Nanopore signals, machine learning unlocks new molecular analysis tool

Illustration of voltage-matrix nanopore profiling. The artistic rendering depicts proteins (colored shapes) being analyzed by solid-state nanopores under varying voltage conditions. By combining nanopore signals with machine learning, researchers can discriminate protein mixtures and detect changes in molecular populations.
Image Credit: ©2025 Sotaro Uemura, The University of Tokyo

Understanding molecular diversity is fundamental to biomedical research and diagnostics, but existing analytical tools struggle to distinguish subtle variations in the structure or composition among biomolecules, such as proteins. Researchers at the University of Tokyo have developed a new analytical approach, which helps overcome this problem. The new method, called voltage-matrix nanopore profiling, combines multivoltage solid-state nanopore recordings with machine learning for accurate classification of proteins in complex mixtures, based on the proteins’ intrinsic electrical signatures.

The study, published in Chemical Science, demonstrates how this new framework can identify and classify “molecular individuality” without the need for labels or modifications. The research holds promise of providing a foundation that could lead to more advanced and wider applications of molecular analysis in various areas, including disease diagnosis.

New AI Model for Drug Design Brings More Physics to Bear in Predictions

This illustration shows the mesh of anchoring points the team obtained by discretizing the manifold, an estimation of the distribution of atoms and the probable locations of electrons in the molecule. This is important because, as the authors note in the new paper, treating atoms as solid points "does not fully reflect the spatial extent that real atoms occupy in three-dimensional space."
Image Credit: Liu et al./PNAS

When machine learning is used to suggest new potential scientific insights or directions, algorithms sometimes offer solutions that are not physically sound. Take for example AlphaFold, the AI system that predicts the complex ways in which amino acid chains will fold into 3D protein structures. The system sometimes suggests "unphysical" folds—configurations that are implausible based on the laws of physics—especially when asked to predict the folds for chains that are significantly different from its training data. To limit this type of unphysical result in the realm of drug design, Anima Anandkumar, Bren Professor of Computing and Mathematical Sciences at Caltech, and her colleagues have introduced a new machine learning model called NucleusDiff, which incorporates a simple physical idea into its training, greatly improving the algorithm's performance.

New advances to boost regeneration and plasticity of brain neurons

The study is led by Professor Daniel Tornero and researcher Alba Ortega , from the Faculty of Medicine and Health Sciences and the Institute of Neurosciences of the University of Barcelona
Photo Credit: Courtesy of University of Barcelona

The brain’s mechanisms for repairing injuries caused by trauma or degenerative diseases are not yet known in detail. Now, a study by the University of Barcelona describes a new strategy based on stem cell therapy that could enhance neuronal regeneration and neuroplasticity when this vital organ is damaged. The results reveal that the use of brain-derived neurotrophic factor (BDNF), combined with stem cell-based cell therapies, could help in the treatment of neurodegenerative diseases or brain injuries.

Combining cell therapy with BDNF production

BDNF is a protein that is synthesized mainly in the brain and plays a key role in neuronal development and synaptic plasticity. Several studies have described its potential to promote neuronal survival and growth, findings that are now extended by the new study.

“The findings indicate that BDNF can promote the maturation and increase the activity of neurons generated in the laboratory from donor skin cells. The skin cells must first be reprogrammed to become induced pluripotent stem cells (iPSCs), and then differentiated to obtain neuronal cultures,” says Daniel Tornero, from the UB’s Department of Biomedicine and the CIBER Area for the Neurodegenerative Diseases (CIBERNED).

In this way, the study combines cell therapy with the production of BDNF in the same cells. This study confirms the beneficial effects of this growth factor in neuronal cultures derived from human stem cells, the same cells that are used in cell therapy to treat, for example, stroke in animal models.

Binding power of trapped water demonstrated for the first time

Water molecules are a driving force in the formation of molecular bonds, such as in proteins.
Image Credit: INT, KIT

Water is everywhere – it covers most of the earth, circulates in the human body and can be found in even the smallest molecular niches. But what happens if water does not flow freely but is trapped in such structures? Researchers at the Karlsruhe Institute of Technology (KIT) and Constructor University in Bremen have proven for the first time that "locked" water can influence its environment and strengthen the bond between molecules. This finding could open new avenues for the development of drugs and materials.

Some of the water on Earth is found in tiny nooks and crannies – enclosed in molecular pockets, such as protein binding sites or synthetic receptors. Whether this water behaves neutrally in the presence of other molecules or influences their binding has so far been controversial. "Water molecules usually interact most strongly with each other. However, experimental data showed that water behaves unusually in such narrow pockets", says Dr. Frank Biedermann from KIT's Institute of Nanotechnology. "We have now been able to provide the theoretical basis for these observations and prove that the water in the molecular pockets is energetically tense."

Extra Silver Atom Sparks Breakthrough in Photoluminescence of Silver Nanoclusters

Structural architectures of anion-templated (a) Ag78 and (b) Ag79 NCs. Hydrogen atoms are omitted for clarity.
Image Credit: ©Yuichi Negishi et al.

A team of researchers from Tohoku University, Tokyo University of Science, and the Institute for Molecular Science have uncovered how the precise addition of a single silver (Ag) atom can dramatically transform the light-emitting properties of high-nuclear Ag nanoclusters (NCs). The study reports a remarkable 77-fold increase in photoluminescence (PL) quantum yield (QY) at room temperature - a milestone that paves the way for practical applications in optoelectronics and sensing technologies. The findings were published in the Journal of the American Chemical Society.

Photoluminescence quantum yield is an important metric used to evaluate the efficiency of photoluminescence, which is how well a material can absorb energy and convert it into light. Improving PLQY positively impacts technology such as OLEDs in TV screens.

Scientists develop novel RNA- or DNA-based substances to protect plants from viruses

The new active ingredients can be used to protect plants against viruses.
Photo Credit: Uni Halle / Markus Scholz

Individually tailored RNA or DNA-based molecules are able to reliably fight off viral infections in plants, according to a new study by the Martin Luther University Halle-Wittenberg (MLU), which was published in the International Journal of Molecular Sciences. The researchers were able to fend off a common virus using the new active substances in up to 90 per cent of cases. They also developed a method for finding substances tailored specifically to the virus. The team has now patented the method.

During a viral infection, the plant’s cells are hijacked by the virus to multiply itself. Key products of this process are viral RNA molecules that serve as blueprints for the production of proteins. "A virus cannot reproduce without producing its proteins," explains Professor Sven-Erik Behrens from the Institute of Biochemistry and Biotechnology at MLU. For years, his team has been working on ways to disrupt this process and degrade the viral RNA molecules inside the cells. 

In the new study, the researchers describe how this can be achieved using the so-called "antisense" method. It relies on short, synthetically produced DNA molecules known as antisense oligonucleotides (ASOs). In the plant cells, the ASOs direct cellular enzymes acting as scissors towards the foreign RNA so they can degrade it. "For this process to work, it is crucial to identify a suitable target structure in the viral RNA which the enzyme scissors can attach to," explains Behrens. However, finding those accessible sites is really tricky: most potential target RNA molecules have a very complex structure, and they are also masked by other cell components. "This makes it even more difficult to attack them directly," says Behrens.