Investigation of the biosynthesis of exopolysaccharides within the biofilm matrix of Pseudomonas aeruginosa and Pseudomonas syringae pv. actinidiea : a thesis presented in partial fulfilment of the requirements for degree of Doctor of Philosophy in Microbiology and Genetics at Massey University, Manawatu, New Zealand

Polysaccharides are highly abundant natural biopolymers, which have biologically significant structural functions in living organisms. Various polysaccharides, with specific physicochemical properties, contribute to biofilm formation; defined as cell aggregations surrounded by extracellular polymeric substances. They are also important in the context of bacterial pathogenesis, while some have been harnessed for industrial and biomedical applications due to their unique chemical compositions and properties. In present study, we aimed at studying biofilm formation by Pseudomonas aeruginosa and P. syringae pv. actinidiae, respectively known as human and plant pathogens. In this context we focused on the production of exopolysaccharides, which predominantly constitute the biofilm matrix of these pathogenic bacteria. Here, we uncovered that the polysaccharide isolated from P. syringae pv. actinidiae biofilm mainly consists of rhamnose, fucose and glucose and it was cautiously introduced as a novel polysaccharide. In the context of disease control, and developing a management program, we provided some evidences for the effectiveness of chlorine dioxide and kasugamycin in the control of the bacteria living in both biofilm and planktonic modes. Furthermore, we investigated alginate biosynthesis as major polysaccharide contributing to mucoid biofilm formation by P. aeruginosa. We generated various mutants producing a variety of alginates with different chemical compositions. Also, this enabled us to analyse functional relationships of protein subunits involved in multiple steps of alginate biosynthesis including alginate polymerization, modification and secretion. We present evidence that while alginate unravelled that while alginate is polymerised and translocated across the membrane by a multiprotein complex, acetylation and epimerisation events positively and negatively correlated with the polymerization of the alginate or molecular mass, respectively. Analysis of the biofilms showed that biofilm architecture and cell-to-cell interactions were differently impacted by various compositions of the alginates. Also, this study provided insights into the c-di-GMP mediated activation of alginate polymerization upon binding to c-di-GMP as well as assigning functional roles to Alg8 and Alg44 including their subcellular localization and distribution. Here, we also used current knowledge of the alginate biosynthesis pathway to assess the production of alginate from biotechnologically accepted heterologous hosts including Escherichia coli and Bacillus megaterium strains. Primarily, we evaluated the production and functionality of the minimal protein requirements in nonpathogenic heterologous hosts, required for producing alginate precursor, and proceeding into polymerization and secretion steps. Overall, we concluded that polysaccharides play a major role in the formation of bacterial biofilms while chemical composition is a key determinant for biofilm architecture and development. This contribution to understanding the biosynthesis of bacterial polysaccharides and their properties could provide the necessary knowledge not only for developing novel therapeutics, but also for harnessing such biopolymers for various industrial applications and production via biotechnological procedures

Design and fabrication of field-effect III-V Schottky junction solar cells

“A new concept of field-effect photovoltaic devices with a focus on design and fabrication of single and multi-junction solar cells using III-V materials has been shown and proved. Schottky solar cells based on metal-(insulator)-semiconductor (M-I-S) structure have been designed and fabricated using various wide bandgap semiconductors, such as GaAs and Al0.3Ga0.7As. A secondary bias layer has been introduced to the device structure, in which it creates additional band bending and subsequently depletion region at the flat band regions on the top surface of the device. It should be mentioned that the bias layer is designed to be electrically isolated from the main current collection contacts, in order to prevent the decrease in Schottky barrier height due to change in applied forward voltage or external load resistance. The electrical and optical characterization results from these Isolated Collection and Biasing Schottky Solar Cells (ICBS) show an improvement in photovoltaic response compared to conventional Schottky junction solar cells. This demonstrates the effectiveness of this novel strategy to design and fabricate high-efficiency multi-junction solar cells”--Abstract, page iii

Effect of Convection Associated with Cross-Section Change During Directional Solidification of Binary Alloys on Dendritic Array Morphology and Macrosegregation

This dissertation explores the role of different types of convection on macrosegregation and on dendritic array morphology of two aluminum alloys directionally solidified through cylindrical graphite molds having both cross-section decrease and increase. Al- 19 wt. % Cu and Al-7 wt. % Si alloys were directionally solidified at two growth speed of 10 and 29.1 µm s-1 and examined for longitudinal and radial macrosegregation, and for primary dendrite spacing and dendrite trunk diameter. Directional solidification of these alloys through constant cross-section showed clustering of primary dendrites and parabolic-shaped radial macrosegregation profile, indicative of “steepling convection” in the mushy-zone. The degree of radial macrosegregation increased with decreased growth speed. The Al- 19 wt. % Cu samples, grown under similar conditions as Al-7 wt. % Si, showed more radial macrosegregation because of more intense “stepling convection” caused by their one order of magnitude larger coefficient of solutal expansion.Positive macrosegregation right before, followed by negative macrosegregation right after an abrupt cross-section decrease (from 9.5 mm diameter to 3.2 mm diameter), were observed in both alloys; this is because of the combined effect of thermosolutal convection and area-change-driven shrinkage flow in the contraction region. The degree of macrosegregation was found to be higher in the Al- 19 wt. % Cu samples. Strong area-change-driven shrinkage flow changes the parabolic-shape radial macrosegregation in the larger diameter section before contraction to “S-shaped” profile. But in the smaller diameter section after the contraction very low degree of radial macrosegregation was found.The samples solidified through an abrupt cross-section increase (from 3.2 mm diameter to 9.5 mm diameter) showed negative macrosegregation right after the cross-section increase on the expansion platform. During the transition to steady-state after the expansion, radial macrosegregation profile in locations close to the expansion was found to be “S-shaped”. This is attributed to the redistribution of solute-rich liquid ahead of the mushy-zone as it transitions from the narrow portion below into the large diameter portion above. Solutal remelting and fragmentation of dendrite branches, and floating of these fragmented pieces appear to be responsible for spurious grains formation in Al- 19 wt. % Cu samples after the cross-section expansion. New grain formation was not observed in Al-7 wt. % Si in similar locations; it is believed that this is due to the sinking of the fragmented dendrite branches in this alloy.Experimentally observed radial and axial macrosegregations agree well with the results obtained from the numerical simulations carried out by Dr. Mark Lauer and Prof. David R. Poirier at the University of Arizona.Trunk Diameter (TD) of dendritic array appears to respond more readily to the changing growth conditions as compared to the Nearest Neighbor Spacing (NNS) of primary dendrites

