Hundreds of proteins have been detected in phloem and xylem sap, even though the cells involved in long distance phloem and xylem transport are incapable of protein synthesis at maturity. We are now beginning to learn the identity and function of these proteins, but this knowledge is generally limited to annual plants. The first objective of this study was to identify phloem and xylem sap proteins in the perennial, poplar. Using LC-MS/MS, 48 proteins were identified in poplar phloem exudate and 98 proteins were identified in xylem sap. A large number of phloem exudate proteins are insect defense proteins that include protease inhibitors and polyphenol oxidase and also members of the pop3/SPI gene family, whereas a number of xylem sap proteins were pathogenesis-related proteins such as thaumatin-like proteins (TLPs) and chitinases that function in pathogen defense. The importance of xylem sap proteins in pathogen defense has been previously demonstrated, however, the role of phloem proteins in insect defense is currently unknown. A major question to be addressed in order to understand the function of phloem proteins is if they are differentially regulated in response to insect herbivory. The second objective of this study was to identify poplar phloem proteins differentially regulated in response to simulated insect feeding. Using two-dimensional gel electrophoresis, two proteins, PtTLP1 and pop3.1, were consistently upregulated 24 hours post-wounding. The third objective of this study was to produce antibodies against these proteins to use to further characterize their expression and localization patterns. Antibodies were also produced against another phloem exudate protein, pop3.4, which is 40% similar to pop3.1. The origin of all three proteins inside sieve elements was confirmed with immunolocalization. PtTLP 1, pop3.1 and pop3.4 antisera labelled organelle-like structures in sieve elements and also phloem parenchyma cells. For PtTLP1, these structures were identified as starch and starch containing plastids. All three antisera also labelled cell wall proteins in different cell types. Overall, this study represents the first large-scale analysis of phloem and xylem sap proteomes from a perennial and describes the first observation of wound-inducible phloem sap proteins.

A large and extremely diverse number of insects harbour maternally transmitted bacterial symbionts. Some symbionts manipulate host reproduction in order to benefit their own fitness, and the most common of these reproductive manipulations is cytoplasmic incompatibility (CI). In CI, uninfected females produce few or no viable progeny when mated to infected males. The bacterial endosymbiont Cardinium causes CI in its host, Encarsia pergandiella (Hymenoptera: Aphelinidae). I used population cages with varying initial infection frequencies to test a model of CI invasion. Cardinium was found to spread rapidly in all populations, even in cases where the initial infection frequency was well below the predicted invasion threshold frequency. Male age can also be an important factor in CI dynamics. I tested the effect of male age on the level of incompatibility induced by Cardinium in E. pergandiella. Male age was found to have a negligible effect on CI strength.

Long isolation and the island environment of Madagascar has led to the evolution of a number of unusual traits in the Lemuriformes, including reproductive synchrony, sexual monomorphism, female dominance, and female feeding priority. Though gestation and lactation are costly in all mammals, the unpredictable and often harsh environment of Madagascar may have led to the selection of particular adaptive traits which offset some of the high costs of reproduction in female lemurs. Sex differences in feeding behavior between male and female Lemur catta, which have been documented previously may he a reflection of increased reproductive female nutritional need, although differences in actual nutritional intake has not been examined. In August and September of 2005 I collected 217 hours of focal feeding data on 9 male and 9 gestating female L. catta from two social groups. at the Beza Mahafaly Special Reserve in southwestern Madagascar. Additionally, I collected representative samples of all plant foods eaten by the focal animals. Since reproductive females have higher metabolic needs, I predicted that when compared to males, gestating females would consume more, feed for longer periods, and ingest higher relative amounts of crude protein and minerals. and lower relative amounts of fiber. Additionally, since the two focal social groups have similar and over-lapping home ranges, I predicted that no feeding differences (amount consumed. time spent feeding, ingestion of crude protein, minerals and fiber) would be present between social groups. I found no statistically significant differences in feeding behavior between males and females. while nutritional sex differences were limited to females consuming increased phosphorus (P= 0.004) and potassium (P=0.015 ). Furthermore, although I detected no between group differences nutrient consumption or amount of food consumption Green Group did spend significantly more time foraging, when compared to Red Group (P=0.004). These data may be explained by the prior activity of cyclone Ernest. which greatly reduced food availability and caused a fruiting failure of Tamarindus indica, a keystone resource of gallery forest L. catta. Additionally, although both focal groups ventured outside of the forest to forage on agricultural or introduced plant species. Green Group only fed on crop foods on one occasion. while Red Group fed daily on the easily processed crop foods, which may have decreased their foraging time. Ability to exploit novel resources and adapt to environmental extremes may be a key feature enabling L. catta to persist alongside humans in the harsh environment of Madagascar.

