Bio21 - Research Publications
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ItemSpectroscopic study of L-DOPA and dopamine binding on novel gold nanoparticles towards more efficient drug-delivery system for Parkinson's disease(PERGAMON-ELSEVIER SCIENCE LTD, 2022-03-05)Nano-drug delivery systems may potentially overcome current challenges in the treatment of Parkinson's disease (PD) by enabling targeted delivery and more efficient blood-brain penetration ability. This study investigates novel gold nanoparticles (AuNPs) to be used as delivery systems for L-DOPA and dopamine by considering their binding capabilities in the presence and absence of a model protein, bovine serum albumin (BSA). Four different AuNPs were prepared by surface functionalization with polyethylene glycol (PEG), 1-adamantylamine (Ad), 1-adamantylglycine (AdGly), and peptidoglycan monomer (PGM). Fluorescence and UV-Vis measurements demonstrated the strongest binding affinity and L-DOPA/dopamine loading efficiency for PGM-functionalized AuNPs with negligible impact of the serum protein presence. Thermodynamic analysis revealed a spontaneous binding process between L-DOPA or dopamine and AuNPs that predominantly occurred through van der Waals interactions/hydrogen bonds or electrostatic interactions. These results represent PGM-functionalized AuNPs as the most efficient at L-DOPA and dopamine binding with a potential to become a drug-delivery system for neurodegenerative diseases. Detailed investigation of L-DOPA/dopamine interactions with different AuNPs was described here for the first time. Moreover, this study highlights a cost- and time-effective methodology for evaluating drug binding to nanomaterials.
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ItemGrowth of Gold Nanorods: A SAXS Study(AMER CHEMICAL SOC, 2021-09-16)Using simultaneous, in situ optical spectroscopy and time-resolved, small-angle X-ray scattering (SAXS), we have directly monitored the seeded growth of nearly monodisperse gold nanorods using hydroquinone as the reductant. Growth of the rods is much slower than with the ascorbate ion, allowing the rate of growth along both the longitudinal and transverse directions to be independently determined. The thickness of the stabilizing CTAB layer (3.2 ± 0.3 nm) has also been extracted. We find that increasing the hydrogen tetrachloroaurate(III) concentration produces longer rods, while conversely, increasing the hydroquinone concentration reduces the final aspect ratio. The final number of gold rods is smaller than the initial number of seed particles and decreases in the presence of larger concentrations of HAuCl4. The SAXS data reveal an early transition from a spherical morphology to an ellipsoidal one and then to spherically capped cylinders. The growth curve exhibits at least three distinct regimes: an initial phase comprising spherical seed growth, followed by symmetry breaking and slow elongation. A third phase is marked by rapid rod growth and increases in the aspect ratio. This process is temporally well resolved from the initial symmetry breaking but typically occurs when the rods are around 6 nm in diameter using hydroquinone as the reductant. The results provide qualitative support for the “popcorn model” proposed by Edgar et al. [ Formation of Gold Nanorods by a Stochastic “Popcorn” Mechanism. ACS Nano 2012, 6, 1116 1125 ].
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ItemNo Preview AvailablePolymeric Nanoneedle Arrays Mediate Stiffness‐Independent Intracellular Delivery (Adv. Funct. Mater. 3/2022)(Wiley, 2022-01)In article number 2104828, Yaping Chen, Nicolas H. Voelcker, Roey Elnathan, and co-workers demonstrate the fabrication of relatively low-cost and high throughput polymeric nanoneedles from cell culture polystyrene. The nanoneedles with precise geometry are imprinted directly on polystyrene from the cell culture petri dish via nanoimprint lithography. The nanoneedles arrays can precisely manipulate cellular processes and mediate intracellular delivery in mammalian cells. This presents opportunities for novel integration of nanostructures into traditional polymeric cell cultureware.
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ItemA sandwich-like structural model revealed for quasi-2D perovskite films(Royal Society of Chemistry, 2021-04-28)The excellent performance and stability of perovskite solar cells (PSCs) based on quasi-2D Ruddlesden–Popper perovskites (RPPs) holds promise for their commercialization. Further improvement in the performance of 2D PSCs requires a detailed understanding of the microstructure of the quasi-2D perovskite films. Based on scanning transmission electron microscopy (STEM), time-resolved photoluminescence, and transient absorption measurements, a new sandwich-like structural model is proposed to describe the phase distribution of RPPs. In contrast to the conventional gradient distribution, it is found that small-n RPPs are sandwiched between large-n RPP phase layers at the front and back sides owing to crystallization initiated from both interfaces during film formation. This sandwich-like distribution profile facilitates excitons funneling from the film interior to both surfaces for dissociation while free carriers transport via large-n channels that permeate the film to ensure efficient charge collection by the corresponding electrodes, which is favorable for high-performance photovoltaics. This discovery provides a new fundamental understanding of the operating principles of 2D PSCs and has valuable implications for the design and optimization strategies of optoelectronic devices based on quasi-2D RPPs films.
