Deafness is the most common sensory deficit in humans, affecting 278 million people worldwide. Non-syndromic hearing loss (NSHL), hearing loss not associated with other symptoms, is the most common type of hearing loss and most NSHL in developed countries is due to a genetic cause. The inner ear is a remarkably complex organ, and as such, there are estimated to be hundreds of genes with mutations that can cause hearing loss. To date, 62 of these genes have been identified. This extreme genetic heterogeneity has made comprehensive genetic testing for deafness all but impossible due to low-throughput genetic testing methods that sequence a single gene at a time. The human genome project was completed in 2003. Soon after, genomic technologies, including massively parallel sequencing, were developed. MPS gives the ability to sequence millions or billions of DNA base-pairs of the genome simultaneously. The goal of my thesis work was to use these newly developed genomic technologies to create a comprehensive genetic testing platform for deafness and use this platform to answer key scientific questions about genetic deafness. This platform would need to be relatively inexpensive, highly sensitive, and accurate enough for clinical diagnostics. In order to accomplish this goal we first determined the best methods to use for this platform by comparing available methods for isolation of all exons of all genes implicated in deafness and massively parallel sequencers. We performed this pilot study on a limited number of patient samples, but were able to determine that solution-phase targeted genomic enrichment (TGE) and Illumina sequencing presented the best combination of sensitivity and cost. We decided to call this platform and diagnostic pipeline OtoSCOPE®. Also during this study we identified several weaknesses with the standard method for TGE that we sought to improve. The next aim was to focus on these weaknesses to develop an improved protocol for TGE that was highly reproducible and efficient. We developed a new protocol and tested the limits of sequencer capacity. These findings allowed us to translate OtoSCOPE® to the clinical setting and use it to perform comprehensive genetic testing on a large number of individuals in research studies. Finally, we used the OtoSCOPE® platform to answer crucial questions about genetic deafness that had remained unanswered due to the low-throughput genetic testing methods available previously. By screening 1,000 normal hearing individuals from 6 populations we determined the carrier frequency for non-DFNB1 recessive deafness-causing mutations to be 3.3%. Our findings will also help us to interpret variants uncovered during analysis of deafness genes in affected individuals. When we used OtoSCOPE® to screen 100 individuals with apparent genetic deafness, we were able to provide a genetic diagnosis in 45%, a large increase compared to previous gene-by-gene sequencing methods. Because it provides a pinpointed etiological diagnosis, genetic testing with a comprehensive platform like OtoSCOPE® could provide an attractive alternative to the newborn hearing screen. In addition, this research lays the groundwork for molecular therapies to restore or reverse hearing loss that are tailored to specific genes or genetic mutations. Therefore, a molecular diagnosis with a comprehensive platform like OtoSCOPE® is integral for those affected by hearing loss.

Twentieth century human settlement within the Tampa Bay watershed was linked to a dramatic mid-century decline in bay water quality and loss of seagrass acreage. Decades of direct and indirect nutrient discharges to the bay from phosphorus mining, fertilizer manufacturing, and wastewater treatment, as examples, impaired the estuary. In the past twenty years, regional stakeholders have worked to improve the bay water quality by reducing point and non-point source nutrient loading to the bay. Lakes within the Tampa Bay watershed may play an important role in attenuating the flow of nutrients into the bay. This study hypothesized that between 1990 and 2007 lake water concentrations of total phosphorus (TP) and chlorophyll-a, as well as the ratio of total nitrogen to total phosphorus (TN:TP), have changed for selected lakes in the Tampa Bay watershed. During this period, the watershed underwent a rapid shift in land use as groves and farms became shopping malls and new homes. A two-way analysis of variance (ANOVA) revealed that for 10 lakes clustered in the northern portion of the Tampa Bay watershed and classified as oligotrophic or mesotrophic, observed increases in water concentrations of TP and chlorophyll-a were statistically significant. For 6 lakes classified as hypereutrophic and scattered across the watershed, observed decreases in water TP concentrations were statistically significant, while chlorophyll-a concentrations did not change. For both groups of lakes, the TN:TP ratio declined significantly; however, oligotrophic and mesotrophic lakes were phosphorus-limited but hypereutrophic lakes were nitrogen-limited, based on this ratio. A second hypothesis of this study was that lake water concentrations of TP, total nitrogen (TN) and chlorophyll-a were lower in lakes that had more coverage of submerged aquatic vegetation, as vegetation suppresses re-suspension of sediments and is a reservoir for nitrogen and phosphorus and a surface for biofilms. The results of a one-way ANOVA showed that for 34 lakes within the Tampa Bay watershed, lakes with a greater than 20 percent volume infested by macrophytes (PVI), water concentrations of TP and chlorophyll-a but not TN were statistically lower than for lakes with a less than 20 PVI.

