Biology Theses and Dissertations

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The Abundance and Distribution of Transparent Exopolymer Particles in the Turbidity Maximum Region of Chesapeake Bay
(2010) Malpezzi, Michael A.; Crump, Byron C; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Transparent exopolymer particle (TEP) concentrations were measured in the turbidity maximum (ETM) region of Chesapeake Bay during eight research cruises over a two-year period. TEP concentrations ranged from <100 to >2500 ug XG eq l^-1 and accounted for an estimated average of 31% ± 14 of POC. Spatially averaged TEP and chl a concentrations were positively correlated over the two year period, although these parameters were rarely correlated within cruises. Peak TEP concentrations were often separated from chl a maxima, suggesting that formation and concentration processes are more responsible for TEP concentrations than the proximity to precursor source material. Significant correlations between TEP and phaeophytin, POC, DOC, TSS and level of stratification were observed during some sampling periods. Settling tube experiments revealed a positive correlation between TEP concentration and the fraction of settling particulate matter. A hypothetical model for TEP formation and concentration in estuaries is proposed.
Acclimation of marine macrophytes (Saccharina latissima and Zostera marina) to water flow
(2008-05-12) Jordan, Terry Lynn; Koch, Evamaria; Davison, Ian; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
I examined the physiological response of two marine macrophytes, the brown alga Saccharina latissima and the angiosperm Zostera marina, to water flow in nature and in controlled experiments. Limitation of photosynthesis of both species by the availability of dissolved inorganic carbon (DIC) was increased under low current velocities. Physiological acclimation to low water flow occurred via upregulation of DIC uptake mechanisms in both S. latissima and Z. marina. Both species increased their ability to generate CO2 in the boundary layer by increasing external carbonic anhydrase and in Z. marina by also increasing proton extrusion and photosynthetic capacity. Changes in the xanthophyll-cycle in low-flow grown S. latissima increased non-photochemical quenching, thus reducing photodamage when photosynthesis was limited by DIC uptake. Water flow also affected root length in Z. marina but root length and below ground biomass were also significantly affected by sediment type, an indirect effect of water flow.
THE ACOUSTIC QUALITIES THAT INFLUENCE AUDITORY OBJECT AND EVENT RECOGNITION
(2019) Ogg, Mattson Wallace; Slevc, L. Robert; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Throughout the course of a given day, human listeners encounter an immense variety of sounds in their environment. These are quickly transformed into mental representations of objects and events in the world, which guide more complex cognitive processes and behaviors. Through five experiments in this dissertation, I investigated the rapid formation of auditory object and event representations (i.e., shortly after sound onset) with a particular focus on understanding what acoustic information the auditory system uses to support this recognition process. The first three experiments analyzed behavioral (dissimilarity ratings in Experiment 1; duration-gated identification in Experiment 2) and neural (MEG decoding in Experiment 3) responses to a diverse array of natural sound recordings as a function of the acoustic qualities of the stimuli and their temporal development alongside participants’ concurrently developing responses. The findings from these studies highlight the importance of acoustic qualities related to noisiness, spectral envelope, spectrotemporal change over time, and change in fundamental frequency over time for sound recognition. Two additional studies further tested these results via syntheszied stimuli that explicitly manipulated these acoustic cues, interspersed among a new set of natural sounds. Findings from these acoustic manipulations as well as replications of my previous findings (with new stimuli and tasks) again revealed the importance of aperiodicity, spectral envelope, spectral variability and fundamental frequency in sound-category representations. Moreover, analyses of the synthesized stimuli suggested that aperiodicity is a particularly robust cue for some categories and that speech is difficult to characterize acoustically, at least based on this set of acoustic dimensions and synthesis approach. While the study of the perception of these acoustic cues has a long history, a fuller understanding of how these qualities contribute to natural auditory object recognition in humans has been difficult to glean. This is in part because behaviorally important categories of sound (studied together in this work) have previously been studied in isolation. By bringing these literatures together over these five experiments, this dissertation begins to outline a feature space that encapsulates many different behaviorally relevant sounds with dimensions related to aperiodicity, spectral envelope, spectral variability and fundamental frequency.
