Category: ESRF

Unveiling the secrets of biofilms

Unveiling the secrets of biofilms

Most bacteria have the ability to form communities, biofilms, that adhere to a wide variety of surfaces and are difficult to remove. This can lead to major problems, for example in hospitals or in the food industry. Now, an international team led by Hebrew University, Jerusalem, and the Technical University Dresden, has studied a model system for biofilms at the synchrotron radiation facilities BESSY II at HZB and the ESRF and found out what role the structures within the biofilm play in the distribution of nutrients and water.

Bacterial biofilms can thrive on almost all types of surfaces: We find them on rocks and plants, on teeth and mucous membranes, but also on contact lenses, medical implants or catheters, in the hoses of the dairy industry or drinking water pipes, where they can pose a serious threat to human health. Some biofilms are also useful, for example, in the production of cheese, where specific types of biofilms not only produce the many tiny holes, but also provide its delicious taste.

Tissue with special structures

“Biofilms are not just a collection of very many bacteria, but a tissue with special structures,” explains Prof. Liraz Chai from the Hebrew University in Jerusalem. Together, the bacteria form a protective layer of carbohydrates and proteins, the so-called extracellular matrix. This matrix protects the from disinfectants, UV radiation or desiccation and ensures that biofilms are really difficult to remove mechanically or eradicate chemically. However, the matrix is not a homogeneous sludge: “It’s a bit like in a leaf of plants, there are specialized structures, for example water channels residing in tiny wrinkles,” says Chai. But what role these structures play and what happens at the molecular level in a biofilm was not known until now. Together with Prof. Yael Politi, TU Dresden, an expert in the characterization of biological materials, Chai therefore applied for measurement time at the synchrotron radiation source BESSY II at HZB.

“The good thing about BESSY II is that we can map quite large areas. By combining X-ray diffraction with fluorescence, not only can we analyze the molecular structures across the biofilm very precisely, but we can also simultaneously track the accumulation of certain metal ions that are transported in the biofilm and learn about some of their biological roles” Yael Politi points out.

Read more on the HZB website

Image: When bacteria join together to form communities, they may build complex structures. The photo shows wild-type Bacillus subtilis biofilms.

Credit: © Liraz Chai/HUJI

Time to fly! One scientist’s story of being inspired and inspiring others

Time to fly! One scientist’s story of being inspired and inspiring others

Shiva Shirani is from Iran and is currently completing a PhD at the University of Malaga. Shiva’s research area is Synchrotron X-ray imaging applied to cementitious material with the goal to decrease our CO2 footprint and protect the planet. Many participants in our #LightSourceSelfies campaign have talked about the need to overcome setbacks and failure. There will always be challenges but success will come. Shiva’s research ideas led to her being granted an OPEN SESAME Fellowship to become a young scientific visitor at ID19 tomography beamline at the ESRF. But prior to this, there were setbacks. Shiva’s story, which she tells with honestly and passion, charts these setbacks and how she eventually found people who believed in her ideas. People who helped Shiva find her “two wings to fly”.

One of these people was the late Claudio Ferrero, one of Shiva’s supervisors at the ESRF. Claudio recognised the unique way that Shiva shares her passion for science with the world via Twitter and Instagram and encouraged her to continue this inspirational science communication. In the early stages of planning the #LightSourceSelfies campaign, Lightsources.org and SESAME recognised this too! We were delighted when Shiva agreed to participate in our campaign and we are very grateful to the ESRF who subsequently helped Shiva with the filming.

Here we present Shiva Shirani’s #LightSourceSelfie!

SESAME’s #LightSourceSelfie featuring Shiva Shirani
More to life than light

More to life than light

The #LightSourceSelfies video campaign highlights the dedication and enthusiasm that is felt by those working in this field. To maintain a sense of physical and mental wellbeing, it is also important to make time for non-work related things like family, hobbies and interests. This montage, with contributors from the ESRF, ALS, MAX IV and Diamond, gives a flavour of the wide range of activities that those in the light source community enjoy when they are not working.

Nights!

Nights!

Experimental time at light sources is very precious. When a synchrotron or X-ray Free Electron Laser (XFEL) is in operating mode the goal is to allocate as many experimental shifts to external scientists and in-house research as possible. This includes night shifts! So, how do light source users survive the night shifts? #LightSourceSelfies brings you top tips from scientists based at, or using, 5 light sources in our collaboration – the ESRF, Advanced Light Source (ALS), ANSTO’s Australian Synchrotron, CHESS and the PAL XFEL.

