cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/25555704.v1
title: Investigating the Role of Microglia in Retinal Regeneration of the Adult Zebrafish Retina

description: The zebrafish possesses a remarkable ability to regenerate dying retinal neurons in response to retinal injury. Both microglia and Müller glia play integral roles in this regenerative process. Resident Müller glia respond to damage by reprogramming and undergoing asymmetric cell division to generate neuronal progenitor cells. These progenitor cells continue to proliferate and differentiate into the lost neurons. In contrast, microglia become reactive, phagocytose dying cells, and release inflammatory signals into the surrounding tissue following damage. In recent years, there has been heightened attention in elucidating the intricate interplay between retinal regeneration and the immune system. Here I demonstrate that microglia become reactive and phagocytose dying photoreceptors following light damage. I also show that chemokines and inflammatory cytokines are differentially expressed during retinal regeneration, where the expression of a subset of pro-inflammatory cytokine genes is upregulated shortly after light damage and the expression of a subset of anti-inflammatory cytokine
genes is delayed before increasing their expression. Both pro-inflammatory cytokine IL- 1ß and anti-inflammatory cytokine IL-10 are essential for Müller glia proliferation in the light-damaged retinas. The absence of either IL-1ß or IL-10 results in fewer PCNA+ Müller glia in the damaged retinas. However, IL-1ß is sufficient to induce Müller glia proliferation in the undamaged retinas. While IL-10 is unable to induce Müller glia proliferation in undamaged retinas, it induces the Müller glia to adopt a gliotic cell morphology and expression of several gliotic genes. Together, these findings demonstrate the essential role of inflammatory cytokines IL-1ß and IL-10 in regeneration in the adult zebrafish retina.
DOI: 10.7274/25586226
title: Habitat and Angler Influences on Recreational Fisheries Ecology and Management

description: Recreational fisheries are socially and economically important systems but difficult to manage. Recreational fisheries provide food, contribute to economic growth through tourism by visiting anglers, and offer human health benefits . Globally, recreational fisheries are worth US 190 billion annually . Recreational fisheries are quite complex, making management a challenge that requires multifaceted solutions. Challenges of over-exploitation, species extinction, warming waters, and declines in fish productivity can be difficult to address. Although extremely complex, three key components of recreational fisheries are: anglers, habitat, and fish populations. Indeed, many fisheries challenges arise due to complex angler effort dynamics, declines in natural habitat structures, and interspecific variability in fish life histories. In the face of these challenges, managers must identify and build understanding of the most effective leverage points of these social-ecological systems as well as important but unmanageable variables. 

In my dissertation research, I investigated the strength of habitat and angler feedbacks on recreational fish populations. The results of my research will signal to managers which leverage points are most influential to fish populations and where adaptation to unmanageable variables will be needed. I used long-term fisheries dependent and independent data to evaluate habitat and interspecific factors that determine differences in catch-abundance relationships among sport fish. I also evaluated the impacts of habitat on juvenile survival and adult fish movement and growth using a before-after control-impact (BACI) design in a whole-lake experiment. In another whole-lake experiment using a BACI design, I manipulated angler effort to test whether angler effort influenced catch rates through fish behavior or hook memory. In my dissertation, I used whole-lake experiments, long-term data, and statistical models to investigate and identify system components and tools that may aid in future management of recreational fisheries.
DOI: 10.7274/25586226.v1
title: Habitat and Angler Influences on Recreational Fisheries Ecology and Management

description: Recreational fisheries are socially and economically important systems but difficult to manage. Recreational fisheries provide food, contribute to economic growth through tourism by visiting anglers, and offer human health benefits . Globally, recreational fisheries are worth US 190 billion annually . Recreational fisheries are quite complex, making management a challenge that requires multifaceted solutions. Challenges of over-exploitation, species extinction, warming waters, and declines in fish productivity can be difficult to address. Although extremely complex, three key components of recreational fisheries are: anglers, habitat, and fish populations. Indeed, many fisheries challenges arise due to complex angler effort dynamics, declines in natural habitat structures, and interspecific variability in fish life histories. In the face of these challenges, managers must identify and build understanding of the most effective leverage points of these social-ecological systems as well as important but unmanageable variables. 

