Friday, August 25, 2023

SARS-CoV-2: how the history of human populations influences their immune response


Peer-Reviewed Publication

INSTITUT PASTEUR




During the COVID-19 pandemic, the clinical spectrum observed among people infected with SARS-CoV-2 ranged from asymptomatic carriage to death. Researchers at the Institut Pasteur, the CNRS and the Collège de France, in collaboration with researchers around the world1, have investigated the extent and drivers of differences in immune responses to SARS-CoV-2 across populations from Central Africa, Western Europe and East Asia. They show that latent cytomegalovirus infection and human genetic factors, driven by natural selection, contribute to population differences in immune response to SARS-CoV-2 and the severity of COVID-19. Understanding the factors underlying such population disparities could help to improve patient management in future epidemics. These results were published on August 9, 2023 in Nature.

The Institut Pasteur’s Human Evolutionary Genetics Unit2 , led by Lluis Quintana-Murci, investigates how human populations differ in their immune responses to infection. These differences may result from different environmental exposures or from past population history, including natural selection, shaping the patterns of genetic diversity of human groups. In this study, published in Nature, the scientists investigated the extent and causes of disparities in the responses to the SARS-CoV-2 virus, focusing on populations from different geographic and ethnic backgrounds.

During the COVID-19 pandemic, the SARS-CoV-2 virus caused a wide range of clinical manifestation, from asymptomatic infection to fatal disease. Although advanced age remains a primary risk factor, male gender, comorbidities and various human genetic and immunological factors also contribute to disease severity. To study variations in immune responses to SARS-CoV-2 across human populations, scientists exposed immune blood cells from 222 healthy donors from Central Africa, Western Europe, and East Asia to the virus.

Single-cell RNA sequencing was used to analyze the SARS-CoV-2 responses of 22 blood cell types. These data were then combined with serological and genetic information collected from the same individuals, making it possible to assess the degree of disparity between populations in terms of their immune responses to SARS-CoV-2, and to identify contributing factors.

Scientists have identified around 900 genes that that respond differently to SARS-CoV-2 between populations. Using statistical genetic analyses, they show that these disparities are mainly due to variation in blood cellular composition: the proportion of each cell type differs from one population to another. We know that blood cell composition can be influenced by environmental factors such as exposure to cytomegalovirus (a human infection of the herpes family, which is usually harmless) and cytomegalovirus prevalence varies widely among populations: Central Africans present 99% seropositivity, in contrast to only 50% in East Asians and 32% in Europeans. The team found that an individual’s environment, specifically latent cytomegalovirus infection, will thus influence the immune cell response to SARS-CoV-2.

Furthermore, the scientists have identified around 1,200 human genes whose expression in response to SARS-CoV-2 is under the control of human genetic factors and the frequency of the alleles3 that regulate these genes can vary between the populations studied. Using population genetics approaches, they have identified recurrent selection events targeting genes involved in anti-viral functions. "We know that infectious agents have had a strong impact on human survival and exerted massive selective pressures that have shaped population genetic variation. We show that past natural selection has impacted present immune responses to SARS-CoV-2, particularly in people of East Asian ancestry, in whom coronaviruses generated strong selective pressures around 25,000 years ago," explains Maxime Rotival, a researcher in the Institut Pasteur's Human Evolutionary Genetics Unit and co-last author of the study.

Between 1.5% and 2% of the genomes of Europeans and Asians is of Neanderthal origin. There is growing evidence of links between Neanderthal ancestry and present-day immunity to infection. By comparing the 1,200 genes identified with the Neanderthal genome, the scientists have discovered dozens of genes that both alter antiviral mechanisms and result from ancient introgression between Neanderthals and modern humans (Homo sapiens). "Previous studies have shown the link between some of the genes identified in our study and the severity of COVID-19. Our comprehensive population-based study highlights the direct impact of genetic variants governing immune responses to SARS-CoV-2 on the severity of COVID-19. It also establishes links between past evolutionary events, such as natural selection or Neanderthal admixture, and current population disparities in immune responses and disease risk," explains Lluis Quintana-Murci, Head of the Human Evolutionary Genetics Unit at the Institut Pasteur, Professor at the Collège de France and co-last author of the study.

"By identifying the precise cellular and molecular pathways of the genetic variants associated with COVID-19 severity, this study paves the way for precision medicine strategies that could either identify high-risk individuals or facilitate the development of new treatments," adds Darragh Duffy, Head of the Institut Pasteur's Translational Immunology Unit.

