PLOS Biology: New Articles

A binding-activated CRISPR/dCas13X imaging system enables precise RNA tracking in plants

2026-10-06T14:00:00Z

by Jiayu Zhang, Yiran Tao, Yun Zhao, Miaomiao Lei, Yucheng Shen, Qicong Li, Chenxu Liu, Jiuyuan Bai

Visualizing the spatiotemporal dynamics of native RNA molecules with single-transcript-level sensitivity in living plant cells remains a formidable challenge due to the high background noise caused by the unique cellular architecture of plants. Here, using transiently transformed Nicotiana benthamiana cells and stable Arabidopsis thaliana lines, we present a high-signal-to-noise RNA imaging platform that couples CRISPR–dCas13X with a binding-associated fluorescence stabilization strategy. We identified a novel plant-specific degron that selectively targets unbound probes for proteasomal degradation while preserving target-associated signal in a manner consistent with binding-dependent protection, enabling high-fidelity detection of endogenous mRNA puncta with minimal perturbation. Leveraging this platform, we characterized dynamics of FT mRNA trafficking in living plant cells, including plasmodesmata-targeting, cell-to-cell trafficking, and long-distance movement. Loss-of-function analysis further identified the established RNA-binding protein GRP7 as a factor that contributes to efficient FT mRNA transport. This work establishes a useful toolkit for investigating plant RNA biology and provides mechanistic insight into the systemic transport of florigenic signals.

Inadequate antibody validation places substantial numbers of animal and human tissue samples at risk of waste

2026-10-06T14:00:00Z

by Michael Biddle, Jemma Cooper, Katherine Blades, Dominic Ruddy, Eva M. Krockow, Harvinder Virk

Lack of antibody validation by researchers frequently misdirects biomedical research, yet the ethical consequences—particularly avoidable use of animal and human biological materials—remain unquantified. Using focus groups (n = 12), surveys (n = 107), and systematic analysis of 785 publications, we examined how researchers select and validate antibodies, and quantified the downstream ethical costs. Antibody selection is substantially influenced by social factors such as previous laboratory use and peer recommendations, while systematic evaluation of performance characteristics remains limited. From a dataset of 614 antibodies subjected to rigorous characterisation using knockout controls, 97 (15.8%) failed across all tested applications; we systematically searched for publications linked to these antibodies. Within the 760 publications (those where validation status could be confirmed), only 120 (15.8%) presented any validation evidence—despite 72.0% of surveyed researchers reporting having used at least one recommended validation method. The remaining 640 papers reported a minimum of 8,064 animal samples and 4,424 human tissue samples used with antibodies of demonstrated poor performance and without evidence of fitness for the specific experimental purpose; we describe these as samples at risk of waste. Reserving the term waste for samples used with reagents since withdrawn from sale, and therefore irreproducible, conservative extrapolation gives lower-bound, order-of-magnitude estimates of millions of animal and human tissue samples consumed globally. Researchers identified time, cost, and lack of supervisor support as primary barriers, whilst strongly supporting open data sharing, dedicated validation funding, and publisher requirements as solutions. These findings provide a first quantification of the ethical costs of inadequate antibody validation and highlight the need for coordinated stakeholder interventions to reduce avoidable biological sample waste in biomedical research.

Actionable solutions to address antibody validation failures

2026-10-06T14:00:00Z

by Katherine Blades, Michael Biddle, Robert Froud, Eva M. Krockow, Harvinder Virk

The experimental use of antibodies that have not been validated for context-specific use frequently misdirects biomedical research. Experimental results that derive from the use of inadequately validated antibodies are estimated to waste over $1 billion annually in the United States alone and to consume millions of animal and human biological samples in experiments whose conclusions may be unreliable. Community validation frameworks, reporting standards, and independent characterisation initiatives have made important progress, and multi-stakeholder coordination efforts are emerging. However, the research community lacks a formally developed, consensus-based action plan that specifies what each stakeholder group should do, by when, and with what priority. We conducted a modified Delphi study with international experts representing academic researchers, scientific publishers, research funders, antibody manufacturers, and institutional research leaders to develop actionable recommendations for improving antibody validation, selection, and reporting practices. Thirty-two participants rated 33 proposed actions on effectiveness and feasibility using 9-point scales, with consensus assessed using the RAND/UCLA Appropriateness Method. Over two rounds, the panel achieved consensus on 15 items as both effective and feasible for implementation by 2030. These spanned institutional actions (training in antibody validation, integration into research integrity frameworks, support for local expertise networks), funder actions (dedicated validation budgets, grant application requirements, endorsement of community reporting standards), publisher actions (complete antibody reporting packages, clear validation standards), manufacturer actions (assignment of unique identifiers at source), and cross-stakeholder coordination (a shared roadmap for improvement). An additional 15 items were rated as effective but with uncertain feasibility, reflecting a consistent pattern in which the panel agreed on the value of proposed interventions but expressed reservations about realistic implementation timelines. One item was rejected by the panel with concerns around effectiveness and feasibility. Participants described four interconnected barriers to progress: diffuse ownership of the problem across stakeholders; market dynamics that inadequately reward antibody quality; difficulty justifying investment when returns are distributed across the research system; and coordination challenges among actors with different incentive structures. These barriers are addressable through coordinated action, and the findings complement existing technical and data-sharing initiatives by providing the structured, expert-informed policy framework to help translate awareness of the problem into concrete practice and policy changes.

