Cloning, bioinformatics analysis, and expression of the dust mite allergen Der f 5 of Dermatophagoides farinae

Crude extracts of house dust mites are used clinically for diagnosis and immunotherapy of allergic diseases, including bronchial asthma, perennial rhinitis, and atopic dermatitis. However, crude extracts are complexes with non-allergenic antigens and lack effective concentrations of important allergens, resulting in several side effects. Dermatophagoides farinae (Hughes; Acari: Pyroglyphidae) is one of the predominant sources of dust mite allergens, which has more than 30 groups of allergen. The cDNA coding for the group 5 allergen of D. farinae from China was cloned, sequenced and expressed. According to alignment using the VECTOR NTI 9.0 software, there were eight mismatched nucleotides in five cDNA clones resulting in seven incompatible amino acid residues, suggesting that the Der f 5 allergen might have sequence polymorphism. Bioinformatics analysis revealed that the matured Der f 5 allergen has a molecular mass of 13604.03 Da, a theoretical pI of 5.43 and is probably hydrophobic and cytoplasmic. Similarities in amino acid sequences between Der f 5 and allergens of other domestic mite species, viz. Der p 5, Blo t 5, Sui m 5, and Lep d 5, were 79, 48, 53, and 37%, respectively. Phylogenetic analysis indicated that Der f 5 and Der p 5 clustered together. Blo t 5 and Ale o 5 also clustered together, although Blomia tropicalis and Aleuroglyphus ovatus belong to different mite families, viz. Echimyopodidae and Acaridae, respectively.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Phylogenetic Analysis of Avidins and Expression of Novel Avidins from Lactrodectus hesperus and Hoeflea phototrophica

Avidins (Avds) are homotetrameric or homodimeric glycoproteins with typically less than 130 amino acid residues per monomer. They form a highly stable, non-covalent complex with biotin (vitamin H) with Kd = 10-15 M (for chicken Avd). The best-studied Avds are the chicken Avd from Gallus gallus and streptavidin from Streptomyces avidinii, although other Avd studies have also included Avds from various origins, e.g., from frogs, fishes, mushrooms and from many different bacteria. Several engineered Avds have been reported as well, e.g., dual-chain Avds (dcAvds) and single-chain Avds (scAvds), circular permutants with up to four simultaneously modifiable ligand-binding sites. These engineered Avds along with the many native Avds have potential to be used in various nanobiotechnological applications. In this study, we made a structure-based alignment representing all currently available sequences of Avds and studied the evolutionary relationship of Avds using phylogenetic analysis. First, we created an initial multiple sequence alignment of Avds using 42 closely related sequences, guided by the known Avd crystal structures. Next, we searched for non-redundant Avd sequences from various online databases, including National Centre for Biotechnology Information and the Universal Protein Resource; the identified sequences were added to the initial alignment to expand it to a final alignment of 242 Avd sequences. The MEGA software package was used to create distance matrices and a phylogenetic tree. Bootstrap reproducibility of the tree was poor at multiple nodes and may reflect on several possible issues with the data: the sequence length compared is relatively short and, whereas some positions are highly conserved and functional, others can vary without impinging on the structure or the function, so there are few informative sites; it may be that periods of rapid duplication have led to paralogs and that the differences among them are within the error limit of the data; and there may be other yet unknown reasons. Principle component analysis applied to alternative distance data did segregate the major groups, and success is likely due to the multivariate consideration of all the information. Furthermore, based on our extensive alignment and phylogenetic analysis, we expressed two novel Avds, lacavidin from Lactrodectus Hesperus, a western black widow spider, and hoefavidin from Hoeflea phototrophica, an aerobic marine bacterium, the ultimate aim being to determine their X-ray structures. These Avds were selected because of their unique sequences: lacavidin has an N-terminal Avd-like domain but a long C-terminal overhang, whereas hoefavidin was thought to be a dimeric Avd. Both these Avds could be used as novel scaffolds in biotechnological applications.

Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.

