Biology Theses and Dissertations

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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.
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.
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.
Methane Biogeochemistry and Microbial Communities in Natural and Restored Freshwater Depressional Wetlands
(2024) Hamovit, Nora David; Yarwood, Stephanie A; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas. Wetland CH4 emissions are dependent on rates of microbial CH4 production (methanogenesis) and consumption (methanotrophy). These processes vary spatially and temporally with environmental conditions, edaphic characteristics, and microbial community structure, making it difficult to predict wetland CH4 emissions. This high variability can be further pronounced in restored wetlands that have undergone environmental and edaphic disturbances. The following work aims to understand this variability by assessing patterns of methanogenesis and methanotrophy, and their associated microbial communities, across natural and restored freshwater depressional wetlands on the Delmarva Peninsula (USA). Sites addressed in this work were restored from agricultural land between 1986 and 2004 through multiple programs funded by the United States Department of Agriculture (USDA). In the first set of experiments, we identified a high abundance of active acetoclastic methanogens in intact core incubations from a restored wetland suggesting a higher potential for methanogenesis in situ compared to the natural wetland assessed. The co-occurrence of active methanogens and Fe-reducing bacteria in these restored wetland cores contradicted the hypothesis that loss of competition may allow methanogens to be the primary users of acetate. Following assessments across vegetative-hydrologic zones in a series of restored wetlands of varying ages, and their natural counterparts, highlighted vegetation type and extent as a driver of methanogen community abundance, composition, and activity. In turn, restored wetlands showed elevated potentials rates of methanogenesis compared to natural sites. Potential rates of methanotrophy (aerobic and anaerobic), however, were also elevated in restored wetlands, which could constrain CH4 emissions in situ. Variability of environmental conditions (ie. hydrology and vegetation) and edaphic measures (ie. soil organic matter (SOM)) across all sites sampled are reflected in distinct microbial community composition and CH4 biogeochemistry. Clear patterns of SOC accumulation and CH4 biogeochemistry with restoration age were not observed for these wetlands, and variability in environmental conditions and edaphic measures across the sites (restored and natural), emphasize the need for continued monitoring and maintenance of the wetlands. Our results suggest efforts to manage herbaceous vegetation extent and maintain regular seasonal hydrology in future restorations may help prevent high potentials for CH4 production, and thus emissions.
INTERACTIONS OF SOCIAL EXPERIENCE, ALCOHOL SENSITIVITY, AND THE SEROTONERGIC SYSTEM
(2024) Ho, Ta-wen; Herberholz, Jens; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Social isolation has been shown to correlate with increased alcohol consumption in various animal species. In humans, a decreased sensitivity to acute alcohol is correlated with future alcohol dependence and addiction. A plausible explanation for this correlation is that alcohol sensitivity decreases after isolation; however, our understanding of the mechanistic interaction between social isolation and sensitivity to acute alcohol is still in its infancy. The serotonergic system is one promising candidate that could be involved in this interaction because of its wide range of behavioral and physiological effects, especially those related to social experiences. In my dissertation, I investigated the roles of the serotonergic (5-HT) system with three separate aims: In the first aim, I measured the effects of several 5-HT agents (neurotoxin, reuptake blocker, and receptor agonist/antagonists) in freely-behaving crayfish that were communally housed (COMs) or individually isolated (ISOs) prior to ethanol (EtOH) exposure. I found that 5-HT is important in regulating the social differences in EtOH sensitivity, and 5-HT2βPRO receptors emerged as candidates to produce this interaction between 5-HT and EtOH. My results from this aim suggest that these receptors are downregulated in isolated crayfish, leading to reduced behavioral EtOH sensitivity. The second aim employed single-cell neurophysiology and pharmacology in the lateral giant (LG) circuit of reduced ex vivo crayfish preparations to investigate the cellular-molecular mechanisms that underlie the interaction between 5-HT and specific EtOH receptor targets. I found that the LG neurons are stimulated by EtOH, and social differences in EtOH sensitivity between COMs and ISOs are paralleled at the level of these single neurons. Specifically, my results suggest that social isolation causes downregulation of 5-HT2βPRO receptors and 5-HT1αPRO receptors on the LG neurons and upregulation of these receptors subtypes in GABAergic neurons that send feed-forward inhibition onto the LG neurons. In my third aim, I developed a wearable, miniature, cyclic voltammetry device that is capable of detecting (injected) monoamine neurotransmitters (including 5-HT) in freely-behaving crayfish. With improved sensor sensitivity in the future, this will allow measurements of 5-HT release patterns in crayfish with different social histories, including during EtOH exposure. Together, the results from my dissertation will inform work in other model systems and improve our understanding of the interactions between social experience, the 5-HT system, and alcohol use.
