Synchrotron radiation source SESAME welcomed as associated partner
>Read more on the DESY website
and another article on the ALBA website. Please find here all news about the LEAPS initiative.
New Synchrotron Light Source is the largest and most complex research structure ever built in Brazil
The Brazilian President, Michel Temer, and the Minister of Science, Technology, Innovation and Communications, Gilberto Kassab, participated on Wednesday 14th November in the ceremony commemorating the first stage of the new Brazilian Synchrotron Light Source, Sirius, in the Brazilian Center for Research in Energy and Materials (CNPEM), in Campinas (SP). Started in 2012, Sirius is the largest project in Brazilian science, a state-of-the-art research infrastructure, strategic for cutting-edge scientific research and for finding solutions to global problems in areas such as health, agriculture, energy and the environment.
This first stage includes the conclusion of the construction works of the building that houses the entire research infrastructure, in addition to the assembly of the Linear and Booster Accelerators. The Storage Ring is currently being assembled.
The delivery of the next stage of the project, scheduled for the second half of 2019, includes the start of the Sirius operation and the opening of the first six beamlines for researchers. The complete project includes seven other beamlines, expected to be opened in 2021. However, the number of beamlines can be gradually expanded, reaching up to 40 experimental stations.
A high-precision X-ray technique, tested at PETRA III, could catch cancer at an earlier stage and facilitate the development and control of pharmaceutical drugs. The test at DESY’s synchrotron radiation source, which used so-called X-ray fluorescence for that purpose, has proved very promising, as is now being reported in the journal Scientific Reports by a research team headed by Florian Grüner from the University of Hamburg. The technique is said to offer the prospect of carrying out such X-ray studies not only with higher precision than existing methods but also with less of a dose impact. However, before the method can be used in a clinical setting, it still has to undergo numerous stages of development.
The idea behind the procedure is simple: tiny nanoparticles of gold having a diameter of twelve nanometres (millionths of a millimetre) are functionalised with antibodies using biochemical methods. “A solution containing such nanoparticles is injected into the patient,” explains Grüner, a professor of physics at the Centre for Free-Electron Laser Science (CFEL), a cooperative venture between DESY, the University of Hamburg and the Max Planck Society. “The particles migrate through the body, where the antibodies can latch onto a tumour that may be present.” When the corresponding parts of the patient’s body are scanned using a pencil X-ray beam, the gold particles emit characteristic X-ray fluorescence signals, which are recorded by a special detector. The hope is that this will permit the detection of tiny tumours that cannot be found using current methods.
Image: Gold nanoparticles spiked with antibodies can specifically attach to tumors or other targets in the organism and can be detected there by X-ray fluorescence.
Credit: Meletios Verras [Source]
The results are important for the development of organic solar cells. The study has now been published in the journal PCCP, and its illustration selected for the cover.
Transition-metal complexes – that is a cumbersome word for a class of molecules with important properties: An element from the group of transition metals sits in the centre. The outer electrons of the transition-metal atom are located in cloverleaf-like extended d-orbitals that can be easily influenced by external excitation. Some transition-metal complexes act as catalysts to accelerate certain chemical reactions, and others can even convert sunlight into electricity. The well-known dye solar cell developed by Michael Graetzel (EPFL) in the 1990s is based on a ruthenium complex.
Why not Iron?
However, it has not yet been possible to replace the rare and expensive transition metal ruthenium with a less expensive element, such as iron. This is astonishing, because the same number of electrons is found on extended outer d-orbitals of iron. However, excitation with light from the visible region does not release long-lived charge carriers in most of the iron complex compounds investigated so far.
Image: The illustration shows a molecule with an iron atom at its centre, bound to 4 CN groups and a bipyridine molecule. The highest occupied iron orbital is shown as a green-red cloud. As soon as a cyan group is present, the outer iron orbitals are observed to delocalize so that electrons are also densely present around the nitrogen atoms.
