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In This Issue Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22
Proceedings of the National Academy of Sciences, Volume 122, Issue 16, April 2025.
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Dynamical-generative downscaling of climate model ensembles Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Ignacio Lopez-Gomez, Zhong Yi Wan, Leonardo Zepeda-Núñez, Tapio Schneider, John Anderson, Fei Sha
Regional high-resolution climate projections are crucial for many applications, such as agriculture, hydrology, and natural hazard risk assessment. Dynamical downscaling, the state-of-the-art method to produce localized future climate information, involves running a regional climate model (RCM) driven by an Earth System Model (ESM), but it is too computationally expensive to apply to large climate
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Lab earthquakes reveal a wide range of rupture behaviors controlled by fault bends Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Tom Gabrieli, Yuval Tal
Natural faults are typically nonplanar and exhibit multiple bends, which deviate from the general fault orientation at different angles. However, while such deviations are considered a key factor controlling earthquake propagation and, hence, its intensity and magnitude, direct experimental evidence of how bends affect earthquake ruptures is nearly nonexistent. Here, we present direct experimental
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Comparative analysis of STP6 and STP10 unravels molecular selectivity in sugar transport proteins Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Camilla Gottlieb Andersen, Laust Bavnhøj, Søren Brag, Anastasiia Bohush, Adriana Chrenková, Jan Heiner Driller, Bjørn Panyella Pedersen
The distribution of sugars is crucial for plant energy, signaling, and defense mechanisms. Sugar Transport Proteins (STPs) are Sugar Porters (SPs) that mediate proton-driven cellular uptake of glucose. Some STPs also transport fructose, while others remain highly selective for only glucose. What determines this selectivity, allowing STPs to distinguish between compounds with highly similar chemical
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Five-body recombination of identical bosons Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Michael D. Higgins, Chris H. Greene
This work treats resonant collisions between five identical ultracold bosons in the framework of the adiabatic hyperspherical representation. The five-body recombination rate coefficient is quantified using a semiclassical description in conjunction with an analysis of the lowest five-body hyperspherical adiabatic potential curves in a scattering length regime with no universal weakly bound tetramers
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Host use drives convergent evolution in clownfish Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Théo Gaboriau, Anna Marcionetti, Alberto Garcia-Jimenez, Sarah Schmid, Lucy M. Fitzgerald, Baptiste Micheli, Benjamin Titus, Nicolas Salamin
Clownfishes (Amphiprioninae) are a fascinating example of a marine radiation. From a central Pacific ancestor, they quickly colonized the coral reefs of the Indo-Pacific and diversified independently on each side of the Indo-Australian Archipelago. Their association with sea anemones has been proposed to be a key innovation that enabled the clownfish radiation. However, this intuition has little empirical
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Biofilm architecture determines the dissemination of conjugative plasmids Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Sarah Djermoun, Daniel K. H. Rode, Eva Jiménez-Siebert, Niklas Netter, Christian Lesterlin, Knut Drescher, Sarah Bigot
Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic resistance among bacteria. While the molecular mechanisms of conjugation have been extensively studied, our understanding of plasmid transfer dynamics within spatially structured bacterial communities and the influence of community architecture on plasmid dissemination
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Prevalence of simplex compression in adversarial deep neural networks Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Yang Cao, Yanbo Chen, Weiwei Liu
Neural collapse (NC) reveals that the last layer of the network can capture data representations, leading to similar outputs for examples within the same class, while outputs for examples from different classes form a simplex equiangular tight frame (ETF) structure. This phenomenon has garnered significant attention due to its implications on the intrinsic properties of neural networks. Interestingly
