Lightsources.org

Shining a new light on biological cells

2018/09/072018/09/12

Combined X-ray and fluorescence microscope reveals unseen molecular details

A research team from the University of Göttingen has commissioned at the X-ray source PETRA III at DESY a worldwide unique microscope combination to gain novel insights into biological cells. The team led by Tim Salditt and Sarah Köster describes the combined X-ray and optical fluorescence microscope in the journal Nature Communications. To test the performance of the device installed at DESY’s measuring station P10, the scientists investigated heart muscle cells with their new method.

Modern light microscopy provides with ever sharper images important new insights into the interior processes of biological cells, but highest resolution is obtained only for the fraction of biomolecules which emit fluorescence light. For this purpose, small fluorescent markers have to be first attached to the molecules of interest, for example proteins or DNA. The controlled switching of the fluorescent dye in the so-called STED (stimulated emission depletion) microscope then enables highest resolution down to a few billionth of a meter, according to principle of optical switching between on- and off-state introduced by Nobel prize winner Stefan Hell from Göttingen.

Image: STED image (left) and X-ray imaging (right) of the same cardiac tissue cell from a rat. For STED, the network of actin filaments in the cell, which is important for the cell’s mechanical properties, have been labeled with a fluorescent dye. Contrast in the X-ray image, on the other hand, is directly related to the total electron density, with contributions of labeled and unlabeled molecules. By having both contrasts at hand, the structure of the cell can be imaged in a more complete manner, with the two imaging modalities “informing each other”.
Credit: University of Göttingen, M. Bernhardt et al.

A closer look of zink behaviour under extreme conditions

2018/09/062018/09/20

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.

These results can help to understand the processes and phenomena happening in the Earth’s interior.

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.

>Read more on the ALBA website

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.

Nanoparticles form supercrystals under pressure

2018/09/062018/09/10

Investigations at Diamond may lead to easier ways to synthesise nanoparticle supercrystals

Self-assembly and crystallisation of nanoparticles (NPs) is generally a complex process, based on the evaporation or precipitation of NP-building blocks. Obtaining high-quality supercrystals is slow, dependent on forming and maintaining homogenous crystallisation conditions. Recent studies have used applied pressure as a homogeneous method to induce various structural transformations and phase transitions in pre-ordered nanoparticle assemblies. Now, in work recently published in the Journal of Physical Chemistry Letters, a team of German researchers studying solutions of gold nanoparticles coated with poly(ethylene glycol)- (PEG-) based ligands has discovered that supercrystals can be induced to form rapidly within the whole suspension.

Figure: 2D SAXS patterns of PEG-coated gold nanoparticles (AuNP) with 2 M CsCl added at different pressures. Left: 1 bar; Middle: 4000 bar; Right: After pressure release at 1 bar. The scheme on top illustrates the structural assembly of the coated AuNPs at different pressures: At 1 bar, the particle ensemble is in an amorphous, liquid state. Upon reaching the crystallization pressure, face-centred cubic crystallites are formed by the AuNPs. After pressure release, the AuNPs return to the liquid state.

Yves Petroff takes over as Director of the LNLS

2018/09/062018/10/23

French physicist was Director-General of the largest European synchrotron between 1993 and 2001 and LNLS’ Scientific Director from 2009 to 2013.

In ceremony held on the morning of August 29th, Yves Pierre Petroff became Director of the Brazilian Synchrotron Light Laboratory (LNLS). Yves Petroff was LNLS’ Scientific Director from November 2009 to March 2013. During the ceremony, Rogério Cesar de Cerqueira Leite, Chairman of the Board of Directors of CNPEM, and Antonio José Roque da Silva, CNPEM’s Director-General and former LNLS Director, highlighted Pretroff’s competence and his history within LNLS.

Yves Petroff is one of the world’s leading specialists in the use of synchrotron light. He received his doctorate in physics from the Ecole Normale Supèrieure of the University of Paris in 1970. Later, he went to the University of California, Berkeley, from 1971 to 1975. During this period, Yves Petroff worked on the investigation of optical properties of solids, having made important developments in the area of Resonant Raman Effect.

