Ge/Si quantum dot formation from non-uniform cluster fluxes

The controlled growth of ultra-small Ge/Si quantum dot (QD) nuclei (≈1 nm) suitable for the synthesis of uniform nanopatterns with high surface coverage, is simulated using atom-only and size non-uniform cluster fluxes. It is found that seed nuclei of more uniform sizes are formed when clusters of non-uniform size are deposited. This counter-intuitive result is explained via adatom-nanocluster interactions on Si(100) surfaces. Our results are supported by experimental data on the geometric characteristics of QD patterns synthesized by nanocluster deposition. This is followed by a description of the role of plasmas as non-uniform cluster sources and the impact on surface dynamics. The technique challenges conventional growth modes and is promising for deterministic synthesis of nanodot arrays.

Suppression of cluster ions during particle formation events in the atmosphere

Cluster ions and charged and neutral nanoparticle concentrations were monitored using a neutral cluster and air ion spectrometer (NAIS) over a period of one year in Brisbane, Australia. The study yielded 242 complete days of usable data, of which particle formation events were observed on 101 days. Small, intermediate and large ion concentrations were evaluated in real time. In the diurnal cycle, small ion concentration was highest during the second half of the night while large ion concentrations were a maximum during the day. The small ion concentration showed a decrease when the large ion concentration increased. Particle formation was generally followed by a peak in the intermediate ion concentration. The rate of increase of intermediate ions was used as the criteria for identifying particle formation events. Such events were followed by a period of growth to larger sizes and usually occurred between 8 am and 2 pm. Particle formation events were found to be related to the wind direction. The gaseous precursors for the production of secondary particles in the urban environment of Brisbane have been shown to be ammonia and sulfuric acid. During these events, the nanoparticle number concentrations in the size range 1.6 to 42 nm, which were normally lower than 1x104 cm-3, often exceeded 5x104 cm-3 with occasional values over 1x105 cm-3. Cluster ions generally occurred in number concentrations between 300 and 600 cm-3 but decreased significantly to about 200 cm-3 during particle formation events. This was accompanied by an increase in the large ion concentration. We calculated the fraction of nanoparticles that were charged and investigated the occurrence of possible overcharging during particle formation events. Overcharging is defined as the condition where the charged fraction of particles is higher than in charge equilibrium. This can occur when cluster ions attach to neutral particles in the atmosphere, giving rise to larger concentrations of charged particles in the short term. Ion-induced nucleation is one of the mechanisms of particle formation in the atmosphere, and overcharging has previously been considered as an indicator of this process. The possible role of ions in particle formation was investigated.

Reactive Oxygen Species and Reactive Nitrogen Species in Epigenetic Modifications

For the normal homeostasis of a cell, there must be a balance between radical oxygen species/radical nitrogen species (ROS/RNS) production and the neutralization of these species by antioxidant scavenging. In times of stress, this balance is not maintained, and the result is oxidative stress. This stress can affect many pathways in the body and result in pathological consequences. Recent evidence suggests that ROS/RNS can affect the epigenetic regulation of genes by affecting the function of histone and DNA modifying enzymes, thus affecting phenotypic changes within the cellular environment. In the following chapter, we provide a broad overview of how oxidative stress induced by ROS/RNS can affect epigenetics, and using lung disease as our model we link the connection between these processes.

Pulmonary innate immunity in children with protracted bacterial bronchitis

Objective To determine bronchoalveolar lavage (BAL) levels of 3 innate immunity components (human alpha-defensin-2 [hBD2], mannose-binding lectin [MBL], and surfactant protein-A [SP-A], the relationship with airway neutrophilia and infection, and cytokine production of stimulated BAL cells in children with current protracted bacterial bronchitis (PBB), children with resolved PBB (PBB well), and controls. Study design BAL of 102 children (mean age 2.8 years) fulfilling predefined criteria of current PBB (n=61), PBB well (n=20), and controls (n=21) was cultured (quantitative bacteriology) and viruses examined by polymerase chain reaction. hBD2, MBL, and SP-A were measured, and cytokine production of lipopolysaccharide-stimulated BAL cells were determined. Results Median hBD2 and MBL levels were significantly higher in the current PBB group (hBD2 = 164.4, IQR 0-435.5pg/mL; MBL = 1.7, 0.4-4ng/mL) than in the PBB well group (hBD2 = 0, IQR 0-85.2; MBL = 0.6, IQR 0.03-2.9) and controls (hBD2 = 3.6, IQR 0-126; MBL = 0.4, IQR 0.02-79). hBD2 was significantly higher in children with airway infection (n = 54; median 76.9, IQR 0-397.3) compared with those without (n = 48; 0, IQR 0-236.3), P=0.04. SP-A levels and cytokine production of stimulated BAL cells were similar between groups. Conclusion In children's airways, hBD2, but not MBL and SP-A, relates to inflammation and infection. In children with PBB, mechanisms involving airway hBD2 and MBL are augmented. These pulmonary innate immunity components and the ability of BAL cells to respond to stimuli are unlikely to be deficient.

