published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

This thesis details investigations into the photophysical properties of lanthanide ions in a number of different systems. The preparation and characterisation of lanthanide containing surfactant salts of the type Ln(A0T)(_3) (Ln = Tb, Nd, Eu, AOT = bis-(2-ethylhexyl) sulfosuccinate) is described. Small angle neutron scattering experiments have been used to determine the size and shape of reverse micelles formed by these surfactants in water/cyclohexane microemulsions. The luminescence lifetimes of the lanthanide ions have been used to investigate the solvation environment within reverse micelle systems as a function of water content. The use of lanthanide complexes based on 1,4,7,10-tetraazacyclododecane bearing phenanthridine antenna in luminescence microscopy has been explored. Samples such as silica particles, onion skin cells and guinea pig heart cells have been imaged. Time- resolved measurements have allowed time gating of the sample from a fluorescent background and lifetime maps of the images have been obtained. The preparation and characterisation of deuteriated complexes of dota (1,4,7,10- tetraazacyclododecane-1,4,7,10-tetraacetic acid) with lanthanide ions is described. Selective deuteriation of both the ring and arm sites allow the relative quenching effects of C-H/D oscillators to be determined for various lanthanides in a series of structurally well defined complexes. Finally, investigations into the distance dependence of the energy transfer between aromatic chromophores and lanthanide ions have been undertaken. The synthesis of a model system linking a phenanthridine donor to a europium complex by poly(valine) spacer units is described. Preliminary photophysical results show that the quantum yield of emission by europium decreases as the distance between the donor acceptor pair is increased.

This thesis introduces a new reverse engineering tool development practice by presenting the development of PowerExcelRigi, a reverse engineering tool built by leveraging Rigi and two selected host tools, PowerPoint and Excel. PowerPoint and Excel, both components of the Microsoft Office Suite, were selected as the host tools for this project because of their large user base, excellent enduser programmability and strong visualization capabilities. The original Rigi reverse engineering tool is used as the backend data engine to make use of its graph computing capabilities. Using PowerExcelRigi, users appreciate the familiar user interface of Excel and PowerPoint and at the same time benefit from the efficiency of Rigi. A custom toolbar in Excel provides a means to perform several reverse engineering tasks. This toolbar follows the standard Office user interface design and seamlessly integrates reverse engineering tasks into the Office environment. Reverse engineering tasks implemented include reusing given program artifacts from Rigi format program fact files, analyzing the artifacts and visualization the analysis results by using Excel, and then reproducing Rigi graphs in PowerPoint. Some Rigi scripts demonstrating typical Rigi functionality have been executed entirely through the Office interface without noticeably using Rigi. Excel and Rigi use a loose, file-based data interchange method to interoperate with each other. In comparison to a new tool with a dedicated user interface, PowerExcelRigi offers users the benefit of the cognitive support derived from their familiarity with the host tool, which decreases the learning barrier to using the new tool. This approach will ... 111 help solve the low adoption problem suffered by many reverse engineering tools. At the same time, development cost is significantly reduced by reusing Rigi, Excel and Powerpoint as existing components. We believe this to be a promising direction for the development of lower-cost, more adoptable low reverse engineering tools.

Reverse engineering (RE) tools can help people extract and understand high level abstractions of subject systems to facilitate software maintenance. However, many of these tools suffer adoption problems in industrial practice. Based on the assumption that industrial users are more likely to accept tools built on top of their current working platforms, the ACRE project (Adoption Centric Reverse Engineering) aims to attack the adoption problem by extending some commonly used tool platforms to implement RE features, rather than writing RE applications from scratch. As part of the ACRE project, my research aims to find a solution for building RE tools on top of a particular Commercial-Off-The-Shelf (COTS) host product-Lotus NotesIDomino and validating feasibility of this approach. My hypothesis is that it is practical to build tools on top of Lotus NotesIDomino to provide RE functionality and to exploit selected features of the host product, such as CSCW (Computer Supported Collaborative Work) features, to facilitate RE tasks. In this thesis, I discuss the benefits and drawbacks of building tools with Lotus NotesIDomino. I propose a solution-the ACRENotes Framework consisting of three layers: Data, Control and Presentation. This framework provides a methodology for using Lotus NotesIDomino to store, manipulate and render RE data. It also offers a Notes template and reusable libraries as a starter kit. Based on this framework, I implemented the prototype application CREST (Collaborative Reverse Engineering Support Tool), which provides selected collaborative RE features. By comparing CREST with Rigi, a traditional stand-alone RE research tool, I discuss CREST'S advantages and disadvantages. Given this prototype tool and the lessons learned, I believe that building RE tools on top of the COTS product Lotus Notes/Domino is feasible and practical.

