A5081648949- Advanced Fluorescence Microscopy Techniques
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Cell Image Analysis Techniques
- RNA and protein synthesis mechanisms
- Computational Physics and Python Applications
- Optical Coherence Tomography Applications
- Advanced Electron Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Ophthalmology and Visual Impairment Studies
- Photoacoustic and Ultrasonic Imaging
- Advanced Biosensing Techniques and Applications
- Microtubule and mitosis dynamics
- Advanced X-ray Imaging Techniques
- RNA modifications and cancer
- Image Processing Techniques and Applications
- Chromosomal and Genetic Variations
- Immunotherapy and Immune Responses
- Cancer Research and Treatments
- Ocular Disorders and Treatments
- Cellular transport and secretion
- Single-cell and spatial transcriptomics
- Microfluidic and Bio-sensing Technologies
- DNA and Nucleic Acid Chemistry
- Ubiquitin and proteasome pathways
University of Oxford
2015-2024
Oxford Nanoimaging (United Kingdom)
2019
Ollscoil na Gaillimhe – University of Galway
2009-2019
University of Leeds
2018
Janelia Research Campus
2018
University of Cambridge
2018
Imaging Center
2018
Howard Hughes Medical Institute
2018
Johnson & Johnson (United States)
2014
Advanced FIB-SEM and 3D-SIM imaging uncover cohesin-independent chromatin arrangement into structural functional modules.
Rapid cryopreservation of biological specimens is the gold standard for visualizing cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope 3D super-resolution fluorescence cryo-imaging correlation with cryo-electron microscopy or cryo-soft X-ray tomography. We provide full instructions replicating instrument mostly from off-the-shelf components...
Visualizing Xist RNA dynamics The noncoding Xist, which controls the process of X chromosome inactivation in mammals, accumulates and spreads over from it is transcribed. underlying basis for this unusual behavior poorly understood. Using a new imaging approach called RNA-SPLIT time-resolved analysis molecules at super-resolution, Rodermund et al. analyzed fundamental parameters normal cells after perturbation factors implicated function. authors provide insights into localization...
Centrioles organise centrosomes and cilia, these organelles have an important role in many cell processes. In flies, the centriole protein Ana1 is required for assembly of functional cilia. It has recently been shown that Cep135 (also known as Bld10) initially recruits to newly formed centrioles, then Asl (known Cep152 mammals) promote conversion centrioles into centrosomes. Here, we show ana1 mutants lack detectable vivo, irreversibly incorporated during their appears play a more...
Centrosomes comprise a pair of centrioles surrounded by matrix pericentriolar material (PCM). In vertebrate cells, Pericentrin plays an important part in mitotic PCM assembly, but the Drosophila Pericentrin-like protein (PLP) appears to have more minor role fly cells. Here we investigate function PLP during rapid cycles early embryo. Unexpectedly, find that is specifically enriched outer-most regions PCM, where it largely co-localizes with scaffold Cnn. absence outer be structurally...
While post-transcriptional control is thought to be required at the periphery of neurons and glia, its extent unclear. Here, we investigate systematically spatial distribution expression mRNA single molecule sensitivity their corresponding proteins 200 YFP trap lines across intact Drosophila nervous system. 97.5% genes studied showed discordance between they encode in least one region These data suggest that regulation very common, helping explain complexity We also discovered 68.5% these...
Limbal ring (also known as 'circle') contact lenses are becoming increasingly popular, especially in Asian markets because of their eye-enhancing effects. The pigment particles that give the effects these can be found on front or back surface lens 'enclosed' within matrix. purpose this research was to evaluate location and roughness seven types 'circle' lenses.Scanning electron microscopic (SEM) analysis performed using a variable pressure Hitachi S3400N instrument discern placement...
ABSTRACT Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural functional nuclear somatic cells. We identify linked domains (CDs) composed irregular ∼200-300-nm-wide aggregates nucleosomes that can overlap with individual topologically associating are distinct from...