Uracil-driven ROS signaling and larval TrpA1-B neuron activation are required for priming the adult Drosophila gustatory response to bacteria

2026-10-05T14:00:00Z

by Romane Milleville, Gérard Manière, Martine Berthelot-Grosjean, Olivier Lamotte, Yaël Grosjean, Julien Royet, C. Léopold Kurz

Animals perceive their immediate environment through their sensory systems. While these systems rely on well-defined neuronal circuits and receptor proteins encoded by the genome, they can also be modulated by internal physiological conditions or exogenous factors. We have previously shown that the presence of certain pathogenic bacteria in the larval gut can alter the specificity of bacterial peptidoglycan recognition in the adults that emerge from these larvae. However, the nature of the bacterial signal and the host cells and molecules involved in receiving and transducing this signal remained unknown. Our results identify uracil as the bacterial metabolite responsible for this priming and demonstrate that the effect is mediated by Duox-dependent production of reactive oxygen species (ROS) in the larval gut. We further show that specific expression of TrpA1 isoforms in a Gr66a-expressing neuron of the larval terminal organ is required for the adult response. Together, these findings reveal uracil as the bacterial cue and the Duo/ROS signaling and TrpA1/Gr66a modules as key mediators linking larval gut microbial signals and host integration to subsequent sensory system modulation in the adult.

Integrated multi-omics analysis reveals the molecular landscape and therapeutic strategies in Chinese cervical cancer patients

2026-10-05T14:00:00Z

by Tao Pan, Xucui Zhuang, Ya Zhang, Jiyu Guo, Si Li, Can Zhang, Lili Han, Fuxia Li, Yueying Gao, Jinyang Yu, Yongsheng Li, Chaoyang Sun

Genomic or transcriptomic sequencing guides the precision of cervical cancer (CC) diagnosis; however, the molecular profile of Asian patients remains poorly understood. We established a comprehensive multi-omics cohort comprising 112 tumor-normal adjacent tissue pairs from Chinese CC patients. Our integrated analysis revealed a mutational burden comparable to other populations, with three major mutational signatures primarily attributed to APOBEC-associated, age-associated, and DNA repair-associated biological categories. Multi-omics profiling elucidated the functional consequences of somatic mutations and copy number variations, identifying PIK3CA, EP300, and MPRIP as key driver events. We further uncovered both concordant and discordant activation patterns across cancer-related signaling pathways. Transcriptomic and proteomic analyses nominated cell cycle regulation, epithelial-mesenchymal transition, and LAMC2 as promising diagnostic and therapeutic targets. Comprehensive immune characterization enabled stratification of patients into three major immune phenotypes with varying microenvironmental profiles. This study provides valuable resources and novel insights into the molecular architecture of cervical cancer in the Chinese population, identifying potential biomarkers to guide precision detection and immunotherapy strategies.

Moral and perceptual conflict processing are implemented by distinct brain activation and functional connectivity patterns

2026-10-05T14:00:00Z

by Ruida Zhu, Marcus Grueschow, Marius Moisa, Chao Liu, Christian C. Ruff

While humans resemble other primates in terms of motor and perceptual abilities, our behavior is uniquely characterized by morality—the ability to choose our actions based on specific ethical values. The evolutionary origins and neurobiological basis of moral behavior are debated intensely, with opposing proposals about whether moral decisions rely on domain-general decision-making neural circuitry (neural common currency hypothesis) or on unique neural processes that were shaped by evolutionary pressures associated with life in groups (social brain hypothesis). Here we examine the potential overlap between moral and perceptual decision-making, by combining functional magnetic resonance imaging with computational modeling of behavior in a novel task requiring human participants to make alternating moral and perceptual choices on identical stimuli. At the algorithmic level, we found that moral and perceptual choices were well fit by the same sequential sampling model, which allowed us to quantify and directly compare conflicts between the choice alternatives for both types of decision-making. At the implementational level, moral and perceptual choice conflicts were represented by distinct neural activity patterns; in fact, neural signals in some brain areas (e.g., temporoparietal junction) encoded the strength of the two types of conflict in opposite directions. Our findings suggest that while similar computational decision mechanisms underlie both moral and perceptual choices, their neural implementation is fundamentally different, supporting the social brain hypothesis.

Why are some neurons spared in neurodegeneration? Cellular subtype identity maintenance as a candidate threshold-setting mechanism

2026-10-05T14:00:00Z

by Dong Won Kim

Neurodegenerative diseases often damage some neuronal populations while sparing closely related neighbors. But instead of asking why some neurons die, should we be asking why some survive? This Essay proposes that a neuron’s capacity to sustain the gene-regulatory machinery that maintains its subtype identity helps set the stress threshold beyond which recovery fails. The initiating insult may be metabolic, proteostatic, inflammatory, or arise from the surrounding tissue, but it is the cell’s capacity for maintenance that will determine where the tipping point lies: above a critical level, the identity program recovers, whereas below it, regulatory loss becomes self-sustaining. Such a framing could have implications for how neuronal vulnerability to neurodegeneration is understood.