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Trophic convergence of marine vertebrate communities worldwide Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-25 Juan David González-Trujillo, Jorge Assis, Ester Serrão, Mark John Costello, Eliza Fragkopoulou, Manuel Mendoza, Miguel B. Araújo
Biogeographic regions arise due to constraints on species ranges, fostering lineage divergence as a result. Yet, convergent evolution means that evolutionary distinct lineages can share similar characteristics when subjected to similar environmental conditions. The ecological convergence of distinct regions has been demonstrated in terrestrial communities, but it remains uncertain if marine systems
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Conserved C143 forms a branched intermediate in Hedgehog autoprocessing: A cancer drug discovery target against Hedgehog signaling Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Shannon Faris, Ke Xia, Andrew G. Wagner, Zihan Xu, Nathan Smith, José-Luis Giner, Brian Callahan, Jian Xie, Chunyu Wang
Hedgehog (Hh) signaling plays fundamental roles in embryonic development while its abnormal activation in adults is associated with cancer. Hh targeting drugs have gained FDA approval but resistance emerged quickly, underlining the need for novel types of Hh inhibitors. Hh signaling is initiated by the Hh ligand, generated from the autoprocessing of Hh precursor. However, the catalytic role of a highly
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Patulin and Xestoquinol are inhibitors of DNA topoisomerase 1 Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Emanuela Tumini, Ralf E. Wellinger, Emilia Herrera-Moyano, Patricia Navarro-Cansino, María García-Rubio, Daniel Salas-Lloret, Alejandro Losada, María J. Muñoz-Alonso, Hélène Gaillard, Rosa Luna, Andrés Aguilera
DNA topoisomerase 1 (TOP1) is essential for transcription, replication, and repair. Its function relies on two catalytic steps, DNA breakage and rejoining. Inhibitors of the second step prevent DNA rejoining and lead to persistent DNA breaks, acting as topoisomerase poisons, used as anticancer drugs. However, reliable inhibitors of the first step are not available. Here, we provide genetic and molecular
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Bounded dissipation law and profiles of turbulent velocity moments in wall flows Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Xi Chen, Katepalli R. Sreenivasan
Understanding the effects of solid boundaries on turbulent fluctuations remains a long-standing challenge. Available data on mean-square fluctuations in these flows show apparent contradiction with classical scaling. We had earlier proposed an alternative model based on the principle of bounded dissipation. Despite its putative success, a conclusive outcome requires much higher Reynolds numbers than
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Disentangling conduction pathways at the ionic–electronic interface in EMI-TFSI-covered graphene transistors Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Mathieu Lizée, Ali Esfandiar, Eva Panoni, Artem Mischenko, Pierre-Louis Taberna, Patrice Simon, Lydéric Bocquet
Transport of electrons and ions at carbon surfaces immersed in electrolytes is instrumental for a wide variety of membrane processes as well as energy storage in batteries and supercapacitors. Ion transport in a nanoporous electrode strongly depends on its electronic conductance and on the interfacial capacitance with the electrolyte. In this study, we use in-plane impedance spectroscopy to disentangle
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Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Forson Gao, Fuzhou Ye, Martin Buck, Xiaodong Zhang
Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ 54 . σ 54 recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does
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Evolutionary feedbacks for Drosophila aggression revealed through experimental evolution Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Anna R. Girardeau, Grace E. Enochs, Julia B. Saltz
Evolutionary feedbacks occur when evolution in one generation alters the environment experienced by subsequent generations and are an expected result of indirect genetic effects (IGEs). Hypotheses abound for the role of evolutionary feedbacks in climate change, agriculture, community dynamics, population persistence, social interactions, the genetic basis of evolution, and more, but evolutionary feedbacks
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Infrared light stimulates the cochlea through a mechanical displacement detected and amplified by hair cells Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Julien B. Azimzadeh, Patricia M. Quiñones, John S. Oghalai, Anthony J. Ricci