Sculpting Sounds: INTRINSIC PHYSIOLOGY AND INHIBITORY ANATOMY OF THE AVIAN AUDITORY BRAINSTEM
(2024) Baldassano, James; MacLeod, Katrina; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Soundwaves are rapidly modulated, multi-dimensional stimuli. The cochlea decomposes these signals into frequency and intensity information which is conveyed via the auditory nerve into the brain. How does the brain manage to extract these multidimensional signals from auditory nerve activity? How does it sculpt this input so that both the microsecond precision of “where?” and the spectrotemporal modulations of “what?” are encoded with high fidelity? Birds are powerful models for studying early auditory processing because they interact with sounds similarly to mammals but have a simpler neuronal architecture. We describe the intrinsic physiology and anatomy and auditory brainstem neurons involved in spectrotemporal processing. In birds, the auditory nerve synapses onto two anatomically distinct cochlear nuclei, cochlear nucleus magnocellularis (NM) which encodes frequency/timing information, and the more heterogeneous cochlear nucleus angularis (NA) which encodes intensity information. NA has been shown to encode the acoustic envelope, likely through a subset of neurons that respond preferentially to modulations in their inputs via an adaptive spike threshold. We first examined the intrinsic basis of this adaptive threshold and found that a dendrotoxin-sensitive low threshold potassium conductance is responsible for it. In addition to the intrinsic properties of neurons, inhibition sculpts a number of auditory processes. The majority of inhibition in the avian auditory brainstem originates in the superior olivary nucleus (SON), which has multiple response types & projects either to multiple lower order ipsilateral nuclei, including NA & NM, or to the contralateral SON. Retrograde labeling experiments have demonstrated that these projections originate from distinct populations of SON neurons, however it is not clear if there is a relationship between response types and postsynaptic target. We used in vitro electrophysiology and neuronal reconstruction to establish a relationship between response types and targets. While the function of inhibition is well documented in timing circuits, its role in intensity processing is less clear. We used dynamic clamp to model inhibitory conductances while recording from NA neurons in vitro to determine how inhibition impacts the range of inputs that a NA neuron can encode before its firing rate saturates.
SEROTONIN REGULATES AN OLFACTORY CRITICAL PERIOD IN DROSOPHILA
(2024) Mallick, Ahana; Araneda, Ricardo; Gaudry, Quentin; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Serotonin (5-HT) is known to modulate early development during critical periods when experience drives heightened levels of plasticity in sensory systems. Studies in the somatosensory and visual cortices implicate multiple target points of serotonergic modulation, yet the underlying cellular and molecular mechanisms of 5-HT modulation of critical period plasticity remain elusive. Here, we take advantage of the genetically tractable olfactory system of Drosophila to investigate how 5-HT modulates critical period plasticity (CPP) in the CO2 sensing circuit of fruit flies. During the critical period, chronic exposure to CO2 has been shown to increase the volume of the CO2 sensing V glomerulus. We found that 5-HT release by serotonergic neurons in the antennal lobe (AL) is required for increase in the volume of the V glomerulus. Furthermore, signaling via the 5-HT1B, 5-HT2B and 5-HT7 receptors in different neuronal populations is also required during the critical period. Olfactory CPP is known to involve local inhibitory networks and consistent with this we found that knocking down 5-HT7 receptors in a subset of GABAergic local interneurons was sufficient to block CPP, as was knocking down GABA receptors expressed by olfactory sensory neurons (OSNs). Additionally, 5-HT2B expression in the cognate OSNs sensing CO2 is also essential for CPP indicating that direct modulation of OSNs also contributes to the olfactory CPP. Furthermore, 5-HT1B expression by serotonergic neurons in the olfactory system is also required during the critical period. Our study reveals that 5HT modulation of multiple neuronal targets is necessary for experience-dependent structural changes in an odor processing circuit. Finally, we wanted to isolate the neuromodulatory effects of individual serotonergic neurons. To achieve this, we combined a state-of-the-art technique to sparsely label serotonergic neurons and a computer algorithm to search against 10,000 Gal4 promoter lines and identify candidate lines that would allow individual manipulation of the 110 serotonergic neurons.
Predictors of Peer Interaction Success for Autistic and Non-Autistic Youth
(2024) McNaughton, Kathryn; Redcay, Elizabeth; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Successful peer interactions are a crucial component of mental health and well-being for autistic and non-autistic youth. Factors that influence successful peer interactions are particularly relevant to investigate in middle childhood and adolescence, a developmental period in which peer interactions take on increased importance for mental health. Research into social interactions can involve both individual-level and interindividual-level understanding of interaction outcomes. Individual-level predictors can yield insight into the way one’s own characteristics predict social interaction outcomes, for example, informing theories about how an individual’s social motivation may predict their social enjoyment. However, because research into social interaction challenges and success in autism has historically focused on individual-level contributions of autistic individuals to social interaction outcomes, it is also important to understand interindividual-level mechanisms, such as the similarity or synchrony between individuals, to understand the role both non-autistic and autistic individuals play in shaping social interactions and their outcomes. Therefore, the overarching goal of this dissertation is to evaluate potential neural and behavioral predictors of peer interaction success in autistic and non-autistic youth during middle childhood and adolescence at the individual and interindividual level. First, I demonstrate that neural sensitivity to social-interactive reward is an individual-level predictor of peer interaction enjoyment. Next, I move beyond individual-level neural predictors to interindividual-level neural predictors, providing evidence for how neural similarity to peers may differentially relate to day-to-day interaction success across different interaction types, such as interactions with peers. Finally, I establish smiling synchronization as an interindividual predictor of peer interaction enjoyment. These studies span the neural and behavioral levels of analysis, providing insight into how these levels of analysis can be investigated from both an individual and interindividual perspective. The findings advance understanding of factors that predict peer interaction success, leading to better understanding of opportunities to support successful peer interactions through individual and interindividual interventions with autistic and non-autistic youth.