Action and perception: Neural indices of learning in infants
(2016) Yoo Chon, Kathryn Hye Jin; Fox, Nathan A; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Early human development offers a unique perspective in investigating the potential cognitive and social implications of action and perception. Specifically, during infancy, action production and action perception undergo foundational developments. One essential component to examine developments in action processing is the analysis of others’ actions as meaningful and goal-directed. Little research, however, has examined the underlying neural systems that may be associated with emerging action and perception abilities, and infants’ learning of goal-directed actions. The current study examines the mu rhythm—a brain oscillation found in the electroencephalogram (EEG)—that has been associated with action and perception. Specifically, the present work investigates whether the mu signal is related to 9-month-olds’ learning of a novel goal-directed means-end task. The findings of this study demonstrate a relation between variations in mu rhythm activity and infants’ ability to learn a novel goal-directed means-end action task (compared to a visual pattern learning task used as a comparison task). Additionally, we examined the relations between standardized assessments of early motor competence, infants’ ability to learn a novel goal-directed task, and mu rhythm activity. We found that: 1a) mu rhythm activity during observation of a grasp uniquely predicted infants’ learning on the cane training task, 1b) mu rhythm activity during observation and execution of a grasp did not uniquely predict infants’ learning on the visual pattern learning task (comparison learning task), 2) infants’ motor competence did not predict infants’ learning on the cane training task, 3) mu rhythm activity during observation and execution was not related to infants’ measure of motor competence, and 4) mu rhythm activity did not predict infants’ learning on the cane task above and beyond infants’ motor competence. The results from this study demonstrate that mu rhythm activity is a sensitive measure to detect individual differences in infants’ action and perception abilities, specifically their learning of a novel goal-directed action.
Active female sampling of male display predicts female uncertainty in mate choice
(2009) Cendes, Linda Marie; Borgia, Gerald; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Information on how females use male display elements can be critical in understanding mate choice. Females often passively sample male displays, therefore female use of an element can be difficult to quantify. In satin bowerbirds, female tasting associated with male paint offers an opportunity to study how females actively assess of male display. In a preliminary study, I found that tasting was less common by females during courtships ending in copulation. This suggested that females with a greater proportion of tastes are less certain in their mate choice. I tested this hypothesis in several ways, and each indicated that a greater proportion of tasting was associated with measures suggesting mate choice uncertainty: visiting more times and more males, mating with multiple males, and switching among males. This active sampling behavior allows for examination of female assessment of a single component of male display and to predict certain female characteristics.
Activity-dependent regulation of Schwann cell development by extracellular ATP
(2003-12-05) Stevens, Beth; Davenport, Roger W; Fields, Douglas; Biology
During development, the importance of activity-dependent plasticity in neurons is widely appreciated, but comparatively less is known of the role of electrical activity in controlling glial development. Schwann cells (SCs)--the myelinating cells in the peripheral nervous system--are critically dependent on axons during the perinatal period, but axonal signals controlling SC development and myelination have remained elusive. The onset of high frequency action potential activity along developing peripheral nerves corresponds to the period when SCs are exiting the cell cycle and initiating myelination. We postulated that neural impulse activity could play an instructive role in regulating SC gene expression and function during development. To address these questions, a neuron/SC co-culture system equipped with stimulating electrodes was used to evoke action potentials in dorsal root ganglion neurons (DRGs), and study the ensuing effects in pre-myelinating SCs. We found that SCs can detect neural impulse activity in pre-myelinated axons, and the activity-dependent axon-Schwann cell signaling molecule was identified as extracellular ATP. Activity-dependent release of ATP activated multiple intracellular signaling pathways in SCs, and increased levels of several transcription factors, including CREB, c-fos, and krox-24. Importantly, we found that ATP has profound effects on SC development. Activity-dependent ATP release significantly inhibited SC proliferation, arrested SC differentiation, and completely prevented the formation of myelin. Extracellular ATP can activate multiple types of purinergic receptors; therefore we explored the specific purinergic receptors and signaling pathways that could mediate this form of activity-dependent neuron-SC communication. Using a combination of pharmacological and molecular approaches, we found that pre-myelinating SCs express a far more complex array of ATP receptors (P2X and P2Y) that previously thought. Surprisingly, we discovered that pre-myelinating SCs also express a class of functional adenosine receptors (A2), which are positively coupled to cAMP. Extracellular adenosine, a breakdown product of ATP, regulated MAP Kinase signaling and proliferation in SCs independently of ATP. Collectively, our findings suggest that ATP and adenosine released from electrically active axons activate a complex intracellular signaling network in SCs, whereby ATP and adenosine act together to regulate SC function during development and nervous system plasticity.
