An investigation into the tropospheric chemistry of acidic aerosols and ammonia in the laboratory

This thesis describes a broad range of experiments based on an aerosol flow-tube system to probe the interactions between atmospherically relevant aerosols with trace gases. This apparatus was used to obtain simultaneous optical and size distribution measurements using FTIR and SMPS measurements respectively as a function of relative humidity and aerosol chemical composition. Heterogeneous reactions between various ratios of ammonia gas and acidic aerosols were studied in aerosol form as opposed to bulk solutions. The apparatus is unique, in that it employed two aerosol generation methods to follow the size evolution of the aerosol while allowing detailed spectroscopic investigation of its chemical content. A novel chemiluminescence apparatus was also used to measure [NH4+]. SO2.H2O is an important species as it represents the first intermediate in the overall atmospheric oxidation process of sulfur dioxide to sulfuric acid. This complex was produced within gaseous, aqueous and aerosol SO2 systems. The addition of ammonia, gave mainly hydrogen sulfite tautomers and disulfite ions. These species were prevalent at high humidities enhancing the aqueous nature of sulfur (IV) species. Their weak acidity is evident due to the low [NH4+] produced. An increasing recognition that dicarboxylic acids may contribute significantly to the total acid burden in polluted urban environments is evident in the literature. It was observed that speciation within the oxalic, malonic and succinic systems shifted towards the most ionised form as the relative humidity was increased due to complete protonisation. The addition of ammonia produced ammonium dicarboxylate ions. Less reaction for ammonia with the malonic and succinic species were observed in comparison to the oxalic acid system. This observation coincides with the decrease in acidity of these organic species. The interaction between dicarboxylic acids and ‘sulfurous’/sulfuric acid has not been previously investigated. Therefore the results presented here are original to the field of tropospheric chemistry. SHO3-; S2O52-; HSO4-; SO42- and H1,3,5C2,3,4O4-;C2,3,4O4 2- were the main components found in the complex inorganic-organic systems investigated here. The introduction of ammonia produced ammonium dicarboxylate as well as ammonium disulfite/sulfate ions and increasing the acid concentrations increased the total amount of [NH4+].

Capillary electrophoresis with boron doped diamond electrode for amperometric detection of low molecular weight biological substrate

The research work in this thesis included the sensitive and selective separation of biological substance by capillary electrophoresis with a boron doped diamond electrode for amperometric detection. Chapter 1 introduced the capillary electrophoresis and electrochemical detection. It included the different modes of capillary electrophoresis, polyelectrolyte multilayers coating for open tubular capillary electrochromatography, different modes of electrochemical detection and carbon based electrodes. Chapter 2 showed the synthesized and electropolymerized N-acetyltyramine with a negatively charged sulfobutylether-β-cyclodextrin on a boron doped diamond (BDD) electrode followed by the electropolymerzation of pyrrole to form a stable and permselective film for selective dopamine detection. For comparison, a glassy carbon (GC) electrode with a combined electropolymerized permselective film of polytyramine and polypyrrole-1-propionic acid was used for selective detection of dopamine. The detection limit of dopamine was improved from 100 nM at a GC electrode to 5 nM at a BDD electrode. Chapter 3 showed field-amplified sample stacking using a fused silica capillary coated with gold nanoparticles embedded in poly(diallyldimethylammonium) chloride, which has been investigated for the electrophoretic separation of indoxyl sulphate, homovanillic acid and vanillylmandelic acid. The detection limit of the three analytes obtained by using a boron doped diamond electrode was around 75 nM, which was significantly below their normal physiological levels in biological fluids. This combined separation and detection scheme was applied to the direct analysis of these analytes and other interfereing chemicals including uric and ascorbic acids in urine samples without off-line sample treatment or preconcentration. Chapter 4 showed the selective detection of Pseudomonas Quinolone Signal, PQS for quorum sensing from its precursor HHQ, using a simply boron doped diamond electrode. Furthermore, by combining poly(diallyldimethylammonium) chloride modified fused silica capillary with a BDD electrode for amperometric detection, PQS was separated from HHQ and other analogues. The detection limit of PQS was as low as 65 nM. Different P. aeruginosa mutant strains were studied. Chapter 5 showed the separation of aminothiols by layer-by-layer coating of silica capillary with a boron doped diamond electrode. The capillary was layer-by-layer coated with the polycation poly(diallyldimethylammonium) chloride and negatively charged silica nanoparticles. All the aminothiols was separated and detected using a BDD electrode in an acidic electrolyte. It was a novel scheme for the separation and detection of glutathione reduced and oxidized forms, which is important for estimated overstressed level in the human system.

