Proceedings of the National Academy of Sciences of the United States of America最新文献

{"title":"A symbiotic gene stimulates aggressive behavior favoring the survival of parasitized caterpillars","authors":"Zhiwei Wu, Xiaotong Wu, Zhizhi Wang, Xiqian Ye, Lan Pang, Yanping Wang, Yuenan Zhou, Ting Chen, Sicong Zhou, Zehua Wang, Yifeng Sheng, Qichao Zhang, Jiani Chen, Pu Tang, Xingxing Shen, Jianhua Huang, Jean-Michel Drezen, Michael R. Strand, Xuexin Chen","doi":"10.1073/pnas.2422935122","DOIUrl":"https://doi.org/10.1073/pnas.2422935122","url":null,"abstract":"Animals often exhibit increased aggression in response to starvation, while parasites often manipulate host behavior. In contrast, underlying molecular mechanisms for these behavioral changes are mostly unknown. The diamondback moth, <jats:italic>Plutella xylostella</jats:italic> , is an agricultural pest that feeds on cruciferous plants as larvae, while <jats:italic>Cotesia vestalis</jats:italic> is a parasitoid wasp that parasitizes diamondback moth larvae. In this study, we determined that unparasitized diamondback moth larvae exhibit increased aggression and cannibalism when starved, while starved larvae parasitized by <jats:italic>C. vestalis</jats:italic> were more aggressive than unparasitized larvae. <jats:italic>C. vestalis</jats:italic> harbors a domesticated endogenized virus named Cotesia vestalis bracovirus (CvBV) that wasps inject into parasitized hosts. Starvation increased octopamine (OA) levels in the central nervous system (CNS) of diamondback moth larvae while a series of experiments identified a CvBV-encoded gene product named Assailant that further increased aggression in starved diamondback moth larvae. We determined that Assailant increases OA levels by activating <jats:italic>tyramine beta-hydroxylase</jats:italic> ( <jats:italic>PxTβh</jats:italic> ), which is a key enzyme in the OA biosynthesis pathway. Ectopic expression of <jats:italic>assailant</jats:italic> in <jats:italic>Drosophila melanogaster</jats:italic> likewise upregulated expression of <jats:italic>DmTβh</jats:italic> and OA, which increased aggressive behavior in male flies as measured by a well-established assay. While parasitized hosts are often thought to be at a competitive disadvantage to nonparasitized individuals, our results uncover how a parasitoid uses an endogenized virus to increase host aggression and enhance survival of offspring when competing against unparasitized hosts.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"39 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884760","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":"Challenges to sustainable large-scale shale gas development in China","authors":"Jian Wu, Jingqiang Tan, Jinqi Xu, Lei Li, Gregory C. Beroza, Kevin G. Mumford, Cole Van De Ven, Baixi Chen, Derek Elsworth","doi":"10.1073/pnas.2415192122","DOIUrl":"https://doi.org/10.1073/pnas.2415192122","url":null,"abstract":"China’s shale gas production has grown annually by 21% since 2017 with long-term national energy strategy calling for continued expansion. This large-scale shale gas development is challenged by constraints on water supply. It requires over 6,000 new wells to be drilled within the Yangtze River Basin in South China—one of China’s most populated regions with sensitive ecological and geological conditions, posing significant environmental threats to the hydrosphere, atmosphere, and biosphere. Hydraulic fracturing-induced seismicity also adds to the existing earthquake risk for the Sichuan/Chongqing region. These potential negative impacts challenge both China’s and the United Nations’ sustainable development goals. We explore China’s current shale gas operations in the Yangtze River Basin and their interaction with the environment from these multiple perspectives. We then suggest future improvements to practice that will promote sustainable development to jointly satisfy China’s burgeoning energy needs. We conclude that China’s shale gas industry would benefit from an innovation ecosystem that involves companies and research institutions, and that there is an urgent need to implement environmental regulations for shale gas extraction.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"18 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884764","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":"Integrating single-cell data with biological variables","authors":"Yang Zhou, Qiongyu Sheng, Shuilin Jin","doi":"10.1073/pnas.2416516122","DOIUrl":"https://doi.org/10.1073/pnas.2416516122","url":null,"abstract":"Constructing single-cell atlases requires preserving differences attributable to biological variables, such as cell types, tissue origins, and disease states, while eliminating batch effects. However, existing methods are inadequate in explicitly modeling these biological variables. Here, we introduce SIGNAL, a general framework that leverages biological variables to disentangle biological and technical effects, thereby linking these metadata to data integration. SIGNAL employs a variant of principal component analysis to align multiple batches, enabling the integration of 1 million cells in approximately 2 min. SIGNAL, despite its computational simplicity, surpasses state-of-the-art methods across multiple integration scenarios: 1) heterogeneous datasets, 2) cross-species datasets, 3) simulated datasets, 4) integration on low-quality cell annotations, and 5) reference-based integration. Furthermore, we demonstrate that SIGNAL accurately transfers knowledge from reference to query datasets. Notably, we propose a self-adjustment strategy to restore annotated cell labels potentially distorted during integration. Finally, we apply SIGNAL to multiple large-scale atlases, including a human heart cell atlas containing 2.7 million cells, identifying tissue- and developmental stage-specific subtypes, as well as condition-specific cell states. This underscores SIGNAL’s exceptional capability in multiscale analysis.