In my dissertation research, I investigated the strength of habitat and angler feedbacks on recreational fish populations. The results of my research will signal to managers which leverage points are most influential to fish populations and where adaptation to unmanageable variables will be needed. I used long-term fisheries dependent and independent data to evaluate habitat and interspecific factors that determine differences in catch-abundance relationships among sport fish. I also evaluated the impacts of habitat on juvenile survival and adult fish movement and growth using a before-after control-impact (BACI) design in a whole-lake experiment. In another whole-lake experiment using a BACI design, I manipulated angler effort to test whether angler effort influenced catch rates through fish behavior or hook memory. In my dissertation, I used whole-lake experiments, long-term data, and statistical models to investigate and identify system components and tools that may aid in future management of recreational fisheries.
DOI: 10.7274/25595238
title: Assessing the Cellular and Genetic Mechanisms of Regeneration in the Zebrafish Telencephalon in Response to Blunt-Force Traumatic Brain Injury

description: Traumatic brain injuries represent a large proportion of the global disease burden and can result in several short- and long-term deficits. Though humans possess adult neurogenesis, it is limited. Recently stem cell therapies aimed at transplantation of exogenous stem cells or stimulation of endogenous stem cells has been proposed to treat TBIs. Though promising, these studies show issues with survival, migration, and integration of progenitor cells. This highlights a lack of understanding of mechanisms necessary for regeneration. The zebrafish possess a robust regenerative capacity shown to respond to TBI in various parts of the central nervous system. This study proposes the use of a modified blunt-force TBI in the adult zebrafish telencephalon to examine cellular and molecular mechanisms of regeneration. This model induces a variety of TBI-related pathologies across different injury severities. I assess the mechanisms of cellular repair after severe TBI, which shows proliferation of radial glia, neural progenitors, and neuroblasts. Finally I assessed the genetic underpinnings of regeneration using a snRNA-Seq which suggested a role for PdgfrB in maintenance of the zebrafish NSCs. Perturbation of this pathway led to an increase in proliferating radial glia in the zebrafish telencephalon. Collectively, this study provides a foundation for future studies of injury-induced neuronal regeneration in the adult zebrafish and could be used to find druggable targets to increase neural repair in humans after TBI.
DOI: 10.7274/25595238.v1
title: Assessing the Cellular and Genetic Mechanisms of Regeneration in the Zebrafish Telencephalon in Response to Blunt-Force Traumatic Brain Injury

description: Traumatic brain injuries represent a large proportion of the global disease burden and can result in several short- and long-term deficits. Though humans possess adult neurogenesis, it is limited. Recently stem cell therapies aimed at transplantation of exogenous stem cells or stimulation of endogenous stem cells has been proposed to treat TBIs. Though promising, these studies show issues with survival, migration, and integration of progenitor cells. This highlights a lack of understanding of mechanisms necessary for regeneration. The zebrafish possess a robust regenerative capacity shown to respond to TBI in various parts of the central nervous system. This study proposes the use of a modified blunt-force TBI in the adult zebrafish telencephalon to examine cellular and molecular mechanisms of regeneration. This model induces a variety of TBI-related pathologies across different injury severities. I assess the mechanisms of cellular repair after severe TBI, which shows proliferation of radial glia, neural progenitors, and neuroblasts. Finally I assessed the genetic underpinnings of regeneration using a snRNA-Seq which suggested a role for PdgfrB in maintenance of the zebrafish NSCs. Perturbation of this pathway led to an increase in proliferating radial glia in the zebrafish telencephalon. Collectively, this study provides a foundation for future studies of injury-induced neuronal regeneration in the adult zebrafish and could be used to find druggable targets to increase neural repair in humans after TBI.
DOI: 10.7274/25599471
title: The Known Function and Enigmatic Roles of the Glycine Cleavage System in Development

