursue a healthcare field. We also saw that the event increased their sense of belonging in the pre-health space. Our results are promising and indicate that a touch-point event can have a positive impact on a student’s educational journey. Furthermore, such programs can be done across a variety of disciplines and institutions throughout the academic spectrum to promote diversity and inclusivity in education.

Some genes are on all of the time in most cells, and carry out functions that are essential for life. Unsuprisingly, essential genes are difficult to study, as interfering with their function leads to death. One such critical component is the multi-protein Mediator complex, which is found at every eukaryotic promoter where it coordinates activation of gene expression. My project focuses on one of the core components of the Mediator complex, MEDIATOR21 (MED21). While MED21 is required for gene activation, the Nemhauser Lab recently found that it also plays a role in repression of gene expression through interaction with the corepressor protein TPL. I would like to be able to differentiate the role MED21 plays in activation versus repression using the plant model Arabadopsis. This work is made more complicated by the fact that most mutations in MED21 lead to lethal phenotypes. As an alternative I recently developed a new technology called a molecular switch that turns off MED21 in certain tissues or in reponse to addition of a chemical. The molecular switch relies on the expression of serine integrases that recognize, and recombine the DNA between, two specific DNA sequences. By expressing an integrase portein from a promoter that is only expressed in secondary roots, I can study MED21 loss of function in a small pool of stem cells while the rest of the plant is wild type and healthy. Plants that have undergone this cell-type-specfic switch exhibit several abnormal root phenotypes including agravitropism, increased root formation, and more root hairs. My next experiments include uisng a switch from wild-type MED21 to a mutant form incapable of binding to the corepressor TPL. This study will help us better understand the role MED21 plays in repression versus activation, and how state switching contributes to organogenesis.

Corepressors are proteins found in all eukaryotes that work with DNA-binding proteins to repress many genes. Keeping some genes off, yet ready to quickly turn of if needed, is essential for development and physiology. Our project aims to identify interacting proteins that work with TPL, a conserved plant corepressor, to form a transcriptional repressor complex. To uncover these proteins, we created a visually screenable plant line containing RUBY, a reporter that expresses throughout the plant, turning it dark pink to purple. We next created a synthetic repressor dCas9-TPL and guide RNA (gRNA) construct that binds to and represses the RUBY reporter. Roots of plants with both constructs appeared whitish-pink, indicating dCas9-TPL is transcriptionally repressing RUBY. We then mutagenized 40,000 individuals from this line using the chemical Ethyl methanesulfonante (EMS), which creates new point mutations in random locations throughout the genome. We identified 257 individuals from 129 mutagenized families with dark pink roots, which show that repression by dCas9-TPL has been impaired. Many of these adult plants had phenotypes in addition to appearing pink, including miniaturization, infertility, and irregular growth patterns, suggesting that the mutations we found are affecting other pathways that require TPL. Using Mendelian genetics, we are currently characterizing the mutation types (i.e. homozygosity, recessive, or dominant) as well as establishing complementation groups. We will then backcross the lines with the parent line to eliminate extraneous mutations and perform whole genome sequencing to determine the precise mutation causing loss of repression. This will also tell us if repression was due to mutating a TPL interactor, or mutating one of our reporter or repressor constructs. By finding genes required for TPL to act as a corepressor, we hope to understand conserved mechanisms of corepressor activity across diverse eukaryotes.

In response to changing conditions, organisms express genes to optimize the match between their phenotype and the environment. Understanding the mechanisms for how genes are turned on or off is therefore an important research area. One challenge in conducting this research is that many of the proteins involved in regulating gene expression are essential to life, and disrupting their function can lead to death. My research focuses on the essential gene SPT6, which encodes a protein that works with RNA polymerase during the elongation phase of transcription. Recently, the Nemhauser Lab has found that SPT6 also plays a role in transcriptional repression. My project aims to differentiate the role that SPT6 plays in transcriptional activation and repression by disrupting its expression in Arabidopsis. Given that SPT6 mutants do not survive, here I test the use of a new tool that allows me to remove my gene of interest in a particular tissue at a particular time. The tool is based on a molecular switch that relies on serine integrases which can recombine DNA between two specific sequences. So far, I have worked with my mentor to rescue SPT6 mutants with a target that expresses the wild-type version of SPT6. Once the integrase is expressed, the recombination turns off the SPT6 gene and turns on a fluorescent reporter. I express the integrase from a promoter that is active only in the first stages of making a new root, so I can observe the impact of loss of SPT6 function in a cell type unnecessary for plants to survive in lab conditions. This project promotes an understanding of the multiple roles of SPT6 during the transtition from repression to activation, and as SPT6 is highly conserved across eukaryotes, my work in plants may also contribute to understanding human diseases. 