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884754","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":"Possible evidence of excitonic condensation in a topological insulator","authors":"Ryo Mori, Kazuaki Takasan, Ping Ai, Samuel Ciocys, Kaishu Kawaguchi, Takeshi Kondo, Takahiro Morimoto, Alessandra Lanzara","doi":"10.1073/pnas.2422667122","DOIUrl":"https://doi.org/10.1073/pnas.2422667122","url":null,"abstract":"The transient excitonic condensate is a nonequilibrium electron–hole Bardeen–Cooper–Schrieffer state in a photoexcited semiconductor and semimetal, where electron–hole pairs undergo a phase transition and condense into a single coherent quantum state. Despite numerous experimental works to realize the predicted excitonic condensation phase, experimental evidence still remains elusive. This is largely due to the absence of direct measurements of a material’s transient momentum-dependent electronic structure and the excitonic state in the condensation regime. Here, using time and angle-resolved photoemission spectroscopy, we find direct evidence of a transient excitonic condensate in the spin-polarized spatially indirect excitonic topological states in Bi <jats:sub>2</jats:sub> Te <jats:sub>3</jats:sub> . Accompanying the formation of the excitonic topological states by photoexcitation, we reveal a splitting of the hole’s and electron’s quasi-equilibrium chemical potential followed by the band flattening and backbending of the transient topological surface state. Moreover, within the same momentum range, we report a reshaping of the bulk valence band in the form of a Mexican-hat-like Bogoliubov dispersion—hallmarks of the excitonic condensation, followed by the opening of an energy gap at the Fermi level. The fluence and temperature dependence of these renormalization effects are reminiscent of excitonic condensation within Bardeen–Cooper–Schrieffer (BCS)-like behavior. These results, together with theoretical simulation, point to the possible formation of a transient excitonic condensate and provide opportunities to manipulate topologically protected Bose condensates with light.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"8 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884762","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":"Gag proteins encoded by endogenous retroviruses are required for zebrafish development","authors":"Ni-Chen Chang, Jonathan N. Wells, Andrew Y. Wang, Phillip Schofield, Yi-Chia Huang, Vinh H. Truong, Marcos Simoes-Costa, Cédric Feschotte","doi":"10.1073/pnas.2411446122","DOIUrl":"https://doi.org/10.1073/pnas.2411446122","url":null,"abstract":"Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here, we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane, and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an “addiction” model to explain how active TEs can be integrated into conserved developmental processes.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"43 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884839","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":"Correction for Mukhi et al., Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor.","authors":"","doi":"10.1073/pnas.2508043122","DOIUrl":"https://doi.org/10.1073/pnas.2508043122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"70 1","pages":"e2508043122"},"PeriodicalIF":11.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880196","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":"Biofilm architecture determines the dissemination of conjugative plasmids","authors":"Sarah Djermoun, Daniel K. H. Rode, Eva Jiménez-Siebert, Niklas Netter, Christian Lesterlin, Knut Drescher, Sarah Bigot","doi":"10.1073/pnas.2417452122","DOIUrl":"https://doi.org/10.1073/pnas.2417452122","url":null,"abstract":"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 remains limited. In this study, we use live-cell fluorescence microscopy to investigate the propagation of the broad host range RP4 conjugative plasmid in <jats:italic>Escherichia coli</jats:italic> populations exhibiting varying levels of spatial organization. In high-density, two-dimensional cell monolayers, direct and tight contact between donors and recipients is not only necessary but also sufficient to trigger RP4 plasmid transfer, ensuring optimal plasmid propagation. In three-dimensional mature biofilms, the emergent community architecture limits the ability of donor cells to enter regions with high cell density, which hinders the establishment of direct contacts with recipients and impedes plasmid transfer in biofilms. In contrast, microcolonies, early-stage biofilms, and biofilms with a lower surface coverage leave open access points for donor cells in regions that later emerge as high-cell-density regions in mature biofilms, which facilitates plasmid transfer. These findings reveal the crucial role of bacterial community architecture in determining the efficiency of plasmid dissemination.