To the Editor Dr Molyneaux and colleagues reported the CORAL randomized clinical trial evaluating nalbuphine extended release (ER) for idiopathic pulmonary fibrosis (IPF)–associated cough, an area where evidence-based options remain limited. By pairing 24-hour digital cough monitoring with patient-reported measures, the study provides a useful template for antitussive trials in interstitial lung disease.
Science Journals
The histone variant H2A.Z and DNA methylation are enriched at mutually exclusive genomic segments, though its mechanistic bases remain unclear. Here, we examine DNA methylation’s influence on the intrinsic stability of the H2A.Z nucleosome and chaperone-mediated H2A.Z deposition. Cryo-EM and endonuclease analyses suggest that DNA methylation subtly increases the openness and accessibility of the H2A.Z nucleosome on satellite II-derived DNA sequences. In transcriptionally silent <i>Xenopus</i> egg extracts, H2A.Z preferentially associates with unmethylated DNA though a substantial proportion of H2A.Z is recruited to methylated DNA. Preferential H2A.Z deposition to unmethylated DNA depends on the SRCAP complex, whose DNA binding is suppressed by methylation, while an SRCAP-independent and DNA methylation-insensitive mechanism for H2A.Z deposition also exists. Altogether, we propose that SRCAP drives the biased association of H2A.Z to unmethylated DNA, while additional mechanisms, potentially taking advantage of the subtle DNA methylation-induced physical effects, further assist the exclusion of H2A.Z from methylated DNA.
The US Department of Health and Human Services (HHS) Office of the Surgeon General released an advisory on the harms of excessive screen use for children and adolescents. (There is currently no confirmed US surgeon general.)
Several common food preservatives may be linked to hypertension and cardiovascular disease, a study published in the European Heart Journal found.
JAMA Senior Editor Derek C. Angus, MD, MPH, spoke with Sneha Kannan, MD, MS, assistant professor of critical care medicine at the University of Pittsburgh, about the complex role of private equity in health care for the Healthy Dialogue podcast.
The US Food and Drug Administration (FDA) approved the first treatment for chronic hepatitis delta virus infection, a liver disease that only occurs in people who have hepatitis B virus infection.
Type 2 diabetes may be more prevalent in US children and adolescents than previously thought, according to the first nationally representative estimates, published in JAMA Pediatrics.
This Viewpoint considers controversies regarding osteoporotic fracture prevention strategies, noting that some currently available medications, including estrogen, are underused and poorly understood.
<p>by Maëlan Q. Menétrey, Michael H. Herzog, David Pascucci</p>
In some forms of postdictive phenomena, later events influence the perception of earlier ones, suggesting that conscious perception may be preceded by extended periods of unconscious processing. An example is the Sequential Metacontrast (SQM) paradigm, in which vernier offsets are unconsciously integrated over several hundred milliseconds before conscious perception. Obviously, the integrated percept can only emerge after each individual element in the stream has been processed. Thus, the SQM provides a unique opportunity to dissociate unconscious from conscious stages of visual processing, as these stages are well separated in time. Using electroencephalography (EEG) recordings in human participants during the SQM, we identified two distinct stages of neural activity: an early occipital EEG activity pattern (~200 ms after the initial vernier) associated with unconscious processing, and a later centro-parietal EEG pattern (~400 to 600 ms after SQM onset) associated with the integrated percept and the behavioral report. We propose that the transition between these neural patterns marks the shift from unconscious encoding of individual visual stimuli to their integrated percept.
<p>by Xuhao Shao, Chuansheng Chen, Elizabeth F. Loftus, Bi Zhu</p>
Shared memories of event details are crucial to eyewitness testimony. When different people encode or recall the same event, similar scene-specific neural activity patterns emerge across individual brains. However, it remains unclear whether these patterns are specific to event details and how test expectancy (i.e., expecting free recall or general memory tests) and misinformation affect them. In this study, 100 participants were randomly assigned to view one of two versions of each event. Both versions featured identical scenarios, but with different details. About half of the participants were informed about the upcoming free recall before viewing events, while the others were told to expect a general memory test. Functional magnetic resonance imaging was used to record their brain activity during four stages: viewing original events, initial free recall, reading misinformation, and final free recall of original events. The neuroimaging data were analyzed based on the similarity of neural patterns across participants. Test expectancy increased the similarity of detail-specific neural activity patterns between individuals when they viewed original events in brain regions relevant for visual attention. Misinformation increased the likelihood of people forming shared false memories of event details. People who formed shared false memories exhibited similar detail-specific patterns of activity in the dorsomedial prefrontal cortex when reading misinformation. People who formed shared true memories exhibited similar detail-specific patterns of activity in the inferior parietal lobe when viewing original events, as well as in the ventrolateral prefrontal cortex and middle temporal gyrus when recalling them after exposure to misinformation. Our findings revealed that different brain regions of the default mode network play distinct roles in the encoding and recall of event details shared by individuals.
