Flexible link manipulators (FLM) are well-known for their light mass and small energy consumption compared to rigid link manipulators (RLM). These advantages of FLM are even of greater importance in applications where energy efficiency is crucial, such as in space applications. However, RLM are still preferred over FLM for industrial applications. This is due to the fact that the reliability and predictability of the performance of FLM are not yet as good as those of RLM. The major cause for these drawbacks is link flexibility, which not only makes the dynamic modeling of FLM very challenging, but also turns its end-effector trajectory tracking (EETT) into a complicated control problem. <p>The major objectives of the research undertaken in this project were to develop a dynamic model for a FLM and model-based controllers for the EETT. Therefore, the dynamic model of FLM was first derived. This dynamic model was then used to develop the EETT controllers. <p>A dynamic model of a FLM was derived by means of a novel method using the dynamic model of a single flexible link manipulator on a moving base (SFLMB). The computational efficiency of this method is among its novelties. To obtain the dynamic model, the Lagrange method was adopted. Derivation of the kinetic energy and the calculation of the corresponding derivatives, which are required in the Lagrange method, are complex for the FLM. The new method introduced in this thesis alleviated these complexities by calculating the kinetic energy and the required derivatives only for a SFLMB, which were much simpler than those of the FLM. To verify the derived dynamic model the simulation results for a two-link manipulator, with both links being flexible, were compared with those of full nonlinear finite element analysis. These comparisons showed sound agreement. <p>A new controller for EETT of FLM, which used the singularly perturbed form of the dynamic model and the integral manifold concept, was developed. By using the integral manifold concept the links lateral deflections were approximately represented in terms of the rotations of the links and input torques. Therefore the end-effector displacement, which was composed of the rotations of the links and links lateral deflections, was expressed in terms of the rotations of the links and input torques. The input torques were then selected to reduce the EETT error. The originalities of this controller, which was based on the singularly perturbed form of the dynamic model of FLM, are: (1) it is easy and computationally efficient to implement, and (2) it does not require the time derivative of links lateral deflections, which are impractical to measure. The ease and computational efficiency of the new controller were due to the use of the several properties of the dynamic model of the FLM. This controller was first employed for the EETT of a single flexible link manipulator (SFLM) with a linear model. The novel controller was then extended for the EETT of a class of flexible link manipulators, which were composed of a chain of rigid links with only a flexible end-link (CRFE). Finally it was used for the EETT of a FLM with all links being flexible. The simulation results showed the effectiveness of the new controller. These simulations were conducted on a SFLM, a CRFE (with the first link being rigid and second link being flexible) and finally a two-link manipulator, with both links being flexible. Moreover, the feasibility of the new controller proposed in this thesis was verified by experimental studies carried out using the equipment available in the newly established Robotic Laboratory at the University of Saskatchewan. The experimental verifications were performed on a SFLM and a two-link manipulator, with first link being rigid and second link being flexible.<p>Another new controller was also introduced in this thesis for the EETT of single flexible link manipulators with the linear dynamic model. This controller combined the feedforward torque, which was required to move the end-effector along the desired path, with a feedback controller. The novelty of this EETT controller was in developing a new method for the derivation of the feedforward torque. The feedforward torque was obtained by redefining the desired end-effector trajectory. For the end-effector trajectory redefinition, the summation of the stable exponential functions was used. Simulation studies showed the effectiveness of this new controller. Its feasibility was also proven by experimental verification carried out in the Robotic Laboratory at the University of Saskatchewan.

