What role does Elongator play in brain development?

What role does a tRNA modification complex, called Elongator, play in brain development?

SOLARIS Centre users from the Malopolska Centre of Biotechnology (of the Jagiellonian University, together with Australian, Turkish and Canadian colleagues, have found a link between defects in the cellular protein production machinery and neurodevelopmental disorders (NDDs), characterized by an inability to reach cognitive and motor milestones. Key studies in this publication were conducted using Cryo-EM microscopes located at our center.

The speed rate of protein synthesis is crucial to the integrity of the proteome

Scientists showed how genetic mutations in patients affect the Elongator activity and lead to severe clinical symptoms. The study provided the first clinical evidence for missense mutations in the Elongator accessory subcomplex ELP456 to cause neurodevelopmental disorders. Genome-wide analysis allowed identification of pathogenic variants in patients with severe clinical presentation of NDDs. Further modelling of the patient-derived mutations in mice resembled the complex neurodevelopmental phenotype and revealed neuron-specific consequences of the found genetic mutations.

We report patient-derived substitutions in the accessory ELP456 subcomplex to affect different types of neurons than previously known mutations in the catalytic core of the complex” – explains Dr. hab. Sebastian Glatt, the senior author and head of the Max Planck Research Group, that carried out the experimental work in Krakow. This provides a novel concept in the field that depletion of specific tRNA modifications in patient cells may induce specific changes in the cellular proteomes.

Read more on the SOLARIS website

Arranging gold nanoparticles precisely in three dimensions

Metal nanoparticles have a wide variety of applications many of which stem from the fact that extremely small particles a few nanometres to  10’s of nanometres in diameter can have very different properties from those of the same material at a larger scale (a nanometre is just a billionth of a metre). Such particles are used as catalysts, coloring agents and can even  make antibacterial coatings. Some effects are due to the pattern of the particles and the spacing between them, but these are very difficult to control and particles are typically used in solution where they randomly move around like motes of dust in the air.   

In the current work, scientists based at the Bionanoscience and Biochemistry Laboratory at the Malopolska Centre of Biotechnology (MCB), Jagiellonian University showed that an artificial protein structure, a hollow sphere called a TRAP-cage, was able to act as a scaffold and provide regular-spaced points of attachment for small gold nanoparticles. “TRAP-cage is itself tiny, but at around 15 nm in diameter is still big enough to attach multiple  gold nanoparticles” explained Jonathan Heddle the head of the lab, “The protein cage is made of 12 rings, so overall it looks a little like a 12-sided dice – a dodecahedron.”  The researchers showed that there are spaces equivalent to the corners of the dodecahedron that offer just the right environment to snugly fit the gold nanoparticles inside. As a result, instead of randomly floating around, the particles appear to be constrained into a fixed three-dimensional pattern. It is hoped that the ability to arrange metal nanoparticles in this way may be developed further to produce new materials with useful properties.

Read more on the SOLARIS website

Image: The structure of the protein cage (purple) with three of the embedded gold nanoparticles highlighted (yellow) 

Credit: Jonathan Heddle

New techniques available at SOLARIS synchrotron

From 2022, National Synchroton Radiation Center SOLARIS provides access to two new research techniques. Access to the Scanning Transmission X-ray Microscope and X-ray Absorption Spectroscopy beamline optimized for measurements in the soft and tender energy range, will be possible in the next call for proposals, in March 2022.

Scanning transmission X-ray microscopy (STXM) is a method to obtain a microscopic image of the raster-scanned sample by detecting the transmission intensity of the focused X-rays. The STXM is one of the two end stations of the DEMETER beamline in NSRC SOLARIS. The operating principle of the STXM is scanning of the sample in the focus of the Fresnel zone plate, which for this device is the lens focusing X-rays. In the next step, the detector measures the intensity of the radiation passing through the sample and, on the basis of the intensity images recorded by the detector, it is possible to calculate the absorption X-ray radiation in a selected place of the tested system. The most important measurement mode in STXM is the so-called “image stack” – a series of images are collected as a function of photon energy to obtain a dataset with space (XY) and energy (E) dimensions. A local absorption spectrum can be obtained from the arbitrary region of interest at the image. It allows a detail chemical composition analysis of a measured sample. The source for the STXM end station is elliptically polarized undulator, which enables to cover the energy range from 100 to 2000 eV. The undulator allows measurements using linear, circular and elliptical polarization. Detailed information about the STXM end station you can find here: https://synchrotron.uj.edu.pl/en_GB/linie-badawcze/demeter/STXM.

