Science

Publication Search Results

Now showing 1 - 10 of 76
  • (2021) Arman, Seyedyousef
    Thesis
    Impedance cellular biosensors are amongst a promising type of label-free technologies in providing ongoing insights into physiological function of cells over a period ranging from several minutes to several days. However, detection of a highly specific biomolecular event using traditional impedance assays is technically challenging. The nature of impedance signal relies on the changes in the local ionic environment at the interface, providing many biochemical events at once lacking biomolecular specificity. The next decade is then likely to witness an interest in using developed impedance assays. Impedance-quartz crystal microbalance (QCM), impedance-surface plasmon resonance spectroscopy (SPR), and impedance-optical microscopy are the hybrid approaches that have been employed in the field. Integrating impedance biosensors to another sensing method, in particular new microscopies that enable identification of cellular structures and processes with a high degree of specificity, enhances the potential of traditional assays by providing additional relevant information. Herein an effective approach for accurate interpretation of impedance signal is presented. By development of optical/electrical multi-electrode chips, light was utilized for direct visualization of cell structures and processes on the surface of the microelectrode. It was essential to achieve both high throughput electrical results and high-resolution microscopy images to detect the transient changes inside the cells. Therefore, the strategy of simultaneous dual sensing was developed in three main steps. For the establishment of a reliable dual sensing readout, it was essential to use a commercial biosensing device (known as xCELLigence) in the first step. This approach enabled to compare the electrical results of developed dual biosensing device and a commercial device (as a high throughput assay for electrical measurement of subtle changes within the cell monolayer). The highly sensitive measurement of commercial device also made it possible to investigate the ongoing mechanism behind receptor/ligand activation. The signalling pathway was determined by using different pharmacological inhibitors. In a separate parallel experiment, fluorescence microscopy was used to visualise the specificity of histamine/HeLa cell interaction which was coupled to intracellular calcium rise. While it is assumed these two processes are connected, this could not be determined definitively by the sole biosensing device application. In the second step it was necessary to develop a setup with the capability of data acquisition in both the high throughput electrical setup and high-resolution fluorescence microscopy on a single platform. The first material of choice for the fabrication of this biosensor was ITO because of its electrical conductivity and optical transparency. It was shown that contribution of cells to the overall signal on the surface of ITO depends on the parameters including sensing area and width of microfingers. Furthermore, comparing the ITO results with the identical gold microelectrode revealed the ITO severely lacked sensitivity compared to gold. This was due to a better penetration of the electric field within the cell layer on the gold surface. The addition of a viewing window made a dual sensing readout possible on the gold microelectrode. Finally, the finding were used to maximize the system efficiency and precision for the detection of minute change of cells to the drug. The reduction of the microfingers down to the single cell level led to a more efficient distribution of electric field within cell monolayer. A high density of gold electrode arrays also increased the chance of individual cells blocking the current which was desirable. The added value of the developed biosensor was illustrated by studying GPCR activation in a more thorough manner using simultaneous fluorescence microscopy. The simultaneous optical/electrical experiment was performed as a powerful approach to translate specific intracellular biomolecular event contributing to the morphological changes in cell/drug interaction.

  • (2020) Sadeghi, Behnam
    Thesis
    Classification methods capable of identifying signals or groups of samples, whose geochemical composition is affected by dispersion from mineralisation, are critical in regional and local scale mineral exploration projects. This study compares various population and spatial fractal classification models with several new models to identify populations associated with VMS-style mineralisation in regional till geochemical data from Sweden and both Cyprus-style VMS deposits and anthropogenic contamination in soil data from Cyprus. The new models include concentration-distance from centroids (C-DC), concentration-concentration (C-C), and simulated-based and category-based fractal models applied to representative and simulated samples (CF-R and CF-S). The precision (stability) of the models and spatial uncertainty were tested using Monte Carlo and sequential Gaussian simulations, as well as the effects of pre-processing of the geochemical data. In the Sweden till data, CF-R, spectrum-area (S-A) and the related simulated (SS-A) approach proved more effective in delineating known VMS mineralisation in some regions than single element patterns for mineralisation-related metals such as Cu. In Cyprus, both established and new fractal approaches were marginally more effective at separating areas of known mineralisation (including the major deposits) against a backdrop of generally elevated levels of VMS-related elements in the pillow basalts and underlying sheeted dyke complex. The C-C and C-DC approaches define a contiguous zone whose multivariate patterns are closely linked to either geogenic dispersion or anthropogenic contamination including historical contamination that cuts across current land use zoning. Population or spatial features in geochemical data delineated by different fractal approaches are dependent on the mathematical basis of specific fractal models. Application of a wide range of fractal methods, along with assessment of uncertainty in sample classification and stability of spatial patterns, provides a firmer basis for quantifying the processes and features that control element distributions in regional geochemical data. It also provides criteria for selection of the most effective combination of data pre-processing and fractal modelling to extract desired features or signals in the data.