ACUTE EXERCISE INDUCED MICROSTRUCTURAL AND FUNCTIONAL CHANGES IN THE HIPPOCAMPUS OF OLDER ADULTS
(2023) Callow, Daniel; Carson, Jerome J; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Declining memory function is a common complaint of aging adults and a primary symptom of mild cognitive impairment (MCI) and Alzheimer’s disease (AD). The hippocampus is often the first brain area to exhibit noticeable deficits in age and pathologically-related cognitive decline and is a necessary structure for proper memory function. More specifically, the dentate gyrus (DG) and the third cornu ammonis area (CA3) of the hippocampus directly support mnemonic discrimination (MD), which is the process of reducing interference among new representations and distinctly encoding them as independent memories. Poor MD is associated with age and is a presymptomatic biomarker of cognitive decline and is believed to result from reduced neurogenesis, angiogenesis, and synaptogenesis within the DG/CA3 subregion of the hippocampus. While causes and treatments for memory decline remain elusive, lifestyle interventions, especially physical activity, have received attention as cost-effective and safe means of ameliorating and potentially preventing cognitive decline in a growing aging population. Animal and human studies suggest exercise benefits the hippocampal structure, preserving neurogenesis and angiogenesis in aging rodents and macrostructure and memory in older adults. However, the mechanisms by which exercise affects the human hippocampus remains a significant knowledge gap in the field and is a critical aspect in understanding the long-term impact exercise has on the aging hippocampus. To better address this gap, researchers have begun implementing acute exercise studies, which allow for greater control of non-exercise-related factors, are cheaper and more time efficient to conduct than training studies, and can predict and inform training-related adaptations. Unfortunately, limitations in the study designs, population tested, specificity of cognitive tasks, and spatial resolution of human imaging techniques have posed significant barriers to our understanding of how acute exercise relates to healthy brain aging at the functional and microstructural levels. Therefore, the objective of this dissertation was to expand our understanding of how acute aerobic exercise alters the function and microstructure of the aging hippocampus. Three within-subject studies were conducted comparing the relationship between a 30-minute bout of moderate to vigorous intensity aerobic exercise vs seated rest on MD performance, hippocampal microstructure, and high-resolution hippocampal-subfield microstructure and functional activity in healthy older adults. In study one, acute exercise preserved MD performance compared to decrements exhibited after seated rest in a pre and post-condition study design. In study two, a post-condition-only study design, acute exercise elevated microstructural diffusion within the hippocampus, indicative of a hippocampal neuroinflammatory response and upregulation of neurotrophic factors. Finally, in study three, a post-condition-only study design, we found that acute exercise resulted in lower MD, suppressed MD-related DG/CA3 network hyperactivity (indicative of healthier network function), and led to higher DG/CA3 extracellular diffusion. However, these neuroimaging-based correlates of hippocampal neuroplasticity and network function were not associated with differences in MD performance. These findings suggest that higher-intensity acute exercise can alter memory performance and stimulate neuroplasticity and neurotrophic cascades within the hippocampus and the DG/CA3 subfield, potentially via different mechanisms. Furthermore these results give insight into the immediate neurotrophic and behavioral effects of acute moderate to vigorous intensity aerobic exercise in older adults and provide new methods and tools for better understanding if and how exercise promotes healthy brain aging. Finally, these initial findings lay a foundation for optimizing exercise prescription and identifying future effective exercise treatments.
