Structural analysis of glycans and development of microarrays from Helcobacter pylori cell surface glycome

Helicobacter pylori is a bacterial pathogen that affects more than half of the world’s population with gastro-intestinal diseases and is associated with gastric cancer. The cell surface of H. pylori is decorated with lipopolysaccharides (LPSs) composed of three distinct regions: a variable polysaccharide moiety (O-chain), a structurally conserved core oligosaccharide, and a lipid A region that anchors the LPS to the cell membrane. The O-chain of H. pylori LPS, exhibits unique oligosaccharide structures, such as Lewis (Le) antigens, similar to those present in the gastric mucosa and are involved in interactions with the host. Glucan, heptoglycan, and riban domains are present in the outer core region of some H. pylori LPSs. Amylose-like glycans and mannans are also constituents of some H. pylori strains, possibly co-expressed with LPSs. The complexity of H. pylori LPSs has hampered the establishment of accurate structure-function relationships in interactions with the host, and the design of carbohydrate-based therapeutics, such as vaccines. Carbohydrate microarrays are recent powerful and sensitive tools for studying carbohydrate antigens and, since their emergence, are providing insights into the function of carbohydrates and their involvement in pathogen-host interactions. The major goals of this thesis were the structural analysis of LPSs from H. pylori strains isolated from gastric biopsies of symptomatic Portuguese patients and the construction of a novel pathogen carbohydrate microarray of these LPSs (H. pylori LPS microarray) for interaction studies with proteins. LPSs were extracted from the cell surface of five H. pylori clinical isolates and one NCTC strain (26695) by phenol/water method, fractionated by size exclusion chromatography and analysed by gas chromatography coupled to mass spectrometry. The oligosaccharides released after mild acid treatment of the LPS were analysed by electrospray mass spectrometry. In addition to the conserved core oligosaccharide moieties, structural analyses revealed the presence of type-2 Lex and Ley antigens and N-acetyllactosamine (LacNAc) sequences, typically found in H. pylori strains. Also, the presence of O-6 linked glucose residues, particularly in LPSs from strains 2191 and NCTC 26695, pointed out to the expression of a 6-glucan. Other structural domains, namely ribans, composed of O-2 linked ribofuranose residues were observed in the LPS of most of H. pylori clinical isolates. For the LPS from strain 14382, large amounts of O-3 linked galactose units, pointing to the occurrence of a galactan, a domain recently identified in the LPS of another H. pylori strain. A particular feature to the LPSs from strains 2191 and CI-117 was the detection of large amounts of O-4 linked N-acetylglucosamine (GlcNAc) residues, suggesting the presence of chitin-like glycans, which to our knowledge have not been described for H. pylori strains. For the construction of the H. pylori LPS microarray, the structurally analysed LPSs, as well as LPS-derived oligosaccharide fractions, prepared as neoglycolipid (NGL) probes were noncovalently immobilized onto nitrocellulosecoated glass slides. These were printed together with NGLs of selected sequence defined oligosaccharides, bacterial LPSs and polysaccharides. The H. pylori LPS microarray was probed for recognition with carbohydratebinding proteins (CBPs) of known specificity. These included Le and blood group-related monoclonal antibodies (mAbs), plant lectins, a carbohydratebinding module (CBM) and the mammalian immune receptors DC-SIGN and Dectin-1. The analysis of these CBPs provided new information that complemented the structural analyses and was valuable in the quality control of the constructed microarray. Microarray analysis revealed the occurrence of type-2 Lex and Ley, but not type-1 Lea or Leb antigens, supporting the results obtained in the structural analysis. Furthermore, the H. pylori LPSs were recognised by DC-SIGN, a mammalian lectin known to interact with this bacterium through fucosylated Le epitopes expressed in its LPSs. The -fucose-specific lectin UEA-I, showed restricted binding to probes containing type-2 blood group H sequence and to the LPSs from strains CI-117 and 14382. The presence of H-type-2, as well Htype- 1 in the LPSs from these strains, was confirmed using specific mAbs. Although H-type-1 determinant has been reported for H. pylori LPSs, this is the first report of the presence of H-type-2 determinant. Microarray analysis also revealed that plant lectins known to bind 4-linked GlcNAc chitin oligosaccharide sequences bound H. pylori LPSs. STL, which exhibited restricted and strong binding to 4GlcNAc tri- and pentasaccharides, differentially recognised the LPS from the strain CI-117. The chitin sequences recognised in the LPS could be internal, as no binding was detected to this LPS with WGA, known to be specific for nonreducing terminal of 4GlcNAc sequence. Analyses of the H. pylori LPSs by SDS-PAGE and Western blot with STL provided further evidence for the presence of these novel domains in the O-chain region of this LPS. H. pylori LPS microarray was also applied to analysis of two human sera. The first was from a case infected with H. pylori (H. pylori+ CI-5) and the second was from a non-infected control.The analysis revealed a higher IgG-reactivity towards H. pylori LPSs in the H. pylori+ serum, than the control serum. A specific IgG response was observed to the LPS isolated from the CI-5 strain, which caused the infection. The present thesis has contributed to extension of current knowledge on chemical structures of LPS from H. pylori clinical isolates. Furthermore, the H. pylori LPS microarray constructed enabled the study of interactions with host proteins and showed promise as a tool in serological studies of H. pyloriinfected individuals. Thus, it is anticipated that the use of these complementary approaches may contribute to a better understanding of the molecular complexity of the LPSs and their role in pathogenesis.

