VictorJuiz/thesis huggingface dataset:
Gene-environment Interactions Underlying the Developmental Origins of Health and Disease

Retrospective epidemiological studies of British cohorts have found an inverse relationship between birth size and rates of mortality from cardiovascular disease and stroke. Subsequently, further studies in humans and in animals have demonstrated that there is an inverse relationship with a combination of suboptimal prenatal and postnatal environments and the development of the metabolic syndrome (insulin resistance, hypertension, obesity and dyslipidemia). However, recently it has been reported that not all individuals exposed to these environments develop these conditions, suggesting that an individual’s genotype may contribute to the eventual outcome. Phylogenetically distinct, murine strains allow the genetic dissection of complex phenotypic traits; however, to date, they have not been utilized to evaluate the gene-environment interaction underlying these inverse relationships. Thus, A/J and C57BL/6J mice were subjected to prenatal undernutrition, to model an adverse intra-uterine environment, and although prenatal undernutrition resulted in fetal growth restriction of equal magnitude, remarkable strain differences were observed. At the end of gestation C57BL/6J mice showed significant alterations in fetal organ weights (liver, kidneys and placenta) and glucocorticoids (elevation). Postnatally, C57BL/6J offspring demonstrated catch-up growth, obesity, impaired glucose tolerance, insulin resistance, increased blood pressure, liver dysfunction and altered cardiovascular function compared to strain and gender matched controls. The A/J strain was resistant to the development of prenatal and postnatal pathologies, except they also demonstrated alterations in cardiovascular function. Females of both strains displayed a more moderate phenotype than the males. Although feeding undernutrition mice an atherogenic diet postnatally did not exacerbate the phenotype, postnatal dietary supplementation of omega-3 long chain unsaturated fatty acids completely reversed the undernutrition induced altered metabolic phenotype in C57BL/6J. Microarray analysis revealed that adult A/J and C57BL/6J mice have distinct gene expression profiles, under control dietary conditions, and that this differential strain expression profile changes in adult offspring in response to prenatal undernutrition. The expression profiles predicted onset of metabolic and liver diseases within the C57BL/6J strain, clearly linking the observed phenotype to alterations in gene expression. These expression differences were also linked to inherent strain differences in the genetic code where a disproportionate number of differential expressed genes had function altering polymorphisms.

Keywords: physiology
Advisor: Lye, Stephen J.
Resurrected Bodies: Individual Experiences and Collective Expressions of Organ Transplant in North America

The dissertation is an ethnographic study of religion as conceived and experienced by organ transplant recipients. It is also a cultural study of North America’s collective expressions of transplant as found in Christian journals, popular media, advocacy literature and public policy statements. The study finds evidence that religious metaphors and directives, cosmological figures and theological arguments, rituals, scriptures and places of worship are actively, vociferously, and consciously engaged with organ transplant discourse and with the experience of giving or receiving organs. While the transplant recipients under study cannot be considered representative (being largely advocates for transplant and almost exclusively of Christian background or affiliation), this group was articulate about the ways their new organ invoked the sacred: they described new metaphysical understandings, they spoke of a closer relationship with God, the universe and other human beings, they divulged inexplicable incidents and mystical states of being, they articulated a complex set of ethical prescripts. “Thinking how many times you should have been dead and you’re still here” was for many an imperative to “start to find out why.” I argue that these spiritual seekers traverse a 21st century terrain shaped by the practices and discourses of what Foucault termed “biopower”. The private and public production of sanctified donors and ‘redeemed’ recipients is inextricably bound to the desires of transplant professionals and government officials, and cannot hope to escape the very real commodification of the body that transplant represents. This seeming paradox of ‘the sacred in the secular’ does not make transplant’s religious constructions inauthentic or irrelevant. Religion remains an active and inventive register for the recording of potent bodily experiences of illness, loss and conditional regeneration. Further, the religious activity around transplant affords a window on emerging rites, on contemporary understandings of death and immortality, and on new conversations about miracles and morality. Circuits of biotechnology are not immune to religious influence and inflection – but, simultaneously, contemporary religious meanings, practices and experiences are indelibly shaped by our newfound ability to transplant organs.

