Hantavirus is a dangerous zoonotic viral pathogen that is found across Asia, Europe, and the Americas. This virus causes a range of symptoms from flu-like malaise to heart failure and death. It is normally transmitted to humans via the aerosolized feces or urine of infected rodents. Currently, there are no known treatments for the disease, and it continues to threaten human health in endemic areas. In order to identify possible future therapeutic targets, we ran a meta-analysis of existing transcriptomic data collected from infected human tissue. Several genes and cellular pathways were identified, in addition to several potential therapeutics that warrant additional testing as potential future therapeutics for hantavirus infection. Such genes include, but are not limited to SLC27A3, NOG, AMIGO1, NUSAP1, and CDC25C which have not been previously associated with hantavirus infection. In addition, we identified that RIG-I and MDA5-associated anti-viral response genes are downregulated, while downstream elements of these pathways are upregulated, indicative of immune activation via alternate pathways. Finally, among the potential therapeutics we identified are dinaciclib, alvodicib, and ruxolitinib, which limit cellular replication, as well as ruxolitinib, baricitinib, and tofacitinib, which target other human intracellular pathways that may aid in successful viral infection. Crohn's disease is an autoimmune disorder that affects the digestive system of more than six million people worldwide, with most cases found in North America and Europe. Although the disease can occur throughout the entire digestive tract, the classical sign of disease progression is inflammation of the intestine. There are a number of factors that have been associated with the onset and progression of the disease including diet, antibiotics, stress, and bacterial infections, but no putative cause has been found. As diet and the gut biome play a significant role in disease progression, we aimed to find commonalities in the gut microbiomes of Crohn's patients, even when located in different geographical areas.

Understanding how biodiversity evolves is a major goal in evolutionary developmental biology because changes in developmental processes are tightly linked with evolutionary diversification. Heterochrony--alteration to the rate or timing of development--can significantly alter the appearance of descendant species. Heterochronic shifts in gene expression and associated morphological change may explain the morphological divergence between the threatened June sucker (Chasmistes liorus) and the sympatric Utah sucker (Catostomus ardens) in Utah Lake, UT, USA. June sucker are endemic to Utah Lake and have subterminal mouths adapted for pelagic feeding, while Utah sucker (Catostomus ardens) have ventral mouths adapted for benthic feeding. As larvae, both June sucker and Utah sucker have terminal mouths. However, within the first 14 weeks of development, the Utah sucker's mouth shifts to a ventral position, whereas the June sucker's mouth only shifts to a subterminal position. Using geometric morphometrics and RNA-seq time courses, we document a difference in the timing of shape development and a corresponding change in the timing of gene expression between June sucker and two Utah sucker lineages. Our results suggest that the distinctive mouth morphology in June sucker may be the result of paedomorphosis in which adult June sucker exhibit an intermediate mouth morphology between that of the larval (terminal) and ancestral (ventral) states. On a broader scale, additional Chasmistes / Catostomus pairs exist in the Intermountain West that are also morphologically divergent, but genetically similar. These pairs could be the result of repeated convergent evolution driven by differential expression of genes in response to environmental cues.

No description available.