Although cochlear implants (CI) are the standard of care for profound sensorineural hearing loss they are technically constrained by the tendency of electrical current to spread within the fluid-filled chambers of the cochlea. This limits the resolution of individual electrodes and patients’ perceptions of complex sounds. Infrared irradiation has been proposed as an alternative to electrical stimulation
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Molecular organization of central cholinergic synapses Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Justin S. Rosenthal, Dean Zhang, Jun Yin, Caixia Long, George Yang, Yan Li, Zhiyuan Lu, Wei-Ping Li, Zhiheng Yu, Jiefu Li, Quan Yuan
Synapses have undergone significant diversification and adaptation, contributing to the complexity of the central nervous system. Understanding their molecular architecture is essential for deciphering the brain’s functional evolution. While nicotinic acetylcholine receptors (nAchRs) are widely distributed across metazoan brains, their associated protein networks remain poorly characterized. Using
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Morphogenesis of spin cycloids in a noncollinear antiferromagnet Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Shashank Kumar Ojha, Pratap Pal, Sergei Prokhorenko, Sajid Husain, Maya Ramesh, Xinyan Li, Deokyoung Kang, Peter Meisenheimer, Darrell G. Schlom, Paul Stevenson, Lucas Caretta, Yousra Nahas, Yimo Han, Lane W. Martin, Laurent Bellaiche, Chang-Beom Eom, Ramamoorthy Ramesh
Pattern formation in spin systems with continuous-rotational symmetry (CRS) provides a powerful platform to study emergent complex magnetic phases and topological defects in condensed-matter physics. However, its understanding and correlation with unconventional magnetic order along with high-resolution nanoscale imaging are challenging. Here, we employ scanning nitrogen vacancy (NV) magnetometry to
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Mechanism of read-through enhancement by aminoglycosides and mefloquine Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-24 Olga Kolosova, Yury Zgadzay, Artem Stetsenko, Anastasia P. Sukhinina, Anastasia Atamas, Shamil Validov, Andrey Rogachev, Konstantin Usachev, Lasse Jenner, Sergey E. Dmitriev, Gulnara Yusupova, Albert Guskov, Marat Yusupov
Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of aminoglycosides, particularly in combination with stop-codon read-through enhancers, for developing drugs that can rescue the production of full-length proteins. Using X-ray crystallography and single-particle
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Bridging life satisfaction data and neurobiological measures would elucidate human well-being. Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Anthony Brandt,Cokorda Bagus Jaya Lesmana,Elkhonon Goldberg
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LACE-UP: An ensemble machine-learning method for health subtype classification on multidimensional binary data Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Rebecca Danning, Frank B. Hu, Xihong Lin
Disease and behavior subtype identification is of significant interest in biomedical research. However, in many settings, subtype discovery is limited by a lack of robust statistical clustering methods appropriate for binary data. Here, we introduce LACE-UP [latent class analysis ensembled with UMAP (uniform manifold approximation and projection) and PCA (principal components analysis)], an ensemble
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Elevated UDP-glucuronic acid levels mend drug resistance and stress responses via a protease and a transporter in Cryptococcus gattii Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Sujiraphong Pharkjaksu, Hongyi Cai, Peter J. Walter, Yun C. Chang, Kyung J. Kwon-Chung
UDP-glucuronic acid (UDP-GlcUA) is a nucleotide sugar essential for various biological processes in many organisms, and its excess within the cell can disrupt cellular functions. In Cryptococcus , mutations in the UXS1 gene which encodes an enzyme responsible for converting UDP-GlcUA into UDP-xylose, result in excessive accumulation of UDP-GlcUA and confer resistance to the antifungal drug 5-fluorocytosine
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B cell–derived acetylcholine mitigates skin inflammation in mice through α9 nicotinic acetylcholine receptor–mediated signaling Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Erica Foffi, Francesco Rugolo, Nisha Ramamurthy, Jillian Haight, Simone Helke, Annick You-Ten, Chantal Tobin, Soode Moghadas Jafari, Andrew J. Elia, Thorsten Berger, Eleonora Candi, Gerry Melino, Tak W. Mak
Chronic inflammatory skin disorders are characterized by keratinocyte hyperproliferation and hyperactivation as well as immune cell infiltration. We investigated whether immune cell–derived acetylcholine (ACh) is a modulator of skin inflammation in mice. Here, we identify skin epithelial B cells as a key source of ACh that damps down inflammation. We used imiquimod (IMQ) to induce inflammatory skin
