Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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Item SENSORY AND HORMONAL MECHANISMS OF EARLY LIFE BEHAVIOR IN A SOCIAL CICHLID FISH(2024) Westbrook, Molly; Juntti, Scott; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Studying the ontogeny of animal behavior is fundamental to ethology and allows understanding how behaviors in early life may affect later life success. The social cichlid Astatotilapia burtoni is an excellent model for examining the mechanisms of early life aggression due to the robust social hierarchy enforced by stereotyped, measurable social behaviors. We examine how hormonal signaling affects early life aggression through pharmacology and CRISPR-Cas9 mutants. We test which sensory pathways convey aggression-eliciting stimuli through sensory deprivation experiments. And we identify kinematic features that predict aggression through machine-learning video tracking algorithms. We observe that aggressive behaviors emerge around 17 days post fertilization (dpf), correlating with when the animals transition to free swimming away from the mother. We find that sex steroids subtly organize behavioral circuits for aggression and suggest that unknown additional mechanisms play a leading role. We show that thyroid hormone is not necessary or sufficient for the transition to aggressive behavior. We show that visual signals are necessary for the full expression of aggression, but in the absence of visual signal, low levels of aggression remain. We show that ciliated olfactory receptor signaling maintains low levels of aggression, as mutant animals display higher levels of aggressive behavior between 17 and 24 dpf. Finally, we demonstrate that swimming velocity has potential to predict aggressive instances of behavior. Together, we find multiple levels of control for early life aggressive bouts from sensory input to hormonal organization of brain circuits.Item Algorithmic approaches for investigating DNA Methylation in tumor evolution and heterogeneity(2024) Li, Xuan; Sahinalp, S. Cenk; Mount, Stephen M.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Intratumor heterogeneity and tumor diversity of cancer impose significant challenges on the prospect of personalized cancer diagnosis, treatment, and prognostics. While many studies seek to understand the complex dynamics of cancer with theoretically well-suited biomarkers like DNA mutations, the relative molecular rigidity and sparsity of mutation make it often challenging to reconstruct reliable tumor lineage using mutation profiles in practice. Epigenetic markers like DNA methylation, on the other hand, serve as a promising alternative to elucidate intratumor heterogeneity and tumor diversity. However, systematic research leveraging algorithmic approaches to investigate DNA methylation in the context of tumor evolution and heterogeneity remains limited. Aimed to address critical gaps in computational cancer research, this dissertation presents novel computational frameworks for analyzing DNA methylation at both single-cell and bulk levels and offers insights into methylation-based tumor heterogeneity, tumor evolutionary dynamics, and cellular composition in tumor samples for characterization of the complex epigenetic landscape of tumors. Chapter 2 and Chapter 3 introduce Sgootr (Single-cell Genomic methylatiOn tumOr Tree Reconstruction), the first distance-based computational method to jointly select tumor lineage-informative CpG sites and reconstruct tumor lineages from single-cell methylation data. Sgootr lays the groundwork for understanding tumor evolution through the lens of single-cell methylation profiles. Motivated by the need highlighted in Chapter 2 to overcome imbalances in single-cell methylation data across patient samples for interpretable comparative patient analysis, Chapter 4 presents FALAFL (FAir muLti-sAmple Feature seLection). With integer linear programming (ILP) serving as its algorithmic backbone, FALAFL provides a fast and reliable solution to fairly select CpG sites across different single-cell methylation patient samples to optimally represent the entire patient cohort and identify reliable tumor lineage-informative CpG sites. Finally, Chapter 5 shifts the scope from single-cell to bulk tissue contexts and introduces Qombucha (Quadratic prOgraMming Based tUmor deConvolution with cell HierArchy), which is designed to tackle the challenges of bulk tissue analysis by inferring the methylation profiles of progenitor brain cells and determining cell type composition in bulk glioblastoma (GBM) samples. The work presented in this dissertation demonstrates the power of algorithmic and data science approaches to tackle some of the most pressing challenges in understanding the complexity of cancer epigenomics. With novel computational tools addressing current limitations in methylation data analysis, this work paves the way for further research in tumor evolution, personalized cancer treatment, and biomarker discovery. Overall, the computational frameworks and findings presented here bridge the gap between complex molecular data and clinically meaningful insights in the battle against cancer.Item AUGMENTING TIDAL WETLAND VEGETATION AND ELEVATION MONITORING USING UNOCCUPIED AERIAL SYSTEMS (UAS)(2024) Malmgren, Benjamin