Credit: T. Splettstoesser/HZB
SESAME thus becomes the first Associate of LEAPS.
On signing the Declaration of Association to the LEAPS Consortium with Helmut Dosch, Chair of LEAPS and Chair of the DESY Board of Directors, Rolf Heuer, President of the SESAME Council, said that “it is a great honour for SESAME to be the first Associate of LEAPS; the scientific and technical development of SESAME and visibility of the Centre will greatly benefit from this association”.
Image: Schematic overview from SESAME, find more here.
Graphene, an sp2 bonded sheet of carbon atoms, is still attracting lots of interest almost 15 years after its discovery. Angle-resolved photoemission spectroscopy (ARPES) is a uniquely powerful method to study the electronic structure of graphene and it has been used extensively to study the coupling of electrons to lattice vibrations (phonons) in doped graphene. This electron-phonon coupling (EPC) manifests as a so-called “kink” feature in the electronic band structure probed by ARPES. What is much less explored is the effect of EPC on the phonon structure. A very accurate probe of the phonons in graphene is Raman spectroscopy.
M.G. Hell and colleagues from Germany, Italy, Indonesia, and Japan combined ARPES (carried out at the BaDelPhbeamline – see Figure 1) with low energy electron diffraction (LEED) and Raman spectroscopy (carried out at the University of Cologne in Germany) in a clever way to fully understand the coupled electron-phonon system in alkali metal doped graphene. LEED revealed ordered (1×1), (2×2), and (sqrt3xsqrt3)R30°adsorbate patterns with increasing alkali metal deposition. The ARPES analysis yielded not only the carrier concentration but also the EPC coupling constant. Ultra-High Vacuum (UHV) Raman spectra carried out using identically prepared samples with the very same carrier concentrations provided the EPC induced changes in the phonon frequencies.
Image: Top: ARPES spectra along the Γ-K-M high symmetry direction of the hexagonal Brillouin zone for Cs doped graphene/Ir(111) with increasing Cs deposition. The Dirac energy ED and the observed LEED reconstruction are also indicated. Bottom: Corresponding Fermi surfaces at the indicated charge carrier concentration.
Although firmly located on earth, the Australian Synchrotron’s Terahertz/Far Infrared beamline (THz/Far IR) is one of three synchrotron facilities in the word able to simulate the extreme conditions of distant planetary worlds.
The most recently reported research using the beamline published in Earth and Space Chemistry, involved recreating the pressure and temperatures environments in the hazy atmosphere surrounding Saturn’s moon Titan.
“We are interested in Titan because it is the most Earth-like of the planetary bodies possessing an atmosphere of mostly nitrogen and methane,” said co-author Rebecca Auchettl (pictured above), a PhD candidate who was supervised by Dr Courtney Ennis, formerly of La Trobe University now at the University of Otago in New Zealand.
Image: Co-author Rebecca Auchettl, PhD candidate.
A lot of the physics principles at the foundation of MAX IV are also at the foundation of medical imaging technologies such as nuclear magnetic resonance imaging, x-ray computed tomography and positron emission tomography.
Positron emission spectroscopy is more commonly known as PET imaging. It’s a method used to study metabolic processes in the body as a research tool but also to diagnose disease. An important use today is in the diagnosis of metastases in cancer patients, but it can also be used to diagnose certain types of dementia.
In PET, a positron-emitting radionuclide is injected into a patient and travels around the body until it accumulates somewhere, depending on the chemical composition. For example, the fluorine-18 radionuclide when bound to deoxyglucose accumulates in metabolically active cells which is useful for finding metastases. The radionuclide is unstable and emits positrons which is the antimatter equivalent of an electron. When a positron and an electron inevitably meet, they annihilate one another, producing two pulses of gamma radiation traveling in opposite directions. By placing a detector around a patient, it is possible to measure the gamma radiation and convert the signal into something that can be more easily measured. These detectors are made up of materials known as scintillators which take high energy radiation and emit lower energy radiation that can be detected using fast photodetectors – photomultiplier tubes.