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ItemCharacterising the influence of milk fat towards an application for extrusion-based 3D-printing of casein-whey protein suspensions via the pH-temperature-route(ELSEVIER SCI LTD, 2021-09)This study presents the design and characterisation of casein−whey protein suspensions (8.0/10.0% (w/w) casein and 2.0/2.5% (w/w) whey protein) mixed with dairy fat (1.0, 2.5 and 5.0% (w/w) total fat) processed via the pH−temperature-route in preparation for 3D-printing. Mechanical treatment was applied to significantly decrease the particle size of the milk fat globules and increase surface area, creating small fat globules (<1 μm) covered with proteins, which could act as pseudo protein particles during gelation. Different proteins covered the fat globule surface after mechanical treatment, as a result of differences in the pH adjusted just prior to heating (6.55, 6.9 or 7.1). The protein-fat suspensions appeared similar by transmission electron cryogenic microscopy and the zeta-potential of all particles was unchanged by the heating pH, with a similar charge to the solution (~−20 mV) occurring after acidification (pH 4.8/5.0) at low temperatures (2 °C). A low heating pH (6.55) resulted in increased sol−gel transition temperatures (G՛ = 1 Pa) and a decreased rate of aggregation for protein−fat suspensions. A higher heating pH (6.9 and 7.1) caused an increased rate of aggregation (aggregation rate ≥ 250 Pa/10 K), resulting in materials more promising for application in extrusion-based printing. 3D-printing of formulations into small rectangles, inclusive of a sol−gel transition in a heated nozzle, was conducted to relate the aggregation rate towards printability.
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ItemBrownian Tree‐Shaped Dendrites in Quasi‐2D Perovskite Films and Their Impact on Photovoltaic Performance(Wiley, 2022-05)Quasi-2D Ruddlesden–Popper perovskites (RPPs) are candidates for constructing perovskite solar cells (PSCs) with superior stability due to their tolerance to the external environment. Fully understanding the film growth mechanism and structure is crucial to further improve the performance of 2D-PSCs while maintaining device stability. In this work, the origin of Brownian tree-shaped dendrites formed in hot-cast methylammonium chloride (MACl)-doped BA2MAn−1PbnI3n+1 ( = 5) quasi-2D perovskite films are reported. Investigations based on optical, electronic, atomic force, and fluorescence microscopies reveal that the dendrites are assembled from large-n RPPs-dominated grains, while the nondendritic film area is composed of small-n RPPs grains and associated with film surface pits caused by the evaporation of MACl. It is proposed that these dendrites are grown by the diffusion-limited aggregation of the MA-rich intermediate phase domains that initially crystallize from the precursor. The formation of these dendrites in quasi-2D perovskite films upon MACl doping is accompanied by improved organization and crystallinity of the 2D RPPs, which benefits the photovoltaic performance. This work provides new insights into the formation mechanism of quasi-2D perovskite films that should assist device engineering strategies to further improve the performance of 2D PSCs.
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ItemEffects of altered cellular ultrastructure on energy metabolism in diabetic cardiomyopathy: an in silico study.(The Royal Society, 2022-11-21)Diabetic cardiomyopathy is a leading cause of heart failure in diabetes. At the cellular level, diabetic cardiomyopathy leads to altered mitochondrial energy metabolism and cardiomyocyte ultrastructure. We combined electron microscopy (EM) and computational modelling to understand the impact of diabetes-induced ultrastructural changes on cardiac bioenergetics. We collected transverse micrographs of multiple control and type I diabetic rat cardiomyocytes using EM. Micrographs were converted to finite-element meshes, and bioenergetics was simulated over them using a biophysical model. The simulations also incorporated depressed mitochondrial capacity for oxidative phosphorylation (OXPHOS) and creatine kinase (CK) reactions to simulate diabetes-induced mitochondrial dysfunction. Analysis of micrographs revealed a 14% decline in mitochondrial area fraction in diabetic cardiomyocytes, and an irregular arrangement of mitochondria and myofibrils. Simulations predicted that this irregular arrangement, coupled with the depressed activity of mitochondrial CK enzymes, leads to large spatial variation in adenosine diphosphate (ADP)/adenosine triphosphate (ATP) ratio profile of diabetic cardiomyocytes. However, when spatially averaged, myofibrillar ADP/ATP ratios of a cardiomyocyte do not change with diabetes. Instead, average concentration of inorganic phosphate rises by 40% owing to lower mitochondrial area fraction and dysfunction in OXPHOS. These simulations indicate that a disorganized cellular ultrastructure negatively impacts metabolite transport in diabetic cardiomyopathy. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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ItemCardioVinci: building blocks for virtual cardiac cells using deep learning(ROYAL SOC, 2022-11-21)Advances in electron microscopy (EM) such as electron tomography and focused ion-beam scanning electron microscopy provide unprecedented, three-dimensional views of cardiac ultrastructures within sample volumes ranging from hundreds of nanometres to hundreds of micrometres. The datasets from these samples are typically large, with file sizes ranging from gigabytes to terabytes and the number of image slices within the three-dimensional stack in the hundreds. A significant bottleneck with these large datasets is the time taken to extract and statistically analyse three-dimensional changes in cardiac ultrastructures. This is because of the inherently low contrast and the significant amount of structural detail that is present in EM images. These datasets often require manual annotation, which needs substantial person-hours and may result in only partial segmentation that makes quantitative analysis of the three-dimensional volumes infeasible. We present CardioVinci, a deep learning workflow to automatically segment and statistically quantify the morphologies and spatial assembly of mitochondria, myofibrils and Z-discs with minimal manual annotation. The workflow encodes a probabilistic model of the three-dimensional cardiomyocyte using a generative adversarial network. This generative model can be used to create new models of cardiomyocyte architecture that reflect variations in morphologies and cell architecture found in EM datasets. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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ItemMatrix metalloproteinase-7 is increased in lung bases but not apices in idiopathic pulmonary fibrosis.(European Respiratory Society (ERS), 2022-10)INTRODUCTION: Idiopathic pulmonary fibrosis (IPF) is a progressively fibrotic lung condition with poor prognosis. Matrix metalloproteinase-7 (MMP7) is a protein secreted by epithelial cells in IPF lungs. It is not known if MMP7 expression correlates with fibrotic changes in lung tissue. METHODS: Tissue samples from lung apices and bases were obtained from 20 IPF patients and 14 non-diseased control (NDC) donors. In formalin-fixed paraffin-embedded sections, histological assessment of fibrosis was performed; overall MMP7 positivity was assessed by immunohistochemistry and MMP7+ cells were quantified using multiplex immunohistochemistry. Protein expression of MMP7 in whole lung lysates was quantified by Western blotting. Bulk tissue transcriptomic profiles of 101 samples were analysed using RNA sequencing technologies. RESULTS: Lung tissue from IPF bases was more fibrotic than in apices. MMP7 protein is elevated in IPF lung base tissue. In IPF whole lung lysates, MMP7 protein levels are increased compared to NDC donors and was increased in IPF lung bases compared to apices. MMP7 protein levels correlated with MMP7 gene expression levels in lung tissue. MMP7 transcript levels were increased in IPF base compared to NDC base lung tissue and increased in IPF base tissue compared to IPF apex tissue. CONCLUSIONS: Our cross-sectional study suggests that lung epithelial MMP7 expression increases as the tissue becomes more fibrotic and identifies a potentially nonepithelial or immune-cell source. Mechanisms of disease progression in IPF are still unclear, and our study suggests aberrant MMP7 production may be a histological starting point of lung tissue fibrosis.
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ItemSystematic Down-Selection of Repurposed Drug Candidates for COVID-19(MDPI, 2022-10)SARS-CoV-2 is the cause of the COVID-19 pandemic which has claimed more than 6.5 million lives worldwide, devastating the economy and overwhelming healthcare systems globally. The development of new drug molecules and vaccines has played a critical role in managing the pandemic; however, new variants of concern still pose a significant threat as the current vaccines cannot prevent all infections. This situation calls for the collaboration of biomedical scientists and healthcare workers across the world. Repurposing approved drugs is an effective way of fast-tracking new treatments for recently emerged diseases. To this end, we have assembled and curated a database consisting of 7817 compounds from the Compounds Australia Open Drug collection. We developed a set of eight filters based on indicators of efficacy and safety that were applied sequentially to down-select drugs that showed promise for drug repurposing efforts against SARS-CoV-2. Considerable effort was made to evaluate approximately 14,000 assay data points for SARS-CoV-2 FDA/TGA-approved drugs and provide an average activity score for 3539 compounds. The filtering process identified 12 FDA-approved molecules with established safety profiles that have plausible mechanisms for treating COVID-19 disease. The methodology developed in our study provides a template for prioritising drug candidates that can be repurposed for the safe, efficacious, and cost-effective treatment of COVID-19, long COVID, or any other future disease. We present our database in an easy-to-use interactive interface (CoviRx that was also developed to enable the scientific community to access to the data of over 7000 potential drugs and to implement alternative prioritisation and down-selection strategies.