Gülberk Bayraktar, Josephine K Dannersø, Sean D S Hansen, Lisbeth Schmidt Laursen, U Valentin Nägerl, Poul Nissen
{"title":"Double periodicity of the AnkyrinG-associated complex in the axon initial segment.","authors":"Gülberk Bayraktar, Josephine K Dannersø, Sean D S Hansen, Lisbeth Schmidt Laursen, U Valentin Nägerl, Poul Nissen","doi":"10.1073/pnas.2612539123","DOIUrl":"https://doi.org/10.1073/pnas.2612539123","url":null,"abstract":"<p><p>The axon initial segment (AIS), situated within the first 20 to 60 µm of the axon, is essential for action potential generation and maintenance of axonal identity [M. N. Rasband, <i>Nat. Rev. Neurosci.</i> <b>11</b>, 552-562 (2010)]. Its structure relies on the beta (β)-IV-spectrin/AnkyrinG (AnkG) scaffold arranged periodically underneath the plasma membrane, harboring diverse membrane proteins [K. Xu, G. Zhong, X. Zhuang, <i>Science</i> <b>339</b>, 452-456 (2013); K. L. Hedstrom, Y. Ogawa, M. N. Rasband, <i>J. Cell Biol.</i> <b>183</b>, 635-640 (2008)]. Although a ~190-nm cytoskeletal periodic organization is well established, the precise stoichiometry and spatial arrangement of AIS proteins within the ~190-nm spatial period remain rudimentary, mostly for lack of sufficient spatial resolution and labeling efficiency. Here, using expansion microscopy and cryoelectron tomography, which overcome these technical limitations, we present data on the organization of the AnkG-associated complex within the ~190-nm spatial period. We demonstrate that exactly two AnkG molecules are situated within each period and with their C termini separated by ~80 nm. By contrast, the AnkG-associated cell-adhesion protein neurofascin-186 appears in clusters of varying sizes that are consistent with the periodic organization of AnkG pairs, yet suggesting a more complex molecular arrangement between the two molecules. Altogether, our approach provides insights into AIS molecular organization and protein stoichiometry.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2612539123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149166921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multidimensional vulnerabilities of informal settlements in the Urban South.","authors":"Mingxing Chen, Wenming Song, Dadao Lu, Yu Deng, Chenglong Wang, Huiping Jiang, Yuyu Zhou, Murray W Scown, Liangkan Chen, Jing Ma, Heran Zheng, Xuemei Bai","doi":"10.1073/pnas.2523034123","DOIUrl":"https://doi.org/10.1073/pnas.2523034123","url":null,"abstract":"<p><p>Informal settlements are widespread and rapidly growing, often associated with high vulnerabilities. However, global-scale understanding on their spatial distribution and complexity of vulnerability is limited. Here, we delineate the informal settlements across a sample of 1,914 cities of the Global South by integrating Sentinel-2 imagery with deep learning models, and we explore the heterogeneity of vulnerability using Urban Informal Settlement Vulnerability Index that encompasses living conditions, social infrastructure, and environmental risk. We found that Urban Informal Settlements cover 12.94 ± 2.52% of their total urban areas (approximately 34.04 × 10<sup>3</sup> km<sup>2</sup>), especially in sub-Saharan Africa, South Asia, and Middle Asia. Sub-Saharan African cities have the highest vulnerability of informal settlements, with 31.75 ± 6.20% of total urban areas being occupied by informal settlements, while East Asian cities exhibit relatively low vulnerability across all dimensions. We also find that urban informal settlements with high environmental exposure are widespread in the Global South, and there is a significantly polarized distribution between \"low\" and \"high\" vulnerability categories. The findings highlight the disparate distribution of multidimensional vulnerability in informal settlements across the Urban South, providing a comparative evidence base for further local assessment and context-specific policy discussions related to SDG 11.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2523034123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaoli Dong, Alexander J Richardson, Rachata Muneepeerakul