 

This research was funded by the institutes mentioned above, and the French National Research Agency (ANR) (COVID-19-POPCELL, POPCELL-REG, COVIFERON), the European Horizon Health 2021 program (UNDINE), the French Foundation for Medical Research (FRM), the Allianz/Institut de France Foundation and the Fondation de France.


[1] Institut Imagine (France), Ghent University (Belgium), University of Rome (Italy), University of Detroit (USA), The Rockefeller University (USA), C2I Hong Kong (China), University of Melbourne (Australia).

[2] At the CNRS, this unit is known as the "Evolutionary Genomics, Modeling and Health Unit" (CNRS/Institut Pasteur).

[3] An allele is a version of a gene that is caused by a mutation. A gene has several alleles that perform the same function as the original gene, but in their own specific ways.

 

Source

Dissecting human population variation in single-cell responses to SARSCoV-2, Nature, 9 August 2023

Yann Aquino1,2,27, Aurelie Bisiaux1,27, Zhi Li1,27, Mary O'Neill1,27, Javier Mendoza-Revilla1, Sarah Helene Merkling3, Gaspard Kerner1, Milena Hasan4, Valentina Libri4, Vincent Bondet5,Nikaia Smith5, Camille de Cevins6,7, Mickael Menager6,7, Francesca Luca8,9,10, Roger Pique-Regi8,9, Giovanna Barba-Spaeth11, Stefano Pietropaoli11, Olivier Schwartz12, Geert Leroux-Roels13, Cheuk-Kwong Lee14, Kathy Leung15,16, Joseph T.K. Wu15,16, Malik Peiris17,18,19,Roberto Bruzzone18,19, Laurent Abel20,21,22, Jean-Laurent Casanova20,21,22,23,24, Sophie A.Valkenburg18,25, Darragh Duffy5,19, Etienne Patin1, Maxime Rotival1,28* & Lluis Quintana-Murci1,26,28*

1. Institut Pasteur, Universite Paris Cite, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France.
2. Sorbonne Universite, College Doctoral, Paris, France.
3. Institut Pasteur, Universite Paris Cite, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France.
4. Institut Pasteur, Universite Paris Cite, Cytometry and Biomarkers UTechS, Paris, France.
5. Institut Pasteur, Universite Paris Cite, Translational Immunology Unit, Paris, France.
6. Universite Paris Cite, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
7. Labtech Single-Cell@Imagine, Imagine Institute, INSERM UMR1163, Paris, France
8. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
9. Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
10. Department of Biology, University of Rome Tor Vergata, Rome, Italy
11. Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Structural Virology Unit, Paris, France.
12. Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Virus and Immunity Unit, Paris, France.
13. Ghent University and University Hospital, Ghent, Belgium.
14. Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China.
15. WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
16. Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
17. Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
18. HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
19. Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
20. St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA.
21. Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France.
22. Imagine Institute, Paris Cite University, Paris, France.
23. Department of Pediatrics, Necker Hospital for Sick Children, Paris, France.
24. Howard Hughes Medical Institute, New York, NY, USA.
25. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
26. Chair Human Genomics and Evolution, College de France, Paris, France.
27. These authors contributed equally.
28. These authors jointly supervised this work.

https://doi.org/10.1038/s41586-023-06422-9

 

 

New study finds ways to suppress lithium plating in automotive batteries for faster charging electric vehicles


Peer-Reviewed Publication

QUEEN MARY UNIVERSITY OF LONDON

Image 

IMAGE: THE DISTRIBUTION OF LITHIUM CONCENTRATION IS INDICATED BY COLOURS DURING THE CHARGING PROCESS OF A GRAPHITE NEGATIVE ELECTRODE view more 

CREDIT: XUEKUN LU ET AL/NATURE COMMUNICATIONS




A new study led by Dr. Xuekun Lu from Queen Mary University of London in collaboration with an international team of researchers from the UK and USA has found a way to prevent lithium plating in electric vehicle batteries, which could lead to faster charging times. The paper was published in the journal Nature Communications

Lithium plating is a phenomenon that can occur in lithium-ion batteries during fast charging. It occurs when lithium ions build up on the surface of the battery's negative electrode instead of intercalating into it, forming a layer of metallic lithium that continues growing. This can damage the battery, shorten its lifespan, and cause short-circuits that can lead to fire and explosion. 

