Transcriptional Characterization of Neuron Differentiation in Hydra vulgaris

The number of research organisms used to study nervous system development and function has substantially increased in recent years due to advances in technology, such as single cell RNA sequencing. This has enabled researchers to characterize the neuronal transcriptional diversity in a wide range of organisms. However, very few comprehensive transcriptional descriptions of adult nervous systems currently exist. Here, we provide a transcriptional analysis of the entire Hydra vulgaris adult nervous system. Although Hydra shares many of the same experimental advantages as well-established invertebrate models, such as small size, optical transparency, and ability to test gene function, it is also able to regenerate its entire nervous system from adult stem cells. This makes Hydra an excellent model for studying nervous system development and regeneration at the whole-organism level. Although Hydra has been studied for over 300 years, the Hydra nervous system has never been fully defined on a molecular level. Prior to this work, the diversity, transcriptional profiles, and developmental lineages of Hydra neurons were unknown. In this dissertation, I present an extensive set of resources characterizing the homeostatic Hydra nervous system. Chapter 1 describes the generation of a whole-animal single-cell RNA-seq atlas for Hydra vulgaris. This includes the first molecular map of the Hydra nervous system, identification of 11 transcriptionally distinct neuronal subtypes, and first validated molecular markers for endodermal neuronal subtypes. Chapter 2 presents the most comprehensive transcriptional characterization of the adult Hydra nervous system to date. This includes both differentiation and transdifferentiation pathways and the identification of the chromatin states of Hydra’s 11 neuronal subtypes. The appendix includes additional manuscripts that were collaborative efforts stemming from my thesis work

Using GIS to Identify and Predict Environmental Racism in Indiana

The environmental racism movement calls for the recognition that minority communities and individuals are burdened with a disproportionate share of environmental risk. In this project, we examine the relationship between race, socioeconomics, location, environmental and health hazards in Indiana using Geographic Information Systems. Specifically, we investigated the location of hazardous waste sites, industrial emissions, groundwater contamination, and negatively associated health effects including birth defects, endocrine disrupters, and cancer. Using data obtained from publicly available government and census websites, we investigated the correlation between geographic equity and hazardous environmental exposure in Indiana. Our results suggested that minority groups (black, asian, hispanic) lived in areas of higher environmental and hazardous impact. Furthermore, areas with a higher environmental and hazard index were more likely to be in areas of high child poverty. Our results suggest correlation between a hazardous index and negative health effects, mainly birth defects. However, we did not find significance relating industrial emissions and health effects, but given a longer study and access to more specific data we believe that we might find a correlation between emissions and negative health effects

Multiple neuronal networks coordinate Hydra mechanosensory behavior

Hydra vulgaris is an emerging model organism for neuroscience due to its small size, transparency, genetic tractability, and regenerative nervous system; however, fundamental properties of its sensorimotor behaviors remain unknown. Here, we use microfluidic devices combined with fluorescent calcium imaging and surgical resectioning to study how the diffuse nervous system coordinates Hydra's mechanosensory response. Mechanical stimuli cause animals to contract, and we find this response relies on at least two distinct networks of neurons in the oral and aboral regions of the animal. Different activity patterns arise in these networks depending on whether the animal is contracting spontaneously or contracting in response to mechanical stimulation. Together, these findings improve our understanding of how Hydra's diffuse nervous system coordinates sensorimotor behaviors. These insights help reveal how sensory information is processed in an animal with a diffuse, radially symmetric neural architecture unlike the dense, bilaterally symmetric nervous systems found in most model organisms

Data from: Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

The adult Hydra polyp continually renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We sequenced 24,985 Hydra single-cell transcriptomes and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified gene modules and putative regulators expressed along these trajectories, thus creating a comprehensive molecular map of all developmental lineages in the adult animal. In addition, we built a gene expression map of the Hydra nervous system. Our work constitutes a resource for addressing questions regarding the evolution of metazoan developmental processes and nervous system function

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

The adult Hydra polyp continually renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We sequenced 24,985 Hydra single-cell transcriptomes and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified gene modules and putative regulators expressed along these trajectories, thus creating a comprehensive molecular map of all developmental lineages in the adult animal. In addition, we built a gene expression map of the Hydra nervous system. Our work constitutes a resource for addressing questions regarding the evolution of metazoan developmental processes and nervous system function

Dissection of the in vitro developmental program of Hammondia hammondi reveals a link between stress sensitivity and life cycle flexibility in Toxoplasma gondii

Most eukaryotic parasites are obligately heteroxenous, requiring sequential infection of different host species in order to survive. Toxoplasma gondii is a rare exception to this rule, having a uniquely facultative heteroxenous life cycle. To understand the origins of this phenomenon, we compared development and stress responses in T. gondii to those of its its obligately heteroxenous relative, Hammondia hammondi and have identified multiple H. hammondi growth states that are distinct from those in T. gondii. Of these, the most dramatic difference was that H. hammondi was refractory to stressors that robustly induce cyst formation in T. gondii, and this was reflected most dramatically in its unchanging transcriptome after stress exposure. We also found that H. hammondi could be propagated in vitro for up to 8 days post-excystation, and we exploited this to generate the first ever transgenic H. hammondi line. Overall our data show that H. hammondi zoites grow as stringently regulated, unique life stages that are distinct from T. gondii tachyzoites, and implicate stress sensitivity as a potential developmental innovation that increased the flexibility of the T. gondii life cycle

A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state.

The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type-specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago