COVID-19 – Lightsources.org

Researchers visualise in 3D how SARS-CoV-2 replicates in cells

2023/11/142023/11/21

The use of different microscopy and tomography techniques, including synchrotron light, unveils how lung cells are modified along the infection in cell culture models. The work is the result of the European consortium CoCID (Compact Cell Imaging Device) with the participation of CSIC groups and the ALBA Synchrotron.

The covid-19 pandemic has affected more than 770 million people and has caused the death of nearly seven million people around the world. Its huge impact on health and global economy has promoted research in the field since 2020, although it is still necessary to understand how this infection makes progress with the aim of finding specific solutions to this pathogen. Now, a team from the Spanish National Research Council (CSIC) and the ALBA Synchrotron publishes in the journal ACS Nano the results obtained after three-dimensional analysis of the interior of an infected cell.

Members of the National Centre of Biotechnology (CNB-CSIC) and the ALBA Synchrotron, the only synchrotron light source in Spain located in Cerdanyola del Vallès (Barcelona), have imaged in three dimensions the interior of human lung epithelium cells, the primary target of the virus, and the severe structural changes caused by SARS-CoV-2 infection.

Pablo Gastaminza, CNB-CSIC researcher and main author of the work, explains the alterations they found: “when comparing an uninfected cell with an infected one, we can see that the virus multiplication machinery forms vesicles and tubules as well as remarkable signs of stress on cellular organelles such as mitochondria and the endoplasmic reticulum.”

The study is part of the collaboration established within the European CoCID (Compact Cell Imaging Device) consortium. It combines the use of molecular biology, virology and three types of microscopy techniques. One of them is the so-called soft X-ray cryo-tomography (Cryo-SXT), a technology available only in four places all over the world, including the MISTRAL beamline at the ALBA Synchrotron. This technique allows “to generate three-dimensional maps of the ultrastructure of complete cells, reconstructing their total volume and providing extra information to other techniques like electron microscopy,” according to Eva Pereiro, head of the MISTRAL beamline at ALBA.

Read more on ALBA website

Image: Three-dimensional images of a fragment of a control cell (left) and a cell infected with SARS-CoV-2 (right). The cell nucleus is highlighted in purple, healthy mitochondria in green, and mitochondria modified by the infection in red, the vacuoles in light blue, the viral factory in yellow and the viral particles in blue.

Credit: ALBA Synchrotron/CNB-CSIC

Funding for Diamond-II approved

2023/09/062023/09/06

The Department for Science, Innovation and Technology together with Wellcome, one of the world’s largest biomedical charities, today (Wednesday 6th September) announced approval for the innovative update and expansion programme to the UK’s national synchrotron, Diamond Light Source, at a total project cost of £519.4M. The investment will see 86% come from the UK Government and 14% from Wellcome, the same proportion that has funded Diamond from its beginning.

The full approval of the upgrade, Diamond-II, is part of a major investment drive in cutting-edge facilities to keep UK researchers and innovators at the forefront of discovery and help address global challenges.

Sir Adrian Smith, Chair of the Board of Diamond Light Source and President of the Royal Society comments:

We are delighted that the government and the Wellcome Trust have agreed this substantial investment in science infrastructure which will ensure the UK is at the forefront of world class science. This investment in Diamond-II will strengthen the UK’s global scientific leadership and confirms the UK’s commitment to building on the success Diamond has achieved so far.

Secretary of State for Science, Innovation and Technology, the Rt Hon Michelle Donelan MP, said:

Our national synchrotron may fly under the radar as we go about our daily lives, but it has been crucial to some of the most defining discoveries in recent history – from kickstarting Covid drug development that allowed us to protect millions of Britons to advancing treatment for HIV.

Our investment will ensure one of the most pioneering scientific facilities in the world continues to advance discoveries that transform our health and prosperity, while creating jobs, growing the UK economy and ensuring our country remains a scientific powerhouse.

The overall transformational Diamond-II upgrade will take several years of planning and implementation. This will include a “dark period” of 18 months during which there will be no synchrotron light for the user community, followed by a period to fully launch the new facility with three new flagship beamlines and major upgrades to many other beamlines.

Read more on the Diamond website

Image: Touring Diamond’s experimental hall during celebrations to mark the funding announcement for Diamond-II.
L to R: Dr Richard Walker, Technical Director and Senior Responsible Owner for Diamond-II, Beth Thompson MBE Chief Strategy Officer at Wellcome, Dr Adrian Mancuso, Diamond’s Physical Science Director, Prof Sir Dave Stuart, Diamond’s Life Sciences Director, Secretary of State for Science, Innovation and Technology, the Rt Hon Michelle Donelan MP, Sir Adrian Smith, Chair of the Board of Diamond, and Executive Chair of STFC Professor Mark Thomson.

Credit: Diamond Light Source

Treating COVID-19 by inhibiting viral replication

2023/01/312023/02/23

When SARS-CoV-2, the virus that causes COVID-19, enters a person’s cells, it hijacks those cells to make more viruses. First SARS-CoV-2 releases its RNA into the host cell. Then the host ribosomes translate the viral RNA into two giant protein chains (polyproteins). One protein in the giant chain, called MPro, cleaves the chain into smaller proteins, which help create more viruses and, therefore, more infection. Because of MPro’s role in initiating the viral replication process, the protein has become a target for antiviral drug developers. Recently, a team of scientists using high-brightness x-rays at the U.S. Department of Energy’s Advanced Photon Source (APS) has determined x-ray crystallographic structures of MPro cleaving the polyprotein at ten cleavage sites. Their findings, published in the journal Nature Communications, provide information about the mechanistic steps and molecular interactions that initiate viral replication, which can be used to inform antiviral therapeutic development for COVID-19, as well as other conditions for which MPro may be responsible.

Viruses can’t reproduce on their own; they need a human or animal cell to make other viruses and continue their infectious rampage. The SARS-CoV-2 virus, which causes COVID-19, employs its spike protein to enter a human cell. Once inside, the virus’s protective coating dissolves, and it dumps its genetic material—RNA—into the host cell. This RNA contains all the instructions the virus needs to replicate. What’s more, it comes in a handy form that is ready for a human cell to translate into proteins that will compose the next generation of viruses.

The SARS-CoV-2 RNA includes instructions for four proteins that make up the virus’s structure—its spike protein, protective coating, and the like—and sixteen proteins that replicate the virus. The replication process begins when the host’s ribosomes translate the replication genes into two gigantic protein chains called polyproteins.

Before replication can continue, however, these gigantic chains must be chopped up into their constituent proteins. Remarkably, the molecule that does the chopping is itself contained in the polyprotein and must hack its way out of the chain before attending to its neighbors.

Read more on the APS website

Image: Fig. 1. The amino acid residues preceding the SARS-CoV-2 polyprotein cleavage site between non-structural proteins nsp10 and nsp11 are shown in yellow. These residues are bound within the Mpro acceptor active site groove (grey semitransparent molecular surface).

Structural evidence that rodents facilitated the evolution of the SARS-CoV-2 Omicron variant

2022/12/192023/02/02

The omicron variant of COVID-19 was identified in the fall of 2021. It stood out from all of the other variants because of the many mutations that simultaneously occurred in its spike protein¹. So far, surveillance and bioinformatics have been the main scientific tools in tracking COVID-19 evolution. Eventually, however, understanding COVID-19 evolution comes down to understanding the functions of key viral mutations. This is where structural biology kicks in and plays a critical role in tracking COVID-19 evolution.

In a study recently published in the journal Proceedings of National Academy of Sciences USA, Dr. Fang Li and colleagues at the University of Minnesota determined the high-resolution crystal structure of the omicron strain’s spike protein and its mouse receptor (Fig. 1A)², using macromolecular cystallography x-ray data measured at Beam Line 12-1 of SSRL. Through detailed analysis, the researchers identified three mutations (Q493R, Q498R, and Y505H) in the omicron spike protein that are specifically adapted to two residues (Asn31 and His353) in the mouse receptor (Fig. 1B, 1C). After searching all of the available receptor sequences in the database, the researchers found that only the receptor from mice contains Asn31 and His353, while the receptors from several other rodent species contain one but not both Asn31 and His353. Thus, the researchers hypothesized that rodents, particularly mice, played a role in the omicron evolution. In contrast, these three mutations in omicron are structurally incompatible with the corresponding two residues (Lys31 and Lys353) in the human receptor (Fig.1D, 1E)², further suggesting that non-human animal reservoirs facilitated the omicron evolution.

Read more on the SSRL website

Image: Figure 1 (C) Structural details of the omicron RBD/mouse ACE2 interface showing Arg498 and His353 in omicron RBD are both structurally adapted to His353 in mouse ACE2.

Long COVID and pulmonary fibrosis better understood thanks to innovative techniques

2022/11/012022/11/03

An international team of researchers has revealed how scarring occurs in Long-COVID and pulmonary fibrosis using innovative blood biomarkers and X-ray technology. This study, published in The Lancet – eBioMedicine, contributes to the knowledge on the pathophysiology of severe COVID-19 and thus its treatment.

Long-COVID syndrome, or the origin of the long-term consequences of SARS-CoV-2 infection, is still not fully understood, more than two years after the onset of the pandemic. In particular, the long-term changes in lung tissue following severe COVID-19 disease pose significant limitations for many patients. Some of these patients continue to develop post-COVID pulmonary fibrosis, which is characterised by rapid scarring of the lung tissue.

Until now, the scientific community didn’t understand the underlying mechanisms of this scarring and of specific blood markers that can predict this process. Now, an international research team led by doctors and researchers at the Institute of Pathology at the RWTH Aachen University Hospital, the Hannover Medical School (MHH), HELIOS University Hospital in Wuppertal, and the University Medical Center Mainz, in collaboration with scientists at University College London (UCL) and the European Synchrotron (ESRF), has uncovered the mechanism that modifies the connective tissue of the lung in severe COVID-19. By combining the latest in imaging and molecular biology techniques this multidisciplinary team uncovered a mechanism by which the connective tissue of the lung is modified in severe COVID-19. They have demonstrated how COVID-19 changes the structure of the finest blood vessels in the lung and found molecular markers of this damage in the blood of patients that might ultimately help diagnose and treat the condition.

Unlocking the doors to effective COVID-19 treatments

2022/09/282022/10/03

Developing therapeutics for COVID-19 should lessen the length and severity of the illness, keeping more people out of the hospital and improving patient outcomes.

A team of interdisciplinary researchers from the Institut National de la Recherche Scientifique (INRS) are hoping to identify effective COVID-19 therapeutics. With help from the Canadian Light Source (CLS) at the University of Saskatchewan, the team has been able to visualize the interaction between inhibitory molecules and viral proteins. This allows researchers to see if their drug designs work as intended.

“We have libraries of molecular fragments and drug candidates that we are testing,” said Michael Maddalena, a research intern in Steven LaPlante’s lab at INRS. “We are screening to see if they are active and actually stick to the virus’ proteins or to essential human receptors where we think there are opportunities for drugs.”

This research targets the proteins of the SARS-CoV-2 virus that are involved in its replication and survival. Their work also targets the essential human receptors that the virus depends on to enter human cells. Drugs that stick to human receptors are unlikely to be susceptible to viral mutants — ensuring that new therapeutics will be effective against new variants.

Read more on the CLS website

Image: The LaPlante research team

Natural substances show promise against coronavirus

2022/08/182022/08/18

X-ray screening identifies compounds blocking a major corona enzyme

Three natural compounds present in foods like green tea, olive oil and red wine are promising candidates for the development of drugs against the coronavirus. In a comprehensive screening of a large library of natural substances at DESY’s X-ray source PETRA III the compounds bound to a central enzyme vital for the replication of the coronavirus. All three compounds are already used as active substances in existing drugs, as the team headed by Christian Betzel from the University of Hamburg and Alke Meents from DESY reports in the journal Communications Biology. However, if and when a corona drug can be developed on the basis of these compounds remains to be investigated.

“We tested 500 substances from the Karachi Library of Natural Compounds if they bind to the papain-like protease of the novel coronavirus, which is one of the main targets for an antiviral drug,” explains the study’s main author Vasundara Srinivasan from the University of Hamburg. “A compound that binds to the enzyme at the right place can stop it from working.”

The papain-like protease (PL^pro) is a vital enzyme for virus replication: When a cell is hijacked by the coronavirus, it is forced to produce building blocks for new virus particles. These proteins are manufactured as a long string. PL^pro then acts like a molecular pair of scissors, cutting the proteins from the string. If this process is blocked, the proteins cannot assemble new virus particles.

Read more on the DESY website

Image: The paper’s main author Vasundara Srinivasan at an X-ray set-up to test protein crystals in the lab.

Credit: University of Hamburg, Susanna Gevorgyan

New discoveries into how the body stores zinc

2022/05/252022/06/01

Zinc deficiency is a global health problem affecting many people and results in a weak immune system in adults and especially in children. This is a challenge for health systems and is quite evident in the Mexican population, for example. Seeking explanations, researchers in Mexico teamed up with international synchrotron experts and gained new insights from studying Drosophila fruit flies, which are known to be a decent model system for human zinc metabolism.

Thanks to beamtime at BESSY II and at the SLS (PSI), they were able to show that the zinc stores in Drosophila flies depend on the tryptophan content of their diet.

“The first experiments were done on the KMC-3 spectroscopy beamline,” relates DFG Fellow Nils Schuth, who is currently researching in Mexico at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav). “We took organs from a fruit fly and performed direct measurements of the tissue. We gained very revealing information from the data. That was the first step, which already brought us forward. In a second step, we then compared the biological results with various synthesised chemical complexes.”

The project started in 2019. Then came the pandemic and travel restrictions. The next measurements were therefore performed at the Paul Scherrer Institute (PSI) on the SLS, where the two research institutes were already cooperating. In the spring of 2021, new measurements performed at BESSY II confirmed their discoveries.

Read more on the HZB website

Image: Confocal images of the kidney-like Malpighian tubule from a Drosophila larva at two magnifications. More details in the main article.

Credit: © Erika Garay (Cinvestav)

Trigger of rare blood clots with AstraZeneca and other COVID vaccines found by scientists

2021/12/092021/12/14

understanding rare blood clots caused by some COVID vaccines – important first to prevention

A collaborative team from the School of Medicine at the University of Cardiff, Wales and a range of US institutions used the UK’s national synchrotron, Diamond Light Source, to help reveal the details of how a protein in the blood is attracted to a key component of Adenovirus based vaccines.

It is believed this protein kicks off a chain reaction, involving the immune system, that can culminate in extremely rare but dangerous blood clots. The Cardiff team were given emergency government funding to find the answers. In collaboration with scientists in the US and from AstraZeneca, they set out to collect data on the structure of the vaccines and perform computer simulations and related experiments to try and uncover why some of the vaccines based on Adenoviruses were causing blood clots in rare cases.

Moderna and BioNTech are based on mRNA, whereas AstraZeneca and Johnson & Johnson are based on Adenoviruses. Blood clots have only been associated with vaccines that use Adenoviruses.

#LightSourceSelfies – Light Source scientists are innovators

2021/11/172021/11/17

Kathryn Janzen is an Associate Scientist and User Experience Coordinator at the Canadian Light Source. During her #LightSourceSelfie, Kathryn reflects on the light source community saying “The contacts between light sources are really important and everyone is very interested in sharing ideas. We’re also really interested in innovating and finding new ways to use the light source and finding new applications for old techniques.”

EBS X-rays show lung vessels altered by COVID-19

2021/11/042021/12/16

The damage caused by Covid-19 to the lungs’ smallest blood vessels has been intricately captured using high-energy X-rays emitted by a special type of particle accelerator.

Scientists from UCL and the European Synchrotron Research Facility (ESRF) used a new revolutionary imaging technology called Hierarchical Phase-Contrast Tomography (HiP-CT), to scan donated human organs, including lungs from a Covid-19 donor.

Using HiP-CT, the research team, which includes clinicians in Germany and France, have seen how severe Covid-19 infection ‘shunts’ blood between the two separate systems – the capillaries which oxygenate the blood and those which feed the lung tissue itself. Such cross-linking stops the patient’s blood from being properly oxygenated, which was previously hypothesised but not proven.

HiP-CT enables 3D mapping across a range of scales, allowing clinicians to view the whole organ as never before by imaging it as a whole and then zooming down to cellular level

Insights into coronavirus proteins using SAXS

2021/07/062021/07/15

A collaboration led by researchers from the European Molecular Biology Laboratory (EMBL) used small angle X-ray scattering (SAXS) at the European XFEL and obtained interesting data on samples containing coronavirus spike proteins including proteins of the isolated receptor biding domain. The results can, for example, help investigate how antibodies bind to the virus. This gives researchers a new tool that may improve understanding of our bodies’ immune response to coronavirus and help to develop medical strategies to overcome COVID-19

SAXS is a powerful technique as it allows researchers to gain insights into protein shape and function at the micro- and nanoscales. The technique has proven to be extremely useful in investigating macromolecular structures such as proteins, especially because it removes the need to crystallize these samples. This means researchers can study the sample in its native form under physiological conditions under which biological reactions occur.

Read more on the European XFEL website

Image: Seen here, the instrument SPB/SFX, where the SAXS experiment was carried out. Using this instrument researchers can study the three-dimensional structures of biological objects. Examples are biological molecules including crystals of macromolecules and macromolecular complexes as well as viruses, organelles, and cells.

Credit: European XFEL / Jan Hosan

Research finds possible key to long term COVID-19 symptoms

2021/06/172021/06/28

Key Points

Researchers from La Trobe University have identified a key mechanism that may link COVID-19 infection and lung damage
Lung damage is one of the possible long term effects of COVID-19
The macromolecular crystallography beamlines at the Australian Synchrotron continue to provide insights into the structural biology of COVID-19

The Macromolecular and microfocus beamlines at the Australian Synchrotron continue to be an invaluable resource for studies in structural biology relating to COVID-19.

This week researchers from La Trobe University reported that they have identified a key mechanism in how SARS-CoV-2 damages lung tissue.

Some patients report long term-COVID symptoms affecting their breathing for months after recovering from an initial COVID-19 infection.

Read more on ANSTO website

Target selection for COVID-19 antibody therapeutics

2021/05/212021/06/03

SCIENTIFIC ACHIEVEMENT

Protein-structure studies at the Advanced Light Source (ALS) helped demonstrate that the primary target of antibody-based COVID-19 immunity is the part of the virus’s spike protein that can most easily mutate.

SIGNIFICANCE AND IMPACT

This work anticipated the rise of SARS-CoV-2 variants and guides the selection of antibody therapeutics that are likely to be more resistant to immune escape.

A better understanding of immunity

To better predict the course of the COVID-19 pandemic and to develop the best new therapeutics, researchers need to understand what regions of the SARS-CoV-2 virus are most critical to the immune response and how likely these regions are to mutate and evade immunity.

Two recent papers, relying in part on protein-structure studies at the ALS, have provided detailed information about the SARS-CoV-2 virus that causes COVID-19 and the human immune response to it. The results reveal where the virus surface protein is most likely to mutate, what the consequences of those mutations may be, and which types of antibodies may be the most effective therapeutics.

Read more on the ALS website

Image: Left: Composite model of the SARS-CoV-2 spike protein trimer with six mAbs shown bound to one RBD (Piccoli et al.). Right: The first RBD–ACE2 complex structure where the RBD is a variant, in this case N439K; the figure highlights a new interaction between the N439K residue and ACE2 (Thomson et al.).

How remdesivir works against the coronavirus

2021/05/112021/06/08

Researchers at Goethe University Frankfurt, in cooperation with the Paul Scherrer Institute PSI, have probably discovered another, previously unknown mechanism of action of the antiviral remdesivir. Using structural analyses, they have discovered that a decomposition product of the virostatic agent remdesivir binds to the viral protein nsP3 of Sars-CoV-2. This protein helps the virus suppress host cell defence mechanisms. The discovery may be important for the development of new drugs to combat Sars-CoV-2 and other RNA viruses.

The virostatic agent remdesivir disrupts an important step in the propagation of RNA viruses, to which Sars-CoV-2 also belongs: the reproduction of the virus’s own genetic material. This provides the blueprint for the production of new virus particles by the host cell and is present as RNA matrices. To accelerate their reproduction, however, RNA viruses cause the RNA matrices to be copied. To do so, they use a specific protein of their own (an RNA polymerase), which is blocked by remdesivir. Strictly speaking, remdesivir does not do this itself, but rather a substance that is synthesized from remdesivir in five steps when the active agent penetrates a cell.

In the second of these five steps, an intermediate is formed from remdesivir, a substance with the somewhat unwieldy name GS-441524 (in scientific terms: a remdesivir metabolite). GS-441524 is a virostatic agent as well. As the scientists in the group headed by Stefan Knapp from the Institute for Pharmaceutical Chemistry at Goethe University Frankfurt have discovered, GS-441524 targets a Sars-CoV-2 protein called nsP3.

Read more on the PSI website

Image: May Sharpe of PSI’s Macromolecules and Bioimaging Laboratory

Credit: Paul Scherrer Institute/Markus Fischer

Innovations against COVID-19 outbreak presented to MHESI Minister

2021/04/222021/05/13

Adjunct Prof. Dr. Anek Laothamatas, the Minister of Higher Education, Science, and Innovation (MHESI), Thailand, had a visit to the field hospital at Suranaree University of Technology (SUT), Nakhon Ratchasima, on Thursday, 22 April 2021. On this occasion, the Minister visited an exhibition on innovations created and presented by SLRI to prevent the spread of COVID-19 at SUT Administration Building.

In supporting the handling of COVID-19 situation, SLRI researchers created outstanding various innovations. The first innovation is studying and developing Thai silk mask for use as an alternative to surgical mask. In this research, SLRI researchers applied synchrotron light to analyze three-dimensional structure of Pak Thong Chai silk and later created the silk mask for use as alternative to surgical mask. The result showed that the created silk mask was more than 80% efficient at PM 2.5 and 0.3 micron filtration capacity. The mask was also better than masks made of other fibers using for droplet transmission prevention and it was durable. The mask development not only helps solving shortage of surgical mask but also increases quality of natural fabric in the region and raises income of community enterprise in Nakhon Ratchasima.

Another innovation created by SLRI is the development of particle permeation test for surgical mask. A high-speed camera was applied for the test to examine permeation of sneeze and cough droplets through the mask. The camera can take photos at high frame rate of up to 1,300 frames per second. In studying permeation of sneeze and cough droplets, the qualified rate is just 200 frames per second to examine droplet permeation through the mask and detect motion occurred during recording and the researchers can examine droplet permeation through surgical masks. The result showed that the created silk mask was better than a surgical mask at preventing saliva droplet permeation.