Marine fish play a significant yet understudied role in the oceanic carbon cycle through the production of magnesium-rich calcium carbonate (CaCO3) precipitates known as ichthyocarbonates. These deposits form in the gut of marine teleost fish in response to salinity, serving as part of their osmoregulation strategy. Through this, marine fish may contribute as much as 9.04 Pg of CaCO3 per year in global new carbonate production, being equivalent to or potentially higher than the production by coccolithophores and pelagic foraminifera. Despite their ecological relevance, the biological mechanisms driving ichthyocarbonate precipitation remain to be fully resolved. Intriguingly, bacteria are consistently found in intimate association with ichthyocarbonate precipitates. Given the widespread capacity of prokaryotes to mediate CaCO₃ precipitation, this association points to a previously unexplored microbial contribution to the process. To investigate the potential role of bacteria in ichthyocarbonate production, we subjected Gulf toadfish (Opsanus beta) to salinity treatments common to their native range and known to elicit changes in CaCO3 precipitation. To assess the respective contributions of the host and its microbiota to ichthyocarbonate formation in the gut, we characterized the microbiome across the toadfish gut and performed meta-transcriptomic analysis. Across the toadfish gut, we identify a high abundance of vibrios associated with ichthyocarbonates with the metabolic potential for CaCO3 precipitation. Specifically, we observe the expression of the transcriptional activator of urease (ureR) by Photobacterium damselae subsp. damselae, which can induce the precipitation of CaCO3 via the production of bicarbonate. We demonstrate that CaCO₃ precipitation in marine fish may not solely be a host-driven process, but potentially the result of a functional symbiosis with gut-associated Vibrio bacteria. We hypothesize that just as photosymbionts enable corals to build reefs, fish hosts, along with their microbial partners, may synergistically contribute to oceanic carbonate production. This discovery, if confirmed, expands the role of symbiosis in marine biomineralization and underscores its broader influence on global biogeochemical cycles.

Cryptococcus neoformans is an environmental pathogen that remodels its cellular physiology to survive within mammals and, in susceptible hosts, cause life-threatening meningoencephalitis. Of the many distinctions between the external environment and mammalian tissues, CO2 concentration in the host is two orders of magnitude higher than in the environment and represents a critical stress for C. neoformans. C. neoformans strains that do not replicate at host CO2 concentrations are less virulent in mouse models of infection, further supporting CO2 tolerance as a virulence trait. To further understand the genetic determinants of C. neoformans CO2 tolerance, we performed a near genome-wide screen for deletion mutants with altered CO2 fitness using a competitive growth assay. A total of 301 of 4,692 deletion mutants showed altered CO2 tolerance (245 reduced fitness; 56 increased fitness) demonstrating the global effect of host CO2 on C. neoformans physiology. Based on this data set as well as a metabolomic analysis of C. neoformans adaptation to host CO2, we show that remodeling of central carbon metabolism, oxidative stress buffering, and membrane homeostasis represent an integrated response to CO2 stress that is mediated in part by the TOR-Ypk1 signaling axis. We propose that CO2-induced capsule formation leads to reduced cellular glucose which, in turn, triggers remodeling of central carbon metabolism toward utilization of alternative carbon sources and increased mitochondrial respiration/reactive oxygen generation. Thus, these data provide a near genome-wide profile of the genetic determinants of C. neoformans CO2 tolerance as well as a model for how this important environmental human fungal pathogen alters its physiology to proliferate in the host.

Virulent bacteriophages infecting Klebsiella pneumoniae often show capsule-driven host tropism due to the presence of capsule-specific depolymerases. Yet for temperate phages the genetic and functional basis of such capsular specificity remains less well understood. Depolymerases appear unexpectedly rare in prophage genomes, raising unresolved questions about which prophage genes mediate capsular specificity, whether this apparent scarcity reflects biological or ecological differences versus annotation limitation, and whether prophage-encoded receptor-binding proteins (RBPs) are functionally active. To address these questions, we analysed 3,900 Klebsiella genomes from diverse ecological niches to identify prophage-encoded proteins mediating capsular specificity. We conducted a genome-wide association study (GWAS) correlating prophage protein clusters (from 8,105 prophages) with confidently assigned bacterial K-loci. GWAS revealed statistically supported predictors of capsular specificity for 16 of the 35 most diverse K-loci analysed. These predictors were dominated by diverse RBPs, including classical [Formula: see text]-helix depolymerases (6 predictors), SGNH-domain hydrolases predicted to deacetylate polysaccharides (6 predictors), and structurally novel RBPs lacking known depolymerase folds (2 predictors). Nearly one-third of K-loci yielded no statistically significant predictors. A targeted experimental screen of 50 candidate prophage depolymerases showed that 34 failed to yield detectable recombinant expression, and neither sequence similarity, structural prediction, nor prophage genomic context reliably predicted activity. Of the 14 active enzymes, 5 targeted a K-type different from that predicted of their bacterial host, and enzyme specificity was not consistently explained by sequence or structural homology. Comparison with GWAS predictions revealed that 10 of the 12 strongest GWAS predictors were experimentally validated, while 2 remained inconclusive. Together, these results highlight the intrinsic difficulty of predicting activity and capsular specificity of prophage-encoded RBPs from genomic information alone. Finally, analysis of 4,598 high-completeness prophages revealed that SGNH-domain hydrolases are among the most prevalent enzymatic domains in prophage RBPs. Two SGNH-domain RBPs identified by GWAS were experimentally confirmed as active esterases, supporting capsule deacetylation as a widespread alternative to polysaccharide depolymerisation in temperate phages. Our findings reveal that Klebsiella prophages encode structurally diverse RBPs, suggesting temperate phages may rely not only on depolymerisation but also on capsule modification-such as deacetylation-for infection. This also suggests that capsule modification may contribute to phage-host interactions in ways not fully captured by current K-locus assignments, with potential implications for phage specificity, competition and vaccine design.

