How deadly parasites ‘glide’ into human cells

X-ray analysis reveals structure of molecular machinery of malaria and toxoplasmosis pathogens

An investigation at DESY’s X-ray source PETRA III provides new insights into the molecular machinery by which certain parasites travel through the human organism. The study, led by Christian Löw from the Hamburg branch of the European Molecular Biology Laboratory EMBL, analyzed the so-called gliding movement of the malaria and toxoplasmosis parasites. The results, which the interdisciplinary team presents in the journal Communications Biology, can aid the search for new drugs against the pathogens.

In biological terms, gliding refers to the type of movement during which a cell moves along a surface without changing its shape. This form of movement is unique to parasites from the phylum Apicomplexa, such as Plasmodium and Toxoplasma. Both parasites, which are transmitted by mosquitoes and cats, have an enormous impact on global heath. Plasmodium causes 228 million malaria infections and around 400 000 deaths per year. Toxoplasma, which infects even one third of the human population, can cause severe symptoms in some people, and is particularly dangerous during pregnancy.

Read more on the DESY PETRA III website

Image: Molecular structure of essential light chain (ELC) protein in Plasmodium glideosome. Blue represents the electron density of the protein, with bonds between atoms indicated in yellow and water molecules indicated in red. The crystal structure at a resolution of 1.5 Ångström (0.15 millionths of a millimetre) was obtained at the EMBL beamlines at DESY’S X-ray source PETRA III. Credit: EMBL, Samuel Pazicky

Searching for the chemistry of life

Study shows possible new way to create DNA base pairs

In the search for the chemical origins of life, researchers have found a possible alternative path for the emergence of the characteristic DNA pattern: According to the experiments, the characteristic DNA base pairs can form by dry heating, without water or other solvents. The team led by Ivan Halasz from the Ruđer Bošković Institute and Ernest Meštrović from the pharmaceutical company Xellia presents its observations from DESY’s X-ray source PETRA III in the journal Chemical Communications.

“One of the most intriguing questions in the search for the origin of life is how the chemical selection occurred and how the first biomolecules formed,” says Tomislav Stolar from the Ruđer Bošković Institute in Zagreb, the first author on the paper. While living cells control the production of biomolecules with their sophisticated machinery, the first molecular and supramolecular building blocks of life were likely created by pure chemistry and without enzyme catalysis. For their study, the scientists investigated the formation of nucleobase pairs that act as molecular recognition units in the Deoxyribonucleic Acid (DNA).

Read more on the PETRA III (DESY) website

Image: From the mixture of all four nucleobases, A:T pairs emerged at about 100 degrees Celsius and G:C pairs formed at 200 degrees Celsius. Credit: Ruđer Bošković Institute, Ivan Halasz

High-pressure study advances understanding of promising battery materials

X-ray investigation shows systematic distortion of the crystal lattice of high-entropy oxides

In a high-pressure X-ray study, scientists have gained new insights into the characteristics of a promising new class of materials for batteries and other applications. The team led by Qiaoshi Zeng from the Center for High Pressure Science in China used the brilliant X-rays from DESY’s research light source PETRA III to analyse a so-called high-entropy oxide (HEO) under increasing pressure. The study, published in the journal Materials Today Advances is a first, but very important step paving a way for a broader picture and solid understanding of HEO materials.

Modern society requires industry to manufacture efficiently sustainable products for everyday life, for example batteries for smart phones. About five years ago, a new class of materials emerged that appears to be very promising for the design of new applications, especially batteries. These high-entropy oxides consist of at least five metals that are distributed randomly in a common simple crystal lattice, while their crystal structure can be different from each metal’s generic lattice. A popular example of a HEO material consists of 20 per cent each of cobalt, copper, magnesium, nickel and zinc for every oxygen atom, or (Co0.2Cu0.2Mg0.2Ni0.2Zn0.2)O.

Read more on the DESY website

Image: Example of a high-entropy oxide between the anvils of a diamond anvil cell used to exert increasing pressure on the sample. Credit: Center of High Pressure Science, Qiaoshi Zeng

Milling towards Green Chemistry

Real-time X-ray investigations reveal strong influence of milling equipment on mechanochemical reactions

The result of mechanochemical synthesis can be altered simply by selecting different milling jars and balls. Using the bright X-ray light from PETRA III (shown in green), the team was able to follow the formation of different polymorphs live. (Credit: McGill University, Luzia Germann)

The physical properties of milling jars and balls used in mechanically driven chemical reactions have a considerable influence on the reaction mechanism and outcome. Achieved at PETRA III, this is the result of a time-resolved X-ray study of mechanochemical syntheses. It shows that the material of milling jars, as well as the size and material of the milling balls can be specifically used to control the results of mechanochemical co-crystallisations, as Luzia S. Germann from McGill University (Canada) and co-workers report in the Royal Society of Chemistry’s journal Chemical Science.

