Scientists produce 3-D chemical maps of single bacteria

Researchers at NSLS-II used ultrabright x-rays to generate 3-D nanoscale maps of a single bacteria’s chemical composition with unparalleled spatial resolution.

Scientists at the National Synchrotron Light Source II (NSLS-II)—a U.S. Department of Energy (DOE) Office of Science User Facility at DOE’s Brookhaven National Laboratory—have used ultrabright x-rays to image single bacteria with higher spatial resolution than ever before. Their work, published in Scientific Reports, demonstrates an x-ray imaging technique, called x-ray fluorescence microscopy (XRF), as an effective approach to produce 3-D images of small biological samples.

“For the very first time, we used nanoscale XRF to image bacteria down to the resolution of a cell membrane,” said Lisa Miller, a scientist at NSLS-II and a co-author of the paper. “Imaging cells at the level of the membrane is critical for understanding the cell’s role in various diseases and developing advanced medical treatments.”
The record-breaking resolution of the x-ray images was made possible by the advanced capabilities of the Hard X-ray Nanoprobe (HXN) beamline, an experimental station at NSLS-II with novel nanofocusing optics and exceptional stability.
“HXN is the first XRF beamline to generate a 3-D image with this kind of resolution,” Miller said.

>Read more on the NSLS-II at Brookhaven National Laboratory website

Image: NSLS-II scientist Tiffany Victor is shown at the Hard X-ray Nanoprobe, where her team produced 3-D chemical maps of single bacteria with nanoscale resolution.

Transition metal complexes: mixed works better

A team at BESSY II has investigated how various iron-complex compounds process energy from incident light. They were able to show why certain compounds have the potential to convert light into electrical energy. 

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.

>Read more on the Bessy II at HZB website

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 becomes the first associate of LEAPS

At its first Plenary Meeting that is being held at DESY on 12-14 November, the Members of LEAPS (League of European Accelerator-Based Photon Sources) unanimously decided to grant SESAME Associate status.

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”.

>Read more on the SESAME website

Image: Schematic overview from SESAME, find more here.

The quest for better medical imaging at MAX IV

Advances in the world of physics often quickly lead to advances in the world of medical diagnostics. From the moment Wilhelm Röntgen discovered X-rays he was using them to look through his wife’s hand.

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.

>Read more on the MAX IV Laboratory website


Graphene on the way to superconductivity

Scientists at HZB have found evidence that double layers of graphene have a property that may let them conduct current completely without resistance. They probed the bandstructure at BESSY II with extremely high resolution ARPES and could identify a flat area at a surprising location.

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.

>Read more on the BESSY II at HZB website

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

Unlocking the secrets of metal-insulator transitions

X-ray photon correlation spectroscopy at NSLS-II’s CSX beamline used to understand electrical conductivity transitions in magnetite.

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.

>Read more on the NSLS-II at Brookhaven National Laboratory website

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.

Researchers create most complete high-res atomic movie of photosynthesis to date

In a major step forward, SLAC’s X-ray laser captures all four stable states of the process that produces the oxygen we breathe, as well as fleeting steps in between. The work opens doors to understanding the past and creating a greener future.

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.

Explosion of life

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.

>Read more on the SLAC website (for LCLS)
>Read also the article on the Berkeley website (for ALS)

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)

SESAME host to delegation from Helmholtz Association of German research centres

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.

>Read more on the Synchrotron light for Experimental Science and Applications in the Middle East (SESAME) website

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.
Credit: DESY

New insight into high-temperature superconductors

Researchers have found evidence for an acoustic plasmon or “sound wave”, which has been predicted for layered systems and suggested to play a role in mediating high temperature superconductivity.

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.

>Read more on the European Synchrotron website

Image: Overview of the beamline ID32 at the ESRF.
Credits: P. Jayet

The ESRF CryoEM excels in its first year

In November 2017, a Titan Krios cryo-electron microscope (cryo-EM) was inaugurated at the ESRF, the European Synchrotron, France. Data collected on this cryo-EM features in a Nature publication describing the activation cycle of a serotonin receptor, which is targeted by medication against chemotherapy- and radiotherapy-induced nausea.

“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.

>Read more on the European Synchrotron website

Image: A close-up view of the Cryo-EM at the ESRF.
Credit: S. Candé.

Mycoplasma genitalium’s cell adhesion mechanism revealed

Mycoplasma genitalium is a sexually transmitted bacterium responsible for several genitourinary disorders.

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.

>Read more on the ALBA website

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.


When is a laser a real laser?

Pulsed lasers are intense and coherent light sources, and the latest category is that of Free Electron Lasers, such as FERMI. First order coherence is a familiar phenomenon, and is manifested for example in diffraction phenomena. This represents the correlation between the amplitudesof a wave at different points in space (transverse coherence) or time (longitudinal coherence.) However, a high degree of first order coherence is not enough to define a laser, according to the Nobel laureate Roy Glauber, who stated that a laser can be defined as a source that is coherent in all orders. The higher order correlations are between intensityat different points in time and space. How are these correlations measured? For this one has to look at the statistics of the photons.
Glauber’s work was inspired by the famous Hanbury Brown and Twiss experiment, in which coincidences of photons (i.e. correlations) were measured of photons coming from distant stars. By varying the distance between two detectors, they were able to determine the degree of coherence of the star, and extract other information. This is the key to measuring the second order coherence of a light source: the intensity of light at different points is measured in coincidence, and statistical analysis is made. This experiment is considered by many as initiating the whole field of quantum optics. Now a team led by Ivan Vartaniants (DESY, Hamburg, and the National Research Nuclear University, Moscow) has performed a Hanbury Brown and Twiss experiment at FERMI. Instead of the two discrete photodetectors used originally, a CCD detector was used. Since all of the photons arrive in less than 100 fs, there is no need to use coincidence methods: the signal is naturally synchronised.