Flexible link manipulators (FLM) are well-known for their light mass and small energy consumption compared to rigid link manipulators (RLM). These advantages of FLM are even of greater importance in applications where energy efficiency is crucial, such as in space applications. However, RLM are still preferred over FLM for industrial applications. This is due to the fact that the reliability and predictability of the performance of FLM are not yet as good as those of RLM. The major cause for these drawbacks is link flexibility, which not only makes the dynamic modeling of FLM very challenging, but also turns its end-effector trajectory tracking (EETT) into a complicated control problem. <p>The major objectives of the research undertaken in this project were to develop a dynamic model for a FLM and model-based controllers for the EETT. Therefore, the dynamic model of FLM was first derived. This dynamic model was then used to develop the EETT controllers. <p>A dynamic model of a FLM was derived by means of a novel method using the dynamic model of a single flexible link manipulator on a moving base (SFLMB). The computational efficiency of this method is among its novelties. To obtain the dynamic model, the Lagrange method was adopted. Derivation of the kinetic energy and the calculation of the corresponding derivatives, which are required in the Lagrange method, are complex for the FLM. The new method introduced in this thesis alleviated these complexities by calculating the kinetic energy and the required derivatives only for a SFLMB, which were much simpler than those of the FLM. To verify the derived dynamic model the simulation results for a two-link manipulator, with both links being flexible, were compared with those of full nonlinear finite element analysis. These comparisons showed sound agreement. <p>A new controller for EETT of FLM, which used the singularly perturbed form of the dynamic model and the integral manifold concept, was developed. By using the integral manifold concept the links lateral deflections were approximately represented in terms of the rotations of the links and input torques. Therefore the end-effector displacement, which was composed of the rotations of the links and links lateral deflections, was expressed in terms of the rotations of the links and input torques. The input torques were then selected to reduce the EETT error. The originalities of this controller, which was based on the singularly perturbed form of the dynamic model of FLM, are: (1) it is easy and computationally efficient to implement, and (2) it does not require the time derivative of links lateral deflections, which are impractical to measure. The ease and computational efficiency of the new controller were due to the use of the several properties of the dynamic model of the FLM. This controller was first employed for the EETT of a single flexible link manipulator (SFLM) with a linear model. The novel controller was then extended for the EETT of a class of flexible link manipulators, which were composed of a chain of rigid links with only a flexible end-link (CRFE). Finally it was used for the EETT of a FLM with all links being flexible. The simulation results showed the effectiveness of the new controller. These simulations were conducted on a SFLM, a CRFE (with the first link being rigid and second link being flexible) and finally a two-link manipulator, with both links being flexible. Moreover, the feasibility of the new controller proposed in this thesis was verified by experimental studies carried out using the equipment available in the newly established Robotic Laboratory at the University of Saskatchewan. The experimental verifications were performed on a SFLM and a two-link manipulator, with first link being rigid and second link being flexible.<p>Another new controller was also introduced in this thesis for the EETT of single flexible link manipulators with the linear dynamic model. This controller combined the feedforward torque, which was required to move the end-effector along the desired path, with a feedback controller. The novelty of this EETT controller was in developing a new method for the derivation of the feedforward torque. The feedforward torque was obtained by redefining the desired end-effector trajectory. For the end-effector trajectory redefinition, the summation of the stable exponential functions was used. Simulation studies showed the effectiveness of this new controller. Its feasibility was also proven by experimental verification carried out in the Robotic Laboratory at the University of Saskatchewan.

No description available.

