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Viridin and viridiol, along with wortmannin, metabolized by filamentous fungus Trichoderma virens, are identical furanosteroids with high-potent inhibitory activity towards phosphatidylinositol 3-kinase (PI3K) that associates the growth of tumor cells. Therefore, structure-activity relationship study (SAR) of these furanosteroids contributes to the development of novel drugs. However, rational supply methods have not been established yet. In this study, we generated an efficient method to produce both viridin and viridiol by using a unique pH regulated T. virens culture manner. Besides, we successfully obtained β-viridin (epimer of viridin) crystal and X-ray structure, of which the CAS number was registered without stereochemistry. Furthermore, applying the original method to stable isotope study, we also obtained [U- 13 C]-viridn and [U- 13 C]-viridol by using [U- 13 C 6 ]-glucose as a carbon source replacing normal glucose which can be used to elucidate the biosynthesis pathway of furanosteroids., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Photoimmunotherapy (PIT) is a potent modality for cancer treatment. The conventional PIT regimen involves the systemic delivery of an antibody-photoabsorber conjugate, followed by a 24-h waiting period to ensure adequate localisation on the target cells. Subsequent exposure to near-infrared (NIR) light selectively damages the target cells. We aimed to improve the efficacy of PIT in vivo by evaluating the effects of the different routes of conjugate administration on treatment outcomes., Methods: Subcutaneous Lewis lung carcinoma tumours were established in mice, targeting cluster of differentiation (CD)44 with an anti-CD44 antibody conjugated to IRDye700DX (IR700). The conjugate was administered via the intravenous or intratumoural route followed by the assessment of antibody binding and therapeutic effects of PIT., Findings: Compared to intravenous administration, intratumoural delivery of the CD44-IR700 conjugate significantly increased the number of cells binding to the conjugate by >five-fold. This method, combined with NIR light irradiation, halved tumour growth when compared to intravenous delivery. Reducing the interval between intratumoural injection and NIR light exposure to 30 min did not diminish efficacy, thereby demonstrating the feasibility of a 1-h procedure., Interpretation: Intratumoural administration of the antibody-photoabsorber conjugate enhanced the efficacy of PIT in vivo. A simplified, 1-h procedure involving conjugate tumour injection followed by irradiation emerged as a potent cancer treatment strategy., Funding: This study was supported by the Japan Society for the Promotion of Science, the Japan Agency for Medical Research and Development, Japan Science and Technology Agency, and the Osaka Medical Research Foundation for Intractable Diseases., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 The Authors. Published by Elsevier B.V. All rights reserved.)

Contrast transfer function (CTF) estimation is essential to the data processing workflow of cryo-electron tomography (cryoET). Here, we present a protocol for CTF estimation of the cryoET tilt series with CTFMeasure. CTFMeasure can estimate the CTF parameters together with the absolute tilt angle offset of the sample. We describe steps for configuring the input files and estimating the CTF parameters and the absolute tilt angle offset of the input tilt series. We then detail procedures for visualizing the power spectra and analyzing the output files. For complete details on the use and execution of this protocol, please refer to Zhang et al. 1 ., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024. Published by Elsevier Inc.)

Optical regulation of transcription using chemical compounds is an effective strategy to manipulate gene expression spatiotemporally. Conventional caging approaches with photoremovable protecting groups may require intense UV-light exposure and release potentially toxic byproducts. To address these problems, here we developed a light-mediated transcriptional regulation system by combining a caging-group-free photoactivatable dye PaX 560 and a multidrug-binding transcriptional regulator QacR. The cationic dye generated from PaX 560 through traceless photoconversion bound QacR and reduced its repressor function, resulting in transcriptional activation. Importantly, this system allowed transcriptional activation with a large dynamic range under mild visible light exposure and simultaneous detection of the state of the photoactivated effector. This module was integrated into the T7 RNA polymerase expression system to demonstrate light-activated transcription in vitro and in living cells., (© 2024 The Author(s). Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Natural protein-protein communications, such as those between transcription factors (TFs) and RNA polymerases/ribosomes, underpin cell-free biosensing systems operating on the transcription/translation (TXTL) paradigm. However, their deployment in field analysis is hampered by the delayed response (hour-level) and the complex composition of in vitro TXTL systems. For this purpose, we present a de novo-designed ligand-responsive artificial protein-protein communication (LIRAC) by redefining the connection between TFs and non-interacting CRISPR/Cas enzymes. By rationally designing a chimeric DNA adaptor and precisely regulating its binding affinities to both proteins, LIRAC immediately transduces target-induced TF allostery into rapid CRISPR/Cas enzyme activation within a homogeneous system. Consequently, LIRAC obviates the need for RNA/protein biosynthesis inherent to conventional TXTL-based cell-free systems, substantially reducing reaction complexity and time (from hours to 10 minutes) with improved sensitivity and tunable dynamic range. Moreover, LIRAC exhibits excellent versatility and programmability for rapidly and sensitively detecting diverse contaminants, including antibiotics, heavy metal ions, and preservatives. It also enables the creation of a multi-protein communication-based tristate logic for the intelligent detection of multiple contaminants. Integrated with portable devices, LIRAC has been proven effective in the field analysis of environmental samples and personal care products, showcasing its potential for environmental and health monitoring., (© 2024 Wiley-VCH GmbH.)

