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A continental scale analysis reveals widespread root bimodality

Author Correction: Characteristics of the first confirmed case of human infection with mpox virus clade Ib in China

Take caution in using LLMs as human surrogates

Recent studies suggest large language models (LLMs) can generate human-like responses, aligning with human behavior in economic experiments, surveys, and political discourse. This has led many to propose that LLMs can be used as surrogates or simulations for humans in social science research. However, LLMs differ fundamentally from humans, relying on probabilistic patterns, absent the embodied experiences or survival objectives that shape human cognition. We assess the reasoning depth of LLMs using the 11-20 money request game. Nearly all advanced approaches fail to replicate human behavior distributions across many models. The causes of failure are diverse and unpredictable, relating to input language, roles, safeguarding, and more. These results warrant caution in using LLMs as surrogates or for simulating human behavior in research.

Bladder cancer variants share aggressive features including a CA125+ cell state and targetable TM4SF1 expression

Abstract Histologic variant (HV) subtypes of bladder cancer are clinically aggressive tumors that are more resistant to standard therapy compared to conventional urothelial carcinoma (UC). Little is known about the transcriptional programs that account for their biological differences. Here we show using single cell analysis that HVs harbor a tumor cell state characterized by expression of MUC16 (CA125), MUC4, and KRT24. This cell state is enriched in metastases, predicted to be highly resistant to chemotherapy, and linked with poor survival. We also find enriched expression of TM4SF1, a transmembrane protein, in HV tumor cells. Chimeric antigen receptor (CAR) T cells engineered against TM4SF1 protein demonstrated in vitro and in vivo activity against bladder cancer cell lines in a TM4SF1 expression-dependent manner, highlighting its potential as a therapeutic target.

TRPML2 in distinct states reveals the activation and modulation principles of the TRPML family

Structural basis of the hepatitis B virus X protein in complex with DDB1

A cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this approach is the hepatitis B virus (HBV) X protein (HBx), which is a key factor that promotes transcription from cccDNA. However, the HBx structure remains unsolved. Here, we present the cryoelectron microscopy structure of HBx in complex with DDB1, which is an essential complex for cccDNA transcription. In this structure, hydrophobic interactions within HBx were identified, and mutational analysis highlighted their importance in the HBV life cycle. Our biochemical analysis revealed that the HBx–DDB1 complex directly interacts simultaneously with NSE3, which is a component of the SMC5/6 complex, and Spindlin1. Additionally, HBx–DDB1 complex dynamics were explored via high-speed atomic force microscopy. These findings provide comprehensive insights into the structure and function of HBx in HBV replication.

Spectral properties of two superconducting artificial atoms coupled to a resonator in the ultrastrong coupling regime

Circulating cell-free DNA methylation patterns indicate cellular sources of allograft injury after liver transplant

Abstract Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed 130 blood samples collected from 44 patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to an atlas of cell-type-specific DNA methylation patterns derived from 476 methylomes of purified cells. For liver cell types, DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and functionally important regulatory regions. We find that multi-tissue cellular damages post-transplant recover in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA within the first month indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and intervention.

Nuclear deformability increases PARPi sensitivity in BRCA1-deficient cells by increasing microtubule-dependent DNA break mobility

Abstract Microtubules and nuclear transmembrane SUN1/2 proteins promote the mobility of DNA Double Strand Breaks (DSBs) induced by ionizing radiation and the misrepair of one-ended DSBs induced in BRCA1-deficient cells by Poly(ADP-ribose) polymerase inhibitors (PARPi). However, whether microtubules promote aberrant DSBs repair by altering the nuclear structure and whether the nuclear structure itself plays a role in these processes is still unclear. Here we show that microtubule-dependent DSBs mobility in BRCA1-deficient cells after PARPi treatment is associated with nuclear envelope (NE) invaginations. Furthermore, increasing NE invaginations by Lmna deletion or inhibition of sphingolipid synthesis increases DSBs mobility, chromosomal aberrations, and PARPi cytotoxicity in BRCA1-deficient cells. These findings reveal a functional connection between the NE and DSB repair and suggest that drugs increasing NE deformability will enhance PARPi therapy efficacy in BRCA1-deficient cancers.

