cells – Lightsources.org

Bringing cryo-correlative hard X-ray microscopy to life science

2026/02/272026/03/11

Scientists led by the ESRF, UGA and INSERM have developed cryo-correlative nano-imaging, a new technique that combines lab cryo-fluorescence microscopy, cryo X-ray fluorescence nanoimaging and phase-contrast nano-tomography on ID16A. The results are published in ACS Nano.

Biologists have long wanted to answer a deceptively simple question: what are the structures we see inside cells actually made of? Visible light fluorescence microscopy shows where organelles are, but not their chemical composition. Hard X-rays can map the chemistry but do not necessarily see the organelles. Cryo-correlative nanoprobe work remains rare, particularly for 3D elemental imaging of whole frozen cells.

A new study at ID16A beamline of the ESRF offers a practical solution. An international team has developed an integrated cryogenic workflow that links laboratory cryo-fluorescence microscopy to targeted cryo X-ray fluorescence (XRF) nano-imaging and phase-contrast nano-tomography.

With this new method, they have tracked therapeutic nanoparticles from the European ScanNtreat project as they moved through cancer cells, showing both where the particles went and what happened to them.

The first author of the publication, Dmitry Karpov, former ESRF scientist and now researcher at the Université Grenoble Alpes, explains how this new development can lead to applications: “This is an example of what the ESRF aims to do: to turn cutting-edge instrumentation into discoveries with direct impact on people’s lives, in this case for medicine and life sciences”.

Read more on the ESRF website

MCB JU researchers discovered a mechanism regulating the essential process of hypusination

2024/10/302024/10/30

A research team from the Malopolska Centre of Biotechnology at Jagiellonian University (MCB UJ), led by dr hab. Przemysław Grudnik, in collaboration with scientists from the Medical College of Wisconsin, has uncovered an unusual role of the ERK1/2 kinases in the regulation of a unique post translational modification, hypusination. This breakthrough not only bridges a gap in our understanding of the mechanisms controlling hypusination, an essential process for the human body, but also reveals a surprising function of ERK1/2. These findings have recently been published in the scientific journal “Cell Reports”.

Hypusination is a highly specific modification of eukaryotic translation factor 5A (eIF5A), and deoxyhypusine synthase (DHPS) is responsible for catalyzing the first and limiting step of this process. Hypusination enables eIF5A to facilitate the synthesis of other proteins in the cells, which is a fundamental process. Despite its critical function in cellular homeostasis, the regulation of hypusination remains elusive. Researchers at MCB have started to unravel the mechanisms controlling hypusination and have shown the new unexpected finding that the extracellular signal regulated kinases 1/2 (ERK1/2) perform a non kinase function by directly interacting with DHPS to regulate hypusination. ERK1/2 are key enzymes in a signaling pathway, which is crucial in regulating cell growth, differentiation, and cell survival in human bodies. Until now, these proteins have been studied for their enzymatic (kinase) activity, which allows them to activate other proteins through phosphorylation (adding phosphate groups).

Researchers at MCB employed cryo-electron microscopy (cryo EM) to study the structure of the DHPS ERK2 complex. The data revealed that ERK2 binds to DHPS at the entrance to its active site, effectively blocking access for eIF5A. The findings also highlight how cellular signaling via the Raf/MEK/ERK pathway modulates ERK1/2 association with DHPS. When this pathway is activated, the interaction between ERK1/2 and DHPS decreases, allowing eIF5A to be hypusinated. Moreover, ERK1/2’s kinase activity controls how much DHPS and eIF5A the cell produces. This discovery provides fresh insights into how cells regulate essential processes such as protein synthesis in response to external signals.

Read more on the SOLARIS website

Image: Dr hab. Przemysław Grudnik (on the right) and Paweł Kochanowski (on the left) are holding a model of the DHPS-ERK2 complex.

