Spatial Transcriptomics Reveals Changes in Cell Type Proportions within Diseased Lung Tissue

Description

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease (ILD) that results in the permanent scarring and damage of lung tissue. Currently, there is no known cause or viable treatment for this disease, and the majority of patients either receive

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease (ILD) that results in the permanent scarring and damage of lung tissue. Currently, there is no known cause or viable treatment for this disease, and the majority of patients either receive a lung transplant or succumb to the disease within five years of diagnosis. This project centers around studying IPF through analyzing gene expression patterns in healthy vs. diseased lung tissue via spatial transcriptomics. Spatial transcriptomics is the study of individual RNA transcripts within cells on a spatial level. With the novel technology MERFISH, we can detect gene expression in a spatial context with single-cell resolution, allowing us to make inferences about certain patterns of gene expression that are solely driven by the pathology of the disease. A total of 120 cells were selected from 21 different lung samples - 6 healthy; 15 ILD. Within those lung samples, selected from 4 different tissue features - control, less fibrotic, more fibrotic, and cystic. We built an analysis pipeline in R to analyze cell type composition around these features at different distances from the center cell (0-75, 76-150, and 150-225 μm). Cell types were annotated at both a broad (less specific) and fine (more specific) level. Upon analyzing the relationship between the proportions of various cell types and distance from tissue features, we found that within the broad cell type annotation level, airway epithelium cells had a negative relationship with distance and were statistically significant through linear regression models. Within the fine cell type annotation level, ciliated/secretory cells displayed this same trend. The results above support our current understanding of cystic tissue in lung tissue, and is a foundation for understanding disease pathology as a whole.

Date Created
2023-05
Agent

Coding and Non-coding RNA Expression in Rodent Models of Cocaine Craving

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Description
Substance use disorders (SUDs) are difficult to treat, in part because drug craving can be elicited by exposure to drug-associated environments and cues within the environment. Furthermore, this craving becomes more pronounced as abstinence progresses and it can take months

Substance use disorders (SUDs) are difficult to treat, in part because drug craving can be elicited by exposure to drug-associated environments and cues within the environment. Furthermore, this craving becomes more pronounced as abstinence progresses and it can take months to years for cue-elicited craving to finally wane. This important hallmark of addiction is modeled in rodents by exposing them to light/tone cues associated with the self-administration (SA) of cocaine. Cue exposure results in drug-seeking behavior, an animal analogue for drug craving. The overarching goal of this dissertation was to use the rodent SA model to explore the nucleus accumbens (NAc), a key brain region in the neural pathway of craving, and examine ribonucleic acid (RNA) expression that may underlie cocaine-seeking behavior. This includes messenger RNAs (mRNAs), which encode directly for proteins, and non-coding RNAs, which are important regulators of mRNA expression and cellular function. My first experiment aimed to identify non-coding microRNAs, which directly target and suppress mRNA expression, that are differentially expressed in animals with high or low cocaine-seeking behavior. In the second study, I compared RNA-sequencing (RNA-seq) datasets from rodent models of cocaine abstinence and developed a novel workflow to narrow candidate genes. In the final experiment, I utilized RNA-seq and reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) to identify and explore non-coding, circular RNAs that may influence gene regulatory networks and impact drug-seeking behavior. Overall, these studies promote our understanding of the neurogenetic mechanisms of craving and they suggest recommendations for improving the experimental design of future neurogenomic studies.
Date Created
2022
Agent

Effects of SWR-5 on cocaine self-administration and D3-mediated behavior

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Description
The epidemic of drug addiction continues to grow at an alarming rate and cocaine-related overdoses have increased by more than 33% over the last decade. Cocaine targets the mesolimbic reward system in the brain to produce the “high” felt when

The epidemic of drug addiction continues to grow at an alarming rate and cocaine-related overdoses have increased by more than 33% over the last decade. Cocaine targets the mesolimbic reward system in the brain to produce the “high” felt when taking cocaine. There is currently no single cure for psychostimulant abuse, but researchers continue to find viable therapeutic options. Dopamine receptors have been a recent target for researchers. We tested a novel D3R-antagonist, SWR-5, with 905-fold D3/D2 selectivity, on addiction using a rat self- administration model and hypothesized that it would reduce motivation for cocaine. SWR-5 significantly reduced cocaine intake on a high-effort PR schedule at a dose of 10 mg/kg but did not affect sucrose intake. Also, SWR-5 did not affect either spontaneous or cocaine-induced locomotion. From our results, we concluded that SWR-5 affects motivation for cocaine, not sucrose, and does not produce adverse locomotor effects. Further research would include taking a behavioral economics approach to determine the cost/benefit ratio of taking the drug, as well as performing cue reinstatement tests to solidify whether SWR-5 plays a role in cocaine-seeking behavior.
Date Created
2020-05
Agent

Handling the Heat: Plasticity of an Arthropod Pest in Response to the Urban Heat Island

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Description
In recent years, ecologists have begun to study the effects of urbanization on species diversity. While urban areas generally suffer decreased biodiversity, some species, termed “urban exploiters”, not only live in the city but depend on urban resources to thrive.

In recent years, ecologists have begun to study the effects of urbanization on species diversity. While urban areas generally suffer decreased biodiversity, some species, termed “urban exploiters”, not only live in the city but depend on urban resources to thrive. It is hypothesized that urban exploiters may succeed in part due to phenotypic plasticity, in which organisms rapidly adjust their physiology or behavior to adapt to novel environmental contexts. In the city, it may be adaptive to display thermal plasticity, as the urban heat island effect caused by concrete and asphalt infrastructure prevents cooling at night. In this study, we observed the decorated cricket Gryllodes sigillatus, an invasive urban exploiter found in metropolitan Phoenix, in two separate experiments. We hypothesized that heat tolerance and activity are both plastic traits in this species. In Experiment 1, we predicted that knock-down time, a measure of heat tolerance, would be negatively affected by acclimation to a laboratory environment. Our results suggest that heat tolerance is affected by recent thermal regimes and that laboratory acclimation decreases knock-down time. In Experiment 2, we predicted that activity would increase with temperature until a point of extreme heat, at which point activity would decline. Statistical analysis for the second experiment reveals that activity decreases at 33°C, a natural urban extreme. This suggests either that 33°C is a thermal limit to physiology or that G. sigillatus is able to alter its behavior to exploit local thermal heterogeneity.
Date Created
2015-05
Agent