A; Palinkas, Cindy M; Staver, Lorie W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal wetlands provide numerous ecosystem services that promote coastal resilience. Live vegetation coverage and elevation are key metrics for assessing the health of these crucial systems. However, traditional monitoring methods can be resource- intensive, intrusive, and lack adequate spatial and temporal resolution. This thesis explores the immense potential of Unoccupied Aerial Systems (UAS, or “drones”) for expanding coastal monitoring capabilities. Chapter 1 compared two tree-based classifiers against in situ observations for estimating live vegetation percent cover. While agreement with field observations varied among both model types, random forest models proved to be more robust than simple thresholding decision stump models when applied to validation data. Chapter 2 evaluated the accuracy of Digital Surface Models (DSMs) generated from drone imagery with Structure-from-Motion, and the influence of vegetation presence on vertical error. While vegetation presence significantly increased vertical error rates, it did not explain all differences in elevation model accuracy across sites. Together, this work underscores the role drones can play in connecting researchers and management practitioners with meaningful data to drive decision- making.Item Impact of salinity on morphology, growth, and pigment profiles of Scenedesmus obliquus HTB1 under ambient air and elevated CO2 (10%) conditions(2024) Jiao, Fanglue; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Certain microalgal species tolerate high CO2 concentrations and proliferate faster with elevated CO2 than with ambient air. This feature makes them attractive for carbon sequestration, a tool for mitigating climate change due to increasing atmospheric CO2. Scenedesmus species are among these microalgae. Scenedesmus obliquus strain HTB1 is a microalgal strain isolated from the Baltimore Inner Harbor (brackish water) and has shown a faster growth with 10% CO2 compared to air. However, how HTB1 grows under different salinity and if the salt response is affected by elevated CO2 remains elusive. Two experiments were set up to address these questions. The first experiment tested the impact of salinity gradient (0, 17.5, 20, 22.5, 25, 27.5, and 30 ppt) on HTB1 under ambient air. With increasing salinity, HTB1 cells became smaller, and the cultures changed color from green to brown, yellowish brown, and then to pale white. The pigment analysis showed that HTB1 reduced several pigments (i.e. zeaxanthin, lutein, chlorophyll b) in response to salt stress. However, HTB1 produced higher concentrations of canthaxanthin under the salt stress. The growth of HTB1 decreased with increasing salinity and was inhibited when the salinity was greater than 22.5 ppt. In the second experiment, we compared the impact of salinity (0, 10, and 20 ppt) on HTB1 under air and 10% CO2, respectively. HTB1 cultures showed little color change with increasing salinity under 10% CO2. In contrast, the change of culture color from dark green to brown was observed with increasing salinity when HTB1 was grown with air. Interestingly, the growth of HTB1 was less inhibited with salt under 10% CO2 than with air, suggesting that elevated CO2 mitigates the salt stress of HTB1. Lutein and canthaxanthin increased with increasing salinity when HTB1 was grown with 10% CO2. Our results indicate that increased salinity affects the growth of Scenedesmus obliquus HTB1 more with air than with 10% CO2. This study provides insight into the impact of salt stress on algal morphology, growth, and pigment composition.Item DEVELOPMENT AND EVALUATION OF SPATIALLY-EXPLICIT POPULATION MODELS FOR ESTIMATING THE ABUNDANCE OF CHESAPEAKE BAY FISHES(2024) Nehemiah, Samara; Wilberg, Michael J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although fish populations typically experience spatially varying abundance and fishing mortality, stock assessments that inform management decisions commonly model a population that is assumed to be well-mixed with homogenous mortality rates. When assumptions about population mixing are not met, these models can result in biased estimates. Spatial population estimates are particularly beneficial to the Chesapeake Bay because this region faces unique challenges as a result of climate change and fishing pressure. However, use of spatial population models for fisheries management relies on models that can provide more accurate estimates of biological parameters than non-spatial models. Objectives for this research were to 1) develop and implement a multi-stock, spatially-explicit population model for Striped Bass (Morone saxatilis) to estimate abundance and fishing mortality in the Chesapeake Bay and along the Atlantic coast; 2) assess the performance of spatially-explicit models compared to spatially-implicit models (i.e., fleets-as-areas) to estimate abundance, determine how improved data quality (e.g., stock composition) affects model performance, and determine the effect of aging error on model accuracy; and 3) determine how spatial model performance is affected by potential changes in population dynamics resulting from climate change (e.g., time-varying natural mortality). The population model was a two-stock model with two