No description available.

<p>One of the main problems our actual society faces is the shortage of water. Despite the great effort made by authorities and researchers, multiple countries with poor economic resources are experiencing serious difficulties derivative of water scarcity. Desalination provides a feasible solution for inland and coastal areas. Through literature and reviewed articles analysis the reader will meet the actual issues regarding designing a desalination plant, and more over with reverse osmosis (RO) processes, which are the main arguments of this work. One of the big deals is the environmental concern when handling the concentrate disposal. Another important point about desalination processes is the increasingly interest in coupling the units with renewable energy sources (RES). The results point out that regardless of the efforts made until today, additional achievement is required in fields such as membrane’s structure materials for RO method, concentrate disposal systems, governmental water policies review and update, and greater distinction researches between brackish water and seawater RO desalination processes. Taking into consideration the previous outcomes it is finally concluded that some particular steps must be accomplished when beginning a desalination plant design.</p>

Swine influenza (SI) is an acute, highly contagious, respiratory disease of swine. The causative agent of SI infections is swine influenza virus (SIV). SIV is a type A influenza virus classified into the Orthomyxoviridae family and is an enveloped particle with a genome composed of eight negative-orientated RNA segments.<p> The mortality rate of influenza disease in pigs is generally low but morbidity can reach up to 100%. SI infections considerably contribute to respiratory disease in post-weaning pigs, causing significant economic losses due to an increase in the number of days pigs need to reach market weight. In addition, SI infections possess significant human public health concerns. Vaccination is the primary method for the prevention of SI. Currently available vaccines against SI are a combination of two inactivated antigenically distinct SIVs with oil adjuvant. The application of these vaccines induce mainly humoral immune responses. In contrast, application of live attenuated influenza vaccines (LAIV) mimics natural infection and induce strong, long-lived cell-mediated and humoral immunity. Furthermore, LAIV induces cross-protective immunity against different subtypes of influenza A viruses. LAIVs are developed for human and equine influenza viruses but at present no LAIV is available for SIVs.<p> The critical step in influenza virus infection is an initial interaction between virus and cell surface carbohydrates followed by receptor-mediated endocytosis and fusion of the viral and endosomal membranes. Influenza virus entry into cells is mediated by the viral surface glycoprotein hemagglutinin (HA). HA is primary synthesized as a polypeptide in HA0 form. In order to be infectious, HA0 must be cleaved by host proteases into HA1 and HA2 subunits. Therefore, this process is crucial determinant for virus pathogenicity.<p> Our objective was to generate a live attenuated SIVs, particularly a viruses with a modified HA cleavage site resistant to activation during natural infection but which can be activated in vitro by an exogenous protease. Using the reverse genetics technique, we generated two mutant SIVs of strain A/SW/SK/18789/02 (H1N1) containing a modified cleavage site within their HA. Mutant A/SW/SK-R345V (R345V) contained a mutation within HA segment at amino acid (AA) position 345 from Arginine (Arg) to Valine (Val) while the second mutant, A/SW/SK-R345A (R345A) encoded Alanine (Ala) instead of Arginine (Arg) at position AA345 on HA. We showed that HA cleavage in both mutants was strictly dependent on the presence of human neutrophil elastase in tissue culture. These tissue-culture grown mutant SIVs showed similar growth properties in terms of plaque size and growth kinetics, compared to the wild type virus. Both mutant SIVs were able to preserve introduced mutations after multiple passages in tissue culture suggesting that AA substitution within HA cleavage site did not alter genetic stability in the presence of appropriate protease. Furthermore, these mutant SIVs were highly attenuated in pigs but capable of inducing significant cell-mediated and humoral immune responses after two vaccinations via intratracheal (IT) and intranasal (IN) routes. Immune responses induced by vaccination with elastase dependent SIV were sufficient to confer full protection against parental homologous and antigenic variant of H1N1 SIVs and partial protection from heterologous subtypic H3N2 after the challenge. Therefore, elastase-dependent mutant SIV could serve as live vaccine against antigenically distinct swine influenza viruses in pigs.

