Development of gene expression-based biomarkers of exposure to metals and pesticides in the freshwater amphipod Hyalella azteca

Ecological risk assessment (ERA) is a framework for monitoring risks of exposure and adverse effects of environmental stressors to populations or communities of interest. One tool of ERA is the biomarker, which is a characteristic of an organism that reliably indicates exposure to or effects of a stressor like chemical pollution. Traditional biomarkers which rely on characteristics at the tissue level and higher often detect only acute exposures to stressors. Sensitive molecular biomarkers may detect lower stressor levels than traditional biomarkers, which helps inform risk mitigation and restoration efforts before populations and communities are irreversibly affected. In this study I developed gene expression-based molecular biomarkers of exposure to metals and insecticides in the model toxicological freshwater amphipod Hyalella azteca. My goals were to not only create sensitive molecular biomarkers for these chemicals, but also to show the utility and versatility of H. azteca in molecular studies for toxicology and risk assessment. I sequenced and assembled the H. azteca transcriptome to identify reference and stress-response gene transcripts suitable for expression monitoring. I exposed H. azteca to sub-lethal concentrations of metals (cadmium and copper) and insecticides (DDT, permethrin, and imidacloprid). Reference genes used to create normalization factors were determined for each exposure using the programs BestKeeper, GeNorm, and NormFinder. Both metals increased expression of a nuclear transcription factor (Cnc), an ABC transporter (Mrp4), and a heat shock protein (Hsp90), giving evidence of general metal exposure signature. Cadmium uniquely increased expression of a DNA repair protein (Rad51) and increased Mrp4 expression more than copper (7-fold increase compared to 2-fold increase). Together these may be unique biomarkers distinguishing cadmium and copper exposures. DDT increased expression of Hsp90, Mrp4, and the immune response gene Lgbp. Permethrin increased expression of a cytochrome P450 (Cyp2j2) and decreased expression of the immune response gene Lectin-1. Imidacloprid did not affect gene expression. Unique biomarkers were seen for DDT and permethrin, but the genes studied were not sensitive enough to detect imidacloprid at the levels used here. I demonstrated that gene expression in H. azteca detects specific chemical exposures at sub-lethal concentrations, making expression monitoring using this amphipod a useful and sensitive biomarker for risk assessment of chemical exposure.

Changes in the community structure of urban and rural forest patches in Baltimore from 1998 to 2015

Urban forests are often highly fragmented with many exotic species. Altered disturbance regimes and environmental pollutants influence urban forest vegetation. One of the best ways to understand the impacts of land-use on forest composition is through long-term research. In 1998, the Baltimore Ecosystem Study established eight forest plots to investigate the impacts of urbanization on natural ecosystems. Four plots were located in urban forest patches and four were located in rural forests. In 2015, I revisited these plots to measure abundances and quantify change in forest composition, diversity, and structure. Sapling, shrub, and seedling abundance were reduced in the rural plots. Alpha diversity and turnover was lower in the rural plots. Beta diversity was reduced in the rural plots. The structure of the urban plots was mostly unchanged, except for a highly reduced sapling layer. Beta diversity in the urban plots was consistent across surveys due to high species turnover.

Air Entrainment in the Turbulent Ship Hull Boundary Layer

Turbulent fluctuations in the vicinity of the water free surface along a flat, vertically oriented surface-piercing plate are studied experimentally using a laboratory-scale experiment. In this experiment, a meter-wide stainless steel belt travels horizontally in a loop around two rollers with vertically oriented axes, which are separated by 7.5 meters. This belt device is mounted inside a large water tank with the water level set just below the top edge of the belt. The belt, rollers, and supporting frame are contained within a sheet metal box to keep the device dry except for one 6-meter-long straight test section between rollers. The belt is launched from rest with an acceleration of up to 3-g in order to quickly reach steady state velocity. This creates a temporally evolving boundary layer analogous to the spatially evolving boundary layer created along a flat-sided ship moving at the same velocity, with a length equivalent to the length of belt that has passed the measurement region since the belt motion began. Surface profile measurements in planes normal to the belt surface are conducted using cinematic Laser Induced Fluorescence and quantitative surface profiles are extracted at each instant in time. Using these measurements, free surface fluctuations are examined and the propagation behavior of these free surface ripples is studied. It is found that free surface fluctuations are generated in a region close to the belt surface, where sub-surface velocity fluctuations influence the behavior of these free surface features. These rapidly-changing surface features close to the belt appear to lead to the generation of freely-propagating waves far from the belt, outside the influence of the boundary layer. Sub-surface PIV measurements are performed in order to study the modification of the boundary layer flow field due to the effects of the water free surface. Cinematic planar PIV measurements are performed in horizontal planes parallel to the free surface by imaging the flow from underneath the tank, providing streamwise and wall-normal velocity fields. Additional planar PIV experiments are performed in vertical planes parallel to the belt surface in order to study the bahvior of streamwise and vertical velocity fields. It is found that the boundary layer grows rapidly near the free surface, leading to an overall thicker boundary layer close to the surface. This rapid boundary layer growth appears to be linked to a process of free surface bursting, the sudden onset of free surface fluctuations. Cinematic white light movies are recorded from beneath the water surface in order to determine the onset location of air entrainment. In addition, qualitative observations of these processes are made in order to determine the mechanisms leading to air entrainment present in this flow.

The Architecture of Waste: Creating New Avenues for Public Engagement with Trash

The relationship between industry, waste, and urbanism is one fraught with problems across the United States and in particular American cities. The interrelated nature of these systems of flows is in critical need of re-evaluation. This thesis critiques the system of Municipal Solid Waste Management as it currently exists in American cities as a necessary yet undesirable ‘invisible infrastructure’. Industry and waste environments have been pushed to the periphery of urban environments, severing the relationship between the urban environment we inhabit and the one that is required to support the way we live. The flow of garbage from cities of high density to landscapes of waste has created a model of valuing waste as a linear system that separates input from output. This thesis aims to investigate ways that industry, waste, and urban ecologies can work to reinforce one another. The goal of this thesis is to repair the physical and mental separation of waste and public activity through architecture. This thesis will propose ways to tie urban waste infrastructure and public amenities together through the merging of architecture and landscape to create new avenues for public engagement with waste processes.