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Category: chemistry

DNA transcription is a tightly choreographed event: How RNA polymerase II regulates the dance

Life’s instructions are written in DNA, but it is the enzyme RNA polymerase II (Pol II) that reads the script, transcribing RNA in eukaryotic cells and eventually giving rise to proteins. Scientists know that Pol II must advance down the gene in perfect sync with other biological processes; aberrations in the movement of this enzyme have been linked to cancer and aging. But technical hurdles prevented them from precisely determining how this important molecular machine moves along DNA, and what governs its pauses and accelerations.

A new study fills in many of those knowledge gaps. In a paper published in Nature Structural & Molecular Biology, researchers used a single-molecule platform to watch individual mammalian transcription complexes in action. The result is a clear view of how this molecular engine accelerates, pauses, and shifts gears as it transcribes genetic information.

“What’s really striking is how this machine functions almost like a finely tuned automobile,” says Shixin Liu, head of the Laboratory of Nanoscale Biophysics and Biochemistry. “It has the equivalent of multiple gears, or speed modes, each controlled by the binding of different regulatory proteins. We figured out, for the first time, how each gear is controlled.”

Pesticides and other common chemical pollutants are toxic to ‘good’ gut bacteria, lab-based screening indicates

A large-scale laboratory screening of human-made chemicals has identified 168 chemicals that are toxic to bacteria found in the healthy human gut. These chemicals stifle the growth of gut bacteria thought to be vital for health. The research, including the new machine learning model, is published in the journal Nature Microbiology.

Most of these chemicals, likely to enter our bodies through food, water, and environmental exposure, were not previously thought to have any effect on bacteria.

As the bacteria alter their function to try and resist the chemical pollutants, some also become resistant to antibiotics such as ciprofloxacin. If this happens in the human gut, it could make infections harder to treat.

Cellular senescence related gene signature predicts prognosis and immune features in skin cutaneous melanoma

Skin cutaneous melanoma (SKCM) is the deadliest skin cancer, with rising global incidence. Cellular senescence plays an essential role in tumorigenesis, progression, and immune modulation in cancer, however, its role in SKCM prognosis and immunotherapy response remains unclear.

We analyzed 279 senescence-related genes (SRGs) in 469 patients with SKCM from The Cancer Genome Atlas. A cellular senescence-related signature (CSRS) was constructed using univariate and LASSO Cox regression analyses. Kaplan-Meier survival curves and receiver operating characteristic (ROC) analyses were used to evaluate its predictive performance. Consensus clustering based on SRG expression stratified patients into distinct subgroups. External validation was performed using the GSE65904 dataset. We further assessed the association between CSRS, immune cell infiltration, and immunotherapy response. Additionally, immunohistochemistry validated the expression of prognosis-related SRGs and functional assays explored the role of RuvB-like AAA ATPase 2 (RUVBL2) in SKCM cells.

The CSRS effectively stratified patients with SKCM into high-and low-risk groups with significantly different survival outcomes and immune profiles. Moreover, our results suggest that higher levels of cellular senescence may enhance immunosurveillance and promote tumor suppression via a senescence-associated secretory phenotype-dependent mechanism. Based on the expression profiles of 113 SRGs, patients were classified into three distinct clusters, with Cluster 1 associated with the poorest prognosis. Among the identified SRGs, RUVBL2 was markedly upregulated in SKCM cells and its knockdown inhibited cell proliferation.

Using peat as sustainable precursor for fuel cell catalyst materials

Iron-nitrogen-carbon catalysts have the potential to replace the more expensive platinum catalysts currently used in fuel cells. This is shown by a study conducted by researchers from the Helmholtz-Zentrum Berlin (HZB), Physikalisch-Technische Bundesanstalt (PTB) and universities in Tartu and Tallinn, Estonia. The research is published in the journal ACS Nano.

At BESSY II, the team observed the formation of complex microstructures within various samples. They then analyzed which structural parameters were particularly important for fostering the preferred electrochemical reactions. The raw material for such catalysts is well decomposed peat.

Fuel cells convert the chemical energy of hydrogen directly into electrical energy, producing only water. Fuel cells could be an important component in a climate-neutral energy system. The greatest potential for improvement lies in the reduction of costs via the replacement of the electrocatalysts, which are currently based on the precious metal platinum.

