Unique synchrotron visualisation techniques offer new forensic insights into the provenance of radioactive material from the Fukushima nuclear accident to understand the sequence of events related to the accident.
In April 2017, a joint team comprising the University of Bristol, the Japan Atomic Energy Agency (JAEA) and Diamond, the UK’s national synchrotronlight source, undertook the first experiment of its kind to be performed at Diamond. A small radioactive particle (450μm x 280μm x 250 μm) from the Fukushima Daiichi nuclear accident in 2011 underwent a comprehensive and independent analysis of its internal structure and 3D elemental distribution, to establish the source of the material and the potential environmental risks associated with it.
Image: Fukushima Particles research group (L-R): Cristoph Rau (I13), Yukihiko Satou, (researcher from the Collaborative Laboratories for Advanced Decommissioning Science, Japan Atomic Energy Agency), with Tom Scott and Peter Martin (University of Bristol).
Bacteria produce complex nano-harpoons on their cell surface. One of their functions is to harpoon and inject toxins into cells that are close by. Producing such a complex weapon requires lots of different moving components that scientists are still trying to understand. Researchers from the University of Sheffield have been using some of Diamond’s crystallography beamlines to understand a particularly enigmatic piece of this tiny puzzle. The team led by David Rice and Mark Thomas worked on a protein component of the harpoon called TssA which they already knew was an integral piece of the machinery. However, unlike the other components of the harpoon, there are distinct variants of the TssA protein that contain radically different amino acid sequences at one end of the protein. The team showed that the structures of the variable region of two different TssA subunits were completely unrelated and they could assemble into distinctly different multisubunit complexes in terms of their size and geometry. This begged the question as to how different bacteria could use this protein with different structures to produce a harpoon with the same function across all species. They found that despite these differences, there was a very specific conserved region at the other end of the protein. They hypothesise that the conserved region is the part that does the work and helps the harpoon to function whereas the variable region acts as a scaffold. They used I02, I03 and I24 in their study and plan to do follow up work using X-ray crystallography and Cryo-EM such as those at the eBIC centre at Diamond. The research was published in Nature Communications.
Image: Macromolecular Crystallography (MX) at Diamond reveals the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function.
Today sees the launch of an innovative Citizen Science Project by Diamond Light Source, the UK’s national synchrotron science facility. The project uses a crowdsourcing model to call on people of all ages around the world to help speed up the analysis of the terabytes of data that Diamond generates every day. The first task set for citizen scientists is to spend a few minutes looking at a series of screens to identify viruses. More tasks will be set for other targets over the next three years. This will help train Artificial Intelligence systems (AI) and develop new ways of segmenting data, with the aim to automate the data segmentation processes. Doing this will dramatically speed up scientists’ ability to understand their research data in a matter of days rather than the current weeks, allowing for a faster path to understanding disease structures, and perhaps speeding up pathways to drug development.
Unveiled at the American Association for the Advancement of Science in Washington DC, The Diamond “Science Scribbler – Virus Project”, is the first of its kind that members of the public can help with in such a big way. It is funded by the world’s biggest biomedical charity, the Wellcome Trust and being developed in collaboration with Zooniverse, the renowned citizen science web platform.
XFEL Hub collaboration reveals the intermediates of the photosynthetic water oxidation clock
A large international collaborative effort aided by the XFEL Hub at Diamond Light Source has generated the most detailed time-resolved studies to date of a key protein involved in photosynthesis. The pioneering work, recently published in Nature, shows how photosystem II harnesses light energy to produce oxygen – insights that could direct a next generation of photovoltaic cells.
>Read more on the Diamond Light Source website
Image: this figure is issued from a video you can watch here.
New research on beamline I18 at Diamond Light Source investigates preservation techniques for Old Master paintings.
The surface of many Old Master paintings has been affected by the appearance of whitish lead-rich deposits, which are often difficult to fully characterise, thereby hindering conservation. Painted in 1663, Rembrandt’s Homer is an incredibly valuable and much-loved painting. Like many Old Masters it has a long and eventful past, which has taken its toll on the painting’s chemistry. The test of time and environmental factors, combined with the painting’s history, caused a barely visible, whitish crust to form on the surface of the painting. This crust indicates that chemical reactions are occurring which could potentially pose as risk for Homer and other old paintings if not kept in stable museum conditions.