Fusarium graminearum is a major fungal pathogen of wheat and other small grain cereal crops globally, causing Fusarium ear blight (FEB) disease. Like many other plant pathogens, F. graminearum is predicted to produce in planta secreted effector proteins that modulate plant metabolism to suppress or re-programme plant defences. Understanding the molecular functions of Fg effectors will help to elucidate the processes underlying wheat spike colonisation and fungal pathogenicity. With the aim of identifying Fg effector proteins that can suppress host plant defences, I selected using next generation sequencing and bioinformatic analysis, a set of small secreted proteins (SSP) to express in planta using the Barley stripe mosaic virus over-expression system (BSMV-VOX). I then tested whether expression of any of these SSPs enhanced Fg fungal infection of susceptible wheat spikes. Amongst the set of Fg SSP tested, FgSSP8, which encodes a ribonuclease protein, induced strong symptoms of necrosis in N. benthamiana leaves when infiltrated via the BSMV:FgSSP8. Three other genes tested (FgSSP7, FgSSP6 and FgSSP5) enhance FEB disease formation in the majority of the experiments when overexpressed in wheat ears prior to infecting with F. graminearum. FgSSP6 and FgSSP7 belong to the cerato-platanin protein (CPP) family. In several other plant pathogenic fungi, CPPs have been implicated in a number of virulence and plant protection mechanisms, including induction of host plant cell death, binding specific polymers and/or expansin-like activity. FgSSP5 encodes a protein that possesses the pfam domain RALF (Rapid alkalinization factor; PF05498.6). RALF domain-containing proteins are predominately found in plants and play a role in plant development regulating tissue expansion and/or negatively regulating pollen tube elongation. BLAST analyses identified RALF domain containing proteins in a restricted range of different pathogen species. Based on the VOX results and biochemical tests, our hypothesis is that pre-elevated cerato-platanins (FgSSP6 and FgSSP7) levels in the apoplast/surrounding the hyphae could initially shield the hyphae from detection by the plant, but late induce an intense defence response culminating in cell death to benefit the necrotrophic phase of Fg by increasing nutrient availability. FgSSP5 may be a specific virulence factor that manipulates a key plant process, by alkalinising the plant environment during infection, and using the same plant receptor repertoire used to recognise plant proteins. Once the mechanisms are further understood, these genes/proteins could potentially be novel intervention targets either for conventional chemistries and/or for methods such as host-induced gene silencing to achieve FEB disease and/or mycotoxin control. The characterisation of single and double gene deletion F. graminearum mutants is in progress.

Among sheep producers, the parasitic nematode Haemonchus contortus is a major animal health concern. Caribbean hair sheep are more resistant than conventional wool breeds to this blood-feeding, abomasal parasite. Our objective was to determine differences in the immune response associated with parasite-resistant hair and susceptible wool lambs infected with 10,000 H. contortus and in uninfected controls. Animals were sacrificed and abomasum and lymph node tissues were collected at 3 or 27 days post-infection (PI), and for controls on day 17, 27, or 38 relative to d 0 of infected animals. Blood and fecal samples were collected throughout the study. Lower fecal egg counts, higher packed cell volumes, and heavier lymph nodes of infected hair compared to wool lambs, suggests hair lambs have increased parasite resistance. Greater tissue infiltration of eosinophils (P < 0.05) was observed in hair compared to wool sheep by 3 days PI, with no breed differences in globule leukocytes. Total serum IgA and IgE were greater in control hair versus wool sheep (P < 0.05). After 3, 5, and 21 of infection, total serum IgA (P< 0.05), total lymph node IgE (P < 0.01), but not total serum IgE were greater in hair sheep compared to wool sheep. Gene expression was measured between hair and wool lambs for abomasal and lymph node tissues using bovine cDNA microarrays and real-time RT-PCR. Microarray analysis revealed cell survival, endosome function, gut motility, and anti-coagulation pathways are important in abomasal and lymph node tissues during H. contortus infection. Immune genes, including IL-4, IL-4 Ra, IL-12 Rb1, and IL-12 Rb2, are also highly represented in abomasal or lymph node tissue of infected animals. Eleven genes were evaluated using real-time RT-PCR and included TH1 and TH2 cytokines, cytokine receptors, and IgE. Parasite infection leads to increased expression of IL-13 and IgE in both tissues and breeds when compared to control animals. Breed comparison of gene expression shows resistant hair sheep produce a stronger modified TH2-type immune response during infection. Differential cell infiltration, antibody production, and regulation of TH2 cytokines between breeds may be partially responsible for differences in parasite resistance. / Ph. D.