Ontologies provide an organization of language, in the form of a network or graph, which is amenable to computational analysis while remaining human-readable. Although they are used in a variety of disciplines, ontologies in the biomedical field, such as Gene Ontology, are of interest for their role in organizing terminology used to describe—among other concepts—the functions, locations, and processes of genes and gene-products. Due to the consistency and level of automation that ontologies provide for such annotations, methods for finding enriched biological terminology from a set of differentially identified genes in a tissue or cell sample have been developed to aid in the elucidation of disease pathology and unknown biochemical pathways. However, despite their immense utility, biomedical ontologies have significant limitations and caveats. One major issue is that gene annotation enrichment analyses often result in many redundant, individually enriched ontological terms that are highly specific and weakly justified by statistical significance. These large sets of weakly enriched terms are difficult to interpret without manually sorting into appropriate functional or descriptive categories. Also, relationships that organize the terminology within these ontologies do not contain descriptions of semantic scoping or scaling among terms. Therefore, there exists some ambiguity, which complicates the automation of categorizing terms to improve interpretability. We emphasize that existing methods enable the danger of producing incorrect mappings to categories as a result of these ambiguities, unless simplified and incomplete versions of these ontologies are used which omit problematic relations. Such ambiguities could have a significant impact on term categorization, as we have calculated upper boundary estimates of potential false categorizations as high as 121,579 for the misinterpretation of a single scoping relation, has_part, which accounts for approximately 18% of the total possible mappings between terms in the Gene Ontology. However, the omission of problematic relationships results in a significant loss of retrievable information. In the Gene Ontology, this accounts for a 6% reduction for the omission of a single relation. However, this percentage should increase drastically when considering all relations in an ontology. To address these issues, we have developed methods which categorize individual ontology terms into broad, biologically-related concepts to improve the interpretability and statistical significance of gene-annotation enrichment studies, meanwhile addressing the lack of semantic scoping and scaling descriptions among ontological relationships so that annotation enrichment analyses can be performed across a more complete representation of the ontological graph. We show that, when compared to similar term categorization methods, our method produces categorizations that match hand-curated ones with similar or better accuracy, while not requiring the user to compile lists of individual ontology term IDs. Furthermore, our handling of problematic relations produces a more complete representation of ontological information from a scoping perspective, and we demonstrate instances where medically-relevant terms--and by extension putative gene targets--are identified in our annotation enrichment results that would be otherwise missed when using traditional methods. Additionally, we observed a marginal, yet consistent improvement of statistical power in enrichment results when our methods were used, compared to traditional enrichment analyses that utilize ontological ancestors. Finally, using scalable and reproducible data workflow pipelines, we have applied our methods to several genomic, transcriptomic, and proteomic collaborative projects.