  • (2022) Nguyen, Robert
    Thesis
    Data-driven decision making is everywhere in the modern sporting world. The most well-known example of this is the Moneyball movement in Major League Baseball (MLB), which built on research by Sherri Nichols in the 1980s, but sport analytics has also driven major changes in strategy in basketball, the National Football League, and soccer. In Australia, sports analytics has not had quite the same influence in its major domestic codes. In this thesis, we develop tools to assist the analytics community in two major Australian commercial sports. For Australian Rules Football, the largest commercial sport in Australia, data was not readily accessible for the national competition, the Australian Football League (AFL). Data access is fundamental to data analysis, so this has been a major constraint on the capacity of the AFL analytics community to grow. In this thesis, this issued is solved by making AFL data readily accessible through the R package fitzRoy. This package has already proven to be quite successful and has seen uptake from the media, fans, and club analysts. Expected points models are widely used across sports to inform tactical decision making, but as currently implemented, they confound the effects of decisions on points scored and the situations that the decisions tend to be made in. In Chapter 3, a new expected points approach is proposed, which conditions on match situation when estimating the effect of decisions on expected points. Hence we call this a conditional Expected Points (cEP) model. Our cEP model is used to provide new insight into fourth Down (NFL) decision-making in the National Football League, and decision-making when awarded a penalty in Rugby League. The National Rugby League (NRL) is the leading competition of Australia’s second largest commercial sport it is played on a pitch that is 100m long and 70m wide, and the NRL have provided us with detailed event data from the previous five seasons, used in academic research for the first time in this thesis. We found that NRL teams should kick for goal from penalties much more often than is currently the case. In Chapter 4 we develop a live probability model for predicting the winner of a Rugby League game using data that is collected live. This model could be used by the National Rugby League during broadcasts to enhance their coverage by reporting live win probabilities. While most live probability models are constructed using scores only, the availability of live event data meant we could investigate whether models constructed using event data have better predictive performance. We were able to show that in addition to score differential that the addition of covariates such as missed tackles can improve the prediction. Clubs use their own domain knowledge to test their own live win probability theories with the R scripts that are provided to the NRL

  • (2022) Gautam, Shreedhar
    Thesis
    Extracellular vesicles (EVs) are phospholipid membrane bound sacs (vesicles) produced from almost all types of cells. They are found in circulation and contain the cargo biomolecules such as nucleic acids, proteins, lipids, and amino acids. EVs are involved in trafficking these biomolecules between cells and as such have the role in physiological and pathological processes. EVs are heterogenous and revealing their heterogeneity is crucial to understand their explicit physiological and pathological roles. Current isolation techniques cannot sort EVs based on their biogenesis and provides average information instead of each EVs subtype. Thus, single EVs analysis was popular and many surface protein characterization techniques are developed. But there are no techniques available for internal cargo analysis of individual EVs. The overall aim was to develop a technique to analyse internal microRNA cargo content, if possible, for single EVs, if not from the minimum number of EVs. To achieve that goal, light activated electrochemistry, a technique where focused light beam was illuminated on the semiconductor surface and make it electrochemically active was used. The surface was protected against oxidation during electrochemical reactions by grafting self-assembled monolayer of 1,8-nonadiyne. Then, silicon-based surface was patterned with polymers, antibodies, and cells using the light patterns. As a result, the first milestone to prepare light-assisted patterned semiconductor surface was achieved for our overall aim of analysing content of individual EVs. The size range of EVs is 30 to 200 nm, still very low compared to 30 µm which is the best spatial resolution achieved for light activated electrochemistry using crystalline silicon. Thus, chapter 4 developed a technique to improve the spatial resolution of light activated electrochemistry using amorphous silicon. Amorphous silicon has short diffusion length of charge carriers compared to crystalline silicon due to the defect states in band gap called as localized states. So, charge carriers are frequently trapped in these localized states leading to 60 times improvement in spatial resolution to 500 nm. But even this spatial resolution was not enough to analyse individual EVs. So, microRNA content from pool of EVs were detected using the screen-printed electrodes in a high throughput manner instead of single EVs.