Factors Affecting Runnability of Press Forming Equipment

The growth of the food packaging industry has raised more interest in bio-based fibre packing. The use of petroleum based packages is unfriendly to the environment while bio-based is a sustainable option for food packing. In this Master Thesis the aim was to discover how the press forming machineries runnability is affected by parameters of the press and how it also affects formability of paperboard trays. Familiarisation of the working operation parameters was done with the KAMA ST 75 flat-bed die cutting machine and the VP3-70 mould press. Some small test runs of moulding trays where done to get acquainted to the adjustment parameters of the machines. Literature study was done on how paperboards physical properties react to the forces applied during press forming. The study of what kind of defects to the paperboard tray might occur during forming process and the causes for these defects. Also how the parameters of the press forming machine affects formability of the tray. Maintenance procedures was done to the press forming machine to enhance the reliably of production process. Tool alignment measurement was done to determine proper alignment. Laboratory test of the physical properties of the test material was done to find any connection to how the test material performs in press forming. An evaluation criterion was made to evaluate the dimensions and defects of the tray. From the test result a conclusion can be drawn on how the parameters of the press forming process affect the paperboard material. Based on the results the adjustment the parameters of moulding machines to the mechanical properties of paperboard it is possible to produce high quality fibre passed trays for the food packaging industry.

Systematic studies of the effect of pressure on magnetic and electronic properties of La2/3Ca1/3MnO3 thin films with various thicknesses /

Interest in mixed-valent perovskite manganese oxides of La\-xAxMnO^ (v4-divalent alkaline earth Ca, Sr or Ba), whose unusual properties were discovered nearly a half century ago, has recently been revived. The discovery of the colossal magnetoresistance and pressure effects introduced new questions concerning the complex interplay between lattice structure, magnetism and transport in doped perovskite manganites. In this study, we report our experimental investigations of pressure and magnetic field dependencies of La-i/sCai/sMnOs (LCMO) epitaxial films with various thickness on SrTiO$ substrate. An analysis of film thickness dependency of the resistivity of LCMO epitaxial films under pressure and magnetic field has been performed by taking into account substrate contributions. This verifies the correlation of lattice distortion with magnetic and transport properties. Strong dependencies of Mn — O — Mn bond bending and Mn — O bond stretching with pressure as well as Mn spin alignment with magnetic field, and the lattice distortion induced by the substrate are discussed.

The surficial geology, sedimentology and geochemistry of the late glacial sediments and Paleozoic bedrock in the Campbellford area, Ontario, with special reference to the Dummer Complex /

The Dummer Complex extends 180 km along the Precambrian - Paleozoic contact from Tamworth to Lake Simcoe. It is composed of coarse, angular Paleozoic clasts in discontinuous, pitted, hummocky deposits. Deposits are usually separated by bare or boulder strewn bedrock, but have been found in the southern drumlinized till sheet. Dummer Complex deposits show rough alignment with ice-flow. Eskers cross-cut many of the deposits. Dummer sediment subfacies are defined on the basis of dominant coarse grain size and lithology, which relate directly to the underlying Paleozoic formation. Three subglacial tills are identified based on the degree of comminution and distance of transport; the immature facies of the Dummer Complex; the mature facies of the drumlinized till sheet and; the submature facies which is transitional. Carbonate geochemistry was used for till-bedrock correlation in various grain sizes. Of the 3 Paleozoic formations underlying the Dummer Complex, the Gull River Fm. is geochemically distinctive from the Bobcaygeon and Verulam Formations using Ca, Mg, Sr, Cu, Mn, Fe and Na. The Bobcaygeon Fm. and Verulam Fm. can be differentiated using Ca and the Sr/Ca ratio. The immature facies from 1.0 phi and finer is dominated by the non-carbonate, long distance transported component which decreases slightly downice. The submature till facies contains more long distance material than the immature facies. Sr and Mn can be used to correlate the Gull River immature till facies to the underlying bedrock the other subfacies could not be distinguished from each other or their respective source formation. This method proved to be ineffective for sediments with greater than 35% non-carbonate component, due to leaching of elements by the dissolving acid.The Dummer Complex is produced subglacially , as the compressional ice encounters the permeable Paleozoic carbonates. The increased shear strength of the ice and pore pressures in the carbonates results in the basal ice zones becoming debris ladden. Cleaner ice overrides the basal debris . laden dead ice which then acts as the glacier bed. During retreat, the Simcoe lobe stagnates as flow is cut-off by the Algonquin Highlands.

