Developing more nutritious crops to feed a growing world

Using synchrotron light to analyze new varieties of peas could be faster, more environmentally friendly, and help to nourish underfed populations around the world.

With thousands of seed samples produced every growing season, Dr. Tom Warkentin needs fast, accurate and cost-effective techniques to assess the nutritional value of the pea varieties he has developed. Now, thanks to two recent studies, techniques available at the Canadian Light Source (CLS) synchrotron at the University of Saskatchewan show promise for Warkentin and many other plant breeders.

“These studies arose from the question, ‘Can we use the synchrotron to measure the nutrient traits in pea seeds?,’” explained Warkentin, professor of plant science and pulse breeder in the Crop Development Centre at the University of Saskatchewan’s College of Agriculture and Bioresources. “Improving the nutritional value of peas is a higher and higher priority for us in plant breeding so we wanted to look at the standard approaches we’ve been using to measure nutritional traits versus the techniques available at the CLS.”

>Read more on the Canadian Light Source website

Image: Scientists Tom Warkentin, Chithra Karunakaran, Jarvis Stobbs, and David Muir with pea samples at our IDEAS beamline.

NSLS-II scientist named DOE Office of Science Distinguished Fellow

Scientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have garnered two out of five “Distinguished Scientists Fellow” awards announced today by the DOE’s Office of Science.

Theoretical physicist Sally Dawson, a world-leader in calculations aimed at describing the properties of the Higgs boson, and José Rodriguez, a renowned chemist exploring and developing catalysts for energy-related reactions, will each receive $1 million in funding over three years to pursue new research objectives within their respective fields. (…)

José Rodriguez (NSLS-II)

For discoveries of the atomic basis of surface catalysis for the synthesis of sustainable fuels, and for significantly advancing in-situ methods of investigation using synchrotron light sources.”

Rodriguez will devote his funding to the development and construction of new tools for performing extremely rapid, time-resolved measurements to track the reaction mechanisms of catalytic processes as they occur under variable conditions—like those encountered during real-world reactions important to energy applications. These include processes on metal-oxide catalysts frequently used in the production of clean fuels and other “green” chemicals through hydrogenation of carbon monoxide and carbon dioxide, or the conversion of methane to hydrogen.

“At a microscopic level, the structure of a catalyst and the chemical environment around the active sites—where chemical bonds are broken and reformed as reactants transform into new products—change as a function of time, thus determining the reaction mechanism,” said Rodriguez. “We can learn a lot about the nature of the active sites under steady-state conditions, with no variations in temperature, pressure, and reaction rate. But to really understand the details of the reaction mechanism, we need ways to track what happens under transient or variable conditions. This funding will allow us to build new instrumentation that works with existing capabilities so we can study catalysts under variable conditions—and use what we learn to improve their performance.”

>Read more on the NSLS-II website

Gene encapsulation with MOFs for new delivery vectors in gene therapy

A research team from RMIT University, CSIRO Manufacturing, University of New South Wales, Graz University of Technology and the University of Adelaide, in Australia, have demonstrated an easy and efficient method to use nano MOFs for carrying large-size intact gene sets to be applied in gene therapy. Their study reports encapsulation of a complete gene-set in zeolitic imidazolate framework-8 (ZIF-8) MOFs and cellular expression of the gene delivered by the nano MOF composites, with data obtained at the MISTRAL beamline at the ALBA Synchrotron showing intracellular presence of the biocomposite particles.

MOFs (metal-organic frameworks) are porous materials with well-defined geometry and high loading capacity. For biological applications, their high porosity makes these composites an effective strategy for loading and protection of proteins; however, their use for other biomacromolecules such as nucleic acids is still in their infancy. Now, a research team lead by RMIT University from Melbourne has been studying the use of ZIF-8 MOFs as possible gene delivery vectors. The results show encapsulation of a gene-set in ZIF-8 MOFs and its cellular expression, proving that MOFs do not damage the structural and functional activity of the cargo nucleic acid, essential for possible applications in gene therapy as disease treatments.