  • (2022) Cao, Jun
    Thesis
    This thesis focuses on the development and applications of magnetic resonance electrical properties tomography (MREPT), which is an emerging imaging modality to noninvasively obtain the electrical properties of tissues, such as conductivity and permittivity. Chapter 2 describes the general information about human research ethics, MRI scanner, MR sequence and the method of phase-based MREPT implemented in this thesis. Chapter 3 examines the repeatability of phase-based MREPT in the brain conductivity measurement using balanced fast field echo (bFFE) and turbo spin echo (TSE) sequences, and investigate the effects of compressed SENSE, whole-head B_1 shimming and video watching during scan on the measurement precision. Chapter 4 investigates the conductivity signal in response to short-duration visual stimulus, compares the signal and functional activation pathway with that of BOLD, and tests the consistency of functional conductivity imaging (funCI) with visual stimulation across participants. Chapter 5 extends the use of functional conductivity imaging to somatosensory stimulation and trigeminal nerve stimulation to evaluate the consistency of functional conductivity activation across different types of stimuli. In addition, visual adaptation experiment is performed to test if the repetition suppression effect can be observed using funCI. Chapter 6 explores if resting state conductivity networks can be reliably constructed using resting state funCI, evaluates the consistency of persistent homology architectures, and compares the links between nodes in the whole brain. Chapter 7 investigates the feasibility of prostate conductivity imaging using MREPT, and distinctive features in the conductivity distribution between healthy participants and participants with suspected abnormalities.

  • (2022) Wang, Shuangyue
    Thesis
    Two-dimensional transition metal dichalcogenide (TMD) nanocrystals (NCs) exhibit unique optical and electrocatalytic properties. However, the growth of uniform and high-quality NCs of monolayer TMD remains a challenge. Until now, most of them are synthesized via solution-based hydrothermal process or ultrasonic exfoliation method, in which the capping ligands introduced from organic solution often quench the optical and electrocatalytic properties of TMD NCs. Moreover, it is difficult to homogeneously disperse the solution-based TMD NCs on a substrate for device fabrication since the dispersed NCs can easily aggregate. Here, we put forward a novel CVD method to grow closely-spaced TMD NCs and explored the growth mechanism and attempts on the size control. Their applications acting as electrocatalysts and adhesion layer for Au film deposition have been also well displayed. Through the whole chapters of this thesis, the following aspects are highlighted: 1. MoS2 and other TMD nanocrystals have been grown on the c-plane sapphire. The surface oxygen vacancies determine the density of TMD nanocrystals. The MoS2 nanocrystals demonstrate excellent hydrogen evolution reaction and surface-enhanced Raman scattering performance owing to the abundant edges. 2. Deep insights into the growth of MoS2 nanograins have been explored. The surface step edges and lattice structures of the underlying sapphire substrates have a significant influence on the growth behaviors. The step edges could modulate the aggregation of MoS2 nanograins to form unidirectional triangular islands. The Raman spectra of MoS2 demonstrate a linear relationship with the crystal size of MoS2. 3. The orientation of sapphire substrate has an of importance effect on the critical size of MoS2 nanocrystals. The MoS2 nanocrystals have the smallest size on the r-plane sapphire, besides, the MoS2 on r-plane sapphire demonstrates the sintering-resistance feature, which is attributed to the edge-pinning effect when MoS2 edges are anchored on the sapphire surface. 4. The MoS2 nanocrystalline layer was utilized as the adhesion layer for Au film depositing on a sapphire substrate. The Au films on MoS2 displayed superior transmittance and electrical conductivity as well as outstanding thermal stability, which lay in the strong binding of Au film with MoS2 nanocrystalline layer.