New Oxygen-Reduction Electrocatalysts for Alkaline Fuel Cells

2024/08/122024/08/19

Hydrogen fuel cells are among the most promising next-generation power sources for future automotive transportation. Developing efficient, durable, and low-cost electrocatalysts to accelerate the sluggish oxygen reduction reaction (ORR) is urgently needed to advance fuel cell technologies.Now, in a new paper appearing in the Journal of the American Chemical Society, a team of researchers from Cornell and the University of Wisconsin report new catalysts which exhibit superior ORR activity and robust stability. The team has characterized metal–organic framework-derived nonprecious dual metal single-atom catalysts (SACs), consisting of Co–N₄ and Zn–N₄ local structures. Their remarkable performance was validated under realistic fuel cell working conditions, achieving a record-high peak power density of ∼1 W cm^–2 among the reported SACs for alkaline fuel cells. Operando X-ray absorption spectroscopy studies at the PIPOXS beamline at CHEXS revealed that the Co atom in the Co–N₄ structure is the main catalytically active center. This work provides a comprehensive mechanistic understanding of the active sites in the Zn/Co–N–C catalysts and will pave the way for the future design and advancement of high-performance single-site electrocatalysts for fuel cells and other energy applications.

Read more on CHESS website

Image: Isolated Zinc and Cobalt atoms on a metal-organic-framework scaffold occupy local environments which are coordinated by 4 Nitrogen atoms. Using x-ray spectroscopy inside operating hydrogen fuel cells, the Cornell/Wisconsin team (with then-PhD-student Weixuan Xu as first author) were able to directly observe that specifically the Co-N₄ sites were responsible for highly efficient catalysis of the oxygen reduction reaction. As oxygen bonds to a Co-N₄ site, the Co XANES edge shifts to higher energy, providing a clear fingerprint for the reaction mechanism.

Detection of early pancreatic cancer lesions using infrared and machine learning

2024/01/292024/02/01

A group of researchers from the CIRI beamline in their latest publication entitled Pancreatic intraepithelial neoplasia detection and duct pathology grading using FT-IR imaging and machine learning published in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy presented the results of their PanIN classification method, which provides opportunities for early recognition of changes in the cells lining the pancreatic ducts using infrared and machine learning.

Pancreatic intraepithelial neoplasia (PanIN) manifests itself by changes in the cells lining the pancreatic ducts. It is an early pre-cancerous lesion divided into low-grade and high-grade PanIN. In particular, high-grade PanIN is a lesion that often leads to Pancreatic ductal adenocarcinoma (PDAC). In the case of pancreatic cancer, due to the lack of characteristic symptoms of the disease in its early stage, patient survival is low. The basic examination performed to diagnose the disease is to take a fine-needle biopsy from the patient. The most common method of treatment is to remove part of the tissue affected by cancer, which increases the patient’s chances of survival, especially if it is done at an early stage of the disease. Therefore, it is so important to understand the biochemistry of lesions such as PanIN and their progression to cancer.

Read more on SOLARIS website

Image : Scheme of sample collection (figure upper part), and FT-IR imaged TMA processing using: Random Forest classification (figure middle part), PLS Regression (figure bottom part).

New insights into what happens in cells in early Alzheimer’s

2023/12/142023/12/14

Researchers led by the ESRF, the European Synchrotron, have found that amyloid oligomers play a role in speeding up mitochondrial energetics during the early stages of Alzheimer’s, in contrast to what has been previously found in more advanced Alzheimer’s brain tissues.

The origin of Alzheimer’s disease, which affects 30 million people worldwide, is still not clear despite an international research effort and significant progress in research. And yet, identifying the factors driving this incurable neurodegenerative disease is essential to find better ways to diagnose Alzheimer, delay its onset and prevent progression. “Before understanding the pathology, we need to understand the biology”, explains Montse Soler López, head of the Structural Biology group at the ESRF and co-corresponding author of the study.

Alzheimer’s is an incurable disease that normally appears after the age of 65. However, changes in the brain begin 20 years before the disease appears. “We believe that malfunctioning of the mitochondria can take place 20 years before the person shows symptoms of the disease”, explains Soler López. For a long time, researchers have focused on the amyloid plaques in the brain as the potential cause of the disease. However, this hypothesis is currently being reconsidered.