When substrates dictate the route: Deuterium source reshapes hydrogen isotope exchange pathways

A collaboration between the groups of Professor Mónica H. Pérez-Temprano at the Institute of Chemical Research of Catalonia (ICIQ) and Professor Anat Milo at Ben-Gurion University of the Negev has uncovered how the characteristics of specific substrates require certain reaction conditions that determine the course of a chemical reaction, in the context of C–H deuteration reactions.

The study, published in Nature Catalysis, combines detailed experiments with data science rooted in reaction intermediates. By correlating molecular features with reaction outcomes, the researchers reveal that the choice of deuterium source—such as heavy water (D2O), deuterated methanol (CD3OD), or acetic acid-d4 (AcOD-d4)—does more than merely influencing the degree of deuterium incorporation. It can actively alter the reaction pathway, revealing hidden mechanistic complexity that intuition alone could not predict.

Study reveals unexpected link between dopamine and serotonin in the brain

Researchers at Karolinska Institutet, Columbia University and the University of San Francisco, have uncovered a previously unknown mechanism by which dopamine, a key brain chemical vital for movement and motivation, can affect brain activity indirectly by boosting serotonin. The study was published in Science Advances.

Dopamine is a key chemical messenger that supports many essential brain functions, including motivation, movement, and learning. Although dopamine acts throughout the brain, it plays an especially central role in the basal ganglia, a network of interconnected regions responsible for selecting which behaviors we express.

The basal ganglia and dopamine are deeply involved in neuropsychiatric and neurodegenerative diseases, and many widely used medications target this network.

Hidden household toxin triples liver disease risk, study finds

PCE, a dry-cleaning chemical found in many everyday products, has been linked to tripled risk of serious liver damage. Scientists have uncovered a new environmental culprit behind liver disease: tetrachloroethylene (PCE), a chemical used in dry cleaning and household products. The study found that people with PCE exposure were three times more likely to develop severe liver scarring, even when traditional risk factors like alcohol or obesity were absent. The chemical is widespread in air, water, and consumer goods, making it a stealthy threat to public health.

Liver disease most often develops due to one of three major causes: excessive alcohol use, the buildup of fat in the liver associated with obesity, diabetes, and high cholesterol, or viral infections such as hepatitis B and C.

Researchers from Keck Medicine of USC have identified another potential cause of liver damage. A new study published in Liver International links tetrachloroethylene (PCE), a chemical widely used in dry cleaning and found in household products like adhesive glues, spot removers, and stainless steel polish, to serious liver harm.

BPA-Free? New Study Shows Popular Replacements May Harm Human Cells

Researchers report that some chemicals used in printed food-package stickers as replacements for bisphenol A can still disrupt human ovarian cell function. Chemicals that have taken the place of bisphenol A (BPA) in food packaging may cause potentially harmful changes in human ovarian cells, acco

Automated Benchtop Synthesis of a Quadrillion-Plus Member Core@Multishell Nanoparticle Library Using a Massively Generalizable Nanochemical Reaction

Rapidly expanding advances in computational prediction capabilities have led to the identification of many potential materials that were previously unknown, including millions of solid-state compounds and hundreds of nanoparticles with complex compositions and morphologies. Autonomous workflows are being developed to accelerate experimental validation of these bulk and nanoscale materials through synthesis. For colloidal nanoparticles, such strategies have focused primarily on compositionally simple systems, due in part to limitations in the generalizability of chemical reactions and incompatibilities between automated setups and mainstream laboratory methods. As a result, the scope of theoretical versus synthesizable materials is rapidly diverging. Here, we use a simple automated platform to drive a massively generalizable reaction capable of producing more than 651 quadrillion distinct core@multishell nanoparticles using a single set of reaction conditions. As a strategic model system, we chose a family of seven isostructural layered rare earth (RE) oxychloride compounds, REOCl (RE = La, Ce, Pr, Nd, Sm, Gd, Dy), which are well-known 2D materials with composition-dependent optical, electronic, and catalytic properties. By integrating a computer-driven, hobbyist-level pump system with a laboratory-scale synthesis setup, we could grow up to 20 REOCl shells in any sequence on a REOCl nanoparticle core. Reagent injection sequences were programmed to introduce composition gradients, luminescent dopants, and binary through high-entropy solid solutions, which expands the library to a near-infinite scope. We also used ChatGPT to randomly select several core@multishell nanoparticle targets within predefined constraints and then direct the automated setup to synthesize them. This platform, which includes both massively generalizable nanochemical reactions and laboratory-scale automated synthesis, is poised for plug-and-play integration into autonomous materials discovery workflows to expand the translation of prediction to realization through efficient synthesis.

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