HOW BILINGUALS' COMPREHENSION OF CODE-SWITCHES INFLUENCES ATTENTION AND MEMORY
(2024) Salig, Lauren; Novick, Jared; Slevc, L. Robert; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Bilinguals sometimes code-switch between their shared languages. While psycholinguistics research has focused on the challenges of comprehending code-switches compared to single-language utterances, bilinguals seem unhindered by code-switching in communication, suggesting benefits that offset the costs. I hypothesize that bilinguals orient their attention to speech content after hearing a code-switch because they draw a pragmatic inference about its meaning. This hypothesis is based on the pragmatic meaningfulness of code-switches, which speakers may use to emphasize information, signal their identity, or ease production difficulties, inter alia. By considering how code-switches may benefit listeners, this research attempts to better align our psycholinguistic understanding of code-switch processing with actual bilingual language use, while also inspiring future work to investigate how diverse language contexts may facilitate learning in educational settings. In this dissertation, I share the results of three pre-registered experiments with Spanish-English bilinguals that evaluate how hearing a code-switch affects attention and memory. Experiment 1a shows that code-switches increase bilinguals’ self-reported attention to speech content and improve memory for that information, compared to single-language equivalents. Experiment 1b demonstrates that this effect requires bilingual experience, as English-speaking monolinguals did not demonstrate increased attention upon hearing a code-switch. Experiment 2 attempts to replicate these results and establish the time course of the attentional effect using an EEG measure previously associated with attentional engagement (alpha power). However, I conclude that alpha power was not a valid measure of attention to speech content in this experiment. In Experiment 3, bilinguals again showed better memory for information heard in a code-switched context, with a larger benefit for those with more code-switching experience and when listeners believed the code-switches were natural (as opposed to inserted randomly, removing the element of speaker choice). This suggests that the memory benefit comes from drawing a pragmatic inference, which likely requires prior code-switching experience and a belief in code-switches’ communicative purpose. These experiments establish that bilingual listeners derive attentional and memory benefits from ecologically valid code-switches—challenging a simplistic interpretation of the traditional finding of “costs.” Further, these findings motivate future applied work assessing if/how code-switches might benefit learning in educational contexts.
MESOSCALE EDDIES INFLUENCE ZOOPLANKTON DISTRIBUTION AND GRAZING IN THE GULF OF MEXICO
(2024) Atkinson, William August; Coles, Victoria J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Carbon biomass and net primary productivity, for two size classes of phytoplankton in the Gulf of Mexico (GoM), are calculated from ocean color remote sensing data. Combining these estimates with mechanistic ecosystem model equations allows for analysis of how changes in phytoplankton biomass and community structure propagate through the food web to zooplankton. Biomass and grazing rates are calculated for three size classes of zooplankton (small, large, and predatory) by solving equations from the NEMURO model describing the growth of small and large phytoplankton and zooplankton using the remote sensing net primary productivity, biomass, temperature, and mixed layer depth. The ecosystem model and approach are validated for the GoM and used to assess error propagation. An eddy detection algorithm, tuned for the GoM, is used to calculate the phytoplankton and zooplankton biomass within eddy centers, around eddy edges, and in the immediate surroundings of the eddy to determine the impact of cyclonic and anticyclonic eddies and submesoscale edge effects on patterns of trophic transfer variability. Cyclonic eddy centers increase biomass and anticyclonic eddy centers decrease biomass in the oligotrophic GoM. Eddy edges contribute to variability in biomass but to a lesser extent than eddy centers. Zooplankton grazing varies in a similar pattern as biomass, and in this oligotrophic region, most grazing is on the largest size class of prey available. Nutrient injection stimulated by eddy dynamics more strongly projects onto biomass in zooplankton trophic levels and their associated grazing which suggests many eddies in the oligotrophic GoM experience top-down control. An understanding of mesoscale eddy impacts on zooplankton dynamics may explain variations in larval fish growth. Advances in remote sensing that allow the discrimination of phytoplankton functional types, such as the new PACE satellite, will be useful for providing a more complete base of the food web and thus enhance estimation of zooplankton biomass.
