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.

New research possibilities at NanoMAX

X-rays can penetrate materials and are therefore useful for studying chemical processes as they occur inside reactors, cells, and batteries. A common ingredient in such chemical systems is metal nanoparticles, which are often used as catalysts for important reactions. As the NanoMAX beamline provides a very small X-ray focal spot, single nanoparticles can in principle be studied as they perform their catalytic functions.

In this paper, we show that gold nanoparticles sitting inside an electrochemical cell can be imaged at NanoMAX. These preliminary results come from nanoparticles around 60 nm (60 millionths of a millimetre) in size, and we show that even smaller particles could be studied. If successful, future experiments will allow “filming” nanoparticles as they catalyze reactions in real-time, and give new understanding of how catalysis works. That could in turn help design new materials for energy conversion, chemical production, and water purification.

>Read more on the MAX IV Laboratory
Image (extract, full image here): Coherent Bragg imaging of 60 nm Au nanoparticles under electrochemical control at the NanoMAX beamline

Collaboration develops sensitive data protocol

MAX IV pairs up with Sprint Bioscience, a listed drug development company, in a new project to improve how companies can benefit from new, faster X-ray fragment screening experiments, while still protecting their valuable information during analysis at FragMAX.

Recently, the project was granted with 500 000 SEK from Sweden’s innovation agency Vinnova.
More or less, all pharmaceutical drugs are molecules binding to proteins in your body. When doing this, they either initiate or inhibit the process in which the target protein is involved. Proteins are in charge of everything from cells dividing at the right moment to the metabolism of the food you eat or signaling in the brain.

>Read more on the MAX IV website

Image: Sample holders
Credit: Ben Libberton

17 meter long detector chamber delivered to CoSAXS

The experimental techniques used at the CoSAXS beamline will use a huge vacuum vessel with possibilities to accommodate two in-vacuum detectors in the SAXS/WAXS geometry.

A major milestone was reached for the CoSAXS project when this vessel was recently delivered, installed and tested.
The main method that will be used at the CoSAXS beamline is called Small Angle X-ray Scattering (SAXS). By detecting the scattered rays coming from the sample at shallow angles, less than 4° typically, it is possible to learn about the size, shape, and orientation of the small building blocks that make up different samples and how this structure gives these materials their properties. The materials to be studied can come from various sources and in diverse states, for example, plastics from packaging, food and how it is processed or proteins in solution which can be used as drugs.
The “co” in CoSAXS stands for coherence, a quality of the synchrotron light optimized at the MAX IV machine, that loosely could be translated as laser-likeness. In the specific case of X-ray Photon Correlation Spectroscopy (XPCS), it lets the researchers not only measure the structure of the building blocks in the sample but also their dynamics – how they change in time.

>Read more on the MAY IV Laboratory website

New beamline for electron bunch diagnostics

A new diagnostic beamline connected directly to the MAX IV linear accelerator is under construction.

It will enable time-resolved characterization of primarily the ultrashort electron bunches for the FemtoMAX beamline but will also be useful for other time-resolved experiments. The design of the highly specialized beamline components is to a large part done in-house.
Head up and tail down
The linear accelerator accelerates electrons up to high energies. Short bunches containing 109 electrons are delivered from the linear accelerator to make X-ray pulses for the FemtoMAX beamline. The duration of the bunches is in the femtosecond (10-15 s) regime to enable high temporal-resolution measurements at the beamline. The short duration makes the bunches very challenging to characterize with time resolution as conventional detection devices are too slow.
In the new setup, two so-called transverse deflecting cavities (TDC) will make the acquisition of time-resolved data possible. They will in principle add an electromagnetic field that deflects the head of the electron bunch upwards and the tail down so that the first electrons hitting the beam profile analyzer will end up at the top of the screen and the last ones will end up at the bottom. The resulting streak gives a time-resolved measurement of the shape of the bunch but the method will also be used to characterize for example how emittance and energy vary as a function of time.
– Today we rely on calculations and relative measurements for the bunch length delivered to FemtoMAX says project leader Erik Mansten, the TDC is a way for us to verify what we deliver. It also helps us preparing the linac for a possible free electron laser in the future.