Optical confinement and manipulation of matter, or optical trapping, is widely adopted at micro-scales as a research tool in disciplines of biology, engineering, and physics. Microfluidic systems arc attractive from the standpoint of low sample volumes, laminar flow, and viscous damping and offer an ideal environment for trapping of miniaturized objects and microorganisms. Various trapping configurations are presented in this thesis using a custom fabricated consumer-grade optofluidic chip and are of significant scientific and practical importance. Microfluidics and fiber optics are integrated in-plane to achieve several flow-dependent particle trapping mechanisms on-chip. Each mechanism results from a combination of fluid drag and optical scattering forces. Parallel and offset fibers, orthogonally oriented to the flow, show cyclic cross-stream particle transit with flow-dependent particle trajectories and loss. Upstream-angled fibers with flow result in circulatory particle trajectories. Asymmetric angled fibers result in continuous particle circulation whereas symmetry with respect to the flow axis enables both stable trapping and circulation modes. Stable trapping of single particles, self-guided multi-particle arrays and stacked particle assemblies are demonstrated with a single upstream-oriented fiber. Size tuning of trapped multiple particle assemblies is also presented. The planar interaction of fluid drag and optical forces results in novel possibilities for cost-effective on-chip diagnostics, mixing, flow rate monitoring, and cell analysis. An opto-hydrodynamic theory is adopted to verify experimentally observed particle array dynamics in a dual-beam fiber-optic trap. When applied to dielectric microsphere particles, the theory confirms the inhomogeneous self-organization and the spontaneous emergence of self-sustained oscillations in particle arrays. In the presence of small-scale symmetry-breaking, self-sustained oscillations are shown to occur spontaneously from an exchange between the optical scattering and the gradient optical forces, in the absence of inertia that is central to the dynamics of ion traps. Experimental results show non-uniform equilibrium particle spacing and spontaneous self-sustained oscillation for large particle numbers. Self-organization and oscillation is of general interest to other systems involving multi-particle optical interactions.

