Strategic Audit for the Lincoln Inn Family Restaurant and Bakery

B.A. (Bachelor of Arts

Metaorganism Metabolomics: Hydra as a tool for understanding the role of bacterial metabolites in shaping the metabolic landscape of the host

With increased focus on host-microbe dynamics over the past decade, evidence that resident microbes affect host behaviour has mounted. Bacteria may be responsible for some of these effects as they produce a number of neuroactive compounds that could influence nervous system structure and function, leading to changes in behavioural phenotype. In the fresh water cnidarian Hydra, two behaviours are altered by microbiota: contraction frequency and feeding response duration. Here, I investigate the potential of resident microbiota to influence the structure and function of the nervous system in the early metazoan Hydra vulgaris AEP. I assess changes to nervous system structure by looking for altered neurogenesis and nerve cell density in adult polyps and find both unaltered in germ-free animals. This does not rule out the possibility of early-life alterations or smaller-scale changes to nervous system anatomy. Next, I present a metabolomics pipeline to aid in the identification of bacterially- derived, contraction-regulating compounds. Future work in identifying these compounds can take advantage of the new extraction process detailed here, which can easily be reproduced from the isolated stocks of Hydra’s five main colonizing bacterial strains. I demonstrate the utility of the metabolomics pipeline in bioactive molecule identification by identifying a dipeptide potentially responsible for the increased chemotaxis of bacterial colonizers towards germ-free Hydra. This may be a new mechanism for host-led shaping of microbial community composition. Finally, I assess the potential role of Hydra microbiota in influencing nervous system function by searching for in vitro neurotransmitter production by Hydra-associated microbes and find that the microbial community produces gamma-aminobutyric acid (GABA). Metabolic modelling confirmed the presence of GABA-synthesizing enzymes in the genomes of all five main colonizers, though only Duganella seems to possess secretory ability via a GABA transporter. Both GABA and Hydra microbiota are reported to increase the duration of the feeding response, so microbial GABA production may play a role in increasing feeding response duration. As GABA feeds into central carbon metabolism, I further analyse the role of the Hydra metabolite and GABA precursor putrescine on the growth of the bacterial colonizers, and find all colonizers are able to grow in a medium that contains putrescine as a sole carbon and nitrogen source. This suggests that any microbial manipulation of behaviour via GABA is a by-product of core metabolic processes in the bacteria. The work presented here demonstrates the utility of untargeted metabolomics for approaching a mechanistic understanding of host-microbe interactions

Description and seasonal detection of two potential whale calls recorded in the Indian Ocean

Unidentified acoustic signals are recorded by hydrophones placed in the world's oceans. Some of these sounds are suspected to originate from marine mammals. In this study, two acoustic signals recorded by two arrays at Diego Garcia in the northern Indian Ocean are described. Data were available between January 2002 and December 2003. Signals were detected manually using long-term spectral average plots. Time and frequency measurements were taken from a sample of both signals. The first unidentified signal [Diego Garcia Downsweep (DGD)] consisted of two main components. The mean frequency range of the entire signal was 19.3-45.0 Hz, with a mean duration of 36.5 s (n = 22). Detections of DGD at the northern array peaked in the austral summer, though detections at the southern array peaked during winter and spring. The second unidentified signal [Diego Garcia Croak (DGC)] consisted of one component with a mean frequency range of 16.9-49.6 Hz. The mean duration of the signal was 13.1 s (n = 10). Detections of DGC did not follow a clear seasonal pattern. These signals followed characteristics of biological sources, suggesting that they could be whale calls. Fin whale calls and possible blue whales D-calls were also identified in the data.Publisher PDFPeer reviewe

Evaluating the effects of cohesive processes on sediment distribution in an idealized, partially-mixed estuary using a numerical model