ADAPTIVE FLIGHT AND ECHOLOCATION BEHAVIOR IN BATS
(2015) Falk, Ben; Moss, Cynthia F; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Bats use sonar to identify and localize objects as they fly and navigate in the dark. They actively adjust the timing, intensity, and frequency content of their sonar signals in response to task demands. They also control the directional characteristics of their sonar vocalizations with respect to objects in the environment. Bats demonstrate highly maneuverable and agile flight, producing high turn rates and abrupt changes in speed, as they travel through the air to capture insects and avoid obstacles. Bats face the challenge of coordinating flight kinematics with sonar behavior, as they adapt to meet the varied demands of their environment. This thesis includes three studies, one on the comparison of flight and echolocation behavior between an open space and a complex environment, one on the coordination of flight and echolocation behavior during climbing and turning, and one on the flight kinematic changes that occur under wind gust conditions. In the first study, we found that bats adapt the structure of the sonar signals, temporal patterning, and flight speed in response to a change in their environment. We also found that flight stereotypy developed over time in the more complex environment, but not to the extent expected from previous studies of non-foraging bats. We found that the sonar beam aim of the bats predicted flight turn rate, and that the relationship changed as the bats reacted to the obstacles. In the second study, we characterized the coordination of flight and sonar behavior as bats made a steep climb and sharp turns while they navigated a net obstacle. We found the coordinated production of sonar pulses with the wingbeat phase became altered during navigation of tight turns. In the third study, we found that bats adapt wing kinematics to perform under wind gust conditions. By characterizing flight and sonar behaviors in an insectivorous bat species, we find evidence for tight coordination of sensory and motor systems for obstacle navigation and insect capture. Through these studies, we learn about the mechanisms by which mammals and other organisms process sensory information to adapt their behaviors.
Adaptive Mechanisms of an Estuarine Synechococcus based on Genomics, Transcriptomics, and Proteomics
(2016) Marsan, David Wilfred; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Picocyanobacteria are important phytoplankton and primary producers in the ocean. Although extensive work has been conducted for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in coastal and oceanic waters, little is known about those found in estuaries like the Chesapeake Bay. Synechococcus CB0101, an estuarine isolate, is more tolerant to shifts in temperature, salinity, and metal toxicity than coastal and oceanic Synechococcus strains, WH7803 and WH7805. Further, CB0101 has a greater sensitivity to high light intensity, likely due to its adaptation to low light environments. A complete and annotated genome sequence of CB0101 was completed to explore its genetic capacity and to serve as a basis for further molecular analysis. Comparative genomics between CB0101, WH7803, and WH7805 show that CB0101 contains more genes involved in regulation, sensing, and stress response. At the transcript and protein level, CB0101 regulates its metabolic pathways, transport systems, and sensing mechanisms when nitrate and phosphate are limited. Zinc toxicity led to oxidative stress and a global down regulation of photosystems and the translation machinery. From the stress response studies seven chromosomal toxin-antitoxin (TA) genes, were identified in CB0101, which led to the discovery of TA genes in several marine Synechococcus strains. The activation of the relB2/relE1 TA system allows CB0101 to arrest its growth under stressful conditions, but the growth arrest is reversible, once the stressful environment dissipates. The genome of CB0101 contains a relatively large number of genomic island (GI) genes compared to known marine Synechococcus genomes. Interestingly, a massive shutdown (255 out of 343) of GI genes occurred after CB0101 was infected by a lytic phage. On the other hand, phage-encoded host-like proteins (hli, psbA, ThyX) were highly expressed upon phage infection. This research provides new evidence that estuarine Synechococcus like CB0101 have inherited unique genetic machinery, which allows them to be versatile in the estuarine environment.
The adaptive significance and prevalence of courtship feeding in Hawaiian swordtail crickets
(2008-06-04) deCarvalho, Tagide; Shaw, Kerry; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Males of many insect species feed their partner during courtship and mating. Studies of male nutrient donation in various systems have established that nuptial feeding has evolved mostly through sexual selection. Although there is extensive diversity in form, the function of nuptial gifts is typically limited to either facilitating copulation or increasing ejaculate transfer, depending on the time at which the gift is consumed by females. Unlike other insects, the Hawaiian swordtail cricket Laupala (Gryllidae: Trigonidiinae) exhibits serial transfer of nuptial gifts. Males transfer multiple spermless 'micro' spermatophores over several hours before mating at the end of the day (i.e. before the transfer of a single sperm-containing 'macro' spermatophore). By experimental manipulation of male microspermatophore donation, I tested several hypotheses pertaining to the adaptive significance of nuptial gifts in this system. I found that microspermatophore transfer improves insemination, by causing the female reproductive tract to take in more sperm. This result reveals a previously undocumented function for premating nuptial gift donation among insects. Enhanced sperm transfer due to microspermatophore donation may represent male manipulation or an internal mechanism of post-copulatory choice by females. I also performed experimental manipulation of male photoperiod to investigate how time and gender influence nuptial gift production and mating behavior. I found that the timing of mating is limited in males but not females and that the time of pair formation has consequences for the degree of nuptial gift donation, which suggests that both mating timing and microspermatophore number is important for male reproductive success. Finally, I observed the mating behavior of several trigonidiine taxa for a comparative analysis of sexual behavior and found that other genera also utilize spermless microspermatophores, which suggests that microspermatophore donation may be a common nuptial gift strategy among swordtail crickets. The elaborate nuptial feeding behavior of Hawaiian swordtail crickets prior to mating represents a newly discovered strategy to increase male insemination success rather than mating success. Based on this unexpected result, it is worth exploring whether courtship behaviors in other cricket or insect mating systems have also evolved to increase sperm uptake.