A study of the oxygen electrochemistry of ruthenium and iridium

This thesis is concerned with an investigation of the anodic behaviour of ruthenium and iridium in aqueous solution and particularly of oxygen evolution on these metals. The latter process is of major interest in the large-scale production of hydrogen gas by the electrolysis of water. The presence of low levels of ruthenium trichloride ca. 10-4 mol dm-3 in acid solution give a considerable increase in the rate of oxygen evolution from platinum and gold, but not graphite, anodes. The mechanism of this catalytic effect was investigated using potential step and a.c. impedance technique. Earlier suggestions that the effect is due to catalysis by metal ions in solution were proved to be incorrect and it was shown that ruthenium species were incorporated into the surface oxide film. Changes in the oxidation state of these ruthenium species is probably responsible for the lowering of the oxygen overvoltage. Both the theoretical and practical aspects of the reaction were complicated by the fact that at constant potential the rates of both the catalysed and the uncatalysed oxygen evolution processes exhibit an appreciable, continuous decrease with either time or degree of oxidation of the substrate. The anodic behaviour of iridium in the oxide layer region has been investigated using conventional electrochemical techniques such as cyclic voltammetry. Applying a triangular voltage sweep at 10 Hz, 0.01 to 1.50V increases the amount of electric charge which the surface can store in the oxide region. This activation effect and the mechanism of charge storage is discussed in terms of both an expanded lattice theory for oxide growth on noble metals and a more recent theory of irreversible oxide formation with subsequent stoichiometry changes. The lack of hysteresis between the anodic and cathodic peaks at ca. 0.9 V suggests that the process involved here is proton migration in a relatively thick surface layer, i.e. that the reaction involved is some type of oxide-hydroxide transition. Lack of chloride ion inhibition in the anodic region also supports the irreversible oxide formation theory; however, to account for the hydrogen region of the potential sweep a compromise theory involving partial reduction of the outer regions of iridium oxide film is proposed. The loss of charge storage capacity when the activated iridium surface is anodized for a short time above ca. 1.60 V is attributed to loss by corrosion of the outer active layer from the metal surface. The behaviour of iridium at higher anodic potentials in acid solution was investigated. Current-time curves at constant potential and Tafel plots suggested that a change in the mechanism of the oxygen evolution reaction occurs at ca. 1.8 V. Above this potential, corrosion of the metal occurred, giving rise to an absorbance in the visible spectrum of the electrolyte (λ max = 455 nm). It is suggested that the species involved was Ir(O2)2+. A similar investigation in the case of alkaline electrolyte gave no evidence for a change in mechanism at 1.8 V and corrosion of the iridium was not observed. Oxygen evolution overpotentials were much lower for iridium than for platinum in both acidic and alkaline solutions.