  • (2022) Bartolec-Criss, Tara
    Thesis
    The function of a protein is mediated by its ability to form precise three-dimensional structures or specific protein-protein interaction (PPI) interfaces. However, it has been challenging to study these aspects of the proteome at scale, in sufficient detail, and in a generalisable way. Cross-linking mass spectrometry (XL-MS) performed on high complexity samples (such as entire organelles or cells) theoretically enables the large scale mapping and monitoring of protein structural conformations and PPI interfaces in native proteoforms. However, as the large scale XL-MS field is young and historically driven by the reporting of technological innovations, assessment of the biological accuracy (and overall utility) of large scale XL-MS studies is still largely underexplored. This thesis applies large scale XL-MS to two eukaryotic systems (Saccharomyces cerevisiae and cultured human cells) and is presented as three independent studies. Firstly, it reports the first budding yeast XL-MS interactome, generated by cross-linking intact nuclei isolated from wild-type cells with DSSO. The wealth of yeast interactome data enabled identification of an inflated false discovery rate for cross-links representing PPIs, and development of a novel quality control approach. Surprisingly, the high confidence PPIs were substantially orthogonal to historical binary interactome mapping efforts. Subsequently, it reports the largest XL-MS dataset currently available for any species, generated by diversifying analyses (cross-linkers, mass spectrometry analyses, software) performed on organelles isolated from human HEK293 cells. Here, we show how the ~30,000 low-resolution distance constraints generated in near-native proteoforms can be used to uniquely (1) contextualise regions within existing experimental protein structures, (2) annotate interfaces in PPIs and multi-protein complexes, and (3) validate structures predicted by computational modellers like AlphaFold. Finally, this thesis reports the use of quantitative XL-MS to explore links between gene function and cellular phenotype, comparing wild-type yeast with a highly pleiotropic deletion strain (Δhpm1) using SILAC multiplexing and PIR cross-linking of intact cells. The untargeted comparison of structural conformations and PPIs uniquely enabled insights into phenotypes entirely invisible to investigation of protein abundance alone. This thesis will therefore argue that XL-MS is the missing link in the systems biology toolbox.