Particulate matter (PM) suspended in air varies in size from nanometers to micrometers and contains a wide range of chemical components, including organic compounds, black carbon (soot), inorganic minerals and metals. Atmospheric aerosols are generated from either primary sources like volcanic eruptions, re-suspended soil dust, sea spray, vegetative detritus, fossil fuel and biomass combustion emissions; or secondary atmospheric reactions via gas-to-particle conversion of atmospheric gases. Particle size, abundance, and chemical composition determine how a particle interacts with light and other atmospheric constituents (e.g. gases, water vapor) in addition to its impact on human health. While atmospheric scientists have been working on characterizing atmospheric aerosols for many years, major gaps persist in understanding the properties of many globally-important sources. This dissertation provides new understanding of the chemical composition of biomass burning and sea spray aerosols. PM emissions from biomass burning vary by fuel, and depend on fuel type and composition, moisture content, and combustion conditions. Although biomass smoke is critically important in global climate and local-regional health impacts, the physical and chemical composition of biomass burning aerosol is still not fully understood in the case of peat, agricultural residues and cooking fires. The Fire Laboratory at Missoula Experiments (FLAME) were designed to fulfill these gaps to improve our understanding in both historically undersampled and well-studied fuels while adding new instrumentation and experimental methods to provide previously unavailable information on chemical properties of biomass burning emissions. Globally-important biomass fuels were combusted in a controlled environment, and PM was chemically characterized to compute fuel based emission factors (EF) as the amount of chemical species released per unit mass of fuel burned. We showed that chemical composition of PM varies for different fuel types and certain fuels types (e.g., peat and ocote) emit considerably high concentrations of polycyclic aromatic compounds that are associated with negative health effects. We also showed that PM from biomass smoke contains fluoride for the first time, at approximately 0.1% by weight. With respect to the annual global emissions of PM due to biomass burning, this makes biomass burning an important source of fluoride to the atmosphere. Further, peatland fire emissions are one of the most understudied atmospheric aerosol sources but are a major source of greenhouse gases globally and cause severe air quality problems in Asia. This thesis provides the first field-based emissions characterization study, for samples collected at peat burning sites in Central Kalimantan, Indonesia. Using these EFs and estimates of the mass of fuel burned, it was estimated that 3.2 - 11 Tg of PM2.5 were emitted to atmosphere during 2015 El Niño peat fire episode which is ~10 % of estimated total annual PM flux for biomass burning. Overall, these studies computed more representative EFs for previously undersampled sources like peat, and previously unidentified chemical species like fluoride that can be used to update regional and global emission inventories. The concentration and composition of organic compounds in sea spray aerosol (SSA) alters its optical properties, hygroscopicity, cloud condensation, and ice nucleation properties and thus affects Earth’s radiative budget. In the past, SSA has been difficult to characterize, because of low concentrations relative to background pollutants. Nascent SSA was generated during a mesocosm, using a wave-flume at the University of California, San Diego and was characterized for saccharides and inorganic ions in order to assess their relative enrichment in fine (PM2.5) and coarse (PM10-2.5) SSA and sea surface microlayer (SSML) relative to seawater. For the first time, we showed that saccharides comprise a significant fraction of organic matter in fine and coarse SSA contributing 11 % and 27 %, respectively. Relative to sodium, saccharides were enriched 14-1314 times in fine SSA, 3-138 times in coarse SSA, but only up to 1.0-16.2 times in SSML. The saccharide and ion concentration in SSML and persistent whitecap foam was quantitatively assessed by another mesocosm study performed under controlled conditions. We demonstrated that relative to sodium, saccharides were enriched 1.7-6.4 times in SSML and 2.1-12 times in foam. Higher enrichment of saccharides in foam over the SSML indicates that surface active organic compounds become increasingly enriched on aged bubble film surfaces. Similarly, we showed that fine SSA contains saccharides characteristic of energy-related polysaccharides, while coarse SSA contains saccharides that are characteristic of structure-related polysaccharides. The ultrafiltration studies showed that structure-related polysaccharides effectively coagulate to form large particulate organic matter and size is likely the reason for their exclusion from small SSA. The enrichment of organic species in SSML, foam and SSA led to an enrichment of inorganic ions probably through chelation with organic molecules. Mean enrichment factors for major ions demonstrated the highest enrichment in fine SSA for potassium (1.3), magnesium (1.4), and calcium (1.7). Consequently, due to these organic and inorganic enrichments, SSA develops a significantly different chemical profile compared to seawater. These improved chemical profiles of SSA should be used to develop laboratory proxies to further study the transfer of organic matter across the ocean-air interface and the physical properties of SSA. . Overall, the results presented in this dissertation provide new chemical profiles for previously understudied emission sources like peatland fire emissions, and previously unquantified chemical species like F- in biomass burning emissions and enrichment of saccharides and ions in SSA. These data could be used in updating regional and global emission inventories, atmospheric modeling and human exposure studies.