Keywords: organ transplant
religion
anthropology
cultural theory
medical sociology
Advisor: Klassen, Pamela
Investigation of Community Dynamics and Dechlorination Processes in Chlorinated Ethane-degrading Microbial Cultures

The purpose of this research was to investigate the microorganisms, genetics and biochemistry of anaerobic dechlorination of chlorinated ethanes, which are common groundwater contaminants. Specifically, this project used mixed microbial cultures to study the dechlorination of 1,2-dichloroethane (1,2-DCA), 1,1,2-trichloroethane (1,1,2-TCA) and 1,1,1-trichloroethane (1,1,1-TCA). A mixed microbial culture enriched from a contaminated multilayered aquifer in West Louisiana dechlorinated 1,2-DCA, 1,1,2-TCA, tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride (VC) to non-toxic ethene when amended with ethanol as the electron donor. 16S rRNA gene sequence analysis revealed the presence of the putative dechlorinating organisms Dehalobacter and Dehalococcoides spp. Denaturing gradient gel electrophoresis analysis and quantitative PCR (qPCR) with species-specific primers demonstrated that both organisms grew during the dichloroelimination of 1,2-DCA to ethene. Conversely, during the dichloroelimination of 1,1,2-TCA to VC only Dehalobacter grew, while during the reductive dechlorination of VC to ethene only Dehalococcoides grew. Further enrichment with 1,2-DCA, H2 and acetate yielded a co-culture of Dehalobacter and Acetobacterium spp. that did not dechlorinate other chlorinated ethanes or ethenes. Dehalobacter grew in the presence but not in the absence of 1,2-DCA, while Acetobacterium growth was not affected by 1,2-DCA. A novel putative Dehalobacter-associated 1,2-DCA reductive dehalogenase gene was identified and was shown to be transcribed only in the presence of 1,2-DCA. An enrichment microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States was also studied. This culture, referred to as MS, reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) when amended with methanol, ethanol, acetate and lactate. 16S rRNA gene sequence analysis revealed the presence of the putative dechlorinating organism Dehalobacter sp., whose growth during 1,1,1-TCA and 1,1-DCA dechlorination was confirmed by qPCR. In the presence of chlorinated ethenes, dechlorination 1,1,1-TCA by the culture MS was slowed, while dechlorination of 1,1-DCA was completely inhibited. Experiments with cell-free extracts and whole cell suspensions of culture MS suggested that chlorinated ethenes have direct inhibitory effects on 1,1,1-TCA reductive dehalogenase(s), while the inhibition of 1,1-DCA dechlorination may be due to effects on non-dehalogenase components of Dehalobacter sp. cells. Additionally, two novel reductive dehalogenase genes associated with 1,1,1-TCA reductive dechlorination were identified.

Keywords: bioremediation
microbial ecology
reductive dechlorination
chlorinated ethanes
Advisor: Edwards, Elizabeth A.
Photography and Trauma in Photo-fiction: Literary Montage in the Writings of Jonathan Safran Foer, Aleksandar Hemon and W. G. Sebald

Located on the interstice between Media Studies and Literary Theory, my dissertation explores the emerging genre of photo-fiction -- literary works that incorporate photographic images into the manuscripts -- and its impact on the commemoration of traumatic historical events. I argue that the way we represent and remember historical traumas is dependent on the media in which images emanating from these events are produced and circulated; put differently, the context of these images shapes our engagement with them. By examining literary works that incorporate photographs into their printed text, I explore textual and visual representations of historical trauma (such as the two World Wars, the Balkan wars of the Nineties, and 9/11). The authors whose works I analyze (Jonathan Safran Foer, Aleksandar Hemon, W.G. Sebald) grant photography a new status: the inserted images transcend traditional “authentification strategies” and draw attention to the convergence of realism and indexicality featured by these photographs. These authors’ employment of photographs from various media (television, internet, printed press, encyclopedias and archives) questions not only the technical qualities of each medium but the veracity and accuracy of evidence. Photography’s capacity to secure and store information is put radically into question, not only because the new contexts of these images, but because of the manipulations and reconfigurations the movement between media has brought about. Drawing on Walter Benjamin’s concept of the literary montage, I suggest that literature provides an apt arena to examine the reception to images. By literary montage I mean the opening up of a new dimension in which visual and verbal elements are juxtaposed, and the disjunctions and gaps between them encourage readers to become active participants in the creation of narrative. Photo-fiction’s interplay between images and texts therefore not only sheds light on the mechanics of representation, but demand from its audience to reflect on the way we interpret and respond to historical traumas in a society saturated with images.

