Science Journals

<p>by Anubhav Dhar, Sucheta Dey, Sanjana Mullick, Nishant Kumar Suman, Maxime C. van Zwam, Nishaant Kumar Palani Balaji, Angana Ghosh, Deepak Nair, Koen van den Dries, Sudarshan Gadadhar, Saravanan Palani</p> Expansion microscopy (ExM) has revolutionized super-resolution imaging in cell biology due to its simple and inexpensive workflow. The use of ExM has revealed several novel insights into the nanoscale architectures of cellular protein complexes, especially the microtubule cytoskeleton in model and non-model systems. Despite tremendous progress in expansion microscopy protocols that preserve cellular ultrastructure (U-ExM), compatible probes for imaging actin isoforms with U-ExM are still lacking and have hindered the study of diverse actin isoforms and networks across model systems. Here, we use IntAct, an internally tagged actin that incorporates into cellular actin networks, to develop and optimize U-ExM for diverse actin structures in yeast, mammalian cells, and primary neurons. Using ALFA-tagged IntAct variants, we achieve robust visualization of actin patches, cables, and rings in yeast, as well as diverse actin architectures including the cortex, stress fibers, filopodia, and lamellipodia in mammalian cells at improved resolution. In primary hippocampal neurons, IntAct efficiently labels actin throughout the soma and neuronal projections, revealing strong enrichment at dendritic spines and synaptic boutons. Notably, we observe a periodic organization of F-actin along axons consistent with the membrane-associated periodic cytoskeleton, thereby resolving the periodic, sub-diffraction actin ring organization. We also detect transient nuclear actin filaments using IntAct-U-ExM underscoring the advantages offered by our approach to image understudied actin structures. Overall, we demonstrate the effectiveness of IntAct-U-ExM for performing super-resolution imaging of various actin structures in an isoform-specific manner and highlight the potential of IntA…

<p>by Yagmur Ozturk, Solal Pirelli, Reese A. K. Richardson</p> Investigating the integrity of published scientific papers is key to the scientific process, but the necessary knowledge is in short supply. We present COSIG, an open collection of meta-scientific guides enabling anyone to perform forensic peer review. Investigating the integrity of published scientific papers is key to the scientific process, but the necessary knowledge is in short supply. This Community Page presents COSIG, an open collection of meta-scientific guides enabling anyone to perform forensic peer review.

<p>by Mingzi Xu, Lata Kalra</p> How does the tempo of animal communication signals evolve? This Primer explores two recent reports published in PLOS Biology, identifying a hotspot of signal tempos between 0.5-4 Hz and independently hypothesizing that delta waves in the receivers’ brains may drive the evolution of this pattern.

<p>by Thi D. Nguyen, Mia J. Konjikusic, Lorenzo M. Del Castillo, Roshanak Irannejad, Jeremy F. Reiter</p> Hedgehog (HH) signaling in vertebrates is dependent on the primary cilium, an organelle that scaffolds signal transduction. HH signals induce ciliary enrichment of Smoothened (SMO) and ciliary departure of the G protein-coupled receptor (GPCR) GPR161 to trigger GLI activation of the HH transcriptional program. Recently, SMO has been shown to inhibit protein kinase A (PKA). To test the hypothesis that SMO inhibits PKA at cilia to activate the HH signal transduction pathway, we developed a ciliary PKA reporter. Ciliary PKA activity was graded during zebrafish development. Activation of the HH signal transduction pathway by either Sonic hedgehog (SHH) or SMO agonist (SAG) inhibited ciliary PKA activity. Blocking SMO phosphorylation by GRK2/3 prevented ciliary SMO from inhibiting ciliary PKA activity. The SMO C-terminal PKA pseudosubstrate site was critical for SMO-mediated inhibition of ciliary PKA activity. A ciliary GPCR, SSTR3, activated ciliary PKA and induced HH transcriptional responses in NIH-3T3 cells via a different mechanism: activation of Gα_i/o. A different ciliary GPCR, GPR161, possesses an A-Kinase Anchoring Protein (AKAP), which we found was critical for the ciliary localization of the catalytic subunit of PKA (PKA-C) to promote ciliary PKA activity. We propose that HH signal transduction is inhibited by GPR161-mediated ciliary enrichment of PKA-C, and activated by GRK2/3-phosphorylated SMO inhibition of ciliary PKA activity.