Mechanochemistry has recently gained a lot of attention as a cornerstone of green and environmentally-friendly solvent-free synthetic methods. The results of the synchrotron X-ray powder diffraction experiments will contribute to a better understanding of mechanochemical processes and how they can be used in the future to explore the synthesis of new materials.

Read more on the DESY website

Image: The result of mechanochemical synthesis can be altered simply by selecting different milling jars and balls. Using the bright X-ray light from PETRA III (shown in green), the team was able to follow the formation of different polymorphs live. (Credit: McGill University, Luzia Germann)

Nanocrystals arrange themselves to form new lattices

Tiny structure that conducts electricity anisotropically offers foundation for new electronic components

Electronic components such as light-emitting diodes or solar cells can never be too minute. The smaller they are, the less power they consume and the wider the range of possible applications. In order to explore smaller and smaller worlds, scientists are constantly on the lookout for new materials with interesting properties. A research team from the University of Tübingen, working with colleagues at DESY and from Russia, has now made such a discovery.

Three-dimensional lattice of nanocrystals and semiconducting molecules. The precise arrangement of the nanocrystals allows current in the form of electrons (e-) to flow in certain directions. Illustration: University of Tübingen, Andre Maier.The scientists attached semiconducting organic molecules to inorganic nanocrystals to form ordered, three-dimensional lattices that have a uniform superstructure and are electrical conductors. “For the first time ever, we were able to determine a correlation between the conductivity and the direction of electrical transport in such lattices made up of nanocrystals,” said Marcus Scheele from the University of Tübingen, one of the team’s two leaders, adding that this is hugely significant in terms of their use in electronic components.

Read more on the DESY website

Image: Three-dimensional lattice of nanocrystals and semiconduction molecules. The prcise arrangement of the nanocrystals allows current in the form of electrons (e-) to flow in certain directions. Illustration: University of Tübingen, Andre Maier.

Unravelling the secrets of the malaria parasite

PETRA III helps to identify a new kind of protein in Plasmodium falciparum

For the first time, scientists have identified a lipocalin protein in the malaria parasite Plasmodium falciparum. The discovery helps to better understand the life cycle of the parasite that is a major health burden in large parts of the world. The cooperation between the groups of Tim Gilberger from the Centre for Structural Systems Biology CSSB (Cellular Parasitology Department at Bernhard Nocht Institute for Tropical Medicine/ Universität Hamburg) at DESY and Matthias Wilmanns from the Hamburg branch of the European Molecular Biology Laboratory EMBL describes the discovery in the journal Cell Reports. CSSB is a cooperation of nine institutions, including DESY, that have deputed scientists to the centre.

With an estimated 228 million cases per year worldwide and more than 400,000 deaths, malaria remains one of the most important human health threats. There is no vaccine commercially available. While biologists have revealed many details about how the malaria parasite rapidly feeds on and transforms its host’s red blood cells, there are many unsolved mysteries surrounding the parasite’s life cycle. Using the microscopic facilities available at CSSB in combination with EMBL’s X-ray beamlines at DESY’s research light source PETRA III, the team unraveled a small piece of this mystery with the identification and characterization of the first lipocalin in the most virulent malaria parasite species P. falciparum.

Read more on the PETRA III (at DESY) website

Image: Ribbon diagram of the protein structure of Plasmodium falciparum Lipocalin PfLCN that comes in tertramers, i.e. complexes of four identical molecules. Fluorescence micrographs of the parasite (upper right and lower left) show that the lipocalin accumulates in vacuoles.

Credit: BNITM/EMBL, Paul-Christian Burda/Thomas Crosskey [Source]

Scientists discover new forms of feldspars

High-pressure experiments reveal unknown variants of common mineral

In high-pressure experiments, scientists have discovered new forms of the common mineral feldspar. At moderate temperatures, these hitherto unknown variants are stable at pressures of Earth’s upper mantle, where common feldspar normally cannot exist. The discovery could change the view at cold subducting plates and the interpretation of seismologic signatures, as the team around DESY scientist Anna Pakhomova and Leonid Dubrovinsky from Bayerisches Geoinstitut in Bayreuth report in the journal Nature Communications.Feldspars represent a group of rock forming minerals that are highly abundant on Earth and make up roughly 60 per cent of Earth’s crust. The most common feldspars are anorthite, (CaSi2Al2O8), albite (NaAlSi3O8), and microcline (KAlSi3O8). At ambient conditions, the aluminium and silicon atoms in the crystal are each bonded to four oxygen atoms, forming AlOand SiO4 tetrahedra.