The primary objective of this research was to develop a landscape-oriented, process-based approach that can enhance understanding and prediction of SOC fluxes in IMLs by incorporating the key mechanisms impacting soil carbon dynamics when moving from the soilscape to the landscape. The mechanisms that are considered to be the focus of this study are redistribution of SOC due to erosion and deposition without neglecting the importance of litter incorporation into the soil column, decomposition due to microbial activity, and physical and chemical stabilization of carbon. To accomplish this objective, field experiments were performed to examine how selective entrainment of different soil size fractions, quantified through the enrichment ratio (ER), varies with management and hillslope position. Differential modes in soil mobilization between rill and interrill areas were either elevated or dampened depending on the prevalent management practice, the gradient of the site and landscape position. Sites where sediment and runoff fluxes were highest were found to have lower ER values (around unity) due to the mobilization of all size classes making static and dynamic samples almost identical. The size fractions analyzed in these experiments were found to have varying levels of carbon associated with them, especially the larger aggregates, which encapsulate organic material. Neglecting them in transport estimates could lead to large errors in predicted fluxes of SOC. For this reason, a careful attention was placed on identifying how aggregate stability varies with respect to management and hillslope position, through controlled experiments looking size distributions to reflect tillage disturbance and aggregate stability to assess resistance to rainsplash. Lastly, a landscape-oriented modeling framework was developed that captures not only the SOC spatial heterogeneity in IMLs but also determines the impacts that redistribution has on this heterogeneity and ultimately on SOC dynamics. The integrative modeling framework considers the collective effects of both rainsplash/rainfall- and tillage-induced erosion on SOC redistribution in IMLs through an ER-module developed and woven within this framework to connect an upland erosion model with a soil biogeochemical model. It provides not only size fraction updates to the active layer and ER values, but also explicitly considers the effects of splash-driven interrill erosion on those ER estimates. The model was applied to twentieth-century changes in SOC across a representative agricultural hillslope in the study watershed and compared to recent SOC data. The chronosequence in SOC storage within the erosional zone revealed that soils were continually depleted of the rich organic matter long after the 1930’s “Dust bowl” due to enhanced erosion that accompanied agricultural practices. However, conservation tillage and enhanced crop production that began in the late 1980’s reversed the downward trend in SOC losses, causing nearly 26% of the lost SOC to be regained. Results from this study can be used to aid policy and decision makers in developing a food-system that accounts for the co-evolution of human and natural activity, to develop sustainable agro-ecosystems through the use of data supported recommended best management practices.