Nitrous oxide emissions from fertilized, irrigated cotton (Gossypium hirsutum L.) in the Aral Sea Basin, Uzbekistan : influence of nitrogen applications and irrigation practices

Nitrous oxide emissions were monitored at three sites over a 2-year period in irrigated cotton fields in Khorezm, Uzbekistan, a region located in the arid deserts of the Aral Sea Basin. The fields were managed using different fertilizer management strategies and irrigation water regimes. N2O emissions varied widely between years, within 1 year throughout the vegetation season, and between the sites. The amount of irrigation water applied, the amount and type of N fertilizer used, and topsoil temperature had the greatest effect on these emissions. Very high N2O emissions of up to 3000 μg N2O-N m−2 h−1 were measured in periods following N-fertilizer application in combination with irrigation events. These “emission pulses” accounted for 80–95% of the total N2O emissions between April and September and varied from 0.9 to 6.5 kg N2O-N ha−1.. Emission factors (EF), uncorrected for background emission, ranged from 0.4% to 2.6% of total N applied, corresponding to an average EF of 1.48% of applied N fertilizer lost as N2O-N. This is in line with the default global average value of 1.25% of applied N used in calculations of N2O emissions by the Intergovernmental Panel on Climate Change. During the emission pulses, which were triggered by high soil moisture and high availability of mineral N, a clear diurnal pattern of N2O emissions was observed, driven by daily changes in topsoil temperature. For these periods, air sampling from 8:00 to 10:00 and from 18:00 to 20:00 was found to best represent the mean daily N2O flux rates. The wet topsoil conditions caused by irrigation favored the production of N2O from NO3− fertilizers, but not from NH4+ fertilizers, thus indicating that denitrification was the main process causing N2O emissions. It is therefore argued that there is scope for reducing N2O emission from irrigated cotton production; i.e. through the exclusive use of NH4+ fertilizers. Advanced application and irrigation techniques such as subsurface fertilizer application, drip irrigation and fertigation may also minimize N2O emission from this regionally dominant agro-ecosystem.

Investigating the effect of internal fixation stiffness on metaphyseal fracture healing in a mouse model

This project examined the differences in healing of metaphyseal bone, when the implants of variable stiffness are used for fracture fixation. This knowledge is important in development of novel orthopaedic implants, used in orthopaedic surgery to stabilise the fractures. Dr Koval used a mouse model to create a fracture, and then assessed its healing with a combination of mechanical testing, microcomputed tomography and histomorphometric examination.

Ethnic cluster lifecycle : a case of Chinese restaurants in South East Queensland

Immigrant entrepreneurs tend to start businesses within their ethnic enclave (EE), as it is an integral part of their social and cultural context and the location where ethnic resources reside (Logan, Alba, & Stults, 2003). Ethnic enclaves can be seen as a form of geographic cluster, China Towns are exemplar EEs, easily identified by the clustering of Chinese restaurants and other ethnic businesses in one central location. Studies on EE thus far have neglected the life cycles stages of EE and its impact on the business experiences of the entrepreneurs. In this paper, we track the formation, growth and decline of an EE. We argue that EE is a special industrial cluster and as such it follows the growth conditions proposed by the cluster life cycle theory (Menzel & Fornahl, 2009). We report a mixed method study of Chinese Restaurants in South East Queensland. Based on multiple sources of data, we concluded that changes in government policies leading to a sharp increase of immigrant numbers from a distinctive culture group can lead to the initiation and growth of the EE. Continuous incoming of new immigrants and increase competition within the cluster mark the mature stage of the EE, making the growth condition more favourable “inside” the cluster. A decline in new immigrants from the same ethnic group and the increased competition within the EE may eventually lead to the decline of such an industrial cluster, thus providing more favorable condition for growth of business outside the cluster.

Clinically-based automatic implant fitting for shape optimization of fracture fixation plates

Complex bone contour and anatomical variations between individual bones complicate the process of deriving an implant shape that fits majority of the population. This thesis proposes an automatic fitting method for anatomically-precontoured plates based on clinical requirements, and investigated if 100% anatomical fit for a group of bone is achievable through manual bending of one plate shape. It was found that, for the plate used, 100% fit is impossible to achieve through manual bending alone. Rather, newly-developed shapes are also required to obtain anatomical fit in areas with more complex bone contour.

The antigen 43 structure reveals a molecular velcro-like mechanism of autotransporter-mediated bacterial clumping

Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms.

Discovery of an archetypal protein transport system in bacterial outer membranes

Bacteria have mechanisms to export proteins for diverse purposes, including colonization of hosts and pathogenesis. A small number of archetypal bacterial secretion machines have been found in several groups of bacteria and mediate a fundamentally distinct secretion process. Perhaps erroneously, proteins called 'autotransporters' have long been thought to be one of these protein secretion systems. Mounting evidence suggests that autotransporters might be substrates to be secreted, not an autonomous transporter system. We have discovered a new translocation and assembly module (TAM) that promotes efficient secretion of autotransporters in proteobacteria. Functional analysis of the TAM in Citrobacter rodentium, Salmonella enterica and Escherichia coli showed that it consists of an Omp85-family protein, TamA, in the outer membrane and TamB in the inner membrane of diverse bacterial species. The discovery of the TAM provides a new target for the development of therapies to inhibit colonization by bacterial pathogens.