ESRF appoints two new Directors of Research

ESRF appoints two new Directors of Research

Gema Martínez-Criado and Annalisa Pastore have been appointed new ESRF directors of research. Martínez-Criado will cover Condensed Matter and Physical and Material Sciences and Pastore Life Sciences, Chemistry and Soft Matter Science.

In its statement, the ESRF Council « unanimously approved the appointments, for a five-year period starting on 01 January 2022, of Dr Gema Martínez Criado, from the Spanish Research Council’s Materials Science Institute of Madrid, as Director of Research for Condensed Matter and Physical and Material Sciences, and of Professor Annalisa Pastore, from King’s College London University, as Director of Research for Life Sciences, Chemistry and Soft Matter Science. » The ESRF Council also « acknowledged the fact that both of these positions were being filled by female candidates of high calibre and expressed the full trust of the Council to continue to lead, in the coming year, the efforts required to fully capitalise on the world leading performances of the EBS storage ring and suite of beamlines.”

Read more on the ESRF website

Image: Gema Martínez-Criado (left) and Annalisa Pastore (right) have been appointed new ESRF directors of research

Credit: ESRF

Mind the gap – ESRF tracks defects triggered by composites in root fillings

Mind the gap – ESRF tracks defects triggered by composites in root fillings

Polymer composite fillings of root-canal treated teeth can fail over time. Scientists led by the Charité University in Berlin (Germany) have found that this is not because of the dentist’s lack of skills but rather because of stresses that build up and deform the biomaterial just after it is placed. The results are published in Acta Biomaterialia.

It is one of the most peculiar images that can come to mind: a dentist restoring severely destroyed teeth and placing fillings on a beamline at a synchrotron. It is, however, exactly what happened on beamline ID19 a while back, when a team from the Charité and TU Universities in Berlin and the ESRF examined how well composite fillings adapt to cavities in the tooth root canal orifice.

To treat cavities in teeth, dentists expose solid tooth tissue prior to “filling” the volume of missing structure with rigid biomaterials that sustain chewing forces. In the past, dentists used metals such as amalgam or gold, but today they mostly use composite materials, made of polymer and glass. Such materials, which are well resistant to damage and highly aesthetic, allow rapid recovery of tooth function. However, composites tend to fail in the long run, especially in root-canal filled teeth.

Read more on the ESRF website

Image: Kerstin Bitter placing a filling on a tooth on ID19’s experimental hutch.

Credit: P. Zaslansky.

A recipe for successful science

A recipe for successful science

Synchrotrons and free electron lasers (FELs) look stunning. The experimental equipment is state-of-the-art, which makes being a light source user both exhilarating and nerve racking. A key ingredient for success is excellent support from the beamline staff on the experimental station you are using. As Kuda Jakata, a postdoc who supports users at the ESRF in Grenoble, France, says in this #LightSourceSelfie, “The light sources community, they are very helpful people and they actually want to push boundaries and so they work hard and they do a lot of really interesting science.”

#LightSourceSelfies Monday Montage!
EBS X-rays show lung vessels altered by COVID-19

EBS X-rays show lung vessels altered by COVID-19

The damage caused by Covid-19 to the lungs’ smallest blood vessels has been intricately captured using high-energy X-rays emitted by a special type of particle accelerator.


Scientists from UCL and the European Synchrotron Research Facility (ESRF) used a new revolutionary imaging technology called Hierarchical Phase-Contrast Tomography (HiP-CT), to scan donated human organs, including lungs from a Covid-19 donor.


Using HiP-CT, the research team, which includes clinicians in Germany and France, have seen how severe Covid-19 infection ‘shunts’ blood between the two separate systems – the capillaries which oxygenate the blood and those which feed the lung tissue itself. Such cross-linking stops the patient’s blood from being properly oxygenated, which was previously hypothesised but not proven.


HiP-CT enables 3D mapping across a range of scales, allowing clinicians to view the whole organ as never before by imaging it as a whole and then zooming down to cellular level

Read more on the ESRF website

Image: Left: Scientists Claire Walsh, UCL and Paul Tafforeau, ESRF, during experiments at the ESRF, the European Synchrotron, France. (Credit S.Candé/ESRF)

Credit: S.Candé/ESRF

Conservation boost for 500-year-old shipwreck

Conservation boost for 500-year-old shipwreck

The ESRF has allowed scientists to discover nanoparticles that could lead to degradation in a 500-year-old shipwreck: the Mary Rose, an English warship.