Adenyl Cyclase and Its Relationship to Insect Diapause in the European Corn Borer, Ostrinia Nubilalis (Hubner)
(1978) Gelman, Dale Berkman; Lockard, J. David; Hayes, Dora K.; Botany and Science Teaching; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
The purpose of this study was to determine if there is a link between adenyl cyclase activity and the diapause condition in the European corn borer, Ostrinia nubilalis. Insects inhabiting those latitudes where cold and warm seasons alternate with one another have evolved mechanisms which allow them to remain dormant (in a state of diapause) during the winter months of the year. Photoperiod, as well as temperature and humidity, has been shown to control the onset, maintenance and termination of insect diapause. In recent years, evidence supporting a role for the cyclic AMP system, including adenyl cyclase, as well as a role for one or more biogenic amines in the pathway between light reception and the neuroendocrine regulation of the insect life cycle and in the multitude of neuroendocrine pathways controlling insect growth and metamorphosis has been accumulating. In light of this evidence, it was decided to investigate the effects of two light regimens, short day (diapausing-inducing) and long day (pupation-inducing), on adenyl cyclase activity of various stages of fifth instar European corn borer larval heads, and to determine the effects of the biogenic amine neurotransmitters, norepinephrine, octopamine, and dopamine on this activity. Adenyl cyclase activity was measured by a modification of the method of Krishna, et al., (1968). A summary of the results follows. In head extracts of fifth instar European corn borer larvae reared under both long day and short day photoperiodic regimens, adenyl cyclase activity in the presence of sodium fluoride increased as the larvae progressed through early, middle and mature stages. In long day larval heads, activity decreased in late prepupae and reached a low in pharate pupae. In contrast, adenyl cyclase activity in short day larval heads peaked in early diapause and then returned to prediapause levels during late diapause. Norepinephrine significantly enhanced adenyl cyclase activity only in early diapause larval head extracts, while octopamine significantly enhanced adenyl cyclase activity in head extracts of late short day mature and early diapause larvae. Dopamine was ineffective as an activator. An analysis of the combined effect of neurotransmitter and developmental stage revealed that in general, a given neurotransmitter in combination with short day larval head extracts resulted in higher adenyl cyclase levels than that neurotransmitter in combination with long day head extracts.
Age, growth and recruitment of Hudson River shortnose sturgeon (Acipenser brevirostrum)
(2005-08-10) Woodland, Ryan Jordan; Secor, David H.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Shortnose sturgeon (Acipenser brevirostrum), an Endangered Species, has experienced a several-fold increase in abundance in the Hudson River in recent decades. Age structure and growth were investigated to evaluate the hypothesis that improvements in water quality during the late 1970s stimulated population recovery. Specimens were captured using gill nets bi-monthly 2003 to 2004. Annuli in fin spine sections were determined to form at an annual rate and yielded age estimates of 5-30 years for sizes 49-105cm Total Length (n=554). Hindcast year-class strengths, corrected for gill net mesh selectivity and cumulative mortality indicated high recruitments (28,000-43,000 yearlings) during 1986-1992, which were preceded and succeeded by c. 5 year-periods of lower recruitment (5,000-15,000 yearlings). Results indicated that Hudson River shortnose sturgeon abundance increased due to the formation of several strong year-classes occurring about five years subsequent to improved water quality in important nursery and forage habitats in the upper Hudson River estuary.