>Read more on the MAX IV website

Image: These copper disks are going to become transverse deflecting cavities for the new diagnostic beamline.

Why having your head in the clouds could be a really good thing

The ATMOS research group in the NANOMO unit, led by Nønne Prisle, Associate Professor at the University of Oulu, are trying to find out what kind of chemistry is happening in cloud droplets and tiny nanometer-sized aerosol particles in the atmosphere. This knowledge could eventually, hopefully, give us more accurate theoretical models to understand the ongoing climate change.
– The only thing that can halter climate change is to stop emitting CO2. Nønne Prisle is very, very clear on that. Even so, she says, if we want to take any other step to try to counter climate change, we really need to know what’s going on in the clouds since these processes could be quite critical.
The ATMOS team are using the beamline HIPPIE at MAX IV being so-called commissioning experts, which means that the experiment is done both to provide useful data but also to verify the capacity and capability of the beamline experimental station.

>Read more on the MAX IV Laboratory website

Image: From left to right: Robert Seidel, Helmholtz Zentrum Berlin; Nønne Prisle, Kamal Raj and Jack Lin, University of Oulu at the HIPPIE beamline.

Capturing protein motion at FemtoMAX

Your body contains a large variety of different proteins. They are big, complex molecules with diverse functions, from transporting oxygen in your blood to making your muscles contract.

Many proteins change their shape and move as they perform their task. A research team from the University of Gothenburg recently visited the beamline FemtoMAX to develop a method for studying moving proteins. They use electric fields to stimulate motion of the proteins in a sample while imaging them with the X-ray beam.
To study how proteins move, we need something to nudge them and then image them after they have changed position. Certain proteins are activated by light and in that case, the researchers can hit them with a laser pulse to provoke the motion. However, that is far from always the case. In the method being developed by the Gothenburg team, the proteins are instead subjected to an electric field that make them move.
The field is synchronized to the short, femtosecond scale (10-15 s) X-ray pulses delivered at beamline FemtoMAX. Each X-ray pulse hitting the sample is like taking a photograph using extremely short shutter speed, just like trying to get sharp images of players on a football field. The X-ray pulses at FemtoMAX are short enough to let the researchers capture the instantaneous position of the protein. By varying the time between the electric field and the X-ray pulse they can see different stages of the movement and even put the frames together as a movie of the protein motion.

>Read more on the MAX IV Laboratory website

HIPPIE provides a closer look at water filtration

Clean fresh water is a scarce resource. Areas of the world suffering from drought have to filter the salt out of seawater to make it drinkable. In other areas, the water may instead have a high content of toxic compounds, such as arsenic.
If you think about a water filter as a kind of strainer with tiny holes through it, you would assume that since it does a pretty good job of filtering out the small ions of normal table salt, sodium, and chloride, from seawater it would work even better for the larger arsenic compounds. This is however not the case when it comes to desalination – the technology for producing fresh water from seawater; quite the opposite actually. While sodium and chloride are removed effectively, other, much larger contaminants pass through the filtration materials that are typically used. That indicates there must be another mechanism at work here.

>Read more on the MAX IV Laboratory website

Students use AI for sample positioning at BioMAX

The samples at BioMAX beamline are very sensitive biomolecule crystals. It could, for example, be one of the many proteins you have in your body. They only last for a short time in the intense X-ray light before being damaged and needs to be placed exactly right before the researchers switch on the beam. In their masters’ project, Isak Lindhé, and Jonathan Schurmann have used methods of artificial intelligence to train the computer how to do it.

Hundreds of thousands of proteins
You have hundreds of thousands of different proteins in your body. They do everything from transporting oxygen in your blood to letting your cells take up nutrients after you’ve eaten or make your heart beat. And when things go wrong, you get prescribed medication. The pharmaceutical molecules connect to the proteins in your body to change how they work. To develop new pharmaceuticals with few side effects, the researchers, therefore, need to understand what different proteins look like in detail.