{"title":"Evolution shapes ecosystem resilience through spatial self-organization.","authors":"Xiaoli Dong, Alexander J Richardson, Rachata Muneepeerakul","doi":"10.1073/pnas.2536473123","DOIUrl":"https://doi.org/10.1073/pnas.2536473123","url":null,"abstract":"<p><p>Drylands are globally widespread and ecologically important but vulnerable to climate change. Many exhibit spatially self-organized vegetation patterns that enhance resilience by enabling vegetation to reorganize their patterns under drying, thereby optimizing water use and maintaining productivity. Plants can also undergo evolution in response to environmental change. Although both spatial self-organization and rapid evolution are fundamental mechanisms of resilience, their interaction remains largely unknown. Using a theoretical model, we examine how these mechanisms interact to shape vegetation transitions-abrupt or gradual-and ecosystem resilience under climatic drying. We find that pattern formation can suppress adaptation by maintaining soil moisture beneath vegetation patches despite rainfall decline, thereby limiting selection for increased drought tolerance. However, this suppression is largely alleviated under the variable rainfall typical of drylands. In turn, evolution feeds back on self-organization by increasing the spatial plasticity of vegetation patterns and their ability to reorganize under changing climate, although this positive effect weakens as evolutionary rate increases. Considering direct (adaptation) and indirect (pattern-mediated) effects, evolution enhances resilience, with indirect effects via pattern plasticity dominating. Within model scenarios spanning plausible rainfall variability and relative evolutionary-to-ecological rates, more than half of vegetation transitions are abrupt involving biomass losses exceeding 50%, highlighting a potential mechanism underlying recent global observations of widespread abrupt vegetation losses in drylands. These results demonstrate that evolution and spatial self-organization jointly determine dryland resilience under environmental change and highlight the unexpected role of evolution in patterned landscapes, calling for integrative approaches to predict ecosystem responses in a changing world.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2536473123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ecology must shape AI before AI reshapes ecology.","authors":"George Roff","doi":"10.1073/pnas.2619925123","DOIUrl":"https://doi.org/10.1073/pnas.2619925123","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2619925123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149148557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cell identity competes with surface tension to determine stromal organization in tumor spheroids beyond the CAF shell paradigm.","authors":"Claire Wilhelm","doi":"10.1073/pnas.2624455123","DOIUrl":"https://doi.org/10.1073/pnas.2624455123","url":null,"abstract":"<p><p>Cancer-associated fibroblasts (CAFs) are often found forming a peripheral stromal barrier around tumors. Here, this paradigm is challenged using microfabricated 3D cancer-CAF spheroid models combined with quantitative magnetic force tensiometry. A surface tension atlas is established for eight cancer cell lines, three CAF populations, and heterotypic tumor-CAF assemblies, spanning nearly two orders of magnitude. Surface tension is first shown to govern spheroid morphology and modulate drug response. Besides, CAFs consistently occupy the highest end of the surface tension hierarchy, predicting core rather than peripheral localization and directly challenging the shell paradigm. Yet confocal imaging reveals not only central accumulation but also complete CAF-tumor mixing, including in spheroids where cancer cells exhibit surface tensions nearly two orders of magnitude lower than CAFs. Surface tension alone therefore fails to predict CAF organization. Instead, the epithelial-to-mesenchymal transition (EMT) state of cancer cells emerges as a major determinant: epithelial-like tumors promote CAF core accumulation, whereas mesenchymal-like states favor persistent mixing. Peripheral CAF localization emerges only under restricted conditions combining high tumor cohesion and sequential stromal recruitment. Together, these results identify surface tension, EMT state, and assembly chronology as joint determinants of tumor-stroma architecture, revealing a context-dependent organization landscape rather than a universal CAF shell.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2624455123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sunbochen Tang, Themistoklis P Sapsis, Navid Azizan