Almost 40 years ago, a salvage operation brought to the surface the Mary Rose warship, which used to be Henry VIII’s favourite warship and sank in 1545. Throughout these years, scientists have been using conservation treatments to preserve it. Unfortunately, the remains of the ship are vulnerable to degradation after spending more than 400 years at the bottom of the sea, where harmful deposits collected inside the ship’s wooden hull.

A team of researchers, led by the University of Sheffield, has used ctPDF, an x-ray technique developed at the European Synchrotron Radiation Facility (ESRF) and Columbia University, to obtain vital information on the nanostructure of substances lodged within the ship’s wood and that could lead to the Mary Rose degrading. 

Researchers were previously unable to obtain information on the nature and structure of these deposits, as they are incredibly diverse and exist on such a small scale. The fragility of the remains also hindered efforts to find out more about the substances.

ctPDF has enabled researchers to identify the harmful deposits for the first time and in a non-destructive way. Serena Cussen, Chair in Functional Nanomaterials at the University of Sheffield and corresponding author of the publication, explains: “This project has brought together researchers from around the world to uncover the nature of potentially harmful deposits lodged within the wooden hull of the Mary Rose. These deposits, when exposed to air, can act to degrade the wood. By understanding their structure, we might understand better these degradation pathways, as well as develop treatments that target their removal”.

Read more on the ESRF website

Image: The hull of the Mary Rose

Credit: The Mary Rose Trust

Uniting science to address climate change

Uniting science to address climate change

Key leaders and researchers from major US and European big science laboratories, namely EIROforum (Europe’s eight largest intergovernmental scientific research organisations, including CERN, EMBL, ESA, ESO, ESRF, EUROfusion, European XFEL and ILL) and the US Department of Energy’s seventeen National Laboratories (Ames, Argonne, Brookhaven, Fermi, Idaho, Jefferson, Los Alamos, Lawrence Berkeley, Lawrence Livermore, NETL, NREL, Oak Ridge, Pacific Northwest, PPPL, SLAC, Sandia and Savannah River), met by videoconference ahead of the United Nations Framework Convention on Climate Change Conference of Parties (COP26).

Sharing the same values, and convinced that science performs best through collaboration, the EIROforum’s directors and NLDC (comprised of directors from the US National Laboratories) affirmed their common commitment to unite science towards a sustainable and resilient global society and economy:

  • By stepping up their scientific collaboration on carbon-neutral energy and climate change
  • By sharing best practices to improve the climate sustainability and carbon footprint of Europe’s and US’s big science facilities
  • By sharing knowledge and fostering public engagement on clean energy and climate change research

Read more on the ESRF website

Image: COP26

Credit: ESRF

One year of ESRF-EBS

One year of ESRF-EBS

One year ago, the ESRF switched on its Extremely Brilliant Source (EBS), a revolutionary new high-energy, fourth-generation synchrotron light source, a €150m project over 2015-2022 funded by ESRF’s 22 partner countries.

An accelerator physics dream saw the light with the launch of the world’s brightest synchrotron source, ESRF-EBS, inspiring many constructions and upgrades of synchrotron light sources around the world. Thanks to its enhanced performances, EBS has opened new vistas for X-rays science, enabling scientists to bring X-ray science into research domains and applications that could not have been imagined a few years ago, and providing invaluable new insight into the microscopic and atomic structure of living matter and materials in all their complexity.

Today, the ESRF celebrates one year of user operation of EBS and one year of exciting new science. “Europe can be proud of this masterpiece of state-of-the-art technology and scientific vision,” says Helmut Dosch, Chair of the ESRF Council.

Read more on the ESRF website

Image: Exterior view of the ESRF-EBS in Grenoble, France

Credit: ESRF

X-ray unveils the creation process of materials on several length scales

X-ray unveils the creation process of materials on several length scales

Nanostructuring often makes materials very powerful in many applications. Some nanomaterials take on the desired complex structures independently during their creation process. Scientists from the University of Hamburg, DESY, ESRF and the Ludwig Maximilians University in Munich have studied the formation of cobalt oxide crystals just a few nanometers in size and how they assemble, while they are still being formed. The results are published in Nature Communications.

