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Scientists chart over 140,000 DNA loops to map human chromosomes in the nucleus

One of the most detailed 3D maps of how the human chromosomes are organized and folded within a cell’s nucleus is published in Nature.

Chromosomes are thread-like structures that carry a cell’s genetic information inside the nucleus. Rather than existing as loose strands or only as the familiar X-shapes seen in textbooks, chromosomes fold into specific three-dimensional forms. How they fold, the structures they form, and their placement play crucial roles in maintaining proper cellular functions, gene expression, and DNA replication.

The team involved in the 4D Nucleome Project, whose goal was to understand the 3D organization of human chromosomes in the nucleus and how it changes over time, identified over 140,000 DNA looping interactions in human embryonic stem cells and fibroblasts. They also presented computational methods that can predict genome folding solely from its DNA sequence, making it easier to determine how genetic variations—including those linked to disease—affect genome structure and function.

Prolonging lung cancer response to EGFR inhibition by targeting the selective advantage of resistant cells

The emergence of resistant subpopulations often underlies the development of resistance to cancer therapy. Here, using a DNA barcoding approach, the authors demonstrate EGFR TKI treatment in non-small cell lung cancer enriches for resistant subpopulation which can be prevented by treatment with the multikinase inhibitor sorafenib via inhibition of MKNK, STAT3 and MCL1.

Artificial Intelligence for Organelle Segmentation in Live-Cell Imaging

JUST PUBLISHED: artificial intelligence for organelle segmentation in live-cell imaging

Click here to read the latest free, Open Access article from Research, a Science Partner Journal.

Investigations into organelles illuminate the intricate interplay of cellular systems, uncovering how specialized structures orchestrate homeostasis, regulate metabolic pathways, and modulate signal transduction. The structural and functional integrity of organelles, including mitochondria, ER, GA, and lysosomes, is critical for cellular health. Deviations in organelle shape and behavior are frequently associated with disease development [51]. Consequently, precise characterization of organelles is crucial for advancing our understanding of cell biology and mechanisms.

Organelle image segmentation is important for extracting precise spatial and structural information, forming the foundation for subsequent quantitative analyses. Unlike whole-cell or nuclear, organelle segmentation is inherently more challenging due to the smaller size, irregular shapes, and intricate distributions of these structures. Additionally, many organelles exhibit dynamic behaviors such as fusion, fission, and trafficking, requiring accurate segmentation across both temporal and spatial dimensions. Advances in segmentation technologies have notably improved the ability to identify and characterize organelles with high-precision accuracy, opening new avenues for understanding cellular functions in health and disease.

Abnormal protein activity found to promote cell migration and spread of glioblastoma

Ever wondered how the different cells in our body communicate with each other to fulfill their different roles-be it cells repairing a tissue injury or immune cells moving towards an invading pathogen (microorganisms that causes disease) to engulf it? To move forward or migrate, cells must exert forces or interact with their surrounding environment. Interestingly, however, a fault in these interactions can also be the reason for spread of deadly cancer cells, such as in glioblastoma or brain tumor. While the importance of these interactions is well-understood, the machinery involved in these interactions at the molecular level remains a mystery.

Now, a team of researchers led by Professor Naoyuki Inagaki from Nara Institute of Science and Technology, Japan, along with Dr. Yonehiro Kanemura from NHO Osaka National Hospital, Japan; Dr. Tatsuo Kinashi from Kansai Medical University, Japan; and Dr. Daisuke Kawauchi from Nagoya City University, Japan, has identified the underlying mechanism involving a protein called shootin1b that promotes cell migration or movement in glioblastoma. The study was published online in Advanced Science on August 13, 2025.

“We discovered that an abnormal activity of shootin1b promotes the movement of cancer cells and spread of glioblastoma, the most common and difficult to treat brain tumor in adults,” explains Professor Inagaki.

Goblet cell-expressed microprotein FXYD3 determines gut homeostasis by maintaining mucus barrier integrity

Yang et al. demonstrate that the goblet cell-expressed microprotein FXYD3 interacts with SERCA2 to regulate ER calcium homeostasis, promoting mucus granule secretion and sialylation. FXYD3 deficiency impairs mucin sialylation and mucus barrier function, increasing susceptibility to intestinal inflammation.

