Rebalancing the Gut: How AI Solved a 25-Year Crohn’s Disease Mystery

Electron micrographs show how macrophages expressing girdin neutralize pathogens by fusing phagosomes (P) with the cell’s lysosomes (L) to form phagolysosomes (PL), compartments where pathogens and cellular debris are broken down (left). This process is crucial for maintaining cellular homeostasis. In the absence of girdin, this fusion fails, allowing pathogens to evade degradation and escape neutralization (right).
Image Credit: UC San Diego Health Sciences

The human gut contains two types of macrophages, or specialized white blood cells, that have very different but equally important roles in maintaining balance in the digestive system. Inflammatory macrophages fight microbial infections, while non-inflammatory macrophages repair damaged tissue. In Crohn’s disease — a form of inflammatory bowel disease (IBD) — an imbalance between these two types of macrophages can result in chronic gut inflammation, damaging the intestinal wall and causing pain and other symptoms. 

Researchers at University of California San Diego School of Medicine have developed a new approach that integrates artificial intelligence (AI) with advanced molecular biology techniques to decode what determines whether a macrophage will become inflammatory or non-inflammatory. 

The study also resolves a longstanding mystery surrounding the role of a gene called NOD2 in this decision-making process. NOD2 was discovered in 2001 and is the first gene linked to a heightened risk for Crohn’s disease.

Researchers decipher a mechanism that determines the complexity of the glucocorticoid receptor

Above, from left to right, Pilar Montanyà-Vallugera, José Luis Torbado-Gardeazábal, Inés Montoya-Novoa and Montse Abella-Monleón. Below, from left to right, Alba Jiménez-Panizo, Pablo Fuentes-Prior, Eva Estébanez-Perpiñá and Andrea Alegre-Martí.
Photo Credit: Courtesy of University of Barcelona

Drugs to treat inflammatory and autoimmune diseases — such as asthma, psoriasis, rheumatoid arthritis or Chrousos syndrome — act mainly through the glucocorticoid receptor (GR). This essential protein regulates vital processes in various tissues, so understanding its structure and function at the molecular level is essential for designing more effective and safer drugs. Now, a study published in the journal Nucleic Acids Research (NAR) has revealed the mechanism of multimerization — the association of different molecules to form complex structures — of the glucocorticoid receptor, a process critical to its physiological function.

Deciphering how the GR forms oligomers — through the binding of several subunits — opens a crucial avenue for developing more selective drugs. These new drugs could modulate this association and thus minimize serious adverse effects, such as immunosuppression or bone loss.

Beavers Impact Ecosystems Above and Below Ground

Photo Credit: Gennady Zakharin

Above ground, we can see changes wrought by beaver ponds such as increases in biodiversity and water retention. But UConn Department of Earth Sciences researcher Lijing Wang says we have a limited understanding of how they impact what happens beneath the ground. In research published in Water Resource Research, Wang and co-authors study how water moves through the soils and subsurface environment and detail new insights into how beaver ponds impact groundwater.

Groundwater can be an important source of water for streams, especially late in a dry summer, it may be the only source of water sustaining a stream, says Wang, and researchers are interested in understanding if and how beaver ponds impact groundwater as these details are important to consider for water management and restoration efforts.

How constant is the fine structure constant?

The thorium crystal 
The core element of the experiment: a crystal containing thorium atoms.
Photo Credit: Technische Universität Wien

Thorium atomic nuclei can be used for very specific precision measurements. This had been suspected for decades, and the search for suitable atomic nucleus states had been ongoing worldwide. In 2024, a team from TU Wien, with the support of international partners, achieved the decisive breakthrough: the long-discussed thorium nuclear transition was found. Shortly afterwards, it was demonstrated that thorium can indeed be used to build high-precision nuclear clocks.

Now the next major success in high-precision research on thorium nuclei has been achieved: when the thorium nucleus changes between different states, it slightly alters its elliptical shape. This also changes the distribution of protons in the nucleus, which in turn alters its electric field. This can be measured so precisely that it allows for better investigation than ever before of the fine structure constant, one of the most important natural constants in physics. This now makes it possible to investigate the question of how constant the fundamental constants of nature really are.

Treating fibrosis with a chemical derived from Lawsonia inermis

Treatment with Lawsone converts a liver with fibrosis into a healthy liver.
Image Credit: Osaka Metropolitan University

Lawsonia inermis is best known for making henna, a versatile dye that is used to change the color of skin and clothes. Now, researchers from Osaka Metropolitan University have found another use for the pigments extracted from the dye: treating liver disease.

Specifically, they could treat liver fibrosis, a disease that causes excess fibrous scar tissue to build up in the liver as a result of chronic liver injury caused by lifestyle choices such as excessive drinking. Patients with liver fibrosis have increased risks of cirrhosis, liver failure, and cancer. Despite 3–4% of the population having the advanced form of the disease, treatment options remain limited.