<p>by Ioanna Morianou, Lee Phillimore, Bhavin S. Khatri, Louise Marston, Matthew Gribble, Austin Burt, Federica Bernardini, Andrew M. Hammond, Tony Nolan, Andrea Crisanti</p>
CRISPR-based gene drives are selfish genetic elements with the potential to spread through entire insect populations for sustainable vector control. Gene drives designed to disrupt the reproductive capacity of females can suppress laboratory populations of the malaria mosquito, <i>Anopheles gambiae</i>. However, any suppressive intervention will inevitably exert an evolutionary pressure for resistance, and the likelihood of resistance emerging at natural population scales remains poorly defined. Here, we present a pipeline to quantify the evolutionary space for resistance, enabling accelerated discovery, engineering, and testing of both natural and drive-induced variants that could reverse gene drive spread. We applied our approach to stress-test a best-in-class suppression gene drive that has evaded resistance in all laboratory-contained releases to date, known as Ag(QFS)1. We showed that previously undetected resistant alleles can arise at low frequency, including a novel type of partially resistant alleles that can perturb drive-invasion dynamics. Integrating experimentally derived resistance rates with population genetic modeling shows that single-target suppression drives are unlikely to be robust at natural mosquito population sizes, even at highly constrained loci. Here, we engineer and validate multiplexed gene drives in <i>Anopheles gambiae</i>, that target multiple conserved sites, actively removing resistant alleles. Our models predict that such gene drives could supress large natural mosquito populations in the field.
<p>by R. Craig MacLean, Adam Mulkern, Liam P. Shaw</p>
Why do even closely-related bacteria differ in their capacity to evolve antibiotic resistance? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic resistance in bacterial genomes is frequently catalyzed by the presence of ‘resistance potentiators’: genes, elements, or pathways that accelerate evolution in a trait-specific manner. Epidemiological evidence suggests that resistance potentiators that modulate phenotypes have been particularly important in successful pathogen lineages. Furthermore, experimental models show that combining antibiotics with inhibitors of resistance potentiators can restrict the evolution of resistance, suggesting that they could be future drug targets or otherwise lead to more evolution-informed antibiotic therapy.
Cancer repeatedly exploits attributes fundamental for morphogenesis to advance malignancy and metastasis. This is illustrated by lineage-specific transcription factors that regulate neural crest migration, representing frequent drivers of malignancy. One such example is the <i>forkhead</i> transcription factor FOXC1, where gain of function is a feature of diverse cancers that is associated with an unfavorable prognosis. Using RNA-, ChIP-sequencing and CRISPR interference, we show that Foxc1 binds a locus in a region of closed chromatin to induce expression of Arhgap36, a tissue-specific inhibitor of protein kinase A. Because PKA is a core Hedgehog (Hh) pathway inhibitor, Foxc1’s induction of Arhgap36 expression increases Hh activity. The function of Sufu, a PKA substrate, and a second essential Hh pathway inhibitor, is likewise impaired. The resulting increased Hh pathway output is resistant to pharmacological inhibition of <i>Smoothened</i>, a phenotype of more aggressive cancers. The Foxc1–Arhgap36 relationship identified in murine cells was further evaluated in neuroblastoma, a neural crest-derived pediatric malignancy. This demonstrated in a cohort of 1348 patients that high levels of ARHGAP36 are predictive of improved 5-year survival. Accordingly, this study has identified as a novel transcription factor which enhances ARHGAP36 expression, one that induces Hh activity in multiple tissues during development. It also establishes a model by which increased levels of FOXC1 via ARHGAP36 and PKA inhibition dysregulate multiple facets of Hh signaling and provides evidence demonstrating relevance to a common neural-crest-derived malignancy.