Structural analysis of Turtle mountain (Alberta) using digital elevation model: Toward a progressive failure

In 1903, the eastern slope of Turtle Mountain (Alberta) was affected by a 30 M m3-rockslide named Frank Slide that resulted in more than 70 casualties. Assuming that the main discontinuity sets, including bedding, control part of the slope morphology, the structural features of Turtle Mountain were investigated using a digital elevation model (DEM). Using new landscape analysis techniques, we have identified three main joint and fault sets. These results are in agreement with those sets identified through field observations. Landscape analysis techniques, using a DEM, confirm and refine the most recent geology model of the Frank Slide. The rockslide was initiated along bedding and a fault at the base of the slope and propagated up slope by a regressive process following a surface composed of pre-existing discontinuities. The DEM analysis also permits the identification of important geological structures along the 1903 slide scar. Based on the so called Sloping Local Base Level (SLBL) an estimation was made of the present unstable volumes in the main scar delimited by the cracks, and around the south area of the scar (South Peak). The SLBL is a method permitting a geometric interpretation of the failure surface based on a DEM. Finally we propose a failure mechanism permitting the progressive failure of the rock mass that considers gentle dipping wedges (30°). The prisms or wedges defined by two discontinuity sets permit the creation of a failure surface by progressive failure. Such structures are more commonly observed in recent rockslides. This method is efficient and is recommended as a preliminary analysis prior to field investigation.

Structural analysis of the Paint Lake Deformation Zone, Northern Ontario /

The Paint Lake Deformation Zone (PLDZ), located within the Superior Province of Canada, demarcates a major structural and lithological break between the Onaman-Tashota Terrane to the north and the Beardmore-Geraldton Belt to the south. The PLDZ is an east-west trending lineament, approximately 50 km in length and up to 1 km in width, comprised of an early ductile component termed the Paint Lake Shear Zone and a late brittle component known as the Paint Lake Fault. Structures associated with PLDZ development including S-, C- and C'-fabrics, stretching lineations, slickensides, C-C' intersection lineations, Z-folds and kinkbands indicate that simple shear deformation dominated during a NW-SE compressional event. Movement along the PLDZ was in a dextral sense consisting of an early differential motion with southside- down and a later strike-slip motion. Although the locus of the PLDZ may in part be lithologically controlled, mylonitization which accompanied shear zone development is not dependent on the lithological type. Conglomerate, intermediate and mafic volcanic units exhibit similar mesoscopic and microscopic structures where transected by the PLDZ. Field mapping, supported by thin section analysis, defines five strain domains increasing in intensity of deformation from shear zone boundary to centre. A change in the dominant microstructural deformation mechanism from dislocation creep to diffusion creep is observed with increasing strain during mylonitization. C'-fabric development is temporally associated with this change. A decrease in the angular relationship between C- and C'-fabrics is observed upon attaining maximum strain intensity. Strain profiling of the PLDZ demonstrates the presence of an outer primary strain gradient which exhibits a simple profile and an inner secondary strain gradient which exhibits a more complex profile. Regionally metamorphosed lithologies of lower greenschist facies outside the PLDZ were subjected to retrograde metamorphism during deformation within the PLDZ.