Sensitivity of staphylococcus epidermidis to chlorhexidine and associated resistance properties

Staphylococcus epidermidis are common Gram-positive bacteria and are responsible for a number of life-threatening nosocomial infections. Treatment of S. epidermidis infection is problematic because the organism is usually resistant to many antibiotics. The high degree of resistance of this organism to a range of antibiotics and disinfectants is widely known. The aims of this thesis were to investigate and evaluate the susceptibility of isolates of S. epidermidis from various infections to chlorhexidine (CHX) and to other disinfectants such as benzalkonium chloride (BKC), triclosan (TLN) and povidone-iodine (PI). In addition, the mechanisms of resistance of S. epidermidis to chlorhexidine (the original isolates and strains adapted to chlorhexidine by serial passage) were examined and co-resistance to clinically relevant antibiotics investigated. In 3 of the 11 S. epidermidis strains passaged in increasing concentrations of chlorhexidine, resistance to the disinfectant arose (16-fold). These strains were examined further, each showing stable chlorhexidine resistance. Co-resistance to other disinfectants such as BKC, TLN and PI and changes in cell surface hydrophobicity were observed. Increases in resistance were accompanied by an increase in the proportion of neutral lipids and phospholipids in the cell membrane. This increase was most marked in diphosphatidylglycerol. These observations suggest that some strains of S. epidermidis can become resistant to chlorhexidine and related disinfectants/antiseptics by continual exposure. The mechanisms of resistance appear to be related to changes in membrane lipid compositions

Characterisation of MIMO radio propagation channels

Due to the incessant requirement for higher performance radio systems, wireless designers have been constantly seeking ways to improve spectrum efficiency, link reliability, service quality, and radio network coverage. During the past few years, space-time technology which employs multiple antennas along with suitable signalling schemes and receiver architectures has been seen as a powerful tool for the implementation of the aforementioned requirements. In particular, the concept of communications via Multiple-Input Multiple-Output (MIMO) links has emerged as one of the major contending ideas for next generation ad-hoc and cellular systems. This is inherently due to the capacities expected when multiple antennas are employed at both ends of the radio link. Such a mobile radio propagation channel constitutes a MIMO system. Multiple antenna technologies and in particular MIMO signalling are envisaged for a number of standards such as the next generation of Wireless Local Area Network (WLAN) technology known as 802.1 ln and the development of the Worldwide Interoperability for Microwave Access (WiMAX) project, such as the 802.16e. For the efficient design, performance evaluation and deployment of such multiple antenna (space-time) systems, it becomes increasingly important to understand the characteristics of the spatial radio channel. This criterion has led to the development of new sounding systems, which can measure both spatial and temporal channel information. In this thesis, a novel semi-sequential wideband MIMO sounder is presented, which is suitable for high-resolution radio channel measurements. The sounder produces a frequency modulated continuous wave (FMCW) or chirp signal with variable bandwidth, centre frequency and waveform repetition rate. It has programmable bandwidth up to 300 MHz and waveform repetition rates up to 300 Hz, and could be used to measure conventional high- resolution delay/Doppler information as well as spatial channel information such as Direction of Arrival (DOA) and Direction of Departure (DOD). Notably the knowledge of the angular information at the link ends could be used to properly design and develop systems such as smart antennas. This thesis examines the theory of multiple antenna propagation channels, the sounding architecture required for the measurement of such spatial channel information and the signal processing which is used to quantify and analyse such measurement data. Over 700 measurement files were collected corresponding to over 175,000 impulse responses with different sounder and antenna array configurations. These included measurements in the Universal Mobile Telecommunication Systems Frequency Division Duplex (UMTS-FDD) uplink band, the 2.25 GHz and 5.8 GHz bands allocated for studio broadcast MIMO video links, and the 2.4 GHz and 5.8 GHz ISM bands allocated for Wireless Local Area Network (WLAN) activity as well as for a wide range of future systems defined in the WiMAX project. The measurements were collected predominantly for indoor and some outdoor multiple antenna channels using sounding signals with 60 MHz, 96 MHz and 240 MHz bandwidth. A wide range of different MIMO antenna array configurations are examined in this thesis with varying space, time and frequency resolutions. Measurements can be generally subdivided into three main categories, namely measurements at different locations in the environment (static), measurements while moving at regular intervals step by step (spatial), and measurements while the receiver (or transmitter) is on the move (dynamic). High-scattering as well as time-varying MIMO channels are examined for different antenna array structures