Accurate pose estimation underpins quantitative analysis of behavior, yet many deep learning-based tracking tools remain optimized for offline workflows that rely on fragmented software pipelines, workstation-grade GPUs, or external middleware to enable real-time deployment. Here, we present an integrated software-hardware ecosystem for pose estimation that spans dataset creation, model training, offline analysis, and real-time deployment on embedded edge-computing devices. SqueakPose Studio provides a software suite for whole-frame, deep learning-based pose estimation that unifies dataset creation, manual and model-assisted labeling, model training, validation, and large-scale offline inference. The system leverages modern object-detection architectures to enable efficient end-to-end training and inference without patch-based sampling or multistage post-processing, and supports execution on CPUs, GPUs, and Apple Silicon. For experimental settings requiring continuous recording and synchronized data acquisition, SqueakView enables real-time model deployment, video capture, and sensor logging on embedded edge-computing hardware, while MouseHouse provides a compact, modular enclosure designed for home cage-based experiments that integrates embedded GPU compute, microcontroller-based timing, and peripheral I/O. A shared data format and deterministic timing architecture ensure consistency across offline analysis and real-time deployment. Together, SqueakPose Studio, SqueakView, and MouseHouse provide a unified platform for pose estimation that supports both conventional offline analysis and embedded, real-time experimentation, without reliance on workstation-grade hardware or external middleware.
Loss of function mutations of Cx32, which is expressed in Schwann cells, cause X-linked Charcot-Marie-Tooth disease, a slowly progressive peripheral neuropathy. Action potential propagation causes Cx32 hemichannels in the Schwann cell paranode to open. As Cx32 hemichannels are directly sensitive to CO<sub>2</sub>, we have tested whether CO<sub>2</sub> produced in the axon, as a consequence of the energetic demands of action potential propagation, might gate Cx32 hemichannels. Using isolated sciatic nerve from the mouse, we found that the critical components required for intercellular CO<sub>2</sub> signaling are present (nodal mitochondria, the source of CO<sub>2</sub>; a CO<sub>2</sub>-permeable aquaporin, AQP1; paranodal Cx32; and carbonic anhydrase). We have used a membrane impermeant fluorescent dye, FITC, to demonstrate the opening of Cx32 in Schwann cells in response to an external CO<sub>2</sub> stimulus or during action potential propagation in the isolated nerve. Pharmacological manipulations of AQP1 or carbonic anhydrase activity altered Cx32 gating during action potential firing. Expression of a modified Cx32 subunit, Cx32<sup>DN</sup>, that coassembles with Cx32<sup>WT</sup>, revealed that the activity-dependent dye loading of Schwann cells depended upon CO<sub>2</sub> binding to Cx32. CO<sub>2</sub> can, therefore, mediate neuron-to-glia signaling via connexins. CO<sub>2</sub> permeable aquaporins and carbonic anhydrase are key components of this signaling mechanism.
A coma pattern-based autofocusing method resolves bacterial cold shock response at single-cell level
Imaging-based single-cell physiological profiling holds great potential for uncovering fundamental bacterial cold shock response (CSR) mechanisms, but its application is impeded by severe focus drift during rapid temperature downshifts required for CSR induction. Here, we introduce LUNA (Locking Under Nanoscale Accuracy), an innovative autofocusing method that leverages the coma pattern of detection light to characterize focus drift. LUNA improves the focusing precision down to 3 nm and extends the focusing range to at least 40 times the objective depth of focus. These advancements enable us to investigate the complete dynamics of bacterial single-cell CSR, revealing continuous cellular growth and division. We resolve a three-phase adaptation process characterized by distinct growth deceleration dynamics, and show that bacterial cells maintain robust size regulation and coordinate uniform adaptation to cold shock through synchronized growth and elapsed cycles. Notably, a model based on scattering theory reconciles the paradox between the growth lag of batch culture and continuous single-cell growth. These findings fundamentally transform our understanding of bacterial CSR and highlight LUNA’s excellent potential for expanding state-of-the-art research in biology.
Lipid packing is a fundamental characteristic of bilayer membranes. Yet, we lack detailed mechanistic understanding of how lipid packing directly affects membrane-associated cellular processes. Here, we address this by focusing on caveolae, small Ω-shaped invaginations of the plasma membrane, which serve as key regulators of cellular lipid sorting and mechano-responses. In addition to caveolae coat proteins, the lipid membrane is a core component of caveolae that critically impacts their biogenesis, morphology, and stability. We show that the small compound Dyngo-4a adsorbs and inserts into the membrane, resulting in a dramatic dynamin-independent inhibition of caveola dynamics. Analysis of model membranes in combination with molecular dynamics simulations revealed that a substantial amount of Dyngo-4a was inserted and positioned at the level of cholesterol in the bilayer, affecting lipid order in a cholesterol-dependent manner. Dyngo-4a treatment resulted in decreased lipid packing of the plasma membrane. This prevented caveolae internalization and lateral diffusion without affecting their morphology, associated proteins, or the overall cell stiffness. Artificially increasing plasma membrane cholesterol levels was found to counteract the block in caveola dynamics caused by Dyngo-4a. Therefore, we propose that the outer leaflet lipid packing of cholesterol in the plasma membrane critically contributes to the confinement of caveolae to the plasma membrane.