description: Nonketotic hyperglycinemia (NKH) is a devastating neurometabolic disease that affects every 1 in 76,000 people worldwide. NKH is caused by an inborn error in the glycine cleavage system (GCS), a four-protein complex that functions to break down glycine, methylate folate, and produce one-carbon units to be utilized in other metabolic pathways. Patients suffer from a wide variety of symptoms including seizures, musculoskeletal defects, brain patterning abnormalities, and developmental deviations in other organ systems, including the kidney. Mutations in glycine decarboxylase (GLDC)and aminomethyltransferase (AMT) are responsible for ~80% and ~20% of NKH cases, respectively. Gldc and Amt deficient mouse models have connected the GCS to neural tube and brain development, however, the role of these proteins in kidney development is unresolved. While mouse models are highly genetically similar to humans, there are drawbacks to mice in developmental studies, such as small litters and in utero fertilization. Here, we have employed the zebrafish as an alternative model to study nephrogenesis in NKH, as zebrafish share ~70% of genes with humans, develop ex utero, and generate hundreds of embryos at a time. We have created two novel genetic loss of function models of NKH by targeting gldc and amt. In each NKH zebrafish model, we found decreased survivability, cartilaginous abnormalities, and brain patterning irregularities, recapitulating what has been noted in human patients. Further, both disease models displayed altered fluid homeostasis due to compromised renal clearance. We investigated the effects of glycine accumulation through exogenous treatment, where we discovered similar alterations in nephron patterning to the gldc morphant model. Additionally, all phenotypes were dose dependent, suggesting severity corresponds to amount of glycine that has accumulated. amt models exhibited some unique phenotypes, including a tail kink phenotype and cloacal cysts. We conducted a novel assay to analyze cloacal function through the addition of a fluorescent molecule, NaGreen. We collected live videos of amt deficient animals where we observed a blind ending lumen and an inability to excrete. To probe the genetic cascade responsible for these phenotypes, we utilized a BMP antagonist as BMP signaling has been implicated in cloacal and tail development. We discovered a novel connection between BMP signaling and amt, suggesting dysregulation of amt causes an increase in BMP signaling. Here, we uncovered a new relationship between the GCS, nephrogenic specification, and cloacal development. With the continued use of these models, we will gain a better understanding of the pathophysiology of NKH, which can provide avenues for advancement in therapeutics.
DOI: 10.7274/25599471.v1
title: The Known Function and Enigmatic Roles of the Glycine Cleavage System in Development

description: Nonketotic hyperglycinemia (NKH) is a devastating neurometabolic disease that affects every 1 in 76,000 people worldwide. NKH is caused by an inborn error in the glycine cleavage system (GCS), a four-protein complex that functions to break down glycine, methylate folate, and produce one-carbon units to be utilized in other metabolic pathways. Patients suffer from a wide variety of symptoms including seizures, musculoskeletal defects, brain patterning abnormalities, and developmental deviations in other organ systems, including the kidney. Mutations in glycine decarboxylase (GLDC)and aminomethyltransferase (AMT) are responsible for ~80% and ~20% of NKH cases, respectively. Gldc and Amt deficient mouse models have connected the GCS to neural tube and brain development, however, the role of these proteins in kidney development is unresolved. While mouse models are highly genetically similar to humans, there are drawbacks to mice in developmental studies, such as small litters and in utero fertilization. Here, we have employed the zebrafish as an alternative model to study nephrogenesis in NKH, as zebrafish share ~70% of genes with humans, develop ex utero, and generate hundreds of embryos at a time. We have created two novel genetic loss of function models of NKH by targeting gldc and amt. In each NKH zebrafish model, we found decreased survivability, cartilaginous abnormalities, and brain patterning irregularities, recapitulating what has been noted in human patients. Further, both disease models displayed altered fluid homeostasis due to compromised renal clearance. We investigated the effects of glycine accumulation through exogenous treatment, where we discovered similar alterations in nephron patterning to the gldc morphant model. Additionally, all phenotypes were dose dependent, suggesting severity corresponds to amount of glycine that has accumulated. amt models exhibited some unique phenotypes, including a tail kink phenotype and cloacal cysts. We conducted a novel assay to analyze cloacal function through the addition of a fluorescent molecule, NaGreen. We collected live videos of amt deficient animals where we observed a blind ending lumen and an inability to excrete. To probe the genetic cascade responsible for these phenotypes, we utilized a BMP antagonist as BMP signaling has been implicated in cloacal and tail development. We discovered a novel connection between BMP signaling and amt, suggesting dysregulation of amt causes an increase in BMP signaling. Here, we uncovered a new relationship between the GCS, nephrogenic specification, and cloacal development. With the continued use of these models, we will gain a better understanding of the pathophysiology of NKH, which can provide avenues for advancement in therapeutics.
DOI: 10.7274/25602474
title: Uncovering the Contributions of ESX-1 Substrates to Protein Secretion and Virulence in <em>Mycobacterium marinum</em>