The research of my thesis focused on the use of transcriptomic open discovery approaches to interrogate the molecular basis of two distinct yet related neurological disorders that are both associated with cognitive decline, Temporal Lobe Epilepsy and Alzheimer’s Disease. Interestingly, a potential role for compromised synaptogenesis early in disease was common to both, as was the direct role that neurons may play in brain inflammatory processes involving glia. Temporal lobe epilepsy (TLE) is a progressive disorder mediated by pathological changes in molecular cascades and hippocampal neural circuit remodeling that results in spontaneous seizures and cognitive dysfunction. Targeting these cascades may provide disease-modifying treatments for TLE patients. Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) inhibitors have emerged as potential disease-modifying therapies; however, a more detailed understanding of the contribution of JAK/STAT signaling to epileptogenesis is required to increase the potential therapeutic efficacy and reduce adverse effects associated with un-targeted JAK/STAT inhibition. With our collaborators, my lab developed a mouse line in which tamoxifen treatment conditionally abolishes STAT3 signaling from forebrain excitatory neurons (nSTAT3KO). Seizure frequency (continuous in vivo electroencephalography) and memory (contextual fear conditioning and motor learning) were analyzed in wildtype (Wt) and nSTAT3KO mice after intrahippocampal kainate (IHKA) injection as a model of TLE. Selective STAT3 KO in excitatory neurons reduced seizure progression and hippocampal memory deficits without reducing the extent of cell death or mossy fiber sprouting induced by IHKA injection. In my thesis, RNA was extracted from harvested hippocampi 24 h after IHKA and libraries were prepared for bulk RNA-sequencing (70–80 million reads/sample) using the NextSeq 500 Illumina system. 3190 genes were differentially expressed in Wt mice injected with KA vs saline (fold change |1.5|, FDR=<0.05). Ingenuity Pathway Analysis (IPA) revealed significant enrichment in 2 overarching sets of pathways: 1) those related to synaptic signaling and 2) those related to inflammation. As expected, many of the IHKA-induced genes were previously associated with epilepsy or seizure disorders (260 for Seizure Disorder, 267 for Epilepsy or Neurodevelopmental Disorder), and Seizure Disorder had the highest activation score in Neurological Disease based on gene expression patterns. Interestingly, a closer analysis of the IHKA-induced gene set revealed an enrichment of STAT3-associated genes (216), most of which were upregulated by IHKA. Compared to the 3190 Differentially Expressed Genes (DEGs) between IHKA and saline-injected Wt mice 24 hours after SE, more than half of these DEGs (1609) were rescued when comparing IHKA-injected nSTAT3KO mice and saline-injected Wt mice, indicating a significant rescue of gene expression when nSTAT3 is absent in excitatory neurons. While nSTAT3 KO influences the expression of genes in many different pathways, including the reversal of genes whose expression was inhibited in pathways of learning and memory by IHKA, the greatest surprise came from the predicted regulatory control over microglial function. nSTAT3KO mice displayed the greatest number of rescued DEGs compared to IHKA-injected WT mice in pathways that regulate inflammation and ion transport, and while inflammation was an expected response to IHKA, we were surprised to find evidence for its rescue in nSTAT3 KO mice. We also interrogated the expression of the Alzheimer’s disease genome as modeled using a rat model (TgF344-AD ) of familial AD that allows for behavioral and molecular characterization of AD, and expresses an endogenous pathogenic form of tau in addition to Abeta oligomers and plaques. AD is a neuropsychiatric disorder characterized initially by short term memory loss and disorientation, followed by declining cognitive functioning, and eventually, death. Widespread failure of 99% of AD drugs that make it to clinical trials has led to renewed interest in early signatures of disease in hopes of altering disease trajectory through early intervention. Key to such efforts is capturing a molecular window into AD at its earliest stages. The TgF344-AD rat shows overt pathology (including Aβ plaques, frank neuronal loss, and endogenous tau pathology) at 16 and 26 mo, but only to a very limited extent at 6 mo (Towne, 2013). Thus, in my thesis research, we set out to uncover any cell-type specific transcriptomic alterations that may be present in advance of major behavioral deficits or appearance of pathology, given that a strong body of literature suggests a long pre-symptomatic stage of illness in which subtle abnormalities may be present. 10x Genomics’ v3 gene expression assays were used to perform snRNA-seq on freshly dissected hippocampi from 6 mos, 9 mos and 19 mos littermate pairs of Tg and Wt rats (n=16 for 6 months and 9 months, with 8 for 19 months). ~2000 cells/subject were collected, and cDNA libraries were sequenced to a depth of ~120k reads/nuclei. Interestingly, data analysis revealed wide-scale gene changes in dentate granule cells (DGCs) and non-DGC excitatory neurons (Excit Ns) at 6 mos, suggestive of a significant decrease in synaptogenesis in Tg vs their Wt littermates, as well as small increases in cholesterol biosynthesis in the Tg rats in these cell types. By 9 months, some differentially expressed genes were observed across genotype in classes of glial cells, but the strongest impact on gene expression could still be seen in Excit Ns and DGCs, which continued to display evidence of decreased synaptogenesis, though to a lesser extent than at 6 mos. Interestingly, 9 mos Tg rats displayed an even stronger upregulation in genes related to cholesterol biosynthesis than 6 mos for both DGCs and Excit Ns. At 19 months, cholesterol and steroid biosynthesis were amongst the top biological pathways enriched for in Excit Ns and Inhibitory neurons of the Tg, to an even greater extent than changes in synaptogenesis. Altogether, our results suggest the transcriptional basis for a profound suppression of synapse formation or maintenance during early stages of illness in the TgF344-AD rat model, as well as abnormalities in neuronal cholesterol biosynthesis. Given that cholesterol is a key component of plasma membranes and lipid rafts, structures needed for the generation of new synapses and the stability of their receptor populations, it may be that deficiencies in the available cholesterol of Tg neuronal cells is leading to the impaired synaptogenesis in these cell types. Future work will focus on identifying whether these transcriptional alterations can be detected at even earlier time points, whether they are prescient for changes at the membrane in vivo that are correlated with memory impairment, and whether they are related to the alterations in the genome seen in our acquired epilepsy models, suggesting a common theme for the brain’s genomic response to injury of the hippocampus. / 2025-02-12T00:00:00Z