Carbon atoms have diverse possibilities to form bonds. Pure carbon can therefore occur in many forms, as diamond, graphite, as nanotubes, football molecules or as a honeycomb-net with hexagonal meshes, graphene. This exotic, strictly two-dimensional material conducts electricity excellently, but is not a superconductor. But perhaps this can be changed.
A complicated option for superconductivity
In April 2018, a group at MIT, USA, showed that it is possible to generate a form of superconductivity in a system of two layers of graphene under very specific conditions: To do this, the two hexagonal nets must be twisted against each other by exactly the magic angle of 1.1°. Under this condition a flat band forms in the electronic structure. The preparation of samples from two layers of graphene with such an exactly adjusted twist is complex, and not suitable for mass production. Nevertheless, the study has attracted a lot of attention among experts.
Image: The data show that In the case of the two-layer graphene, a flat part of bandstructure only 200 milli-electron volts below the Fermi energy. Credit: HZB
By using an x-ray technique available at the National Synchrotron Light Source II (NSLS-II), scientists found that the metal-insulator transition in the correlated material magnetite is a two-step process. The researchers from the University of California Davis published their paper in the journal Physical Review Letters. NSLS-II, a U.S. Department of Energy (DOE) Office of Science user facility located at Brookhaven National Laboratory, has unique features that allow the technique to be applied with stability and control over long periods of time.
“Correlated materials have interesting electronic, magnetic, and structural properties, and we try to understand how those properties change when their temperature is changed or under the application of light pulses, or an electric field” said Roopali Kukreja, a UC Davis professor and the lead author of the paper. One such property is electrical conductivity, which determines whether a material is metallic or an insulator.
If a material is a good conductor of electricity, it is usually metallic, and if it is not, it is then known as an insulator. In the case of magnetite, temperature can change whether the material is a conductor or insulator. For the published study, the researchers’ goal was to see how the magnetite changed from insulator to metallic at the atomic level as it got hotter.
Image: Professor Roopali Kukreja from the University of California in Davis and the CSX team Wen Hu, Claudio Mazzoli, and Andi Barbour prepare the beamline for the next set of experiments.
Despite its role in shaping life as we know it, many aspects of photosynthesis remain a mystery. An international collaboration between scientists at SLAC National Accelerator Laboratory, Lawrence Berkeley National Laboratory and several other institutions is working to change that. The researchers used SLAC’s Linac Coherent Light Source (LCLS) X-ray laser to capture the most complete and highest-resolution picture to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe. The results were published in Nature today.
When Earth formed about 4.5 billion years ago, the planet’s landscape was almost nothing like what it is today. Junko Yano, one of the authors of the study and a senior scientist at Berkeley Lab, describes it as “hellish.” Meteors sizzled through a carbon dioxide-rich atmosphere and volcanoes flooded the surface with magmatic seas.
Over the next 2.5 billion years, water vapor accumulating in the air started to rain down and form oceans where the very first life appeared in the form of single-celled organisms. But it wasn’t until one of those specks of life mutated and developed the ability to harness light from the sun and turn it into energy, releasing oxygen molecules from water in the process, that Earth started to evolve into the planet it is today. This process, oxygenic photosynthesis, is considered one of nature’s crown jewels and has remained relatively unchanged in the more than 2 billion years since it emerged.
Image: Using SLAC’s X-ray laser, researchers have captured the most complete high-res atomic movie to date of Photosystem II, a key protein complex in plants, algae and cyanobacteria responsible for splitting water and producing the oxygen we breathe.
