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Synthetic marine habitats such as artificial reefs (ARs) are deployed to offset marine habitat losses and aid conservation of marine communities, including species at risk. Though environmental benefit is often assumed, AR’s ability to support northern temperate marine fish communities has rarely been tested. The structural orientation and location of a reef can strongly influence biodiversity and productivity of faunal communities inhabiting it. For ARs, understanding how reef characteristics affect species and community composition are key in optimizing their use in conservation initiatives. I used ROV and sonar to survey threatened rockfish (Sebastes spp.) and other groundfish species associated with 18 ARs and natural reefs (NRs) along the northeast Pacific coastal shelf, along the coast of BC, Canada. In my second chapter, I investigate how ARs compare to NRs in achieving conservation objectives as measured by fish abundance and species richness. I found that community composition significantly differed between NRs and ARs. ARs had high variability in rockfish abundance, while NRs consistently supported intermediate rockfish abundances. Groundfish diversity was markedly greater on NRs. Depth and relief significantly explained variability in abundance and species richness. Interestingly, rockfish abundance was negatively associated with proximity to nearest rockfish conservation area. In my third chapter, I assess variation between AR fish communities on six reefs to better understand efficacy of meeting conservation objectives. I quantified structural characteristics of each reef using high-definition sonar data to create three-dimensional models and calculate measurements of reef structure. I also examined the effects of surrounding habitat associated with reef locations. I found that depth, conservation status, rugosity, and reef age significantly explained rockfish abundance. Groundfish species richness was significantly associated with conservation status, relief, reef size, and an interaction between depth and reef age. This research is a first step in proposing underlying mechanisms for differences between fish communities on ARs in BC, and which reef attributes facilitate successful contributions to conservation. Though ARs show promise in the conservation of some threatened species, the maintenance of diverse fish communities may depend on protection of heterogeneous natural reef communities. Given that a critical component of AR success is structure, using three-dimensional technologies can be used as a tool to understand species-habitat association on existing reefs and help predict the success of future reefs. / Graduate

Changes in the productivity of temperate forests have important implications for atmospheric carbon dioxide (CO2) concentrations, and many efforts have focused on methods to monitor both gross and net primary productivity in temperate forests. Remotely sensed vegetation indices provide spatially extensive measures of vegetation activity, and the Enhanced Vegetation Index (EVI) has been widely linked to photosynthetic activity of vegetation. Networks of tree ring width (TRW) chronologies provide ground-based estimates of annual net carbon (C) uptake in forests, and time series of EVI and TRW may capture common productivity signals. Robust correlations between mean TRW and EVI may enhance spatial extrapolations of TRW-based productivity estimates, ultimately improving understanding of spatio-temporal variability in forest productivity. The research presented in this thesis investigates potential empirical relationships between networks of TRW chronologies and time series of Landsat EVI and Landsat-based phenological metrics in the Northeast United States. We hypothesized that mean TRW is positively correlated with mean monthly EVI during the growing season, EVI integrated over the growing season, and growing season length. Results indicate that correlations between TRW and EVI are largely not significant in this region. The complex response of tree growth to a variety of limiting climatic factors in temperate forests may decouple measures of TRW growth and canopy reflectance. However, results also indicate that there may be important lag effects in which EVI affects mean TRW during the following year. These findings may improve understanding of links between C uptake and growth of tree stems over large spatial scales.

This thesis examines the hypothesis that, in southern New South Wales and northeast Victoria, Australia, palatable taxa of E. curvula offer advantages that complement those of the species that are traditionally sown in temperate pastures in a landscape context.This hypothesis was based on a review of literature showing that, prior to European settlement, the vegetation, the landscape and the climate were broadly in balance, and the wateruse pattern of the vegetation of southeastern Australia resulted in water being used more-or-less completely by the end of summer. This maximised the capacity of the soil to take up and store water during autumn and winter.Three grazing experiments and one spaced-plant species evaluation study were used to assess the role of summer-growing, C4 Eragrostis curvula in pastures in the temperate zone of southeastern Australia.Issues relating to pasture production and the productivity of wool-growing sheep were investigated. Factors affecting the sustainability of the pastures and their potential on and off site impacts were emphasised.Modelling was used to explore issues of water use, arising from the grazing experiments. It is concluded that the persistence, production, water use patterns, and the adaptability of palatable varieties of E. curvula make it a useful and complementary addition to the range of species that are currently available for use as sown pastures in southern Australia. / Doctor of Philosophy (PhD)