Uncovering what drives select biomolecules to form phase-separated condensates in vivo and identifying their physiological significance are topics of fundamental importance. Here, we show that nitrogen-starved Escherichia coli produces long-chain polyphosphates, which scaffold the RNA chaperone Hfq into high molecular weight complexes, which eventually phase separate together with components of the RNA translation and processing machinery. The presence of polyphosphate within these condensates controls Hfq function by selectively stabilizing polyadenylated RNAs involved in transcription and protein translation and by promoting interactions with translation- and RNA-metabolism-associated proteins involved in de novo protein synthesis. Lack of polyphosphate significantly impairs condensate formation, increases cell death, and hinders recovery from N-starvation. In functional analogy, we demonstrate that polyP contributes specifically to the formation of Processing (P)-bodies in human cell lines, revealing that a single, highly conserved and ancestral polyanion serves as a modulator for functional phase-separated condensate formation across the tree of life.

P2X receptors are ATP-gated cation channels, and the P2X3 subtype plays crucial roles in peripheral sensory neurons, including in chronic pain and chronic cough. Accordingly, P2X3 receptors have attracted substantial interest as a therapeutic target. Gefapixant, a negative allosteric modulator (NAM) of P2X3 receptors, has been approved in some countries for the treatment of chronic cough; however, its limited selectivity for P2X3 homomers over P2X2/P2X3 heteromers is associated with taste disturbance as a prominent adverse effect. These limitations have motivated the development of next-generation NAMs with improved subtype selectivity, but their subtype-specific allosteric inhibition mechanisms are unclear. Here, we report the cryo-EM structure of the human P2X3 receptor in complex with ATP and the P2X3-selective next-generation NAM sivopixant, an investigational drug. Sivopixant binds to an allosteric site at the portal of the central pocket in the extracellular domain, and structure-based mutational analysis by electrophysiology identifies key residues required for sivopixant-dependent inhibition of human P2X3 receptors. Structural comparisons across P2X subtypes, together with patch-clamp analyses of gain-of-function mutants that confer sensitivity to two investigational drugs, sivopixant and camlipixant, provided a broadly applicable structural framework for subtype selectivity. Furthermore, structural comparisons with apo and ATP-bound open states of P2X3 receptors, together with molecular dynamics simulations, revealed that sivopixant expands the upper-body domain to suppress the lower-body movements required for channel activation, thereby preventing channel opening even in the presence of ATP.

Humans and other animals learn the value of candidate actions by interacting with their environment, which invariably requires the exertion of effort. Dopamine has been implicated in both effort and reward learning, but little is known about how these processes interact. In this double-blind study, healthy young adults (N = 42) were randomized to receive either high-dose sulpiride (a post-synaptic D2-receptor antagonist) or placebo. Participants then completed a novel two-armed bandit task, in which they weighed the effort costs associated with each option against their expected rewards. Overall, learning accuracy was lower on sulpiride compared to placebo. Computational modeling revealed that this was driven by the capacity of effort to significantly modulate learning rates on placebo but, critically, not on sulpiride. Simulations showed that the capacity of effort to modulate learning rates plays an adaptive role by improving performance in agents whose learning would otherwise be compromised by low motivation. Together, these data provide causal evidence that dopamine supports the relationship between effort and learning, and reveal a novel role for dopamine in shaping how humans learn from the consequences of their actions.