A tedious task
To get high-quality data from a sample it needs to be correctly positioned in the X-ray beam. The conventional model for finding the right position is to scan the sample in the beam to optimize the position. At MAX IV, the X-ray light is very intense, which is good because smaller crystals can be used. But at the same time, very often the sample can’t be scanned in the beam since it would be damaged long before the right position is found. The researchers, therefore, have to perform the rather tedious task of positioning it manually.

>Read more on the MAX IV Laboratory website

First commissioning results for insertion devices published

The intense X-ray light for each of the MAX IV beamlines is generated when fast electrons fly through an array of magnets, placed in a so-called insertion device.

In a recent report, our insertion device team present the commissioning results for the first nine of these beamline specific instruments.
At synchrotrons like MAX IV, we accelerate electrons to velocities close to the speed of light. The electrons are injected into storage rings where they travel turn after turn inside a vacuum tube, guided by the strong forces of hundreds of carefully tuned magnets. At certain places along the electron path, the magnets are arranged in arrays called insertion devices that make the electrons wiggle from side to side as they fly through. When the electrons perform this motion, they emit energy in the form of intense X-rays. Each beamline needs its dedicated insertion device, built to produce X-rays optimised for the measurement techniques performed there.
The insertion device team have now published the first commissioning results. At the time the report was written, twelve insertion devices were installed, and nine successfully commissioned to deliver according to specifications. Six of them have been built in-house, and two are transferred from the old MAX-lab and refurbished. The remaining insertion devices come from Hitachi and our French synchrotron colleague SOLEIL.

>Read more on the MAX IV Laboratory website

Towards upscaling the production of graphene nanoribbons for electronics

Two-dimensional sheets of graphene in the form of ribbons a few tens of nanometers across have unique properties that are highly interesting for use in future electronics.

Researchers have now for the first time fully characterised nanoribbons grown in both the two possible configurations on the same wafer with a clear route towards upscaling the production.
Graphene in the form of nanoribbons show so called ballistic transport, which means that the material does not heat up when a current flow through it. This opens up an interesting path towards high speed, low power nanoelectronics. The nanoribbon form may also let graphene behave more like a semiconductor, which is the type of material found in transistors and diodes. The properties of graphene nanoribbons are closely related to the precise structure of the edges of the ribbon. Also, the symmetry of the graphene structure lets the edges take two different configurations, so called zigzag and armchair, depending on the direction of the long respective short edge of the ribbon.

See some video interviews and the entire article on the MAX IV website

Biological material discovered in Jurassic fossil

Ichthyosaurs were reptiles that roamed the Jurassic oceans 180 million years ago. They are extremely well studied and the form will probably be instantly recognisable from museums and textbooks. They resemble modern toothed whales such as dolphins and this similarity led researchers to hypothesise that the two creatures had similar strategies for survival in the marine environment. However, until now, there was little evidence to support this hypothesis. The research team led by Lund researcher Johan Lindgren went on the search for biological material within fossils to help solve this puzzle. After a lot of preparation in the lab and traveling around the world to perform experiments, they discovered that the fossil contained remnants of smooth skin and subcutaneous blubber. This is compelling evidence that the Ichthyosaurs were indeed warm-blooded and confirms the previous hypothesis. Lindgren showed visible delight when he described how you could see that the 180-million-year-old blubber was indeed visibly flexible after treatment in his laboratory.

>Read more on the MAX IV Laboratory website

Image: MAX IV’s Anders Engdahl was part of a team that published a landmark study about biological tissue found in a Jurassic fossil. The work published this week in Nature is one of the most comprehensive studies of its kind and sheds new light on the life of a prehistoric sea creature.

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

 

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.

The search for clean hydrogen fuel

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.

>Read more on the MAX IV Laboratory website

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

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.

>Read more on the MAXIV Laboratory website