A paper in ChemComm (Royal Society of Chemistry) has been published by a team of conservation scientists from the Mauritshuis in the Hague and the Rijksmuseum in Amsterdam, University of Amsterdam and scientists from Finden Ltd, UCL and Diamond Light Source, the UK’s National Synchrotron. Called “Unravelling the spatial dependency of the complex solid-state chemistry of Pb in a paint micro-sample from Rembrandt’s Homer using XRD-CT,” this paper is particularly timely given the celebrations occurring in 2019 to mark 350 years since the death of Rembrandt and the Dutch Golden Age. A paint micro-sample from Rembrandt’s Homer was imaged using X-ray Diffraction Computed Tomography (XRD-CT) in order to understand the evolving solid-state Pb chemistry from the painting surface and beneath.
Image: Stephen Price, Lead author from Diamond Light Source and Finden Ltd.
When you think about the theory of relativity, physics might be the first thing you think about.
But here at Diamond Light Source, our unique facility and state of the art instrument means that even our engineering teams must keep relativity in mind. In our last Year of Engineering spotlight piece, learn more about the unique engineering opportunities that present themselves when working at a synchrotron.
There are many areas where science and engineering work together, but relativity rarely makes an appearance. Most of our daily challenges can be solved by using simpler classical mechanics, where we (correctly) assume that objects travel at speeds which are a minute fraction of the speed of light, and weigh many times less than planets or stars. However, two engineering applications used every day at Diamond involve conditions which breach those assumptions, and so they must enter the strange world of relativity.
If you mention Einstein’s theory of relativity to a physicist, they will tell you how it provides a more accurate solution to any classical mechanics problem – but often with a lot more work involved! Inside Diamond’s linac and booster accelerators, the presence of relativistic effects instead allows for some clever engineering solutions which simplify the difficult task of controlling the movement of five billion electrons.
Image: The linac, with the gun at the far end and the accelerating structures coming towards us. The electrons are already more than 0.95 times the speed of light by the time they emerge from the copper rings at the back.
The inner workings of a lethal giant freshwater prawn virus have been revealed by an international team of researchers using data gathered at Diamond Light Source. The results reveal a possible new class of virus and presents the prospect of tackling a disease that can devastate prawn farms around the world.
The detailed structure of a virus that can devastate valuable freshwater prawn fisheries has been revealed by an international team using image data collected in the Electron Bio-Imaging Centre (eBIC) based at Diamond Light Source. The researchers produced high-resolution images of virus like particles, VLP’s, composed of virus shell proteins which they compared with lower resolution images of the complete virus purified from prawn larvae. They found strong similarities between the two suggesting that the more detailed VLP images are a good representation of the intact virus. This research, exposing the inner workings of the MrNV, could make it easier to develop ways of combating the economically important disease, but also suggests that it belongs in a new, separate, group of nodaviruses.
The researchers used the rapidly developing technique of cryo-electron microscopy, cryoEM, which has the ability to produce very high-resolution images of frozen virus particles. Images so detailed that the positions of individual atoms could be inferred. Recent breakthroughs in this technique have transformed the study of relatively large biological complexes like viruses allowing researchers to determine their structures comparatively quickly. The data to produce the MrNV structure described here was captured in two days at the eBIC facility.
Image: 3D model of the MrNV
Credit: Dr David Bhella
First users from the University of Southampton investigated proteins involved in nutrient uptake of photosynthetic or cyanobacteria to understand how these phytoplankton thrive under scarce nutrient conditions.
The work has immense global significance for biofuels production and biotechnology. This beamline marks the completion of Diamond’s original Phase III funding on time and within budget.
First users have now been welcomed by Diamond Light Source, the UK’s national synchrotron light source on its new VMXm beamline. The Versatile Macromolecular Crystallography micro/nanofocus (VMXm) beamline becomes the 32nd operational beamline to open its doors to users, completing the portfolio of seven beamlines dedicated to macromolecular crystallography.