Large-scale patterns of species richness have been attributed to ecological limits, variation in diversification rates, and differences in evolutionary time, yet the relative importance of these drivers remains debated. Here, we present a unifying framework distinguishing four richness-generating scenarios, defined by contrasting roles of evolutionary time and speciation rates, which yields explicit and testable predictions for how evolutionary time, speciation, and environmental factors influence species richness. We applied this framework by analyzing 129 distinct, nonoverlapping clades spanning amphibians, reptiles, birds, and mammals. For each clade, we integrated historical biogeographic reconstructions, multiple estimates of speciation rates, and GIS-based environmental data. Using structural equation modeling, we quantified the direct and indirect effects of evolutionary time, speciation rates, and environmental conditions (productivity, temperature, and precipitation) on species richness. We further tested whether these effects varied systematically with clade-level traits, including age, physiology, diversity, and geographic extent. Productivity emerged as the dominant predictor of species richness, exerting strong and consistent direct effects that were largely invariant to clade traits. In contrast, speciation rates contributed little to species richness, while the influence of evolutionary time was highly context-dependent and most pronounced in younger clades. Temperature showed consistent direct effects not mediated by productivity, evolutionary time, or speciation rates, whereas precipitation influenced richness primarily via productivity. Together, our results support a productivity-driven equilibrium view of species richness, in which diversity reflects a balance between speciation and extinction regulated by energy availability. Deviations from equilibrium dynamics, particularly in younger clades, highlight the role of evolutionary history on biodiversity gradients.

Coronaviruses (CoVs) rely heavily on host lipid metabolism for efficient replication, but the specific host pathways involved remain incompletely defined. Here, we identify the non-vesicular cholesterol transport protein GRAMD1C as a key host factor required for the replication of multiple coronaviruses across α, β, and δ genera, including TGEV, PEDV, HCoV-229E, SARS-CoV-2, MHV, and PDCoV. Mechanistically, GRAMD1C is recruited to the replication factory through its interaction with the viral nonstructural proteins 3 and 4 (nsp3 and nsp4). Transmission electron microscopy (TEM) analysis revealed that GRAMD1C facilitates the formation of replication double-membrane vesicles (DMVs). Further domain rescue and inhibitor experiments demonstrated that GRAMD1C's cholesterol transport activity is essential for viral replication. Moreover, GRAMD1C-deficient and inhibitor-treated mice exhibited reduced viral replication, underscoring its critical role in vivo. Collectively, our findings expand the current understanding of the importance of non-vesicular cholesterol transport in viral replication and highlight GRAMD1C as a promising broad-spectrum antiviral target.

Osteogenesis depends on the self-renewal and differentiation of mesenchymal stem cells (MSCs). Emerging research underscores the regulatory functions of RNA methylation on bone homeostasis. Here, we show PCIF1, the N6,2'-O-dimethyladenosine (m6Am) methyltransferase, is essential for maintaining bone mass and promoting osteogenic differentiation of MSCs. Multiple complementary analyses-including GWAS, TWAS, and single-cell transcriptomics-collectively point to PCIF1 as a regulator of human bone mineral traits and early-stage mesenchymal differentiation. Global or MSC-specific Pcif1 deletion elicits osteoporotic pathology in mice, although myeloid cell-specific Pcif1 knockout does not induce femur bone alterations. Mechanistically, Pcif1 knockout decreases m6Am signals of Wnt-related genes (Wnt11, Fzd4, and Fgfr2) and accelerates mRNA degradation. This down-regulates active β-Catenin protein, and thus impairs osteogenic function of MSCs. Additionally, the WNT agonist attenuates the osteoporosis-like phenotype induced by Pcif1 deletion. These findings highlight the crucial role of PCIF1-mediated m6Am modification in regulating osteogenesis and suggest potential therapeutic implications for bone disorders.

Human spatial navigation relies on the brain’s ability to visually represent the 3D layout of the environment. To understand how the brain encodes the layout information, it is crucial to identify the key features of environmental layout and how they are processed in the human brain. The vector coding principle, which highlight the role of boundary distance and orientation, provides a theoretical framework supported by physiological evidence from rodents. In this study, we developed a reconstruction approach to quantitatively estimate 3D layout information from natural indoor scene images. This approach enabled analyses of fMRI data from the large-scale Natural Scenes Dataset (NSD) using vector-based models of 3D layout. To validate the NSD-based results and examine task-related dynamics, we further conducted fMRI and MEG experiments with navigation-related and non-navigational tasks. Controlling for low-, mid-, and high-level visual and semantic features of natural indoor scenes, we found a spatiotemporal dissociation between boundary distance and orientation representations in the human brain. Relative distance was encoded in the early visual cortex during early processing in a task-invariant manner, whereas orientation was represented in scene-selective higher visual areas during later processing and was modulated by navigation-related tasks. Importantly, task modulation manifested as enhanced orientation coding in early visual cortex, potentially reflecting top-down feedback and short-term maintenance mechanisms. Together, these findings provide a novel perspective on how the human brain represents navigation-relevant information about the immediate surrounding environment, advancing our understanding of the neural mechanisms that link perception to action in spatial navigation.