Nanomaterials have special properties that make them more effective than conventional materials in various applications. In sensors and catalysts (in green energy production, such as water splitting into energy-rich hydrogen and oxygen) the important chemical processes happen at the surface. Nanostructured materials, even in small amounts, provide a very large surface and are therefore suitable for this kind of applications.

Further potential arises due to the variety of shapes and material combinations that are conceivable on the nanoscale. However, establishing the exact shape of these nanostructures can be a tedious process. Researchers focus on nanocrystals that independently form complex structures without any external influence, for example by sticking together (assembling). This increases their effectiveness in important technological applications, such as green energy generation or sensor technology.

“Often nanoparticles arrange themselves independently, as if following a blueprint, and take on new shapes,” explains Lukas Grote, one of the main authors of the study and scientist at DESY and the University of Hamburg. “Now, however, we want to understand why they are doing this and what steps they go through on the way to their final form. That is why we follow the formation of nanomaterials in real time using high-intensity X-rays. ” For some of the experiments, the researchers used the European Synchrotron Radiation Facility (ESRF) and DESY’s synchrotron radiation source PETRA III.

Read more on the ESRF website

Image: X-rays from a synchrotron radiation source are both attenuated (absorbed) and deflected (scattered) by matter. Depending on which of these interactions is measured with a certain X-ray technology, conclusions can be drawn about different stages of the development process of a nanomaterial. If you combine both X-ray absorption and X-ray scattering, you can decipher all the steps from the starting material (left) to the fully assembled nanostructures (right).

Credit: Nature Communications

New fossil sheds light on the evolution of how dinosaurs breathed

New fossil sheds light on the evolution of how dinosaurs breathed

An international team of scientists has used high-powered X-rays at the European Synchrotron to show how an extinct South African 200-million-year-old dinosaur, Heterodontosaurus tucki, breathed. The study, published in eLife, demonstrates that not all dinosaurs breathed in the same way.

In 2016, scientists from the Evolutionary Studies Institute at the University of the Witwatersrand in Johannesburg, South Africa, came to the ESRF, the European Synchrotron in Grenoble, France, the brightest synchrotron light source, for an exceptional study: to scan the complete skeleton of a small, 200-million-year-old plant-eating dinosaur. The dinosaur specimen is the most complete fossil ever discovered of a species known as Heterodontosaurus tucki. The fossil was found in 2009 in the Eastern Cape of South Africa by study co-author, Billy de Klerk of the Albany Museum, Makhanda, South Africa. “A farmer friend of mine called my attention to the specimen”, says de Klerk, “and when I saw it I immediately knew we had something special on our hands.”

Fast forward some years: the team of scientists use scans and new algorithms developed by ESRF scientists to virtually reconstruct the skeleton of Heterodontosaurus in unprecedented detail, and thus show how this extinct dinosaur breathed. “This specimen represents a turning point in understanding how dinosaurs evolved” explains Viktor Radermacher, corresponding author, a South African PhD student and now at the University of Minnesota, US.

Read more on the ESRF website

Image: The skull of the Heterodontosaurus tucki dinosaur.

Credit: ESRF

Dramatic impact of crystallographic conflict on material properties

Dramatic impact of crystallographic conflict on material properties

Many material properties are associated with structural disorder that exhibits local periodicity or correlations. A new form of this phenomenon exhibiting strong disorder-phonon coupling has been shown to arise in response to crystallographic conflict, with dramatic phonon lifetime suppression.

In recent years there has been a rapidly growing understanding that, hidden within the globally periodic structures of many crystals, various forms of disorder may exist that could form ‘locally periodic’ states, which the language of classic crystallography fails to describe. Such phenomena are commonly referred to as ‘correlated disorder’ and in many functional materials, from leading ferroelectric and thermoelectric candidates to photovoltaic perovskites and ionic conductors, this correlated deviation from perfect periodicity plays a pivotal role in governing functionality. As such, understanding the role of disorder, and the correlations that exist within it, is one of the defining challenges for the development of future functional materials.

Read more on the ESRF website

Image: Fig. 1: a) Reciprocal space reconstructions of the (hk2)s plane. All three samples investigated are shown with relevant at. % Mo indicated. Reflections are categorised and indexed in the bottom right quadrant, parent Bragg peaks (black) and diffuse superstructure reflections from two different domains (blue/green). b) Orientational relationship between parent (blue) and superstructure (red) unit cells for one of six possible domains. All atoms in the “shear plane” (highlighted red) move collinearly with the direction of motion indicated by arrows on the plane edge. Alternate planes, demarcated by I, I, III, … , move in antiphase. c) Top-down view showing the 45◦ relationship between the parent and superstructure. d) Schematic of the atomic motions in a “phonon plane.” Blue dashed and red dotted lines refer to interatomic bonding in the parent and superstructure unit cells, respectively.