>Read more on the FERMI at Elettra Sincrotrone Trieste website

Figure 1.  Difference between chaotic and coherent light sources. (a) photon correlation map for FERMI operated in seeded mode. (b) corresponding spectrum. (c) correlation map for FERMI operated in Self Amplified Stimulated Emission mode (the mode of operation of most Free Electron Lasers). (d) corresponding spectrum.
Credit: Reprinted from O. Yu. Gorobtsov et al, Nature Communications 9 (2018) 4498. (Copyright Nature Publishing Group)

Analysing the structure of biopolymers for the food industry

A research group from the Institute of Agrochemistry and Food Technology (IATA-CSIC) in Valencia is using scattering techniques at the ALBA Synchrotron to develop new packaging systems made of biopolymers, an environmentally friendly solution for the food industry.

Plastic is the packaging material of most of the food we consume nowadays. This results in a severe problem as common plastics are made of petroleum – a limited resource with highly variable price – and supposes a huge environmental impact – most plastic wastes need more than 400 years to decompose.

Researchers from the Food Safety and Preservation department of the Institute of Agrochemistry and Food Technology (IATA-CSIC), located in Paterna (Valencia), are looking for more sustainable ways of producing food packaging with appropriate mechanical and chemical properties. They are investigating biopolymers that can be made from biomass such as algae.
“We need to look for alternative sources which do not compete with food. This is why marine resources such as algae and microalgae are very interesting. They proliferate very quickly, grow in a wide variety of environments and do not interfere with food production”, according to Ámparo López-Rubio, researcher at the IATA-CSIC.

>Read more on the ALBA website

Image: At the left, Juan Carlos Martínez, scientist from the ALBA Synchrotron with users Amparo López Rubio and Marta Martínez Sanz from IATA-CSIC at the NCD-SWEET experimental hutch.

Expanding the infrared nanospectroscopy window

The ability to investigate heterogeneous materials at nanometer scales and far-infrared energies will benefit a wide range of fields, from condensed matter physics to biology.

Scientific studies require tools that match the natural length and energy scales of the phenomena under investigation. For many questions in biology, quantum materials, and electronics, this means nanometer spatial resolution combined with far-infrared energies. For example, scientists might want to study collective electron oscillations in quantum materials for optoelectronic circuits, or the characteristic vibration modes of protein molecules in biological systems.

A recently developed infrared technique—synchrotron infrared nanospectroscopy (SINS)—combines broadband synchrotron light with atomic-force microscopes to enable infrared imaging and spectroscopy at the nanoscale. However, the technique could only be used in a narrow range of the electromagnetic spectrum that excluded far-infrared wavelengths, due to a scarcity of suitable light sources and detectors for that range. In this work, researchers extended SINS to far-infrared wavelengths, opening up a whole new experimental regime.

> Read more on the Advanced Lightsource at Berkeley Lab website

Image: Left: Nanoscale images of SiO2 hole array, obtained using atomic-force microscopy (AFM, top) and synchrotron infrared nanospectroscopy (SINS, bottom), demonstrating SINS contrast between patterned SiO2 and underlying Si substrate with ~30 nm spatial resolution (inset). Scale bar = 200 nm. Right: SINS broadband spectroscopic data for SiO2, taken along dotted line in images at left, showing amplitude (top) and phase (bottom) information from asymmetric  Si–O stretching (1200 cm–1) and bending (460 cm–1) modes. The lower-energy bending mode had previously been inaccessible with this technique.

The human behind the beamline

Happy Birthday, Felix Bloch – 23rd October 1905

Felix Bloch was born on this day (23rd October) in 1905 in Zürich, Switzerland. He got a Ph.D. in 1928 studying under Werner Heisenberg. In his thesis, he established the quantum theory of solids describing how electrons moved through crystalline materials using Bloch waves. The phenomena he described are observed today using the technique ARPES which is carried out at the Bloch beamline at MAX IV.

>Read more on the MAX IV Laboratory website

Image: Detail of a Max Bloch illustration. To discover the entire illustration click here.
Credit: Emelie Hilner.

Targeting bacteria that cause meningitis and sepsis

The work provides molecular-level information about how the antibody confers broad immunity against a variable target and suggests strategies for further improvement of available vaccines.

Our central nervous systems (brain and spinal cord) are surrounded by three membranes called “meninges.” Meningitis is caused by the swelling of these membranes, resulting in headache, fever, and neck stiffness. Most cases of meningitis in the United States are the result of viral infections and are relatively mild. However, meningitis caused by bacterial infection, if left untreated, can be deadly or lead to serious complications, including hearing loss and neurologic damage.

The bacterium responsible for meningitis (Neisseria meningitidis) can also infect the bloodstream, causing another life-threatening condition known as sepsis. N. meningitidis is spread through close contact (coughing or kissing) or lengthy contact (e.g. in dorm rooms or military barracks). In this work, researchers were interested in understanding how humans develop immunity to bacterial meningitis and sepsis, collectively known as meningococcal disease, by vaccination with a new protein-based vaccine.

>Read more on the Advanced Light Source website

Image: The work provides molecular-level information about how the antibody confers broad immunity against a variable target and suggests strategies for further improvement of available vaccines.