A series of model steels containing copper levels up to 0.48wt%, nickel up to 0.22wt% and silicon levels of 0.52wt% were oxidised in air at 1050 and 1150??C, and in a CO2-N2 mixture at 1250??C for times of up to 3 hours. The scaling kinetics were measured and the behaviour of copper-rich phase formation at the scale/metal interface was investigated. When oxidised at 1050/1150??C, significant quantities of copper-rich phase were observed for most model steels. The relatively high oxidation rate under these conditions led to the rapid development of a copper-rich layer with little copper diffusing into the metal. However, when oxidised at 1250??C, the copper-rich phase did not form for a significant amount of time; and for some model steels, not at all. This was attributed to the considerably lower oxidation rate and the fact that more copper was found to have diffused into the metal. Alloying additions of nickel and silicon were found to be beneficial in reducing the amount of copper-rich phase measured at the scale/metal interface under the conditions investigated at 1150??C and 1250??C. This occurred because nickel and silicon addition promoted the occlusion of copper-rich phase into the scale. Copper enrichment during oxidation was modelled using a numerical description of the diffusion processes involved. Predictions of the time for commencement of copper-rich phase formation at 1250??C were in close agreement with observation. Agreement between predicted and observed copper-rich layer thickness was less successful under conditions where occlusion was significant, and the measured thickness varied non-uniformly with time. The cracking susceptibility of the model steels was examined using a hot compression test. Oxidation was performed in air at 1050, 1150 and 1250??C and most specimens were compressed at 1050??C. The amount of cracking was found to increase with the amount of copper-rich phase precipitated at the scale/metal interface during oxidation. In general, nickel addition reduced the amount of cracking at all temperatures; and under some conditions prevented cracking altogether. Silicon reduced or completely suppressed cracking when the subscale formed was liquid. The beneficial effects of nickel and silicon addition were attributed to their effect of promoting copper occlusion.

This project aims at investigating the effect of CO2 enrichment on the growth and gas exchange of C3, C3-C4 and C4 Panicum grasses. Potted plants were grown in soil under well watered conditions, in artificially lit environmentally controlled cabinets or naturally lit greenhouses at varying levels of CO2 enrichment. CO2 enrichment enhanced the dry weight of C3 and C4 Panicum species under optimal light and N supplies, but had no effect on the total leaf N or TNC concentrations. The high-CO2 induced photosynthetic reaction in the C3 species was accompanied by a reduced Rubisco concentration and was related to the conservation of the relative growth rate of the plant. Elevated CO2 had no effect on the photosynthetic capacity of the C4 species, but enhanced its CO2 assimilation rates under high light and N supplies. The effect of elevated CO2 on the leaf and stem anatomy reflected increased carbon supply at high CO2 in the C3 grass, and reduced transpiratory demand at high CO2 in C4 grasses. Consequently, it is clear that both C3 and C4 grasses are likely to be more productive under rising atmospheric CO2 concentrations. / Doctor of Philosophy (PhD)

This thesis examined whether it is possible to enhance core elements of the information processing system with specific forms of environmental stimulation. The first series of experiments demonstrated that a preweaning environmental enrichment procedure that provided 60 minutes of daily multisensory stimulation accelerated the development of long-term contextual memory and enhanced inhibitory processing in young rats. That is, whilst stimulated and non-stimulated rats exhibited long-term memory of a context at 26 days of age, only stimulated rats showed this ability at 18 days of age. In addition, stimulated rats showed a faster rate of extinction of long-term contextual memory at 21 days of age, which was taken as evidence of enhanced inhibitory learning (i.e., context ??? no US) in these rats. Subsequent experiments with adult rats demonstrated that a combination of preweaning multisensory stimulation and postweaning rearing in an enriched environment improved the (1) specificity of long-term contextual memory, (2) speed of contextual information processing, and (3) availability of attentional resources. More specifically, enriched-reared rats demonstrated superior ability to discriminate between two similar contexts in comparison to standard-reared rats. In addition, enriched-reared rats showed superior memory of a context when there was limited time available to form a memory of that context. This finding was taken to indicate that rats that receive environmental enrichment are able to process contextual information more rapidly. Finally, standard-, but not enriched-, reared rats showed less conditioning to a discrete stimulus when it was presented in combination with a stronger stimulus during training compared to when it was presented by itself. The finding that enriched-reared rats did not show this overshadowing effect suggests that these rats have greater availability of attentional resources to divide between two stimuli that are competing for attention. The experiments with rats were followed by two experiments with children that investigated the effects of a computerised cognitive training procedure on