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"Simpson, David A."
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Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types
Background
MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore have the potential to mediate intercellular communication. It has been suggested that certain miRNAs may be selectively exported, although the mechanism has yet to be identified. Manipulation of the miRNA content of EVs will be important for future therapeutic applications. We therefore wished to assess which endogenous miRNAs are enriched in EVs and how effectively an overexpressed miRNA would be exported.
Results
Small RNA libraries from HEK293T cells and vesicles before or after transfection with a vector for miR-146a overexpression were analysed by deep sequencing. A subset of miRNAs was found to be enriched in EVs; pathway analysis of their predicted target genes suggests a potential role in regulation of endocytosis. RT-qPCR in additional cell types and analysis of publicly available data revealed that many of these miRNAs tend to be widely preferentially exported. Whilst overexpressed miR-146a was highly enriched both in transfected cells and their EVs, the cellular:EV ratios of endogenous miRNAs were not grossly altered. MiR-451 was consistently the most highly exported miRNA in many different cell types. Intriguingly, Argonaute2 (Ago2) is required for miR-451 maturation and knock out of Ago2 has been shown to decrease expression of other preferentially exported miRNAs (eg miR-150 and miR-142-3p).
Conclusion
The global expression data provided by deep sequencing confirms that specific miRNAs are enriched in EVs released by HEK293T cells. Observation of similar patterns in a range of cell types suggests that a common mechanism for selective miRNA export may exist.
Journal Article
Quantitative profiling of lifespan-dependent cell-cell communication potential reveals dynamic ligand-receptor network shifts across mouse tissues
Cell-to-cell communication (CCC) is a tightly regulated process essential for tissue development and homeostasis, but can become dysregulated during ageing. While CCC is inherently complex and remains incompletely characterised, advances in single-cell RNA sequencing (scRNA-seq) have enabled large-scale, unbiased inference of intercellular interactions which offers broad-spectrum information that complements traditional protein-based assays. Unlike these targeted assays, transcriptomic approaches enable systematic inference and exploration of both known and potentially novel ligand-receptor (LR) interactions. In this study, we applied LIgand-receptor ANalysis frAmework (LIANA), which integrates multiple inference methods to derive consensus CCC predictions, to scRNA-seq data for four mouse organs (liver, lung, heart, and kidney), spanning key life stages: post-natal development, adulthood and ageing. Our analysis revealed dynamic, organ-specific CCC patterns characterised by both gains and losses of LR interactions over time, reflecting lifespan-dependent shifts in transcriptome-inferred intercellular communication potential. To quantify these shifts, we developed a two-phase comparative framework and introduced the Shrink and Expand (SE) score to capture directional changes in inferred LR interaction sets between any two biological states. Applying this framework generated a curated dataset of LR pairs and their predicted changes, capturing the repertoire of putative interactions across organs and states and enabling robust, interpretable comparisons of organ-specific and coinciding patterns of change across multiple organs. For instance, CD44 and ITGB1 were found to undergo highly dynamic changes across timepoints and organs, suggesting that they may act as central nodes in predicted age-dependent communication changes. This generalisable approach supports quantitative comparisons of inferred CCC across diverse states, including development, ageing, disease, or treatment conditions, and provides a resource for prioritising candidate interactions for drug target discovery for further experimental validation while exploring context-specific shifts in predicted intercellular communication.
Journal Article
Electron paramagnetic resonance microscopy using spins in diamond under ambient conditions
Magnetic resonance spectroscopy is one of the most important tools in chemical and bio-medical research. However, sensitivity limitations typically restrict imaging resolution to ~ 10 µm. Here we bring quantum control to the detection of chemical systems to demonstrate high-resolution electron spin imaging using the quantum properties of an array of nitrogen-vacancy centres in diamond. Our electron paramagnetic resonance microscope selectively images electronic spin species by precisely tuning a magnetic field to bring the quantum probes into resonance with the external target spins. This provides diffraction limited spatial resolution of the target spin species over a field of view of 50 × 50 µm
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with a spin sensitivity of 10
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spins per voxel or ∼100 zmol. The ability to perform spectroscopy and dynamically monitor spin-dependent redox reactions at these scales enables the development of electron spin resonance and zepto-chemistry in the physical and life sciences.
Electron paramagnetic resonance spectroscopy has important scientific and medical uses but improving the resolution of conventional methods requires cryogenic, vacuum environments. Simpson et al. show nitrogen vacancy centres can be used for sub-micronmetre imaging with improved sensitivity in ambient conditions.
Journal Article
Quantum probe hyperpolarisation of molecular nuclear spins
Hyperpolarisation of nuclear spins is important in overcoming sensitivity and resolution limitations of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. Current hyperpolarisation techniques require high magnetic fields, low temperatures, or catalysts. Alternatively, the emergence of room temperature spin qubits has opened new pathways to achieve direct nuclear spin hyperpolarisation. Employing a microwave-free cross-relaxation induced polarisation protocol applied to a nitrogen vacancy qubit, we demonstrate quantum probe hyperpolarisation of external molecular nuclear spins to ~50% under ambient conditions, showing a single qubit increasing the polarisation of ~10
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nuclear spins by six orders of magnitude over the thermal background. Results are verified against a detailed theoretical treatment, which also describes how the system can be scaled up to a universal quantum hyperpolarisation platform for macroscopic samples. Our results demonstrate the prospects for this approach to nuclear spin hyperpolarisation for molecular imaging and spectroscopy and its potential to extend beyond into other scientific areas.