sub-annual time-steps and two regions with stock and age-specific occupancy probabilities representing movement into and out of the Chesapeake Bay. Fishing mortality was estimated to be higher in the Ocean than the Chesapeake Bay, and abundance increased during 1982-2004 for both stocks before declining slightly until 2017. Simulations were conducted to test the ability of models to estimate abundance and fishing mortality under alternative scenarios of data availability and quality. Spatially-explicit estimates were approximately unbiased when they closely matched the assumptions of the data generating model. Models that ignored potential aging bias in datasets resulted in highly biased estimates of abundance and fishing mortality. Although the performance of all models degraded under most climate change scenarios, spatially-explicit models produced the most accurate model estimates compared to fleets-as-areas models. This research highlights the potential benefits of implementing spatially-explicit population models for Striped Bass and ecologically valuable fish species in the Chesapeake Bay.Item EFFECTS OF AGE ON CONTEXT BENEFIT FOR UNDERSTANDING COCHLEAR-IMPLANT PROCESSED SPEECH(2024) Tinnemore, Anna; Gordon-Salant, Sandra; Goupell, Matthew J; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The number of people over 65 years old in the United States is rapidly growing as the generation known as “Baby Boomers” reaches this milestone. Currently, at least 16 million of these older adults struggle to communicate effectively because of disabling hearing loss. An increasing number of older adults with hearing loss are electing to receive a cochlear implant (CI) to partially restore their ability to communicate effectively. CIs provide access to speech information, albeit in a highly degraded form. This degradation can frequently make individual words unclear. While predictive sentence contexts can often be used to resolve individual unclear words, there are many factors that either enhance or diminish the benefit of sentence contexts. This dissertation presents three complementary studies designed to address some of these factors, specifically: (1) the location of the unclear word in the context sentence, (2) how much background noise is present, and (3) individual factors such as age and hearing loss. The first study assessed the effect of context for adult listeners with acoustic hearing when a target word is presented in different levels of background noise at the beginning or end of sentences that vary in predictive context. Both context sentences and target words were spectrally degraded as a simulation of sound processed by a CI. The second study evaluated how listeners with CIs use context under the same conditions of background noise, sentence position, and predictive contexts as the group with acoustic hearing. The third study used eye-tracking methodology to infer information about the real-time processing of degraded speech across ages in a group of people who had acoustic hearing and a group of people who used CIs. Results from these studies indicate that target words at the beginning of the context sentence are more likely to be interpreted to be consistent with the following context sentence than target words at the end of the context sentences. In addition, the age of the listener interacted with some of the other experimental variables to predict phoneme categorization performance and response times in both listener groups. In the study of real-time language processing, there were no significant differences in the gaze trajectories between listeners with CIs and listeners with acoustic hearing. Together, these studies confirm that older listeners can use context in a manner similar to younger listeners, although at a slower speed. These studies expand the field’s knowledge of the importance of an unclear word’s location within a sentence and draw attention to the strategies employed by individual listeners to use context. The results of these experiments provide vital data needed to assess the current usage of context in the aging population with CIs and to develop age-specific auditory rehabilitation efforts for improved communication.Item Investigating the Microbial Diversity and Ecophysiology of Filamentous Cyanobacteria on the Susquehanna Flats, Chesapeake Bay(2024) Keller, Shayna Aryn; O'Neil, Judith M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Susquehanna Flats is a biodiverse and resilient submerged aquatic vegetation (SAV) bed just below the mouth of the Susquehanna River in the Chesapeake Bay. The Susquehanna River, the largest tributary of the Chesapeake Bay, discharges more water than all other tributaries in the Bay combined. This makes the SAV bed at the Susquehanna Flats important for nutrient removal of the water discharged into the headwaters of the Bay. The Susquehanna Flats is also a unique part of the oligohaline portion of the Chesapeake Bay as it is one of the most prolific and diverse SAV beds that make up ~8% of SAV in the Chesapeake Bay. The SAV bed was devastated by Hurricane Agnes in 1972 and did not reappear until the early 2000s when an extended dry period and long-term reductions in nutrient loading facilitated its resurgence. Since then, it has recovered to be the most abundant and biodiverse