>Read more on the ALBA website

Image: Left: Confocal laser scanning microscope images of plGFP@ZIF-8 transfected into human prostate cancer epithelial cells. See the entire image here.

The driving force behind Cornell Compact Undulators at CHESS

Researchers at CHESS are working to further improve the already impressive CHESS Compact Undulator, or CCU.

Within the new NSF-funded CHEXS award, Sasha Temnykh is developing a new driving mechanisms that will add variable gap control and even better tuning of the device, both desirable qualities for a variety of experimental needs.

Undulators are critical devices for the creation of brilliant X-rays at CHESS and other lightsources around the world. With the recent CHESS-U upgrade, the Cornell Electron Storage Ring, CESR, is now outfitted with seven new insertion devices. As the beam circulates around CESR, it passes through a series of alternating magnets in the undulators, resulting in X-rays that are roughly 20 times brighter than those produced prior to the upgrade, making CHESS an even more powerful X-ray source.

Researchers at CHESS lead by Sasha Temnykh are working continuously to improve the already impressive CHESS Compact Undulator, or CCU. The CCUs are about ten times more compact, lighter, and less expensive compared to conventional insertion devices typically used at other lightsource. They also require a significant shorter fabrication time. Nine CCUs have already been constructed in industry from the Cornell-held patent, and according to KYMA, the manufacturer of the CCU, other labs are starting to show interest in the device.

>Read more on the CHESS website

Image: Sasha Temnykh is the driving force behind the Cornell Compact Undulator design and development. 

Synergistic Co−Mn oxide catalyst for oxygen reduction reactions

Researchers employed synchrotron-based X-ray absorption spectroscopy (XAS) at CHESS to investigate the synergistic interaction of bimetallic Co1.5Mn1.5O4/C catalysts… under real-time operando electrochemical conditions.

Identifying the catalytically active site(s) in the oxygen reduction reaction (ORR) is critical to the development of fuel cells and other technologies. Researchers employed synchrotron-based X-ray absorption spectroscopy (XAS) at CHESS to investigate the synergistic interaction of bimetallic Co1.5Mn1.5O4/C catalysts – which exhibit impressive ORR activity in alkaline fuel cells – under real-time operando electrochemical conditions. Under steady state conditions, both Mn and Co valences decreased at lower potentials, indicating the conversion from Mn-(III,IV) and Co(III) to Mn(II,III) and Co(II), respectively. Changes in the Co and Mn valence states are simultaneous and exhibited periodic patterns that tracked the cyclic potential sweeps.

>Read more on the CHESS website

Image: Schematic of the in situ XAS electrochemical cell. Working electrode (WE, catalyst on carbon paper) and counter electrode (CE, carbon rod) were immersed in 1 M KOH solution. The reference electrode was connected to the cell by a salt bridge to minimize IR drops caused by the resistance in the thin electrolyte layer within the X-ray window.

All SQS experiment stations up and running

Three new experiment stations expand the scientific possibilities in the field of soft X-ray science.

The soft X-ray instrument for Small Quantum Systems (SQS) welcomed its first users at the end of 2018. Now, almost a year later, the SQS team and collaborators have completed their ambitious plan to install and commission all three experiment stations, each specifically designed for different types of experiments and samples, ranging from atoms and small molecules to large clusters, nanoparticles and biomolecules. We look at how the instrument has developed during the past year, how important collaboration has been for the success of SQS so far, and what lies ahead.

>Read more on the European XFEL website

Image: SQS scientist Rebecca Boll makes final adjustments on the AQS experiment station before the first users arrive at the end of 2018.
Credit: European XFEL

CLS celebrates 20th anniversary of its launch

From the discovery of an enzyme able to turn any blood into a universal donor type, to a process that creates plastic from sunshine and pollution, to identifying heat-tolerance traits in pea varieties, scientific advances achieved at the Canadian Light Source at the University of Saskatchewan (USask) are being celebrated asv the institution marks the 20th anniversary of its launch. “This unique-in-Canada research centre arose from an unprecedented level of collaboration among governments, universities, and industry in Canada, and represents the single largest investment in Canadian science,” said USask President Peter Stoicheff.  “Strongly endorsed two decades ago by many other universities across Canada and by an international scientific panel, the CLS has made possible cutting-edge research that benefits human and animal health, agriculture, advanced materials, and the environment. For USask’s research community, it has helped us be the university the world needs.”