One of the main problems our actual society faces is the shortage of water. Despite the great effort made by authorities and researchers, multiple countries with poor economic resources are experiencing serious difficulties derivative of water scarcity. Desalination provides a feasible solution for inland and coastal areas. Through literature and reviewed articles analysis the reader will meet the actual issues regarding designing a desalination plant, and more over with reverse osmosis (RO) processes, which are the main arguments of this work. One of the big deals is the environmental concern when handling the concentrate disposal. Another important point about desalination processes is the increasingly interest in coupling the units with renewable energy sources (RES). The results point out that regardless of the efforts made until today, additional achievement is required in fields such as membrane’s structure materials for RO method, concentrate disposal systems, governmental water policies review and update, and greater distinction researches between brackish water and seawater RO desalination processes. Taking into consideration the previous outcomes it is finally concluded that some particular steps must be accomplished when beginning a desalination plant design.

Swine influenza (SI) is an acute, highly contagious, respiratory disease of swine. The causative agent of SI infections is swine influenza virus (SIV). SIV is a type A influenza virus classified into the Orthomyxoviridae family and is an enveloped particle with a genome composed of eight negative-orientated RNA segments.<p> The mortality rate of influenza disease in pigs is generally low but morbidity can reach up to 100%. SI infections considerably contribute to respiratory disease in post-weaning pigs, causing significant economic losses due to an increase in the number of days pigs need to reach market weight. In addition, SI infections possess significant human public health concerns. Vaccination is the primary method for the prevention of SI. Currently available vaccines against SI are a combination of two inactivated antigenically distinct SIVs with oil adjuvant. The application of these vaccines induce mainly humoral immune responses. In contrast, application of live attenuated influenza vaccines (LAIV) mimics natural infection and induce strong, long-lived cell-mediated and humoral immunity. Furthermore, LAIV induces cross-protective immunity against different subtypes of influenza A viruses. LAIVs are developed for human and equine influenza viruses but at present no LAIV is available for SIVs.<p> The critical step in influenza virus infection is an initial interaction between virus and cell surface carbohydrates followed by receptor-mediated endocytosis and fusion of the viral and endosomal membranes. Influenza virus entry into cells is mediated by the viral surface glycoprotein hemagglutinin (HA). HA is primary synthesized as a polypeptide in HA0 form. In order to be infectious, HA0 must be cleaved by host proteases into HA1 and HA2 subunits. Therefore, this process is crucial determinant for virus pathogenicity.<p> Our objective was to generate a live attenuated SIVs, particularly a viruses with a modified HA cleavage site resistant to activation during natural infection but which can be activated in vitro by an exogenous protease. Using the reverse genetics technique, we generated two mutant SIVs of strain A/SW/SK/18789/02 (H1N1) containing a modified cleavage site within their HA. Mutant A/SW/SK-R345V (R345V) contained a mutation within HA segment at amino acid (AA) position 345 from Arginine (Arg) to Valine (Val) while the second mutant, A/SW/SK-R345A (R345A) encoded Alanine (Ala) instead of Arginine (Arg) at position AA345 on HA. We showed that HA cleavage in both mutants was strictly dependent on the presence of human neutrophil elastase in tissue culture. These tissue-culture grown mutant SIVs showed similar growth properties in terms of plaque size and growth kinetics, compared to the wild type virus. Both mutant SIVs were able to preserve introduced mutations after multiple passages in tissue culture suggesting that AA substitution within HA cleavage site did not alter genetic stability in the presence of appropriate protease. Furthermore, these mutant SIVs were highly attenuated in pigs but capable of inducing significant cell-mediated and humoral immune responses after two vaccinations via intratracheal (IT) and intranasal (IN) routes. Immune responses induced by vaccination with elastase dependent SIV were sufficient to confer full protection against parental homologous and antigenic variant of H1N1 SIVs and partial protection from heterologous subtypic H3N2 after the challenge. Therefore, elastase-dependent mutant SIV could serve as live vaccine against antigenically distinct swine influenza viruses in pigs.

A survey performed over existing two pilot-scale and two full-scale RO desalination facilities to study the current status of boron rejection showed a highest rejection 85% leading to permeate boron concentration of 0.52 mg/L, and recent studies predicted a cost increase due to incorporation of boron reduction systems. Mathematical models were developed to study the process performance and related cost implications. The deterministic process model was verified with pilot-scale experiment performed using a single spiral wound module and was later modified to represent the full-scale design options available to meet the required water quality criteria. Then the selected full-scale design options were simulated to predict their performance in terms of recovery and boron rejection. For cost analysis, to account for uncertainty probability models were developed for stochastic inputs to the cost estimation model and were used with operating parameters from the full-scale simulations to determine the expected total cost of water produced. Later, a sensitivity analysis was performed to observe the effect of change in uncertainty of inputs. Further, the applications of the deterministic process model are suggested.