Now Soler López’s team, together with scientist Irina Gutsche at the Institut de Biologie Structurale (CNRS, CEA, Université Grenoble Alpes) and researchers at the EMBL, conduct a new line of research focusing on aging factors, such as mitochondrial dysfunction. Mitochondria are often referred to as the “powerhouse of cell” because of their essential role in energy production. Over time, mitochondria suffer oxidative stress and this leads to their malfunction. A recent finding indicates that individuals with Alzheimer’s may exhibit an accumulation of amyloids within mitochondria, challenging the previously belief that amyloids were solely present outside neurons.

Read more on the ESRF website

Quantitative analysis of cell organelles with artificial intelligence

2023/07/182023/07/20

The analysis of cryo-X-Ray-microscopy data still requires a lot of time. Scientists developed a convolutional neural network, which identifies structures at high accuracy within a few minutes.

BESSY II’s high-brilliance X-rays can be used to produce microscopic images with spatial resolution down to a few tens of nanometres. Whole cell volumes can be examined without the need for complex sample preparation as in electron microscopy. Under the X-ray microscope, the tiny cell organelles with their fine structures and boundary membranes appear clear and detailed, even in three dimensions. This makes cryo x-ray tomography ideal for studying changes in cell structures caused, for example, by external triggers. Until now, however, the evaluation of 3D tomograms has required largely manual and labour-intensive data analysis. To overcome this problem, teams led by computer scientist Prof. Dr. Frank Noé and cell biologist Prof. Dr. Helge Ewers (both from Freie Universität Berlin) have now collaborated with the X-ray microscopy department at HZB. The computer science team has developed a novel, self-learning algorithm. This AI-based analysis method is based on the automated detection of subcellular structures and accelerates the quantitative analysis of 3D X-ray data sets. The 3D images of the interior of biological samples were acquired at the U41 beamline at BESSY II.

“In this study, we have now shown how well the AI-based analysis of cell volumes works, using mammalian cells from cell cultures that have so-called filopodia,” says Dr Stephan Werner, an expert in X-ray microscopy at HZB. Mammalian cells have a complex structure with many different cell organelles, each of which has to fulfil different cellular functions. Filopodia are protrusions of the cell membrane and serve in particular for cell migration. “For cryo X-ray microscopy, the cell samples are first shock-frozen, so quickly that no ice crystals form inside the cell. This leaves the cells in an almost natural state and allows us to study the structural influence of external factors inside the cell,” Werner explains.

“Our work has already aroused considerable interest among experts,” says first author Michael Dyhr from Freie Universität Berlin. The neural network correctly recognises about 70% of the existing cell features within a very short time, thus enabling a very fast evaluation of the data set. “In the future, we could use this new analysis method to investigate how cells react to environmental influences such as nanoparticles, viruses or carcinogens much faster and more reliably than before,” says Dyhr.

Image: The images show part of a frozen mammalian cell. On the left is a section from the 3D X-ray tomogram (scale: 2 μm). The right figure shows the reconstructed cell volume after applying the new AI-supported algorithm

Credit: HZB

Understanding how motor proteins shape our cells

2022/08/092022/08/11

Understanding the busy networks inside our cells can help researchers develop new cancer treatments and prevent dangerous fungal infections.

With the help of the Canadian Light Source (CLS) at the University of Saskatchewan, a research team led by John Allingham from Queen’s University and Hernando Sosa from the Albert Einstein College of Medicine has shed light on a protein that regulates the intricate microscopic networks that give cells their shape and helps ship important molecules to diverse locations.

Using the CMCF beamline at the CLS and the cryo-EM facility at the Simons Electron Microscopy Center (SEMC) at the New York Structural Biology Center, the team found the missing pieces of an important puzzle.

In their published work, they are the first group to clearly describe the mechanism of action of a tiny motor protein called Kinesin-8 that enables it to control the structures of microtubule fiber networks inside the cell.

Read more on the CLS website

Image: Cells, Canadian Light Source.

Safely studying dangerous infections just got a lot easier

2022/02/252022/03/17

An extremely fast new 3D imaging method can show how cells respond to infection and to possible treatments

To combat a pandemic, science needs to move quickly. With safe and effective vaccines now widely available and a handful of promising COVID-19 treatments coming soon, there’s no doubt that many aspects of biological research have been successfully accelerated in the past two years.