Reconstructing and investigating the geometry underlying data is a fundamental task in single-cell analysis, yet no unified framework exists for learning, evaluating, and diagnosing representations that faithfully preserve it. We present TopoMetry, a geometry-aware framework that learns intrinsic coordinate systems directly from the data and refines them into high-fidelity <i>spectral scaffolds</i>. These scaffolds capture both local neighborhoods and global structures, supporting downstream analyses such as clustering and visualization. In benchmarks across diverse single-cell datasets, TopoMetry preserved geometry more reliably than standard workflows and revealed biological signals otherwise obscured, including unexpected transcriptional diversity among T cells and links between RNA-defined subpopulations, and clonal expansion. The full analysis can be executed with a single line of code to generate a comprehensive report, making the framework both powerful and accessible. Beyond individual findings, TopoMetry warrants a shift of focus from static two-dimensional projections to the systematic learning and evaluation of geometry itself, enabling more accurate exploration of cellular diversity.
Choosing a clinical specialty is a critical decision for physician-scientist trainees, influencing both clinical practice and research trajectory. This article provides a structured approach to specialty selection, emphasizing the importance of aligning clinical interests with long-term research goals, evaluating training pathways, and considering lifestyle implications. Physician-scientists, including MD-PhD and other dual-degree graduates, as well as MD graduates with research-intensive training, often pursue specialties with established research pathways. We outline key decision-making factors, including mentorship, clinical exposure, research commitment, and financial sustainability. Additionally, we compare research track and categorical residency pathways, detailing differences in training structure, funding opportunities, and career outcomes. The article explores the evolving role of physician-scientists across career stages, from residency through senior faculty leadership, highlighting strategies to maintain research engagement while balancing clinical responsibilities. By critically evaluating these factors and leveraging mentorship and institutional support, physician-scientists can make informed decisions that align with their aspirations, ensuring a fulfilling and impactful career in both medicine and research.
Cortical control of movement is a distributed computation spanning multiple densely interconnected regions. Although we have rich anatomical atlases and a coarse understanding of how function maps to areas and subregions, we lack a detailed account of how behaviorally relevant activity is organized across the cortical sheet. Here, we trained head-fixed mice to perform a 15-target reach-to-grasp task while we performed cellular-resolution, two-photon calcium imaging across five regions of sensorimotor cortex (>39,000 layer 2/3 neurons). We characterized each neuron’s trial-averaged peri-event activity with interpretable metrics and mapped these response properties across areas, revealing large-scale spatial structure. Neuronal response profiles often shifted abruptly at anatomical borders: motor areas showed sharper tuning and more linear relationships with target location, whereas somatosensory areas displayed more heterogeneous response patterns. Neural response properties also differed according to somatotopic representation. Nonlinear dimensionality reduction of the neural feature matrix revealed that areas varied in their average response profiles, but that areas did not have well-separated feature distributions; instead, each area contained subpopulations. Neurons in each subpopulation had characteristic response profiles and were distributed across multiple cortical areas. The spatial distributions of the subpopulations overlapped, with neurons from different subpopulations salt-and-pepper intermingled in the overlap zones. Together, these results describe novel activity structure across sensorimotor cortex and identify several distinct but spatially overlapping subpopulations with characteristic activity patterns during reach-to-grasp behavior.
We report a minimally disruptive labeling strategy for stress granule protein, G3BP Stress Granule Assembly Factor 1 (G3BP1), and ALS-linked protein, TAR DNA-binding protein 43 (TDP-43), using the fluorescent non-canonical amino acid Anap. By integrating the genetic code expansion (GCE) with rational site selection, we achieved precise incorporation of Anap that preserves protein structure and function. In live cells and neurons, Anap labeling faithfully recapitulated localization, stress-induced dynamics, and recovery behavior, outperforming conventional fluorescent tags, and enabling physiologically relevant visualization of protein pathobiology.