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A simple method for mapping the location of cross-β-forming regions within protein domains of low sequence complexity Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Jinge Gu, Xiaoming Zhou, Lillian Sutherland, Glen Liszczak, Steven L. McKnight
Protein domains of low sequence complexity are unable to fold into stable, three-dimensional structures. In test tube studies, these unusual polypeptide regions can self-associate in a manner causing phase separation from aqueous solution. This form of protein:protein interaction has been implicated in numerous examples of dynamic morphological organization within eukaryotic cells. In several cases
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Neuronal autophagy controls excitability via ryanodine receptor–mediated regulation of calcium-activated potassium channel function Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Gaga Kochlamazashvili, Aarti Swaminathan, Alexander Stumpf, Amit Kumar, York Posor, Dietmar Schmitz, Volker Haucke, Marijn Kuijpers
Glutamate-mediated neuronal hyperexcitation plays a causative role in eliciting seizures and promoting epileptogenesis. Recent data suggest that altered autophagy can contribute to the occurrence of epilepsy. We examined the role of autophagy in neuronal physiology by generating knockout mice conditionally lacking the essential autophagy protein ATG5 in glutamatergic neurons. We demonstrate that conditional
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A selfish supergene causes meiotic drive through both sexes in Drosophila Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Graeme L. Keais, Chadi M. Saad-Roy, Emmanuel Gonzalez-Sqalli, Candice N. Powell, Loren H. Rieseberg, Ryan M. R. Gawryluk, P. van den Driessche, Kevin H.-C. Wei, Benjamin Loppin, Steve J. Perlman
Meiotic drivers are selfish genetic elements that bias their own transmission during meiosis or gamete formation. Due to the fundamental differences between male and female meiosis in animals and plants, meiotic drivers operate through distinct mechanisms in the two sexes: In females, they exploit the asymmetry of meiosis to ensure their inclusion in the egg, whereas in males, they eliminate competing
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Fungal Argonaute proteins act in bidirectional cross-kingdom RNA interference during plant infection Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 An-Po Cheng, Lihong Huang, Lorenz Oberkofler, Nathan R. Johnson, Adrian-Stefan Glodeanu, Kyra Stillman, Arne Weiberg
Argonaute (AGO) proteins bind to small RNAs to induce RNA interference (RNAi), a conserved gene regulatory mechanism in animal, plant, and fungal kingdoms. Small RNAs of the fungal plant pathogen Botrytis cinerea were previously shown to translocate into plant cells and to bind to the host AGO, which induced cross-kingdom RNAi to promote infection. However, the role of pathogen AGOs during host infection
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Pathogen growth and virulence dynamics drive the host evolution against coinfections Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Srijan Seal, Dipendra Nath Basu, Kripanjali Ghosh, Aryan Ramachandran, Rintu Kutum, Triveni Shelke, Ishaan Gupta, Imroze Khan
The occurrence of coinfections, where hosts are simultaneously infected by multiple pathogens, is widespread in nature and has significant negative impacts on global health. In humans, over one-sixth of the world’s population is affected by coinfections, contributing to several diseases. However, despite the broad ecological relevance and impact on global health, most biomedical research has focused
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The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Ling-Qi Zhang, Jiang Mao, Geoffrey K. Aguirre, Alan A. Stocker
The tilt illusion—a bias in the perceived orientation of a center stimulus induced by an oriented surround—illustrates how context shapes visual perception. Although extensively studied for decades, we still lack a comprehensive account of the illusion that connects its behavioral and neural characteristics. Here, we demonstrate that the tilt illusion originates from dynamic changes in neural coding
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Distinct oxytocin signaling pathways synergistically mediate rescue-like behavior in mice Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Feng-Rui Zhang, Juan Liu, Jieqi Wen, Zi-Yan Zhang, Yijia Li, Eric Song, Li Hu, Zhou-Feng Chen
Spontaneous rescue behavior enhances the well-being and survival of social animals, yet the neural mechanisms underlying the recognition and response to conspecifics in need remain unclear. Here, we report that observer mice experience distress when encountering anesthetized conspecifics, prompting spontaneous rescue-like behavior toward the unconscious mice. This behavior facilitates the earlier awakening