Keywords: photo-fiction
visual culture
trauma
photography
Literary Montage
context
media
memory
Jonathan Safran Foer
W. G. Sebald
Aleksandar Hemon
Advisor: Hutcheon, Linda
Development of a High-throughput Electrokinetically-controlled Heterogeneous Immunoassay Microfluidic Chip

This thesis was on the development of a high-throughput electrokinetically-controlled heterogeneous immunoassay (EK-IA) microfluidic chip for clinical application. Through a series of experimental studies, a high-throughput EK-IA was developed. This EK-IA was capable of automatically screening multiple analytes from up to 10 samples in parallel, in only 26 min. Flow control in an integrated microfluidic network was realized by numerical simulation of the transport processes. This EK-IA was successfully applied to detect E. coli O157:H7 antibody and H. pylori antibody from human sera with satisfactory accuracy. Simultaneous screening of both antibodies from human sera was also achieved, demonstrating the potential of this EK-IA for efficiently detecting multiple pathogenic infections in clinical settings. Preliminary work on the application of EK-IA to detect biomarkers of embryo development in embryo culture media also yielded good results. In addition to the experimental studies, the reaction kinetics of this microfluidic EK-IA has also been investigated, using both numerical simulation and a modified Damköhler number. Targeted towards a more sensitive assay, the influences of several important parameters on the reaction kinetics were studied. This EK-IA holds great promise for automated and high-throughput immunoassay in clinical environments.

Keywords: microfluidic
immunoassay
electrokinetic
lab-on-a-chip
Advisor: Li, Dongqing
Sun, Yu
The Influence of Release Modality on Synaptic Transmission at a Developing Central Synapse

The auditory brainstem is comprised of a number of synapses specialized for the transmission of high-fidelity synaptic signals. Within the first three postnatal weeks, these pathways acquire the ability to process high-frequency signals without compromising timing information. However, little is known regarding developmental adaptations which confer this ability. Situated in the sound localization pathway, the calyx of Held-medial nucleus of the trapezoid body synapse provides an ideal model for investigating such adaptations as both the pre- and postsynaptic neurons are accessible to electrophysiological experimentation. Using this synapse, we have shown herein that the spatial coupling between voltage-gated calcium channels (VGCCs) and synaptic vesicles (SVs) tightens during development. Immature synapses use a loosely-coupled arrangement of many N- and P/Q-type VGCCs (“microdomain” modality) while mature synapses use a tightly-coupled arrangement of fewer P/Q-type VGCCs, to release SVs (“nanodomain” modality). As a consequence of this tightening, synaptic delay (SD) shortens. By fluorescence- and electron microscopy of SVs near active zones, we further identified the filamentous protein septin 5 as a molecular substrate, differentiating the two release modalities, which may act as a spatial barrier separating VGCCs and SVs in immature synapses. Finally, we have demonstrated that changes in release modality affect the nature of short-term plasticity observed at this synapse. Using trains of action potentials as presynaptic voltage-commands, we showed that, downstream of calcium influx, the microdomain modality promotes short-term facilitation in excitatory postsynaptic currents (IEPSC), and calcium-dependent decreases in SD, with these being absent in synapses employing the nanodomain modality. In contrast, we found that as a result of depletion of SVs, short-term depression of IEPSC dominates in synapses using the nanodomain modality, and correlates with calcium-dependent increases in SD. These findings imply that the type of release modality has a significant impact on the strength and timing of synaptic responses. The microdomain modality imparts greater dynamic range in timing and strength, but does so at the cost of efficiency and fidelity, while the nanodomain modality is a key accomplishment consolidating the high-fidelity abilities of this synapse.

Keywords: Calyx of Held
MNTB
Synaptic Transmission
Calcium Channels
Development
Synaptic Plasticity
Synaptic Delay
Cooperativity
Release Modality
Vesicle Release
Advisor: Wang, Lu-Yang
Mechanisms of Presynaptic CaV2.2 (N-type) Modulation

Neurotransmitter release at presynaptic terminals is a complex process involving calcium ion influx through voltage-gated calcium channels (CaV). In addition to their role as entry points through which calcium influx may occur, CaV are now understood to be fundamental components of a common release-site complex that is highly adapted for modulation. Consistent with this model, I investigated mechanisms of modulating a presynaptic calcium channel, CaV2.2, via a heterotrimeric G-protein pathway. Using the patch-clamp technique, I demonstrated in chick dorsal root ganglion (DRG) neurons that the slow kinetics of G-protein inhibition of CaV2.2 via GTPgammaS were limited by the rate of GDP dissociation from the G-protein nucleotide binding site. In addition, I investigated the role of G-protein regulation of CaV2.2 currents evoked by action potential-like stimuli. Here, I characterized an inhibited current that was advanced in time with respect to uninhibited controls. These currents exhibited a shorter latency to current activation and faster deactivation. These findings may have important physiological ramifications on signal transduction and timing. In addition to G-protein regulation, presynaptic CaV2.2 have been demonstrated to exhibit a resistance to voltage-dependent inactivation (VDI), a property thought to be important in determining channel availability and synaptic excitability. I demonstrated a role for dynamic palmitoylation in conferring resistance to VDI in presynaptic terminals of the chick ciliary ganglion. Using tunicamycin, an inhibitor of palmitoylation, I induced a hyperpolarizing shift in the steady-state-inactivation (SSI) profile of presynaptic CaV2.2. Finally, I examined the role of a CaV interacting protein, Munc18, as a potential regulator of CaV. I probed for alterations in CaV2.2 function in DRG neurons that had been transfected with Munc18 or Munc18 siRNA. Despite the intimate interaction between Munc18 and CaV2.2, no major effects on the fundamental characteristics of CaV2.2 function were observed. However, a hyperpolarizing shift in the inactivation profile of CaV2.2 was determined in DRG neurons in which Munc18 was knocked down. It is not clear if this was a direct consequence of Munc18 perturbation.