In the early 1970s, the first generation of synchrotron accelerators began to be built, focused primarily on particle physics. In 1975, Yves Petroff returned to France to work in the ACO, one of the first synchrotrons in the world, located in Orsay. Pioneering work was performed by Petroff’s team on the use of synchrotron light to understand the properties of solids. His group was also the first in the world to build a Free Electron Laser in the region of visible light.

European XFEL celebrates one year of user operation

2018/09/05

At the beginning of September, staff and users of the world’s largest X-ray laser facility celebrate a successful first year of user operation.

Since September 2017, over 500 scientists from more than 20 countries from across the globe have visited European XFEL in Schenefeld in north Germany for their week long experiments. The first research results were published just days ago on 28 August; more publications are in preparation for the following weeks.

For the first and second round of experiments scheduled from September 2017 to October 2018, 123 international groups of scientists submitted their proposals for experiment. Of these, 26 groups were selected by an international panel of experts to carry out their research at the two instruments—the SPB/SFX instrument (Single Particles, Clusters and Biomolecules / Serial Femtosecond Crystallography) and the FXE instrument (Femtosecond X-Ray Experiments). The experiments range from method development to biomolecule structure determination and studies of extremely fast processes in small molecules and chemical reactions. Submissions for the user experiments at the remaining four instruments scheduled to start operation between the end of 2018 and mid-2019 are currently being evaluated.

>Read more on the European XFEL website

Image: The European XFEL birthday cake shows the map of the underground tunnel system. It was cut by Nicole Elleuche (Administrative Director European XFEL), Robert Feidenhans’l (Managing Director European XFEL), as well as Maria Faury (Chair of the European XFEL Council) and distributed to European XFEL and DESY staff.

Thailand is planning to build its ‘second’ Synchrotron Light Source

2018/08/312018/08/31

Synchrotron light source is the national infrastructure in science and technology for its contribution of research analysis from downstream, midstream, to upstream levels. Being an effective tool for advanced research, synchrotron promotes research targeting industrial applications for product development and innovation.

Thailand’s synchrotron radiation facility, the 2nd generation synchrotron light source, generates electron beam energy at 1.2 GeV covering spectral range from infrared to low-energy X-Rays. With such energy, the capacity of industrial and medical research is restricted due to the necessity of wider research techniques requiring higher energy and intensity of light. To produce high-energy X-Rays, Thailand should be compelled to develop the 4th generation of synchrotron light source with 2.5 times higher electron energy and 100,000 times higher intensity. This improvement aim to enhance research framework and facility service of Thailand to the leading position in medical, industrial, material, agricultural, food, and commercial research, including application and basic research, as well as becoming one of the top leaders in science and technology of Asia Pacific continent.

Image: Architectural model of Thailand’s future second Synchrotron Light Source

Direct Observation of the Kinetics of Gas–Solid Reactions

2018/08/312018/09/10

… using in-situ kinetic and spectroscopic techniques.

Copper oxide is a widely used adsorptive material that removes trace amounts of H₂S from various process streams via chemical reaction to form copper sulfide. At room temperature the thermodynamics favor a near complete conversion of CuO to copper sulfide in the presence of H₂S. However, in application, the extent of conversion of the CuO to copper sulfide during reaction can be influenced by many factors, including the initial crystalline state of the CuO, and the rate at which solid products accumulate on the reactive surfaces or within pores of the CuO particles. This incomplete utilization of CuO is problematic for industrial applications because it typically leads to oversized equipment and/or frequent process shutdowns. Developing fundamental insight at the atomic scale for this reaction could overcome these limitations by providing a rational basis for the design of new materials and by leading to predictive models that allow for current materials to be operated toward their thermodynamic limits. Thus, experiments that combine reaction kinetic testing while also simultaneously capturing chemical and structural changes in the solid phase at multiple length scales are necessary to elucidate the fundamentals of these reactions at various length scales.