Squamous cell carcinoma of the bronchus is the second most common and fatal subtype of lung cancer. In the process of squamous carcinogenesis, the normal bronchial epithelium undergoes a series of histologic transformations known as the metaplasia-dysplasia-carcinoma sequence. These intermediate histologic patterns are called premalignant lesions, and occur prior to the development of cancer. Compared to early stage cancer, survival following resection of premalignant lesions approaches 100%, highlighting the promise of lung cancer interception. However, because of our lack of understanding of the molecular events during squamous carcinogenesis, we are currently unable to predict which lesions will progress to cancer, and we do not have molecular targets for noninvasive treatment. The work in this thesis seeks to improve our understanding of the changes associated with grades of premalignant histology and progression at the level of single cells. I analyzed single cell RNA sequencing data from a cohort of 41 lesions from 26 patients, encompassing the normal-appearing bronchus, premalignant lesions, and early stage carcinoma. I described histology-associated changes in basal cells. Basal cells from low grade lesions expressed genes related to the maintenance of the normal epithelium, while basal cells from high grade lesions expressed genes related to the cell cycle and detoxification of the airway from smoking toxicants. Secondly, I identified a high grade lesion undergoing the epithelial-to-mesenchymal transition. These cells transitioned from a high grade basal cell state, lost their expression of basal cell markers, and expressed canonical EMT genes, including SPARC, FN1, and MMP2. Finally, I identified shifts in T cell subtypes and widespread expression of exhaustion markers PD-1, CTLA4, LAG3, and TIGIT co-occurring with high grade basal cells. Secondly, I leveraged our single cell data to identify gene modules associated with histology and progression in bulk RNA sequencing data. I identified a module of genes expressed in B and dendritic cells involved in antigen presentation through the MHC II pathway whose expression was decreased in progressive lesions. I also identified a module of stromal-expressed genes that were less expressed in progressive lesions, which had previously been unidentified. Associations between module expression and progression were validated in a second data set. This work improves our understanding of the signaling and interactions between cell types associated with histology and progression of premalignant lesions. These findings may be used to improve our prognostication and treatment of premalignant lesions.

No description available.

Functionality of Cnidarian symbiosis with Symbiodiniaceae is fundamental to reef ecosystem success. Symbiodiniaceae cells have a complex life history, which, in hospite, is controlled by the host. In addition to the endosymbiotic lifestyle, they can exist free-living cells which diurnally alternate between a coccoid, vegetative night-time form to a day-time motile, flagellated cell. Their cell division cycle is gated by external light cues, and correlates with transitions in cell morphology. In contrast, endosymbiotic cells have an elongated G1 phase – demonstrating a de-coupling of cell cycle from 24-hour cycle in response to symbiosis. Furthermore, daughters of dividing endosymbiotic Symbiodiniaceae remain as coccoid cells, de-coupling morphological and cell division cycles. How this occurs remains unknown. The answer may lie in crystalline uric acid deposits, which are present only in motile, daytime cells, correlating with G1 and S phase. These store excess nitrogen and are quickly metabolized in low nitrogen availability. They also function as an eyespot. The influence of uric acid on the life cycle of free-living and endosymbiotic Symbiodiniaceae is unknown. In this study, I treated cultures of B. minutum with allopurinol, an inhibitor of uric acid synthesis. Flow cytometry showed that allopurinol the reduced growth rate and ratio of coccoid:motile cell cultures. RNA sequencing and differential gene expression analysis identified biological processes enriched in allopurinol treatment. I hypothesize that an intracellular lack of nitrogen imposed lack of uric acid crystals stimulates the General Amino Acid Control pathway. This represses translation, explaining the downregulation of ribosomal proteins, and upregulates amino acid and purine de novo biosynthesis pathways. Repression of translation may slow cellular growth and the G1 phase of the cell cycle, reducing number of cells meeting the size threshold for G1/S transition. Without uric acid deposits, cells may lack a functioning eyespot and not receive light cues which usually trigger morphological transitioning. This may suppress the motile morphology of free-living Symbiodiniaceae and cells in hospite even though the cell division cycle progresses, albeit more slowly. Genes involved in biosynthesis of flagella, thecal plates and the eyespot are upregulated, suggesting suppression of the motile form may act downstream of transcription.