Molecules with ‘hyperpolarised’ nuclear spins can be used to improve MRI performance but require an efficient polarisation method. Broadway et al. demonstrate a quantum control protocol using a nitrogen vacancy centre inside a diamond to hyperpolarise protons within molecules deposited on the surface.
Journal Article
A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma
Background
Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expression profiles is required to maximise miRNA biomarker discovery. Although developments in small RNA-Seq technology have improved detection of plasma-based miRNAs, the low RNA content and sequencing bias introduced during library preparation remain challenging. In this study we compare commercially available RNA extraction methods using MagnaZol (Bioo Scientific) or miRNeasy (QIAGEN) and three library preparation methods - CleanTag (TriLink), NEXTflex (Bioo Scientific) and QIAseq (QIAGEN) - which aim to address one or both of these issues.
Results
Different RNA extractions and library preparation protocols result in differential detection of miRNAs. A greater proportion of reads mapped to miRNAs in libraries prepared with MagnaZol RNA than with miRNeasy RNA. Libraries prepared using QIAseq demonstrated the greatest miRNA diversity with many more very low abundance miRNAs detected (~ 2–3 fold more with < 10 reads), whilst CleanTag detected the fewest individual miRNAs and considerably over-represented miR-486-5p. Libraries prepared with QIAseq had the strongest correlation with RT-qPCR quantification. Analysis of unique molecular indices (UMIs) incorporated in the QIAseq protocol indicate that little PCR bias is introduced during small RNA library preparation.
Conclusions
Small RNAs were consistently detected using all RNA extraction and library preparation protocols tested, but with some miRNAs at significantly different levels. Choice of the most suitable protocol should be informed by the relative importance of minimising the total sequencing required, detection of rare miRNAs or absolute quantification.
Journal Article
Proximal nitrogen reduces the fluorescence quantum yield of nitrogen-vacancy centres in diamond
The nitrogen-vacancy colour centre in diamond is emerging as one of the most important solid-state quantum systems. It has applications to fields including high-precision sensing, quantum computing, single photon communication, metrology, nanoscale magnetic imaging and biosensing. For all of these applications, a high quantum yield of emitted photons is desirable. However, diamond samples engineered to have high densities of nitrogen-vacancy centres show levels of brightness varying significantly within single batches, or even within the same sample. Here we show that nearby nitrogen impurities quench emission of nitrogen-vacancy centres via non-radiative transitions, resulting in a reduced fluorescence quantum yield. We monitored the emission properties of nitrogen-vacancy centre ensembles from synthetic diamond samples with different concentrations of nitrogen impurities. All samples were irradiated with high energy electrons to create high densities of nitrogen-vacancy centres relative to the concentration of nitrogen impurities. While at low nitrogen densities of 1.81 ppm we measured a lifetime of 13.9 ns, we observed a strong reduction in lifetime with increasing nitrogen density. We measure a lifetime as low as 4.4 ns at a nitrogen density of 380 ppm. The change in lifetime matches a reduction in relative fluorescence quantum yield from 77.4% to 32% with an increase in nitrogen density from 88 ppm to 380 ppm, respectively. These results will inform the conditions required to optimise the properties of diamond crystals devices based on the fluorescence of nitrogen-vacancy centres. Furthermore, this work provides insights into the origin of inhomogeneities observed in high-density nitrogen-vacancy ensembles within diamonds and nanodiamonds.
Journal Article
Magneto-optical imaging of thin magnetic films using spins in diamond
Imaging the fields of magnetic materials provides crucial insight into the physical and chemical processes surrounding magnetism and has been a key ingredient in the spectacular development of magnetic data storage. Existing approaches using the magneto-optic Kerr effect, x-ray and electron microscopy have limitations that constrain further development and there is increasing demand for imaging and characterisation of magnetic phenomena in real time with high spatial resolution. Here we show how the magneto-optical response of an array of negatively-charged nitrogen-vacancy spins in diamond can be used to image and map the sub-micron stray magnetic field patterns from thin ferromagnetic films. Using optically detected magnetic resonance, we demonstrate wide-field magnetic imaging over 100 × 100 μm
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with sub-micron spatial resolution at video frame rates, under ambient conditions. We demonstrate an all-optical spin relaxation contrast imaging approach which can image magnetic structures in the absence of an applied microwave field. Straightforward extensions promise imaging with sub-μT sensitivity and sub-optical spatial and millisecond temporal resolution. This work establishes practical diamond-based wide-field microscopy for rapid high-sensitivity characterisation and imaging of magnetic samples, with the capability for investigating magnetic phenomena such as domain wall and skyrmion dynamics and the spin Hall effect in metals.
Journal Article
Genome-wide transcriptome profiling of human trabecular meshwork cells treated with TGF-β2
Glaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.
Journal Article