Previous studies were successful in semi-quantitatively relating properties of materials to performance in fixed-bed systems, however, differences in performance were often attributed to physical properties at the >10 mm scale (e.g., surface area, pore volume, bulk density). The effects of molecular scale material characteristics (e.g., microscopic shape, metal oxide crystallite size, and surface composition) were rarely investigated, thus, it is difficult to extend the conclusions from these studies across a broad range of conditions and materials.

>Read more on the SSRL at SLAC website

Image (extract): (A) CuO and CuS concentration maps derived from XANES analysis of TXM images of individual CuO particle during reaction with 1000 ppm H₂S. (B) Fractional conversion versus time (derived from linear combination fitting of Cu K-edge XANES) of fixed beds of CuO particles consisting of 2 different crystallite sizes (red circles are 2.8 nm and blue squares are 28 nm) and of individual CuO particles. See the entire figure here.

Empowering multicomponent cathode materials for sodium ion batteries

2018/08/312018/09/10

…by exploring three-dimensional compositional heterogeneities

Energy storage devices have revolutionized the modern electronics industry by enabling the widespread application of portable electronic devices. Moreover, these storage devices also have the potential to reduce the dependence on fossil fuels by implementing electric vehicles in the market. To date, lithium ion batteries have dominated the market because of the high energy density delivered by them. However, one should look into the sustenance of such devices because Li is not one of the most abundant metals on Earth’s crust. Thus, developing an alternative to lithium ion batteries has become one of the key issues to ensure the sustainable future of energy storage devices. Sodium ion batteries provide one such alternative. Out of all the components of a battery, cathode materials play one of the key roles in determining the overall performance of such batteries. Unfortunately, sodium-ion batteries have been lagging behind their lithium ion counterpart in terms of performance. Thus, new design strategies must be undertaken in order to improve the performance of cathode materials for sodium ion batteries.

>Read more on the SSRL at SLAC website

Image (extract): Three-dimensional elemental associations of pristine Na_0.9Cu_0.2Fe_0.28Mn_0.52O₂ studied through transmission x-ray tomography. a) Visualizing the surface elemental associations at different angles with different colors corresponding to different association, and b) 2D cross-sectional association maps showing the bulk elemental associations. [Energy Environ. Sci., DOI: 10.1039/C8EE00309B (2018)] See entire figure here.

Just like lego – studying flexible protein for drug delivery

2018/08/302018/09/06

Researchers from the Sapienza University of Rome and its spin-off company MoLiRom (Italy) are spending the weekend at the ESRF to study a protein that could potentially transport anticancer drugs.

Ferritin is a large spherical protein (20 times bigger than haemoglobin) that stores iron within its cavity in every organism. Just like a lego playset, Ferritin assembles and disassembles. It is also naturally targeted to cancer cells. These are the reasons why Ferritin is a great candidate as a drug-transport protein to fight cancer. An international team of scientists from “Sapienza” University of Rome and the SME MoLiRom (Italy) came to the ESRF to explore a special kind of ferritin that shows promising properties. “This is an archaebacterial ferritin that have transformed into a humanised ferritin to try to tackle cancer cells”, explains Matilde Trabuco, a scientist at the Italian SME MoLiRom.

The mechanism looks simple enough: “Ferritin has a natural attraction to cancer cells. If we encapsulate anti-cancer drugs inside it, it will act as a Trojan horse to go inside cells, then it will open up and deliver the drug”.

Ferritins have been widely used as scaffolds for drug-delivery and diagnostics due to their characteristic cage-like structure. Most ferritins are stable and disassemble only by a harsh pH jump that greatly limits the type of possible cargo. The humanised ferritin was engineered to combine assembly at milder conditions with specific targeting of human cancer cells.

Strain research on rotating bearings wins Fylde prize for best paper

2018/08/302018/09/04

The paper – “Dynamic contact strain measurement by time‐resolved stroboscopic energy dispersive synchrotron X‐ray diffraction,” was the result of a collaboration between the Universities of Sheffield, Bristol, Oxford and Diamond Light Source. The researchers set themselves the challenge not just of measuring the strain in a bearing, but of capturing the measurement while the bearing was rotating and under load. This involved using a special stroboscopic X-ray diffraction technique to measure the strain in the rotating piece of machinery.