ALGAL TOXICITY AND FORMATION OF HALOGENATED ORGANIC COMPOUNDS IN BALLAST WATER AFTER OXIDATIVE TREATMENT
(2019) Ziegler, Gregory; Tamburri, Mario N; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Ballast water plays a vital role in the stabilization and operations of modern ships, and it is estimated that 3 to 5 billion tons of ballast water are transferred around the world each year. However, the discharge of ballast water has led to the release of non-indigenous species, and costly and ecologically damaging biological invasions. To combat this serious problem, ballast water discharge is now regulated and ballast water management systems (BWMS) have been developed to meet required discharge limits for the release of live organisms. The most common BWMS rely on chlorination of ballast water to kill planktonic organisms but also result in the formation of disinfection by-products (DBPs) and the potential for aquatic toxicity. The research in this thesis was conducted to advance the understanding of treated ballast water toxicity, and to document the formation of higher molecular weight DBPs using ultrahigh resolution mass spectrometry. Research was conducted with commercial BWMS that were based on either direct chlorination (Ch. 2 & 3) or in-situ electrochlorination (Ch. 2 & 4). Ballast water treatment was conducted in estuarine waters of the Port of Baltimore (Patapsco River, Maryland). In Chapter 2, I tested the algal toxicity of discharged ballast water from four BWMS at the time of discharge and monthly thereafter, showing the longevity of the toxic effect of treated water on micro algae. In Chapters 3 and 4, I used ultrahigh resolution mass spectrometry to identify the molecular composition of dissolved organic matter (DOM) and halogenated DBPs after oxidative treatment of ballast water. By comparing samples before and after direct chlorination, I was able to document the changes in dissolved organic matter and the formation of numerous halogenated DBPs (Ch. 3). In Chapter 4, I was able to document the change in brominated DBPs after a period of 92 days, showing the relative persistence of dibrominated compounds. This work together demonstrates that use of traditional water treatment to solve one environmental problem may, in fact, cause other unintended consequences to aquatic ecosystems.
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.
Alternate state theory and tidal freshwater mudflat experimental ecology on Anacostia River, Washington, D.C.
(2007-11-13) may, peter; Kangas, Patrick; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The concept that multiple community states may alternately exist for some ecosystems has been the subject of controversy for decades. This theory is tested and applied to the mudflats of the low/middle marsh intertidal zone of two restored freshwater tidal marshes on the Anacostia River. It is believed that experimental exclosures exposed strong species interactions and provided a window with which to view the potential alternate existence of two structurally different systems, intertidal mudflat and emergent marsh. The occurrence, persistence and community composition of the two ecosystem states are examined through experimental exclosures at the two marsh restoration study areas. The power of large grazers to deflect the goals of wetland restoration practitioners is studied in the context of alternate state theory. Initially unvegetated mudflat, native marsh vegetation emerged within exclosure study areas at two restoration sites. Resident Canada geese (Branta canadensis maxima) decimated planted areas of restored marsh left open to grazing, returning marsh to unvegetated mudflats. Data from exclosures are presented on macrophyte community composition, sediment elevation, bird, fish, invertebrate and algae associations from two separate sets of Anacostia River experimental exclosure sites, one covering 588 m2, the other covering 2,700 m2. Results support the hypothesized alternate existence of the two system states in the same space and relative time, each dependant upon the access of a critical mass of large grazers. A description of the mudflat biotic community and its interconnectivity is discussed as an important feature of the Anacostia River system. An emergy analysis of each state and an accounting of fisheries energy flow is conducted. Information collected relating to the pre-restoration (tidal mudflat) and post-restoration (emergent marsh) physical and biological conditions are detailed and analyzed. A determination of the emergy inputs for a large-scale marsh restoration project are calculated and as a final analysis, economic (emdollar) equivalents are developed to compare the yield of fisheries production supplied by mudflats vs. a restored and mature emergent freshwater tidal marsh. Through these studies support is given to valuing mudflats as important system components of Anacostia River.