Breadth of ACE2 receptor usage predicts host range and antigenic relatedness across bat sarbecoviruses

2026-10-01T14:00:00Z

by Nazia Thakur, Joseph Newman, Dongchun Ni, Jeffrey Seow, Abigail L. Hay, Yeonjae Lee, Ayush Upadhyay, Babatunde E. Ekundayo, John A. Hammond, Thomas P. Peacock, Kelvin Lau, Katie J. Doores, Dalan Bailey

Sarbecoviruses interact with their receptor, angiotensin-converting enzyme 2 (ACE2), via the receptor-binding domain (RBD) of Spike, the immunodominant target for neutralising antibodies. Understanding the interplay and correlation between ACE2-determined host range and antigenicity is vitally important for understanding the zoonotic potential of related bat sarbecoviruses. Using binding assays, pseudotype-entry assays and a diverse panel of mammalian ACE2 proteins, we examined the host range and related antigenicity of multiple bat coronaviruses. Broad bat ACE2 usage (a generalist phenotype) was most common in clade 1 sarbecoviruses, including SARS-CoV-2 and the BANAL isolates from Laos. In contrast, clade 3 (e.g., RhGB07) and 5 (e.g., Rc-o319) sarbecoviruses exhibited more restricted ACE2 usage (a specialist phenotype). A novel structure for RhGB07 Spike further helped to identify RBD residues associated with this receptor specialism. Interestingly, the generalist phenotypes were largely maintained with more diverse mammalian receptor libraries, including human, non-human primate, livestock, rodent ACE2 and potential intermediate reservoir hosts (e.g., civet, racoon dog, pangolin), while specialists, like RhGB07, exhibited wider phenotypic diversity. The impact of SARS-CoV-2’s continued evolution in humans was also examined, identifying an expanding and/or shifting pattern of generalism for variants, especially Omicron and its sub-lineages. Furthermore, we compared and correlated these entry phenotypes with antigenicity using sera from SARS-CoV-2 convalescent individuals. Clade 1 viruses, phylogenetically related to SARS-CoV-2, were antigenically the most similar, with robust evidence for cross-neutralisation; however, there was still evidence for limited cross-neutralisation across the entire sub-genus. Finally, using monoclonal antibodies, derived from COVID-19 vaccinees with breakthrough infections, we pin-pointed the antibody epitope classes responsible for wider neutralisation. Our research indicates that generalist ACE2-using sarbecoviruses are phylogenetically and antigenically related to SARS-CoV-2.

Targeting of conserved spike epitopes enables broad antibody neutralisation of diverse bat sarbecoviruses

2026-10-01T14:00:00Z

by Ayush Upadhyay, Jeffrey Seow, Yilmaz Alguel, Joseph Newman, Nazia Thakur, Abigail L. Hay, Jerry C. H. Tam, Andrea Nans, Richard J. Orton, Dalan Bailey, Peter Cherepanov, Katie J. Doores

The continuing evolution of SARS-CoV-2 variants of concern, and the increasing spillover potential of sarbecoviruses into the human population presents an important and urgent need to discover cross-reactive monoclonal antibodies (mAbs) for future therapeutic use and identify conserved neutralising epitopes that can be used for rationale design of broadly protective sarbecovirus vaccines. Here we study the neutralising epitopes on WIV-1 Spike of three mAbs that confer broad sarbecovirus and SARS-CoV-2 variant neutralisation, including XEC, JN.1, and XFG. mAb V1WT_06 binds a highly conserved RBD site V epitope that is mediated by the heavy chain alone. V1WT_06 contact residues are highly conserved in circulating viruses suggesting that the epitope is evolutionarily and functionally constrained. mAbs V1WT_41 and VA14_26 bind overlapping RBD class 4 epitopes with differing angles of approach that impact on the degree of ACE2 competition. We show that neutralisation by these mAbs is maintained when virus entry is via Japanese horseshoe bat and Halcyon horseshoe bat ACE2s. These mAbs are ideal candidates for therapeutic antibody development and inform the rational design of pan-betacoronavirus vaccines.

Adaptive introgression between two Drosophila species enhances heat tolerance despite barriers to gene flow

2026-09-30T14:00:00Z

by Noora Poikela, Rhonda R. Snook, Jonna Kulmuni, Michael G. Ritchie

As global temperatures rise and heat waves become more frequent, populations must adapt rapidly to avoid local extinctions. Adaptive introgression allows species to quickly acquire adaptive genetic material from close relatives. However, certain genomic regions, containing barrier loci, may resist introgression. We experimentally tested whether strong heat stress selection can overcome such barriers and facilitate the transfer of adaptive alleles to improve heat tolerance. We also examined whether chromosomal inversions, which can tightly link adaptive and barrier loci through reduced recombination, promote or prevent introgression. We conducted a hybridize, evolve, and re-sequence experiment by crossing the heat-sensitive D. flavomontana with the more heat-tolerant D. montana, exposing heat-selection lines to transient heat for three generations while maintaining control lines. We also mapped long-term barriers to gene flow between natural populations using a demographically explicit genome scan. The heat-selection lines exhibited approximately twice the introgression and higher male fertility under heat stress compared to control lines and the heat-sensitive parental D. flavomontana. This introgression was primarily located in colinear autosomal regions and correlated with improved heat tolerance. Some introgression occurred also in inverted autosomal regions in the heat-selection lines but not in the control lines. The X chromosome, with three overlapping inversions, resisted introgression in both heat-selection and control lines, thereby maintaining a strong species barrier. Finally, genetic barriers in the control lines significantly overlapped with long-term barriers, but this overlap was less pronounced in the heat-selection lines. Our study demonstrates that strong selection can lead to adaptive introgression despite long-standing genetic barriers. These findings highlight that introgression can serve as a rapid source of adaptive genetic material under stressful thermal conditions, potentially mitigating climate-induced population extinctions.