S1–S8 Figs were uploaded incorrectly. Please see the correct S1–S8 Figs below. Supporting information S1 Fig. Behavior plots for both rules. A: Cartoon showing the organization of the AM pure tones in each rule for ferret B. “T” is a go stimulus, “R” is a reference stimulus. Ferret A would be the same, but with T and R locations reversed. B: Measured psychometric curves for ferret A, for each rule. C: Same as B, but for ferret B. (EPS) S2 Fig. Demonstration of the method used for judging anatomical correspondences. In order to judge the anatomical location of any particular micromanipulator position, information from all anatomical images was taken into account. The images for each ferret were taken at anterio-posterior steps of 200 micrometers. Images on the left are anterior, and on the right are posterior. The AP position estimates can be used for comparison to pages 86, 92, 98, 104, and 110 of the Radtke-Schuller ferret atlas [17]. Particularly important landmarks in this case include the cruciate sulcus, which branches out from the interhemispheric fissure in a Y formation. Moving anterior from the branch point, it becomes more and more lateral. Also important and reliable as an anatomical anchor is the corpus callosum: when it is present, the large blood vessel in the intrahemispheric fissure has a “gap” in the image. Moving anterior, the corpus callosum is no longer present. This transition, according to the atlas, happens in between 26.1 and 25.5 mm anterior to the occipital crest. The example slice in the text was ferret A at −25.9. Green boxes surround the locations used for repeated recordings; an arrow at the bottom points to the recording location used as an example throughout the text. (EPS) S3 Fig. Replication of example figures from Figs 1, 2, and 3 for all slices and both ferrets. The ferret and estimated slice AP position are noted on the left of each row. The example slice from the main text is in the second row. A, E, I, M: Percents correctly …

<p>by Theophane Piette, Chundra Cathcart, Chiaria Barbieri, Keesha Martin Ming, Didier Grandjean, Balthasar Bickel, Eloïse Déaux, Anne-Lise Giraud</p> Acoustic communication is crucial for survival across the animal kingdom, with acoustic signals being shaped by the interaction of producer and receiver selective pressures. While spectral features’ variation reflects species-specific selection, the evolutionary history of acoustic communication rhythms, i.e., the rhythmic modulations of acoustic signals, remains unknown. Using data from 98 species spanning primarily mammals and birds, with additional representation from amphibians, reptiles, fishes, and insects, we investigate the origins of acoustic communication rhythms, notably whether they are shaped by the producer’s anatomical characteristics, environmental constraints, or social complexity. Regression models which controlled for phylogenetic relatedness did not support an influence of these species-specific selective forces; instead, explicit phylogenetic models of trait evolution showed that most species’ rhythms are conserved around an evolutionary optimum of 2.7 Hz that falls within the neural delta range (1–4 Hz) and predates mammalian divergence. Given the known conserved brain oscillations across species and delta involvement in active sensing, we propose that, unlike spectral features, acoustic rhythm could be governed by a universal neural mechanism facilitating effective intra and interspecific communication via a shared channel that has persisted through evolutionary times.

<p>by Mckenna Eklund, Edan Foley</p> Mutations in the innate immune receptor NOD2 are the greatest single genetic risk factor for Crohn’s disease, yet the mechanisms by which NOD2 regulates intestinal homeostasis remain unclear. We used a CRISPR-generated zebrafish model to determine the impacts of NOD2 deficiency on intestinal health. In cellular, molecular, and transcriptomic studies, we uncovered substantial effects of NOD2 deficiency on epithelial and immune compartments, including deregulated expression of developmental pathways that establish and maintain the gut epithelium, and an unexpected increase in the expression of multiple estrogen-response genes. In functional assays, we uncovered a mechanistic link between estrogenic signals and NOD2-deficiency phenotypes, whereby exposure to estrogen alone replicated the effects of NOD2-deficiency, and treatment with the estrogen receptor modulator tamoxifen reverted the epithelial defects observed in <i>nod2</i> mutants. Our findings identify a NOD2-estrogen regulatory axis that supports intestinal homeostasis and suggest that hormonal signaling may contribute to sex-specific aspects of Crohn’s disease.

<p>by Hiroki Oishi, Vladimir K. Berezovskii, Margaret S. Livingstone, Kevin S. Weiner, Michael J. Arcaro</p> Neural activity depends on energy metabolism, yet the extent to which regional variation in cortical metabolic architecture reflects the functional and perceptual demands of visual processing remains unclear. In the primate visual system, retinotopic eccentricity, the topographic mapping of visual space relative to gaze, provides a large-scale organizational axis along which spatial resolution and selectivity for behaviorally relevant visual categories vary systematically. Here, we tested whether cortical metabolic architecture reflects this axis by aligning in vivo fMRI maps of eccentricity and visual category selectivity with <i>ex vivo</i> cytochrome oxidase (CO) histology, a marker of oxidative metabolism, in macaque visual cortex. We found that the middle lateral (ML) face-selective region, which is biased toward central vision, exhibited higher CO intensity than the lateral place patch (LPP), a scene-selective region biased toward peripheral vision. More broadly, CO intensity covaried with eccentricity within both ML and LPP and across occipitotemporal visual cortex, though eccentricity only partially accounted for the elevated CO in ML. These findings reveal a close correspondence between cortical metabolic architecture and retinotopic organization, suggesting that the distribution of cortical metabolic resources is shaped by both visual field organization and the processing demands of perceptual specialization.

<p>by Marc de Manuel, Molly Przeworski, Natanael Spisak, Anastasia Stolyarova</p> Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation burdens at the end of lifespans are comparable across mammals. These observations point to a key role for natural selection in shaping mutation rates. This Essay summarizes the patterns identified to date and outlines existing theories for how selection pressures might shape mutation rates in animal germline and soma. An understanding of what sets the mutation rate of a given cell type in a species requires better integration of genetics and development with population processes of selection and genetic drift.

<p>by Abul K. Tarafder, Miles Graham, Luke K. Davis, Shawna Pratt, Jan Böhning, Pavithra Manivannan, Zhexin Wang, Camila M. Clemente, Aaron Weimann, R. Andres Floto, Raymond J. Owens, George A. O’Toole, Philip Pearce, Tanmay A. M. Bharat</p> All bacterial biofilms contain an extracellular matrix rich in filamentous molecules that self-associate, conferring emergent properties to bacteria, including antibiotic tolerance. <i>Pseudomonas aeruginosa</i> is a human pathogen that forms biofilms in diverse infectious settings, where the upregulation of a filamentous bacteriophage Pf4, has been shown to be a key virulence factor that protects bacteria from antibiotics. Here, we modeled biophysical characteristics of biofilm-linked liquid crystalline droplets formed by Pf4, which predicted that sub-stoichiometric phage binders had the ability to disrupt liquid crystals by changing the surface properties of the phage. We tested this prediction by developing nanobodies targeting the outer surface of the Pf4 phage, which disrupted in vitro reconstituted droplets, promoted antibiotic diffusion into bacteria, disrupted <i>P. aeruginosa</i> biofilm formation under a variety of conditions, and abolished antibiotic tolerance of biofilms. The inhibition strategy illustrated in this study could be extended to biofilms of other pathogenic bacteria, where filamentous molecules are pervasive in the extracellular matrix. Furthermore, our findings exemplify how targeting a biophysical mechanism, rather than a defined biochemical target, is a promising avenue for intervention, with the potential of applying this concept to other disease-related contexts.

<p>by Federica Palma, Melanie Hennart, Keith A. Jolley, Chiara Crestani, Kelly L. Wyres, Sebastien Bridel, Corin A. Yeats, Bryan Brancotte, Brice Raffestin, Sophia David, Margaret M.C. Lam, Radosław Izdebski, Virginie Passet, Carla Rodrigues, Martin Rethoret-Pasty, Audrey Combary, Solene Cottis, Martin C.J. Maiden, David M. Aanensen, Kathryn E. Holt, Alexis Criscuolo, Sylvain Brisse</p> Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cgMLST) holds great promise for standardized high-resolution strain genotyping. However, this approach faces challenges including classification instability and disconnection of new nomenclature from widely adopted classical MLST identifiers. This Essay discusses the cgMLST-based Life Identification Number (LIN) method, recently proposed as a stable multilevel strain taxonomy system applicable to most bacterial pathogens, covering how LIN codes are implemented and used in practice for precise strain definitions and epidemiological tracking.

<p>by Boris Taillefer, Florian Schattenberg, Thierry Doan, Susann Müller, Eric Cascales</p> The type VI secretion system (T6SS) is a widespread nanoweapon deployed by bacteria to eliminate competitors in polymicrobial environments, allowing niche colonization or host invasion. Fluorescent microscopy recordings have shown that T6SS expression and/or activation is heterogeneous in clonal populations of many bacterial species. However, it is still unknown whether T6SS heterogeneity is genetically controlled or arises from stochastic processes and what its physiological relevance is. Here, we report that enteroaggregative <i>Escherichia coli</i> (EAEC) exhibits stable phenotypic heterogeneity in T6SS expression. Under iron-limiting conditions, the Sci1 T6SS is expressed in only a subset of the population, creating distinct ON and OFF subpopulations in a reversible, heritable, and epigenetically controlled equilibrium. This heterogeneity is governed by the interplay between the iron-responsive regulator Fur- and Dam-dependent DNA methylation at the <i>sci1</i> promoter. Mutations in Fur binding sites or GATC methylation motifs shift the population to homogeneous ON or OFF states, respectively. Functional analyses reveal that while ON cells mediate antibacterial activity, OFF cells buffer the population against lethal retaliatory responses from defensive T6SS⁺ competitors. Our results suggest that T6SS heterogeneity in EAEC represents a finely tuned attenuation strategy optimizing the trade-off between competitive killing and survival in hostile microbial communities. This work uncovers a novel layer of regulation in T6SS deployment and highlights phenotypic heterogeneity as an adaptive trait in interbacterial warfare.

<p>by Lucas M. Bietti, Adrian Bangerter</p> Artificial intelligence (AI) is rapidly transforming scientific writing by expanding access and efficiency, yet it risks decoupling writing from thinking. Scientific writing is a core cognitive and epistemic practice that must be cultivated and preserved alongside AI use. The use of large language models is rapidly transforming the scientific writing process, making it quicker and easier to write research papers. However, this Perspective urges caution when using such tools, arguing that it can risk decoupling writing from thinking.

<p>by Fuxi Rong, Yaqi Zhang, Fangrui Ni, Lantian Zhang, Mingxin Yu, Zheyuan Hong, Muhammad Fahad, Yuxin Shen, Chuanjia Liu, Shengke Tian, Dezhi Wu, Liang Wu</p> In plants, a subset of miRNA precursors can yield multiple mature miRNAs; however, how they simultaneously regulate a single biological process remains poorly understood. Cadmium (Cd) is a non-essential heavy metal toxic to plants, posing serious risks to human health via the food chain. As rice is a major dietary source of Cd, elucidating the molecular mechanisms underlying Cd accumulation is crucial for ensuring food safety. Here, we show that a pair of miRNAs derived from the <i>MIR408</i> precursor cooperatively represses Cd uptake in roots by targeting distinct genes, consequently reducing Cd accumulation in rice grains. miR408-5p inhibits translation of <i>Heavy metal-associated Isoprenylated Plant Protein 9</i> (<i>HIPP19</i>), which is specifically expressed in exodermis and endodermis cells and facilitates Cd binding. Meanwhile, miR408-3p cleaves <i>Uclacyanin 7</i> (<i>UCL7</i>) mRNA, leading to enhance the activity of superoxide dismutases (SODs), and increase production of reactive oxygen species (ROS), particularly hydrogen peroxide (H₂O₂), which in turn suppresses Cd absorption and accumulation. Furthermore, knockout mutants of <i>HIPP19</i> and <i>UCL7</i>, as well as <i>MIR408</i> overexpressing lines, exhibit significantly decreased Cd content in grains, while the accumulation of other essential metals remains comparable to that of wild-type plants. These findings establish a promising strategy for producing “low-Cd rice” without compromising agronomic traits for food safety.

<p>by William B. Mair, Ines Alvarez-Garcia</p> Aging affects us all, but we still do not know how the process evolves or if we can modulate its pace. This issue of PLOS Biology presents a Collection of articles that explores different aspects of aging, discussing what challenges still need to be overcome. Aging affects us all, but we still do not know how the process evolves or if we can modulate its pace. This Editorial presents a Collection of articles that explores different aspects of aging, discussing what challenges still need to be overcome.

<p>by Jiasong Li, Lingwei Tang, Xinhang Wei, Yumin Chen, Haibing Xu</p> Flexible goal‑directed navigation requires integrating changing goal information with a stable spatial map, yet how cortico-hippocampal circuits accomplish this remains unclear. We simultaneously recorded medial orbitofrontal cortex (mOFC) and dorsal CA1 (dCA1) while rats learned daily changing goal locations on a cheeseboard maze. Rats rapidly learned new goal locations and retained memory for them in the post‑probe session. Both regions contained goal‑related neuronal representations, but their profiles differed: dCA1 showed stronger spatial specificity, whereas mOFC showed more prominent learning‑related updating of goal‑related activity. Combining dCA1 and mOFC activity improved decoding of behavioral stage and learning block relative to either region alone, consistent with complementary contributions to ongoing behavior and learning state. Across learning, these population‑level differences were accompanied by stronger theta‑range synchronization and theta–gamma coupling during navigation than during goal periods. A recurrent network model with dynamic synaptic efficacy captured qualitative features of efficient acquisition and flexible goal updating, providing a candidate computational framework for how learning‑related temporal coordination could contribute to adaptive navigation.

<p>by Chengchao Ding, Xinyi Ashley Liu, Fushun Zhang, Saori Uematsu, Shu-Bing Qian, Yan Xiang</p> Schlafens proteins (SLFNs) are interferon-inducible regulators of RNA metabolism that influence antiviral defense and cell fate. Human SLFN14 is a ribosome-associated endoribonuclease whose pathogenic variants cause autosomal dominant inherited thrombocytopenia (IT), but the molecular basis of this disorder remains unclear. Here, using HEK293T cells expressing human SLFN14 variants, we show that SLFN14 represses global protein synthesis through selective cleavage of type II tRNAs. IT-linked mutations alter SLFN14 RNA substrate specificity, enhancing depletion of type II tRNAs while reducing rRNA cleavage. This shift promotes ribosome stalling at codons decoded by type II tRNAs, triggering global translational arrest, stress signaling, and cell death. These findings reveal how altered RNA targeting by SLFN14 can drive disease and highlight selective tRNA targeting as a mechanism than regulates translation and cell fate.

<p>by Frans Nordén, Irene Zanettin, Mikael Lundqvist, Artin Arshamian, Johan N. Lundström</p> Perceived stimulus intensity is a core feature of sensory experience, yet how it emerges in the human olfactory system remains unknown. Here, we demonstrate that oscillatory dynamics in the human olfactory bulb (OB) and piriform cortex (PC) primarily encode subjective perceived intensity rather than physical concentration. Using noninvasive electrobulbogram recordings, we show that early gamma-band activity in the OB reflects bottom-up transmission of perceived intensity to the PC, which in turn sends top-down beta-band feedback that modulates OB activity via phase–amplitude coupling and transient beta bursts. This bidirectional communication supports a dynamic updating mechanism that maintains perceptual constancy across varying environmental odor concentrations. Our findings reveal a previously uncharacterized oscillatory framework for intensity coding in the human olfactory system, highlighting the primacy of perception over stimulus properties and offering a mechanistic basis for predictive processing in early sensory circuits.