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"2 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875780","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":"Comparative analysis of STP6 and STP10 unravels molecular selectivity in sugar transport proteins","authors":"Camilla Gottlieb Andersen, Laust Bavnhøj, Søren Brag, Anastasiia Bohush, Adriana Chrenková, Jan Heiner Driller, Bjørn Panyella Pedersen","doi":"10.1073/pnas.2417370122","DOIUrl":"https://doi.org/10.1073/pnas.2417370122","url":null,"abstract":"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 composition, remains unknown. Here, we present the structure of <jats:italic>Arabidopsis thaliana</jats:italic> STP6 in an inward-occluded conformational state with glucose bound and demonstrate its role as both a glucose and fructose transporter. We perform a comparative analysis of STP6 with the glucose-selective STP10 using in vivo and in vitro systems, demonstrating how different experimental setups strongly influence kinetic transport properties. We analyze the properties of the monosaccharide binding site and show that the position of a single methyl group in the binding site is sufficient to shuffle glucose and fructose specificity, providing detailed insights into the fine-tuned dynamics of affinity-induced specificity for sugar uptake. Altogether, these findings enhance our understanding of sugar selectivity in STPs and more broadly SP proteins.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"75 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875771","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":"Host use drives convergent evolution in clownfish","authors":"Théo Gaboriau, Anna Marcionetti, Alberto Garcia-Jimenez, Sarah Schmid, Lucy M. Fitzgerald, Baptiste Micheli, Benjamin Titus, Nicolas Salamin","doi":"10.1073/pnas.2419716122","DOIUrl":"https://doi.org/10.1073/pnas.2419716122","url":null,"abstract":"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 or theoretical support given our current knowledge of the group. To date, no ecological variable has been identified to explain clownfish niche partitioning, phenotypic evolution, species co-occurrence, and thus, the adaptive aspect of the group’s radiation. Our study solves this long-standing mystery by testing the influence of sea anemone host use on phenotypic divergence. We provide a major revision of the known clownfish-sea anemone host associations, accounting for the biologically relevant aspects of host associations. We gathered whole-genome data for all 28 clownfish species and reconstructed a fully supported species tree for the Amphiprioninae. Integrating this data into comparative genomic approaches, we demonstrate that the host sea anemones are the drivers of convergent evolution in clownfish color pattern and morphology. During the diversification of this group, clownfishes in different regions that associate with the same hosts have evolved similar phenotypes. Comparative genomics also reveals several genes under convergent positive selection linked to host specialization events. Our findings reveal that the sea anemone host plays a crucial role in driving clownfish diversification. This highlights how a strong mutualistic interaction can promote the diversification of entire clades by influencing their phenotypes, defining their geographic distribution, and ultimately contributing to their evolutionary and ecological success.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"3 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875774","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":"Lab earthquakes reveal a wide range of rupture behaviors controlled by fault bends","authors":"Tom Gabrieli, Yuval Tal","doi":"10.1073/pnas.2425471122","DOIUrl":"https://doi.org/10.1073/pnas.2425471122","url":null,"abstract":"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 observations of the interaction of dynamic frictional ruptures with fault (double-) bends of different angles. Using ultrahigh-speed photography, we capture highly detailed full-field images of the complex rupture dynamics that evolve as lab earthquakes in an analog material [poly(methylmethacrylate)] propagate through fault bends, as well as the resulting near-field ground motions. Releasing bends, which extend as the fault slips, intensify the rupture by promoting a transition to supershear propagation speeds (i.e., above the medium shear wave velocities) and a crack-like rupture style with spread-out slip, while restraining bends, which contract as the fault slips, slow or arrest the rupture. Surprisingly, we find that secondary back-propagating supershear ruptures are spontaneously triggered at intermediate-angle restraining bends. These constraints on the effect of natural fault geometry on the behavior and extent of earthquake ruptures have significant implications for earthquake source physics, seismic hazards, and the interpretation of seismic data.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"15 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875772","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}