School of Physics - Research Publications
Now showing items 1-12 of 1276
Gene set enrichment analysis for genome-wide DNA methylation data
DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions. GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis. Benchmarking analyses demonstrate GOmeth outperforms other approaches, and GOregion is the first method for gene set testing of differentially methylated regions. Both methods are publicly available in the missMethyl Bioconductor R package.
Live cell dynamics of the NF-Y transcription factor
(NATURE RESEARCH, 2021-05-26)
Transcription factors (TFs) are core players in the control of gene expression, evolutionarily selected to recognise a subset of specific DNA sequences and nucleate the recruitment of the transcriptional machinery. How TFs assemble and move in the nucleus to locate and bind their DNA targets and cause a transcriptional response, remains mostly unclear. NF-Y is a highly conserved, heterotrimeric TF with important roles in both housekeeping and lineage-specific gene expression, functioning as a promoter organiser. Despite a large number of biochemical, structural and genomic studies of NF-Y, there is a lack of experiments in single living cells; therefore, basic assumptions of NF-Y biology remain unproven in vivo. Here we employ a series of dynamic fluorescence microscopy methods (FLIM-FRET, NB, RICS and FRAP) to study NF-Y dynamics and complex formation in live cells. Specifically, we provide quantitative measurement of NF-Y subunit association and diffusion kinetics in the nucleus that collectively suggest NF-Y to move and bind chromatin as a trimeric complex in vivo.
Nanophotonics enhanced coverslip for phase imaging in biology
The ability to visualise transparent objects such as live cells is central to understanding biological processes. Here we experimentally demonstrate a novel nanostructured coverslip that converts phase information to high-contrast intensity images. This compact device enables real-time, all-optical generation of pseudo three-dimensional images of phase objects on transmission. We show that by placing unstained human cancer cells on the device, the internal structure within the cells can be clearly seen. Our research demonstrates the significant potential of nanophotonic devices for integration into compact imaging and medical diagnostic devices. The nanophotonics enhanced coverslip (NEC) enables ultra-compact phase imaging of samples placed directly on top of the device. Visualisation of artificial phase objects and unstained biological cells is demonstrated.
Advances in Carbon-Based Microfiber Electrodes for Neural Interfacing
(FRONTIERS MEDIA SA, 2021-04-12)
Neural interfacing devices using penetrating microelectrode arrays have emerged as an important tool in both neuroscience research and medical applications. These implantable microelectrode arrays enable communication between man-made devices and the nervous system by detecting and/or evoking neuronal activities. Recent years have seen rapid development of electrodes fabricated using flexible, ultrathin carbon-based microfibers. Compared to electrodes fabricated using rigid materials and larger cross-sections, these microfiber electrodes have been shown to reduce foreign body responses after implantation, with improved signal-to-noise ratio for neural recording and enhanced resolution for neural stimulation. Here, we review recent progress of carbon-based microfiber electrodes in terms of material composition and fabrication technology. The remaining challenges and future directions for development of these arrays will also be discussed. Overall, these microfiber electrodes are expected to improve the longevity and reliability of neural interfacing devices.
Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor
(LIPPINCOTT WILLIAMS & WILKINS, 2021-04-20)
BACKGROUND: Despite in-depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals governing postnatal maturation of the human heart. METHODS: Single-nucleus RNA sequencing of 54 140 nuclei from 9 human donors was used to profile transcriptional changes in diverse cardiac cell types during maturation from fetal stages to adulthood. Bulk RNA sequencing and the Assay for Transposase-Accessible Chromatin using sequencing were used to further validate transcriptional changes and to profile alterations in the chromatin accessibility landscape in purified cardiomyocyte nuclei from 21 human donors. Functional validation studies of sex steroids implicated in cardiac maturation were performed in human pluripotent stem cell-derived cardiac organoids and mice. RESULTS: Our data identify the progesterone receptor as a key mediator of sex-dependent transcriptional programs during cardiomyocyte maturation. Functional validation studies in human cardiac organoids and mice demonstrate that the progesterone receptor drives sex-specific metabolic programs and maturation of cardiac contractile properties. CONCLUSIONS: These data provide a blueprint for understanding human heart maturation in both sexes and reveal an important role for the progesterone receptor in human heart development.
Clustering of the ζ-Chain Can Initiate T Cell Receptor Signaling.
(MDPI AG, 2020-05-15)
T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of ζ-chain in a light controlled manner. We showed that spatial clustering of the ζ-chain intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of ζ-chain, Zap70, PLCγ, ERK and initiated Ca2+ flux. In reconstituted COS-7 cells, only Lck expression was required to initiate ζ-chain phosphorylation upon ζ-chain clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed ζ-chain clusters at the plasma membrane. Taken together, our data demonstrated the biophysical relevance of receptor clustering in TCR signaling.
Simple route toward efficient frequency conversion for generation of fully coherent supercontinua in the mid-IR and UV range.