Nightjars trade off cruising speed efficiency for hovering capabilities and link upstroke thrust production with restricted wing folding

2026-09-30T14:00:00Z

by L. Christoffer Johansson, Gabriel Norevik, Sonja Friman, Anders Hedenström

The European nightjar (Caprimulgus europaeus) is a long-distance migrant that also uses slow, hovering, flight as part of its feeding ecology. This reflects complex tradeoffs in aerodynamic mechanisms and makes studies of their flight performance, in relation to their wing shape, particularly interesting. Here we reveal, using wake visualization and aerodynamic measurements of nightjars flying in a wind tunnel, a unique double tip vortex phenomenon at cruising speeds. This correlates with reduced span efficiency at these flight speeds, suggesting relatively high costs of generating lift. Our interpretation is that the nightjar’s broad, slotted wing tip shape promotes lift during slow flight while incurring reduced aerodynamic efficiency at faster speeds. In addition, we found outer wing upstroke thrust generation during cruising flight—a characteristic previously attributed to bats and hummingbirds—in nightjars. This challenges an existing paradigm that considers an active upstroke to primarily add weight support in birds. Our kinematic analysis suggests this phenomenon may stem from constraints on wing folding during the upstroke, something that may apply generally to flapping flight. Our results highlight the tradeoffs seen in animals engaged in multiple costly behaviors with different aerodynamics optimization criteria based on ecological demands and offer potential solutions applicable in bioinspired engineering.

Intrinsic timescale develops hierarchically from sensorimotor to association cortex in youth and stabilizes in adulthood

2026-09-29T14:00:00Z

by Golia Shafiei, Joëlle Bagautdinova, Valerie J. Sydnor, Dani S. Bassett, Deanna M. Barch, Matthew Cieslak, Yong Fan, Elizabeth Flook, Alexandre R. Franco, Gregory Kiar, Audrey C. Luo, Michael P. Milham, Linden Parkes, Taylor Salo, Leah H. Somerville, Tien T. Tong, Russell T. Shinohara, Theodore D. Satterthwaite

Intrinsic timescale is a commonly used measure of spontaneous neural dynamics that quantifies the temporal window of processing of neuronal populations. Intrinsic timescale displays a hierarchical cortical organization across multiple species and imaging modalities, with shorter timescales in sensorimotor cortex compared to association cortex. However, less is known about how intrinsic timescale evolves during human brain development and whether its cortical maturation patterns generalize to independent developmental samples. Here we estimate the intrinsic timescale in two independent cross-sectional datasets of youth (HCPD: n = 565; HBN: n = 729; age range 8–22 years) and investigate its neurodevelopmental patterns. We find that developmental patterns in the intrinsic timescale follow a hierarchical pattern that recapitulates an axis spanning sensorimotor to association cortices (S–A axis). Our analysis of an independent healthy young adult dataset (HCPYA: n = 973, age range 22–37 years) underscores the specificity of these developmental findings, suggesting that the intrinsic timescale develops along the S–A axis in youth and stabilizes in adulthood. Together, these results reveal convergence between major axes of cortical organization and development, highlighting intrinsic timescale as a principled marker of hierarchical brain maturation in youth.

Correction: Correction: Data-driven analyses of motor impairments in animal models of neurological disorders

2026-09-29T14:00:00Z

by The PLOS One Staff

A trade-off between fungal biofilm formation and persistence in the host

2026-09-29T14:00:00Z

by Shannon Esher Righi

Fungal biofilm formation has long been considered an important virulence trait. A new study on Candida parapsilosis outbreak isolates in PLOS Biology challenges this, finding that low biofilm-producing strains are better adapted for immune evasion and survival. Fungal biofilm formation has long been considered an important virulence trait. A new study on Candida parapsilosis outbreak isolates in PLOS Biology challenges this, finding that low biofilm-producing strains are better adapted for immune evasion and survival.

Intestinal lipid metabolism controls molecular and behavioral immunity through NHR-68 and gut–brain signaling in Caenorhabditis elegans

2026-09-29T14:00:00Z

by Jie Ren, Yu Sang, Young-Mo Kim, Ernesto S. Nakayasu, Alejandro Aballay

Animals must allocate limited energetic resources across competing defense programs in response to infection. Here, we show that the conserved nuclear hormone receptor NHR-68 integrates fatty acid metabolism with the neural control of molecular and behavioral immunity in Caenorhabditis elegans. Acting in parallel with NHR-10, NHR-68 controls genes involved in polyunsaturated fatty acid (PUFA) metabolism. Loss of NHR-68 disrupts linoleic acid (LA) homeostasis, impairing pathogen avoidance behavior. Supplementation with LA restores avoidance, and fat-3 inhibition, which elevates LA, enhances pathogen avoidance, whereas loss of LA synthesis by fat-2 inhibition diminishes this behavior, indicating that LA promotes behavioral immunity. We further show that NHR-68 acts in the intestine to regulate linoleic acid homeostasis, and that changes in intestinal lipid metabolism influence an AWC-dependent pathogen-avoidance circuit through intestine-to-neuron communication. NHR-68 suppresses activation of the PMK-1/p38 MAPK and DAF-16/FOXO pathways, which mediate molecular immune responses. These findings identify a gut-brain transcriptional circuit that connects intestinal lipid metabolism to neural and immune outputs, revealing a mechanism by which the metabolic state coordinates behavioral and molecular defenses to optimize host protection.