Dr. Xuekun Lu explains that lithium plating can be significantly mitigated by optimizing the microstructure of the graphite negative electrode. The graphite negative electrode is made up of randomly distributed tiny particles, and fine-tuning the particle and electrode morphology for a homogeneous reaction activity and reduced local lithium saturation is the key to suppress lithium plating and improve the battery's performance.

"Our research has revealed that the lithiation mechanisms of graphite particles vary under distinct conditions, depending on their surface morphology, size, shape and orientation. It largely affects the lithium distribution and the propensity of lithium plating," said Dr. Lu. “Assisted by a pioneering 3D battery model, we can capture when and where lithium plating initiates and how fast it grows. This is a significant breakthrough that could have a major impact on the future of electric vehicles.” 

The study provides new insights into developing advanced fast charging protocols by improving the understanding of the physical processes of lithium redistribution within graphite particles during fast charging. This knowledge could lead to an efficient charging process while minimising the risk of lithium plating.  

In addition to faster charging times, the study also found that refining the microstructure of the graphite electrode can improve the battery's energy density. This means that electric cars could travel further on a single charge. 

These findings are a major breakthrough in the development of electric vehicle batteries. They could lead to faster-charging, longer-lasting, and safer electric cars, which would make them a more attractive option for consumers. 

 

Social media does not cause depression in children and young people


Yes, kids spend a lot of time on social media. And the prevalence of depression in youths has increased. But there's no evidence of a causal link

Peer-Reviewed Publication

NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY




“The prevalence of anxiety and depression has increased. As has the use of social media. Many people therefore believe that there has to be a correlation,” says Silje Steinsbekk, a professor at the Norwegian University of Science and Technology's (NTNU) Department of Psychology.

But that is not the case if we are to believe the results of the study “Social media behaviours and symptoms of anxiety and depression. A four-wave cohort study from age 10-16 years”.

Trondheim Early Secure Study

In the Trondheim Early Secure Study research project, researchers followed 800 children in Trondheim over a six-year period in order to look for correlations between the use of social media and the development of symptoms of mental illness.

“We have collected data every other year, from the year in which the children were ten years old until they turned 16 years of age. This enabled us to follow the children during the transition from childhood to adolescence. Symptoms of anxiety and depression have been identified through diagnostic interviews with both the children and their parents,” Steinsbekk explains.

The outcome of the study was the same for both boys and girls. The results were the same regardless of whether the children published posts and pictures via their own social media pages or whether they liked and commented on posts published by others.

Increased use of social media did not lead to more symptoms of anxiety and depression. Nor was it the case that those who developed more symptoms of anxiety and depression over time changed their social media habits.

Norwegian researchers find weak correlations

A number of studies have been conducted in recent years looking at the correlation between the use of social media on the part of children and young people and their mental health.

Some studies have found that the use of social media promotes mental health, while others find that it has a negative impact. But the majority of the correlations are weak, according to Steinsbekk.

“Mental health is often broadly defined in the studies and covers everything from self-esteem to depression. Data is often collected using questionnaires. It is unclear what has actually been measured and the focus has often been on frequency, i.e. how much time young people have spent on social media," Steinsbekk said

“By following the same subjects over a number of years, recording symptoms of mental illness through in-depth interviews and examining various types of social media use, our study has enabled us to take a more detailed look and provide a more nuanced picture of the correlations,” Steinsbekk said.

Previous studies conducted by the same research group show that around five per cent of young people in Norway experience depression. The prevalence is lower in children.

One in ten children meet the criteria for an anxiety disorder at least once during the period between the ages of four and 14 years.

“Young people’s use of social media is a topic that often creates strong emotions, and there is a lot of concern among both parents and professionals," she said.

“We are hoping to contribute more knowledge about how social media affects young people's development and ability to function in society. Who is particularly vulnerable? Who benefits from social media? Does the way in which social media is used matter?," she said.

Social support and less loneliness

Steinsbekk and her colleagues previously found that girls who like and comment on other people’s posts on social media develop a poorer body image over time, but this was not the case for boys. Posting to their own social media accounts had no impact on self-esteem, for both boys or girls.

Over the coming years, researchers will also examine how different experiences on social media, such as cyberbullying and posting nude pictures, affect young people's development and functioning in society.