information-processing speed. These experiments demonstrated that 30-minutes per weekday of training in rapid decision-making for three to five weeks improved children???s performance on two tests of processing speed (i.e., a choice reaction time and odd-man-out task). In addition, the speeded training improved children???s ability to sustain their attention and inhibit impulsive responses on a continuous performance test (Test of Variables of Attention). The cognitive training procedure had no effect on children???s performance on a measure of fluid intelligence (Raven???s Standard Progressive Matrices). The results of the experiments reported in this thesis suggest that a number of fundamental cognitive processes can be modified by environmental conditions that place increasing demands on the information-processing system. A neurobiological model, focusing on myelin, axon diameter, and the glutamatergic, glucocorticoid, noradrenergic, and cholinergic systems, was proposed in order to explain the observed effects of environmental stimulation on cognition in children and rats. The rationale for attempting to enhance fundamental cognitive processes was that improving these processes should ultimately improve general intellectual functioning. With respect to this aim, the correlational data from the present experiments with children revealed promising trends towards greater improvements on the tests of fundamental cognitive processes in those children in the training group with slower processing speed at the start of the intervention. This finding suggests that cognitive training may be even more effective at enhancing processing speed and other fundamental cognitive processes in children with intellectual impairments???who reportedly have slower processing speed than normal children. However, the extent to which training-related improvements in fundamental cognitive processes generalise to improvements in general cognitive functioning is unclear. That is, there is insufficient evidence that processing speed and other fundamental cognitive processes are causally related to intelligence. It is therefore essential that future cognitive training research is mindful of related developments within the intelligence and information processing literature.

Doctor of Philosophy / Zoological gardens, or zoos, keep and display wild animals, mainly for the purposes of education, conservation and biological research. However, it is evident that a significant component of zoos is the vast number of people who visit them, since without the support of visitors, zoos would not be financially viable and would cease to exist. This research investigates the behaviours of these visitors and develops an understanding of their awareness relating to what they see and do while they are in the zoo, along with their motivations for visiting. The study focuses on two major metropolitan zoos in Australia: Adelaide (in South Australia) and Taronga (in Sydney, New South Wales). A brief historical account contextualises changes, raising awareness of the significance of visitors to the livelihood of zoos. More and more zoos are integrating into their management routines different programmes that relate to the care and welfare of the animals. Despite recent growth in scientific attention, which has focused on human-animal relationships, little research has been conducted relating to the human visitor in the zoo. To date, decisions made by administrators have been based upon assumptions of the visitors’ understanding of the work of zoos rather than on actual quantitative findings. This empirical research is significant in that it uses both quantitative and qualitative methods to appraise factual data and information. The data from unobtrusive tracking observations at different exhibits, combined with the results of questionnaire surveys, are used to explore and assess the perceptions of visitors. In developing a demographic profile of the people who visit zoos, this work considers the motivations and the frequency of visitors. Various factors that influence the viewing patterns of visitors are explored to assess the popularity of exhibits, and the perceptions of visitors relating to animals and enclosures are investigated, to assess the diverse levels of satisfaction. Case studies explore the perceptions and understandings of visitors towards the use of enrichment items, the use of signs and labels, and a hypothetical approach to the feeding of carnivores in zoos. The results are important in that they contribute essential knowledge that describes the perceptions of a wide range of people who visit zoos, along with their expectations, since it is crucial for these institutions to maintain their popularity with the public.

Over the past six years, a part-time withdrawal-from-mainstream-class enrichment program for gifted and talented children has been operating at the Holt Primary School in the Australian Capital Territory. In keeping with the neighbourhood school policy of the ACT Schools Authority, the program caters only for children within the school and has included those from grades three to six. Based on Renzulli's Enrichment Triad Model, the program has a thematic approach which provides opportunities for participants to pursue both group and individual research on topics of interest to them. Identified children remain in the program for as long as possible and some have continued for as long as three years when resources have been available. This Action Research Study by the Co-ordinator of the program describes the setting up, objectives, identification methods, resources and evaluation.