X-ray Absorption Spectroscopy beamline – SOLABS is a bending magnet beamline dedicated to X-ray absorption spectroscopy (XAS) in the energy range from 1 keV to 15 keV. The beamline was especially designed for XAS measurements in the tender X-ray range, i.e., at the K absorption edges of important elements such as P, S, Si, Al and Mg. Besides, the energy range also includes K-edges of heavier elements up to Se, L-edges of elements up to Bi and some M-edges of elements including U, which allows investigation of a variety of highly relevant materials. Due to this straightforward concept without any optical components such as lenses or mirrors, SOLABS can be quickly aligned and easily operated.  At the beamline spectroscopic experiments in different measurement modes and with various sample environments are possible. XAS is a non-destructive, element-specific characterization method that can be applied to both crystalline and amorphous materials, liquids and samples in the gas phase. Detailed information about the SOLABS beamline and the features of its end station can be found here: https://synchrotron.uj.edu.pl/en_GB/linie-badawcze/solabs

Agnieszka Cudek

The Head of Communication, SOLARIS National Synchrotron Radiation Centre

To apply for beamtime, please visit the SOLARIS website

A welcoming and friendly community awaits!

Challenges are part of daily life at a synchrotron. In his #LightSourceSelfie, Tomasz talks about the importance of flexibility and how teams work together, adjusting to overcome challenges and get things done. When describing the synchrotron community, Tomasz says, “I think it is one of the most welcoming and friendly communities I have ever met.” Tomasz is driven by curiosity and the need to help others. He says, “Light sources are a nice combination of both because I can actually help people to solve their problems, their interesting scientific problems, and this gives me the everyday fulfilment.”

After over a decade working in infrared spectroscopy, Tomasz is excited that SOLARIS now has funding to construct an infrared beamline that will allow scientists to do cutting edge infrared imaging experiments of cells and tissues primarily for cancer diagnostics and understanding of biological systems.

To find out more about SOLARIS, visit https://lightsources.org/lightsources-of-the-world/europe/synchrotron-solaris/

Science Advances cover dedicated to research results on Cryo-EM

The research carried out at NCPS SOLARIS with the use of electron cryomicroscopy and at the Malopolska Biotechnology Centre, and at the British National Electron Bioimaging Center eBIC (Diamond Light Source) allowed to solve the structure of the protein responsible for introducing compounds necessary for the life of bacterial cells. The exceptional importance of the research was honored with a dedicated, unique image by Alina Kurokhtina published on the cover of Science Advances!

Bacterial species are under continuous warfare with each other for access to nutrients. To gain an advantage in this struggle, they produce antibacterial compounds that target and kill their competitors. Different species of bacteria, including ones that live inside us, can battle each other for scarce resources using a variety of tactics. Now, researchers from the laboratories of Prof Jonathan Heddle from Malopolska Centre of Biotechnology, Jagiellonian University, Krakow and Dr Konstantinos Beis at Research Complex at Harwell /Imperial College, London, have uncovered the mechanism of one such tactic in work that may eventually lead to the development of new antibacterials.

Read more on the SOLARIS website

Image: A view of the determined SbmA structure in gold

Credit: Alina Kurokhtina

Retrovirus research using Cryo-EM

Reverse transcription involves the conversion of single-stranded RNA to double-stranded DNA. This is a key step in the replication of retroviruses, catalyzed by the enzyme reverse transcriptase. Retroviruses are divided into two subfamilies, one of which, Spumaretrovirinae, has a different proliferation cycle and a different reverse transcriptase domain structure. The presented studies provide the first structural description of the nucleic acid binding by viral reverse transferase, demonstrating its ability to change the oligomeric state depending on the type of bound nucleic acid.

Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA, a crucial process for the replication of retroviruses. Foamy viruses (FV) possess a unique RT which is a fusion with the protease (PR) domain. The mechanism of substrate binding by this enzyme has been unknown. The authors report a crystal structure of monomeric full-length marmoset FV (MFV) PR-RT in complex with an RNA/DNA hybrid substrate. Moreover, the describtion of a structure of MFV PR-RT with RNase H deletion in complex with a dsDNA substrate in which the enzyme forms an asymmetric homodimer has been presented. Cryo-electron microscopy reconstruction of full-length MFV PR-RT – dsDNA complex confirmed the dimeric architecture. These findings represent the first structural description of nucleic acid binding by a foamy viral RT and demonstrate its ability to change its oligomeric state depending on the type of bound nucleic acid. 

Read more on the SOLARIS website

Image: Model of FV

New insights into the photochemical activity of titanium dioxide

Not so many compounds are as important to industry and medicine today as titanium dioxide (TiO2). The electronic structure of transition metal oxides is an important factor determining the chemical and optical properties of materials. Specifically for metal-oxide structures, the crystal-field interaction determines the shape and occupancy of electronic orbitals. Consequently, the crystal-field splitting and resulting unoccupied state populations can be foreseen as modeling factors of the photochemical activity. The research on titanium dioxide inaugurated the presence of IFJ PAN scientists in research programs carried out at the SOLARIS synchrotron. The measurements, co-financed by the National Science Center, were carried out at the XAS beamline.

In many chemical reactions, TiO2 appears as a catalyst. As a pigment, it occurs in plastics, paints, and cosmetics, while in medical implants, it guarantees their high biocompatibility. A group of scientists from the Institute of Nuclear Physics of the Polish Academy of Sciences (IFJ PAN) in Krakow, led by Dr. Jakub Szlachetka, engaged in research on the oxidation processes of the outer layers of titanium samples and related changes in the electronic structure of this material. Scientists from the IFJ PAN conducted their latest measurements, co-financed by the National Science Center, at the XAS beamline. They analyzed how X-rays are absorbed by the surface layers of titanium samples previously produced at the Institute under carefully controlled conditions.

Read more on the SOLARIS website

Scientist from the SOLARIS team awarded with the prestigious ERC Grant

Dr Sebastian Glatt the member of SOLARIS Team and the researcher from Małopolska Centre of Biotechnology (MCB) of the Jagiellonian University has received the ERC Consolidator Grant worth almost 2 million euro. His research will contribute to the better understanding of molecular mechanisms behind the fundamental processes of high clinical relevance, which shape and control the functioning of cellular protein in all living organisms.

Since 2008, the European Research Council (ERC) has been awarding grants for ground-breaking research conducted in the European Union member states and associated countries. The ERC consolidator grant has been addressed to experienced and  deserved researchers. The recently published list of this year’s Consolidator Grant winners comprises 327 researchers from 23 European countries, who will receive 655 million euro in total. Three of the winning projects will be carried out at Polish universities: the AGH University of Science and Technology in Kraków, the University of Warsaw and the Jagiellonian University. The last one is represented by the project “Deciphering the role of RNA modifications during ribosomal decoding and protein synthesis” by Dr Sebastian Glatt. This is the first grant of the European Research Council in the field of life sciences, which received a researcher from the Jagiellonian University.

Read more on the SOLARIS website

Image: Dr Sebastian Glatt with colleagues in the lab


PHELIX beamline is ready to research

Synchrotron light has finally been observed for the first time on a sample at the end station of the experimental beamline PHELIX. This success is the crowning achievement of three years of hard work designing, constructing, fitting, and tuning its components to the synchrotron beam.   

The installation of this new beamline began in mid-2018. In March of 2020, the final elements were delivered. Then on 18th September 2020, the scientific supervisors of beamline, Dr. Magdalena Szczepanik – Ciba and Tomasz Sobol, announced readiness for test experiments using the synchrotron beam.  

The first results testing the capabilities with the active beam of the analyser at the PHELIX end station were performed using the sample of gold in the presence of a specialist from the SPECS company, Dr. Robert Reichelt. As  a result of testing this calibration material, among others, the XPS Au4f spectrum was acquired (see pic.1). Additionally, an angle – resolved and spin – resolved measurements were performed .

