Despite the brain being a 3D structure with a complex topography and spatial relationships, neuroscientists currently rely on 2D visualizations. These less informative visualizations obscure the distances between 3D regions, and hinder scientists’ ability to perceive functional correlations and anatomical connections. To provide a more decipherable method of exploring the structure and function of the brain, we built neuroscience tools specifically aimed toward exploratory 3D data visualization. I worked on the development of a Universal Renderer for Neuroscience (Urchin) that lets users plot their data in its original 3D anatomical context. Urchin can perform a variety of different functions such as displaying certain features (e.g. neurons, brain regions, or contextual objects such as probes), or interactively exploring the data within context of brain location via mouse and keyboard navigation. This not only paves the way for new methods of data analysis but also creates a deeper understanding of the structure and patterns found within the data. I worked on building Urchin within the Unity platform, implementing features to enhance data exploration and analysis via scripting in C. Some examples of functionality that I built include implementing 3D mesh rendering for brain regions, primitive models, and changing materials. I also established a proxy server that allows for secure communication between client side browser applications and python notebooks. Along with this, I developed a more intuitive and efficient python API that allows people with minimal coding experience to run the renderer visualizations with ease. Urchin enhances neuroscience research and education by providing a more interactive and immersive experience, allowing students and the public to directly engage with diverse data sets and investigate different aspects and features of the brain.

Electrophysiology experiments targeting deep brain structures require extensive training and expertise. However, even experienced researchers face challenges in placing electrodes precisely within a target location, particularly when using multiple electrodes simultaneously. On average, there is a 400-um (standard deviation) of human error when targeting Bregma and navigating to insertion coordinates. Slow setup time and human error can lead to unnecessary stress in experimental animals and prevent scientists from focusing on data collection. Our laboratory developed an experiment planning tool called Pinpoint to address these challenges. However, even with interactive tools, a typical two-probe experiment setup can take over an hour, increasing as more probes are added in complex experiments. To reduce time inefficiencies and lower the risk of human error, we developed an electrode manipulator automation platform for Pinpoint. Our platform consists of a server application called Ephys Link, which unifies communication between Pinpoint and various electrode manipulator platforms. With Ephys Link, scientists can view the electrodes they are using in their experiment live inside the virtual brain and pre-plan insertions for multiple probes. They can then simply press a button to have their probes automatically move to their chosen targets. We expect our automation pipeline to make multi-probe electrophysiology an easier and more accessible task for researchers, enabling them to focus on gathering high-quality data rather than managing the geometry of their experiments. To measure the impact of our automation platform, we plan to use positional logging, timed recordings, and researcher feedback to evaluate the efficacy of the pipeline in speeding up electrophysiology experiments. We expect to see increased targeting precision, reduced time setup time, and overall productivity boosts for researchers. By reducing electrophysiology's difficulty and time-consuming nature, our automation pipeline helps researchers alleviate cumbersome experiment setups and prevent unnecessary stress on experimental animals.

Clearance of wound infections can be hindered by a bacterial biofilm; a complex extracellular matrix (EM) secreted by adherent bacteria that allows them to evade the host immune system and obviate antibiotics. A novel, synthetic peptide—known as an anti-α-sheet inhibitor—can disrupt biofilm stability by inhibiting the formation of amyloid fibrils, which contribute to the biofilm EM. This project aims to design and characterize alginate porous scaffolds that elute these synthetic peptides, for use as anti-biofilm wound dressings. The physical properties and peptide release kinetics of the scaffolds will be optimized for clinical applications, supported by in vitro efficacy studies with live bacteria. This project draws upon past work from the Bryers Research Group on engineering infection immunity and tissue scaffolds, in which biofilms are prevalent. Results of this project will provide an alternative approach to biofilm prevention, thus reducing the burden of biofilm-related infection complications.

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

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