Mobile genes are commonly found in bacteria, and they are capable of being transferred between unrelated bacterial cells via a process termed horizontal gene transfer (HGT). Mobile genes that undergo HGT can evolve in various “host” bacteria and thereby evolve in several different genomic backgrounds. In a recent publication, my lab constructed a mathematical model to assess the effects of HGT (i.e “host-switching”) on mobile gene evolution. I have built upon this work by probing additional factors that may influence mobile gene evolution. In phase one of my project, I compared the original evolutionary model used in the publication to a newly expanded, more ecologically realistic model in which growth rates of the bacteria depend on resource availability. To compare the models, I ran simulations with both models on a set of bacterial-host pairs and compared the resulting evolutionary outcomes from both models. I found that the categorical effect of HGT occurring (i.e. HGT confers a higher, lower, or neutral change in host fitness) was the same across both models, indicating that ecological factors are less predictive of mobile gene evolutionary outcomes. For the second phase of my experiment, I assessed the effect of variable HGT rate on mobile gene evolutionary outcomes. I ran simulations using a set of bacterial host-pairs while varying the HGT rate along a biologically relevant range, and found a positive correlation between HGT rate and the magnitude of positive fitness effects conferred by a mobile gene that has undergone HGT. This indicates that HGT rates play an important role in governing the evolutionary outcomes of mobile genes. Using evolutionary simulations has allowed us to gain insight into the predictive factors governing mobile gene evolution and thereby mobile gene-containing bacterial evolution. This is especially important, as many genes conferring antibiotic resistance are mobile.

In mammals, circadian rhythms are regulated by a hierarchy of oscillators governed by a central circadian pacemaker in the suprachiasmatic nucleus (SCN), which is principally entrained by the light-dark (LD) cycle. Recent experiments in our lab have revealed that cyclic 24-h fearful stimuli can act as a potent nonphotic zeitgeber, entraining circadian rhythms of behavior in mice and rats. This discovery utilized a naturalistic rodent cage with a safe nesting area separated from a foraging area where feeding and drinking occur. While foraging behaviors naturally occur at night, when the foraging area is rendered dangerous by nocturnal aversive stimuli (footshocks), animals entrain behaviors to the shock schedule by shifting activity to the daytime. Under conditions of fear-entrainment, SCN clock gene expression remains loyal to the LD cycle and the SCN is necessary but not sufficient for sustaining diurnal activity. Therefore, we propose the existence of extra-SCN fear-entrained oscillators capable of overriding SCN output and influencing behavioral timing. Here, we subjected 16 mice to either diurnal shocks (DS; control) or nocturnal shocks (NS) under a 12:12 LD cycle. Following confirmation of fear-entrainment, animals were released into constant conditions and sacrificed between 24-36h after the last presentation of footshocks, either CT 1 or CT13. Brains were dissected, sliced, prepared for immunohistochemistry processing, and c-Fos protein quantification is currently underway in the SCN, basolateral amygdala, paraventricular nucleus of the thalamus, and dentate gyrus. We hypothesize that c-Fos expression within the SCN will align with the LD cycle, while centers involved in fear processing and memory will exhibit altered levels of c-Fos expression in response to time-specific fear. Results from this study may be useful for identifying putative brain regions containing fear-entrainable oscillator(s).

Land plants have evolved the ability to uptake silicon from the soil and deposit it as silica-based structures called phytoliths in their tissues. Phytoliths are hypothesized to play a variety of roles in plants including contributing to structural support, defense against abiotic stressors such as drought, and herbivore deterrence. Grasses (Family Poaceae) in particular are known for their high silica concentrations of up to 40% of dry mass. We are investigating whether or not high silica concentrations are more common in grassland species and are associated with C4 photosynthesis. This directly tests the “C4-grazer hypothesis,” which states that, compared to other species, C4 grasses (i.e., those with adaptations allowing more efficient photosynthesis under hot and dry conditions relative to the ancestral C3 photosynthesis) have evolved increased silica accumulation as a response to ungulate herbivory in grassland environments. Using material from herbariums across the world, we have prepared 482 grass leaf samples for analysis. Our samples derive from approximately 200 species from all 12 subfamilies of Poaceae. These samples are analyzed using a portable X-ray fluorescence spectrometer to measure silicon concentration, which serves as a proxy for accumulated silica. To do so, we have established a custom calibration and protocol for measurements. Preliminary results show that high silica concentrations have evolved in a range of grasses, including species occupying both open grasslands and shady forest habitats, and both C3 and C4. This suggests that the mechanisms and influences on silica accumulation may depend not only on photosynthetic pathway and herbivory pressure, but may also depend on other evolutionary and environmental factors. Overall, this research will improve our understanding of how grasses adapt to stressors that will worsen under climate change, and how grasses might contribute to global carbon-silicon cycling.

