In the study, published March 8 in Circulation Research, the researchers showed that boosting levels of a sphingolipid called S1P in artery-lining endothelial cells slows the development and progression of coronary artery disease in an animal model. The lead author was Dr. Onorina Laura Manzo, a postdoctoral researcher in the laboratory of Dr. Annarita Di Lorenzo, an associate professor of pathology and laboratory medicine at Weill Cornell Medicine.

Sphingolipids are named for the enigmatic sphinx of ancient mythology because their functions in biology traditionally have been somewhat mysterious. In recent years, there has been increasing evidence of their relevance in coronary artery disease; bloodstream levels of S1P, for example, are lower in patients with this condition. But the precise roles of these lipids have remained unclear.

In the new study, the researchers sought a better understanding of those roles — and of sphingolipids’ potential as therapeutic targets. Despite the availability of cholesterol-lowering drugs and other interventions, coronary artery disease — the underlying cause of most heart attacks and many strokes — continues to be the world’s leading cause of mortality, affecting more than 20 million people in the United States alone.

Using a novel mouse model developed by the same group, the researchers found that blood pressure-related stress on arteries — which eventually will induce coronary artery disease — triggers an increase in S1P production in endothelial cells, as part of a protective response. This response normally is only temporary, but deleting a protein called NOGO-B, which inhibits S1P production, allows the rise in endothelial S1P production to be sustained — and made the animals much more resistant to coronary artery disease and associated mortality.

Another key finding is related to a different group of sphingolipids called ceramides. Prior studies have linked coronary artery disease to high bloodstream levels of some ceramides, and their causative role in the disease has been widely assumed. In their model, however, the researchers observed that while ceramide levels were high in the bloodstream, levels in artery-lining endothelial cells remained about the same regardless of coronary artery disease status. This suggests that the current view of ceramides’ role in the disease should be revised.

All in all, the findings lay the foundation for the development of drugs that boost S1P to treat or prevent coronary artery disease, the researchers concluded.

The work reported in this story was supported by the National Heart, Lung, and Blood Institute, part of the National Institutes of Health, through grant numbers R01HL126913 and R01HL152195 and a Harold S. Geneen Charitable Trust Award for Coronary Heart Disease Research.

“We looked at how the rates of fluid production with oil and gas compare to natural background circulation of water and showed how humans have made a big impact on the circulation of fluids in the subsurface,” said Jennifer McIntosh, a professor in the UArizona Department of Hydrology and Atmospheric Sciences and senior author of a paper in the journal Earth’s Future detailing the findings.

“The deep subsurface is out of sight and out of mind for most people, and we thought it was important to provide some context to these proposed activities, especially when it comes to our environmental impacts,” said lead study author Grant Ferguson, an adjunct professor in the UArizona Department of Hydrology and Atmospheric Sciences and a professor in the University of Saskatchewan’s School of Environment and Sustainability.

In the future, these human-induced fluid fluxes are projected to increase with strategies that are proposed as solutions for climate change, according the study. Such strategies include: geologic carbon sequestration, which is capturing and storing atmospheric carbon dioxide in underground porous rocks; geothermal energy production, which involves circulating water through hot rocks for generating electricity; and lithium extraction from underground mineral-rich brine for powering electric vehicles. The study was done in collaboration with researchers from the University of Saskatchewan in Canada, Harvard University, Northwestern University, the Korea Institute of Geosciences and Mineral Resources, and Linnaeus University in Sweden.

“Responsible management of the subsurface is central to any hope for a green transition, sustainable future and keeping warming below a few degrees,” said Peter Reiners, a professor in the UArizona Department of Geosciences and a co-author of the study.

With oil and natural gas production, there is always some amount of water, typically saline, that comes from the deep subsurface, McIntosh said. The underground water is often millions of years old and acquires its salinity either from evaporation of ancient seawater or from reaction with rocks and minerals. For more efficient oil recovery, more water from near-surface sources is added to the salt water to make up for the amount of oil removed and to maintain reservoir pressures. The blended saline water then gets reinjected into the subsurface. This becomes a cycle of producing fluid and reinjecting it to the deep subsurface.

The same process happens in lithium extraction, geothermal energy production and geologic carbon sequestration, the operations of which involve leftover saline water from the underground that is reinjected.

“We show that the fluid injection rates or recharge rates from those oil and gas activities is greater than what naturally occurs,” McIntosh said.

Using existing data from various sources, including measurements of fluid movements related to oil and gas extraction and water injections for geothermal energy, the team found that the current fluid movement rates induced by human activities are higher compared to how fluids moved before human intervention.

As human activities like carbon capture and sequestration and lithium extraction ramp up, the researchers also predicted how these activities might be recorded in the geological record, which is the history of Earth as recorded in the rocks that make up its crust.

Human activities have the potential to alter not just the deep subsurface fluids but also the microbes that live down there, McIntosh said. As fluids move around, microbial environments may be altered by changes in water chemistry or by bringing new microbial communities from Earth’s surface to the underground.

For example, with hydraulic fracturing, a technique that is used to break underground rocks with pressurized liquids for extracting oil and gas, a deep rock formation that previously didn’t have any detectable number of microbes might have a sudden bloom of microbial activity.

