Inhibition of respiratory syncytial virus by nasally administered siRNA modified with F-ANA

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Integration of geochemical and biological modifications in mining areas: waters, sediments and diatoms

The development of mining activities over thousands of years in the region of Aljustrel is nowadays visible as a vast area of ore tailings, slag and host rocks of sulphides mineralization. The generation of acidic waters by the alteration of pyritic minerals - Acid Mine Drainage (AMD) - causes a significant impact on the river system both in the south of the village (Rib ª. Água Forte) and in the north of it (Rib ª. Água Azeda and Barranco do Farrobo), which is reflected in extremely low pH values (< 3) and high concentrations of As, Cd, Cu, Fe, Mn, Pb, Zn and sulphates. This study aimed to assess the environmental impacts extent, integrating geochemical (surface waters and stream sediments) and biological (diatoms) parameters. Three groups of sites were defined, based on sediments and water analysis, which integration with diatom data showed the same association of groups: Group 1- impacted, with acidic pH (1.9-5.1), high metal contents (0.4-1975 mg L-1) and Fe-Mg-sulphate waters, being metals more bioavailable in waters in cationic form (Me2+); mineralogically the sediments were characterized by phyllosilicates and sulphates/oxy-hydroxysulphate phases, easily solubilized, retaining a high amount of metals when precipitated; dominant taxon was Pinnularia aljustrelica (a new species); Group 2- slightly impacted, weak acid to neutral pH (5.0-6.8), metal contents not so high (0.2-25 mg L-1) and Fe-Mg-sulphate to Mg-chloride waters; dominant taxa were Brachysira neglectissima and Achnanthidium minutissimum; Group 3- unimpacted, alkaline pH (7.0-8.4), low metal contents (0-7 mg L-1) with Mg-chloride waters. In this group, metals were associated to the primary phases (e.g. sulphides), not so easily available; the existence of high chloride contents explained the presence of typical taxa of brackish/marine (e.g. Entomoneis paludosa) waters. Taxonomical aspects of the diatoms were studied (discovery of a new species: Pinnularia aljustrelica Luis, Almeida et Ector sp. nov.), as well as morphometric (size decrease of diatoms valves, as well as the appearance of deformed valves of Eunotia exigua in Group 1 and A. minutissimum in Group 2) and physiological (effective to assess the effects of metals/acidity in the photosynthetic efficiency through PAM Fluorometry) aspects. A study was carried out in an artificial river system (microcosm) that aimed to mimic Aljustrel’s extreme conditions in controlled laboratory conditions. The chronic effects of Fe, SO42- and acidity in field biofilms, inoculated in the artificial rivers, were evaluated as well as their contribution to the communities’ tolerance to metal toxicity, through acute tests with two metals (Cu and Zn). In general, the effects caused by low pH values and high concentrations of Fe and SO42- were reflected at the community level by the decrease in diversity, the predominance of acidophilic species, the decrease in photosynthetic efficiency and the increase of enzymatic (e.g. catalase, superoxide dismutase) and non-enzymatic activities (e.g. total glutathione and total phytochelatins). However, it was possible to verify that acidity performed a protective effect in the communities, upon Cu and Zn addition. A comparative study between Aljustrel mining area and New Brunswick mining area was carried out, both with similar mining and geological conditions, reflected in similar diatom communities in both mines, but in very different geographic and climatic areas.

Temporal modifications in bone following spinal cord injury in rats

Introduction: The aim of this study was to investigate the temporal modifications in bone mass, bone biomechanical properties and bone morphology in spinal cord injured rats 2, 4 and 6 weeks after a transection. Material and methods: Control animals were randomly distributed into four groups (n = 10 each group): control group (CG) - control animals sacrificed immediately after surgery; spinal cord-injured 2 weeks (2W) - spinal cord-injured animals sacrificed 2 weeks after surgery; spinal cord-injured 4 weeks (4W) - spinal cord-injured animals sacrificed 4 weeks after surgery; spinal cord-injured 6 weeks (6W) - spinal cord-injured animals sacrificed 6 weeks after surgery. Results: Biomechanical properties of the right tibia were determined by a threepoint bending test and injured animals showed a statistically significant decrease in maximal load compared to control animals. The right femur was used for densitometric analysis and bone mineral content of the animals sacrificed 4 and 6 weeks after surgery was significantly higher compared to the control animals and animals sacrificed 2 weeks after surgery. Histopathological and morphological analysis of tibiae revealed intense resorptive areas in the group 2 weeks after injury only. Conclusions: The results of this study show that this rat model is a valuable tool to investigate bone remodeling processes specifically associated with SCI. Taken together, our results suggest that spinal cord injury induced bone loss within 2 weeks after injury in rats.

Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples

Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. © 2013 Elsevier B.V.

Use of narrow mass-window, high-resolution extracted product ion chromatograms for the sensitive and selective identification of protein modifications

Protein modifications, including oxidative modifications, glycosylations, and oxidized lipid-protein adducts, are becoming increasingly important as biomarkers and in understanding disease etiology. There has been a great deal of interest in mapping these on Apo B100 from low density lipoprotein (LDL). We have used extracted ion chromatograms of product ions generated using a very narrow mass window from high-resolution tandem mass spectrometric data collected on a rapid scanning quadrupole time-of-flight (QTOF) instrument, to selectively and sensitively detect modified peptides and identify the site and nature of a number of protein modifications in parallel. We have demonstrated the utility of this method by characterizing for the first time oxidized phospholipid adducts to LDL and human serum albumin and for the detection of glycosylation and kynurenin formation from the oxidation of tryptophan residues in LDL. © 2013 American Chemical Society.

Lipoxidation adducts with peptides and proteins:deleterious modifications or signalling mechanisms?

Protein lipoxidation refers to the modification by electrophilic lipid oxidation products to form covalent adducts, which for many years has been considered as a deleterious consequence of oxidative stress. Oxidized lipids or phospholipids containing carbonyl moieties react readily with lysine to form Schiff bases; alternatively, oxidation products containing α,β-unsaturated moieties are susceptible to nucleophilic attack by cysteine, histidine or lysine residues to yield Michael adducts, overall corresponding to a large number of possible protein adducts. The most common detection methods for lipoxidized proteins take advantage of the presence of reactive carbonyl groups to add labels, or use antibodies. These methods have limitations in terms of specificity and identification of the modification site. The latter question is satisfactorily addressed by mass spectrometry, which enables the characterization of the adduct structure. This has allowed the identification of lipoxidized proteins in physiological and pathological situations. While in many cases lipoxidation interferes with protein function, causing inhibition of enzymatic activity and increased immunogenicity, there are a small number of cases where lipoxidation results in gain of function or activity. For certain proteins lipoxidation may represent a form of redox signaling, although more work is required to confirm the physiological relevance and mechanisms of such processes. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. © 2013 Elsevier B.V.

Targeted mass spectrometry methods for detecting oxidative post-translational modifications

Oxidative post-translational modifications (oxPTMs) can alter the function of proteins, and are important in the redox regulation of cell behaviour. The most informative technique to detect and locate oxPTMs within proteins is mass spectrometry (MS). However, proteomic MS data are usually searched against theoretical databases using statistical search engines, and the occurrence of unspecified or multiple modifications, or other unexpected features, can lead to failure to detect the modifications and erroneous identifications of oxPTMs. We have developed a new approach for mining data from accurate mass instruments that allows multiple modifications to be examined. Accurate mass extracted ion chromatograms (XIC) for specific reporter ions from peptides containing oxPTMs were generated from standard LC-MSMS data acquired on a rapid-scanning high-resolution mass spectrometer (ABSciex 5600 Triple TOF). The method was tested using proteins from human plasma or isolated LDL. A variety of modifications including chlorotyrosine, nitrotyrosine, kynurenine, oxidation of lysine, and oxidized phospholipid adducts were detected. For example, the use of a reporter ion at 184.074 Da/e, corresponding to phosphocholine, was used to identify for the first time intact oxidized phosphatidylcholine adducts on LDL. In all cases the modifications were confirmed by manual sequencing. ApoB-100 containing oxidized lipid adducts was detected even in healthy human samples, as well as LDL from patients with chronic kidney disease. The accurate mass XIC method gave a lower false positive rate than normal database searching using statistical search engines, and identified more oxidatively modified peptides. A major advantage was that additional modifications could be searched after data collection, and multiple modifications on a single peptide identified. The oxPTMs present on albumin and ApoB-100 have potential as indicators of oxidative damage in ageing or inflammatory diseases.

Case definition and holistic model modifications required for building elements

This project is an extension of a previous CRC project (220-059-B) which developed a program for life prediction of gutters in Queensland schools. A number of sources of information on service life of metallic building components were formed into databases linked to a Case-Based Reasoning Engine which extracted relevant cases from each source.

Report : holistic model modifications for selected building elements

This project is an extension of a previous CRC project (220-059-B) which developed a program for life prediction of gutters in Queensland schools. A number of sources of information on service life of metallic building components were formed into databases linked to a Case-Based Reasoning Engine which extracted relevant cases from each source.