During the latest open call for the beamtime the applications on the PHELIX beamline where included for the first time. This line will use soft X-ray radiation. The end-station will enable a wide range of spectroscopic and absorption researches, characterised by different surface sensitivity. Besides acquiring standard, high-resolution spectra, it will allow e.g. for the mapping of band structure in three dimensions and for the detection of spin in three dimensions.  

Users will thus be able to conduct research on new materials, thin films, and multi-layer systems, catalysers and biomaterials, as well as research on solids, on spin-polarised surface states, and on chemical reactions taking place on the surface.

Read more on the SOLARIS website

Image:  From left Tomasz Sobol, Dr. Robert Reichelt, Dr. Magdalena Szczepanik – Ciba. Credit – Solaris

Expansion of SOLARIS experimental hall

The SOLARIS Centre has been awarded by the Ministry of Science and Higher Education a grant for the expansion of the experimental hall. This long-awaited decision opens up new perspectives for the development of the Centre.

The area of ​​the synchrotron hall will be increased by over two thousand square meters. This space will enable the construction of four new beamlines, which require a long distance of the sample from the synchrotron radiation source. These new facilities include the SOLCRYS beamline for the structural research. The beamline end stations will enable analyses of the structure of proteins, viruses, nucleic acids, and polymers. These studies provide knowledge on the molecular structure of the basic building blocks of living organisms, including the architecture of macromolecules. Research carried out on the beamline will be used, among others, in biological sciences, medicine (drug design and discovery), chemistry, and materials science. SOLCRYS will be the only research infrastructure of this type not only in Poland, but also in the entire Central and Eastern Europe.

Read more on the SOLARIS website

Image: Visualisation of the new building.

PHELIX beamline – delivery of analyzer and spin detector

On July 22, 2020, the last components of the PHELIX end station were delivered to SOLARIS. The delivery included a high-resolution hemispherical photoelectron energy analyzer and a VLEED spin detector.

The PHELIX end station will be exceptional: it will allow scientists to perform circular dichroism measurements (CD-ARPES) and provide direct insights into the spin texture of electron states (SP-ARPES) in the same UHV system and for the same sample. Both of these methods give information about the electron spin, but the interpretation of the CD-ARPES results alone can be challenging. However, the combination of these two methods has a number of advantages allowing for the better understanding of the systems, as it excludes differences in quality between samples and the risk of surface contamination when transferring the sample between experimental systems. Both of these factors significantly affect the obtained results, and the limited control over them reduces the reliability of the research. To our knowledge, the PHELIX beamline will be one of the very few facilities in the world where such combined measurements can be performed.

Read more on the SOLARIS website

Faster diagnosis of esophageal cancer

Scientists from SOLARIS National Synchrotron Radiation Centre (Kraków, Poland), University of Exeter (UK), Beckman Institute (University of Illinois at Urbana-Champaign – USA), and Institute of Nuclear Physics Polish Academy of Sciences (Kraków, Poland) performed research that will facilitate the rapid and automated diagnosis of esophageal cancer.

Dr. Tomasz Wróbel`s group focuses on cancer detection through a combination of Infrared Imaging (IR) and the use of Machine Learning (ML) algorithms. Thanks to this approach, it is possible to develop an effective model, which will allow histopathologists to confirm the diseased area automatically and in a much shorter time.

Infrared Imaging (IR), which will soon also be available on the newly built beamline at SOLARIS, has found widespread use in biomedical research over the last couple of decades and is currently being introduced into clinical diagnostics.

Read more on the Solaris website

Image: The above graphic shows two esophageal biopsies: the top of the graphic contains a biopsy taken from a patient suffering from esophageal cancer, the bottom of the graphic contains a biopsy taken from a healthy patient. In the left part of the graphic, microscopic images of the mentioned biopsies are visible after the H&E staining (Hematoxylin and Eosin) (in this image of the stained biopsy, the histopathologist visually assigns tissue types), in the middle of the graphic, biopsy images obtained using infrared imaging are visible, the right part of the graphic presents a histological picture of a biopsy obtained after assigning tissues and structures to three classes (cancer, other, benign) by Machine Learning (ML).

Red – cancer
Blue – other
Green – benign

Cryo-electron microscopy for industry coming soon to SOLARIS

The SOLARIS Centre and the Malopolska Centre of Biotechnology (Jagiellonian University) won a two-stage competition for the purchase of an electron microscopy for industrial research.