Synergistic hydrogen embrittlement in high-strength steels

Hydrogen embrittlement (HE) remains a critical scientific challenge in building reliable infrastructure for a carbon-free hydrogen economy. Predictive models for hydrogen-induced material failure are still lacking, largely due to an incomplete understanding of hydrogen’s effects on deformation behavior, especially in multiphase alloys with complex compositions and microstructures. Here, we demonstrate a synergistic hydrogen embrittlement (SHE) phenomenon in high-strength martensitic steels, where hydrogen interacts with carbon in solution to activate hydrogen-enhanced localized plasticity (HELP). Microcantilever bending tests revealed greater hydrogen susceptibility with higher carbon content, evidenced by a significant reduction in work-hardening capacity, promoting slip localization and reduced ductility. First-principles calculations and theoretical modeling revealed that carbon intensifies hydrogen–dislocation interactions and amplifies hydrogen redistribution around screw dislocations, inhibiting cross-slip. This work integrates experimental and modeling approaches to elucidate the synergistic interactions between hydrogen and solute elements, providing critical insights for designing high-strength, hydrogen-tolerant structural materials.

Publisher Correction: A machine learning and centrifugal microfluidics platform for bedside prediction of sepsis

Antlers on does: An unexpected role of macrophages in deer biology

Antlers, a male deer secondary sex characteristic, are unique mammalian appendages that fully regenerate annually, under androgen regulation. Stem cells located in the antlerogenic periosteum (AP), a tissue overlaying the frontal crest of both male and female deer, play a crucial role in antlerogenesis. Nonetheless, the underlying molecular mechanisms as to how antlerogenesis is regulated by androgens remain largely unexplored. Here, we show that androgens regulate antler growth via macrophages. Bulk RNA sequencing revealed a significant enrichment of immune-related factors in the androgen-activated antlerogenic periosteum (AAP), and single-cell RNA sequencing identified a cluster of AAP cells overexpressing macrophage chemokine CCL2. Additionally, the presence of a substantial number of monocytes/macrophages was detected in the skin overlying the AAP. Histological examination confirmed macrophage accumulation in the AAP. Removal of macrophages with clodronate effectively inhibited antler generation in male sika deer as well as in nude mice engrafted with the AP. Furthermore, testosterone up-regulated CCL2 expression in the AP cells (APCs), thus enhancing their chemotactic effect on recruitment of macrophages. Remarkably, female sika deer developed antlers following local injection of CCL2, autologous macrophages, or even immune response inducer lipopolysaccharide (LPS). Therefore, macrophages play an essential role in deer antler generation.

Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar

Plague continues to pose a public health problem in multiple regions of the world, including Madagascar, where it is characterized by a pronounced seasonal pattern. The drivers of plague seasonality remain poorly understood. Using a deterministic compartmental model, calibrated to rat and flea capture data, serological data collected in active rural foci, and human plague surveillance data, we analyzed the effects of seasonal rat and flea population dynamics on plague transmission. The models that incorporated seasonal fluctuations in rat and flea populations provided better predictive performances than those that did not. We found that a simpler mass-action model also performed well. Driven by these seasonal changes, the effective reproduction number (R e ) between rats peaks at 1.45 [95% credible interval (CI): 1.41, 1.48] in October and falls to 0.6 (95% CI: 0.57, 0.63) in March. We estimated that 0.5% (95% CI: 0.2%, 0.9%) of rats are infected annually, indicating that plague is not the main driver of rat population changes. Using our model, we evaluated intervention strategies and found that targeting both rats and their fleas at the start of the epidemic season (July–September) was the most effective approach for reducing human plague cases. Such an approach contrasts with the reactive strategy currently employed in Madagascar. Our findings highlight the role of flea and rat populations in plague seasonality and identify strategies that could be deployed in Madagascar to better control plague epidemics.