Diverse pathogens secrete effector proteins into plant cells to manipulate host cellular processes. The genome of Hyaloperonospora arabidopsidis (Hpa), the causative agent of downy mildew of Arabidopsis, contains at least 134 candidate RXLR effector genes. These genes contain an RXLR motif required for effector entry into host cells. Only a small subset of these candidate effectors is conserved in related oomycetes. Here, we describe a comparative functional characterization of the Hpa RXLR effector HaRxL96 and a homologous gene, PsAvh163, from the soybean pathogen Phytophthora sojae. HaRxL96 and PsAvh163 are induced during early stages of infection and carry a functional RXLR motif that is sufficient for protein uptake into plant cells. Both effectors can suppress or activate immune responses in soybean, Nicotiana, and Arabidopsis. Several SA-responsive defense genes are suppressed in Arabidopsis Col:HaRxL96 and Col:PsAvh163 during an incompatible interaction with Hpa Emoy2. Both effectors are localized to the nucleus and cytoplasm of plant cells. Nuclear localization of both effectors is required for proper virulence functions, including suppression of basal resistance and RPP4-mediated immunity to virulent and avirulent Hpa, respectively. In addition, both effectors interact with plant U-box (PUB) proteins that are conserved between diverse plant species. The targeted PUB proteins are negative regulators of plant immunity in Arabidopsis. These experiments demonstrate that evolutionarily-conserved effectors from different oomycete species can suppress immunity in plant species that are divergent from the source pathogen's primary host. / Ph. D.

Ducted fan VTOL UAVs are currently being designed for use by the Army for surveillance and reconnaissance in the battlefield. The vehicle tested in this research is part of the Honeywell MAV program. Able to be carried in a backpack by a single soldier, it has a duct diameter of 11.5-in. and weighs approximately 20-lbs at takeoff. It is designed for flight up to 50-knots with fan speeds varying between 5000 and 8500 RPM. Reynolds numbers, based on the duct diameter, were on the order of Re = 0.96 x 106 to 4.6 x 106. Various control effectors were mounted to the vehicle and tested for maximum control authority to reduce the nose-up pitch moment created during forward flight or with crosswinds present. Static and wind tunnel tests were conducted to measure each control effector's performance. Box vanes, mounted downstream of the duct, utilized four assemblies, each with three vanes and one flap. This configuration showed adequate results in generating a nose-down pitch moment. Duct deflectors, mounted on the windward strut upstream of the duct, reduced the windward lift produced by both the fan and duct, resulting in a nose-down pitch moment. Opposed vanes, utilizing two vanes and flaps for each of the four assemblies, were designed with the same surface area as the box vanes. With each pair capable of independent vane movement, the opposed vanes were tested with the vanes rotating in tandem for a basic elevator deflection and with the leading edges touching, disrupting the flow at the duct exit. Opposed vanes combined the capabilities of the box vanes and duct deflector. Results show that the opposed vanes were the most practical control effector, offering the most control authority for maximum nose-down pitch moment (up to 80% better) with minimal loss in thrust. / Master of Science

Unlike mammals, plants do not have specific immune cells. However, plants can still recognize pathogens and defend themselves. They do that by recognizing microbial-associated molecular patterns (MAMPs) and secreted pathogen proteins, called effectors. MAMP-triggered immunity (MTI) relies on recognition of MAMPs by leucine-rich repeats (LRRs) pattern-recognition receptors (PRRs). The best-studied LRR PRR is Flagellin-Sensitive 2 (Fls2), the receptor of a 22-amino acid long epitope of bacterial flagellin, called flg22. In this project, alleles of FLS2 of different tomato cultivars were sequenced and compared to each other to get insight into natural selection acting on FLS2 and to identify residues important for ligand binding. This information may be used in the future to engineer Fls2 for improved ability to recognize flagellin. MTI can be suppressed by effectors secreted by bacteria into plant cells through the type III secretion system. On the other hand, plants are equipped with repertoires of resistance proteins, which can recognize some pathogen effectors. If a pathogen carries an effector that is recognized, effector-triggered immunity (ETI) is activated and the plant is resistant. Here, eggplant breeding lines were screened for their ability to activate ETI upon recognition of effectors of the soil borne pathogen Ralstonia solanacearum, a causative agent of bacterial wilt. Four effectors were found to trigger plant defenses in some of the lines. This is the first step in cloning the genes coding for the responsible resistance proteins. These genes may be used in the future for engineering tomato and potato for resistance to bacterial wilt. / Master of Science in Life Sciences