Kr-Ar laser Raman spectrometer for low temperature measurements /

A Czerny Mount double monochromator is used to measure Raman scattered radiation near 90" from a crystalline, Silicon sample. Incident light is provided by a mixed gas Kr-Ar laser, operating at 5145 A. The double monochromator is calibrated to true wavelength by comparison of Kr and Ar emission Une positions (A) to grating position (A) display [1]. The relationship was found to be hnear and can be described by, y = 1.219873a; - 1209.32, (1) where y is true wavelength (A) and xis grating position display (A). The Raman emission spectra are collected via C"*""*" encoded software, which displays a mV signal from a Photodetector and allows stepping control of the gratings via an A/D interface. [2] The software collection parameters, detector temperature and optics are optimised to yield the best quality spectra. The inclusion of a cryostat allows for temperatmre dependent capabihty ranging from 4 K to w 350 K. Silicon Stokes temperatm-e dependent Raman spectra, generally show agreement with Uterature results [3] in their frequency haxdening, FWHM reduction and intensity increase as temperature is reduced. Tests reveal that a re-alignment of the double monochromator is necessary before spectral resolution can approach literature standard. This has not yet been carried out due to time constraints.

Teachers' perspectives on the implementation of expectations-based curricula /

This qualitative study examines teachers' experiences implementing new standardized curricula in Ontario schools. This new curricula contained several policy changes and an expectations based format which directed what knowledge and skills students were to demonstrate in each subject. This level of specificity of subject-content served to control teachers in relation to curricula; however, data suggested that at the same time, teachers had enormous flexibility in terms of pedagogy. Four secondary teachers who were implementing a Grade 10 course in the 2000-2001 school year participated in the study. The qualitative framework supported the researcher's emphasis on examining the participants' perspectives on the implementation of expectation-based curricula. Data collected included transcripts from interviews conducted with teacher participants and a representative of the Ontario Ministry of Education and Training, field notes, and a research journal. Many of the factors often cited in the literature as influencing implementation practices were found to have affected the participants' experiences of curriculum implementation: time, professional development, and teachers' beliefs, particularly concerning students. In addition, the format of the policy documents proved to both control and free teachers during the implementation process. Participants believed that the number of specific expectations did not provide them an opportunity to add content to the curriculum; at the same time, teachers also noted that the general format of the policy document allowed them to direct instruction to match students' needs and their own teaching preferences. Alignment between teachers' beliefs about education and their understanding of the new curriculum affected the ways in which many participants adapted during the implementation process.

Developing a numerical inverse-theory-based extraction of orientation-dependent relaxation rates from partially- relaxed spectra

Second-rank tensor interactions, such as quadrupolar interactions between the spin- 1 deuterium nuclei and the electric field gradients created by chemical bonds, are affected by rapid random molecular motions that modulate the orientation of the molecule with respect to the external magnetic field. In biological and model membrane systems, where a distribution of dynamically averaged anisotropies (quadrupolar splittings, chemical shift anisotropies, etc.) is present and where, in addition, various parts of the sample may undergo a partial magnetic alignment, the numerical analysis of the resulting Nuclear Magnetic Resonance (NMR) spectra is a mathematically ill-posed problem. However, numerical methods (de-Pakeing, Tikhonov regularization) exist that allow for a simultaneous determination of both the anisotropy and orientational distributions. An additional complication arises when relaxation is taken into account. This work presents a method of obtaining the orientation dependence of the relaxation rates that can be used for the analysis of the molecular motions on a broad range of time scales. An arbitrary set of exponential decay rates is described by a three-term truncated Legendre polynomial expansion in the orientation dependence, as appropriate for a second-rank tensor interaction, and a linear approximation to the individual decay rates is made. Thus a severe numerical instability caused by the presence of noise in the experimental data is avoided. At the same time, enough flexibility in the inversion algorithm is retained to achieve a meaningful mapping from raw experimental data to a set of intermediate, model-free

The Canada Not For Profit Corporations Act: Perceived impact on the governance of federal sport organizations

This thesis examined the impact of the Canada Not-for-Profit Corporations Act (2009) on the governance of national sport organizations (NSO). The impact of the legislation was explored through the perceptions of NSO executive leaders and by analyzing the by-laws in effect before the legislation. The legislation was perceived to have the greatest impact on enhancing accountability, specifically affecting membership categories and director selection. The interview data showed that the legislation was necessary to enhance accountability in many NSOs. The Respondents also demonstrated that they understood the goals sought through the legislation. The data also showed that the boards of NSOs were already in alignment with the goals of the legislation. With respect to governance, the data indicated that NSOs rely almost exclusively on their regional sport associations as voting stakeholders. An emerging issue that came out of the results was the role of athletes in the governance of sport organizations.