{"title":"Learning dissipative chaotic dynamics with boundedness guarantees.","authors":"Sunbochen Tang, Themistoklis P Sapsis, Navid Azizan","doi":"10.1073/pnas.2533077123","DOIUrl":"https://doi.org/10.1073/pnas.2533077123","url":null,"abstract":"<p><p>Chaotic dynamics, commonly seen in weather systems and fluid turbulence, are characterized by their sensitivity to initial conditions, which makes accurate prediction challenging. Recent approaches have focused on developing data-driven models that attempt to preserve invariant statistics over long horizons since many chaotic systems exhibit dissipative behaviors and ergodicity. Despite the recent progress in such models, they are still often prone to generating unbounded trajectories, leading to invalid statistics evaluation. To address this fundamental challenge, we introduce a modular framework that provides formal guarantees of trajectory boundedness for neural network chaotic dynamics models. Our core contribution is a dissipative projection layer that leverages control-theoretic principles to ensure the learned system is dissipative. Specifically, our framework simultaneously learns a dynamics emulator and an energy-like function, where the latter is used to construct an algebraic dissipative constraint within the projection layer. Furthermore, the learned invariant level set provides an outer estimate for the system's strange attractor, which is known to be difficult to characterize due to its complex geometry. We demonstrate our model's ability to produce bounded long-horizon forecasts that preserve invariant statistics for chaotic dynamical systems, including Lorenz 96 and a reduced-order model of the Kuramoto-Sivashinsky equation.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2533077123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Quiescence to proliferation transition regulates asynchronous mitochondrial DNA replication dynamics.","authors":"Kiyoshi Miyagawa, Noriko Hosoya","doi":"10.1073/pnas.2602028123","DOIUrl":"https://doi.org/10.1073/pnas.2602028123","url":null,"abstract":"<p><p>Each human cell contains hundreds to thousands of mitochondrial DNA (mtDNA) copies, only a small fraction of which replicates independently of the cell cycle. An asynchronous replication of the leading and lagging strands has been proposed to represent a major replication mode in mitochondria, complicating the investigation of mechanisms that regulate mtDNA replication. Using single-DNA-molecule analysis that distinguishes the origins and timing of replication of each strand, we show that the mitochondrial DNA replication machinery responds to the transition from quiescence to proliferation by dynamically dissociating strand-specific replication rates and modulating the physiological requirements for factors involved in replication and transcription. During this response, the requirement for mitochondrial RNA polymerase (POLRMT) in replication initiation increases, whereas that for primase-polymerase (PrimPol), which is thought to function in DNA repriming at DNA lesions, eventually decreases. Thus, precise quantification of mtDNA replication rates at the single-strand level reveals the temporally dynamic nature of the mtDNA replication machinery during the transition from quiescence to proliferation.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2602028123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenzheng Shi, Christopher E Miles, Jungsik Noh, Gaudenz Danuser, Alex Mogilner
{"title":"Reconstructing actin dynamics of the leading edge from observational data.","authors":"Wenzheng Shi, Christopher E Miles, Jungsik Noh, Gaudenz Danuser, Alex Mogilner","doi":"10.1073/pnas.2603666123","DOIUrl":"https://doi.org/10.1073/pnas.2603666123","url":null,"abstract":"<p><p>Mesenchymal cell migration starts with the protrusion of the cell's leading edge, enabled by the branching growth of the actin network. Two crucial molecular players in protrusion are actin filaments and the Arp2/3 complex, the branching agent. Traditionally, protrusion models are intuited from several perturbative experiments. Recent multiplex microscopy imaging data promise to change this paradigm by providing measurements of naturally fluctuating densities of key proteins at the leading edge of unperturbed cells. We report an attempt to reconstruct the mechanistic protrusion model from such data. We analyze fluctuations of densities of actin filaments and Arp2/3 complex and cell edge velocity using phase space and regression analysis to reconstruct linearized dynamics of the coupled actin-Arp2/3-velocity system. We then build a nonlinear model of these dynamics based on previous knowledge of this system and parsimony. The resulting models recover the rates of reactions and mechanical and transport processes in the lamellipodium from a single nonperturbative experiment. The models posit that the dominant nonlinear term in the lamellipodial dynamics corresponds to the retrograde flow of the actin network in the cell frame. The models suggest that the protrusion is dominated by a damped oscillatory cycle resulting from a combination of positive feedback from the Arp2/3 complex to protrusion velocity and negative feedback from actin density to the velocity.