When a virus attacks, the body’s immune response has two basic layers of defense: the innate and the adaptive immune systems. While the adaptive immune system grows stronger against a specific pathogen as the body is exposed to it multiple times and which forms the basis of vaccinations, the innate immune system is an assortment of molecular mechanisms that work against a broad range of pathogens at a basic level. The Kobe University virologist SHOJI Ikuo says, “The new coronavirus, however, is so infectious that we wondered what clever mechanisms the virus employs to evade the innate immune system so effectively.”

Shoji’s team previously worked on the immune response to hepatitis viruses and investigated the role of a molecular tag called “ISG15” the innate immune system attaches to the virus’s building blocks. Having learned that the novel coronavirus has an enzyme that is especially effective in removing this tag, he decided to use his team’s expertise to elucidate the effect of the ISG15 tag on the coronavirus and the mechanism of the virus’s countermeasures.

In a paper in the Journal of Virology, the Kobe University-led team is now the first to report that the ISG15 tag gets attached to a specific location on the virus’s nucleocapsid protein, the scaffold that packages the pathogen’s genetic material. For the virus to assemble, many copies of the nucleocapsid protein need to attach to each other, but the ISG15 tag prevents this, which is the mechanism behind the tag’s antiviral action. “However, the novel coronavirus also has an enzyme that can remove the tags from its nucleocapsid, recovering its ability to assemble new viruses and thus overcoming the innate immune response,” explains Shoji.

The novel coronavirus shares many traits with the SARS and MERS viruses, which all belong to the same family of viruses. And these viruses, too, have an enzyme that can remove the ISG15 tag. However, Shoji’s team found that their versions are less efficient at it than the one in the novel coronavirus. And in fact, it has been reported recently that the previous viruses’ enzymes have a different primary target. “These results suggest that the novel coronavirus is simply better at evading this aspect of the innate immune system’s defense mechanism, which explains why it is so infectious,” says Shoji.

But understanding just why the novel coronavirus is so effective also points the way to developing more effective treatments. The Kobe University researcher explains: “We may be able to develop new antiviral drugs if we can inhibit the function of the viral enzyme that removes the ISG15 tag. Future therapeutic strategies may also include antiviral agents that directly target the nucleocapsid protein, or a combination of these two approaches.”

This research was funded by the Kansai Economic Federation, the Hyogo Science and Technology Association (grant 3501) and the Ministry of Education, Culture, Sports, Science and Technology Japan (grant 18042-203556). It was conducted in collaboration with researchers from Universitas Gadjah Mada, Niigata University, the University of Yamanashi, Hokkaido University and Osaka University.

The term kokumi derives from Japanese and refers to a full-bodied and long-lasting taste experience. The taste impression is particularly pronounced in aged cheeses, mainly due to the increasing concentration of gamma-glutamyl dipeptides. These are small molecules that consist of a link between glutamic acid and another amino acid.

Depending on how the two amino acids are linked, researchers distinguish between gamma-, alpha-, and X-glutamyl dipeptides, with the latter two not contributing to the kokumi effect. The high polarity of the glutamyl dipeptides, as well as their great structural similarity with different flavor contributions, represent a major challenge for food analysis.

Efficient analysis method developed

Nevertheless, the team led by principal investigator Andreas Dunkel of the Leibniz Institute has succeeded in developing a new efficient analysis method based on ultra-high performance liquid chromatography-mass spectrometry. For the first time, it can precisely and selectively determine the concentrations of all 56 gamma-glutamyl dipeptide variants in just 22 minutes. Optimized sample preparation makes it possible to analyze 60 cheese samples per day.

“This is a significant improvement compared to other methods. Our tests have shown that our method is faster, more efficient, and yet reliable — it delivers reproducible results and detects even the smallest concentrations,” says first author Sonja Maria Fröhlich, a doctoral student at the Leibniz Institute. To further investigate the influence of ripening time on gamma-glutamyl dipeptide concentrations, the researchers applied the method to 122 cheese samples from Europe and the USA after the test phase. The ripening times of the cheese ranged from two weeks to 15 years.

Mold cultures accelerate flavor development

The results show that, as expected, the concentrations of glutamyl dipeptides increase with increasing ripeness. “Interestingly, the addition of blue and white mold cultures led to significantly higher gamma-glutamyl dipeptide concentrations, even at shorter ripening times,” says Andreas Dunkel, who heads the Integrative Food Systems Analysisresearch group at the Leibniz Institute.

The food chemist adds: “The concentration profiles we have determined for different stages of ripening and different types of cheese can be used in the future as a database for prediction models. The latter could, for example, be used to objectively monitor flavor development during cheese ripening, to shorten ripening times, or to develop new plant-based cheese products with high consumer acceptance.”

“In the sense of an interdisciplinary, food systems biology research approach, one of our goals is to combine analytical research results with bioinformatic methods to develop predictive models suitable to support sustainable food production. This is also the starting point of the project led by Andreas Dunkel,” concludes Veronika Somoza, director of the Leibniz Institute.

However, Van Overwalle’s research extends beyond motor functions, exploring the cerebellum’s involvement in social and cognitive abilities. His findings reveal that abnormalities in the cerebellum not only lead to motor deficits but are also linked to emotional and behavioral disorders. He references research on individuals with autism, demonstrating how non-invasive brain stimulation techniques like magnetic stimulation can improve social task performance.