Construction of the synchrotron facility on the USask campus began in 1999 and its official opening was held Oct. 22, 2004. Since then, thousands of scientists from across Canada and around the world have come to the CLS to run experiments that could not be done elsewhere in Canada.

>Read more on the Canadian Light Source website

Worldwide scientific collaboration develops catalysis breakthrough

A new article  just published in Nature Catalysis shows the simple ways of controlling the structure of platinum nanoparticles and tuning their catalytic properties. 

Research led by Cardiff Catalysis Institute (CCI) in collaboration with scientists from Lehigh University, Jazan University, Zhejiang University, Glasgow University, University of Bologna, Research Complex at Harwell (RCaH), and University College London have combined their unique skills to develop and understand using advanced characterisation methods (particularly TEM and B18 at Diamond Light Source), how it is possible to use a simple preparation method to control and manipulate the structures of metal nanoparticles. These metal nanoparticles are widely used by industry as innovative catalysts for the production of bulk chemicals like polymers, liquid fuels (e.g., diesel, petrol) and other speciality chemicals (pharmaceutical products).

>Read more on the Diamond Light Source website

Image: Andy Beale works at Diamond Light Source.

Structure and functional binding epitopes of VISTA

V-domain Ig Suppressor of T-cell Activation (VISTA) is an immune checkpoint protein involved in the regulation of T cell activity. Checkpoint proteins are overexpressed by cancer cells or surrounding immune cells and prevent anti-tumor activity by co-opting natural regulation mechanisms to escape immune clearance. Compared to healthy tissues, VISTA is upregulated on tumor infiltrating leukocytes, including high expression on myeloid-derived suppressor cells (MDSCs). Through VISTA signaling, these inhibitory immune cells prevent effective antigen presentation and indirectly promote tumor growth. VISTA is implicated in a number of human cancers including skin (melanoma), prostate, colon, pancreatic, ovarian, endome­trial, and non-small cell lung. VISTA is a known member of the B7 protein family but the mechanism of action is still unclear as VISTA has been shown to function as both a ligand1,2 and a receptor3.  In the model of VISTA as a receptor, the proposed ligand of interaction is V-set and immunoglobulin domain containing 3 (VSIG3)4,5.

>Read more on the SSRL website

Image: Structure of human VISTA with extended C-C’ loop (blue), mapped VSTB/VSIG3 binding epitope (red), and disulfide bonds (yellow).

Synchrotron light for deciphering Friedreich’s Ataxia

A team from the Germans Trias i Pujol Research Institute (IGTP) in Badalona is performing an experiment at the ALBA Synchrotron to obtain for the first time 3D images of cells with this disease.

Friedreich’s ataxia affects more than 3,000 people in Spain, causing serious mobility problems and other severe illnesses such as heart disease. At present there is no treatment to prevent or cure the disease.

Friedreich’s ataxia is a rare neurodegenerative disease that progressively damages mobility, balance and coordination. It is an inherited disease, caused by a genetic mutation, that can appear when both parents are carriers. A research group from the Germans Trias i Pujol Research Institute (IGTP), at the Can Ruti Campus in Badalona, led by Dr. Antoni Matilla, is looking into the causes and possible treatments for this disease that results in high disability and an important decrease in the patients’ quality of life.

“Today there is no treatment or cure for Friedreich’s ataxia. It is necessary to try to understand how the disease develops in order to propose therapeutic solutions”, says Dr. Ivelisse Sánchez, co-Principal Investigator of this project at the Neurogenetics Unit of the IGTP. Researchers are now analysing donors’ cells in the ALBA Synchrotron to see the changes caused by the disease.

>Read more on the ALBA website

Image: Dr. Ivelisse Sánchez, co-Principal Investigator of the project, and pre-doctoral researcher Eudald Balagué at the MISTRAL beamline.