Epistasis and pleiotropy constrain the evolution of cross-reactive breadth in a broadly neutralizing influenza antibody

2026-09-28T14:00:00Z

by Katrine E. Dailey, Yiquan Wang, Qi Wen Teo, Chaoyang Wang, Huibin Lv, Ruipeng Lei, Meixuan Tong, Lucia A. Rodriguez, Letianchu Wang, Nicholas C. Wu

The highly conserved influenza virus hemagglutinin (HA) stem domain is a major target for broadly neutralizing antibodies (bnAbs). However, despite being discovered more than a decade ago, the IGHV1-69-encoded CR9114 remains the only HA stem bnAb that cross-reacts with both influenza A and B viruses. To investigate the constraints on the breadth evolution of CR9114, this study performs four deep mutational scanning experiments to compare the binding affinity landscapes of the germline and somatic CR9114 against H1 HA, H3 HA, and influenza B virus HA. Many mutations that minimally affect or even improve the H1 HA binding are detrimental for binding to H3 HA and influenza B virus HA. We further reveal the prevalence of epistasis in IGHV1-69 HA stem bnAbs. Overall, our findings provide a mechanistic explanation for the scarcity of HA stem bnAbs with cross-reactivity against both influenza A and B viruses, and have important implications for developing broadly protective influenza vaccines.

A developmental single-cell atlas of the Drosophila visual system glia reveals cell type diversification and subcellular mRNA compartmentalization

2026-09-28T14:00:00Z

by Amanda A. G. Ferreira, Sergio Córdoba, Raghuvanshi Rajesh, Ben Jiwon Choi, Claude Desplan

Glial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated the glial cells from two large single-cell mRNA-sequencing (scRNA-seq) atlases of the developing Drosophila visual system. This allowed us to identify all glial cell types from larval to adult stages and follow their developmental trajectories to understand how the diversity of glial types is generated during development. We show that whereas most glial types, such as chiasm glia, gradually change their transcriptome as they mature during development, neuropil glia that transcriptionally appear as a single-cell class in larvae, splits into ensheathing (EG) and astrocyte-like (ALG) glia types during pupal stages. We have experimentally validated these developmental trajectories and identified the genetic markers expressed through the differentiation between EG and ALG classes. Unexpectedly, our analysis of scRNA-seq datasets allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their processes. We have identified that processes are enriched for distinct mRNAs that were validated in vivo. This work provides the most detailed transcriptomic analysis of optic lobe glia during development and helps explain the expansion of glial diversity observed in the adult visual system. We also present an innovative computational approach to identify mRNA species that are differentially localized to cell bodies or cellular processes.

Whole-organ single-cell mapping defines growth dynamics and clonal organization in developing and adult zebrafish livers

2026-09-28T14:00:00Z

by Hsiao-Yuh Roan, Xuejiao Tian, Wei-Chen Chu, Chia-Ming Lee, Hsin Chen, Fiorency Santoso, Chung-Han Wang, Yu-Hsiu Liu, Uday Kumar, He-Yun Hsiao, Chiou-Hwa Yuh, Bi-Chang Chen, Chen-Hui Chen

Vertebrate organs undergo massive growth during the post-embryonic period. Yet, our understanding of how this organ-wide process is organized at single-cell resolution has been limited by an inability to monitor individual cells of different types throughout intact adult organs. Here we establish an integrated workflow of whole adult-organ expansion microscopy (WAO-ExM) that enables in toto single-cell-resolved visualization of every hepatocyte within a complete adult vertebrate liver. Using transgenic reporters to label hepatocyte nuclei, we quantified cell expansion dynamics across the entire post-embryonic growth period, finding that an intact adult liver spanning ~5 mm thickness had an average of 1,265,206 hepatocytes. The data further revealed a non-linear growth regimen in which cell number increased by 538-fold, with a temporally concentrated burst that was not reflective of overall body growth. Integration of lineage tracing with WAO-ExM revealed that cell number increases were driven by a few hepatocytes undergoing drastic clonal expansion at the whole-organ scale. Disruption of extracellular matrix laminins decoupled liver shaping from total cell number increases, suggesting independent regulatory control of tissue architecture and cell proliferation. We also utilized WAO-ExM to monitor diseased livers and other adult organs, including heart and pancreas. Altogether, these findings bridge micrometer-scale cell behaviors with centimeter-scale organ growth, and establish a generalizable platform for adult vertebrate organs to be fully resolved at bona fide single-cell resolution.

Ancient inversion polymorphisms associate with sexually selected traits across natural guppy populations

2026-09-23T14:00:00Z

by Yuying Lin, Wouter van der Bijl, Judith E. Mank

Understanding the distribution, frequency, and long-term persistence of chromosomal inversions in natural populations is key to understanding population evolution and adaptive processes. Inversions often span multiple genes, are subject to strong selective pressures and can affect complex traits. Here, we used an unbiased method to identify inversions in guppies from three different Trinidadian rivers with paired high- and low-predation populations which differ in a wide range of morphological, behavioural and life-history traits. We identified 22 inversions, ranging in age from 1 to 6 million years, which are widespread across the genome and predate the colonisation of each river. We were able to verify the breakpoints for all but one of these inversions using linked reads. We find three inversions that are significantly associated with local adaptation syndromes in high- versus low-predation populations, however, none are reciprocally fixed throughout all three replicate rivers. Additionally, we observe seven additional inversions maintained in all three rivers without evidence of local adaptation. Simulations reveal that the level of inversion polymorphism that we observe is far greater than expected under a neutral model. We observed a significant overlap between polymorphic inversions and loci previously implicated in male ornament pattern variation in guppies, suggesting that negative frequency-dependent selection due to female preference for male pattern novelty explains the maintenance of inversion polymorphisms. Overall, our results show the role of sexual selection in the long-term maintenance of inversion polymorphisms, and an interplay between sexual and natural selection in frequency dynamics.