<p>by Jennifer L. Garrison</p> Classifying ovaries solely as reproductive organs has obscured their role as systemic regulators of female physiology. This Perspective makes the case that ovarian aging is a primary determinant of healthspan and belongs at the center of geroscience. Classifying ovaries solely as reproductive organs has obscured their role as systemic regulators of female physiology. This Perspective discusses that ovarian aging is a primary determinant of healthspan and belongs at the center of geroscience.

<p>by The PLOS Biology Staff </p>

<p>by Sara Alam, Linda Partridge, Nazif Alic</p> Globally, the growing proportion of older individuals is imposing personal and societal costs. However, interventions that slow aging are possible; for example, dampened nutrient signaling pathway activity in animal models promotes better health later in life. Recent findings indicate that such interventions have long-term effects even when applied transiently in early adulthood, forming a “physiological memory.” Similar memory has been extensively documented in human epidemiology, where the health of older people is shaped by their earlier environmental exposures, such as diet composition. This Essay argues that the study of the biology of aging should encompass determinants of healthspan across the entire life course.

<p>by Priscila Chiavellini, Vittorio Sebastiano</p> Aging is typically framed as a one-way, irreversible accumulation of molecular damage in cells and tissues, leading to progressive functional decline. Yet mammalian reproduction, and particularly female reproduction, reveals a striking exception to this rule. Despite residing within an aging organism and within a fast-aging ovarian tissue environment, oocytes give rise to embryos that begin life with restored developmental potential and youthful molecular organization. By reframing ovarian biology as a model for rejuvenation rather than solely as a site of reproductive decline, this Essay proposes that the ovary offers a powerful blueprint for advancing the biology of aging and longevity.

<p>by The PLOS Biology Editors </p>

<p>by Susmit Mhatre, Darcie L. Moore</p> The field of human adult neurogenesis has been controversial despite mounting evidence. The authors propose moving beyond debating the existence of adult neurogenesis and towards discovering strategies to harness endogenous stem cell potential for resilience against cognitive aging. The field of human adult neurogenesis has been controversial despite mounting evidence. This Perspective proposes moving beyond debating the existence of adult neurogenesis, and towards discovering strategies to harness endogenous stem cell potential for resilience against cognitive aging.

<p>by Garrison W. Bullard, Lauren B. Buckley, Joel G. Kingsolver</p> Predicting survival of ectotherms in stressful and variable thermal environments is an essential challenge in this era of heat waves and climate change. Recent thermal death time (TDT) models, based on an exponential relationship between average time to death (or failure) <i>t</i>_f and temperature, enable accounting for average survival responses to both the magnitude and duration of stressful temperatures. However, extending these deterministic and probabilistic models to predict patterns of survival in fluctuating temperatures currently requires additional assumptions: e.g., that injury accumulation due to heat stress is additive across temperatures, and that the shape of the cumulative survival curve does not change with temperature. We evaluate these assumptions and their consequences by using a parametric survival model and available data on failure (knockdown) times of adult <i>Drosophila.</i> We find that the variance in log(<i>t</i>_f) increases with increasing constant temperatures in most <i>Drosophila</i> species, resulting in changes in the shape of the failure density and survival curves across temperatures. We compare predictions of three deterministic and probabilistic models that differ in their TDT assumptions using <i>D. melanogaster</i> data in fluctuating (but stressful) temperatures. All three models consistently underestimate observed median failure times except at extremely high temperatures, suggesting non-additivity of heat injury accumulation. Our parametric model, incorporating temperature-dependent variance, provides more accurate predictions of cumulative survival curves in fluctuating temperatures. Our findings highlight the importance of understanding both mean and variation in failure times, and how these change across temperatures, for modeling survival in fluctuating thermal environments.