Read more on the DESY website

Image : The crystal structure of the feldspar anorthite under normal conditions (left) and the newly discovered high-pressure variant (right). Under normal conditions, the silicon and aluminium atoms form tetrahedra (yellow and blue) with four oxygen atoms each (red). Under high pressure polyhedra with five and six oxygen atoms are formed. Calcium atoms (grey) lie in between. The black lines outline the so-called unit cell, the smallest unit of a crystal lattice. 

Credit : DESY, Anna Pakhomova

Plastic from Wood

X-ray analysis points the way to lignin-based components made to measure

The biopolymer lignin is a by-product of papermaking and a promising raw material for manufacturing sustainable plastic materials. However, the quality of this naturally occurring product is not as uniform as that of petroleum-based plastics. An X-ray analysis carried out at DESY reveals for the first time how the internal molecular structure of different lignin products is related to the macroscopic properties of the respective materials. The study, which has been published in the journal Applied Polymer Materials, provides an approach for a systematic understanding of lignin as a raw material to allow for production of lignin-based bioplastics with different properties, depending on the specific application.

Read more on the PETRA III at DESY website (opens in a new tab)”>>Read more on the PETRA III at DESY website

Image: Lignin is a promising raw material (left) for thermoplast (right) production.
Credit: KTH Stockholm, Marcus Jawerth

Double X-ray vision helps tuberculosis and osteoporosis research

Combination measurement shows distribution of metals in biological samples

With an advanced X-ray combination technique, scientists have traced nanocarriers for tuberculosis drugs within cells with very high precision. The method combines two sophisticated scanning X-ray measurements and can locate minute amounts of various metals in biological samples at very high resolution, as a team around DESY scientist Karolina Stachnik reports in the journal Scientific Reports. To illustrate its versatility, the researchers have also used the combination method to map the calcium content in human bone, an analysis that can benefit osteoporosis research.“Metals play key roles in numerous biological processes, from the oxygen transport in our red blood cells and the mineralisation of bones to the detrimental accumulation of metals in nerve cells as seen in diseases like Alzheimer’s,” explains Stachnik who works in the Center for Free-Electron Laser Science CFEL at DESY. High-energy X-rays make metals light up in fluorescence, a method that is very sensitive even to tiny amounts. “However, the X-ray fluorescence measurements usually do not show the ultrastructure of a cell, for example,” says DESY scientist Alke Meents who led the research. “If you want to exactly locate the metals within your sample, you have to combine the measurements with an imaging technique.” The ultrastructure comprises the details of the cell morphology that are not visible under an optical microscope.

>Read More on the DESY Website

Image: Two agglomerates of antibiotic-loaded iron nanocontainers (red) in a macrophage. Credit: Stachnik et al., „Scientific Reports“, CC BY 4.0

Tuneable self-organisation of liquid crystals in nanopores

Innovative path to novel materials with adaptive electrical and optical properties

A team of researchers has used X-rays from DESY’s research light source PETRA III to explore the amazingly diverse self-organisation of liquid crystals in nanometre-sized pores. The study, led by Patrick Huber from the Hamburg University of Technology (TUHH), shows how liquid crystals arrange themselves in pores of different sizes, exhibiting different electrical and optical properties. These could be of interest for applications such as sensors and novel optical metamaterials, as the group around first author Kathrin Sentker from TUHH reports in the journal Nanoscale. The research, which Huber presented at the annual DESY Users’ Meeting running until this Friday, will be continued within the framework of the planned Centre for Multiscale Materials Systems (CIMMS), in which TUHH, University of Hamburg, Helmholtz-Zentrum Geesthacht and DESY are involved and for which the Hamburg Science Authority has just approved approximately four million euros funding.

The researchers had studied a special liquid crystal material called HAT6 (2,3,6,7,10,11-hexakis(hexyloxy)triphenylene; C54H84O6), whose single molecules are disc-shaped. Below about 70 degrees Celsius, they arrange themselves into a liquid crystal; by heating to about 100 degrees, the order can be broken. The scientists filled this material into pores in an aluminium oxide substrate and cooled it down. The cylindrical pores were 17 to 160 nanometres (millionths of a millimeter) in diameter, 0.1 millimetres long and situated on a regular, hexagonal lattice.