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Mixing individual and collective behaviors to predict out-of-routine mobility Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-23 Sebastiano Bontorin, Simone Centellegher, Riccardo Gallotti, Luca Pappalardo, Bruno Lepri, Massimiliano Luca
Predicting human displacements is crucial for addressing various societal challenges, including urban design, traffic congestion, epidemic management, and migration dynamics. While predictive models like deep learning and Markov models offer insights into individual mobility, they often struggle with out-of-routine behaviors. Our study introduces an approach that dynamically integrates individual and
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FlgY, PflA, and PflB form a spoke–ring network in the high-torque flagellar motor of Helicobacter pylori Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Shoichi Tachiyama, Kyle Rosinke, Mohammad F. Khan, Xiaotian Zhou, Yue Xin, Jack M. Botting, Jian Yue, Anna Roujeinikova, Timothy R. Hoover, Jun Liu
Helicobacter pylori has evolved distinct flagellar motility to colonize the human stomach. Rotation of the H. pylori flagella is driven by one of the largest known bacterial flagellar motors. In addition to the core motor components found in Escherichia coli and Salmonella enterica , the flagellar motor in H. pylori possesses many accessories that enable the bacteria to penetrate the gastric mucus
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Opioid receptors reveal a discrete cellular mechanism of endosomal G protein activation Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Nicole M. Fisher, Mark von Zastrow
Many GPCRs initiate a second phase of G protein-mediated signaling from endosomes. This inherently requires the GPCR to increase cognate G protein activity on the endosome surface. G s -coupled GPCRs are thought to achieve this by internalizing and mediating a second round of allosteric coupling to G proteins on the endosome membrane. Here, we provide evidence that the μ-opioid receptor (MOR), a G
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Horizontal transfer of nuclear DNA in transmissible cancer Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Kevin Gori, Adrian Baez-Ortega, Andrea Strakova, Maximilian R. Stammnitz, Jinhong Wang, Jonathan Chan, Katherine Hughes, Sophia Belkhir, Maurine Hammel, Daniela Moralli, James Bancroft, Edward Drydale, Karen M. Allum, María Verónica Brignone, Anne M. Corrigan, Karina F. de Castro, Edward M. Donelan, Ibikunle A. Faramade, Alison Hayes, Nataliia Ignatenko, Rockson Karmacharya, Debbie Koenig, Marta Lanza-Perea
Horizontal transfer of nuclear DNA between cells of host and cancer is a potential source of adaptive variation in cancer cells. An understanding of the frequency and significance of this process in naturally occurring tumors is, however, lacking. We screened for this phenomenon in the transmissible cancers of dogs and Tasmanian devils and found an instance in the canine transmissible venereal tumor
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Relaxation to universal non-Maxwellian equilibria in a collisionless plasma Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Robert J. Ewart, Michael L. Nastac, Pablo J. Bilbao, Thales Silva, Luís O. Silva, Alexander A. Schekochihin
Generic equilibria are derived for turbulent relaxing plasmas via an entropy-maximization procedure that accounts for the short-time conservation of certain collisionless invariants. The conservation of these collisionless invariants endows the system with a partial “memory” of its prior conditions but is imperfect on long time scales due to the development of a turbulent cascade to small scales, which
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Extreme weather variability on hot rocky exoplanet 55 Cancri e explained by magma temperature–cloud feedback Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Kaitlyn Loftus, Yangcheng Luo, Bowen Fan, Edwin S. Kite
Observations of the hot rocky exoplanet 55 Cancri e report significant but unexplained variability in brightness across visible and infrared bands, e.g., on subweekly timescales, its mid-infrared brightness temperature fluctuates by approximately 1,400 K (with hundreds of Kelvin uncertainty). We propose a magma temperature–cloud feedback as a potential explanation that relies on the planet’s atmosphere
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Ligand-binding pockets in RNA and where to find them Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Seth D. Veenbaas, Jordan T. Koehn, Patrick S. Irving, Nicole N. Lama, Kevin M. Weeks
RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules—via well-defined ligand-binding pockets—to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA–ligand interactions remains unrealized
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Proteostasis landscapes of cystic fibrosis variants reveal drug response vulnerability Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Eli Fritz McDonald, Minsoo Kim, John A. Olson, Jens Meiler, Lars Plate
Cystic fibrosis (CF) is a lethal genetic disorder caused by variants in CF transmembrane conductance regulator (CFTR). Many variants are treatable with correctors, which enhance the folding and trafficking of CFTR. However, approximately 3% of persons with CF harbor poorly responsive variants. Here, we used affinity purification mass spectrometry proteomics to profile the protein homeostasis (proteostasis)
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Annihilation-limited long-range exciton transport in high-mobility conjugated copolymer films Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Yuping Shi, Partha P. Roy, Naoki Higashitarumizu, Tsung-Yen Lee, Quanwei Li, Ali Javey, Katharina Landfester, Iain McCulloch, Graham R. Fleming
A combination of ultrafast, long-range, and low-loss excitation energy transfer from the photoreceptor location to a functionally active site is essential for cost-effective polymeric semiconductors. Delocalized electronic wavefunctions along π-conjugated polymer (CP) backbone can enable efficient intrachain transport, while interchain transport is generally thought slow and lossy due to weak chain–chain
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A unified framework for hydromechanical signaling can explain transmission of local and long-distance signals in plants Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Vesna Bacheva, Fulton E. Rockwell, Jean-Baptiste Salmon, Jesse D. Woodson, Margaret H. Frank, Abraham D. Stroock
Local wounding in plants triggers signals that travel locally within the wounded leaf or systemically through the vasculature to distant leaves. Our understanding of the mechanisms of initiation and propagation of this ubiquitous class of signals remains incomplete. Here, we develop a unifying framework based on poroelastic dynamics to study two coupled biophysical processes—propagation of pressure
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NAT10 exacerbates acute renal inflammation by enhancing N4-acetylcytidine modification of the CCL2/CXCL1 axis Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Jia-nan Wang, Xiao-guo Suo, Ju-tao Yu, Qi-chao Luo, Ming-lu Ji, Meng-meng Zhang, Qi Zhu, Xin-ran Cheng, Chao Hou, Xin Chen, Fang Wang, Chuan-hui Xu, Chao Li, Shuai-shuai Xie, Jie Wei, Dan-feng Zhang, Xin-ru Zhang, Zhi-juan Wang, Yu-hang Dong, Sai Zhu, Li-jin Peng, Xiang-yu Li, Hai-yong Chen, Tao Xu, Juan Jin, Fei Xavier Chen, Xiao-ming Meng
Inflammation plays an essential role in eliminating microbial pathogens and repairing tissues, while sustained inflammation accelerates kidney damage and disease progression. Therefore, understanding the mechanisms of the inflammatory response is vital for developing therapies for inflammatory kidney diseases like acute kidney injury (AKI), which currently lacks effective treatment. Here, we identified
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Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Joshua L. Dickerson, Katerina Naydenova, Mathew J. Peet, Hugh Wilson, Biplob Nandy, Greg McMullan, Robert Morrison, Christopher J. Russo
The physical limit in determining the atomic structure of biological molecules is radiation damage. In electron cryomicroscopy, there have been numerous attempts to reduce the effects of radiation damage by cooling the specimen beyond liquid-nitrogen temperatures, yet all failed to realize the potential improvement for single-particle structure determination. We have identified the physical causes
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Phospholipid flippase ATP11A brokers uterine epithelial integrity and function Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Alexa Krala, Aleksandra O. Tsolova, Bethany N. Radford, Anshul S. Jadli, Xiang Zhao, Danielle Blackwell, Ankita Narang, Wendy Dean, Myriam Hemberger
Uterine adaptations driven by the steroid hormones estrogen and progesterone are pivotal for embryo implantation and, ultimately, for a successful pregnancy. Here, we show in mice that genetic ablation of the membrane lipid flippase Atp11a causes severe deficits in this hormonal response and profound defects in the morphological organization and transcriptional profile of the uterine epithelial compartment
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40 Hz sensory stimulation enhances CA3–CA1 coordination and prospective coding during navigation in a mouse model of Alzheimer’s disease Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-22 Abigail L. Paulson, Lu Zhang, Ashley M. Prichard, Annabelle C. Singer