Structural analysis of interior layered deposits in north and south Coprates Chasma, Mars

Interior layered deposits within an embayment in the northern as well as near the southern wall of Coprates Chasma in the Valles Marineris, Mars are studied using HRSC, CTX, HiRISE and CRISM data. In the northern embayment, layered deposits outcrop in three separate locations (a western deposit, a central deposit and an eastern deposit). The central layered deposit in the north has a stratigraphic thickness of 2 km. The western layered deposit abuts against the chasma wall appearing to have a relatively un-eroded depositional surface. The eastern deposit is near a landslide scar which appears to have exposed basement layering showing downward displacement. This northern embayment is suggested to have been an ancestral basin. The triangular edged deposit near the southern wall of Coprates Chasma has an elongated mound protruding from the central edge and is suggested to be the outer limits of a fault block which is back rotated 6° south. The rotation may be the result of the Valles Marineris opening.

STRUCTURAL ANALYSIS, LAYER THICKNESS MEASUREMENTS AND MINERALOGICAL INVESTIGATION OF THE LARGE INTERIOR LAYERED DEPOSIT WITHIN GANGES CHASMA, VALLES MARINERIS, MARS

The interior layered deposit (ILD) in Ganges Chasma, Valles Marineris, is a 4.25 km high mound that extends approximately 110 km from west to east. The deposition, deformation, and erosion history of the Ganges ILD records aids in identifying the processes that formed and shaped the Chasma. To interpret structural and geomorphic processes acting on the ILD, multiple layer attitudes and layer thickness transects were conducted on the Ganges ILD. Mineralogical data was analyzed to determine correlations between materials and landforms. Layer thickness measurements indicate that the majority of layers are between 0.5 m and 4 m throughout the ILD. Three major benches dominate the Ganges ILD. Layer thicknesses increase at the ILD benches, suggesting that the benches are formed from the gradual thickening of layers. This indicates that the benches are depositional features draping over basement topography. Layer attitudes indicate overall shallow dips generally confined to a North-South direction that locally appear to follow bench topography. Layering is disrupted on a scale of 40 m to 150 m in 12 separate locations throughout the ILD. In all locations, underlying layering is disturbed by overlying folded layers in a trough-like geometry. These features are interpreted to have formed as submarine channels in a lacustrine setting, subsequently infilled by sediments. Subsequently, the channels were eroded to the present topography, resulting in the thin, curved layering observed. Data cannot conclusively support one ILD formation hypothesis, but does indicate that the Ganges ILD postdates Chasma formation. The presence of water altered minerals, consistently thin layering, and layer orientations provide strong evidence that the ILD formed in a lacustrine setting.