EXPANDING THE HISTORIC NARRATIVE OF AFRICAN AMERICAN WATERMEN IN CHESAPEAKE BAY COMMERCIAL FISHERIES: PRESERVING CULTURAL HERITAGE AND ENSURING FUTURE AFRICAN AMERICAN MARITIME PARTICIPATION THROUGH A SOCIAL-ECOLOGICAL SYSTEMS PERSPECTIVE
(2024) Black, Imani; Gray, Dr. Matthew; Shaffer, Dr. Jen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
This thesis investigates African Americans' historical and contemporary contributions to the Chesapeake Bay commercial fishing industry, employing a social-ecological system (SES) framework to explore their roles, challenges, and the decline in their participation. Utilizing methods such as oral histories, participant observations, and historical analysis, the research highlights the significant yet underrecognized contributions of African American communities to the maritime heritage of Chesapeake Bay. Through in-depth interviews with African American watermen, historians, and community members, the study examines their achievements, obstacles, and the impacts of ecological and social change on their participation trends. Additionally, it assesses the influence of prominent African American coastal communities on commercial fisheries and discusses strategies for future engagement and adaptation in a rapidly evolving industry. The findings challenge prevailing perceptions of marginal involvement by revealing substantial African American participation across various aspects of the fisheries, emphasizing the importance of acknowledging this legacy and promoting diversity and inclusion for industry sustainability. By showcasing the rich heritage and ongoing excellence of Black maritime traditions in Chesapeake Bay, this thesis underscores the critical need for greater recognition of African American contributions to the Bay’s preservation, restoration, and strong ties to the cultural heritage that have built the coastal communities along its shoreline.
The Role of Urban Agriculture in Baltimore Food Systems
(2024) Mathews, Meghna Anjali; Zhang, Xin; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The United States is one of the most agriculturally productive countries; and yet, food insecurityremains a significant issue. Urban agriculture in Baltimore, Maryland should be studied further because of its potential to address food insecurity while overcoming systemic barriers created and embedded within food systems. While numerous previous studies have explored food insecurity, knowledge gaps still exist regarding how urban agriculture has influenced food accessibility, and how availability, cultural values of foods, etc. can be improved through increased production and distribution practices of fresher fruits and vegetables in Healthy Food Priority Areas. To address these knowledge gaps, we queried food insecure community members and urban farmers in Baltimore, Maryland to better understand the underlying factors that influence low fruit and vegetable consumption and how they can be mitigated through the establishment of urban agriculture. Urban farmers were interviewed in detail about their production and distribution patterns, and factors influencing the low consumption of fresh fruits and vegetables by community members in Baltimore. Food insecure individuals were asked about their food consumption habits and the accessibility of fruit and vegetables, their food purchasing behavior and related challenges, and community needs. Results indicate that while accessibility and availability are two main factors in fresh produce consumption, there are other important factors that might have received limited attention in existing literature. Our interviews revealed that income, cultural value, and a lack of knowledge in food preparation are key factors in low consumption and purchase of fresh fruits and vegetables. To address the underlying factors and improve the accessibility and availability of fresh produce to low-income communities, it is important to assess community needs and provide policy recommendations that can potentially enhance their nutrition. Ensuring access to individuals with limited resources is a critical component of advancing social justice.
MODULATION OF SIGNALING IN THE ANTERIOR CINGULATE CORTEX AND ITS IMPACT ON DECISION-MAKING
(2024) Vazquez, Daniela; Roesch, Matthew R; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Attentional deficits are defining hallmarks of some of the most prevalent and disruptive neuropsychiatric disorders—including attention deficit hyperactivity disorder (ADHD) and substance abuse disorders. The anterior cingulate cortex (ACC) is a brain region that is highly implicated in shifting attention allocation towards relevant stimuli after unexpected events or outcomes occur. Importantly, increases in attention facilitate flexible learning, as attention allows you to dynamically filter relevant and necessary information during decision-making. My dissertation work seeks to identify the ACC as a novel point of intervention for the treatment of neuropsychiatric and addiction disorders by providing an in-depth perspective on its involvement in cognitive control and attentional processes.My research explores the neural correlates of decision-making by using electrophysiology to record single unit activity while rats perform a complex reward-based decision-making task, and employing chemical, optogenetic, and epigenetic manipulations to modulate attentional correlates in the ACC. I explored the ACC’s role in attention—and how it is impacted by drug use—using electrophysiology to record from ACC neurons as both cocaine-exposed and drug-naïve rats performed a reward-guided decision-making task. Using this task, we found a dose-dependent attenuation of ACC signaling after cocaine self-administration, which was correlated with decreases in task performance and attention to the task. Rats that had self-administered large amounts of cocaine had diminished neural responsiveness to cues, which translated into reductions in behavioral measures of attention, disruptions in cognitive flexibility, and decision-making impairments. These results both supported previous findings establishing the ACC’s role in attentional allocation, and revealed an intake-dependent effect of drugs on decision-making and neural encoding. In aim 2, we wanted to be able to precisely modulate ACC activity in order to better interrogate the role of the ACC in the absence of confounding variables (e.g. cocaine use results in the dysregulation of various neural circuits), and conduct within-subject analyses. Thus, in our next experiment we used optogenetics to inactivate the ACC, and found that ACC inhibition severely impaired task engagement, as evinced by reductions in trial initiations, and trial and session completions—resulting in overall impaired session performance. In order to disambiguate whether these behavioral deficits resulted from ACC impairment dysregulating downstream action-outcome encoding, we performed chemical lesions of the ACC, and recorded neural activity from the dorsomedial striatum (DMS)—a downstream brain region that is importantly involved in goal-directed behavior—as rats performed the previously mentioned decision-making task. Again, we found that ACC lesions resulted in disrupted attention to the task, and similar behavioral deficits to the ones we observed following cocaine use. Interestingly, we found that DMS encoding was minimally impacted, reinforcing that the observed decision-making deficits stem from disruptions in attentional signaling and not dysregulations in downstream action-outcome encoding. In the aforementioned experiments, we employed an array of techniques to dissect how disrupting ACC signaling in a variety of manners impacted task performance and engagement, so for our final experiment we sought to explore a therapeutically relevant way to potentially repair signaling disruptions that lead to the breakdown in attentional signaling. Thus, we turned to epigenetics—specifically, decreasing the expression of HDAC5, an enzyme that is involved in negatively regulating gene expression—to explore whether epigenetic changes might map onto specific alterations of neural activity and behavior. Surprisingly, we found that HDAC5 knockdown in the ACC dysregulates attentional signals that are necessary for flexible and adaptive decision-making. Together, these studies established that signaling in the functional ACC is importantly involved in attention, and that dampening these signals leads to decision-making impairments and decreased task engagement, notably characterized by significant reductions in the proportion of initiated and completed trials, and prolonged periods of inattention.