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2603666123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149207786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lida Aeindartehran, Luke Kwan, Ibrahim Tahir, Daniel K Unruh, Maria Petrov, William B Stoll, Alejandro Alvarez, Jia-Sen Hu, Ejaz Ahmed, Nilanjan Seal, Nathan Taton, Anja Milenkova, Robert E Dinnebier, Murillo Longo Martins, Yongqiang Cheng, Anibal J Ramirez-Cuesta, Jin S Zhang, Michael T Ruggiero, Panče Naumov, Tomče Runčevski
{"title":"Ice-ray pentagonal packing of pseudo-fivefold helices.","authors":"Lida Aeindartehran, Luke Kwan, Ibrahim Tahir, Daniel K Unruh, Maria Petrov, William B Stoll, Alejandro Alvarez, Jia-Sen Hu, Ejaz Ahmed, Nilanjan Seal, Nathan Taton, Anja Milenkova, Robert E Dinnebier, Murillo Longo Martins, Yongqiang Cheng, Anibal J Ramirez-Cuesta, Jin S Zhang, Michael T Ruggiero, Panče Naumov, Tomče Runčevski","doi":"10.1073/pnas.2608878123","DOIUrl":"https://doi.org/10.1073/pnas.2608878123","url":null,"abstract":"<p><p>While fivefold point symmetry is common in nature, fivefold spatial symmetry is seldom observed. Regular pentagons cannot tile a plane without leaving voids, and even the densest \"ice-ray\" packing is exceptionally rare. Fivefold helices are equally elusive. We report a small molecule that self-assembles into hydrogen-bonded pseudo-fivefold helices and adopts an ice-ray pentagonal packing motif over crystallographic length scales using peripheral disorder that partially occupies regions that would otherwise be void in an ideal pentagonal tessellation. The resulting structure exhibits weak and nondirectional interhelical interactions within the (<i>bc</i>) plane and comparatively strong and directional intrahelical hydrogen bonding along the <i>a</i> axis. This structural anisotropy gives rise to single crystals with large aspect ratios and distinct mechanical behavior. This realization of two rare structural motifs within a single crystal shows the capability of simple organic molecules to form complex structures and highlights an untapped potential for symmetry engineering in molecular solids through the interplay of intermolecular interactions with pronounced differences in strength and directionality.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2608878123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jianhui Ye, An Yan, Qiting Fang, Yijie Liu, Chunyang Li
{"title":"Shading enhances Se accumulation in tea leaves through promoting CsMYB7-like-mediated conversion of Se (VI) to Se (IV).","authors":"Jianhui Ye, An Yan, Qiting Fang, Yijie Liu, Chunyang Li","doi":"10.1073/pnas.2535927123","DOIUrl":"https://doi.org/10.1073/pnas.2535927123","url":null,"abstract":"<p><p>Limited selenium (Se) accumulation in agricultural products contributes to widespread dietary Se deficiency, posing a global nutritional threat. Efficient agronomic strategies to enhance Se biofortification in crops are still lacking. Here, we reveal the synergistic effects of shading and Se nanoparticles application on Se biofortification in tea leaves. Field experiments demonstrate that shading enhances Se accumulation in tea leaves under sufficient Se supply, through activating Se metabolism pathway. We identify CsAPR1 functions at the early stage of Se assimilation, catalyzing the reduction of Se (VI). The transcription of <i>CsAPR1</i> is activated by CsMYB7-like and is further promoted by shading through interaction with CsbHLH70. Under sunlight, CsHY5 competes with CsbHLH70 for binding to CsMYB7-like, thereby attenuating CsMYB7-like-mediated transcription of <i>CsAPR1</i> and suppressing Se accumulation in tea plants. Our findings reveal the molecular mechanisms underlying shade-induced enhancement of Se biofortification, offering insights and strategies for Se-enriched crop production.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 42","pages":"e2535927123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}