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

2018/11/082018/11/08

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.

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)

Funds for the latest generation of electron cryomicroscopy

2018/11/062018/11/22

The Polish Ministry of Science and Higher Education handed over to SOLARIS the official decision to establish the National Cryo-EM Centre at the Polish partner facility, granting the requested financial support.

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.

>Read more on the SOLARIS website

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]

SESAME host to delegation from Helmholtz Association of German research centres

2018/11/062018/11/08

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.
Credit: DESY

New insight into high-temperature superconductors

2018/11/052018/11/13

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.

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

The ESRF CryoEM excels in its first year

2018/10/312018/11/04

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.

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

Mycoplasma genitalium’s cell adhesion mechanism revealed

2018/10/312018/11/08

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?

2018/10/312018/11/04

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.

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

2018/10/302018/10/31

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

2018/10/262018/11/04

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.

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

2018/10/232018/10/24

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.

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

Targeting bacteria that cause meningitis and sepsis

2018/10/222018/10/25

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.

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.

50 years later, Wilson Lab stays cutting edge

2018/10/192018/11/05

October 2018 marks the 50^thanniversary of the dedication of the Wilson Synchrotron Laboratory.

Initially built for $11million and promising to deliver cutting-edge research in elementary particle physics, it was the NSF’s largest project at that time. Fifty years later, the lab is going through its biggest upgrade in decades.
Chris Conolly looks at the concrete floor of Wilson Lab, eyeing up the numerous holes drilled by one of the contractors for the upgrade project. These one-inch holes pockmark the 10,000sf experimental hall of the Wilson Synchrotron Laboratory. In a way, these holes represent the numerous experiments conducted over the past 50 years.

There are a lot of holes. 652 to be exact, as the CHESS X-ray Technical Director and CHESS-U beamline project manager easily points out.
“It’s almost like being an archaeologist”, says Conolly, as he walks through the maze of newly constructed hutches in the experimental hall. He stops near the sector II hutches, “especially this spot here,” he says, presenting a repeating pattern of drilled holes arcing across the floor. The pattern spans a total of about 25 feet, and Chris, who has been with CHESS for the past 18 years, has no idea what was held down by the bolts marked in the floor.

Image: Robert Wilson, right, was the architect behind Wilson Lab, as well as many of the subsequent experiments. Wilson later went over to Fermilab to design their famed building.

Extremely small magnetic nanostructures with invisibility cloak

2018/10/192018/10/25

Future data storage technology

In novel concepts of magnetic data storage, it is intended to send small magnetic bits back and forth in a chip structure, store them densely packed and read them out later. The magnetic stray field generates problems when trying to generate particularly tiny bits. Now, researchers at the Max Born Institute (MBI), the Massachusetts Institute of Technology (MIT) and DESY were able to put an “invisibility cloak” over the magnetic structures. In this fashion, the magnetic stray field can be reduced, allowing for small yet mobile bits. The results were published in Nature Nanotechnology.

For physicists, magnetism is intimately coupled to rotating motion of electrons in atoms. Orbiting around the atomic nucleus as well as around their own axis, electrons generate the magnetic moment of the atom. The magnetic stray field associated with that magnetic moment is the property we know from e.g. a bar magnet we use to fix notes on pinboard. It is also the magnetic stray field that is used to read the information from a magnetic hard disk drive. In today’s hard disks, a single magnetic bit has a size of about 15 x 45 nanometer, about 1.000.000.000.000 of those would fit on a stamp.

One vision for a novel concept to store data magnetically is to send the magnetic bits back and forth in a memory chip via current pulses, in order to store them at a suitable place in the chip and retrieve them later. Here, the magnetic stray field is a bit of a curse, as it prevents that the bits can be made smaller for even denser packing of the information. On the other hand, the magnetic moment underlying the stray field is required to be able to move the structures around.

Credit: MIT, L. Caretta/M. Huang [Source]

2018 ALS User Meeting Highlights

2018/10/192018/10/25

Past, present, and future converged at the ALS User Meeting, held October 2–4, 2018. About 480 registrants helped celebrate the 25th anniversary of first light at the ALS and the announcement of CD-1 approval for the ALS Upgrade project (ALS-U), a major federal milestone. Users’ Executive Committee (UEC) Chair Will Chueh kicked things off by acknowledging the organizers—UEC members Jennifer Ciezak-Jenkins, Alex Frañó, and Michael Jacobs—and thanking the ALS for its support. He also explained the organizing principle behind the program: to engage student and young-scientist users and strengthen interactions between users in general. Jeff Neaton, Berkeley Lab’s Associate Laboratory Director for Energy Sciences, then extended an official welcome to attendees. He noted that it’s been an exciting year for the ALS, which gained a new director, Steve Kevan, in addition to CD-1 approval for ALS-U.

Image: Plenary session, Day 1.
Credit: Peter DaSilva/Berkeley Lab

The search for clean hydrogen fuel

2018/10/192018/10/22

The world is transitioning away from fossil fuels and hydrogen is poised to be the replacement.

Two things are needed if we are to make the transition to a low carbon, “hydrogen economy” they are clean and high yielding sources of hydrogen, as well as efficient means of producing and storing energy using hydrogen.

Hydrogen powered cars are the perfect case study for how a hydrogen-fuelled future would look. While they work and show a great deal of promise, the best examples of hydrogen being used in fuel require very clean sources of hydrogen. If the source of hydrogen is mixed with contaminants like carbon monoxide, the efficiency of the fuel goes down and causes downstream problems in the fuel cell.

A team from KTH led by Jonas Weissenrieder is visiting MAX IV this week to try and solve this exact problem, how can we generate clean hydrogen for fuel cells? The team is working on a process to catalyse the oxidation of carbon monoxide, which adversely affects fuel cell performance, to harmless carbon dioxide. The catalysis reaction must be selective, and not affect the hydrogen gas that could be oxidised to water which is not great for running car engines.

Acid-base equilibria: not exactly like you remember in chemistry class

2018/10/18

Work published in the Royal Society of Chemistry with the support of the Helmholtz Association through the Center for Free-Electron Laser Science at DESY, MAX IV Laboratory, Lund University, Sweden, European Research Council (ERC) under the European Union’s Horizon 2020 and the Academy of Finland.

Remember doing titrations in chemistry class? Adding acid drop-by-drop to the beaker and the moment you took your eye off it the solution completely changed colour.
We learned in chemistry that by doing this titration, we were actually affecting an important equilibrium in the beaker between acids and bases. This equilibrium was first described at the turn of the 20th century by American biochemist Lawrence Henderson and modified by Karl Hasselbalch giving us the Henderson-Hasselbalch equation. The discovery and subsequent study of acids and bases using this equation has led to the discovery of many important phenomena in the natural world from as how cells function to how materials are formed.

However, after years of study, an idea arose that questioned the validity of the Henderson-Hasselbalch equation, what happens at the surface? If you have a beaker filled with a dilute acid, what happens at the very top atomic layer? The top layer of a liquid in a beaker is special for many reasons, but if you’re a dissolved molecule, it means that you’re no longer surrounded by water on all sides. For hydrophobic molecules, this means that it is favourable to be at the surface. With this in mind, the scientists took another look at the Henderson-Hasselbalch equilibrium equation and thought that it couldn’t work at the surface. Many studies have measured indicator chemical species, and determined that the Henderson-Hasselbalch equation does not seem to apply at the surface, and concluded that the concentration of hydronium or hydroxide ions, which determines the acidity/basicity, is different at the air-liquid interface than in the bulk.