Custom-built microscopes often require control of multiple hardware devices and precise coordination. It is also desirable to have a solution that scalable complex systems translatable between components from different manufacturers. Here we report Python-Microscope, free open-source Python library for high-performance arbitrarily custom microscope systems. Python-Microscope offers simple use Python-based tools, abstracting differences physical by providing defined interface device types....
<ns3:p>We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user allows next-generation near instantaneous navigation the entire slide landscape efficient selection specimens interest automated acquisition without use eyepieces. Cockpit uses “Python-Microscope” (Microscope) high-performance coordinated wide range...
Advanced fluorescence imaging methods require careful matching of excitation sources, dichroics, emission filters, detectors, and dyes to operate at their best. This complex task is often left guesswork, preventing optimal dye:filter combinations, particularly for multicolour applications. To overcome this challenge we developed SPEKcheck, a web application visualise the efficiency light path in microscope. The software reports values dye, collection emitted fluorescence, "brightness" score,...
Abstract Core histone proteins H2A, H2B, H3, and H4 are encoded by a large family of genes distributed across the human genome. Canonical core histones contribute majority to bulk chromatin packaging, in 4 clusters 65 coding comprising 17 for 18 15 H4, along with at least total pseudogenes. The canonical display variation that gives rise 11 2 unique protein isoforms. Although highly conserved overall, these isoforms represent surprising seldom recognised amino acid identity as low 77%...
Abstract Rapid cryo-preservation of biological specimens is the gold standard for visualising cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope 3D super-resolution fluorescence cryo-imaging correlation with cryo electron microscopy or soft X-ray tomography. We provide full instructions replicating instrument mostly from off-the-shelf...
Abstract We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based GUI environment for precision control of both simple and elaborate bespoke microscope systems. The user allows next-generation near-instantaneous navigation the entire slide landscape efficient selection specimens interest automated acquisition without use eyepieces. Cockpit uses “Python-Microscope” (Microscope) high-performance coordinated wide range hardware devices using...
<ns4:p>BeamDelta is a tool to help align optical systems. It greatly assists in assembling bespoke systems by providing live view of the current laser beam position and reference position. Even simple setup has multiple degrees freedom that affect alignment paths. These rise exponentially with complexity system. The process aligning all components for specific system often esoteric poorly documented, if it documented at all. Alignment methods used rely on visual inspection beams impinging...
<ns4:p>We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user allows next-generation near instantaneous navigation the entire slide landscape efficient selection specimens interest automated acquisition without use eyepieces. Cockpit uses “Python-Microscope” (Microscope) high-performance coordinated wide range...
Summary While post-transcriptional control is thought to be required at the periphery of neurons and glia, its extent unclear. Here, we investigate systematically spatial distribution expression mRNA single molecule sensitivity their corresponding proteins 200 YFP trap protein lines across intact Drosophila nervous system. 98% genes studied showed discordance between they encode in least one region These data suggest that regulation very common, helping explain complexity We also discovered...
Abstract Xist RNA directs the process of X-chromosome inactivation in mammals by spreading cis along chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms -confinement, we established a sequential dual color labeling, super-resolution imaging approach trace individual molecules over time, enabling us define fundamental parameters spreading. We demonstrate feedback mechanism linking synthesis degradation, an...
Abstract Custom built microscopes often require control of multiple hardware devices and precise coordination. It is also desirable to have a solution that scalable complex systems translatable between components from different manufacturers. Here we report Python-Microscope, free open source Python library for high performance arbitrarily custom microscope systems. Python-Microscope offers simple use Python-based tools, abstracting differences physical by providing defined interface device...
Abstract 3D structured illumination microscopy (3D-SIM) doubles the resolution of fluorescence imaging in lateral and axial directions increases contrast both fixed live specimens. However, 3D-SIM has so far not been widely applied to deep thick tissues due its sensitivity specimen-induced aberrations, making method difficult apply beyond 10 µm depth. Furthermore, available an upright configuration, limiting use for while manipulating specimen, example with electrophysiology. Here, we have...