Credit: Gregory Stewart, SLAC National Accelerator Laboratory)
The successful application is the result of an agreement and cooperation of 17 leading scientific institutions in Poland in the area of structural biology. This very unique nation-wide consortium, led by Dr. Sebastian Glatt (the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków) and Dr. hab. Marcin Nowotny (the International Institute of Molecular and Cell Biology, Warsaw), was not only key to bring this breakthrough research technique to Poland, but also exemplifies how scientists from around the country are able to work efficiently together for a greater common goal. This state-of-the-art microscope will allow its users to follow the progress of other international research centres and will transfer Polish and international scientists into the first class of structural biology.
The advances made in cryo-EM have revolutionized the field of structural biology over the last decade. The increased recognition of this technology has also culminated in the Chemistry Nobel Prize being awarded to its creators in 2017. The development of this technique has opened up new research horizons, which resulted in a long list of groundbreaking studies published in the most prestigious scientific journals. Foremost, the anticipated results are extremely relevant for a better understanding of the function of the human body, of the formation of human diseases and of processes like aging, and can lead to the development of new effective therapies. Structural biology has already contributed to a huge progress in the treatment of various human diseases, including cancer, Alzheimer’s disease and obesity. Last but not least, the presence of a high-end cryo-electron microscope at SOLARIS means that Krakow will attract national and international structural biologists.
Image: The image of mimivirus made with the use of a cryo-electron microscope.
Credit: Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, et al. (2009) [CC BY 2.5]
On 25th October, SESAME was host to a delegation from the Helmholtz Association of German Research Centres consisting of 43 persons. It was headed by Professor Otmar Wiestler, President of the Association.
The visiting delegation was shown round SESAME’s experimental hall and was able to see at first hand two of the Phase I beamlines that are already in operation, namely the XAFS/XRF (X-ray absorption fine structure/X-ray fluorescence) spectroscopy and IR (infrared) spectromicroscopy beamlines, as well as a further two Phase I beamlines, the MS (materials science) and MX (Macromolecular crystallography) beamlines, that are under construction and are expected to come on stream in two-three years.
During the visit, Otmar Wiestler informed SESAME that five research centres of the Helmholtz Association will be taking part in construction of a soft X-ray beamline for SESAME under the leadership of DESY (Deutsches Elektronen-Synchrotron). This is another of SESAME’s Phase I beamlines. The five research centres – DESY, FZJ (Forschungszentrum Jülich), HZB (Helmholtz-Zentrum Berlin), HZDR (Helmholtz-Zentrum Dresden-Rossendorf), and KIT (Karlsruher Institut für Technologie) – will be constructing a complete undulator beamline with monochromator and refocussing optics and a small chamber to conduct absorption and fluorescence yield experiments. The capital value of this work would be of the order of €3.5 million.
Given that the European Union has very recently informed SESAME that it will be providing €6 million for construction of its tomography beamline, SESAME will have six of its seven Phase I beamlines in operation relatively soon.
Image: (from left to right) Rolf Heuer, President SESAME Council, Otmar Wiestler, President Helmholtz Association, Khaled Toukan, SESAME Director, Walid Zidan, SESAME Administrative Director, and Rene Röspel, Member of the Bundestag and Vice-Chairman of the Science Committee of the Bundestag.
When electrical current propagates through a conducting material, energy dissipates due to the conductor’s electrical resistance. In a superconductor, however, the resistance can vanish completely if the material is cooled to extremely low temperatures. Such dissipationless supercurrent would be highly desirable for a plethora of electronic and technological applications, and has spawn decades of intense research dedicated to find materials with superconducting properties at elevated temperatures.
While all superconducting materials reported until the 1980’s had to be cooled below 30 K, the game changed in 1986, when the first superconductors based on copper oxide materials were discovered. These so-called high-temperature superconductors are composed of stacked layers of copper-oxygen planes and some show zero electrical resistance well above 100 K. By understanding the mechanisms mediating superconductivity in the copper oxides, the scientific community hopes to become able to devise novel materials that show zero resistance even at room temperature. However, a comprehensive understanding of these mechanisms has yet remained elusive. Nonetheless, superconductors are used already today in some technological applications, such as magnetic resonance imaging devices in the field of medicine. Future applications of room temperature superconductors could revolutionize the fields of electrical power storage and transmission, and enable rapid public transport by magnetically levitated trains.