“Our study finds that if Kari or Knut increasingly like and post on Instagram or Snapchat, they are no more likely to develop symptoms of anxiety and depression. But that does not mean that they are not having negative experiences on social media, or feeling addicted or excluded. Some may be particularly vulnerable and those are the ones we need to identify,” Steinsbekk says.

At the same time, Steinsbekk also notes that there are positive aspects of social media.

“Social media provides a venue for community and belonging, making it easy to stay in touch with friends and family. Social media can be a platform for social support and help protect against loneliness for young people with few friends.

The Trondheim Early Secure Study has collected data from thousands of children and their parents every year since the subjects were four years of age. The subjects are now 20 years old and the ninth data collection round will take place this autumn.

Source:

Silje Steinsbekk, Jacqueline Nesi, Lars Wichstrøm: Social media behaviors and symptoms of anxiety and depression. A four-wave cohort study from age 10–16 years. Available online 1 July 2023. Science Direct
https://doi.org/10.1016/j.chb.2023.107859

 

New dual-arm robot achieves bimanual tasks by learning from simulation


Peer-Reviewed Publication

UNIVERSITY OF BRISTOL

Fig 1 

IMAGE: DUAL ARM ROBOT HOLDING CRISP view more 

CREDIT: YIJIONG LIN



An innovative bimanual robot displays tactile sensitivity close to human-level dexterity using AI to inform its actions.

The new Bi-Touch system, designed by scientists at the University of Bristol and based at the Bristol Robotics Laboratory, allows robots to carry out manual tasks by sensing what to do from a digital helper.

The findings, published in IEEE Robotics and Automation Letters, show how an AI agent interprets its environment through tactile and proprioceptive feedback, and then control the robots' behaviours, enabling precise sensing, gentle interaction, and effective object manipulation to accomplish robotic tasks.

This development could revolutionise industries such as fruit picking, domestic service, and eventually recreate touch in artificial limbs.

Lead author Yijiong Lin from the Faculty of Engineering, explained: “With our Bi-Touch system, we can easily train AI agents in a virtual world within a couple of hours to achieve bimanual tasks that are tailored towards the touch. And more importantly, we can directly apply these agents from the virtual world to the real world without further training.

“The tactile bimanual agent can solve tasks even under unexpected perturbations and manipulate delicate objects in a gentle way.”

Bimanual manipulation with tactile feedback will be key to human-level robot dexterity. However, this topic is less explored than single-arm settings, partly due to the availability of suitable hardware along with the complexity of designing effective controllers for tasks with relatively large state-action spaces. The team were able to develop a tactile dual-arm robotic system using recent advances in AI and robotic tactile sensing.

The researchers built up a virtual world (simulation) that contained two robot arms equipped with tactile sensors. They then design reward functions and a goal-update mechanism that could encourage the robot agents to learn to achieve the bimanual tasks and developed a real-world tactile dual-arm robot system to which they could directly apply the agent.

The robot learns bimanual skills through Deep Reinforcement Learning (Deep-RL), one of the most advanced techniques in the field of robot learning. It is designed to teach robots to do things by letting them learn from trial and error akin to training a dog with rewards and punishments.

For robotic manipulation, the robot learns to make decisions by attempting various behaviours to achieve designated tasks, for example, lifting up objects without dropping or breaking them. When it succeeds, it gets a reward, and when it fails, it learns what not to do. With time, it figures out the best ways to grab things using these rewards and punishments. The AI agent is visually blind relying only on proprioceptive feedback  – a body’s ability to sense movement, action and location and tactile feedback.

They were able to successfully enable to the dual arm robot to successfully safely lift items as fragile as a single Pringle crisp.

Co-author Professor Nathan Lepora added: “Our Bi-Touch system showcases a promising approach with affordable software and hardware for learning bimanual behaviours with touch in simulation, which can be directly applied to the real world. Our developed tactile dual-arm robot simulation allows further research on more different tasks as the code will be open-source, which is ideal for developing other downstream tasks.”

Yijiong concluded: “Our Bi-Touch system allows a tactile dual-arm robot to learn sorely from simulation, and to achieve various manipulation tasks in a gentle way in the real world.

“And now we can easily train AI agents in a virtual world within a couple of hours to achieve bimanual tasks that are tailored towards the touch.”

 

Paper:

‘Bi-Touch: Bimanual Tactile Manipulation With Sim-to-Real Deep Reinforcement Learning’ by Yijiong Lin, Nathan Lepora et al in IEEE Robotics and Automation Letters.