  • (2022) Gutierrez Chavez, Carolina
    Thesis
    Microbial motility is a survival strategy. Bacteria utilise motility in growth and reproduction to protect against desiccation and antibiotics, defend against competitors, colonise new habitats, and find nutrient-rich environments. Antarctica is the most extreme and pristine region on Earth. Here, soils are exposed to low temperatures, considerable levels of UV radiation, strong winds, extreme drought, and low availability of nutrients. Currently, there are no reports of motility in polar soil bacteria. Due to the extreme conditions in the Antarctic continent, we used these polar desert soils as a study model. We hypothesise that Antarctic soils are an ideal environment for bacteria to perform motility to find more favourable conditions. In this thesis, we describe for the first-time mechanisms of motility by Antarctic soil bacteria. As model microorganisms, we selected bacteria from the genera Streptomyces and Arthrobacter, belonging to the phylum Actinomycetota, the most abundant in East Antarctic soils. The first aim was to investigate the incidence and behaviour of Antarctic Streptomyces performing exploration. The genus Streptomyces had been described as a group of sessile bacteria. In 2017, the phenomenon of Streptomyces exploration was described for the first-time as a mechanism of translocation performed by Streptomyces cells through biotic and abiotic surfaces to facilitate access to distant nutrients. It was reported that the incidence of wild-type Streptomyces strains exhibiting exploration was ~10%. In addition, two critical conditions involved in the exploration process were described, glucose depletion and alkaline pH in the medium produced by the synthesis of volatile organic compounds (VOCs). Here, we screened 57 Streptomyces strains previously isolated from four sites in Eastern Antarctica. We found that 22.8% did not exhibit exploration capabilities, and 19.4% showed exploration behaviour in glucose depletion and alkaline environments. In contrast, 57.8% exhibited exploration at neutral pH or in the presence of glucose. These findings about the incidence of glucose-independent exploration suggest that the exploratory behaviour might be encouraged by searching for alternative carbon sources due to the low nutrient availability in East Antarctic soils. The second aim was to provide insight into potential compounds involved in Streptomyces exploration. Here, we obtained a fraction with emulsifying, antimicrobial, and haemolytic activities from the secretome of Streptomyces INR7 explorer cells. LC-MS analysis of the fraction and bioactive predictors revealed that a LysM-containing peptide with amphipathic properties is the responsible for the antibacterial and haemolytic activities. Furthermore, genomic annotation and sequence alignment indicate that the peptide is part of a protein belonging to the resuscitation-promoting factors family, contributing to physiological processes of cell wall remodelling and metabolic activation of dormant cells. The third aim was to describe whether Antarctic Arthrobacter isolates can use microbial hitchhiking as a motility strategy to migrate across the fungal hyphae of Antarctomyces psychrotrophicus. So far, Arthrobacter bacteria have been associated with active motility, also known as flagella-dependent motility. Flagella-assisted displacement is typical in aqueous environments; however, East Antarctic soils are exposed to arid and hyperarid conditions, suggesting that the motility of Arthrobacter isolates from these polar desert soils might be challenging. Here, we found that microbial hitchhiking facilitates the migration of Arthrobacter strains previously isolated from Antarctic soils. Hitchhiking is a form of transportation where microorganisms with null or limited motility, known as 'hitchhikers' or 'riders', use the motility of nearby motile organisms known as 'carriers' or 'host' to move. In soils, fungi facilitate the migration of bacteria over short and long distances by forming 'networks' or 'highways' on which bacteria can travel actively, passively or by direct attachment to the fungal hyphae. By using SEM, motility screening, flagella identification and hitchhiking assays, we found that of 17 Arthrobacter strains examined, 14 migrated through the fungus A. psychrotrophicus. The results suggest that Arthrobacter isolates migrated by three mechanisms: two strains travelled flagella-dependent motility, seven isolates translocated by flagella-independent motility and five strains migrated by direct attachment to the fungal surface. These findings provide evidence that Antarctic soil bacteria, specifically members of the genera Streptomyces and Arthrobacter, exhibit a high incidence of motility. We propose that motility could be a survival strategy used by bacteria to cope with the extreme conditions in Antarctica.

  • (2022) Guan, Peiyuan
    Thesis
    Cathode is the key component in lithium-ion batteries (LIBs) and it determines the performance of LIBs to a large extent. Recently, layered-structure Ni-rich cathode has attracted concentrated research attention due to its high theoretical capacity and energy density, which showed great potential as an alternative for the current dominant LiCoO2 in the energy market. Intrinsically, the high Ni content led to an excellent discharge capacity; however, the high reactivity of Ni also caused an capacity fading resulting from the undesired side reactions during prolonged cycling. Therefore, a trade-off between high capacity and long cycle life obstruction of the commercializing process of Ni-rich cathode in modern LIBs. In this case, this work attempt to employing surface modification strategy to stabilize the cyclability of Ni-rich cathodes by perovskite oxides. Because they provide a variety of outstanding physical and chemical properties. Most importantly, several materials, including metal oxide, fluoride, phosphate, etc. have been investigated as surface coating layer for the electrochemical property enhancement; however, perovskite oxide is still rarely mentioned. THus, this work firstly used a typical perovskite oxide, strontium titanate (STO) and its diverse modified forms, as surface modifier coated onto Ni-rich cathodes, respectively. In detail, chapter 4 demonstrates that the STO surface coating on NCM811 could effectively enhance its cycling stability. The effect of the heat treatment after perovskite oxide surface coating is studied and disclosed in chapter 5. In chapter 6, NCA is covered by STO with the defect-rich surface, exhibiting a better rate performance due to the higher electronic and ionic conductivity possessed by the coating layer. At last, as-prepared Nb-doped STO onto NCM811 could act as a buffer layer to suppress the dissolution of transition metal ions resulting from the electrolyte decomposed HF attacking and robust the Li diffusion channel during the charge-discharge process. The current study offers a systematically understanding of the positive effect of perovskite oxide materials-based surface modification on Ni-rich cathodes. It confirms the feasibility of improving the electrochemical performances of Ni-rich oxides by preventing the deleterious side reactions accompanied by reducing Li residues on the cathode surface, which is of great significance to the optimization of the cathode material for next-generation LIB for electric vehicles.

