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.

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.

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 the face of a global crisis, the poaching of pangolins (Manis spp) has emerged as a dire threat, with Africa at the epicenter of this illicit trade; these enigmatic creatures, sought after for their scales and meat, face exploitation driven by illegal activities that endanger their populations and disrupt the balance of the African ecosystems. Studying the lineage distributions of pangolins could prove crucial for their protection as it provides valuable insights into their evolutionary history, genetic diversity, and ecological adaptations. This information may be essential for formulating effective conservation strategies, understanding their vulnerabilities to diseases, and identifying key habitats for preservation. We aim to address these gaps, by exploring whether pangolin (Manis temminckii) lineages from Mozambique can be genetically distinguished from those from Southern Africa and by investigating the region of origin for two scale samples seized by law enforcement in Singapore in 2019. We conducted genetic and phylogenetic species delineation by sequencing two mitochondrial genes, Cytochrome b oxidase (cytb) and the Control Region (D-loop), from pangolin skin tissues from 10 villages in 3 provinces in Mozambique to complement existing data from Southern Africa. We will then use RAxML (Randomized Axelerated Maximum Likelihood) for phylogenetic analysis and to estimate phylogenetic trees based on our collected data. This multi-locus approach ensures robust species delineation and provides essential support for species recognition. Our focus on mitochondrial DNA (mtDNA) in Mozambique aims to make a reference map of the distributions of genotypes throughout Southern Africa, and our research contributes valuable genetic insights, offering a nuanced perspective on the spatial dynamics of pangolin populations. Ultimately, these findings play a pivotal role in addressing the complex issue of illegal wildlife poaching in Africa, providing essential resources for conservation efforts and informed management strategies as well as contributing to the field of forensic science for counter wildlife trafficking.

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.