Hemorrhagic fever viruses are a major public health threat in Sub-Saharan Africa. These kinds of viruses cause symptoms ranging from non-specific fevers and body aches to severe, life-threatening bleeding, shock, and multi-organ failure. Previously discovered hemorrhagic fever viruses can cause recurrent or seasonal outbreaks, but new ones continue to emerge. In order to combat these viruses, we need to better understand the aspects of pathogenesis that lead to mortality or survival. I will present analysis of the host immune response to two hemorrhagic fever viruses, Lassa virus and Bundibugyo virus, and how the host response can be used to predict mortality in these diseases. Lassa virus (LASV) was identified over 50 years ago, but it remains understudied and has hence been denoted a “Neglected Tropical Disease”. Clinical studies and experiments were run by our collaborators in Nigeria and Germany. In all, longitudinal blood samples were collected for over two hundred Nigerian Lassa Fever patients and concentrations of over 60 proteins analyzed. I processed the datasets, performed statistical testing, and created logistic regression models for each protein. This modeling allowed me to determine which proteins could be used as a predictive biomarker of mortality and the level of that protein that could best stratify patients who died and survived. I then compared protein levels for the best biomarkers and other markers in the same biological pathways with those of healthy and other febrile illness (non-Lassa Fever) controls. I examined the best biomarkers over time for their utility as biomarkers at later timepoints in hospitalization. Finally, I produced an application using RShiny that incorporated these and other exploratory analyses of the data, which allows users to visualize all the data we had in addition to the plots that were published. The filovirus Bundibugyo ebolavirus (BDBV), a relative of the more well-known Ebola virus (EBOV), first caused an outbreak in people fifteen years ago. Animal models are still being developed and characterized for this virus. Our collaborators in Texas experimentally infected cynomolgus macaques with BDBV and gave them post-exposure treatment with a VSV-based vaccine. These collaborators performed RNA-Seq on longitudinal samples from the infected macaques and sent me these data for analysis. I wrote pipelines to perform RNA-Seq and differential expression analyses on over 600 samples, of which I will focus on a subset here. I found differentially expressed genes for different subsets of the data, and I examined these gene lists using gene set enrichment analysis. I then generated logistic regression models to find differentially expressed genes that could predict mortality or survival. Many of these genes could accurately predict outcome at either late or early timepoints. I then used the top genes found by logistic regression to generate random forest models that could predict mortality over the entire course of disease. / 2025-03-20T00:00:00Z

In the post-genomic era, one of the most important goals for the community of plant biologists is to take full advantage of the knowledge generated by the Arabidopsis thaliana genome project, and to employ state-of-the-art functional genomics techniques to assign function to each gene. This will be achieved through a complete understanding of what all cellular components do, and how they interact with one another to produce a phenotype. Among the proteins encoded by the Arabidopsis genome are 24 related carboxyl methyltransferases that belong to the SABATH family. Several of the SABATH methyltransferases convert plant hormones, like jasmonic acid, indole-3-acetic acid, salicylic acid, gibberellins, and other plant constituents into methyl esters, thereby regulating the biological activity of these molecules and, consequently, myriad important physiological processes. Our research aims to decipher the function of proteins belonging to the SABATH family by applying a combination of genomics tools, including genome-wide expression analysis and gas-chromatography coupled with mass spectrometry-based metabolite profiling. Our results, combined with available biochemical information, provide a better understanding of the physiological role of SABATH methyltransferases, further insights into secondary plant metabolism and deeper knowledge of the consequences of modulating the expression of SABATH methyltransferases, both at the genome-wide expression and metabolite levels. / Ph. D.

As the global population rises, the demand for food increases which underscores a need for improvement in food security. Disease pressures are a major concern surrounding sustainable agriculture. Static crop populations, containing little to no genetic diversity, are vulnerable to diverse pathogen populations. Wild relatives of crop plants are a reservoir for new disease resistance traits that can be introgressed into cultivated crops. The identification of novel disease resistance is of paramount importance because pathogen co-evolution is not only defeating current resistance genes (R genes) but chemical controls as well. Phytophthora sojae (P. sojae), the causal agent of Phytophthora root and stem rot disease, reduces soybean harvests worldwide. We developed an approach to screen for new R genes that recognize core effectors from P. sojae. We expect R genes identified by these screens to be durable because P. sojae requires core effectors for virulence. We utilized effector-based screening to probe Glycine soja germplasm with core RXLR effectors from P. sojae to search for novel R genes. We developed segregating populations from crosses of P. sojae resistant G. soja germplasm with susceptible G. max cultivar Williams to determine inheritance of potential R genes in germplasm that responded to core effectors. We are using marker assisted breeding to map disease resistance traits in recombinant inbred (RI) lines. To better understand pathosystems, we examined host resistance and susceptibility using bioinformatics. We analyzed the interaction between Arabidopsis thaliana ecotype Col-0 and Hyaloperonospora arabidopsidis isolate Emwa1 using a publicly available RNA time-course experiment. We describe a new algorithm to sort genes into time-point specific clusters using activation and repression parameters. Gene ontology annotations were used to identify defense genes with unique expression profiles, and A. thaliana null mutants for these genes were significantly more susceptible to Emwa1 than wild-type. We plan to use these tools to rapidly identify and guide introgression of durable disease resistance into crop species. / Ph. D.