An idealized two-dimensional model is designed to represent a longitudinal section of a partially-mixed estuary, accounting for a freshwater source, tides, and estuarine circulation, but neglecting across-channel variations. The Community Sediment Transport Modeling System (CSTMS) is used to simulate suspended transport, erosion, and deposition within the Regional Ocean Modeling System (ROMS). This version of the model also includes cohesive processes such as consolidation and swelling of the sediment bed; sediment-induced stratification; and variable settling velocities. To better understand the processes controlling fine-grained sediment transport in the York River, VA, the primary features of the idealized estuary mimic that system, and the model uses site-specific field measurements of erodibility and settling properties to constrain sediment transport model parameters. Simulations that include different combinations of cohesive processes are used to determine the impact of bed consolidation and swelling, and sediment-induced stratification on the depositional patterns of various sediment types along the idealized estuary and over a tidal cycle. The sediment classes represent the range of particle settling velocities (ws) seen from in situ observations; and include resilient muddy fecal pellets (ws = 2.4 mm s-1 ), very fine sand (ws = 6 mm s-1 ), lowerdensity flocs (ws = 0.8 mm s-1 ), and unflocculated primary particles (ws = 0.1 mm s-1 ). Slower settling particles preferentially remain in suspension, leading to a more even spatial distribution. Faster settling sediment is more readily trapped in the estuarine region of convergence or estuarine turbidity maximum (ETM). Considering sedimentinduced stratification traps sediment in the lower water column, and bed consolidation limits suspension of lower ws sediment, then the incorporation of these processes are likely to enhance the trapping of relatively higher ws sediment in the ETM region

Desistance from Sexual Offending: A Policy and Research Agenda Whose Time Has Come

For the past three decades or so, criminal justice policies have been enacted under the assumption that individuals who have been convicted of a sex offense are life course persistent sex offenders. In that context, research has been heavily focused on the assessment of risk and the prediction of sexual recidivism. Simultaneously, little to no attention has been given to the majority of individuals convicted of sex offenses who are not arrested or convicted again.Researchers have witnessed a growing gap between scientific knowledge and the sociolegal response to sexual violence and abuse. The current legal landscape carries important social implications and significant life course impact for a growing number of individuals. More recently, theoretical and research breakthroughs in the study of desistance from crime and delinquency have been made that can help shed some light on desistance from sex offending. Desistance research, in the context of sex offending, however, represents serious theoretical, ethical, legal, and methodological challenges. To that end, this article introduces a special issue exploring current themes in desistance research by examining the life course of individuals convicted of a sexual offense while contextualizing their experiences of desistance.No Full Tex

Including fine-grained sediment processes within numerical representations of a partially-mixed estuary, the York River, Virginia

The Community Sediment Transport Modeling System (CSTMS) is being used to represent conditions in the York River, Virginia, a partially-mixed tidal tributary of Chesapeake Bay. Our modeling approach includes both an idealized two-dimensional longitudinal representation of the estuary, and a more realistic full three-dimensional model of the York River. Both have been implemented using versions of the Regional Ocean Modeling System (ROMS). Our modeling efforts have been motivated by a rich set of observation data from in-situ measurements made by acoustic Doppler velocimeters (ADVs), a pulse coherent acoustic Doppler profiler (PC-ADP), a laser in-situ scattering and transmissometry (LISST), and a particle imaging camera system (PICS). Additionally, water column and bed inventories of Beryllium-7 will be used to constrain the three-dimensional model parameters. Within the full three-dimensional model, hydrologic conditions, physical forcing, and sediment characteristics are being used to examine spatial and temporal changes in sediment dynamics in the York River estuary. This version of the CSTMS accounts for suspended transport, erosion, deposition and cohesive processes via consolidation and swelling of the sediment bed, which change the critical shear stress of the seafloor in response to sedimentation. Adjustments to the open boundary conditions for salinity and wind forcing produced model estimates for the summer 2007 that show good agreement with observed sediment concentration, bed stress and other hydrological parameters. We analyzed the sensitivity of calculations of the total eroded mass to the bed consolidation time scale and the critical shear stress for erosion. Further analysis showed model sensitivities to the swelling time scale and the user defined initial and equilibrium critical shear stress profiles. The idealized two-dimensional model is being developed within the Coupled OceanAtmosphere-Waves-Sediment Transport (COAWST) version of the ROMS model family. The idealized model represents a longitudinal section of a partially-mixed estuary, accounting for a freshwater source, tides, and estuarine circulation, but neglecting across-channel variations. The impact of sediment-induced stratification and the flocculation of cohesive sediments on depositional patterns will be evaluated through the addition of these two processes into the twodimensional model. This simplified model will be used as a platform for implementing code to account for sediment-induced stratification and flocculation processes within the CSTMS framework, including our three-dimensional CSTMS model of the York River estuar