INVESTIGATION OF A NOVEL O-GLCNAC MODIFICATION OF A VACCINIA VIRUS CORE PROTEIN
(2024) Zhang, Yunliang; Scull, Margaret; Moss, Bernard; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Vaccinia virus (VACV) is a large, complex, enveloped virus that is the prototypic member of the genus Orthopoxvirus of the Poxviridae family and is well known as the live-virus vaccine that eradicated smallpox. It has a linear, double-stranded DNA genome of approximately 190 kbp that encodes about 200 proteins some of which undergo various post-translational modifications. These modifications are crucial for regulating protein function and influencing the virus behavior within the vertebrate and insect cells. Among these, O-GlcNAcylation is notable for its reversible modulation of protein function, like phosphorylation. Although over 5,000 human proteins have been documented as O-GlcNAcylated, the prevalence and function of this modification in viral proteins remain underexplored.Early studies from the Moss laboratory demonstrated the presence of a 40-kDa protein that contained N-acetylglucosamine in purified virions. The small size of the pronase-digestion product and the absence of other sugars suggested one or few glucosamines. The current study advances this understanding by pinpointing the novel O-linked β-N-acetylglucosamine (O-GlcNAc)-modified protein in VACV infectious particles. Enzymatic labeling of purified virions was performed using the mutant β-1,4-galactosyltransferase (GalT1 (Y289L)) to specifically transfer azido-modified galactose (GalNAz) from UDP-GalNAz to O-GlcNAc residues. Following copper catalyzed azide-alkyne cycloaddition (CuAAC) of biotin or an infrared dye, the candidate O-GlcNAc proteins were detected by SDS-polyacrylamide gel electrophoresis and identified by mass spectrometry (MS). Then using strain-promoted cycloaddition (SPACC) chemistry to attach a polyethylene glycol mass tag of 10 kDa to the O-GlcNAc protein, a significant shift in the electrophoretic mobility of the VACV A4 protein was documented by western blotting. The presence of O-GlcNAc in A4 was confirmed by MS and by binding to specific antibodies. Multiple modification sites were pinpointed using higher-energy collisional dissociation induced electron-transfer dissociation in MS. Further evidence linking cellular protein O-GlcNAc transferase (OGT) to the modification of A4 was derived from experiments conducted with an A4-expressing cell line. Disruption of OGT activity, either through chemical inhibition or knock-down techniques, reduced A4 O-GlcNAc modification without impairing VACV infectivity. This finding suggests that the O-GlcNAc modification of A4 does not play an essential role in VACV infectivity, which is not correlated with the A4 deletion phenotype. Therefore, the specific effects of O-GlcNAc modification on the VACV lifecycle remain elusive, indicating further studies are required to determine the potentially subtle effects of O-GlcNAcylated A4 on the VACV life cycle.
CHARACTERIZING THE ROLES AND MECHANISMS OF CYTONEMES IN ASYMMETRIC SIGNALING AND ORGANIZATIONS IN THE DROSOPHILA MUSCLE PROGENITOR NICHE.