(Springer Science and Business Media LLC, 2017-02)
Fiber supercontinua represent light sources of pivotal importance for a wide range of applications, ranging from optical communications to frequency metrology. Although spectra encompassing more than three octaves can be produced, the applicability of such spectra is strongly hampered due to coherence degradation during spectral broadening. Assuming pulse parameters at the cutting edge of currently available laser technology, we demonstrate the possibility of strongly coherent supercontinuum generation. In a fiber with two zero-dispersion wavelengths a higher-order soliton experiences a temporal breakdown, without any compression or splitting behavior, which leads to nearly complete conversion of input solitonic radiation into resonant nonsolitonic radiation in the dispersive wave regime. As the process is completely deterministic and shows little sensitivity to input noise, the resulting pulses appear to be compressible down to the sub-cycle level and may thus hold a new opportunity for direct generation of attosecond pulses in the visible to near ultraviolet wavelength range.
Effects of edge on graphene plasmons as revealed by infrared nanoimaging.
(Springer Science and Business Media LLC, 2017-02)
We used scattering-type scanning near-field optical microscopy (s-SNOM) to investigate the plasmonic properties of edges in well-defined graphene nanostructures, including sharp tapers, nanoribbons and nanogaps, which were all fabricated via the growth-etching chemical vapor deposition (GECVD) method. The obtained near-field images revealed the localized plasmon modes along the graphene nanoribbon; these modes strongly depended on the size of the graphene pattern, the angle of the tapered graphene and the infrared excitation wavelength. These interesting plasmon modes were verified by numerical simulations and explained by the reflection, and interference of electromagnetic waves at the graphene-SiO2 edge. The constructive interference at the graphene nanogap caused by charge accumulation was demonstrated for the first time. Using the infrared nanoimaging technique, greater plasmon broadening was observed in the zigzag edge than in the armchair edge. Our study suggests that graphene edges should be separated by an effective working distance to avoid the overlapping of localized plasmon modes, which is very important for the design of graphene-based plasmonic circuits and devices.
A mobile endocytic network connects clathrin-independent receptor endocytosis to recycling and promotes T cell activation.
(Springer Science and Business Media LLC, 2018-04-23)
Endocytosis of surface receptors and their polarized recycling back to the plasma membrane are central to many cellular processes, such as cell migration, cytokinesis, basolateral polarity of epithelial cells and T cell activation. Little is known about the mechanisms that control the organization of recycling endosomes and how they connect to receptor endocytosis. Here, we follow the endocytic journey of the T cell receptor (TCR), from internalization at the plasma membrane to recycling back to the immunological synapse. We show that TCR triggering leads to its rapid uptake through a clathrin-independent pathway. Immediately after internalization, TCR is incorporated into a mobile and long-lived endocytic network demarked by the membrane-organizing proteins flotillins. Although flotillins are not required for TCR internalization, they are necessary for its recycling to the immunological synapse. We further show that flotillins are essential for T cell activation, supporting TCR nanoscale organization and signaling.
New Insights into How Trafficking Regulates T Cell Receptor Signaling.
(Frontiers Media SA, 2016)
There is emerging evidence that exocytosis plays an important role in regulating T cell receptor (TCR) signaling. The trafficking molecules involved in lytic granule (LG) secretion in cytotoxic T lymphocytes (CTL) have been well-studied due to the immune disorder known as familial hemophagocytic lymphohistiocytosis (FHLH). However, the knowledge of trafficking machineries regulating the exocytosis of receptors and signaling molecules remains quite limited. In this review, we summarize the reported trafficking molecules involved in the transport of the TCR and downstream signaling molecules to the cell surface. By combining this information with the known knowledge of LG exocytosis and general exocytic trafficking machinery, we attempt to draw a more complete picture of how the TCR signaling network and exocytic trafficking matrix are interconnected to facilitate T cell activation. This also highlights how membrane compartmentalization facilitates the spatiotemporal organization of cellular responses that are essential for immune functions.
Highly responsive MoS2 photodetectors enhanced by graphene quantum dots.
(Springer Science and Business Media LLC, 2015-07-03)
Molybdenum disulphide (MoS2), which is a typical semiconductor from the family of layered transition metal dichalcogenides (TMDs), is an attractive material for optoelectronic and photodetection applications because of its tunable bandgap and high quantum luminescence efficiency. Although a high photoresponsivity of 880-2000 AW(-1) and photogain up to 5000 have been demonstrated in MoS2-based photodetectors, the light absorption and gain mechanisms are two fundamental issues preventing these materials from further improvement. In addition, it is still debated whether monolayer or multilayer MoS2 could deliver better performance. Here, we demonstrate a photoresponsivity of approximately 10(4) AW(-1) and a photogain of approximately 10(7) electrons per photon in an n-n heterostructure photodetector that consists of a multilayer MoS2 thin film covered with a thin layer of graphene quantum dots (GQDs). The enhanced light-matter interaction results from effective charge transfer and the re-absorption of photons, leading to enhanced light absorption and the creation of electron-hole pairs. It is feasible to scale up the device and obtain a fast response, thus making it one step closer to practical applications.