Characterisation of bacteriophage-host interactions in Lactococcus lactis

Lactococcus lactis is used extensively world-wide for the production of fermented dairy products. Bacteriophages (phages) infecting L. lactis can result in slow or incomplete fermentations, or may even cause total fermentation failure. Therefore, bacteriophages disrupting L. lactis fermentation are of economic concern. This thesis employed a multifaceted approach to investigate various molecular aspects of phage-host interaction in L. lactis. The genome sequence of an Irish dairy starter strain, the prophage-cured L. lactis subsp. cremoris UC509.9, was studied. The 2,250,427 bp circular chromosome represents the smallest among its sequenced lactococcal equivalents. The genome displays clear genetic adaptation to the dairy niche in the form of extensive reductive evolution. Gene prediction identified 2066 protein-encoding genes, including 104 which showed significant homology to transposase-specifying genes. Over 9 % of the identified genes appear to be inactivated through stop codons or frame shift mutations. Many pseudogenes were found in genes that are assigned to carbohydrate and amino acid transport and metabolism orthologous groups, reflecting L. lactis UC509.9’s adaptation to the lactose and casein-rich dairy environment. Sequence analysis of the eight plasmids of L. lactis revealed extensive adaptation to the dairy environment. Key industrial phenotypes were mapped and novel lactococcal plasmid-associated genes highlighted. In addition to chromosomally-encoded bacteriophage resistance systems, six functional such systems were identified, including two abortive infection systems, AbiB and AbiD1, explaining the observed phage resistance of L. lactis UC509.9 Molecular analysis suggests that the constitutive expression of AbiB is not lethal to cells, suggesting the protein is expressed in an un/inactivated form. Analysis of 936 species phage sk1-escape mutants of AbiB revealed that all such mutants harbour mutations in orf6, which encodes the major capsid protein. Results suggest that the major capsid protein is required for activation of the AbiB system, although this requires furrther investigations. Temporal transcriptomes of L. lactis UC509.9 undergoing lytic infection with either one of two distinct bacteriophages, Tuc2009 and c2, was determined and compared to the transcriptome of uninfected UC509.9 cells. Whole genome microarrays performed at various time-points post-infection demonstrated a rather modest impact on host transcription. Alterations in the UC509.9 transcriptome during lytic infection appear phage-specific, with a relatively small number of differentially transcribed genes shared between infection with either Tuc2009 or c2. Transcriptional profiles of both bacteriophages during lytic infection was shown to generally correlate with previous studies and allowed the confirmation of previously predicted promoter sequences. Bioinformatic analysis of genomic regions encoding the presumed cell wall polysaccharide (CW PS) biosynthesis gene cluster of several strains of L. lactis was performed. Results demonstrate the presence of three dominant genetic types of this gene cluster, termed type A, B and C. These regions were used for the development of a multiplex PCR to identify CW PS genotype of various lactococcal strains. Analysis of 936 species phage receptor binding protein phylogeny (RBP) and CW PS genotype revealed an apparent correlation between RBP phylogeny and CW PS type, thereby providing a partial explanation for the observed narrow host range of 936 phages. Further analysis of the genetic locus encompassing the presumed CW PS biosynthesis operon of eight strains identified as belonging to the CW PS C (geno)type, revealed the presence of a variable region among the examined strains. The obtained comparative analysis allowed for the identification of five subgroups of the C type, named C1 to C5. We purified an acidic polysaccharide from the cell wall of L. lactis 3107 (C2 subtype) and confirmed that it is structurally different from the CW PS of the C1 subtype L. lactis MG1363. Combinations of genes from the variable region of C2 subtype were amplified from L. lactis 3107 and introduced into a mutant of the C1 subtype L. lactis NZ9000 (a direct derivative of MG1363) deficient in CW PS biosynthesis. The resulting recombinant mutant synthesized a CW PS with a composition characteristic for that of the C2 subtype L. lactis 3107 and not the wildtype C1 L. lactis NZ9000. The recombinant mutant exhibited a changed phage resistance/sensitivity profile consistent with that of L. lactis 3107, which unambiguously demonstrated that L. lactis 3107 CW PS is the host cell surface receptor of two bacteriophages belonging to the P335 species as well as phages that are member of the 936 species. The research presented in this thesis has significantly advanced our understanding of L. lactis bacteriophage-host interactions in several ways. Firstly, the examination of plasmidencoded bacteriophage resistance systems has allowed inferences to be made regarding the mode of action of AbiB, thereby providing a platform for further elucidation of the molecular trigger of this system. Secondly, the phage infection transcriptome data presented, in addition to previous work, has made L. lactis a model organism in terms of transcriptomic studies of bacteriophage-host interactions. And finally, the research described in this thesis has for the first time explicitly revealed the nature of a carbohydrate bacteriophage receptor in L. lactis, while also providing a logical explanation for the observed narrow host ranges exhibited by 936 and P335 phages. Future research in discerning the structures of other L. lactis CW PS, combined with the determination of the molecular interplay between receptor binding proteins of these phages and CW PS will allow an in depth understanding of the mechanism by which the most prevalent lactococcal phages identify and adsorb to their specific host.