Synthesis and modifications of metal oxide nanostructures and their applications

Transition metal oxides are functional materials that have advanced applications in many areas, because of their diverse properties (optical, electrical, magnetic, etc.), hardness, thermal stability and chemical resistance. Novel applications of the nanostructures of these oxides are attracting significant interest as new synthesis methods are developed and new structures are reported. Hydrothermal synthesis is an effective process to prepare various delicate structures of metal oxides on the scales from a few to tens of nanometres, specifically, the highly dispersed intermediate structures which are hardly obtained through pyro-synthesis. In this thesis, a range of new metal oxide (stable and metastable titanate, niobate) nanostructures, namely nanotubes and nanofibres, were synthesised via a hydrothermal process. Further structure modifications were conducted and potential applications in catalysis, photocatalysis, adsorption and construction of ceramic membrane were studied. The morphology evolution during the hydrothermal reaction between Nb2O5 particles and concentrated NaOH was monitored. The study demonstrates that by optimising the reaction parameters (temperature, amount of reactants), one can obtain a variety of nanostructured solids, from intermediate phases niobate bars and fibres to the stable phase cubes. Trititanate (Na2Ti3O7) nanofibres and nanotubes were obtained by the hydrothermal reaction between TiO2 powders or a titanium compound (e.g. TiOSO4·xH2O) and concentrated NaOH solution by controlling the reaction temperature and NaOH concentration. The trititanate possesses a layered structure, and the Na ions that exist between the negative charged titanate layers are exchangeable with other metal ions or H+ ions. The ion-exchange has crucial influence on the phase transition of the exchanged products. The exchange of the sodium ions in the titanate with H+ ions yields protonated titanate (H-titanate) and subsequent phase transformation of the H-titanate enable various TiO2 structures with retained morphology. H-titanate, either nanofibres or tubes, can be converted to pure TiO2(B), pure anatase, mixed TiO2(B) and anatase phases by controlled calcination and by a two-step process of acid-treatment and subsequent calcination. While the controlled calcination of the sodium titanate yield new titanate structures (metastable titanate with formula Na1.5H0.5Ti3O7, with retained fibril morphology) that can be used for removal of radioactive ions and heavy metal ions from water. The structures and morphologies of the metal oxides were characterised by advanced techniques. Titania nanofibres of mixed anatase and TiO2(B) phases, pure anatase and pure TiO2(B) were obtained by calcining H-titanate nanofibres at different temperatures between 300 and 700 °C. The fibril morphology was retained after calcination, which is suitable for transmission electron microscopy (TEM) analysis. It has been found by TEM analysis that in mixed-phase structure the interfaces between anatase and TiO2(B) phases are not random contacts between the engaged crystals of the two phases, but form from the well matched lattice planes of the two phases. For instance, (101) planes in anatase and (101) planes of TiO2(B) are similar in d spaces (~0.18 nm), and they join together to form a stable interface. The interfaces between the two phases act as an one-way valve that permit the transfer of photogenerated charge from anatase to TiO2(B). This reduces the recombination of photogenerated electrons and holes in anatase, enhancing the activity for photocatalytic oxidation. Therefore, the mixed-phase nanofibres exhibited higher photocatalytic activity for degradation of sulforhodamine B (SRB) dye under ultraviolet (UV) light than the nanofibres of either pure phase alone, or the mechanical mixtures (which have no interfaces) of the two pure phase nanofibres with a similar phase composition. This verifies the theory that the difference between the conduction band edges of the two phases may result in charge transfer from one phase to the other, which results in effectively the photogenerated charge separation and thus facilitates the redox reaction involving these charges. Such an interface structure facilitates charge transfer crossing the interfaces. The knowledge acquired in this study is important not only for design of efficient TiO2 photocatalysts but also for understanding the photocatalysis process. Moreover, the fibril titania photocatalysts are of great advantage when they are separated from a liquid for reuse by filtration, sedimentation, or centrifugation, compared to nanoparticles of the same scale. The surface structure of TiO2 also plays a significant role in catalysis and photocatalysis. Four types of large surface area TiO2 nanotubes with different phase compositions (labelled as NTA, NTBA, NTMA and NTM) were synthesised from calcination and acid treatment of the H-titanate nanotubes. Using the in situ FTIR emission spectrescopy (IES), desorption and re-adsorption process of surface OH-groups on oxide surface can be trailed. In this work, the surface OH-group regeneration ability of the TiO2 nanotubes was investigated. The ability of the four samples distinctively different, having the order: NTA > NTBA > NTMA > NTM. The same order was observed for the catalytic when the samples served as photocatalysts for the decomposition of synthetic dye SRB under UV light, as the supports of gold (Au) catalysts (where gold particles were loaded by a colloid-based method) for photodecomposition of formaldehyde under visible light and for catalytic oxidation of CO at low temperatures. Therefore, the ability of TiO2 nanotubes to generate surface OH-groups is an indicator of the catalytic activity. The reason behind the correlation is that the oxygen vacancies at bridging O2- sites of TiO2 surface can generate surface OH-groups and these groups facilitate adsorption and activation of O2 molecules, which is the key step of the oxidation reactions. The structure of the oxygen vacancies at bridging O2- sites is proposed. Also a new mechanism for the photocatalytic formaldehyde decomposition with the Au-TiO2 catalysts is proposed: The visible light absorbed by the gold nanoparticles, due to surface plasmon resonance effect, induces transition of the 6sp electrons of gold to high energy levels. These energetic electrons can migrate to the conduction band of TiO2 and are seized by oxygen molecules. Meanwhile, the gold nanoparticles capture electrons from the formaldehyde molecules adsorbed on them because of gold’s high electronegativity. O2 adsorbed on the TiO2 supports surface are the major electron acceptor. The more O2 adsorbed, the higher the oxidation activity of the photocatalyst will exhibit. The last part of this thesis demonstrates two innovative applications of the titanate nanostructures. Firstly, trititanate and metastable titanate (Na1.5H0.5Ti3O7) nanofibres are used as intelligent absorbents for removal of radioactive cations and heavy metal ions, utilizing the properties of the ion exchange ability, deformable layered structure, and fibril morphology. Environmental contamination with radioactive ions and heavy metal ions can cause a serious threat to the health of a large part of the population. Treatment of the wastes is needed to produce a waste product suitable for long-term storage and disposal. The ion-exchange ability of layered titanate structure permitted adsorption of bivalence toxic cations (Sr2+, Ra2+, Pb2+) from aqueous solution. More importantly, the adsorption is irreversible, due to the deformation of the structure induced by the strong interaction between the adsorbed bivalent cations and negatively charged TiO6 octahedra, and results in permanent entrapment of the toxic bivalent cations in the fibres so that the toxic ions can be safely deposited. Compared to conventional clay and zeolite sorbents, the fibril absorbents are of great advantage as they can be readily dispersed into and separated from a liquid. Secondly, new generation membranes were constructed by using large titanate and small ã-alumina nanofibres as intermediate and top layers, respectively, on a porous alumina substrate via a spin-coating process. Compared to conventional ceramic membranes constructed by spherical particles, the ceramic membrane constructed by the fibres permits high flux because of the large porosity of their separation layers. The voids in the separation layer determine the selectivity and flux of a separation membrane. When the sizes of the voids are similar (which means a similar selectivity of the separation layer), the flux passing through the membrane increases with the volume of the voids which are filtration passages. For the ideal and simplest texture, a mesh constructed with the nanofibres 10 nm thick and having a uniform pore size of 60 nm, the porosity is greater than 73.5 %. In contrast, the porosity of the separation layer that possesses the same pore size but is constructed with metal oxide spherical particles, as in conventional ceramic membranes, is 36% or less. The membrane constructed by titanate nanofibres and a layer of randomly oriented alumina nanofibres was able to filter out 96.8% of latex spheres of 60 nm size, while maintaining a high flux rate between 600 and 900 Lm–2 h–1, more than 15 times higher than the conventional membrane reported in the most recent study.