description: Pathogenic mycobacteria, such as Mycobacterium tuberculosis, infect over 10 million people every year. These numbers have risen over the past few years due to the onset of the COVID-19 pandemic. Pathogenic mycobacteria use the ESX-1 secretion system to avoid degradation. The ESX-1 system transports protein substrates through the mycobacterial cell envelope which lyse the host phagosome. Here, we use genetic, biochemical, and proteomic tools to further understand the secretion and transcriptional mechanisms behind the ESX-1 system. Using the model organism Mycobacterium marinum, we identified the contributions of each ESX-1 substrate to protein secretion and virulence. In doing so, we uncovered a substrate secretion hierarchy for the first time. Our findings support a model in which ESX-1 substrates act as secreted components of the ESX-1 system. Additionally, we identified and characterized a novel ESX-1 transcription factor, EspN, that activates transcription of ESX-1-associated genes. We also found that EspN is important for virulence in vivo. Finally, we constructed a library of ESX-1 substrate double deletion strains to understand the functional relationships between ESX-1 substrates. We identified interactions between substrates that were important in facilitating substrate secretion. We observed unique changes in substrate secretion in a set of double deletion strains, which may suggest that certain ESX-1 substrates are needed to switch between secretion of early, middle, and late substrates. Collectively, our findings deepen our understanding of mycobacterial virulence strategies, which aids in development of targeted therapeutic interventions and diagnostic tools.
DOI: 10.7274/25602474.v1
title: Uncovering the Contributions of ESX-1 Substrates to Protein Secretion and Virulence in <em>Mycobacterium marinum</em>

description: Pathogenic mycobacteria, such as Mycobacterium tuberculosis, infect over 10 million people every year. These numbers have risen over the past few years due to the onset of the COVID-19 pandemic. Pathogenic mycobacteria use the ESX-1 secretion system to avoid degradation. The ESX-1 system transports protein substrates through the mycobacterial cell envelope which lyse the host phagosome. Here, we use genetic, biochemical, and proteomic tools to further understand the secretion and transcriptional mechanisms behind the ESX-1 system. Using the model organism Mycobacterium marinum, we identified the contributions of each ESX-1 substrate to protein secretion and virulence. In doing so, we uncovered a substrate secretion hierarchy for the first time. Our findings support a model in which ESX-1 substrates act as secreted components of the ESX-1 system. Additionally, we identified and characterized a novel ESX-1 transcription factor, EspN, that activates transcription of ESX-1-associated genes. We also found that EspN is important for virulence in vivo. Finally, we constructed a library of ESX-1 substrate double deletion strains to understand the functional relationships between ESX-1 substrates. We identified interactions between substrates that were important in facilitating substrate secretion. We observed unique changes in substrate secretion in a set of double deletion strains, which may suggest that certain ESX-1 substrates are needed to switch between secretion of early, middle, and late substrates. Collectively, our findings deepen our understanding of mycobacterial virulence strategies, which aids in development of targeted therapeutic interventions and diagnostic tools.
DOI: 10.7274/25844299
title: Malaria Diagnosis with Focus in <em>hrp2/3 </em>Deletion