(2024) Patel, Akshay Jitendrakumar; Roy, Sougata; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Tissue development and homeostasis rely on the ability of embryonic or stem cells to efficiently determine whether to multiply for self-renewal or differentiate to generate a wide range of cell types that constitute an adult body. Stem cells determine these fates in the context of a specialized microenvironment or the niche that they occupy. All stem cell niches characterized to date are known to function using two key processes - adhesive interactions and asymmetric growth factor signaling between the niche and stem cells. While adhesion to the niche maintains niche occupancy and stemness, the loss of niche adhesion and occupancy initiates stem cell differentiation. Moreover, niche cells produce secreted growth factors to support stem cell self-renewal. Despite the ability of secreted growth factors to disperse across tissues over a long range, only the niche-adhering stem cells receive the self-renewal signals. The genetically identical daughter cells that lack adhesion to the niche fail to receive self-renewal signals, even when located within one or two cell diameters away, leading to the activation of their post-mitotic fates. Therefore, understanding how asymmetric signal distribution and adhesive interactions are produced and coordinated within the niche is critical to understanding how stem cells determine their identity and prime differentiation to generate or regenerate tissues. This thesis investigated and characterized a new mechanism of asymmetric signaling and cell organization in the Drosophila Adult Muscle Progenitor (AMP) niche. By employing genetic, cell-biological, and high-resolution microscopy techniques, this work discovered that AMPs extend thin polarized actin-based filopodia, called cytonemes, by orienting toward the wing disc niche. Cytonemes play a dual role. Cytonemes help AMPs to physically adhere to the wing disc niche and also directly receive a self-renewal Fibroblast Growth Factor (FGF) through the cytoneme-niche contact sites. AMP cytonemes localize the FGF-receptor (FGFR), called Heartless (Htl), and selectively adhere to the wing disc areas that express two different Htl ligands, Pyramus and Thisbe, both mammalian FGF8 homologs. Htl on these cytonemes directly receives Pyramus and Thisbe through the cytoneme-niche contact sites. Although FGFs are long-range secreted paracrine signals and Htl is the only receptor shared by Pyramus and Thisbe, these FGFs are received and restricted only to the niche-adhering AMPs due to the contact-dependent cytoneme-mediated asymmetric delivery of the signals. Moreover, despite employing a common FGF signal transduction pathway, Thisbe- and Pyramus-signaling initiates divergence of AMP fates into two distinct muscle-specific lineages. These experiments showed that cytoneme-mediated signal communication forms the basis of asymmetric signaling and organization within the AMP niche. We next asked how AMPs determine the niche-specific polarity and affinity of cytonemes. This research discovered that FGF reception and signaling activation in AMPs are required to activate polarized cytoneme formation orienting toward the wing disc niche. Without FGF signaling, AMPs cytonemes fail to polarize and adhere to the FGF-producing niche, causing them to exit the niche and start to differentiate. Thus, while target-specific asymmetric FGF distribution relies on cytonemes, activation of FGF signaling feedback maintains the polarity and adhesion of the signaling cytonemes toward the FGF-producing niche. A consequence of this interdependent relationship between niche adhesion, polarized FGF-reception, and stimulation of FGF signaling feedback is the maintenance of the self-organized niche-specific asymmetric signaling and organization via cytonemes. We next investigated whether the niche-adhering cytonemes receive additional fate-specifying cues, particularly the mechanical cues from the niche. Recent evidence suggests a critical role of mechanical and physical cues in determining stem cell fates. This work discovered that the AMP cytonemes are enriched with a common mechano-transducer, named Talin. AMP-specific genetic manipulation of talin indicates that Talin is critical for cytoneme-mediated niche occupancy and FGF signaling. Using a Talin-based force probe expressed at the physiological levels and FLIM-FRET microscopy, we discovered that Talin experiences pN level force within the cytonemes. These findings suggest that AMPs employ cytonemes not only for receiving FGFs in a restricted polarized manner but also for a mechanosensory function. In conclusion, these results strongly suggest a critical role of cytonemes in coordinating asymmetric signaling and organization in the stem cell niche. In addition, the work provides evidence that the stem cell cytonemes are critical organelles for integrating the inputs and outputs of both growth factor signaling and mechanical cues to sculpt tissues.