New nanoparticles stimulate the immune system to attack ovarian tumors

A team, including researchers in MIT ChemE, designed new nanoparticles that can deliver an immune-stimulating molecule called IL-12 directly to ovarian tumors. When given along with immunotherapy drugs called checkpoint inhibitors, IL-12 helps the immune system launch an attack on cancer cells.

“What’s really exciting is that we’re able to deliver IL-12 directly in the tumor space. And because of the way that this nanomaterial is designed to allow IL-12 to be borne on the surfaces of the cancer cells, we have essentially tricked the cancer into stimulating immune cells to arm themselves against that cancer,” says MIT ChemE Professor Paula Hammond, a senior author of the study.

📸: Courtesy of the researchers.

MIT researchers designed nanoparticles that can deliver an immune-stimulating molecule called IL-12 directly to ovarian tumors. When given to mice along with checkpoint inhibitors, the treatment eliminated metastatic tumors more than 80 percent of the time.

‘Ready-made’ T-cell gene therapy tackles ‘incurable’ T-cell leukemia

A new treatment using genome-edited immune cells, developed by scientists at UCL (University College London) and Great Ormond Street Hospital (GOSH), has shown promising results in helping children and adults fight a rare and aggressive form of blood cancer called T-cell acute lymphoblastic leukemia (T-ALL).

The world-first gene therapy (BE-CAR7) uses base-edited immune cells to treat previously untreatable T-cell leukemia and help patients achieve remission, offering new hope for families facing this aggressive cancer. Base-editing is an advanced version of CRISPR technology, that can precisely change single letters of DNA code inside living cells.

In 2022, researchers from GOSH and UCL delivered the world’s first treatment made using “base-editing” to a 13-year-old girl from Leicester, Alyssa.

Speech-to-reality system creates objects on demand using AI and robotics

Generative AI and robotics are moving us ever closer to the day when we can ask for an object and have it created within a few minutes. In fact, MIT researchers have developed a speech-to-reality system, an AI-driven workflow that allows them to provide input to a robotic arm and “speak objects into existence,” creating things like furniture in as little as five minutes.

With the speech-to-reality system, a robotic arm mounted on a table is able to receive spoken input from a human, such as “I want a simple stool,” and then construct the objects out of modular components. To date, the researchers have used the system to create stools, shelves, chairs, a small table, and even decorative items such as a dog statue.

“We’re connecting natural language processing, 3D generative AI, and robotic assembly,” says Alexander Htet Kyaw, an MIT graduate student and Morningside Academy for Design (MAD) fellow. “These are rapidly advancing areas of research that haven’t been brought together before in a way that you can actually make physical objects just from a simple speech prompt.”

Cosmic knots may finally explain why the Universe exists

Knotted structures once imagined by Lord Kelvin may actually have shaped the universe’s earliest moments, according to new research showing how two powerful symmetries could have created stable “cosmic knots” after the Big Bang. These exotic objects may have briefly dominated the young cosmos, unraveled through quantum tunneling, and produced heavy right-handed neutrinos whose decays tipped the balance toward matter over antimatter.

In 1867, Lord Kelvin pictured atoms as tiny knots in an invisible medium called the ether. That picture turned out to be wrong, since atoms are built from subatomic particles rather than twists in space. Yet his discarded idea of knotted structures may still help explain one of the deepest questions in science: why anything in the universe exists at all.

A team of physicists in Japan has now shown that knotted structures can naturally appear in a realistic particle physics model that also addresses several major mysteries, including the origins of neutrino masses, dark matter, and the strong CP problem. Their study, published in Physical Review Letters, suggests that such “cosmic knots” could have formed in the violently changing early universe, briefly taken over as a dominant form of energy, and then collapsed in a way that slightly favored matter over antimatter. As they formed and decayed, these knots would have stirred spacetime itself, producing a distinctive pattern of gravitational waves that future detectors might be able to pick up, which is rare for a problem that is usually very difficult to test directly.

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