40 Hz sensory stimulation (“flicker”) has emerged as a new technique to potentially mitigate pathology and improve cognition in mouse models of Alzheimer’s disease (AD) pathology. However, it remains unknown how 40 Hz flicker affects neural codes essential for memory. Accordingly, we investigate the effects of 40 Hz flicker on neural representations of experience in the hippocampus of the 5XFAD mouse
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The ins and outs of plant specialized metabolite gene organization. Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Richard A Dixon
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PEARLs of wisdom for ribosome-independent peptide bond synthesis. Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Amy M Weeks
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Start your engines: How migratory fibroblasts respond to and remember mechanical stretch. Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Daphne Weihs
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An algorithmic constraint at the transition to complex life. Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Evandro Ferrada
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Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice—An unbiased functional study Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Hongsup Yoon, Lisa Ann Gerdes, Florian Beigel, Yihui Sun, Janine Kövilein, Jiancheng Wang, Tanja Kuhlmann, Andrea Flierl-Hecht, Dirk Haller, Reinhard Hohlfeld, Sergio E. Baranzini, Hartmut Wekerle, Anneli Peters
We developed a two-tiered strategy aiming to identify gut bacteria functionally linked to the development of multiple sclerosis (MS). First, we compared gut microbial profiles in a cohort of 81 monozygotic twins discordant for MS. This approach allowed to minimize confounding effects by genetic and early environmental factors and identified over 50 differently abundant taxa with the majority of increased
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Linking energetic instability to compositional changes in biological communities Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Taku Kadoya, Kenta Suzuki, Akira Terui
The resilience of an ecological community informs us how it will respond to future environmental disturbances. However, the concept is rarely tested in the context of predicting biodiversity change, particularly at broad spatial and taxonomic scales. Here, we show that measures of instability derived from the resilience of the current state of community compositions greatly improve the predictability
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Mitigation justice Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Peter B. Reich, Kathryn Grace, Arun Agrawal, Harini Nagendra
Mitigating climate change and social injustice are critical, interwoven challenges. Climate change is driven by grossly unequal contributions to elevated greenhouse gas emissions among individuals, socioeconomic groups, and nations. Yet, its deleterious impacts disproportionately affect poor and less powerful nations, and the poor and the less powerful within each nation. This climate injustice prompts
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Four-million-year Marinoan snowball shows multiple routes to deglaciation Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Adrian R. Tasistro-Hart, Francis A. Macdonald, James L. Crowley, Mark D. Schmitz
Twice during the Neoproterozoic Era, Earth experienced runaway ice-albedo catastrophes that resulted in multimillion year, low-latitude glaciations: the Sturtian and Marinoan snowball Earths. In the snowball climate state, CO 2 consumption through silicate weathering collapses, and atmospheric CO 2 accumulates via volcanic outgassing until a sufficiently strong greenhouse causes deglaciation. The duration
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Structure in conversation: Evidence for the vocabulary, semantics, and syntax of prosody Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Nadav Matalon, Eyal Weinreb, Dominik Freche, Erez Volk, Tirza Biron, Elisha Moses, David Biron
Prosody, the musical facet of speech, is pivotal in human communication, and its structure and meaning remain subjects of ongoing research. In this study, we introduce a data-driven model for English prosody, based on large-scale analysis of spontaneous conversations. As a first step, we identify approximately 200 discernible prosodic patterns—which we view as building blocks of the prosodic vocabulary—and
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Abiotic origin of the citric acid cycle intermediates Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Mason McAnally, Jana Bocková, Andrew M. Turner, Nana Hara, Daria Mikhnova, Cornelia Meinert, Ralf I. Kaiser