Field Equilibrium Finite Elements for Structural Analysis

Many finite elements used in structural analysis possess deficiencies like shear locking, incompressibility locking, poor stress predictions within the element domain, violent stress oscillation, poor convergence etc. An approach that can probably overcome many of these problems would be to consider elements in which the assumed displacement functions satisfy the equations of stress field equilibrium. In this method, the finite element will not only have nodal equilibrium of forces, but also have inner stress field equilibrium. The displacement interpolation functions inside each individual element are truncated polynomial solutions of differential equations. Such elements are likely to give better solutions than the existing elements.In this thesis, a new family of finite elements in which the assumed displacement function satisfies the differential equations of stress field equilibrium is proposed. A general procedure for constructing the displacement functions and use of these functions in the generation of elemental stiffness matrices has been developed. The approach to develop field equilibrium elements is quite general and various elements to analyse different types of structures can be formulated from corresponding stress field equilibrium equations. Using this procedure, a nine node quadrilateral element SFCNQ for plane stress analysis, a sixteen node solid element SFCSS for three dimensional stress analysis and a four node quadrilateral element SFCFP for plate bending problems have been formulated.For implementing these elements, computer programs based on modular concepts have been developed. Numerical investigations on the performance of these elements have been carried out through standard test problems for validation purpose. Comparisons involving theoretical closed form solutions as well as results obtained with existing finite elements have also been made. It is found that the new elements perform well in all the situations considered. Solutions in all the cases converge correctly to the exact values. In many cases, convergence is faster when compared with other existing finite elements. The behaviour of field consistent elements would definitely generate a great deal of interest amongst the users of the finite elements.

Thermo-Structural Analysis of 3D Composites

Three dimensional (3D) composites are strong contenders for the structural applications in situations like aerospace,aircraft and automotive industries where multidirectional thermal and mechanical stresses exist. The presence of reinforcement along the thickness direction in 3D composites,increases the through the thickness stiffness and strength properties.The 3D preforms can be manufactured with numerous complex architecture variations to meet the needs of specific applications.For hot structure applications Carbon-Carbon(C-C) composites are generally used,whose property variation with respect to temperature is essential for carrying out the design of hot structures.The thermomechanical behavior of 3D composites is not fully understood and reported.The methodology to find the thermomechanical properties using analytical modelling of 3D woven,3D 4-axes braided and 3D 5-axes braided composites from Representative Unit Cells(RUC's) based on constitutive equations for 3D composites has been dealt in the present study.High Temperature Unidirectional (UD) Carbon-Carbon material properties have been evaluated using analytical methods,viz.,Composite cylinder assemblage Model and Method of Cells based on experiments carried out on Carbon-Carbon fabric composite for a temparature range of 300 degreeK to 2800degreeK.These properties have been used for evaluating the 3D composite properties.From among the existing methods of solution sequences for 3D composites,"3D composite Strength Model" has been identified as the most suitable method.For thegeneration of material properies of RUC's od 3D composites,software has been developed using MATLAB.Correlaton of the analytically determined properties with test results available in literature has been established.Parametric studies on the variation of all the thermomechanical constants for different 3D performs of Carbon-Carbon material have been studied and selection criteria have been formulated for their applications for the hot structures.Procedure for the structural design of hot structures made of 3D Carbon-Carbon composites has been established through the numerical investigations on a Nosecap.Nonlinear transient thermal and nonlinear transient thermo-structural analysis on the Nosecap have been carried out using finite element software NASTRAN.Failure indices have been established for the identified performs,identification of suitable 3D composite based on parametric studies on strength properties and recommendation of this material for Nosecap of RLV based on structural performance have been carried out in this Study.Based on the 3D failure theory the best perform for the Nosecap has been identified as 4-axis 15degree braided composite.

Structural analysis of narratives produced by normal-hearing and deaf children

This dissertation presents two experiments investigating the structural analysis of narratives produced by normal-hearing and hearing-impaired children. The results suggest that the evaluation of deaf children’s language at a discourse level is both possible and more relevant to academic achievement than traditional assessment procedures that focus on assessing language at a word, phrase or sentence level.

First structural analysis of a naphthalene-based poly(ether ketone): Crystal and molecular simulation from X-ray powder data and diffraction modeling

Polycondensation of 2,6-dihydroxynaphthalene with 4,4'-bis(4"-fluorobenzoyl)biphenyl affords a novel, semicrystalline poly(ether ketone) with a melting point of 406 degreesC and glass transition temperature (onset) of 168 degreesC. Molecular modeling and diffraction-simulation studies of this polymer, coupled with data from the single-crystal structure of an oligomer model, have enabled the crystal and molecular structure of the polymer to be determined from X-ray powder data. This structure-the first for any naphthalene-containing poly(ether ketone)-is fully ordered, in monoclinic space group P2(1)/b, with two chains per unit cell. Rietveld refinement against the experimental powder data gave a final agreement factor (R-wp) of 6.7%.