Now, researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) and Heidelberg University in Germany have cranked up the speed of imaging infected cells using soft X-ray tomography, a microscopic imaging technique that can generate incredibly detailed, three-dimensional scans.

Their approach takes mere minutes to gather data that would require weeks of prep and analysis with other methods, giving scientists an easy way to quickly examine how our cells’ internal machinery responds to SARS-CoV-2, or other pathogens, as well as how the cells respond to drugs designed to treat the infection.

“Prior to our imaging technique, if one wanted to know what was going on inside a cell, and to learn what changes had occurred upon an infection, they’d have to go through the process of fixing, slicing, and staining the cells in order to analyze them by electron microscopy. With all the steps involved, it would take weeks to get the answer. We can do it in a day,” said project co-lead Carolyn Larabell, a Berkeley Lab faculty scientist in the Biosciences Area. “So, it really speeds up the process of examining cells, the consequences to infection, and the consequences of treating a patient with a drug that may or may not cure or prevent the disease.”

Taking cellular freeze frames

Larabell is a professor of anatomy at UC San Francisco and director of the National Center for X-Ray Tomography, a facility based at Berkeley Lab’s Advanced Light Source (ALS). The facility’s staff developed soft X-ray tomography (SXT) in the early 2000s to fill in the gaps left by other cellular imaging techniques. They currently offer the SXT to investigators worldwide and continue to refine the approach. As part of a study published in Cell Reports Methods late last year, she and three colleagues performed SXT on human lung cell samples prepared by their colleagues at Heidelberg University and the German Center for Infection Research.

Read more on the Berkeley Lab website

Image: Digital images of cells infected with SARS-CoV-2, created from soft X-ray tomography taken of chemically fixed cells at the Advanced Light Source

Credit: Loconte et al./Berkeley Lab

How deadly parasites ‘glide’ into human cells

2020/10/262020/10/29

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

X-ray microscopy at BESSY II: Nanoparticles can change cells

2020/02/132020/02/13

Nanoparticles easily enter into cells. New insights about how they are distributed and what they do there are shown for the first time by high-resolution 3D microscopy images from BESSY II.

For example, certain nanoparticles accumulate preferentially in certain organelles of the cell. This can increase the energy costs in the cell. “The cell looks like it has just run a marathon, apparently, the cell requires energy to absorb such nanoparticles” says lead author James McNally.
Today, nanoparticles are not only in cosmetic products, but everywhere, in the air, in water, in the soil and in food. Because they are so tiny, they easily enter into the cells in our body. This is also of interest for medical applications: Nanoparticles coated with active ingredients could be specifically introduced into cells, for example to destroy cancer cells. However, there is still much to be learned about how nanoparticles are distributed in the cells, what they do there, and how these effects depend on their size and coating.

Image: 3D architecture of the cell with different organelles: mitochondria (green), lysosomes (purple), multivesicular bodies (red), endoplasmic reticulum (cream).
Credit: Burcu Kepsutlu/HZB

Structure and functional binding epitopes of VISTA

2019/09/302019/10/10

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 ligand^1,2 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).

ALBA collaborates in the discovery of a new muscular disease: myoglobinopathy

2019/03/272019/04/17

An international collaboration led by IDIBELL identifies the first disease caused by a mutation in myoglobin.

At the MIRAS beamline of the ALBA Synchrotron they could demonstrate the presence of oxidized lipids in the damaged muscle cells.
Researchers of the Bellvitge Biomedical Research Institute (IDIBELL) led by Dr. Montse Olivé have described in Nature Communications a new muscular disease caused by a mutation in the myoglobin gene. The study has been possible thanks to a collaboration with a group of geneticists from the University of Western Australia (UWA), led by Prof. Nigel Laing, and researchers from the Karolinska Institute (Stockholm, Sweden).

Myoglobin, the protein that gives muscles their red colour, has as its main function the transportation and intracellular storage of oxygen, acting as an oxygen reservoir when there are low levels (hypoxia) or a total lack thereof (anoxia). It also acts as scavenger of free radicals and other reactive oxygen species, avoiding cell damage due to oxidative stress.