The unique VMXm beamline represents a significant landmark for Diamond. It is a specialist tuneable micro/nanofocus macromolecular crystallography (MX) beamline, with an X-ray beam size of less than 0.5 microns, allowing even the tiniest of samples to be analysed. Integrated into the ‘in vacuum’ sample environment is a scanning electron microscope, making VMXm a hybrid X-ray/cryoEM instrument for detecting and measuring data from nanocrystals. VMXm is aimed at research applications where the production of significant quantities of protein and crystals is difficult.
Image: Principal Beamline Scientist Dr Gwyndaf Evans with his team Dr Jose Trincao, Dr Anna Warren, Dr Emma Beale and Dr Adam Crawshaw. First users – Dr Ivo Tews from Biological Sciences at the University of Southampton and joint Diamond-Southampton PhD student Rachel Bolton investigating proteins involved in nutrient uptake of photosynthetic or cyanobacteria.
We are one step further to uncovering a new way to stave off dengue fever thanks to important work carried out at the I02 beamline at Diamond Light Source.
The study, recently published in Nature Immunology, describes how an antibody effectively targets the dengue virus.
Dengue virus affects hundreds of millions of people worldwide and is an untreatable infection. Secondary infections with dengue can lead to a life-threatening form of the disease due to a phenomenon called antibody-dependent enhancement (ADE). Additionally, efforts to develop a vaccine against the virus have been hindered by ADE.
A huge collaborative effort sought to investigate ADE in dengue, and two antibodies were characterised that bound to the envelope protein of the dengue virus. One of the antibodies was found to be a potent neutraliser of the virus, but importantly was unable to promote ADE.
Image: Fab binding in the context of the mature virion. e, Comparison of 2C8 Fab and 3H5 Fab docked onto a E dimer. 2C8 (green) and 3H5 (orange) Fabs were docked onto PDB ID 3J27 by aligning the EDIII potion of the structures. The Fabs are shown as surfaces and the E dimer is displayed in cartoon representation. A side view is of the E dimer on the viral surface is shown. The approximate location of the viral membrane is shown schematically.
In-depth investigations on I13 to optimise soft tissue synchrotron X-ray microtomography
The Bradbury Lab at King’s College London, headed by Professor Elizabeth Bradbury, investigates damage to the central nervous system (CNS), and how the body responds to it. The traditional way of investigating soft tissue samples such as those of the central nervous system is 2D histology, in which slices are taken, stained and imaged. However, this process has limitations – slice thickness has a lower limit and measurements within cut slices are subject to inaccuracies arising from mechanical processing distortions. The group sent PhD student (now Dr) Merrick Strotton to the Diamond-Manchester Imaging Branchline I13-2 to investigate whether X-ray microtomography (a nominally non-destructive technique for taking a series of 2D images and turning them into a 3D volume) could avoid these issues. It wasn’t clear how to achieve the best possible results, and so alongside the biomedical studies, Dr Strotton worked with Diamond’s Dr Andrew Bodey on a series of methodological investigations on how to optimise imaging for soft tissue samples, the first results of which have recently been published in Scientific Reports.
Image: Segmentation of the low thoracic-high lumbar (T13-L1) level spinal cord sample from background, white & grey matter from spinal cord and vasculature from spinal cord with SuRVoS.
Celebrating the Year of Engineering on Beamline I23
The Year of Engineering (UK) is all about celebrating the world and wonder of the industry, and exploring the wide range of ideas and innovations that Engineering involves. Today, we’re having a look at Diamond’s Beamline I23 – a specially designed instrument for protein crystallography that uses long wavelengths.
There are unique engineering scientific challenges involved in designing a system that will allow researchers to use long wavelengths of Synchrotron radiation effectively. The special cryogenically-cooled sample gripper on I23, is one of the solutions that makes this beamline successful. Learn more about this engineering innovation.