  • (2023) Dela Cruz, Michael Leo
    Thesis
    Biodegradable implant materials are more appropriate for temporary support applications compared with their inert counterparts since the former requires no removal surgery because they naturally degrade and eventually dissolve completely during healing. Iron and its alloys are a possible substitute for the commercial magnesium biodegradable implants because of their superior mechanical properties and slower corrosion rates. The addition of manganese and silicon in iron imparts another interesting property to the material–the shape memory effect. There is copious research on the structure and properties of the biodegradable face centred cubic (FCC) Fe-30Mn-6Si shape memory alloy (SMA) that exhibits the reversible FCC austenite to hexagonal close packed (HCP) ε-martensite transformation. However, recent advances in additive manufacturing of metals, brought by the development of the laser powder bed fusion (LPBF) technique, warrant the need for an investigation on the adaptability of the technique in fabricating this alloy composition. The LPBF technique is limited by the need for specialty raw material powder, and this thesis extends the application of the technique in fabricating the Fe-30Mn-6Si shape memory alloy (SMA) from homogenised powder precursors. More so, LPBF processing of Fe-30Mn-6Si alloy from either pre-alloyed powder or blended powder has not been reported. To successfully fabricate a Fe-30Mn-6Si LPBF product, the influence of key LPBF processing parameters on product quality was identified as a major challenge. This was addressed by investigating the influence of laser power, laser scan speed, laser re-scanning, and their equivalent input energy on the relative density and defect formation. A relative density of over 99% with few processing defects was achieved using the optimised parameters of 175 W laser power, 400 mm/s scan speed, and no re-scanning. The influence of these parameters on the solidification microstructure was also investigated using key techniques, such as X-ray diffraction (XRD) and scanning electron microscopy (SEM) in conjunction with energy dispersive spectroscopy (EDS) and electron backscatter diffraction (EBSD). Further, the simulated thermal profile of the melt pool region as a function of process parameters via single scan track experiments was calculated using the finite element method (FEM). These data were used to explain the key microstructural features observed in the as-solidified microstructure of the LPBF alloy as a function of the processing parameters. The mechanical properties of the LPBF alloy were then assessed by hardness and tensile testing and then compared with a reference alloy produced by arc melting. The hardness of the LPBF as-built alloy was ∼20% higher than the reference alloy. To identify the factors affecting the increased hardness of the former, the influence of grain size and morphology, crystallographic texture, phase constituents (mainly austenite and martensite), and residual strain were investigated. The hardness of the reference alloy was affected mainly by the grain size and residual strain, but for the LPBF-built alloy, the relative volume fractions of austenite and martensite strongly influenced the hardness. Meanwhile, the tensile properties of the LPBF alloy, such as the yield stress, ultimate tensile stress, and ductility, were adversely affected by the internal defects present, such that high temperature homogenisation and hot isostatic pressing (HIP) post-process treatments were investigated to improve these properties. The homogenisation and HIP treatments increased both the tensile strength and ductility of the LPBF-built alloy. Homogenisation altered the grain morphology by promoting recrystallisation and grain growth, and this increased the tensile strength by ∼80%. The hardness, however, decreased due to a reduction in the volume fraction of HCP martensite in the FCC austenitic microstructure. HIP retained some of the columnar microstructure generated by the LPBF process, marginally increased the density, and increased the tensile strength by ∼65%. The improvement in tensile properties through these post-process treatments allowed for the measurement of LPBF alloy’s shape memory behaviour, whereby a tensile recovery strain of 2% was achieved for the HIP-treated alloy. Finally, the biocorrosion behaviour of the LPBF-processed and HIP-treated alloy was investigated, whereby the in vitro corrosion potential and current density of the alloy were determined to be -769 mV and 5.6 μA/cm2, respectively, indicating a reasonable corrosion rate for this material. Overall, this thesis enabled the first demonstration of the shape memory effect in an LPBF-built Fe-based alloy fabricated from homogenised powder, an alloy which also exhibits biodegradable properties.