Image: Overview of the beamline ID32 at the ESRF.
Credits: P. Jayet
“This publication is a true reward for us: the first one in less than a year from inauguration and we hope this kind of rewards will grow in number”, explains Isai Kandiah, ESRF scientist who runs the facility. “It shows the revolution that cryo-EM is leading in structural biology”, she adds. Thanks to cryo-EM, researchers can now freeze biomolecules, including membrane proteins of high medical importance, in several different conformations in action and visualise each of these to atomic resolution. Cryo-EM thus allows researchers to produce snapshots revealing the dynamics of proteins when they interact with other molecules, information that is crucial both for a basic understanding of life’s chemistry and for the development of pharmaceuticals. The user programme of the cryo-electron microscope at the ESRF is run jointly with the European Molecular Biology Laboratory (EMBL), the Institut de Biologie Structurale (IBS) and the Institut Laue-Langevin (ILL).
The research in Nature is a result of an international collaboration of scientists from the Institute of Structural biology (IBS-mixed research unit CEA-CNRS-University Grenoble Alps), CEA, CNRS, the Institut Pasteur, the University of Lorraine (France), the University of Copenhagen (Denmark), the University of Illinois (US) and the biotech company Theranyx. The focus of the paper, featuring data from the ESRF cryo-EM, is the activation cycle of the 5-HT3 receptor, belonging to the family of serotonin receptors. These receptors are well-known because they influence various biological and neurological processes such as anxiety, appetite, mood, nausea, sleep and thermoregulation, among others. Unlike the other serotonin receptors, which are G protein-coupled receptors, 5-HT3 is a neurotransmitter-gated ion channel and changes its conformation during activation. It is present in the brain, as well as in the enteric nervous system, the peripheral nervous system that drives the digestive tract.
Image: A close-up view of the Cryo-EM at the ESRF.
Credit: S. Candé.
An estimated 1% of the adult population is infected with this bacterium. Using XALOC beamline at the ALBA Synchrotron it has been defined the structure of the protein involved in the pathogen’s adhesion process. The discovery opens the door to defining new therapeutic strategies to fight this pathogen which is becoming more and more resistant to antibiotics.
Researchers from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and the Institute of Biotechnology and Biomedicine (IBB-UAB) have discovered the mechanism by which the bacterium Mycoplasma genitalium (Mgen) adheres to human cells. This adhesion is essential for the onset of bacterial infection and subsequent disease development.
Mgen is an emerging pathogen responsible for several infectious genitourinary disorders. In men, it is the most common cause of urethritis (15-20%) while in women, it has been associated with cervicitis, pelvic inflammatory disease, premature birth and spontaneous abortions. So far, it was known that adherence to the genitourinary tract was possible thanks to proteins known as adhesins, which recognise specific cell surface receptors.
In this study, IBMB-CSIC researchers determined the three-dimensional structure of the Mgen’s P110 adhesins interacting with these cell receptors using X-rays diffraction and protein crystallography at the XALOC beamline. “We made a protein crystal of the P110 adhesin bound to these receptors and diffracted with the synchrotron’s X-rays to determine the exact position of the atoms within the protein, and we were able to decipher the three-dimensional structure”, explains IBMB researcher David Aparicio.
Image: Overall structure of P110. Two views, 90° apart from each other, of the extracellular region of P110 that is formed by a large N-domain, with a seven blade β-propeller (green), the crown (brown), and the C-domain (orange). In the right side panel the view is along the central axis of the β-propeller. The situation of the seven blades in the propeller is explicitly indicated showing that the two terminal blades I and VII are close to the C-terminal domain and opposite to the crown.