Nearly 50 years after our first steps on the Moon, rock samples from the Apollo missions still have a lot to tell us about lunar formation, and Earth’s volcanoes.
An international collaboration involving scientists in Tenerife, the US and the UK, are using Diamond, the UK’s national synchrotron light source, to investigate Moon rocks recovered during the Apollo Missions in a brand new way.
Dr. Matt Pankhurst of Instituto Volcanológico de Canarias and NASA lunar principle investigator explains: “We have used a new imaging technique developed at Diamond to carry out 3D mapping of olivine – a common green mineral found in the Earth’s sub-surface and in these Moon rock samples. These maps will be used to improve understanding of the Moon’s ancient volcanic systems and help to understand active geological processes here on Earth.
With this new technique, our team may be able to recover from these Moon rock samples information such as what the patterns of magma flow within the volcanic system were, what the magma storage duration was like, and potentially even identify eruption triggers. The data will be analysed using state-of-the-art diffusion modelling which will establish the history of individual crystals.”
>Read more on the Diamond Light Source website
Image: Dr Matt Pankhurst studies one of the moon rock samples from the Apollo 12 & 15 missions at Diamond Light Source
UK set to be global leader in providing large-scale industrial access to Cryo-EM for drug discovery thanks to new collaboration.
Thermo Fisher Scientific and Diamond Light Source are creating a step change for life sciences sector, a one-stop shop for structural biology and one of largest cryo-EM sites in the world.
An agreement to launch a new cryo-EM capability for use in the life sciences industry sector by Thermo Fisher Scientific, one of the world leaders in high-end scientific instrumentation, and Diamond Light Source, the UK’s national synchrotron and one of the most advanced scientific facilities in the world, was announced today ahead of the official opening of the new national electron bio-imaging centre (eBIC) which will be held at Diamond on September 12th 2018.
This announcement confirms Diamond as one of the major global cryo-EM sites embedded with an abundance of complementary synchrotron-based techniques, and thereby, provides the life sciences sector with an offer not available anywhere else in the world.
Professor Dave Stuart, Life Sciences Director at Diamond and MRC Professor of Structural Biology at the University of Oxford, Department of Clinical Medicine, says, “Access to 21st century scientific tools to push the boundaries of scientific research is essential for both academia and industry, and what we have created here at Diamond is truly unique in the world in terms of size and scale. The new centre offers the opportunity for almost real-time physiology, capturing proteins in action at cryo-temperatures by flash-freezing them at various stages. What Diamond has created with eBIC is an integrated facility for structural biology, which will accelerate R&D for both industry and academic users. The additional advanced instruments made available by Thermo Fisher will position the UK as a global leader in providing large-scale industrial access to cryo-EM for drug discovery research. Our new collaboration provides a step change in our offer for industry users and helps ensure that R&D remains in the UK.”
Image: Close up sample loading Krios I.
Researchers have explored the phase diagram of zinc under high pressure and high temperature conditions, finding evidence of a change in its structural behaviour at 10 GPa. Experiments profited from the brightness of synchrotron light at ALBA and Diamond.
The field of materials science studies the properties and processes of solids to understand and discover their performances. Synchrotron light techniques permit to analyse these materials at extreme conditions (high pressure and high temperature), getting new details and a deep knowledge of them.
Studying the melting behaviours of terrestrial elements and materials at extreme conditions, researchers can understand the phenomena taking place inside them. This information is of great value for discovering how these materials react in the inner core of Earth but also for other industrial applications. Zinc is one of the most abundant elements in Earth’s crust and is used in multiple areas such as construction, ship-building or automobile.
Figure: P-T phase diagram of zinc for P<16 GPa and T<1600K. Square data points correspond to the X-ray diffraction measurements. Solid squares are used for the low pressure hexagonal phase (hcp) and empty symbols for the high pressure hexagonal phase (hcp’). White, red and black circles are melting points from previous studies reported in the literature. The triangles are melting points obtained in the present laser-heating measurements. In the onset of the figure is shown the custom-built vacuum vessel for resistively-heated membrane-type DAC used in the experiments at the ALBA Synchrotron.