Wireless systems that have traditionally been designed using a layered approach have seen a recent paradigm shift to a cross-layered approach where the interactions between two or more layers are considered explicitly in an integrated framework. This dissertation presents new methodologies that aim to improve the performance of wireless systems through consideration of cross-layer based design. The physical (PHY) and the medium access control (MAC) layers are the primary layers responsible for data transmission and user selection/control, respectively, in wireless systems. This dissertation begins with an analysis illustrating the use of multiple antennas and antenna arrays at. the PHY layer. A framework combining space-time block coding and beamforming for uplink in a wireless systems is con¬sidered for studying the trade-offs between antennas and antenna arrays at the receiver. Results indicate that in high noise environments the diversity achieved by using a large number of antennas combats bit error rate (BER) more efficiently than beamforming. On the other hand, in low noise environments beamforming plays an important role in reducing BER by minimizing the effect of interference from other co-channel users. Two approaches of cross-layer design that are currently available are the bottom-up and top-down approaches. The bottom-up approach uses the PHY laver infor¬mation at the MAC and higher layers to make decisions that affect the system performance. Following a bottom-up approach, a new scheduling algorithm is designed that uses the channel state information and direction of arrival information of mobile users to efficiently schedule users for service. Both semi-analytical (based on the probability density and cumulative distribution functions) and numerical frameworks are used to compare the performance of this algorithm with the traditional round-robin and greedy scheduling algorithms. Both the numerical and semi-analytical frameworks which are shown to be consistent with each other yield improved system capacity for the proposed algorithm compared to the traditional algorithms. This is the result of explicitly considering the angular location of mobile users around the base station that results into the reduced interference between simultaneously served users on one other. The effect of channel availability on the scheduling algorithms is also investigated within a queuing framework and the results indicated that the system performance is also dependent on channel availability and traffic conditions. A top-down approach is based on modifying the PHY layer to support the require¬ments or protocols used at the MAC layer to improve system throughput. Following a top-down approach, a new methodology is presented that reduces null depths of a given beam to address the hidden beam problem in IEEE 802.11 systems. The hidden beam problem occurs in carrier sensing multiple access (CSMA) systems when mobile users lying in deep nulls are unable to sense an ongoing downlink transmission and start transmitting data in an uplink. The modified beam with reduced null depths is compared with the original beam in terms of reducing the hidden beam problem when used in non-persistent CSMA systems. The modified beam is shown to improve the throughput of a slotted non-persistent CSMA system significantly when compared to original beam with relatively small changes to directivity and half power beamwidth. The bottom-up and top-down approaches used in this dissertation illustrate that by jointly addressing the PHY and MAC layer issues in an integrated cross-layer framework the performance of wireless systems can be significantly improved.

In this thesis, we study cluster analysis of time series and develop a new mixture model which is effective for such analysis. Our study is motivated by a real life problem of clustering time series of electricity load (demand) for BC Hydro customers. BC Hydro collects electricity load data for selected customers for the purpose of grouping customers into homogeneous classes in terms of the load. Such homogeneous classes or clusters are useful for rate setting and long term generation capacity planning. The BC Hydro data set that we use in this thesis contains 923 load series representing 923 BC Hydro customers. Each load series consists of repeated hourly load measurements over a one year period and thus is a long time series. There are a number of clustering methods in the literature for clustering general multivariate data but these are not effective for clustering such long time series. This is because time series such as the BC Hydro customer’s load series typically have high dimensions and special covariance structures. Existing clustering methods are not designed to accommodate these special characteristics. The contributions of this thesis are the following: We first develop a mixture model based clustering method for time series which cannot only handle their high dimensions but also makes effective use of their special covariance structures. Our method is based on the random effects mixture model, a mixture model which we develop specifically for time series. We devise a special EM algorithm based on the AECM algorithm of Meng and van Dyk (1997) to handle the computation of the random effects mixture model. Once the model is computed, we assign individual time series to clusters by their posterior probabilities of belonging to the components of the mixture model. Then to demonstrate the application of our method, we apply it to analyse BC Hydro data. We obtain a new clustering of the BC Hydro sample which is superior to the existing clustering in terms of relevance and interpretability.

Lithodid crabs present intriguing questions about evolution of reproductive strategies and developmental evolution of asymmetry. Lopholithodes foraminatus (Decapoda: Anomura: Paguroidea) from British Columbia have a biennial reproductive cycle. Eighteen months of egg-brooding included an embryonic diapause of 12 months. Larvae were released over a long period of up to 3 months due to pronounced differential developmental rate that was apparently not due to differential oxygen availability among brooded eggs. I describe the behaviour, growth, and morphology of 4 zoeal stages, a non-feeding glaucothoe, and early juvenile instars. Approximately 25% of glaucothoe showed reversed asymmetry, which was surprising considering its rarity among field collected adults. Incidence of reversed asymmetry was not affected by rearing temperature or by cheliped removal and did not differ among offspring of reversed and normal females. Lability in the direction of asymmetry during development is enigmatic in light of long-term evolutionary stability of this character among lithodids.