>Read more on the ALBA website

Image: Left, Typical μFTIR spectra and their second derivative of the muscle tissue where the lipid region has been highlighted in orange and the protein region in blue; the inset shows the lipid/protein ratio (calculated from the Infrared spectra) on an optical image of a tissue section with sarcoplasmic bodies. The color bar represents intensity of the ratio: blue and red mean low and high lipid content, respectively. The scale bar is 4 microns. Right, Infrared second derivative spectrum of the amide region of one sarcoplasmic body (green) showing an increase of β-sheet structures indicating protein aggregation. Second derivative of the amide region corresponding to the tissue surrounding the sarcoplasmic bodies (black).

A step closer to early detection of multiple sclerosis

2019/03/082019/03/11

Synchrotron techniques identify the critical conditions that alter myelin structure

Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease resulting in the destruction of myelin, a fatty substance that insulates nerves and increases the speed at which signals travel between nerve cells. MS affects more than 2.3 million people worldwide and has no cure. In work recently published in PNAS, a team of researchers from Tel Aviv University and the Technion-Israel Institute of Technology mapped, for the first time, the delicate and complicated force balance between the myelin sheath constituents, and their effect on the myelin structure. This new information will allow the identification of critical components involved in neurodegenerative diseases such as MS.

Structural insights into tiny bacterial harpoons

2019/02/282019/03/07

Bacteria produce complex nano-harpoons on their cell surface. One of their functions is to harpoon and inject toxins into cells that are close by. Producing such a complex weapon requires lots of different moving components that scientists are still trying to understand. Researchers from the University of Sheffield have been using some of Diamond’s crystallography beamlines to understand a particularly enigmatic piece of this tiny puzzle. The team led by David Rice and Mark Thomas worked on a protein component of the harpoon called TssA which they already knew was an integral piece of the machinery. However, unlike the other components of the harpoon, there are distinct variants of the TssA protein that contain radically different amino acid sequences at one end of the protein. The team showed that the structures of the variable region of two different TssA subunits were completely unrelated and they could assemble into distinctly different multisubunit complexes in terms of their size and geometry. This begged the question as to how different bacteria could use this protein with different structures to produce a harpoon with the same function across all species. They found that despite these differences, there was a very specific conserved region at the other end of the protein. They hypothesise that the conserved region is the part that does the work and helps the harpoon to function whereas the variable region acts as a scaffold. They used I02, I03 and I24 in their study and plan to do follow up work using X-ray crystallography and Cryo-EM such as those at the eBIC centre at Diamond. The research was published in Nature Communications.

Image: Macromolecular Crystallography (MX) at Diamond reveals the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function.

A timely solution for the photosynthetic oxygen evolving clock

2019/01/252019/01/31

XFEL Hub collaboration reveals the intermediates of the photosynthetic water oxidation clock

A large international collaborative effort aided by the XFEL Hub at Diamond Light Source has generated the most detailed time-resolved studies to date of a key protein involved in photosynthesis. The pioneering work, recently published in Nature, shows how photosystem II harnesses light energy to produce oxygen – insights that could direct a next generation of photovoltaic cells.
>Read more on the Diamond Light Source website

Image: this figure is issued from a video you can watch here.

Know your ennemy

2018/12/212019/01/08

Light source identifies a key protein interaction during E. coli infection

Escherichia coli is a common source for contaminated water and food products, causing the condition known as gastroenteritis with symptoms that include diarrhea, vomiting, fever, loss of energy, and dehydration. In fact, for children or individuals with weakened immune systems, this bacterial infection in the gut can be life-threatening.

One of the microbes responsible for gastroenteritis, known formally as enteropathogenic E. coli (EPEC), causes infections by directing a pointed, needle-like projection into the human intestinal tract, releasing toxins that make people sick.

“Enteropathogenic E. coli can fire toxic proteins from inside the bacterium right into the cells of your gut lining,” says Dustin Little, a post-doctoral researcher in the Brian Coombes lab at McMaster University’s Department of Biochemistry and Biomedical Sciences.

Image: Dustin Little and Brian Coombes in the lab.
Credit: Dustin Little.