The molecular framework for protometabolism—chemical reactions in a prebiotic environment preceding modern metabolism—has remained unknown in evolutionary biology. Mono-, di-, and tricarboxylic acids that comprise contemporary metabolism, such as the Krebs cycle, are of particular prebiotic relevance and are theorized to predate life on Earth. Researchers have struggled to unravel the molecular origins
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Identifying air quality monitoring deserts in the United States Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Nelson A. Roque, Hailey Andrews, Alexis R. Santos-Lozada
Air quality is associated with adverse health outcomes and mortality risk. While most research has focused on the association between air quality estimates and these outcomes, little is known about the presence of air quality monitoring sites across the United States or the place-level characteristics associated with such placements. We classify counties without a monitoring station as air quality
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Unbalanced social–ecological acceleration led to state formation failure in early medieval Poland Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Adam Izdebski, Sambor Czerwiński, Marek Jankowiak, Marcin Danielewski, Sabina Fiołna, Raphael Gromig, Piotr Guzowski, Negar Haghipour, Irka Hajdas, Piotr Kołaczek, Mariusz Lamentowicz, Katarzyna Marcisz, Jakub Niebieszczański, Paweł Sankiewicz, Bernd Wagner
Rapid social–ecological intensification is a recurrent feature of human history. It occurred in different forms and contexts; its outcomes may have been sustainable or transient. Until recently, such intensifications usually accompanied state formation: Consolidation of political power was often coupled with exponential increase in human exploitation of the environment of a given area. Here, we study
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Ecologically informed solar enables a sustainable energy transition in US croplands Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Matthew A. Sturchio, Adam Gallaher, Steven M. Grodsky
United States (US) croplands are ideal recipient environments for solar photovoltaic (PV) energy because they are flat and have a high solar resource. Perceived threats of solar to agriculture have led some stakeholders to suggest that croplands be exclusively used to produce food. However, 12 million hectares of US croplands, an area about the size of New York State, are already dedicated to corn
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Nonnative tree invaders lead to declines in native tree species richness Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Yunpeng Liu, Samuel M. Scheiner, J. Aaron Hogan, Matthew B. Thomas, Pamela S. Soltis, Robert P. Guralnick, Douglas E. Soltis, Jeremy W. Lichstein
Biological invasions are profoundly altering Earth’s ecosystems, but generalities about the effects of nonnative species on the diversity and productivity of native communities have been elusive. This lack of generality may reflect the limited spatial and temporal extents of most previous studies. Using >5 million tree measurements across eastern US forests from 1995 to 2023, we quantified temporal
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Phase transitions and dimensional cross-over in layered confined solids Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Yong Wang, Junjie Wang, Ge Yao, Zheyong Fan, Enzo Granato, Michael Kosterlitz, Tapio Ala-Nissila, Roberto Car, Jian Sun
The nature of solid phases and cross-over of order–disorder phase transitions from two-dimensional (2D) layers to three-dimensional (3D) bulk in confined atomic systems remain largely unexplained. To this end, we consider noble gases and aluminum confined between graphene sheets at different pressures and temperatures. Using crystal structure search methods and molecular dynamics based on machine-learned
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Rab32 regulates Golgi structure and cell migration through Protein Kinase A–mediated phosphorylation of Optineurin Proc. Natl. Acad. Sci. U.S.A. (IF 9.4) Pub Date : 2025-04-21 Katherine M. Johnson, Maxwell G. Marley, Kristina Drizyte-Miller, Jing Chen, Hong Cao, Nourhan Mostafa, Micah B. Schott, Mark A. McNiven, Gina L. Razidlo
Rab32 is a small GTPase and molecular switch implicated in vesicular trafficking. Rab32 is also an A-Kinase Anchoring Protein (AKAP), which anchors cAMP-dependent Protein Kinase (PKA) to specific subcellular locations and specifies PKA phosphorylation of nearby substrates. Surprisingly, we found that a form of Rab32 deficient in PKA binding (Rab32 L188P) relocalized away from the Golgi apparatus and