Combatting COVID-19 with crystallography and cryo-EM

Combatting COVID-19 with crystallography and cryo-EM

Crystallography and cryo-electron microscopy are vital tools in the fight against COVID-19, allowing researchers to reveal the molecular structures and functions of the SARS-CoV-2 virus, paving the way for new drugs and vaccines. Since the start of the pandemic, the ESRF has mobilised its crystallography and cryo-electron microscopy expertise and made its new Extremely Brilliant Source available as part of the collective effort to address this critical global health challenge.

When the WHO declared the outbreak of COVID-19 a public health emergency of international concern in early 2020, it signalled the start of a race against time for scientists to understand how the newly identified SARS-CoV-2 virus functioned and to develop treatments for the disease. Structural biologists around the world pitched in, determining the structures of most of the 28 proteins encoded by the novel coronavirus. This remarkable collective effort resulted in over a thousand 3D structural models of SARS-CoV-1 and SARS-CoV-2 proteins deposited in the Protein Data Bank (PDB) public archive in just one year [1]. Researchers and drug developers rely on these models to design antiviral drugs, therapies and vaccines. However, the speed and urgency with which the SARS-CoV-2 protein structures were solved means that errors could inevitably slip in, with potentially severe consequences for drug designers targeting certain parts of the virus’s structure. 

Enter the Coronavirus Structural Task Force, an international team of 25 structural biologists offering their time and expertise to fix errors in structural models of the virus’s proteins in order to give drug designers the best possible templates to work from. Gianluca Santoni, crystallography data scientist in the ESRF’s structural biology group, is part of the task force, whose work is detailed in an article recently published in Nature Structural & Molecular Biology [2]. “Every week, we check the PDB for any new protein structure related to SARS-CoV-2,” he explains. “We push structural biology tools and methods to the limit to get every last bit of information from the data, to evaluate the quality and improve the models where possible.” 

To read more visit the ESRF website

Image: The coronavirus research project ‘COVNSP3’ is based on the use of the ESRF’s cryo-electron microscope facility, led by Eaazhisai Kandiah (pictured)

Credit: ESRF/S. Cande.

X-ray tomography as a new tool to analyse the voids in RRP Nb3Sn wires

X-ray tomography as a new tool to analyse the voids in RRP Nb3Sn wires

Scientists have developed a new tool to investigate the internal features of Nb3Sn superconducting wires, combining X-ray tomographic data acquired at beamline ID19 with an unsupervised machine-learning algorithm. The method provides new insights for enhancing wire performance.

Interest in niobium-tin (Nb3Sn) as a material for superconducting wires has recently been renewed because this material has been selected to replace niobium-titanium as the next step in accelerator magnet technology [1]. The design of these magnets relies on the availability of advanced Nb3Sn wires capable of withstanding extreme mechanical and thermal loads. The Restacked Rod Process (RRP) is considered the most promising technology to produce Nb3Sn wires at industrial scale for future accelerator magnets.

Nb3Sn is a brittle superconducting compound that cannot be drawn directly in the form of a wire. Instead, ductile precursor components are embedded in a copper matrix, drawn, brought to the final shape and then heat-treated, so that Nb3Sn forms in a reactive diffusion process. The result is a composite wire with several Nb3Sn sub-elements surrounded by copper. However, the diffusion process can lead to voids, which can play a role in the electro-mechanical and thermal behaviour of the wire. A team of scientists have developed a novel, non-destructive and non-invasive method to investigate the voids in high-performance RRP Nb3Sn superconducting wires, combining X-ray microtomography data at beamline ID19 with an unsupervised machine-learning algorithm, with a view to providing new insights into the development of these wires.

Read more on the ESRF website

Image:Fig. 1: a) 3D cross-section of a RRP Nb3Sn wire: Nb3Sn sub-elements (red), sub-element voids (light blue), copper voids (white), copper matrix (grey). b) Longitudinal cross-section of a void generated by Sn diffusion due to a leak in the sub-element. The void is highlighted in red inside the sub-element and in blue in the copper matrix, showing the sub-element failure point.