Keywords: calcium channel
g-protein
voltage-clamp
DRG
presynaptic
CaV2.2
chick
patch-clamp
Munc18
modulation
ion channel
Advisor: Stanley, Elise F.
Development and Application of a Flow-through Sampler for Semi-volatile Organic Compounds in Air

The investigation of the atmospheric fate and transport of semi-volatile organic compounds (SOCs) often requires the sampling of large volumes of air (>100 m3) in a relatively short period of time. Conventionally high-volume pumps are not suitable for remote areas without access to reliable network power. We have developed a flow through sampler for such situations. It consists of a horizontally-oriented flow-tube, that can collect gaseous and particle-bound SOCs from large volumes of air by turning into the wind and having the wind blow through a porous sampling medium such as polyurethane foam. Through both indoor and outdoor experiments, we quantified its air sampling rate (through battery operated anemometers inside and outside of the flow tube), its sampling efficiency (by theoretical plate number analysis of the break-though curves for PCBs, PAHs, OCPs and PBDEs), and its accuracy (by comparison of concentrations, time trends, temperature dependences and isomer ratios with those obtained by conventional high-volume sampling) under conditions of constant and variable meteorological conditions (wind speed, temperature). The flow-through sampler was deployed to monitor SOC concentrations at a remote Chinese research station located close to Nam Co Lake, Tibet. During the campaign, fifteen 1 month-long samples were taken, corresponding to sample volumes between 5,000 and 20,000 m3. Despite those large sample volumes, only HCB and HCHs experienced break-through, but application of frontal chromatograph theory allows the estimation of breakthrough-corrected air concentrations even for those relatively volatile SOCs. The pesticide levels at Nam Co are generally very low. Most pesticides had higher levels during summer, resulting in a strong temperature dependence. This is correlated with air mass origin across the Himalayas in the Gangetic plains of India and Bangladesh. The flow through sampler constitutes a feasible method for reliably and quantitatively collecting SOCs from large air volumes.

Keywords: Flow-Through Sampler
semi-volatile organic compounds
frontal chromatographic theory
air sampling
Tibet
breakthrough behavior
Advisor: Wania, Frank
Organic Contaminant Release from Melting Snow

Snow efficiently scavenges organic contaminants from the atmosphere. Those chemicals can be released in short, concentrated pulses during spring snowmelt, potentially affecting both aquatic and terrestrial environments. In order to investigate the behavior of organic contaminants in melting snow laboratory experiments were conducted using artificial snow spiked with the organic target substances naphthalene, phenanthrene, pyrene, benzo(ghi)perylene, lindane, and atrazine. The behavior of those substances during melting is dependent on their partitioning between the different phases present within the bulk snow. Very water soluble organic chemicals, such as atrazine, are preferentially released at an early stage of melting similar to inorganic ions. This first chemical flush becomes more pronounced when a deep, aged, and relatively homogeneous snow pack is exposed to intense melting. Hydrophobic substances attached to particles, such as high molecular weight polycyclic aromatic hydrocarbons, are often released at the very end of the melt period. Dirt cones at the surface of a deep snow pack amplify this late chemical enrichment. Whereas chemicals that are clearly hydrophilic or hydrophobic are likely to be released in pulse loads, the snowmelt behavior of chemicals with intermediate partitioning properties, such as lindane, is more dependent on the varying snow pack and melt characteristics. A notable fraction of volatile chemicals may transfer from the melting snow pack to the lower atmosphere due to evaporation. Shallow snow covers in temperate regions with depths below 10cm that are exposed to recurrent melt phases during the winter are less likely to lead to pulse releases. When the melt water runs off as overland flow over frozen ground, pollutants are directly transferred into catchment streams, and their water quality is affected most. Melt water flow along the soil subsurface dilutes and buffers organic contaminant loads. The findings of this laboratory study may assist in the development of contaminant fate models that includes snowmelt processes. The results may further help to explain observations of organic contaminants in natural snow environments.

Keywords: organic contaminants
snow
Advisor: Wania, Frank