Formation of Oil-Particle-Aggregates: Numerical Model Formulation and Calibration

When oil spills occur in turbid waters, the oil droplets and mineral grains can combine to form oil-particle aggregates (OPAs). The formation of OPAs impacts the vertical transport of both the oil and the mineral grains; especially increasing deposition of oil to the seabed. Though the coastal oceans can be very turbid, to date, few numerical ocean models have accounted for aggregation processes that form OPAs. However, interactions between oil and mineral aggregates may be represented using techniques developed to account for sediment aggregation. As part of Consortium for Simulation of Oil Microbial Interactions in the Ocean (CSOMIO), we modified an existing, population dynamics-based sediment flocculation model to develop OPAMOD, a module that accounts for the formation of OPAs. A zero-dimensional model using OPAMOD is shown to be capable of reproducing the size distribution of aggregates from existing laboratory experimental results. Also using the zero-dimensional model, sensitivity tests were performed on two model parameters, the fractal dimension and collision efficiency. Results showed that fractal dimension played a role in the OPA size distribution by influencing the effective particle density, which modified the number concentration of flocs for a given mass concentration. However, the modeled particle characteristics and oil sequestration were relatively insensitive to collision efficiency. To explore OPA formation for an outer continental shelf site, two simulations were conducted using a one-dimensional (vertical) implementation of the model. One scenario had high sediment concentration near the seabed to mimic storm-induced resuspension. The other scenario represented river plume sediment delivery by having high sediment concentration in surface waters. Results showed that OPA formation was sensitive to the vertical distribution of suspended sediment, with the river plume scenario creating more OPA, and sequestering more oil within OPA than the storm resuspension scenario. OPAMOD was developed within the Coupled Ocean-Atmosphere-Wave-and-Sediment Transport (COAWST) modeling system, therefore the methods and parameterizations from this study are transferrable to a three-dimensional coupled oil-sediment-microbial model developed by CSOMIO within the COAWST framework

Adapting Global Service-Learning Project and Community Partnership Outcomes Using a “Tele-engineering” Approach in Response to the COVID-19 Pandemic

The Water Supply in Developing Countries (WSDC) service-learning course at Purdue University has fostered a strong partnership with the La Vega region in the Dominican Republic since 2012. During this time, an interdisciplinary group of engineering and science students has helped design drinking water treatment systems and the group has developed water, sanitation, and health (WASH) education materials. These WASH education and water safety approaches often have been conducted in person in the past. However, with the state of the COVID-19 pandemic and the inability to travel in the fall and spring semesters of the 2020–2021 academic year, the students have been exploring (1) the impact of the pandemic on the community schools in the La Vega province, (2) the impact of the pandemic on the current water treatment systems, and (3) possible solutions to implement a “virtual installation” of a water treatment system at our newest partner school in the community of Desecho. The coronavirus pandemic has ushered in a new way that we may approach our service-learning experiences in the future. More specifically, in the future, it may be more effective to serve as a “virtual consulting firm” of engineers and consultants, rather than builders, for the implementation and design of the water treatment systems. In this way, we may facilitate a partnership that fosters community agency and solution-based approaches to technical issues are led by local community members