<p>Recent changes in the timing of annual events are a sign that climate change is already impacting ecosystems. Carbon sequestration by forests increases with longer growing seasons. Biodiversity can be affected by mis-timing of events through shading interactions and frost damage. Projecting forests' ability to provide these ecosystem services in the future requires an understanding of trees' phenological responses to a new climate. I begin by proposing a first order definition of an `optimal' phenological response to warming: that the mean temperature following budburst should remain essentially constant. Analogously, the temperature preceding senescence can serve the same role. </p><p>To understand which environmental cues will drive future changes in phenology, I assimilate clues from observational and experimental literature. For budburst in woody plants, spring warmth, over-winter chilling and light drive nearly all behavior, but species' responses vary widely. Species using chilling or light as safety mechanisms against budburst during mid-winter thaws are thought to be less able to phenologically track a warming climate. However, I show that even species cued solely by spring warmth are likely to under-track temperature changes. Fall cues are more idiosyncratic, and a plant's driver of senescence is likely to vary from year to year. </p><p>Models are a tempting method to untangle species budburst cues and forecast phenology under warmer climate scenarios. I tested two models' ability to recover parameters used to simulate budburst data. The simpler model was cued only by spring warmth while the complex one modulated warmth requirements with chilling exposure. For the simple model, parameters could be recovered consistently from some, but not all, regions of parameter space. The complex model's parameters were largely unrecoverable. To understand the consequences of parameter uncertainty, I applied both models to an 18 year phenological record of 13 deciduous tree species. While a few species fell into identifiable regions of the simple model's parameter space, most did not, and projected budburst dates had wide parameter-derived uncertainty intervals. These bands were wider still under a 5°C warming scenario. Even greater uncertainty resulted from the complex model.</p><p>To better understand plants' potential for growing season extension I subjected seedlings to warmer climates in a series of open-topped chambers in sites at each end of the eastern deciduous biome. Soil and air were heated to 3 or 5°C above ambient, or left unheated. For nearly all species, warming hastened budburst and germination and delayed senescence. However, these events failed to track temperature changes, happening at warmer temperatures in hotter chambers. Individual species showed a remarkable variability of all events' dates within treatments, and even within chambers. Because phenological traits are heritable, this offers a potential for evolutionary response to climate change.</p><p>This research has shown that while individual trees extend their growing seasons under warmer temperatures, they typically under-respond to the magnitude of warming, suggesting forests' capacity for increased carbon sequestration may reach a limit. However, within populations, trees vary substantially in their phenological responses, forming a possibility for evolutionarily adaptation to changing cues.</p> / Dissertation

Methane fluxes were calculated from measurements carried out at a temperate upland forest in Central Ontario using the eddy covariance method over five months in the summer and fall seasons of 2011. Measurements were made by an off-axis integrated cavity output spectrometer Fast Greenhouse Gas Analyzer (FGGA) which simultaneously measured methane (CH4), carbon dioxide (CO2), and water at 10 Hz sampling rates. Observed methane fluxes showed net uptake of methane over the measurement period with an average uptake flux value (±standard deviation of the mean) of -2.7±0.13 nmol m-2 s-1. Methane fluxes showed a diurnal pattern of increased uptake during the day and increasing uptake with seasonal progression. There was also a significant correlation in methane fluxes with soil water content and wind speed. Comparison of the FGGA measurements to those using a static chamber method and canister sampling showed close agreement in flux and mixing ratio values respectively.

Methane fluxes were calculated from measurements carried out at a temperate upland forest in Central Ontario using the eddy covariance method over five months in the summer and fall seasons of 2011. Measurements were made by an off-axis integrated cavity output spectrometer Fast Greenhouse Gas Analyzer (FGGA) which simultaneously measured methane (CH4), carbon dioxide (CO2), and water at 10 Hz sampling rates. Observed methane fluxes showed net uptake of methane over the measurement period with an average uptake flux value (±standard deviation of the mean) of -2.7±0.13 nmol m-2 s-1. Methane fluxes showed a diurnal pattern of increased uptake during the day and increasing uptake with seasonal progression. There was also a significant correlation in methane fluxes with soil water content and wind speed. Comparison of the FGGA measurements to those using a static chamber method and canister sampling showed close agreement in flux and mixing ratio values respectively.