A comparison of disinfection by-product (DBP) results for 12 surface source waters on Vancouver Island, British Columbia determined that there was a distinct spatial difference in DBP production based on biogeoclimatic ecoregions. The main factors affecting the DBP production between ecoregions was source water quality, water body type (stream versus lake) and treatment strategy. Typically water bodies within an ecoregion exhibit similar water quality and produce similar DBPs. Differences in DBPs between water body types were attributed to the source of natural organic matter (NOM), allochthonous or autochthonous origin, and seasonal variability. Additional source water quality parameters such as pH, chlorophyll a, total phosphorus, water temperature and bromide concentrations support the spatial differences observed in DBP production between ecoregions. These results suggest that source water quality and water body type could be used as a preliminary tool to predict the amount of DBPs a community within a specific ecoregion may be exposed to. A review of a long-term data set determined that changes in treatment strategy significantly affected the DBPs produced. The most distinct changes in DBP production were associated with booster station treatment processes in terms of annual versus seasonal re-chlorination and the decommissioning of a booster station. Sooke reservoir water quality, following an inundation project, changed significantly with respect to water temperature and NOM. The increase in TOC levels did not result in any changes to DBP production, however cooler water temperatures reduced the potential for losses of chlorine residual and for the re-growth of bacteria. The results of this research suggest that the management and protection of drinking water sources, along with treatment strategies, is the most promising way to ensure minimal risk to human health.

In this dissertation I present a detailed survey of molecular line emission (including NH3, C2S, HC5N, N2H+, N2D+ and H2D+) towards clustered star forming Cores in the nearby Ophiuchus molecular cloud, with the aim of characterizing the distribution and kinematics of the dense gas within a clustered star forming environment and compare these results with those found in more isolated star forming regions. I show that the dense Oph Cores present characteristics of both isolated and clustered star forming regions in several key parameters, including Core kinematics, temperatures and chemistry. At the higher gas densities where the N2H+ emission is excited, I show that the presence of an embedded protostar is correlated with increased gas motions. I additionally present evidence of N2H+ depletion from the gas phase, suggesting that in higher density, clustered environments N2H+ may not accurately trace the physical conditions of the densest core gas. I present the distribution of H2D+ and N2D+ across the Oph B Core, and show the distribution is not simple or easily explained by chemical models of evolving, isolated cores. Finally, I summarize the results of this dissertation, the questions it raises concerning the exploration of how stars form in clusters, and discuss how these questions may be answered through upcoming observational surveys and by new telescope facilities.

Natural communities are structured by a complex of direct and indirect species interactions. It is well recognized theoretically that if these interactions are weak, the entire community is more likely to persist. Several mechanisms can weaken a predator-prey interaction. I studied interference among conspecific predators and heterogeneity at the prey level. Incorporating these mechanisms into realistic functional responses is required for accurate model predictions at the community level. However, controversy remains on which dependencies need to be included. Using laboratory microcosms, I was able to demonstrate moderate predator-dependence in my model system. This effect was present even at low predator densities and after accounting for prey depletion. In separate experiments, I experimentally compared the functional responses of a gape-limited predator feeding on its prey in the absence or presence of species outside the predator's diet (non-prey). I demonstrated that both density and diversity of non-prey species can also substantially reduce the strength of predator-prey interactions. I further tested this non-prey effect on a long time-scale, where I compared the population dynamics of predator and prey alone to the dynamics of predator and prey when a non-prey species was present. Prey and predators had both gone extinct at the end of the experiment for all replicates containing only predator and prey. However, in the treatment that included non-prey, all species persisted in 4 out of the 5 replicates until the last day of the experiment. Prey species also spent significantly more time above the detection limit in the treatment with non-prey. In addition, I studied how inducible anti-predator defenses affect an aquatic food web with intraguild predation. I detected substantial clonal variation in the expression of a morphological inducible defense and the long-term experiment showed that the intraguild prey with greater ability to increase their body width as a response to predation also have longer persistence times. These results show that predator interference and prey heterogeneity may be important factors that increase persistence of predator and prey as predicted by theory. Their incorporation into simple food web models can improve our ability to reliably predict community dynamics.