SAV bed within the upper Chesapeake Bay. However, a nitrogen fixing filamentous Cyanobacteria, morphologically identified as Microseira (Lyngbya) wollei, has seasonally bloomed at the Susquehanna Flats since the early 2000s. Over the ensuing decade, anecdotal evidence suggested an overall increase of Cyanobacteria on the SAV beds on the Susquehanna Flats, which raised concerns about the impact of this growth on the resilience of the recovering SAV bed. Despite the consistent summer blooms, the filamentous Cyanobacterial mats and its microbiome at the Susquehanna Flats has not been molecularly identified and its characteristics have not been investigated to date. Additionally, new DNA sequencing technology has become more readily available, and the identification and taxonomy of the Cyanobacteria family Oscillatoriaceae, of which Microseira (Lyngbya) wollei is a part of, has become more refined and organized. Due to this, molecularly identifying the filamentous Cyanobacterial mats and investigating its microbiome has become much easier with current methods that can provide detailed taxonomic information that can help implement management strategies. Using PacBio long-read amplicon sequencing on the 16S rRNA genes and Illumina short-read amplicon sequencing on the nifH genes of the filamentous Cyanobacteria mats and a newly observed mucilaginous Cyanobacteria mat collected at the Susquehanna Flats, the host organisms and microbial compositions were revealed. The results indicate that the dominant filamentous Cyanobacterial mat host is Microseira (Lyngbya) wollei and these mats contain a complex microbial community. The host of a newly observed mucilaginous mats was revealed to be a novel strain of Phormidium sp. To understand the basic nutrient requirements and preferences of the Microseira (Lyngbya) wollei at the Susquehanna Flats, nutrient bioassay growth and nitrogen fixation experiments were initiated to assess its growth and nitrogen fixation qualities. Samples received nutrient treatments of nitrate, phosphate, nitrate + phosphate, and ammonium compared to the growth of control samples that did not receive nutrient treatments in the summers of 2022 and 2023. The results demonstrated that Microseira (Lyngbya) wollei has variable growth rates, with higher rates in the mid to late part of the summer season, with significant growth stimulations from added nitrogen and phosphorus. In terms of nitrogen fixation, rates were higher in the beginning of the season, with significant stimulation with phosphorus additions. It is likely that lower rates measured at the end of the season, were due to the increased availability of regenerated nitrogen within the system. More detailed investigation of the seasonal nutrient dynamics are warranted to fully understand the dynamics between these Cyanobacterial mats and the SAV beds.Item The Impact of Marsh Sill Living Shorelines on Coastal Resilience and Stability: Insights from Maryland's Chesapeake Bay and Coastal Bays(2024) Sun, Limin; Nardin, William WN; Palinkas, Cindy CP; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Climate change and coastal urbanization are accelerating the demand for strategies to reduce shoreline erosion and enhance coastal resilience to storms and sea-level rise. Generally adverse ecological impacts of hardened infrastructure (e.g., seawalls, revetments, and dikes) have led to growing interest in alternative solutions. Living shorelines, increasingly recognized as sustainable Natural and Nature-Based Features (NNBFs; or Nature-Based Solutions (NBSs)) for their dual benefits of stabilizing shorelines while preserving or restoring coastal habitats, represent a promising approach to shoreline stabilization. Marsh sill living shorelines (created marshes with adjacent rock sills) have been extensively constructed in the Chesapeake Bay, notably in Maryland. Despite their popularity, significant uncertainties remain regarding their effectiveness and resiliency, especially during high-energy events. This dissertation investigates the dynamics of marsh sill living shorelines in Maryland’s Chesapeake Bay and Coastal Bays, aiming to fill knowledge gaps and inform effective shoreline stabilization strategies. First, the dissertation examines marsh boundary degradation into open water during high-energy conditions, contrasting mechanisms between living shorelines and natural marshes. Field surveys and numerical modeling reveal that while natural marshes experience erosion through undercutting and slumping at the scarp toe, living shorelines degrade primarily through open-water conversion at the marsh boundary behind rock sills. Differences in sediment characteristics and vegetation between the two ecosystems drive variations in marsh boundary stability between them. Next, the study assesses the impacts of rock sill placement on sediment dynamics and shoreline stability, highlighting the role of tidal gaps in enhancing sediment flux to the marsh and increasing vertical accretion during high-energy events. Numerical modeling demonstrates that while continuous sills mitigate erosion at the marsh edge of living shorelines, they diminish sediment deposition on the marsh platform compared to segmented sills with tidal gaps. Finally, the research identifies key factors driving marsh boundary degradation