Phytoliths are silica bodies inside and around plant cell which hold crucial evolutionary insights into the grass family, Poaceae. This study focuses on phytolith morphology within the PACMAD group, consisting of the Poaceae subfamilies Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae. By examining over 1,500 phytoliths across 114 extant species within these subfamilies, we aim to identify patterns in the distribution and abundance of specific phytolith morphologies, so-called morphotypes. This analysis could help deepen our understanding of both phytolith morphotypes as potential indicators of evolutionary relationships within grasses. We can also use these patterns to determine the taxonomic affinities of fossil phytoliths, which allows us to trace the evolutionary history of grasses in the fossil record. Additionally, we focus on the evolution of C4 photosynthesis, a key adaptation in grasses to dry and hot climates; specifically, how we can use phytolith morphology as an indicator for this evolutionary trait in the fossil record. Through comparative analyses within and beyond the PACMAD clade, we aim to compare phytoliths from modern C3 and C4 grasses to gain a better understanding of the differences between phytoliths from grasses with the two photosynthetic pathways and apply it to fossil phytoliths to better understand when C4 grasses evolved and spread. Furthermore, we emphasize the significance of this research in the context of climate change. By linking phytolith morphotypes to the climatic preferences of extant grasses and applying this information to the fossil record, we can trace past climatic shifts and patterns, learning how grasses adapted to environmental changes. Our preliminary results so far show that there are distinct patterns in phytolith morphology across PACMADs, although, at the genus and species level, there is an overlap in morphological traits that we hope to address with increased data.

Including undergraduate peer facilitators (UPFs) in lectures is often done to support students in large and often challenging introductory science courses. Our team increased UPF involvement by creating BIOL113, an undergraduate-led companion course to BIOL180, the largest biology course at the University of Washington. This study is a part of a larger project that assessed the overall experience of both UPFs and students, and this particular work focuses on the latter. We examined how BIOL113 enhanced students' learning and academic success in Introductory Biology. By incorporting quantitative and qualitative data, we compared the performance of students who received UPF support in this companion class with those who did not. Quantitative data included grades, exam scores, and course completion rates, while qualitative data encompassed students' perceptions of peer facilitation though blast surveys. We found that undergraduate-led programs play a unique role in improving students' learning and including UPFs promoted peer-to-peer interaction and student engagement. Additionally, UPFs serve as relatable role models, providing mentorship and practical guidance. Moreover, programs like BIOL113 have a rare opportunity to disproportionately support students from minoritized groups. Understanding the impact of BIOL113 on students' success can inform instructional strategies, with potential expansion of such programs across the University. 

Many ecologically and economically important coastal invertebrates that live on the seafloor (eg. mussels, oysters, crabs, sea stars) have distinct larval stages that live up in the water column – collectively categorized as meroplankton. Meroplankton may face different environmental conditions than their adult forms that live on the seafloor. Moreover, planktonic larval stages are often more vulnerable to changes in oceanographic conditions than their adult counterparts. A variety of climate-related abiotic stressors (low pH due to ocean acidification, high temperature, low salinity) have been shown to negatively affect a variety of important life processes such as swimming ability, metabolism, growth, and survival in laboratory settings. However, owing to the logistical constraints of measuring oceanographic conditions and plankton abundance in the same time and place, it remains largely unknown which oceanographic variables affect the abundances of different meroplankton taxa in their natural habitat. To identify the oceanographic variables that primarily drive patterns of meroplankton abundance, we collected a two-year time series of oceanographic data (temperature, salinity, pH, dissolved oxygen, turbidity, current velocity) using the Friday Harbor Labs Ocean Observatory (FHLOO), the Salish Sea’s only multi-instrument remote sensing network. We simultaneously collected a two-year time series of plankton abundance for 20 different taxa of meroplankton by performing regular plankton tows at the FHLOO. Here, we focus on the oceanographic drivers of barnacle larvae (nauplii) abundance, as they metamorphose into important fouling organisms that slow boats by attaching themselves to the hulls, but also form ecologically important habitat for other organisms by attaching to rocky shores. We show several transient high temperature, low salinity events caused by freshwater pulses due to seasonal snowmelt into the Fraser River, which outputs into the Salish Sea north of the FHLOO in British Columbia. These hot, low salinity events coincide with spikes in the relative abundance of barnacle nauplii, suggesting that temperature and salinity drive barnacle nauplius abundance in the Salish Sea. Overall, we show the importance of collecting collocated oceanographic and plankton abundance datasets to uncover the climate-change related stressors that drive meroplankton abundance in ecologically important coastal habitats.