Pathogen subversion of neuro-epidermal signaling impairs lysosomal function to disrupt collagen homeostasis in Caenorhabditis elegans

2026-09-22T14:00:00Z

by Qian Li, Yating Liu, Hanyi Chen, Weilie Xiao, Bin Qi

The epidermis relies on collagen-rich extracellular matrices (ECMs) to maintain barrier integrity against pathogens. Lysosomes regulate cuticle collagen turnover, yet how neuronal signaling modulates epidermal lysosomal function and collagen organization during infection remains unclear. Using Pseudomonas aeruginosa PA14-Caenorhabditis elegans infection model, we demonstrate that pathogen-induced neuronal signaling disrupts epidermal lysosomal activity and collagen remodeling. PA14 infection triggers neurons to secrete NSIF-1 (Neuronal Secreted Immune Factor 1), which translocates to the epidermis and impairs lysosomal acidification, maturation, and degradation by suppressing the transcription factor ELT-3. This disruption leads to disorganized collagen structure, compromising cuticle integrity and host resistance. Genetic mutation of nsif-1 restores lysosomal function, enhances collagen density, and improves survival, while neuron-specific nsif-1 knockdown confirms its neuronal origin. Moreover, NSIF-1 inhibits ELT-3 nuclear localization, blocking its role in lysosomal-dependent ECM repair. Our study reveals a neuro-epidermal axis wherein pathogens exploit neuronal signals to disrupt lysosomal function and collagen homeostasis, identifying NSIF-1 and ELT-3 as potential targets to counteract infection-driven ECM dysregulation.

Coordinated P450–UGT detoxification contributes to furanocoumarin tolerance associated with host plant range divergence in Helicoverpa

2026-09-22T14:00:00Z

by Huidong Wang, Yajie Kong, Xinyue Su, Yu Shi, Jianpeng Zhang, Yinjia Wang, Yajuan Xiao, Xing Geng, Jing Song, Yueru Ye, Kairan Zuo, Chris Bass, Shutang Zhou

Plants and herbivorous insects are engaged in a continuous evolutionary arms race driven by chemical defences and counter-defences. How insects integrate distinct detoxification systems to overcome diverse phytochemicals, and how such mechanisms contribute to host-range divergence, remains poorly understood. Here, we uncover a cooperative cytochrome P450–UDP-glycosyltransferase (UGT) cascade that mediates furanocoumarin tolerance in Helicoverpa armigera. Comparative genomic analyses across Helicoverpa and related noctuid species revealed that the UGT33 family is the most extensively expanded and dynamically diversified UGT lineage in Helicoverpa. Targeted CRISPR–Cas9 knockouts of UGT33 gene clusters in polyphagous H. armigera demonstrated their essential roles in detoxifying the furanocoumarins xanthotoxin and imperatorin. Combined metabolic and functional assays further established a sequential detoxification pathway, in which the cytochrome P450 CYP6AE19 catalyses either the O-dealkylation of xanthotoxin to yield xanthotoxol or the aromatic-carbon hydroxylation of xanthotoxin to form 5-hydroxyxanthotoxin, which are subsequently glycosylated by UGT33 enzymes to form their less-toxic glucosides. In contrast, impaired CYP6AE19–UGT33 coordination in the oligophagous Helicoverpa assulta was associated with reduced xanthotoxin detoxification and high sensitivity to this compound. Together, these findings provide direct evidence for coordinated Phase I–Phase II detoxification of a plant defensive compound in insects and show that functional divergence in this pathway contributes to interspecific differences in plant toxin tolerance, which are associated with contrasting dietary breadth in closely related herbivorous insects.

Antibodies targeting phage fiber and nozzle proteins impair Acinetobacter baumannii phage therapy by blocking infection and promoting immune clearance

2026-09-22T14:00:00Z

by Heng Xue, Xinfeng Li, Guibo Rao, Fen Hu, Mingyue Zhong, Paulina Miernikiewicz, Rui Qiu, Sheng Cao, Krystyna Dąbrowska, Hang Yang

Phage therapy represents a promising strategy to tackle the growing threat of antimicrobial resistance. Increasing evidence has demonstrated that phage-specific antibodies may compromise the efficacy of phage therapy. Nevertheless, little is known about how phage protein specificity of antibodies modulates phage therapeutic outcomes. Herein, we utilized AbP20, a podovirus against Acinetobacter baumannii, to explore the effects of antibodies elicited by each structural protein on phage therapy efficacy in a mouse infection model. Intraperitoneal administration of AbP20 once a day for 7 consecutive days induced robust phage-specific antibody responses that impaired phage therapy. Genome-guided antigen screening identified that antibodies elicited by the nozzle and fiber proteins of AbP20, rather than those targeting the portal, capsid, or adaptor proteins, are the dominant drivers of phage therapy failure. Specifically, fiber-specific and nozzle-specific antibodies block bacterial adsorption and genomic injection of AbP20, respectively. Meanwhile, both antibody subsets efficiently induce large phage aggregates and potentiate macrophage phagocytosis via an Fc receptor-independent pathway. An evolved AbP20 variant with improved neutralization escape capacity exhibited comparable antibody-accelerated phagocytosis and host immune clearance, yet partially rescued therapeutic failure caused by neutralizing antibodies. Collectively, this study elucidates that nozzle- and fiber-elicited neutralizing antibodies impair phage therapy via dual synergistic mechanisms, which offers novel insights into the multifaceted modulation of phage-specific antibodies against phage therapeutic efficacy.

Who Eats Whom? A global food web derived from citizen science

2026-09-22T14:00:00Z

by Bradley C. Allf, Aditi Mallavarapu, David W. Kikuchi, Nikhil Vasudeva, Robert R. Dunn

Citizen science contains abundant yet underutilized data about species interactions. We present Who Eats Whom, a database and public engagement tool for searching and visualizing thousands of feeding relationships derived from iNaturalist data. Citizen science photographs contain a vast and underused record of species interactions. This Community Page introduces Who Eats Whom, an interactive, searchable food web created from photographs uploaded to iNaturalist.

