Bio21 - Research Publications
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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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ItemSupramolecular Assembly of Polyphenols and Nucleic Acids by Thermal Cycling for Immune Cell Activation(American Chemical Society (ACS), 2023)Supramolecular assembly of polyphenols and biomacromolecules (proteins and nucleic acids) has emerged as a versatile and simple strategy to construct nanomaterials with biological activity. Here, we report a strategy to finely control the supramolecular assembly of tannic acid and oligonucleotides into uniform and stable nanoparticles by exploiting the thermal cycling of tannic acid. The equilibrium of complexation is investigated, and individual nanoparticles are resolved with nanoscale resolution by using stochastic optical reconstruction microscopy. The nanoparticles incorporating cytosine phosphoguanine (CpG) oligonucleotides are efficiently taken up by cells and trafficked via endo/lysosomal compartments and induce up to a 7-fold increase in tumor necrosis factor secretion in RAW 264.7 macrophage cells compared with naked CpG oligonucleotides. This work highlights the potential of this simple approach to engineer two-component tannic acid–oligonucleotide nanoparticles for the intracellular delivery of therapeutic nucleic acids.
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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, 2021-04-28)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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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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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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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, 2022-10-01)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.
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ItemEntry of the antipsychotic drug, olanzapine, into the developing rat brain in mono- and combination therapies.(F1000 Research Ltd, 2022)Background: Olanzapine is used to treat schizophrenia and bipolar disorder in women of childbearing age. Continuation of psychotropic medications throughout pregnancy and lactation is often required as cessation could be dangerous for both mother and child. However, there is a lack of information on the transfer of these drugs into the developing brain. Methods: Sprague Dawley rats at three developmental ages: embryonic day E19, postnatal day P4 and non-pregnant adult females were administered unlabelled or radiolabelled ( 3H) olanzapine (0.15 mg/kg) either as monotherapy or in combination with each of seven other common medications. Similar injections were administered to pregnant E19 females to investigate placental transfer. Olanzapine in plasma, cerebrospinal fluid (CSF) and brain was measured by liquid scintillation counting after a single dose (acute) or following 5 days of treatment (prolonged). Results: Olanzapine entry into brain and CSF was not age-dependent. Prolonged olanzapine treatment reduced placental transfer from 53% to 46% (p<0.05). Co-administration of digoxin or lamotrigine with olanzapine increased its entry into the fetal brain, whereas paracetamol decreased its entry into the CSF. Placental transfer of olanzapine was increased by co-treatment with cimetidine and digoxin, whereas co-treatment with lamotrigine, paracetamol or valproate led to a substantial decrease. Repeated co-treatment of digoxin and olanzapine increased olanzapine transfer into the brain and CSF, but not across the placenta. Overall entry of olanzapine from maternally administered drugs into the fetal brain was higher after combination therapy with cimetidine and digoxin. Conclusions: Co-administration of olanzapine with some commonly used drugs affected its entry into the fetus and its developing brain to a greater extent than in adults. It appears that protection of the fetal brain for these drugs primarily comes from the placenta rather than from the fetal brain barriers. Results suggest that drug combinations should be used with caution particularly during pregnancy.
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ItemPhosphoproteomic dysregulation in Huntington's disease mice is rescued by environmental enrichment(OXFORD UNIV PRESS, 2022-11-02)Huntington's disease is a fatal autosomal-dominant neurodegenerative disorder, characterized by neuronal cell dysfunction and loss, primarily in the striatum, cortex and hippocampus, causing motor, cognitive and psychiatric impairments. Unfortunately, no treatments are yet available to modify the progression of the disease. Recent evidence from Huntington's disease mouse models suggests that protein phosphorylation (catalysed by kinases and hydrolysed by phosphatases) might be dysregulated, making this major post-translational modification a potential area of interest to find novel therapeutic targets. Furthermore, environmental enrichment, used to model an active lifestyle in preclinical models, has been shown to alleviate Huntington's disease-related motor and cognitive symptoms. However, the molecular mechanisms leading to these therapeutic effects are still largely unknown. In this study, we applied a phosphoproteomics approach combined with proteomic analyses on brain samples from pre-motor symptomatic R6/1 Huntington's disease male mice and their wild-type littermates, after being housed either in environmental enrichment conditions, or in standard housing conditions from 4 to 8 weeks of age (n = 6 per group). We hypothesized that protein phosphorylation dysregulations occur prior to motor onset in this mouse model, in two highly affected brain regions, the striatum and hippocampus. Furthermore, we hypothesized that these phosphoproteome alterations are rescued by environmental enrichment. When comparing 8-week-old Huntington's disease mice and wild-type mice in standard housing conditions, our analysis revealed 229 differentially phosphorylated peptides in the striatum, compared with only 15 differentially phosphorylated peptides in the hippocampus (statistical thresholds fold discovery rate 0.05, fold change 1.5). At the same disease stage, minor differences were found in protein levels, with 24 and 22 proteins dysregulated in the striatum and hippocampus, respectively. Notably, we found no differences in striatal protein phosphorylation and protein expression when comparing Huntington's disease mice and their wild-type littermates in environmentally enriched conditions. In the hippocampus, only four peptides were differentially phosphorylated between the two genotypes under environmentally enriched conditions, and 22 proteins were differentially expressed. Together, our data indicates that protein phosphorylation dysregulations occur in the striatum of Huntington's disease mice, prior to motor symptoms, and that the kinases and phosphatases leading to these changes in protein phosphorylation might be viable drug targets to consider for this disorder. Furthermore, we show that an early environmental intervention was able to rescue the changes observed in protein expression and phosphorylation in the striatum of Huntington's disease mice and might underlie the beneficial effects of environmental enrichment, thus identifying novel therapeutic targets.