Structural analysis of PEO-PBO copolymer monolayers at the air-water interface

X-ray reflectivity (XR) and grazing incidence X-ray diffraction (GIXD) have been used to examine an oxyethylene-b-oxybutylene (E23B8) copolymer film at the air-water interface. The XR data were fitted using both a one- and a two-layer model that outputted the film thickness, roughness, and electron density. The best fit to the experimental data was obtained using a two-layer model (representing the oxyethylene and oxybutylene blocks, respectively), which showed a rapid thickening of the copolymer film at pressures above 7 mN/m. The large roughness values found indicate a significant degree of intermixing between the blocks and back up the GIXD data, which showed no long range lateral ordering within the layer. It was found from the electron density model results that there is a large film densification at 7 mN/m, possibly suggesting conformational changes within the film, even though no such change occurs on the pressure-area isotherm at the same surface pressure.

Synthesis, structural analysis, and magnetic behaviour of three fumarate bridged coordination polymers: five-fold interpenetrated diamond-like net of Ni-II, sheets of Ni-II and Co-II

The hydrothermal reactions of Ni(NO3)(2).6H(2)O, disodium fumarate (fum) and 1,2-bis(4-pyridyl)ethane (bpe)/1,3-bis(4-pyridyl) propane (bpp) in aqueous-methanol medium yield one 3-D and one 2-D metal-organic hybrid material, [Ni(fum)(bpe)] (1) and [Ni(fum)(bpp)(H2O)] (2), respectively. Complex 1 possesses a novel unprecedented structure, the first example of an "unusual mode" of a five-fold distorted interpenetrated network with metal-ligand linkages where the four six-membered windows in each adamantane-type cage are different. The structural characterization of complex 2 evidences a buckled sheet where nickel ions are in a distorted octahedral geometry, with two carboxylic groups, one acting as a bis-chelate, the other as a bis-monodentate ligand. The metal ion completes the coordination sphere through one water molecule and two bpp nitrogens in cis position. Variable-temperature magnetic measurements of complexes 1 and 2 reveal the existence of very weak antiferromagnetic intramolecular interactions and/or the presence of single-ion zero field splitting (D) of isolated Ni-II ions in both the compounds. Experimentally, both the J parameters are close, comparable and very small. Considering zero-field splitting of Ni-II, the calculated D values are in agreement with values reported in the literature for Ni-II ions. Complex 3, [{Co(phen)}(2)(fum)(2)] (phen=1,10-phenanthroline) is obtained by diffusing methanolic solution of 1,10-phenanthroline on an aqueous layer of disodium fumarate and Co(NO3)(2).6H(2)O. It consists of dimeric Co-II(phen) units, doubly bridged by carboxylate groups in a distorted syn-syn fashion. These fumarate anions act as bis-chelates to form corrugated sheets. The 2D layer has a (4,4) topology, with the nodes represented by the centres of the dimers. The magnetic data were fitted ignoring the very weak coupling through the fumarate pathway and using a dimer model.

A structural analysis of M protein in coronavirus assembly and morphology

The M protein of coronavirus plays a central role in virus assembly, turning cellular membranes into workshops where virus and host factors come together to make new virus particles. We investigated how M structure and organization is related to virus shape and size using cryo-electron microscopy, tomography and statistical analysis. We present evidence that suggests M can adopt two conformations and that membrane curvature is regulated by one M conformer. Elongated M protein is associated with rigidity, clusters of spikes and a relatively narrow range of membrane curvature. In contrast, compact M protein is associated with flexibility and low spike density. Analysis of several types of virus-like particles and virions revealed that S protein, N protein and genomic RNA each help to regulate virion size and variation, presumably through interactions with M. These findings provide insight into how M protein functions to promote virus assembly.

Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.