Regeneration programs buffer genetic defects in animal development

2026-09-21T14:00:00Z

by Kazunori Ando, Sushant Bangru, John Welsby, John D. Thompson, Kenneth D. Poss

Regeneration programs enable animals to restore damaged or lost tissues, and the range of stimuli for these programs is incompletely understood. Here, we used zebrafish, a vertebrate species with exceptional regenerative capacity, to identify chemically induced mutations that alter regeneration-associated gene activation. Transgenic zebrafish with a permissive promoter and EGFP cassette inserted in the vicinity of the pro-regenerative factor gene fgf20a were mutagenized, and larvae homozygous for ENU-induced mutations were assessed for disruptions in fgf20a-directed reporter gene expression following fin fold amputation. One line was identified with heritable, elevated fgf20a:EGFP presence in the absence of experimental injury, localized to regions of fin fold tissue undergoing degeneration. Whole-genome sequencing identified a mutation within exon 72 of the fraser syndrome 1 (fras1) gene, mutated in patients with inherited skin disease. fras1 mutant larvae spontaneously displayed broader signatures of regeneration, and zebrafish crispants for homologs of other genes mutated in human developmental diseases also displayed regeneration-associated gene expression in regions of dysmorphology. Tempering Fgf signaling by transgenic expression of a dominant-negative Fgf receptor in fras1 mutants exacerbated the disease phenotype. Our findings provide evidence that regeneration programs are harnessed in response to developmental defects caused by genetic mutations, potentially buffering deleterious phenotypes.

Monovalent cations differentially regulate the activity of eukaryotic fluoride channels and impact fluoride resistance

2026-09-21T14:00:00Z

by Chia-Yu Kang, Sahar Heidari, Sabrina Kolb, Minjun An, Melanie D. Ohi, Hedieh Torabifard, Randy B. Stockbridge

Fluoride is an environmentally prevalent inhibitor of fungi, plants, and other eukaryotes. The fluoride exporter (FEX) is the major resistance mechanism that prevents intracellular fluoride accumulation in eukaryotes. FEX activity is sodium-dependent, but the mechanism for Na⁺ activation and the impact of other cations on FEX function remain poorly understood. Here, we show that sodium and lithium have different effects on channel activity. We leverage these differences to understand how monovalent cations regulate FEX. Functional assays in a reconstituted system show that lithium acts as a competitive antagonist of channel activation by competing with sodium for the central cation binding site. We further demonstrate that lithium markedly reduces fluoride tolerance of yeast. A cryo-EM structure of Candida albicans FEX with Li⁺, together with molecular dynamics (MD) simulations, reveals that differences in the preferred coordination sphere underlie the cation dependence of FEX activity. Whereas sodium binding supports a dynamic structure with a broader pore radius, lithium coordination favors a more rigid conformation that is more compact in the channel’s vestibule. These changes perturb the tilt angle of a pore lining helix, and alter the rotamer of a key phenylalanine in the pore, which together constrict the permeation pathway. In addition to providing general insight into the mechanism of fluoride channel regulation by monovalent cations, these results identify lithium as a previously unknown environmental antagonist of eukaryotic fluoride export and tie cellular fluoride stress tolerance to the abundance of additional ions in the cellular milieu.

The nematode Caenorhabditis elegans has a cationic amphiphilic drug (CAD) defense system

2026-09-21T14:00:00Z

by Levon Tokmakjian, Duhyun Han, Kateryna Sihuta, Aanchal Aggarwal, Somayeh Pirhadi, Yao Wang, Andrew R. Burns, Brittany Cooke, Siyue Ren, Marios Gavrielatos, Jiabao Liu, Henry M. Krause, Carolyn L. Cummins, Justin Nodwell, David R. Koes, Peter J. Roy

Cationic Amphiphilic Drugs (CADs) severely disrupt lysosomal function, which leads to a cellular pathology in humans characterized by excess phospholipids called phospholipidosis. Through a forward genetic screen and mining of published datasets, we discovered that CADs induce the expression of the CYP-35B family of cytochrome P450s and the PGP-13 p-glycoprotein pump via the nuclear receptors NHR-70 and NHR-107 in the nematode C. elegans. A pgp-13 fluorescent reporter revealed hundreds of human drugs that up-regulate the CAD defense system in vivo. Chemoinformatic analyses indicate that the pgp-13 reporter may be useful in identifying CADs that have pathogenic potential in humans. Mutant analyses coupled to metabolomics and structural modeling show that the CYP-35Bs are necessary and sufficient for CAD metabolism, and that CYP-35B2 D311 is key in mediating electrostatic interactions with the positively charged CADs. We also show that CAD metabolites are effluxed via PGP-13 acting partially redundantly with PGP-14 and that an intact defense system is necessary to resist CAD-induced pathology. Finally, we demonstrate that bacteria that likely cohabitate with C. elegans in nature trigger the CAD defense system, providing a plausible explanation for why a pathway that protects against anthropogenic small molecules exists in nematodes.