Researchers Explore How AI Could Shape the Future of Student Learning

Johns Hopkins study reveals the strengths and pitfalls of incorporating chatbots into middle and high school classrooms as a 'co-tutor'
Image Credit: Scientific Frontline / AI generated

As students settle into the new school year, one question looms large: How will artificial intelligence tools like ChatGPT affect their learning? Seeking answers, a team from Johns Hopkins recently introduced a chatbot into a classroom of middle and high school students to act as a co-tutor and study the impact.

The pilot study included 22 students enrolled in the Johns Hopkins Center for Talented Youth's online course Diagnosis: Be the Doctor. It involved two virtual classrooms; both were taught by the same instructor and organized similarly, except for one key difference: Students in one classroom had access to a large language model designed to act like a coach, asking Socratic-style questions as students worked through medical case studies.

Dangerous E. coli strain blocks gut’s defense mechanism to spread infection

Isabella Rauch, Ph.D., is the senior author on a new study published in Nature that reveals how a dangerous strain of E. coli blocks the body’s immune defenses to spread infection.
Photo Credit: OHSU/Christine Torres Hicks

When harmful bacteria that cause food poisoning, such as E. coli, invade through the digestive tract, gut cells usually fight back by pushing infected cells out of the body to stop the infection from spreading.

In a new study published today in Nature, scientists from Genentech, a member of the Roche Group, in collaboration with researchers from Oregon Health & Science University, discovered that a dangerous strain of E. coli — known for causing bloody diarrhea — can block this gut defense, allowing the bacteria to spread more easily.

The bacteria inject a special protein called NleL into gut cells, which breaks down key enzymes, known as ROCK1 and ROCK2, that are needed for infected cells to be expelled. Without this process, the infected cells can’t leave quickly, allowing the bacteria to spread more easily.

Neutrinos ‘flavor’ may hold clues to the universe’s biggest secrets

Inside the Super-Kamiokande detector.
Photo Credit: Kamioka Observatory, ICRR (Institute for Cosmic Ray Research), The University of Tokyo.

In a new analysis, physicists provide the most precise picture yet of how neutrinos change ‘flavor’ as they travel through the cosmos. 

Neutrinos are fundamental particles of the universe, but also some of the most elusive; They pass through everything and can be extremely difficult to detect. While many of their properties are mysterious, scientists know neutrinos come in three types: electron, muon, and tau. 

Understanding these different identities can help scientists learn more about neutrino masses and answer key questions about the evolution of the universe, including why matter came to dominate over antimatter in the early universe, said Zoya Vallari, 

New observation method improves outlook for lithium metal battery

Stacey Bent (left), professor of chemical engineering and of energy science and engineering, Sanzeeda Baig Shuchi (right), chemical engineering PhD student, and Yi Cui (not pictured), professor of materials science and engineering and of energy science and engineering, led the research team that discovered a way to more accurately analyze key chemistries for rechargeable batteries and possibly many other chemistry applications.
Photo Credit: Bill Rivard

Stanford researchers developed a flash-freezing observation method that reveals battery chemistry without altering it, providing new insights to enhance lithium metal batteries.

In science and everyday life, the act of observing or measuring something sometimes changes the thing being observed or measured. You may have experienced this “observer effect” when you measured the pressure of a tire and some air escaped, changing the tire pressure. In investigations of materials involved in critical chemical reactions, scientists can hit the materials with an X-ray beam to reveal details about composition and activity, but that measurement can cause chemical reactions that change the materials. Such changes may have significantly hampered scientists learning how to improve – among many other things – rechargeable batteries.

To address this, Stanford University researchers have developed a new twist to an X-ray technique. They applied their new approach by observing key battery chemistries, and it left the observed battery materials unchanged and did not introduce additional chemical reactions. In doing so, they have advanced knowledge for developing rechargeable lithium metal batteries. This type of battery packs a lot of energy and can be recharged very quickly, but it short-circuits and fails after recharging a handful of times. The new study, published today in Nature, also could advance the understanding of other types of batteries and many materials unrelated to batteries.

Fungal secrets of a sunken ship

Robert Blanchette, a professor at the University of Minnesota, and Claudia Chemello, president and co-founder of Terra Mare Conservation, examine the wood of the USS Cairo.
Photo Credit: Paul Mardikian

University of Minnesota researchers studied the microbial degradation of the USS Cairo, one of the first ironclad and steam powered gunboats used in the United States Civil War. Studies of microbial degradation of historic woods are essential to help protect and preserve important cultural artifacts. 

Built in 1861, the ship hit a torpedo and sank in December 1862 and was recovered about 100 years later from the Yazoo River. It's been on display at the Vicksburg National Military Park in Mississippi. Although the ship has a canopy cover, it is exposed to environmental elements.