that are needed to assess the stability of marsh sill living shorelines. Analysis of eco-geomorphic features and hydrodynamics across 18 living shoreline sites reveals that metrics such as the Unvegetated/Vegetated Ratio (UVVR) and sediment deposition rate often used to assess the resilience of natural marshes also apply to the created marshes of living shorelines. Multivariate analyses further reveal that the Relative Exposure Index (REI) and Gap/Rock (G/R) ratio are crucial predictors of shoreline stability in marsh sill living shorelines, and thus should be particularly considered in shoreline design. By integrating remote sensing, field observations, and numerical modeling, this dissertation advances the understanding of sediment dynamics and stability in living shorelines and provides actionable insights for effective shoreline design and management to promote coastal resilience.Item Becoming a Father: Disentangling the Causes and Consequences of Caregiving Behavior in California Mouse Males(2024) Colt, Maria; Carleton, Karen L; Fisher, Heidi S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In mammals, parental care is critical to offspring survival, however, it can also lead to measurable changes in parents. In the biparental California mouse, Peromyscus californicus, fathers actively care for their offspring, including grooming, huddling, retrieving their pups, and building nests. When fathers engage in caregiving behavior, they also experience increased memory, decreased anxiety-like behavior, and structural neuroplasticity of the hippocampus. However, the trigger, reproduction or caregiving experience, and the molecular pathways that regulate these behavioral and neurological changes, remain unclear. In the first chapter, I compared caregiving behaviors in fathers who have cared for their pups and pup-sensitized non-fathers who have cared for unrelated pups, and I found that pup-sensitized non-fathers were slower to approach pups but eventually spent more time grooming pups, whereas fathers spent more time nest-building. I then compared recognition learning, anxiety-like behaviors, and reproductive investment in fathers, pup-sensitized non-fathers, non-fathers with no caregiving experience, and virgins that were socially housed but had no caregiving experience. I found that experienced fathers exhibited increased recognition memory and decreased anxiety-like behavior compared to virgins and non-fathers, and that virgins had smaller testes and fewer sperm compared to non-fathers yet that first-time fathers had larger testes compared to non-fathers. In the second chapter, I first show that hippocampal dendritic spine density is positively associated with males’ caregiving experience. Then, I compared hippocampal gene expression in fathers, non-fathers, and pup-sensitized non-fathers and performed gene ontology, network, and pathway analyses to identify suites of RNA expression patterns associated with caregiving experience. I found that fathers exhibit an upregulation of genes associated with neurogenesis, glutamatergic synapses, neuronal signaling, cellular components of dendritic spines, and some biological pathways previously linked to maternal care, such as regulation of actin cytoskeleton. Together, my results suggest that caregiving behavior induces important behavioral, structural, and transcriptional changes in the brains of males, even if they are caring for offspring that are not their own.Item NEURAL BASIS OF VIBRATION DETECTION IN LEPIDOSAURIAN REPTILES(2024) Han, Dawei; Carr, Catherine E.; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)There are three potential pathways for detection of substrate vibration: cochlear, otolithic and somatosensory, reviewed in chapter one. How different lepidosaurian reptiles detect substrate vibration from these three pathways was explored from neuroanatomical and physiological perspectives. In chapter two, I described vibration sensitivity and the organization of the brainstem cochlear nuclei in the western snake (Pantherophis obsoletus). The western ratsnake is sensitive to low-frequency vibrations, comparable to other snakes. It has two first-order cochlear nuclei, nucleus magnocellularis (NM) and nucleus angularis (NA), similar to other reptiles. NM is small, while NA is relatively robust. In chapter three, I examined the connections and response properties of nucleus vestibularis ovalis (VeO) in the hindbrain of the tokay gecko (Gekko gecko). VeO receives input from the saccule, and connections of VeO mirror those of the cochlear nuclei, including an ascending projection to the central nucleus of the torus semicircularis. VeO neurons are sensitive to low-frequency vibration. In chapter four, I revisited a classic study to determine the connections and response properties of the snake torus semicircularis. In the western ratsnake, the torus can be divided into a central nucleus and a paratorus, the latter receiving input from the spinal cord, nucleus myelencephali dorsalis in the spinomedullary junction, as well as auditory nuclei. Toral neurons are sensitive to low frequency vibration and have heterogenous response characteristics. In chapter five, I discuss future directions based on findings in my dissertation and highlight the importance of vibration detection for lepidosaurs.