ALTERNATIVE MIGRATORY PATHWAYS OF JUVENILE STRIPED BASS IN THE PATUXENT RIVER ESTUARY, MARYLAND
(2012) Conroy, Christian William; Secor, David H.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Although highly migratory striped bass Morone saxatilis utilize spatially diverse and dynamic estuarine systems as nurseries, early dispersal behaviors have remained largely unknown. Using otolith chemistry, we identified consistent migratory and residence behaviors in juvenile striped bass year classes. Migrants were further separated by size and age into contingents that shared similar ontogenetic dispersal thresholds. We identified a small group of larval dispersers that moved to mesohaline waters prior to reaching 6 mm. Resident juveniles experienced better early growth that migrants. Small migrants had the lowest growth rates prior to dispersal, but afterward showed enhanced growth rate. Positive growth inflections were also observed for a group of migrants that reinvaded freshwater at larger sizes. Striped bass migration seems to be controlled by individual growth trajectories, where movement is driven by poor growth in the natal habitat.
Ambient sound affects movement and calls of bottlenose dolphins
(2021) Fandel, Amber Desneige; Bailey, Helen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Abundant oceanic shipping and more frequent and intense storms are increasing sound levels in aquatic habitats. Understanding how changing soundscapes affect protected species, especially those that use sound to communicate and navigate, is critical. This study utilizes passive acoustic monitoring to investigate the effects of changing ambient sound levels on bottlenose dolphin (Tursiops truncatus) movements, spatial utilization, and social calls in the Mid-Atlantic Bight, USA. By localizing dolphin whistles, I determined that their habitat use changed under higher ambient sound levels and that these elevated sound levels caused dolphins to alter the acoustic characteristics of their calls. The acoustic characteristics of individually identifiable calls (signature whistles) also varied between the sites and regions in which they were recorded. As changes in the underwater soundscape continue in the future, these findings will help inform resource managers about how protected marine mammals may be affected by anthropogenic activities and sounds.
AMPA receptor and synaptic plasticity
(2009) He, Kaiwen; Lee, Hey-Kyoung; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Long-term changes in synaptic strength, such as long-term potentiation (LTP) and long-term depression (LTD), have been proposed to be the cellular correlates of learning and memory formation. In the hippocampus, an area of the brain associated with memory formation, LTP and LTD require functional modification of AMPA receptors (AMPARs). Since AMPARs are the major ionotropic glutamate receptors in the brain, changing the single channel properties and/or the number at synapses can greatly affect excitatory synaptic function. Recent studies highlight that functional recruitment of Ca2+-permeable AMPARs (CP-AMPARs) at synapses is another key regulatory mechanism that alter excitatory synaptic transmission. By combining electrophysiology, biochemistry, and imaging methods, I found that phosphorylation of the GluR1 subunit of AMPAR on the serine-845 site (GluR1-S845) is critical for the functional recruitment of CP-AMPARs. This has functional consequences as CP-AMPARs can be expressed at synapses by various neuronal activities both in vitro and in vivo, such as by LTP, sensory experiences, brain diseases and drug addiction. On the other hand, dephosphorylation of the GluR1-S845 is necessary for producing long-term synaptic depression, which is accompanied by a loss in functional CP-AMPARs. Interestingly, the GluR1-S845 site is not required for the plasticity of dendritic spine structures, which is considered an important mechanism for long-term synaptic plasticity as well as learning and memory formation. These results suggest that the functional change in synaptic transmission and the structural synaptic plasticity may utilize separate signaling cascades. In a parallel study, I demonstrated that the beta-site cleaving enzyme 1 (BACE1), which cleaves the amyloid precursor protein (APP) to release the amyloid beta peptide (Abeta), is also involved in regulating synaptic plasticity. Using mice lacking the BACE1 gene, I found that BACE1 is involved in specific forms of synaptic plasticity as well as presynaptic function. Abnormal accumulation of Abeta by excessive BACE1 activity is thought responsible for triggering the pathology of Alzheimer's disease (AD). However, my results caution the development of AD therapeutics targeting the BACE1 activity. In summary, my studies demonstrate that the function of AMPA receptors can be regulated in multiple ways, including phosphorylation of a single amino acid, and is critically involved in synaptic plasticity that underlies learning and memory formation.