“We’ve seen improvements in the sequence of cognitive tasks in people with autism through magnetic stimulation,” says Van Overwalle. “We’re now testing more complex tasks to see if these effects can be further enhanced, with the ultimate goal of developing practical treatments for people with autism.”

A notable breakthrough is the use of transcranial electrical stimulation (tES), a more affordable and accessible technique compared to magnetic stimulation. While the effects of tES are still limited, the research group is committed to further development, seeing its potential for wide-scale application in the future.

This research offers a fresh perspective on the cerebellum’s role and paves the way for new treatments for psychiatric and neurological conditions, such as autism spectrum disorders. “Our hope is to refine these techniques further to improve social and cognitive functions in people with autism,” concludes Van Overwalle.

The amount of CO₂ removed from the atmosphere via photosynthesis from land plants is known as Terrestrial Gross Primary Production, or GPP. It represents the largest carbon exchange between land and atmosphere on the planet. GPP is typically cited in petagrams of carbon per year. One petagram equals 1 billion metric tons, which is roughly the amount of CO₂ emitted each year from 238 million gas-powered passenger vehicles.

A team of scientists led by Cornell University, with support from the Department of Energy’s Oak Ridge National Laboratory, used new models and measurements to assess GPP from the land at 157 petagrams of carbon per year, up from an estimate of 120 petagrams established 40 years ago and currently used in most estimates of Earth’s carbon cycle. The results are described in the paper, “Terrestrial Photosynthesis Inferred from Plant Carbonyl Sulfide Uptake.”

Researchers developed an integrated model that traces the movement of the chemical compound carbonyl sulfide, or OCS, from the air into leaf chloroplasts, the factories inside plant cells that carry out photosynthesis. The research team quantified photosynthetic activity by tracking OCS. The compound largely follows the same path through a leaf as CO₂, is closely related to photosynthesis and is easier to track and measure than CO₂ diffusion. For these reasons, OCS has been used as a photosynthesis proxy at the plant and leaf levels. This study showed that OCS is well suited to estimate photosynthesis at large scales and over long periods of time, making it a reliable indicator of worldwide GPP.

The team used plant data from a variety of sources to inform model development. One of the sources was the LeafWeb database, established at ORNL in support of the DOE Terrestrial Ecosystem Science Scientific Focus Area, or TES-SFA. LeafWeb collects data about photosynthetic traits from scientists around the world to support carbon cycle modeling. The scientists verified the model results by comparing them with high-resolution data from environmental monitoring towers instead of satellite observations, which can be hindered by clouds, particularly in the tropics.

Key to the new estimate is better representation of a process called mesophyll diffusion — how OCS and CO₂ move from leaves into chloroplasts where carbon fixation occurs. Understanding mesophyll diffusion is essential to figuring out how efficiently plants are conducting photosynthesis, and even how they might adapt to changing environments.

Lianhong Gu, co-author, photosynthesis expert and distinguished staff scientist in ORNL’s Environmental Sciences Division, helped develop the project’s mesophyll conductance model, which represents numerically the diffusion of OCS in leaves, as well as the linkage between OCS diffusion and photosynthesis.

“Figuring out how much CO₂ plants fix each year is a conundrum that scientists have been working on for a while,” Gu said. “The original estimate of 120 petagrams per year was established in the 1980s, and it stuck as we tried to figure out a new approach. It’s important that we get a good handle on global GPP since that initial land carbon uptake affects the rest of our representations of Earth’s carbon cycle.”

“We have to make sure the fundamental processes in the carbon cycle are properly represented in our larger-scale models,” Gu added. “For those Earth-scale simulations to work well, they need to represent the best understanding of the processes at work. This work represents a major step forward in terms of providing a definitive number.”

Pan-tropical rainforests accounted for the biggest difference between previous estimates and the new figures, a finding that was corroborated by ground measurements, Gu said. The discovery suggests that rainforests are a more important natural carbon sink than previously estimated using satellite data.

Understanding how much carbon can be stored in land ecosystems, especially in forests with their large accumulations of biomass in wood, is essential to making predictions of future climate change.

“Nailing down our estimates of GPP with reliable global-scale observations is a critical step in improving our predictions of future CO₂ in the atmosphere, and the consequences for global climate” said Peter Thornton, Corporate Fellow and lead for the Earth Systems Science Section at ORNL.

The results of this study point to the importance of including key processes, such as mesophyll conductance, in model representations of photosynthesis. DOE’s Next Generation Ecosystem Experiments in the Tropics has the goal of advancing model predictions of tropical forest carbon cycle response to climate change. These results can inform new model development that will reduce uncertainty in predictions of tropical forest GPP.

In addition to Cornell’s School of Integrative Plant Sciences, other collaborators on the project were Wageningen University and Research of The Netherlands, Carnegie Institution for Sciences, Colorado State University, University of California Santa Cruz and the NASA Jet Propulsion Laboratory.

Support came from Cornell, the National Science Foundation and the ORNL TES-SFA, sponsored by DOE’s Office of Science Biological and Environmental Research program.