Neuronal activity is driven by the complex interplay between various membrane currents, often located in distinct domains of the spatially extended dendritic tree. How the effect of these currents propagates to the soma and contributes to neuronal output under in vivo conditions is not fully understood. Here, we develop a new method to measure and visualize the contributions of individual membrane currents to the somatic response in spatially extended biophysical model neurons. Our approach relies on the iterative decomposition of the axial current flowing between neighbouring compartments in proportion to the underlying membrane currents measured in the model. We apply this method to visualize the inputs driving hippocampal place cell activity. Our method provides a compact and intuitive description of the various dendritic events underlying subthreshold activity, spiking, or burst firing. By contrasting the dendritic input currents preceding spiking and bursting, we demonstrate that both could occur at highly variable input levels to proximal dendrites (basal and oblique), and that strong distal inputs facilitate, rather than control, the generation of complex spike bursts. Our method opens a novel window onto single-neuron computations that will help to design better models and to interpret the results of in vivo imaging experiments.
<p>by Tal Shay, Christophe O. Benoist, Ricardo Grieshaber-Bouyer</p>
High-throughput single-cell assays reveal data that defies discrete categorization. The ‘cell cloud’ model, grounded in established systems biology principles, offers a framework to navigate biological plasticity alongside technical variability.
Immune cells exist as continuous clouds, not discrete categories. In this Perspective, authors from the Immunological Genome Project reframe immune identity through systems biology, and redirect where immunotherapies should aim: at the dynamics of the cloud, not just its center.
<p>by Tomas G. Aquino, Robert Kim, Nuttida Rungratsameetaweemana</p>
Flexible behavior requires the ability to modulate sensory processing based on task context, yet the circuit-level mechanisms supporting this capacity remain poorly understood. Here, we combine recurrent neural network modeling and neural recordings from mouse visual cortex to investigate how task context shapes sensory coding. Networks trained on an instruction-based discrimination task develop a disinhibitory interneuron-to-interneuron motif that dynamically gates task-relevant sensory information. Perturbation and lesion analyses show that this motif is necessary for task performance and for maintaining distinct sensory representations across contexts. We validate key predictions in mouse visual cortex, where interneuron activity patterns exhibit comparable task-dependent modulation. These results identify a biologically plausible circuit motif that supports flexible sensory processing and link recurrent connectivity structure to adaptive context integration in both artificial and biological systems.
There are a number of errors in the caption for Fig 4, “Farnesylated Ydj1 is required for maintaining Cdc42 levels and its asymmetric distribution,” panels A-C. Please see the complete, correct Fig 4 caption here.
A. Localization of Cdc42-mCherrySW in WT and ydj1 mutants at 27°C. Arrows mark examples of large-budded cells used for Cdc42 quantification in B & C. Scale bar: 3 µm. B. Cdc42-mCherrySW levels in mother (m) and bud (b) compartments of large-budded ydj1Δ cells, grown at 27°C. (left plot) Mean fluorescence intensities from 19 representative mother-bud pairs are plotted. ns, p ≥ 0.05, paired t test. (right plot) The log2 mother-to-bud ratio of Cdc42-mCherrySW mean intensity in WT and ydj1 mutants (n = 52 per strain). The dotted line denotes a symmetric distribution of Cdc42 between mother and bud. **** p < 0.0001 by one-way ANOVA. See also S3D Fig. C. Cdc42 levels in WT and ydj1 mutants, grown at 27°C to mid-log phase. Mean fluorescence intensities of Cdc42-mCherrySW in whole cells (mother and bud combined) are plotted. n = 57 ~ 60 per strain; **** p < 0.0001, unpaired t-tests. Immunoblotting shows Cdc42-mCherrySW in each strain, detected using polyclonal anti-RFP antibodies, and α-tubulin, a loading control. See also S3C Fig. D. Association of Cdc42-mCherrySW with GFP-Ydj1 detected by a visible IP assay (top panel). A control reaction used extracts containing untagged Ydj1 (bottom panel). The data underlying the graphs can be found in S1 Data.
A. Localization of Cdc42-mCherrySW in WT and ydj1 mutants at 27°C. Arrows mark examples of large-budded cells used for Cdc42 quantification in B & C. Scale bar: 3 µm. B. Cdc42-mCherrySW levels in mother (m) and bud (b) compartments of large-budded ydj1Δ cells, grown at 27°C. (left plot) Mean fluorescence intensities from 19 representative mother-bud pairs are plotted. ns, p ≥ 0.05, paired t test. (right plot) The log2 mother-to-bud ratio of Cdc42-mCherrySW mean intensity in WT and ydj1 mutants (n = 52 per strain).…