An Exploration of the Impact of Ontario Integrated Secondary Programs Through the Perceptions of their Graduates

The purpose of this study was to investigate the impact of participating in an integrated program at the secondary level on students’ lives based on their postsecondary perceptions. A basic interpretive qualitative design was employed in this study. Ten semistructured interviews were conducted with graduates of integrated program as the means of data collection. It was found that the integrated programs accomplished objectives in close alignment with the mandated curriculum expectations regarding integrated programs. Some of the most powerful impacts related to students' learning skills, such as collaboration and social skills, and how to create as well as participate in community. A strong connection between participating in integrated programs and vocational guidance was also identified. The results led to the recommendation that integrated programs be explored as a platform for delivering 21st century education as they closely paralleled the objectives prescribed by a number of authors who detailed the role of education in the 21st century.

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

Affiliation: Département de Biochimie, Université de Montréal

L'évolution de la réglementation internationale des investissements directs étrangers dans les Amériques : vers de nouvelles perspectives ?

"Mémoire présenté à la Faculté des études supérieures en vue de l'obtention du grade de LL.M. Droit Dans le cadre du programme de Maîtrise en droit(LL.M.) 2-325-1-0 en option recherche et droit des affaires"

Caractérisation électro-clinique des convulsions fébriles et risque d’épilepsie

Environ 2-3% d’enfants avec convulsions fébriles (CF) développent une épilepsie, mais les outils cliniques existants ne permettent pas d’identifier les enfants susceptibles de développer une épilepsie post-convulsion fébrile. Des études ont mis en évidence des anomalies d’EEG quantifiée, et plus particulièrement en réponse à la stimulation lumineuse intermittente (SLI), chez des patients épileptiques. Aucune étude n’a analysé ces paramètres chez l’enfant avec CF et il importe de déterminer s’ils sont utiles pour évaluer le pronostic des CF. Les objectifs de ce programme de recherche étaient d’identifier, d’une part, des facteurs de risque cliniques qui déterminent le développement de l’épilepsie après des CF et, d’autre part, des marqueurs électrophysiologiques quantitatifs qui différencieraient les enfants avec CF des témoins et pourraient aider à évaluer leur pronostic. Afin de répondre à notre premier objectif, nous avons analysé les dossiers de 482 enfants avec CF, âgés de 3 mois à 6 ans. En utilisant des statistiques de survie, nous avons décrit les facteurs de risque pour développer une épilepsie partielle (antécédents prénataux, retard de développement, CF prolongées et focales) et généralisée (antécédents familiaux d’épilepsie, CF récurrentes et après l’âge de 4 ans). De plus, nous avons identifié trois phénotypes cliniques distincts ayant un pronostic différent : (i) CF simples avec des antécédents familiaux de CF et sans risque d’épilepsie ultérieure; (ii) CF récurrentes avec des antécédents familiaux d’épilepsie et un risque d’épilepsie généralisée; (iii) CF focales avec des antécédents familiaux d’épilepsie et un risque d’épilepsie partielle. Afin de répondre à notre deuxième objectif, nous avons d’abord analysé les potentiels visuels steady-state (PEVSS) évoqués par la SLI (5, 7,5, 10 et 12,5 Hz) en fonction de l’âge. Le tracé EEG de haute densité (128 canaux) a été enregistré chez 61 enfants âgés entre 6 mois et 16 ans et 8 adultes normaux. Nous rapportons un développement topographique différent de l’alignement de phase des composantes des PEVSS de basses (5-15 Hz) et de hautes (30-50 Hz) fréquences. Ainsi, l’alignement de phase des composantes de basses fréquences augmente en fonction de l’âge seulement au niveau des régions occipitale et frontale. Par contre, les composantes de hautes fréquences augmentent au niveau de toutes les régions cérébrales. Puis, en utilisant cette même méthodologie, nous avons investigué si les enfants avec CF présentent des anomalies des composantes gamma (50-100 Hz) des PEVSS auprès de 12 cas de CF, 5 frères et sœurs des enfants avec CF et 15 témoins entre 6 mois et 3 ans. Nous montrons une augmentation de la magnitude et de l’alignement de phase des composantes gamma des PEVSS chez les enfants avec CF comparés au groupe témoin et à la fratrie. Ces travaux ont permis d’identifier des phénotypes électro-cliniques d’intérêt qui différencient les enfants avec CF des enfants témoins et de leur fratrie. L’étape suivante sera de vérifier s’il y a une association entre les anomalies retrouvées, la présentation clinique et le pronostic des CF. Cela pourrait éventuellement aider à identifier les enfants à haut risque de développer une épilepsie et permettre l’institution d’un traitement neuroprotecteur précoce.