CDADC1 is a vertebrate-specific dCTP deaminase that metabolizes gemcitabine and decitabine to prevent cellular toxicity

Cancer therapy is limited by resistance to standard-of-care chemotherapeutic and/or by treatment-associated toxicity. Identifying molecular mechanisms that modulate cellular toxicity is crucial for enhancing treatment efficacy. We characterize CDADC1, a vertebrate-specific orphan enzyme, as an unprecedented eukaryotic dCTP deaminase. CDADC1 catalyzes the conversion of dCTP into dUTP. While bacteria use this activity to sustain proliferation, CDADC1 evolved independently and is not required for mammalian cell proliferation, as demonstrated in cell lines and by the normal growth and standard lifespan of Cdadc1-deficient mice. However, we uncover a role of CDADC1 in metabolizing nucleotide analogs gemcitabine and decitabine. Gain- and loss-of-function assays in cancer cell lines, along with ectopic mouse models of pancreatic cancer, show that CDADC1 reduces these drugs’ efficacy. By the same token, Cdadc1 −/− mice are hypersensitive to gemcitabine. Mechanistically, CDADC1 deaminates the active triphosphate form of gemcitabine and decitabine, rendering them susceptible to inactivation by deoxyuridine triphosphatase. In contrast, the dCMP deaminase DCTD contributes to cell proliferation and promotes gemcitabine and decitabine toxicity. Thus, CDADC1 underpins a previously unrecognized mechanism of intrinsic chemoresistance in cancer cells and has a nonredundant role in protecting from gemcitabine toxicity. CDADC1 reveals a clinically relevant metabolic pathway that might be exploited to enhance the efficacy of deoxycytidine analogs but calls for assessing CDADC1 status to avoid lethal toxicities.

Why grain growth is not curvature flow

Grain growth in polycrystals is traditionally considered a capillarity-driven process, where grain boundaries (GBs) migrate toward their centers of curvature (i.e., mean curvature flow) with a velocity proportional to the local curvature (including extensions to account for anisotropic GB energy and mobility). Experimental and simulation evidence shows that this simplistic view is untrue. We demonstrate that the failure of the classical mean curvature flow description of grain growth mainly originates from the shear deformation naturally coupled with GB motion (i.e., shear coupling). Our findings are built on large-scale microstructure evolution simulations incorporating the fundamental (crystallography-respecting) microscopic mechanism of GB migration. The nature of the deviations from curvature flow revealed in our simulations is consistent with observations in recent experimental studies on different materials. This work also demonstrates how to incorporate the mechanical effects that are essential to the accurate prediction of microstructure evolution.

LDL receptor–mediated endocytosis of <i>Escherichia coli</i> α-hemolysin mediates renal epithelial toxicity

The α-hemolysin (HlyA) of uropathogenic Escherichia coli (UPEC) is a pore-forming toxin (PFT) that is thought to function by disrupting the host cell plasma membrane. Although CD18 (LFA-1) has been implicated as a receptor on myeloid cells, the mechanisms underlying HlyA cytotoxicity to epithelial cells are poorly defined. Here, we show that HlyA secretion by UPEC markedly intensifies renal tubular epithelial injury in a murine model of ascending pyelonephritis. A CRISPR-Cas9 loss-of-function screen in renal collecting duct cells revealed an unexpected requirement for clathrin-mediated endocytosis in HlyA-induced cytotoxicity. Following internalization, HlyA triggered lysosomal permeabilization, resulting in protease leakage, cytoplasmic acidification, and mitochondrial impairment, culminating in rapid epithelial cell death—a pathway distinct from canonical membrane-disrupting mechanisms of other PFTs. Moreover, we identify the low-density lipoprotein receptor (LDLR) as a critical epithelial receptor for HlyA; genetic ablation or competitive inhibition of the HlyA–LDLR interaction fully abrogated cytotoxicity. Our findings detail a paradigm for HlyA function in which epithelial toxicity relies on LDLR-mediated endocytic uptake rather than plasma membrane poration. These mechanistic insights illuminate potential therapeutic strategies to attenuate HlyA-mediated tissue damage during UPEC infections.