MICROBIAL COMMUNITIES IN COASTAL ECOSYSTEMS
(2024) Kim, Carol; Malkin, Sairah Y; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Firstly, I examined microbial community succession along a chronosequence of constructed salt marshes using the Poplar Island restoration project site as a case study. By comparing 16S rRNA gene amplicon sequences across 6 constructed low marshes spanning a chronosequence of 1-16 years at Poplar Island (Chesapeake Bay) and a nearby natural reference marsh, I found strong evidence that the development of soil microbial communities is on a trajectory towards natural marsh conditions following marsh restoration with successional rates within timescales expected for soil development. Results from this study showed the value of microbial communities to serve as effective bioindicators for monitoring the recovery of microbially mediated biogeochemical processes in restored or newly constructed salt marshes, as well as potentially for assessing the marsh inundation period and by extension marsh health and resiliency. Secondly, I conducted a manipulation experiment to explore microbial communities associated with cable bacteria using RNA stable isotope probing (RNA-SIP). I traced the uptake of isotopically labeled bicarbonate and acetate in sediments with baseline and with stimulated cable bacteria activity, to test the hypothesis that cable bacteria activity can stimulate chemoautotrophic bacteria in anaerobic sediments. I used 16S rRNA sequencing to identify the active “incorporators” of bicarbonate (as a tracer of chemoautotrophy) and acetate (as a tracer of heterotrophy). I found that estuarine cable bacteria activity stimulated the chemoautotrophic activity of Gammaproteobacteria (Nitrosomonas, Thioalkalispira-Sulfurivermis) and Campylobacterota (Sulfurovum, Sulfurimonas) at anaerobic depths. This result is not explainable with conventional understanding of chemoautotrophic activity. Rather, this study contributes to the emerging concept that cable bacteria activity stimulates metabolic activities at suboxic sediment depths, potentially by serving as an electron sink for other microbes. Furthermore, I found that heterotrophic activity, measured as 13C-acetate assimilation into RNA, was stimulated amongst known chemoautotrophic sulfur oxidizers at depth, highlighting that metabolic flexibility, and specifically mixotrophy, may be widespread in complex natural sediment environments. Lastly, I characterized the composition and metabolic potential of microbial communities in estuarine sediment enriched with cable bacteria. By using metagenomic and 16S rRNA sequencing, I constructed 23 medium- to high-quality metagenome-assembled genomes (MAGs) that span across 9 phyla. I retrieved MAGs exhibiting mixotrophy and a range of capabilities for extracellular electron transport. This study revealed a diverse range of metabolically flexible communities of microbes that contribute to the biogeochemical cycling of carbon, nitrogen, and sulfur.
EVOLUTION OF THE CRISPR IMMUNE SYSTEM FROM ECOLOGICAL TO MOLECULAR SCALES
(2024) Xiao, Wei; Johnson, Philip LF; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Bacteria and archaea inhabit environments that constantly face viral infections and other external genetic threats. They have evolved an arsenal of defense strategies to protect themselves. My research delves into the CRISPR immune system, the only known adaptive immune system of prokaryotes. My work explores three different dimensions of the CRISPR immune system, ranging from ecological to molecular scales.From an evolutionary perspective, CRISPR is widely distributed across the prokaryotic tree, underscoring its immune effectiveness. However, the CRISPR distribution is uneven and some lineages are devoid of CRISPR. Here, I identify two ecological drivers of the CRISPR immune system. By analyzing both 16S rRNA data and metagenomic data, I find the CRISPR system is favored in less abundant prokaryotes in the saltwater environment and higher diverse prokaryote communities in the human oral environment. On the molecular level, the CRISPR system selects and cleaves its “favorite” DNA segments (also known as “spacers”) from invading viral genomes to form immune memories. I explore how the spacer sequence composition affects its acquisition rate by the CRISPR system. I develop a convolutional neural network model to predict the spacer acquisition rate based on the spacer sequence composition in natural microbial communities. The model interpretation reveals that the PAM-proximal end of the spacer is more important in predicting the spacer abundance, which is consistent with previous findings from controlled experimental studies. Combining these scales, CRISPR repeat sequences coevolve with the rest of the genome. Thus, I explore the potential of utilizing CRISPR repeat sequences for taxonomy profiling. I find a strong relationship between unique repeat sequences and taxonomy in both the RefSeq database and a human metagenomic dataset. Then I show high accuracy when utilizing repeat sequences in taxonomy annotation of human metagenomic contigs. This novel method not only aids in annotating CRISPR arrays but also introduces a novel tool for metagenomic sequence annotation.
INSIGHTS IN ECOLOGY, BEHAVIOR, AND REPRODUCTION FROM VISUAL MODELS OF AFRICAN CICHLIDS
(2024) Gonzalez, Zeke Martin; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Sexual selection has long been proposed to have played an important role in the explosive speciation of east African cichlids. Further, it is known that visual signals are the most salient ones to cichlids when it comes to reproduction. However, studies examining visual signals such as egg spots and size have been historically difficult to conduct due to the relationship between such phenotypes and confounding variables like age. In addition, the results from such studies often conflict and do not highlight clear patterns and hypotheses. In this dissertation, I use a receptor noise limited (RNL) visual model of increasing complexity to examine the discriminability of important visual signals in cichlid ecology, behavior, and evolution. In determining whether cichlid egg spots are truly mimics of cichlids eggs, I quantified fish and egg reflectance and found that two cichlid species are unable to distinguish the colors of eggs and egg spots in the lighting of their natural habitat. In order to bring together these quantitative methodologies with behavioral data, I tested the viability of using virtual stimuli displayed on a monitor to robustly examine how various visual signals affect conspecific male aggression. I found that although the cichlid Metriaclima zebra responds to virtual stimuli with equal aggression as towards live fish, it also responds with equal aggression towards virtual stimuli that differ in egg spot presence, body color, movement, and size. This suggests that virtual stimuli are not useful for behavioral tests in this species. Finally, in order to examine the salience of egg spots and body color in the wild, I calculated chromatic distance as a function of viewing distance for cichlid body colors against biologically-relevant backgrounds, conspecific body colors, and heterospecific body colors. The study shows that M. zebra body colors are discriminable from the space light at up to 5 m, but from the rocks at shorter distance, though distances that are comparable to the spacing of male territories. This suggests that males should be able to discriminate potential conspecific rivals on their breeding territories. Additionally, the visual model shows that M. zebra is highly discriminable from yellow heterospecifics but not so from blue heterospecifics. This dissertation emphasizes the importance of avoiding human biases in studies of cichlid color vision and behavior.