Managing process model complexity via abstract syntax modifications

As a result of the growing adoption of Business Process Management (BPM) technology different stakeholders need to understand and agree upon the process models that are used to configure BPM systems. However, BPM users have problems dealing with the complexity of such models. Therefore, the challenge is to improve the comprehension of process models. While a substantial amount of literature is devoted to this topic, there is no overview of the various mechanisms that exist to deal with managing complexity in (large) process models. It is thus hard to obtain comparative insight into the degree of support offered for various complexity reducing mechanisms by state-of-the-art languages and tools. This paper focuses on complexity reduction mechanisms that affect the abstract syntax of a process model, i.e. the structure of a process model. These mechanisms are captured as patterns, so that they can be described in their most general form and in a language- and tool-independent manner. The paper concludes with a comparative overview of the degree of support for these patterns offered by state-of-the-art languages and language implementations.

Managing process model complexity via concrete syntax modifications

While Business Process Management (BPM) is an established discipline, the increased adoption of BPM technology in recent years has introduced new challenges. One challenge concerns dealing with the ever-growing complexity of business process models. Mechanisms for dealing with this complexity can be classified into two categories: 1) those that are solely concerned with the visual representation of the model and 2) those that change its inner structure. While significant attention is paid to the latter category in the BPM literature, this paper focuses on the former category. It presents a collection of patterns that generalize and conceptualize various existing mechanisms to change the visual representation of a process model. Next, it provides a detailed analysis of the degree of support for these patterns in a number of state-of-the-art languages and tools. This paper concludes with the results of a usability evaluation of the patterns conducted with BPM practitioners.