Nitric oxide (NO) and S-nitrosothiols (SNOs) are widespread signalling molecules that regulate immunity in animals and plants (Wendehenne et al., 2001). Previously, we have reported that Arabidopsis thaliana S-nitrosoglutathione reductase, (AtGSNOR1) modulates the extent of total cellular SNO formation, which subsequently regulates multiple modes of plant disease resistance (Feechan et al., 2005). Loss-of-function mutations in AtGSNOR1, leading to increased SNO levels, have recently been shown to result in S-nitrosylation of the key defence regulators NPR1 and AtSABP3, blunting their activity and subsequently leading to increased pathogen susceptibility (Tada et al., 2008; Wang et al., 2009). Thus, inhibiting AtGSNOR1 function leading to increased SNOs, would potentially provide a good strategy for bacterial effector proteins, delivered by the type III secretion system (TTSS), to promote infection. AtGSNOR1 is constitutively expressed in all organs in Arabidopsis and its expression is induced by wounding stress avirulent and non-host pathogen. Using gas phase chemiluminescence, we show that infection with Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000) resulted in increase SNO levels which is TTSS. At the same time, RT-PCR and GUS analysis indicated that AtGSNOR1 expression was transiently suppressed by PstDC3000 which is also TTSS-dependent. Therefore, PstDC3000 infection suppresses denitrosylase function of AtGSNOR1 to increase SNO levels and this virulence effect is delivered by at least one of the effector protein secreted through TTSS. Several putative cis-acting elements were identified in AtGSNOR1 promoter through deletion analysis including GT-box, W-box and MYB/MYC binding motif. These elements comprise of positive and negative regulators which are critical for the induction and suppression of AtGSNOR1 in response to pathogen infection. A few transgenic plants expressing effector proteins were selected and tested for their suppressive effect on AtGSNOR1 expression during PstDC3000 infection. HopAM1 effector proteins showed the ability to suppress AtGSNOR1 when expressed in planta.

Influenza B virus is a major human pathogen causing highly contagious respiratory disease. It accounts for approximately ~30% of influenza virus infection per year. The effector domain of the NS1 protein of influenza B virus (NS1B protein), encompassing the carboxy terminal two thirds of the protein, suppresses interferon-β (IFN-β) synthesis in virus-infected cells by unknown mechanism(s). The induced IFN-β mediates innate immunity. To elucidate the mechanism by which the NS1B effector domain suppresses the production of IFN-β, we identified cellular proteins that interact with the NS1B effector domain. Two approaches were used. The approach that succeeded employed the transfection into cells of plasmids expressing the NS1B effector domain containing two affinity tags. After double affinity purification, co-purified cellular proteins were identified by mass spectrometry. We identified Brd2 as a cellular protein that interacts with the NS1B protein. We established that Brd2 specifically binds to the NS1B effector domain in vitro, in vivo, and in virus-infected cells. Serial mutagenesis experiments showed the phenylalanine at position 171 (F171) of the NS1B protein is essential for Brd2 binding. To determine the function of the interaction of Brd2 with the NS1B protein, we generated a recombinant virus encoding an NS1B protein in which F at position 171 was replaced by an alanine. The F171A mutant virus was attenuated, and unlike the wild-type virus, induced the synthesis of IFN-β mRNA. IRF3, a key transcription factor for transcription of the IFN-β gene, was activated in mutant virusinfected cells, but not in wild-type virus-infected cells. Transfection assays implicated the activation of the TBK1 kinase as the step in IRF3 activation that is induced in mutant virus-infected cells. We interpreted these results as showing that Brd2 binding to the NS1B protein is required for suppressing IRF3 activation and IFN-β induction. Attempts at further confirmation by depletion of endogenous Brd2 using RNA interference were not successful because of inefficient knock-down efficiency and nonspecific IFN-β induction. A further complication is that another bromodomain protein, Brd4, interacts with the NS1B protein and could compensate for depletion of Brd2. / text