Read more on the PETRA III website

Image: Simulation of the different orders of the liquid crystal, matching the measurements. Simulation: Marco D. Mazza, Max Planck Institute for dynamics and self-organisation and und Loughborough University

Record participation at user meetings of the Hamburg research light sources

More than 1300 participants from 28 countries have registered

For this year’s users’ meetings of the Hamburg X-ray light sources, more participants have registered than ever before: More than 1300 scientists from 28 countries will come to discuss research with DESY’s X-ray source PETRA III, the free-electron laser in Hamburg FLASH and the X-ray laser European XFEL for three days starting this Wednesday. The jointly organised users’ meetings of DESY and European XFEL are the largest gathering of this kind worldwide.

“The steadily increasing number of participants from Germany and abroad shows the great importance of the Hamburg research light sources for the national and international scientific community,” says DESY’s Director for Photon Science, Edgar Weckert. “Hamburg is one of the X-ray capitals of the world.” The brilliant X-ray light from the powerful particle accelerators provides detailed insights into the structure and dynamics of matter at the atomic level. It can be used, for example, to decipher the structure of biomolecules, illuminate innovative materials, film chemical reactions and simulate and study the conditions inside planets and stars.

At the European X-ray laser European XFEL, all six scientific experiment stations are in operation since June. “Our users’ experiences and expertise are crucial for shaping the future of our science and facility”, says European XFEL managing director Robert Feidenhans’l. “The annual users’ meeting, therefore, is an extremely valuable opportunity for users and scientists who work at our facilities to share their experiences of doing experiments at the instruments, and talk about ideas for further development.” In 2019, 890 scientists from 255 institutes in 28 countries participated in experiments at the facility.

> Read more on the PETRA III and FLASH website

> Please find here another article on the European XFEL website

Picture: The jointly organised users’ meetings are the largest gathering of this kind worldwide.
Credit: DESY, Marta Mayer

60 years of DESY – From Hamburg particle accelerator to global research centre

Germany’s largest accelerator centre turns 60 on 18 December 2019

The story of DESY began on 18 December 1959 with the signing of a contract in Hamburg’s town hall. It is a story of success, for global research and for Germany as a science hub! For the past 60 years, fundamental research has been carried out at DESY in Hamburg-Bahrenfeld – which was joined in 1991 by a second DESY site in Zeuthen. In those 60 years, DESY has become a world leader in accelerator technology, structure research, particle physics and astroparticle physics. During these 60 years, DESY has developed pioneering technologies, which have been used by scientists from all over the world to make outstanding advances. Among other things, the gluon was discovered and the structure of ribosomes was determined at DESY.
“It is now a question of the big challenges of our times,” says DESY’s director Professor Helmut Dosch. “We have developed a new generation of research tools in the form of so-called X-ray lasers. These afford fundamental insights in medicine and in materials engineering, for example, which will help shape the world of tomorrow.” DESY offers unique conditions for this: the combination of the radiation sources PETRA III, FLASH and European XFEL means that international scientists can carry out experiments using high-intensity X-rays. In addition to this, DESY offers structure researchers and businesses from all over the world a unique “toolbox” in the form of supplementary methods for manufacturing, processing and examining nano-samples and nanomaterials. DESY’s second site in Zeuthen is also an international magnet as a growing centre of excellence in astroparticle physics. Zeuthen operates the only accelerator in Brandenburg and is one of the largest scientific institutions in the region.

>Read more on the DESY website

Image: Part of the DESY staff in Hamburg holds the DESY-60 logo
Credit: DESY/H. Müller-Elsner

Scientists probe Earth’s deep mantle in the laboratory

Extreme conditions experiments sharpen view of our planet’s interior

Simulating the conditions 2700 kilometres deep underground, scientists have studied an important transformation of the most abundant mineral on Earth, bridgmanite. The results from the Extreme Conditions Beamline at DESY’s X-ray light source PETRA III reveal how bridgmanite turns into a structure known as post-perovskite, a transformation that affects the dynamics of Earth’s lower mantle, including the spreading of seismic waves. The analysis can provide an explanation for a range of peculiar seismic observations, as the team headed by Sébastien Merkel from the Université de Lille in France report in the Journal Nature Communications.
Bridgmanite is a magnesian-iron mineral ((Mg,Fe)SiO3) with a crystal structure that is not stable under ambient conditions. It forms about 660 kilometres below the surface of the Earth, and microcrystalline grains found as inclusions in meteorites are the only samples ever recovered on the surface. “In order to study bridgmanite under the conditions of the lower mantle, we had to produce the mineral first,” explains Merkel. To do so, the scientists compressed tiny amounts of iron-magnesium-silicon-oxide in a diamond anvil cell (DAC), a device that can squeeze samples with high pressure between two small diamond anvils.