The authors will receive their award from the Journal’s Editorial Board and the British Society for Strain Measurement (BSSM) on 30^th August 2018 and have been invited to present their paper at the BSSM’s International Conference on Advances in Experimental Mechanics in Southampton at 29 – 31 August 2018.

Image: The bearing experiment.

Using uranium to create order from disorder

2018/08/302018/08/30

The first demonstration of reversible symmetry lowering phase transformation with heating.

ANSTO’s unique landmark infrastructure has been used to study uranium, the keystone to the nuclear fuel cycle. The advanced instruments at the Australian Synchrotron and the Australian Centre for Neutron Scattering have not only provided high resolution and precision, but also allowed in situ experiments to be carried out under extreme sample environments such as high temperature, high pressure and controlled gas atmosphere.

As part of his joint PhD studies at the University of Sydney and ANSTO, Gabriel Murphy has been investigating the condensed matter chemistry of a crystalline material, oxygen-deficient strontium uranium oxide, SrUO_4-x, which exhibits the unusual property of having ordered defects at high temperatures.

“Strontium uranium oxide is potentially relevant to spent nuclear fuel partitioning and reprocessing,” said Dr Zhaoming Zhang, Gabriel’s ANSTO supervisor and a co-author on the paper with Prof Brendan Kennedy of the University of Sydney that was published recently in Inorganic Chemistry.
Uranium oxides can access several valence states, from tetravalent— encountered commonly in UO₂ nuclear fuels, to pentavalent and hexavalent—encountered in both fuel precursor preparation and fuel reprocessing conditions.
Pertinent to the latter scenario, the common fission daughter Sr-90 may react with oxidised uranium to form ternary phases such as SrUO₄.

Image: Dr Zhaoming Zhang and Gabriel Murphy.

First European XFEL research results published

2018/08/28

High number of X-ray pulses per second reduces time needed for the study of biological structures.

Just days before the first anniversary of the start of European XFEL user operation, the first results based on research performed at the facility have been published. In the journal Nature Communications, the scientists, headed by Prof. Ilme Schlichting from Max-Planck-Institute for Medical Research in Heidelberg, Germany, together with colleagues from Rutgers State University of New Jersey, USA, France, DESY and European XFEL, describe their work using the intense X-ray laser beam to determine the 3D structure of several proteins. They demonstrate, for the first time that, under the conditions used at the time of the experiment an increased number of X-ray pulses per second as produced by the European XFEL can be successfully used to determine the structure of biomolecules. As much faster data collection is therefore possible, the time needed for an experiment could be significantly shortened. The detailed determination of the 3D structure of biomolecules is crucial for providing insights into informing the development of novel drugs to treat diseases.

Prof. Ilme Schlichting said: “Our work shows that under the conditions used data can be collected at European XFEL at a rate much faster than has ever been previously possible. As the time and cost of experiments decrease, very soon many more researchers will be able to perform experiments at high repetition rate X-ray lasers. Our results are therefore of interest not only tor the fields of biology and medicine, but also physics, chemistry and other disciplines.”

>Read more on the European XFEL website

Image: Guest scientist Tokushi Sato working at the sample chamber of the SPB/SFX instrument.
Credit: European XFEL

First-year operational results of the MAX IV 3 GeV ring

2018/08/272018/09/06

If you fly over MAX IV right now and look down, you’ll see a large circular building. The reason for this size and shape is the 528-meter-long 3GeV storage ring which precisely guides bunches of electrons traveling at velocities approaching the speed of light. As the electrons pass through arrays of magnets called insertion devices, they produce bright X-rays which are then used by beamline scientists to do many different types of experiments.

In an article published this month in the Journal of Synchrotron Radiation, the 3 GeV ring team led by Pedro Tavares describe the results for the first year of operation. This important milestone in the MAX IV project provides validation for many of the brand-new concepts that were implemented in the MAX IV design in order to improve the performance of the machine and reduce downtime.

Structure reveals mechanism behind periodic paralysis

2018/08/272018/08/30

The results suggest possible drug designs that could provide relief to patients with a genetic disorder that causes them to be overcome suddenly with profound muscle weakness.