Discoveries map out CRISPR-Cas defence systems in bacteria

For the first time, researchers at the University of Copenhagen have mapped how bacterial cells trigger their defence against outside attacks. This could affect how diseases are fought in the future.

With the aid of highly advanced microscopes and synchrotron sources, researchers from the University of Copenhagen have gained critical insight into how bacteria function as defence mechanisms against attacks from other bacteria and viruses. The study, which has just been published in the renowned journal, Nature Communications, also describes how the defence systems can be activated on cue. This discovery can turn out to be an important cornerstone in fighting diseases in the future.

The researchers have shown how a cell attacked by a virus activates a molecule called COA (Cyclic Oligoadenylate), which in turn activates a so-called protein complex called CSX1 to eradicate the attacker.

>Read more on the MAX IV website

Image: Model of the CSX1 protein complex.

Breaking up buckyballs is hard to do

A new study shows how soccer ball-shaped molecules burst more slowly than expected when blasted with an X-ray laser beam.

As reported in Nature Physics, an international research team observed how soccer ball-shaped molecules made of carbon atoms burst in the beam of an X-ray laser. The molecules, called buckminsterfullerenes – buckyballs for short ­– consist of 60 carbon atoms arranged in alternating pentagons and hexagons like the leather coat of a soccer ball. These molecules were expected to break into fragments after being bombarded with photons, but the researchers watched in real time as buckyballs resisted the attack and delayed their break-up.

The team was led by Nora Berrah, a professor at the University of Connecticut, and included researchers from the Department of Energy’s SLAC National Accelerator Laboratory and the Deutsches Elektronen-Synchrotron (DESY) in Germany. The researchers focused their attention on examining the role of chemical effects, such as chemical bonds and charge transfer, on the buckyball’s fragmentation.

Using X-ray laser pulses from SLAC’s Linac Coherent Light Source (LCLS), the team showed how the bursting process, which takes only a few hundred femtoseconds, or millionths of a billionth of a second, unfolds over time. The results will be important for the analysis of sensitive proteins and other biomolecules, which are also frequently studied using bright X-ray laser flashes, and they also strengthen confidence in protein analysis with X-ray free-electron lasers (XFELs).

>Read more on the Linear Coherent Light Source at SLAC website

Image: An illustration shows how soccer ball-shaped molecules called buckyballs ionize and break up when blasted with an X-ray laser. A team of experimentalists and theorists identified chemical bonds and charge transfers as crucial factors that significantly delayed the fragmentation process by about 600 millionths of a billionth of a second.
Credit: Greg Stewart/SLAC National Accelerator Laboratory

For additional information: article published on the DESY website

A citizen-science computer game for protein design

Using the computer game, “Foldit,” nonexpert citizen scientists designed new proteins whose structures, verified at the Advanced Light Source (ALS), were equivalent in quality to and more structurally diverse than computer-generated designs.

Proteins constitute the biomachinery—the cellular gears and levers—that make our bodies work. When this machinery is running smoothly, nutrients get absorbed, cells regenerate, and so on. When the machinery breaks down, the tools needed to fix the problem (i.e. drug molecules) are often proteins themselves.

Until recently, the pool of proteins available for such therapeutic purposes was limited to those found in nature. But natural proteins represent a small subset of all the possible ways to link 20 amino acids—the basic building blocks of all proteins—into chains hundreds, even thousands, of units long. On top of this, there are countless ways in which any given protein chain can fold—a key aspect of functionality.

In the last 20 years, “de novo” protein design (from scratch as opposed to starting with a known protein) has taken off, promising cheap and effective drugs with fewer side effects. But given the huge number of possibilities available, scientists are limited in their ability to fully explore this vast “protein space.”

>Read more on the Advanced Light Source website on Berkeley Lab

Image: The user interface of Foldit, a free online computer game developed to crowdsource problems in protein modeling. (a) The Foldit score: better models yield higher scores. (b) The design palette allows players to change the amino acids in the protein chain. (c) The “pull” tool allows players to manipulate the 3D structure of the model. (d) The “undo” graph tracks the score as a model is developed and allows players to backtrack. (e) Additional tool selections.