As the climate changes, we are beginning to see the impacts on a global scale. In order to understand how our landscapes will change with future warming, we can look back to see how landscapes were impacted by past warm, variable climates. This project looks to understand how climate variability in the Middle Miocene is expressed in terrestrial sedimentary records. Using X-ray fluorescence (XRF) analysis, we created a high-resolution elemental geochemical profile of sediment samples from Clarkia, ID (~16 Ma). From XRF, elemental concentrations for a host of elements, including Ca, Fe, K, Mn, Sr, Ti, Zn, and Zr, were calculated. Some elements, notably Ca, showed long-term trends but also sections of shorter-term cyclic variability. It is possible that this variability reflects changes in basin weathering rates of Ca-bearing minerals as a function of climate change occurring on timescales of tens to hundreds of thousands of years. Alternatively, Ca concentrations may reflect changes to precipitation of Ca-bearing minerals within the ancient lake, responding to algal productivity. These hypotheses are tested using X-ray diffraction (XRD) to identify minerals and their crystalline structures as well as characterizing the elemental trends from an additional site, Clarkia’s P-40. Understanding the depositional history of the Clarkia lakebeds aids our understanding in how climate impacts Miocene landscapes.

Introductory biology classes are often a stepping stone for students in various STEM majors, as prerequisites or major requirements. For this reason, it is vital that these courses properly prepare students for life beyond their classes, through the ability to apply the knowledge they are gaining to the real world. Because textbooks are often used as preparatory assignments or as the content on which a course is grounded, we decided to focus on this type of circular tool, in order to evaluate the level of humanization in introductory biology courses. We set out to find out the degree to which six popular and prominent introductory biology textbooks humanize science, by positioning the content in a social context. We did this by developing our definition of humanization, and based on this, a continuum of humanization. We then developed a rubric for coding the extent of humanization, with the lowest being scarce humanization and highest being content that centers justice. We also coded topics of biology, from ethics to the environment. The team went through page-by-page and line-by-line to apply the rubric to all six textbooks, including the text as well as questions. In terms of the questions, we found that out of 9262, only 236 questions were humanizing. For the text, out of 9670 pages, there were 1352 humanizing passages. Overall, we found the inclusion of humanizing content to be rare across the six textbooks analyzed, and humanization by inclusion of justice to be particularly rare. We end by giving suggestions to educators, a main one being to pose justice-centered problems to students - a “problem-posing” model of science education.

Plant root signaling is a complex process. An important growth hormone that is hypothesized to regulate this complexity is Auxin; this hormone is known to oscillate in a region of the root that initiates lateral root development. Auxin oscillations are established by auxin exporters called PIN proteins. However, the regulatory mechanism that determines PIN expression and distribution is unknown. In this project, we built an agent-based model in order to characterize expected auxin dynamics and investigate hypothesized PIN regulatory signaling cascades. In the model, each cell is an individual agent that follows a given rule set. Cells independently calculate their growth and the amount their circulatory components change as the root develops. I analyzed previous models and extracted parameters to determine the necessary spatial and circulatory conditions that initiate our model. I constructed the circulation module to calculate the concentration of circulating components and updates information stored in circulation data structures to track how the values have changed after each round simulation. I also implemented the input and output modules for initialization and results export respectively. The model is implemented in Python and was built following test-driven development to ensure all class functions and modules are tested using pre-defined conditions. Preliminary simulation results revealed an oscillatory change in auxin concentration. This agent-based model provides a means to explore the auxin circulation dynamics and interrogate the viability of hypothesized mechanisms that regulate the lateral root development by applying different rule sets.

The latest Eocene Florissant Formation (deposited ~34 million years ago) contains a rich flora and fauna that has received much study by paleobotanists since the 19th century. However, several questions about the ecology and evolution of biota are outstanding and much material remains to be studied. Using observations from a high-definition compound microscope, dichotomous keys, and published literature, I seek to directly analyze and identify an unidentified fossil of a latest Eocene angiosperm, gain a comprehensive view of their surrounding habitat, and contribute to a better understanding of plant-pollinator relationships in the Florissant region. The fossilized angiosperm flower I am studying was collected by Judge Junius Henderson from lacustrine deposits of the Florissant Formation (in modern day Teller County, Colorado). It is a compression fossil with perfectly preserved petals and anthers, providing a rare opportunity for detailed analysis of its anatomy. The rock additionally contains the abdominal region of an insect, which I will attempt to place taxonomically to draw inferences about its ecological role in the Florissant ecosystem. My preliminary studies suggest that the fossil flower belongs to the extinct species Phenanthera petalifera (family unknown)- originally described by Theodore Cockerell in the early 20th century- due to matching dimensions, spatulate appendages, and two-lobed stamens exerted beyond the calyx. The insect is harder to place due to incomplete preservation, but anatomy suggests Aeschneta larvata, a bee fly (family bombyliidae), or a similar insect in order Diptera; I will explore the prominence of these possibilities. Documenting the diversity of plants and potential pollinators in ancient ecosystems existing during past warm climates is crucial for understanding how plant-pollinator relationships might change as anthropogenic warming causes shifts and losses in plant-pollinator niches.