A rare genetic disorder called hypokalemic periodic paralysis (hypoPP) causes sudden, profound muscle weakness in people who occasionally exhibit low levels of potassium in their blood, or hypokalemia. When a patient is hypokalemic, hypoPP affects the function of the muscles responsible for skeletal movement. The disease has been known to stem from mutations in certain membrane proteins that channel and regulate the flow of sodium into cells. Exactly how the mutation affects the proteins’ function, however, was not known.

In earlier work, researchers from the Catterall Lab at the University of Washington had solved the structure of a sodium channel called Na_vAb from a prokaryote (single-celled organism). As a next step, the group decided to see if Na_vAb could serve as a model for studying the mutations that cause hypoPP in humans (eukaryotes), with the goal of finding a way to prevent or treat this disorder.

A leak in the pipe?

In a resting state, muscle-cell membranes keep potassium ions and sodium ions separated, inside and outside the cell, respectively, creating a voltage across the membrane. A chemical signal from a nerve cell sets off a cascade of events that results in sodium ions flowing into the cell, changing the membrane potential and and ultimately triggering muscle contraction.

Image: Three states of the voltage-sensing domain (VSD) of a membrane-channel protein. In the normal state, the water-accessible space (magenta) does not extend through the channel, preventing sodium (gray spheres) from passing through. In the disease state, a clear passage allows sodium to leak through, resulting in muscle paralysis. In the “rescued” state, the binding of guanidinium (blue and yellow spheres) effectively closes the channel and blocks sodium leakage. The red sphere represents the location of the disease-causing mutation. The side-chain sticks represent the voltage sensors of the sodium channel.

Unprecedented 3D images of neurons in healthy and epileptic brains

2018/08/242018/10/08

Results open new perspectives for the study of neurodevelopment and neurodegenerative diseases.

A comprehensive understanding of the brain, its development, and eventual degeneration, depends on the assessment of neuronal number, spatial organization, and connectivity. However, the study of the brain architecture at the level of individual cells is still a major challenge in neuroscience.
In this context, Matheus de Castro Fonseca, from the Brazilian Biosciences National Laboratory (LNBio), and collaborators [1] used the facilities of the Brazilian Synchrotron Light Laboratory (LNLS) to obtain, for the first time, three-dimensional images in high resolution of part of the neuronal circuit, observed directly in the brain and with single cell resolution.

The researchers used the IMX X-Ray Microtomography beamline, in combination with the Golgi-Cox mercury-based impregnation protocol, which proved to be an efficient non-destructive tool for the study of the nervous system. The combination made it possible to observe the points of connectivity and the detailed morphology of a region of the brain, without the need for tissue slicing or clearing.
The mapping of neurons in healthy and unhealthy tissues should improve the research in neurodegenerative and neurodevelopmental diseases. As an example of this possibility, the work presents, for the first time in 3D, the neuronal death in an animal model of epilepsy.

The researchers are now working to extend the technique to animal models of Parkinson’s disease. The intention is to better understand the cellular mechanisms involved in the onset and progression of the disease. In the future, with the inauguration of the new Brazilian synchrotron light source, Sirius, the researchers believe that it will be possible to obtain images at the subcellular level, that is, images of the interior of the neurons.

Image: X-ray microtomography of the cerebral cortex showing the segmentation of individual neurons. Each color represents a single neuron or a group of neurons.

Synchrotrons in Black and White

2018/08/23

Recently on social media, a number of synchrotrons have taken part in the Black and White Challenge. The rules are simple, each facility must take a photo every day, in black and white with no people and post it on social media. You are not allowed to explain what is in the photo or why you chose to post it, you must also nominate one more account to take up the challenge every day.

A few weeks ago, MAX IV was nominated by both ESRF and ALBA Synchrotron to take part in the challenge and we accepted. Below are examples from each challenge, along with links to all the photos on Twitter (account not required).

This is a good opportunity to follow our various social media accounts if you haven’t already. We are very active and post exclusive content there that can’t be found anywhere else.