Q&A with Sakura Pascarelli, new scientific director at European XFEL

European XFEL’s new scientific director talks about her career, her new role and her love for swimming.

On 1 September Sakura Pascarelli joined the European XFEL from the ESRF. In her role as scientific director she is responsible for the development of the four hard X-ray instruments. She spoke to Rosemary Wilson about her career, her new role and her love for swimming.

How did you get into science?

I spent part of my childhood in Burma and Indonesia. The American school system there enabled you to do lessons at your level, meaning you stayed interested and engaged. I really liked maths which I did with kids a few years older than me. I remember also doing experiments. I liked seeing things explode and break and try to understand why. Later on in Italy, I studied physics – not because I was particularly talented, but because I enjoyed it.

You joined ESRF at a time when the facility was still being built. What parallels can you see between that time, and now here at European XFEL?

I went to the ESRF to build one of the first beamlines there. We didn’t know what we would be able to discover or measure with this new machine. Here at European XFEL I see some of that same excitement. That opportunity taught me so much about instrumentation, and coordinating the construction of a beamline. But it is a different world now. Back then a good scientist with a solid background in physics, X-ray optics or instrumentation, could build a group and build a beamline. That is not possible here. This is so much more complicated. Here you need experts in X-rays, lasers, electronics, detectors. We don’t really know how to measure a femtosecond pulse let alone synchronise it with another laser! To run these instruments we need group leaders who are really good managers. This is so important. It is no longer enough for someone to be just a good scientist. At European XFEL we need to make sure the groups are well structured, well managed and that the people are happy. That might be difficult in the beginning when things don’t work, but when people see that their work is recognized, satisfaction and productivity increases.

>Read more on the European XFEL website

Image: European XFEL

New sample holder for protein crystallography

An HZB research team has developed a novel sample holder that considerably facilitates the preparation of protein crystals for structural analysis.

A short video by the team shows how proteins in solution can be crystallised directly onto the new sample holders themselves, then analysed using the MX beamlines at BESSY II. A patent has already been granted and a manufacturer found. Proteins are huge molecules that often have complex three-dimensional structure and morphology that can include side chains, folds, and twists. This three-dimensional shape is often the determining factor of their function in organisms. It is therefore important to understand the structure of proteins both for fundamental research in biology and for the development of new drugs. To accomplish this, proteins are first precipitated from solution as tiny crystals, then analysed using facilities such as the MX beamlines at BESSY II in order to generate a computer image of the macromolecular structure from the data.

>Read more on the BESSY II at HZB website

Image: Up to three indivudal drops may be placed onto the sample holder.
Credit: HZB

Direct evidence of small airway closure in acute respiratory distress syndrome

Airway closure is thought to play an important role in acute respiratory distress syndrome (ARDS).

Airway closure has been imaged for the first time in an ARDS model by synchrotron phase contrast imaging providing direct evidence of this phenomenon.

ARDS is an acute inflammatory lung condition associated with high permeability oedema, surfactant dysfunction and widespread collapse of pulmonary alveoli, called atelectasis, which leads to decreased lung compliance and volume [1]. Clinicians have long suspected that the collapsibility of small airways is increased in this clinical syndrome, causing atelectasis [2,3]. While patients invariably require mechanical ventilation to survive, this life support measure can worsen lung injury due to exaggerated stress and strain applied to the tissue, which is magnified by mechanical inhomogeneity of lung tissue and atelectasis. Efforts to develop ventilation strategies that protect the lung, critically depend on our understanding of the mechanical behaviour of lung tissue and airways at the microscale. However, traditional computed tomography studies have not been able to clearly identify airway closure as a cause of atelectasis, due to their limited spatial resolution. To better identify the mechanisms involved in airway closure, it is necessary to use approaches that allow the study of individual airways. Here, the same individual small airways in intact lungs of anesthetised and mechanically ventilated rabbits with ARDS was studied using high resolution synchrotron phase-contrast computed tomography at beamline ID17.

>Read more on the European Synchrotron (ESRF) website