Gene flow drives periods of both evolutionary stasis and change in a wild bird population

2026-09-21T14:00:00Z

by Simon R. Evans, Henri Bouwmeester, Arie J. van Noordwijk, Marcel E. Visser, Erik Postma

The struggle to explain the absence of evolutionary change in heritable, fitness-related traits of free-living populations has become emblematic of our ignorance of the evolutionary process in the wild. Yet while this ‘paradox of stasis’ has been the subject of much discussion, it is primarily identified a posteriori and rarely subject to direct quantification. We examined the evolution of clutch size in neighbouring populations of great tits (Parus major) before, during and after an experimental evolutionary perturbation. Interannual genetic changes in clutch size were directionally consistent with selection (refuting absolute stasis) but were smaller than predicted by adaptive evolutionary models (supporting relative stasis). Yet accounting for the contribution of post-selective immigration (i.e., explicitly recognising the distinction between adaptation and evolution) greatly improved our forecast accuracy and this tendency toward overprediction. Indeed, attributing interannual genetic change to its contributing demographic processes revealed immigration to be key to explaining periods of both evolutionary stasis and change, with its evolutionary impact varying across time and space in a manner analogous to the dynamism of natural selection. Our multi-decadal study of clutch size evolution thus shows that recognising the impact of gene flow is crucial to explaining contemporary evolutionary change and stasis of a key determinant of life history.

AlloPool is a deep learning framework that infers protein allostery from molecular dynamics simulations

2026-09-21T14:00:00Z

by Matthieu Marfoglia, Miguel A. Pedraza-Joya, Lucas Guirardel, Aisima Chatzi Souleiman, Patrick Barth

Recent advances in artificial intelligence have transformed protein structure prediction and design. However, protein function is governed not only by static structures but also by the conformational dynamics that allow proteins to access distinct functional states. Predicting these dynamic transitions, central to many biological processes, remains challenging due to the scarcity of high-resolution experimental data, which limits the training of machine-learning models for dynamic and energetic property prediction. Here, we present AlloPool, a graph neural network (GNN)-based framework that interprets molecular dynamics simulations by iteratively pruning residue–residue interactions to uncover minimal, time-resolved interaction networks that govern protein conformational dynamics and structural responses to chemical or mechanical perturbations, collectively known as allostery. By integrating temporal attention with graph aggregation, AlloPool learns evolving interaction graphs from equilibrium and non-equilibrium molecular dynamics simulations, enabling accurate reconstruction of dynamic trajectories and the interaction networks that drive conformational transitions. Validated across diverse dynamic protein systems, including binding domains, mechanosensors, signaling receptors, and enzymes, AlloPool maps allosteric communication pathways, predicts the effects of ligand binding, mechanical forces, and mutations, discovers transient dynamic states and outperforms existing machine-learning approaches in dynamic trajectory reconstruction. This advance provides a general framework for interpreting protein dynamics with broad implications for drug discovery, synthetic biology, and protein engineering.

Myelin sheath lengths in the central nervous system scale to axon diameter via oligodendroglial Piezo1

2026-09-21T14:00:00Z

by Amanda R. Young, Ashley Galfano, Jacob Reyngoudt, Ryan W. Lewis, Martha Cash, Beckam Polis, Myah Zalusky, Avipsha Datta, Marie E. Bechler

Myelin sheath lengths vary by an order of magnitude in the central nervous system (CNS) and tune the timing of neuronal signaling. Thus, variation in myelin sheath length has been proposed to coordinate the timing of neuronal signaling to ultimately impact behavior. The mechanisms to establish myelin sheath length are unknown. For decades, reports have documented that in vivo myelin sheath size scales with the diameter of the ensheathed axon. We previously demonstrated diameter is sufficient to instruct myelin sheath lengths formed by rat oligodendrocytes using a synthetic axon culture system. The mechanisms of oligodendrocyte diameter-sensing and its translation into sheath elongation are still unknown. Here, we demonstrate that diameter-sensing and sheath length is locally regulated: each individual myelin sheath responds to the underlying fiber diameter. We uncover a novel mechanism for scaling myelin sheath length to fiber diameter, through mechanosensitive ion channel Piezo1. In mice in vivo, Piezo1 impacts the elongation of myelin sheaths on large diameter axons, recapitulating our in vitro results. Yet, surprisingly, there is no impact on myelin thickness with conditional Piezo1 loss. We propose Piezo1 provides a mechanism to establish hard-wired myelin sheath patterns, where oligodendrocytes transduce axon diameter into generating myelin segments with vastly different lengths.

MucD regulates alginate biosynthesis through the proteolytic control of AlgX and AlgK in Pseudomonas aeruginosa

2026-09-21T14:00:00Z

by Yujun Jiang, Xin-Fu Yan, Rya Ero, Chao Wang, Kanaga Sabapathy, Yong-Gui Gao

Pseudomonas aeruginosa is an opportunistic human pathogen capable of infecting a wide range of tissues and organs. Its persistence during chronic infection is strongly associated with biofilm formation, which depends on extracellular polysaccharides such as alginate. The HtrA-like periplasmic serine protease MucD is a key regulator of bacterial virulence, stress response, and alginate production, yet its molecular mechanism has remained largely unclear. Here, we discovered the alginate acetylation and export proteins AlgX and AlgK as MucD substrates, and characterized their degradation by mass spectrometry and bioinformatic analysis. We further determined the cryo-EM structure of MucD bound to an AlgK-derived substrate peptide, offering atomic insights into MucD oligomerization assembly, substrate recognition, and specificity. Together with structure-guided mutagenesis and biochemical assays, our results revealed that MucD proteolytic activity is governed by an equilibrium between a resting 12-mer and an active trimer. Crucially, we demonstrate that MucD represses alginate biosynthesis post-translationally, in addition to its previously implicated role in transcriptional regulation. These findings define a distinct activation mechanism and regulatory function for MucD and provide new insight into bacterial HtrA-like serine proteases.