Fish Bioacoustics: From Basic Science to Policy
(2024) Colbert, Benjamin; Bailey, Helen R; Popper, Arthur N; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Sound is critically important to fishes. Sound is used to communicate with conspecifics, to detect predators and prey, or to otherwise understand the world around them. Within this dissertation, I used a variety of methods to investigate multiple aspects of fish bioacoustics, including hearing, hearing in noise, the effects of anthropogenic sound, and the morphology of peripheral auditory structures.In Chapter 2, I reviewed international policy on the regulation of underwater sound and the effects of underwater sound on marine and aquatic habitats. I found that while there are increasing efforts to regulate underwater noise, the policy efforts are hampered by a lack of quantifiable metrics associated with impacts of anthropogenic sound in aquatic habitats and species. In Chapter 3, I measured auditory sensitivity of cyprinids using physiological methods. Auditory evoked potentials, a physiological measure of auditory sensitivity, have been used in previous studies to measure hearing sensitivity. However, while physiological methods have their place, they are measuring the sensitivity of the ear rather than the entirety of the auditory pathway. Therefore, I further measured hearing sensitivity of goldfish using behavioral methods that encompass the full auditory pathway. I found that physiological methods tend to underestimate actual hearing sensitivity at frequencies less than 1000 Hz. In Chapter 4, I investigated cyprinid hearing in noise, using both physiological and behavioral measures. Critical ratios were measured for four species of carp and goldfish using auditory evoked potentials. Behavioral methods were also used to measure critical ratios for goldfish. These data represent the first measurements of critical ratios for carp and the first comparative analysis between critical ratios measured using both physiology and behavior. I found that critical ratios for carp increase by as much as 25 dB between 300 Hz and 1500 Hz. I also found that physiological methods likely overestimate actual critical ratios for fish. In Chapter 5, I used micro-computed tomography (micro-CT) and three dimensional geometric morphometrics to compare the peripheral auditory structures of three species of carp. Three dimensional models of the tripus ossicle, the posterior most Weberian ossicle, and the sagitta otolith were created and the shape of these structures for silver carp (Hypophthalmichthys molitrix), bighead carp (H. noblis), and grass carp (Ctenopharyngodon idella) quantified and contrasted. I found that the shape of the tripus differed between the Hypophthalmichthys genus (i.e., silver and bighead carp) and Ctenopharyngodon (grass carp), demonstrating a possible phylogenetic signal in the shape of the Weberian ossicles. In Chapter 6, I studied the response of wild oyster toadfish (Opsanus tau) to underwater radiated noise from boats. I used passive acoustic monitoring to record toadfish vocalizations and vessel passages in the Chesapeake Bay, U.S.A. The effect of acute vessel passage was determined by comparing the number of calls after a vessel had passed to a control period. The effect of both aggregate vessel passage over an hour and environmental variables were investigated using generalized additive mixed models. I found that there was no significant effect on toadfish call rates from acute vessel passage but when vessel generated sound was higher over an hour long period (i.e., aggregate effect), call rate declined.
SPATIOTEMPORAL DISTRIBUTION OF CHESAPEAKE BAY MYSIDS IN THE CHOPTANK AND PATUXENT RIVERS, MARYLAND
(2024) Quill, Danielle; Woodland, Ryan; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The importance of mysids as trophic links in key Chesapeake Bay food webs has been well documented. However, their abundance, distribution, and demographics haven’t been examined in Chesapeake Bay since 1930. The goal of this study was to examine patterns of mysid abundances and demographic dynamics between and within two key Chesapeake Bay tributaries (the Choptank and Patuxent rivers). I hypothesized that mysid abundances would be greater in the Choptank River due to its historically better water quality (particularly dissolved oxygen saturation) than the Patuxent River. Secondarily, I hypothesized that Neomysis americana (hereafter, Neomysis) would be the most abundant mysid species in both the Chopank and Patuxent rivers. Six stations in each river were sampled monthly from May to September of 2018. Numerical dominance of the mysid assemblage in both rivers shifted from Neomysis in the early summer to a mixed-species group belonging to the genus Americamysis (Americamysis spp.) between August and September. Total abundance across genera and abundance of Neomysis were significantly greater in the Choptank River in early summer, then did not differ from Americamysis spp. abundance thereafter. Neomysis abundance was greater than Americamysis spp. from May through June, did not differ from Americamysis spp. abundance in July, and was less abundant than Americamysis spp. from August through September in the Patuxent River. The Patuxent River displayed overall lower dissolved oxygen saturation in the summer, which correlated with lower mysid abundances, providing support for my hypothesis. Understanding the intricacies of mysid population dynamics within nursery areas for ecologically and economically important predators should strengthen ecosystem-based management strategies for those areas.

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