Bacteriophage Lambda (λ) has played a historical role as an essential model contributing to our current understanding of molecular genetics. Lambda’s major capsid protein “gpD” occurs on each capsid at 405 to 420 copies per phage in homotrimeric form and functions to stabilize the head and likely to compact the genomic DNA. The interesting conformation of this protein allows for its exploitation through the genetic fusion of peptides or proteins to either the amino or carboxy terminal end of gpD, while retaining phage assembly functionality and viability. The lytic nature of λ and the conformation of gpD in capsid assembly makes this display system superior to other display options. Despite previous reports of λ as a phage display candidate, decorative control of the phage remains an elusive concept. The primary goal of this study was to design and construct a highly controllable head decoration system governed by two genetic conditional regulation systems; plasmid-mediated temperature sensitive repressor expression and bacterial conditional amber mutation suppression. The historical λ Dam15 conditional allele results in a truncated gpD fragment when translated in nonsuppressor, wild-type E. coli cells, resulting in unassembled, nonviable progeny. I sequenced the Dam15 allele, identifying an amber (UAG) translational stop at the 68th codon. Employing this mutant in combination with a newly created isogenic cellular background utilizing the amber suppressors SupD (Serine), SupE (Glutamine), SupF (Tyrosine) and Sup— (wild type), we sought to control the level of incorporation of undecorated gpD products. As a second dimension, I constructed two separate temperature-inducile plasmids whereby expression of either D or D::eGFP was governed by the λ strong λ CI[Ts]857 temperature-sensitive repressor and expressed from the λ PL strong promoter. Our aim was to measure the decoration of the λ capsid by a D::gfp fusion under varying conditions regulated by both temperature and presence of suppression. This was achieved utilizing this controllable system, enabling the measurement of a variable number of fusions per phage based on diverse genetic and physical environments without significantly compromising phage viability. Surprisingly, both SupE and SupF showed similar levels of Dam15 suppression, even though sequencing data indicated that only SupE could restore the native gpD sequence at amino acid 68 (Q). In contrast, SupD (S), conferred very weak levels of suppression, but imparted an environment for very high decoration of gpD::eGFP per capsid, even at lower (repressed) temperatures. The presence of albeit few wild-type gpD molecules allowed for an even greater display than that of the perceived “100%” decoration scenario provided by the nonsuppressor strain. It appears that the lack of wild-type gpD does not allow for the space required to display the maximum number of fusions and in turn creates an environment that affects both phage assembly and therefore phage viability. Finally, the use of Western blotting, confirmed the presence of gpD::eGFP fusion decoration by employing a polyclonal anti-eGFP antibody. The significance of this work relates to the unique structure of λ’s capsid and its ability to exploit gpD in the design of controlled expression, which is guiding future research examining the fusion of different therapeutic peptides and proteins. Furthermore this approach has important implications specifically for the design of novel vaccines and delivery vehicles for targeted gene therapy in which steric hindrance and avidity are important concerns. The execution of this project employed basic bacterial genetics, phage biology and molecular biology techniques in the construction of bacterial strains and plasmids and the characterization of the phage display system.

Speleothems are considered a reliable proxy for paleoclimatic reconstructions and analysis of stable carbon isotopes in speleothems is used for paleoclimatic reconstructions. However, in temperate areas that lacks C4 vegetation there are uncertainties in how to interpret changes in the δ13C signal. The aim of this study is toincrease the understanding of how the δ13C signal in speleothems from temperateareas can be interpreted. The study was divided in two parts, first a literature studythat focused on interpretations of the δ13C signal in speleothems from temperate areasand a case study in which a comparison of seven 13C records from similarenvironments in the Scandes Mountains and the Alps are made. The results from the literature study were used in the case study to draw conclusions on tree line and vegetation changes during Holocene in central northern Scandinavia. The study showed that trends in interpretation of the δ13C signal in speleothems from temperateareas are that low δ13C values are interpreted as wetter, warmer conditions with higherbio productivity, and high δ13C values are interpreted as colder, drier conditions withlower bio productivity. Further it was found in the study that vegetation changes seen in Holocene pollen data are also seen in δ13C records from Scandinavia. The δ13Csignal in temperate speleothems therefore appears to be related to changes invegetation density and to tree-line changes.

This thesis examined the effect of differences in body surface area-to-lean body mass ratio (AD/LBM) on core temperature cooling rates during cold water immersion (2°C, CWI) and temperate water immersion (26°C, TWI) following exercise-induced hyperthermia (end-exercise rectal temperature of 40°C). Individuals with a High AD/LBM (315 cm2/kg) had a ~1.7-fold greater overall rectal cooling rate relative to those with Low AD/LBM (275 cm2/kg) during both CWI and TWI. Further, overall rectal cooling rates during CWI were ~2.7-fold greater than during TWI for both the High and Low AD/LBM groups. Study findings show that AD/LBM must be considered when determining the duration of the immersion period. However, CWI provides the most effective cooling treatment for EHS patients irrespective of physical differences between individuals.