Methanotrophs are prokaryotes that naturally consume the potent greenhouse gas methane for energy. Through metabolic engineering at an industrial scale, these microorganisms hold potential to mitigate the contribution of methane emissions to global warming. In particular, Methylotuvimicrobium buryatense can sustain robust growth both in nature and experimental settings; it is a promising engineering candidate. To develop a robust metabolic engineering platform using M. buryatense, biologists require a deeper understanding of the genetic mechanisms by which it functions. Here, I present an open-source software tool designed to interactively explore the transcriptome of M. buryatense. By integrating bulk RNA-seq datasets collected from experiments over the past decade and applying an array of unsupervised machine learning clustering algorithms, we cluster genes by their expression profiles in differing growth conditions. These gene clusters are annotated with gene ontology (GO) terms using statistical enrichment analysis to assist in functional interpretation of the clusters and the genes that comprise them. To enhance domain-expert researchers’ ability to explore and drill-down into specific queries, I unify these cluster-specific analyses in a web-hosted tool using interactive data visualization techniques centered on a ReactJS frontend and Azure Cloud backend. With both exploratory and query-focused use cases, this software tool can support M. buryatense biologist workflows for predicting functions of hypothetical proteins, showcase new or confirming putative regulatory processes, and generate new experimental hypotheses from the presented transcriptomic trends.

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

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