Image: The crystal structures of bridgmanite (left) and post-perovskite (right).

Credit: Université de Lille, Sébastien Merkel
>Read more on the PETRA III (DESY) website

Spraying nanopaper

New process produces extremely smooth cellulose layers on an industrial scale

With a new spray coating process, very uniform layers of cellulose nanofibers (CNF) can be produced on an industrial scale. X-ray investigations at DESY’s research light source PETRA III as well as investigations with an atomic force microscope and neutron scattering show how the layer is structured and can be tailored for different purposes like extremely thin, smooth and tough nanopaper. A Swedish-German research team led by DESY scientist Stephan Roth presents its structural analyses in the journal Macromolecules.
“Porous, nanostructured cellulose films have a number of advantageous properties that make them interesting for various applications from ultrastrong bio-active fibres to transparent conductive nanopaper,” explains the main author of the study, Calvin Brett from DESY and the Royal Institute of Technology (KTH) in Stockholm. “They are lightweight and temperature stable, have excellent mechanical properties, a low density and are made from renewable raw materials – cellulose nanofibers are usually made from wood.”

> Read more on the PETRA III at DESY website

Image: A silicon wafer without (top) and with (bottom) nano-cellulose coating. Each wafer is two centimetres wide and ten centimetres long. The coating is just 200 nanometres thin. Credit: DESY/KTH Stockholm, Calvin Brett.

Beryllium configuration with neighbouring oxygen atoms revealed

High-pressure experiments prove 50-year-old theoretical prediction.

In high-pressure experiments at DESY’s X-ray light source PETRA III, scientists have observed a unique configuration of beryllium for the first time: At pressures nearly a million times the average atmospheric pressure, beryllium in a phosphate crystal acquires six neighbouring atoms instead of the usual four. This six-fold coordination had been predicted by theory more than 50 ago, but could not be observed until now in inorganic compounds. DESY scientist Anna Pakhomova and her collaborators report their results in the journal Nature Communications.
“Originally, chemistry textbooks stated that elements like beryllium from the second period of the periodic table could never have more than four neighbours, due to their electron configuration”, explains Pakhomova. “Then around 50 years ago theorists discovered that higher coordinations could actually be possible, but these have adamantly evaded experimental proof in inorganic compounds.” Inorganic compounds are typically those without carbon – apart from a few exceptions like carbon dioxide and carbon monoxide.

>Read more on the PETRA III at DESY website

Image: Transformation of the usual fourfold coordination of beryllium to five- and sixfold with increasing pressure. (Credit: DESY, Anna Pakhomova)

Simulating earthquakes and meteorite impacts in the lab

New device squeezes samples with 1.6 billion atmospheres per second.

A new super-fast high-pressure device at DESY’s X-ray light source PETRA III allows scientists to simulate and study earthquakes and meteorite impacts more realistically in the lab. The new-generation dynamic diamond anvil cell (dDAC), developed by scientists from Lawrence Livermore National Laboratory (LLNL), DESY, the European Synchrotron Radiation Source ESRF, and the universities of Oxford, Bayreuth and Frankfurt/Main, compresses samples faster than any similar device before. The instrument can turn up the pressure at a record rate of 1.6 billion atmospheres per second (160 terapascals per second, TPa/s) and can be used for a wide range of dynamic high-pressure studies. The developers present their new device, that has already proven its capabilities in various materials experiments, in the journal Review of Scientific Instruments.
“For more than half a century the diamond anvil cell or DAC has been the primary tool to create static high pressures to study the physics and chemistry of materials under those extreme conditions, for example to explore the physical properties of materials at the center of the Earth at 3.5 million atmospheres,” said lead author Zsolt Jenei from LLNL. To simulate fast dynamic processes like earthquakes and asteroid impacts more realistically with high compression rates in the lab, Jenei’s team, in collaboration with DESY scientists, now developed a new generation of dynamically driven diamond anvil cell (dDAC), inspired by the pioneering original LLNL design, and coupled it with the new fast X-ray diffraction setup of the Extreme Conditions Beamline P02.2 at PETRA III.

>Read more on the PETRA III at DESY website

Image: Artist’s impression of a meteorite impact.
Credit: NASA