There remain a lot of unknowns about Earth’s deep subsurface and how it is impacted by human activities, and it’s important to continue working on those questions, McIntosh said.

“We need to use the deep subsurface as part of the solution for the climate crisis,” McIntosh said. “Yet, we know more about the surface of Mars than we do about water, rocks and life deep beneath our feet.”

To design these climate-saving plants, scientists in Salk’s Harnessing Plants Initiative are using a sophisticated new research tool called SLEAP — an easy-to-use artificial intelligence (AI) software that tracks multiple features of root growth. Created by Salk Fellow Talmo Pereira, SLEAP was initially designed to track animal movement in the lab. Now, Pereira has teamed up with plant scientist and Salk colleague Professor Wolfgang Busch to apply SLEAP to plants.

In a study published in Plant Phenomics on April 12, 2024, Busch and Pereira debut a new protocol for using SLEAP to analyze plant root phenotypes — how deep and wide they grow, how massive their root systems become, and other physical qualities that, prior to SLEAP, were tedious to measure. The application of SLEAP to plants has already enabled researchers to establish the most extensive catalog of plant root system phenotypes to date.

What’s more, tracking these physical root system characteristics helps scientists find genes affiliated with those characteristics, as well as whether multiple root characteristics are determined by the same genes or independently. This allows the Salk team to determine what genes are most beneficial to their plant designs.

“This collaboration is truly a testament to what makes Salk science so special and impactful,” says Pereira. “We’re not just ‘borrowing’ from different disciplines — we’re really putting them on equal footing in order to create something greater than the sum of its parts.”

Prior to using SLEAP, tracking the physical characteristics of both plants and animals required a lot of labor that slowed the scientific process. If researchers wanted to analyze an image of a plant, they would need to manually flag the parts of the image that were and weren’t plant — frame-by-frame, part-by-part, pixel-by-pixel. Only then could older AI models be applied to process the image and gather data about the plant’s structure.

What sets SLEAP apart is its unique use of both computer vision (the ability for computers to understand images) and deep learning (an AI approach for training a computer to learn and work like the human brain). This combination allows researchers to process images without moving pixel-by-pixel, instead skipping this intermediate labor-intensive step to jump straight from image input to defined plant features.

“We created a robust protocol validated in multiple plant types that cuts down on analysis time and human error, while emphasizing accessibility and ease-of-use — and it required no changes to the actual SLEAP software,” says first author Elizabeth Berrigan, a bioinformatics analyst in Busch’s lab.

Without modifying the baseline technology of SLEAP, the researchers developed a downloadable toolkit for SLEAP called sleap-roots (available as open-source software here). With sleap-roots, SLEAP can process biological traits of root systems like depth, mass, and angle of growth. The Salk team tested the sleap-roots package in a variety of plants, including crop plants like soybeans, rice, and canola, as well as the model plant species Arabidopsis thaliana — a flowering weed in the mustard family. Across the variety of plants trialed, they found the novel SLEAP-based method outperformed existing practices by annotating 1.5 times faster, training the AI model 10 times faster, and predicting plant structure on new data 10 times faster, all with the same or better accuracy than before.

Together with massive genome sequencing efforts for elucidating the genotype data in large numbers of crop varieties, these phenotypic data, such as a plant’s root system growing especially deep in soil, can be extrapolated to understand the genes responsible for creating that especially deep root system.

This step — connecting phenotype and genotype — is crucial in Salk’s mission to create plants that hold on to more carbon and for longer, as those plants will need root systems designed to be deeper and more robust. Implementing this accurate and efficient software will allow the Harnessing Plants Initiative to connect desirable phenotypes to targetable genes with groundbreaking ease and speed.

“We have already been able to create the most extensive catalogue of plant root system phenotypes to date, which is really accelerating our research to create carbon-capturing plants that fight climate change,” says Busch, the Hess Chair in Plant Science at Salk. “SLEAP has been so easy to apply and use, thanks to Talmo’s professional software design, and it’s going to be an indispensable tool in my lab moving forward.”

Accessibility and reproducibility were at the forefront of Pereira’s mind when creating both SLEAP and sleap-roots. Because the software and sleap-roots toolkit are free to use, the researchers are excited to see how sleap-roots will be used around the world. Already, they have begun discussions with NASA scientists hoping to utilize the tool not only to help guide carbon-sequestering plants on Earth, but also to study plants in space.

At Salk, the collaborative team is not yet ready to disband — they are already embarking on a new challenge of analyzing 3D data with SLEAP. Efforts to refine, expand, and share SLEAP and sleap-roots will continue for years to come, but its use in Salk’s Harnessing Plants Initiative is already accelerating plant designs and helping the Institute make an impact on climate change.

Other authors include Lin Wang, Hannah Carrillo, Kimberly Echegoyen, Mikayla Kappes, Jorge Torres, Angel Ai-Perreira, Erica McCoy, Emily Shane, Charles Copeland, Lauren Ragel, Charidimos Georgousakis, Sanghwa Lee, Dawn Reynolds, Avery Talgo, Juan Gonzalez, Ling Zhang, Ashish Rajurkar, Michel Ruiz, Erin Daniels, Liezl Maree, and Shree Pariyar of Salk.

The work was supported by the Bezos Earth Fund, the Hess Corporation, the TED Audacious Project, and the National Institutes of Health (RF1MH132653).