ANALYSIS OF MACROINVERTEBRATE COMMUNITIES IN SEASONAL WETLANDS THROUGH TIME, ACROSS SPACE, AND USING SPECIES TRAITS
(2016) Spadafora, Elanor; Lamp, William O; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Restoration of natural wetlands may be informed by macroinvertebrate community composition. Macroinvertebrate communities of wetlands are influenced by environmental characteristics such as vegetation, soil, hydrology, land use, and isolation. This dissertation explores multiple approaches to the assessment of wetland macroinvertebrate community composition, and demonstrates how these approaches can provide complementary insights into the community ecology of aquatic macroinvertebrates. Specifically, this work focuses on macroinvertebrates of Delmarva Bays, isolated seasonal wetlands found on Maryland’s eastern shore. A comparison of macroinvertebrate community change over a nine years in a restored wetland complex indicated that the macroinvertebrate community of a rehabilitated wetlands more rapidly approximated the community of a reference site than did a newly created wetland. The recovery of a natural macroinvertebrate community in the rehabilitated wetland indicated that wetland rehabilitation should be prioritized over wetland creation and long-term monitoring may be needed to evaluate restoration success. This study also indicated that characteristics of wetland vegetation reflected community composition. The connection between wetland vegetation and macroinvertebrate community composition led to a regional assessment of predaceous diving beetle (Coleoptera: Dytiscidae) community composition in 20 seasonal wetlands, half with and half without sphagnum moss (Sphagnum spp.). Species-level identifications indicated that wetlands with sphagnum support unique and diverse assemblages of beetles. These patterns suggest that sphagnum wetlands provide habitat that supports biodiversity on the Delmarva Peninsula. To compare traits of co-occurring beetles, mandible morphology and temporal and spatial variation were measured between three species of predaceous diving beetles. Based on mandible architecture, all species may consume similarly sized prey, but prey characteristics likely differ in terms of piercing force required for successful capture and consumption. Therefore, different assemblages of aquatic beetles may have different effects on macroinvertebrate community structure. Integrating community-level and species-level data strengthens the association between individual organisms and their ecological role. Effective restoration of imperiled wetlands benefits from this integration, as it informs the management practices that both preserve biodiversity and promote ecosystem services.
ANALYTICAL APPROACHES FOR COMPLEX MULTI-BATCH -OMICS DATASETS AND THEIR APPLICATION TO NEURONAL DEVELOPMENT
(2023) Alexander, Theresa Ann; Speer, Colenso M; El-Sayed, Najib M; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
High-throughput sequencing methods are extremely powerful tools to quantify gene expression in bulk tissue and individual cells. Experimental designs often aim to quantify expression shifts to characterize developmental trajectories, disease states, or cellular drug responses. Experimental and genetic methods are also rapidly evolving to capture specific aspects of gene expression such as in targeting individual cell types, regulatory stages, and spatially resolved cell subcompartments. These studies frequently involve a variety of experimental conditions that require many samples to guarantee sufficient statistical power for subsequent analyses. These studies are frequently processed in multiple batches due to limitations on the number of samples that can be collected, processed, and sequenced at once. To eliminate erroneous results in subsequent analyses, it is necessary to deconvolve non-biological variation (batch effect) from biological signal. Here, we explored variational contributions in multi-batch high throughput sequencing experiments by developing new methods, evaluating heterogeneity-contributors in an axon-TRAP-RiboTag protocol case-study, and highlighting biological results from this protocol. First, we describe iDA, a novel dimensionality reduction method for high-throughput sequencing data. High-dimensional data in complex, multi-batch experiments often result in discrete clustering of samples or cells. Existing unsupervised linear dimensionality reduction methods like PCA often do not resolve discreteness simply with projections of maximum variance. We show that iDA can produce better projections for separating discrete clustering that correlates with known experimental biological and batch factors. Second, we provide a case study of special considerations for a complex, multi-batch high throughput experiment. We investigated the multi-faceted heterogenic contributions of a study using the axon-TRAP-RiboTag translatomic isolation protocol in a neuronal cell type. We show that popular batch-correction methods may reduce signal due to true biological heterogeneity in addition to technical noise. We offer metrics to help identify biological signal-driven batch-differences. Lastly, we employ our understanding of variational contributions in the intrinsically photosensitive retinal ganglion cell (ipRGC) -omics case study to explore the biological transcriptomic and translatomic coordination. Our analysis revealed ipRGCs participate in subcompartment-specific local protein translation. Genetic perturbations of photopigment-driven neuronal activity led to global tissue transcriptomic shifts in both the retina and brain targets, but the ipRGC axonal-specific translatome was unaltered.