Cryptic isoprene emission of soybeans

Isoprene is the most abundant nonmethane biogenic hydrocarbon emitted by some plants, mostly trees. It plays critical roles in atmospheric chemistry by contributing to ozone and aerosol formation. Isoprene also benefits plants, particularly under stress, through its signaling roles. Legume crops like soybean were thought to have evolutionarily lost isoprene synthase (ISPS) and are typically considered nonemitters. Here, we report that damage to soybean leaves by wounding or burning triggered a burst of isoprene emission from the undamaged part of the leaves. In silico analysis identified intact ISPS genes in the soybean genome, with features similar to known ISPSs. Protein made from these gene sequences catalyzed isoprene production in the presence of dimethylallyl diphosphate. Isoprene emission in soybeans was linked to reduced photosynthesis rates and stomatal conductance. Metabolomic analysis showed that leaf damage caused a surge in glyceraldehyde 3-phosphate and pyruvate levels, leading to an increase of most of the methylerythritol 4-phosphate pathway metabolites.

Escalating Israel–Iran conflict damages science labs

Intermediate light adaptation induces oscillatory phototaxis switching and pattern formation in <i>Chlamydomonas</i>

Biological microswimmers exhibit intricate taxis behaviors in response to environmental stimuli and swim in complex trajectories to navigate their environment. How microswimmers respond to stimulus instantaneously, and how adaptation to stimulus influences their long-term behavioral changes, remains largely unclear. Here, we report an oscillatory phototaxis observed in Chlamydomonas reinhardtii at intermediate light intensities, where cells swim back-and-forth under a constant, unidirectional light stimulus due to alternation between positive and negative phototaxis. The phototaxis switching can be captured by the change in phase relationship between eyespot and helical swimming. Oscillatory phototaxis of individual cells leads to a global pattern of millimeter-scale propagating density bands that persists for ∼ 30 min. High-speed imaging and long-time tracking experiments at single-cell level verify a unified phototaxis mechanism that couples light detection, light adaptation, flagella responses, and behavioral switching. By experimentally tracking steady swimming and transient turning states, we verify that phototaxis transition is achieved via the modulation of flagella waveforms and flagella phase difference, which can be captured by a hydrodynamic model accounting for photoresponses. Adaptation acts effectively as an oscillator damper to mediate multipurpose tasking across multiple system levels (subcellular flagella beats, oscillatory phototaxis, colonial pattern formation) and timescales (from milliseconds to over 30 min). This adaptive phototaxis mechanism provides a comprehensive understanding of how microswimmers achieve complex behavioral changes across multiple temporal scales with a single sensor–actuator circuit featuring relatively simple adaptive feedback responses.

Pathogenic variants in the polycystin pore helix cause distinct forms of channel dysfunction

PKD2 is a member of the polycystin subfamily of transient receptor potential (TRP) ion channel subunits which traffic and function in primary cilia organelle membranes. Millions of individuals carry pathogenic genetic variants in PKD2 that cause a life-threatening condition called autosomal dominant polycystic kidney disease (ADPKD). Although ADPKD is a common monogenetic disorder, there is no drug cure or available therapeutics which address the underlying channel dysregulation. Furthermore, the structural and mechanistic impacts of most disease-causing variants are uncharacterized. Using direct cilia electrophysiology, cryogenic electron microscopy (cryo-EM), and superresolution imaging, we have found mechanistic differences in channel dysregulation caused by three germline missense variants located in PKD2’s pore helix 1. Variant C632R reduces protein thermal stability, resulting in impaired channel assembly and abolishes primary cilia trafficking. In contrast, variants F629S and R638C retain native cilia trafficking but exhibit gating defects. Cryo-EM structures (2.7 to 2.8 Å resolution) indicate loss of critical pore helix interactions which precipitate allosteric collapse of the channels inner gate. Results demonstrate how ADPKD-causing mutations cause mechanistically divergent and ranging impacts on PKD2 function, despite their shared structural proximity. These unexpected findings highlight the need for structural and biophysical characterization of polycystin variants, which will guide rational drug development of ADPKD therapeutics.