Funding was awarded by the National Information Processing Institute (OPI PIB) as part of the EU’s Smart Growth Operational Programme.

“We have been trying to purchase a microscope because Polish companies keep asking us about the possibility to carry out measurements using the Cryo-EM technique” – says Michał Młynarczyk, Finance and Administration Deputy Director at SOLARIS. “We expect that the total time allocated for the commercial study will be at least 40% of operational time. The remaining time will be available for academic researchers” –  continues the director.

“We are keen to enable Polish companies to access this exciting new technology, which is developing very fast and is currently becoming the most important one used in structural biology. The achievable results facilitate to understand the cellular mechanisms behind human diseases, the design of new drugs, the optimization of existing drug molecules. The technique is also successfully applied in nanotechnology and other fields” – adds Sebastian Glatt, Max Planck Research Group leader at the Malopolska Centre of Biotechnology – the main partner of SOLARIS in the implementation of this project.

>Read more on the SOLARIS website

Electronics of future: magnetic properties of InSb-Mn

The recent volume of “ACS Nano Letters” presented the results of research conducted at the SOLARIS National Synchrotron Radiation Centre and at the Academic Centre for Materials and Nanotechnology of the University of Science and Technology in Kraków.

The research was led by Dr Katarzyna Hnida-Gut and demonstrated that the magnetic properties of indium antimonide nanowires with an addition of manganese (InSb-Mn) can be controlled by the concentration of the dopants. The ground-breaking aspect of this research was that for the first time in the pulse electrosynthesis process in AAO pores (anodic aluminium oxide) high quality InSb-Mn nanowires were obtained, making use of previously determined optimum conditions for the synthesis of the semiconductor indium antimonide.

Some of the measurements conducted as part of the research project were performed using synchrotron radiation at the SOLARIS Centre in Kraków. Thanks to an experiment conducted on PEEM/XAS beamline, it was possible to determine the local structure in the vicinity of manganese atoms. This allowed for the confirmation of the hypothesis that “the manganese atoms in the studied nanowires form small clusters, such as Mn3. It is precisely these clusters that are the source of the magnetic response at room temperature,” explains Dr. Marcin Sikora, one of the co-authors of the paper.

>Read more on the SOLARIS website

New beamlines at SOLARIS

Environmental protection, nanotechnology, diagnosis of diseases, and even samples of cosmic dust – these are only some of directions in research that will be performed soon thanks to the decision of the Ministry of Science and Higher Education to finance the construction of two new beamlines and  end station at the SOLARIS synchrotron in Kraków.

The new research infrastructure, eagerly awaited by the Polish scientific community, includes:

  • a beamline for infrared spectroscopic studies (FTIR)
  • a beamline for multimodal X-ray imaging (POLYX)
  • a scanning transmission X-ray end station (STXM).

The main research conducted on the FTIR beamline will focus on biomedical aspects, from in vitro  (conducted on cell cultures in laboratory conditions) to ex vivo experiments (on tissues or cells collected from living bodies), in the range of basic research, developing new analytical technologies and diagnostics.

>Read more on the SOLARIS website

PHELIX beamline – undulator installation and hutch construction

The PHELIX beamline construction continues. In October 2018 the light source for the beamline – an undulator – was installed in the storage ring. In November construction of the an optical hutch ended.

The hutch will protect people from radiation hazards. In the near future it will house the first optical components of the beamline.
The next planned steps are the installation of the front-end, i.e. the part of the beamline situated in the storage ring tunnel after the source (January 2019), the installation of the beamline with optical components for X-rays (February-March 2019) and the installation of the end-station (May-June 2019).

The PHELIX beamline will use soft X-rays. Its end station will enable a wide range of spectroscopic and absorption studies characterized by different surface sensitivity. In addition to collecting standard high-resolution spectra, it will allow, for example, to map the band structure in three dimensions and to detect electron spin in three dimensions. Users will, therefore, be able to conduct research on new materials, thin films and multilayers systems, catalysts and biomaterials, surface of bulk compounds, spin polarized surface states, as well as chemical reactions taking place on the surface.

>Read more on the SOLARIS website

Image credit: Agata Chrześcijanek