description: Malaria diagnosis plays a crucial role in the control and eventual elimination of the disease. In many malaria-endemic areas, diagnosis relies on microscopy and rapid diagnostic tests (RDTs). RDTs can yield false-negative results due to various factors, including the presence of parasites with deletions in the hrp2/3 genes which encode the HRP2 and HRP3 proteins detected by most RDTs. This dissertation aimed to develop and test a novel hrp2/3 deletion detection method that can be used not only in the laboratory but also in the field; additionally, the characterization of samples that carry the deletion of hrp2/3 from Kenya, Ghana, Ethiopia, Brazil, and Ecuador was performed.
First, I validated a novel assay for molecular surveillance of hrp2/hrp3 deletions based on droplet digital PCR (ddPCR). The assay quantifies hrp2, hrp3, and a control gene with very high accuracy. I compared side-by-side the performance of the conventional nested PCR (nPCR) assay and ddPCR assay. Then, I apply the ddPCR assay to screen 739 samples from Kenya, Ghana, Ethiopia, Brazil, and Ecuador.
 Second, I optimized hrp2/3 protocols for typing on a portable dPCR platform (LOAA), including simplified DNA extraction protocols and extraction from archived RDTs. I adapted a more efficient method for DNA recovery with RDTs as a sample source. In a pilot study I applied my method to archived RDT samples from Gondar, Ethiopia. 
Third, using the hrp2/3 ddPCR data from Brazilian and Ecuadorian samples, I characterized wild-type parasites and hrp2 deleted parasites by 6 microsatellite markers located in the flanking regions of hrp2. I found that it was impossible to analyze the samples because of the abundant presence of stutter peaks in almost all the markers. However, the marker MS -41, which was present in all the samples, suggested that the hrp2 deleted samples from Brazil were the product of at least one hrp2 deletion event.
In conclusion, this dissertation highlights the importance of molecular diagnosis in halting the transmission of hrp2/3-deletion-carrying parasites for effective malaria control.
DOI: 10.7274/25844299.v1
title: Malaria Diagnosis with Focus in <em>hrp2/3 </em>Deletion

description: Malaria diagnosis plays a crucial role in the control and eventual elimination of the disease. In many malaria-endemic areas, diagnosis relies on microscopy and rapid diagnostic tests (RDTs). RDTs can yield false-negative results due to various factors, including the presence of parasites with deletions in the hrp2/3 genes which encode the HRP2 and HRP3 proteins detected by most RDTs. This dissertation aimed to develop and test a novel hrp2/3 deletion detection method that can be used not only in the laboratory but also in the field; additionally, the characterization of samples that carry the deletion of hrp2/3 from Kenya, Ghana, Ethiopia, Brazil, and Ecuador was performed.
First, I validated a novel assay for molecular surveillance of hrp2/hrp3 deletions based on droplet digital PCR (ddPCR). The assay quantifies hrp2, hrp3, and a control gene with very high accuracy. I compared side-by-side the performance of the conventional nested PCR (nPCR) assay and ddPCR assay. Then, I apply the ddPCR assay to screen 739 samples from Kenya, Ghana, Ethiopia, Brazil, and Ecuador.
 Second, I optimized hrp2/3 protocols for typing on a portable dPCR platform (LOAA), including simplified DNA extraction protocols and extraction from archived RDTs. I adapted a more efficient method for DNA recovery with RDTs as a sample source. In a pilot study I applied my method to archived RDT samples from Gondar, Ethiopia. 
Third, using the hrp2/3 ddPCR data from Brazilian and Ecuadorian samples, I characterized wild-type parasites and hrp2 deleted parasites by 6 microsatellite markers located in the flanking regions of hrp2. I found that it was impossible to analyze the samples because of the abundant presence of stutter peaks in almost all the markers. However, the marker MS -41, which was present in all the samples, suggested that the hrp2 deleted samples from Brazil were the product of at least one hrp2 deletion event.
In conclusion, this dissertation highlights the importance of molecular diagnosis in halting the transmission of hrp2/3-deletion-carrying parasites for effective malaria control.