Aim: Frailty is a mediator between robustness and functional disability. This study examined the association between remission of frailty and incident disability., Methods: The present study analyzed longitudinal data from 2601 community-dwelling older adults who were aged ≥65 years (mean age 70.8 ± 4.5 years, 1307 women [50.2%]) using the Cardiovascular Health Study criteria. Next, examining changes in status from wave 1 (2011) to wave 2 (2015), participants were categorized into a frailty group (those who remained or became frail), a remission of frailty group (those who were frail and became robust) and a robust group (those who remained robust). Cox proportional hazard modeling was used to determine the change of frailty status from wave 1 to wave 2, as well as incident disability at wave 2 (median duration 35 months)., Results: Of those participants who started in the frailty or prefrailty groups at wave 1, 15.8% had an improved frailty status at the 47-month follow up. After adjusting for covariates at baseline, the Cox proportional hazard regression models showed that the hazard ratio of disability among participants who remained robust was significantly less than for those who were in the frailty group (hazard ratio 0.515; 95% confidence interval 0.333-0.796)., Conclusion: Our data confirm that among those whose frailty status improved, the risk of disability was lower than for those who remained frail. Geriatr Gerontol Int 2025; ••: ••-••., (© 2025 Japan Geriatrics Society.)

As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets., Competing Interests: Competing interests: D.M. is a consultant for BiomeSense, Inc., has equity and receives income. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. G.H. is the recipient of the Robert A. Winn Diversity in Clinical Trials: Career Development Award, which is partly funded by Bristol-Meyer Squibb Foundation. B.L. is the owner of InOrder Labs LLC. K.C. has research grant support from Phathom Pharmaceuticals. R.K. is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant for DayTwo, and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, and has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The remaining authors declare no competing interests., (© 2025. The Author(s).)

Gold (or electrum) in hydrothermal fluid precipitates directly from gold sulfide complex and/or partly via suspended nanoparticles. The hydrothermal fluid contains "invisible gold" that is atomically dispersed in sulfide minerals or as nanoparticles with a size of less than 10 nm. However, the contribution of these gold nanoparticles to the formation of native gold and its alloy with silver (electrum) remains unclear. The Higashi-Aogashima Knoll Caldera hydrothermal field, south of Tokyo, Japan, is an area of significant seafloor hydrothermal activity that is known for high-grade gold-containing minerals in sulfide-rich rocks. In this study, dry-polished thin sections were created to minimize sample damage and scanning and transmission electron microscopy were used to investigated the cross-sectional and three-dimensional morphologies of native gold grains in a sulfide-rich mound rock from the Central Cone site of the caldera. The surfaces of the gold grains comprised nanoparticles with sizes of 5-50 nm that were also attached to their periphery, which suggests that gold nanoparticles in deep-sea hydrothermal fluid were involved in the mineralization of the gold. In addition, the distribution of silver was uneven within the gold grains, which suggests that the gold precipitation comprised multiple stages at different temperatures that resulted in the post-deposition or secondary remobilization of silver., Competing Interests: The authors declare no competing interest., (Copyright: © 2025 Okada et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Plants, with intricate molecular networks for environmental adaptation, offer groundbreaking potential for reprogramming with predictive genetic circuits. However, realizing this goal is challenging due to the long cultivation cycle of plants, as well as the lack of reproducible, quantitative methods and well-characterized genetic parts. Here, we establish a rapid (~10 days), quantitative, and predictive framework in plants. A group of orthogonal sensors, modular synthetic promoters, and NOT gates are constructed and quantitatively characterized. A predictive model is developed to predict the designed circuits' behavior accurately. Our versatile and robust framework, validated by constructing 21 two-input circuits with high prediction accuracy (R 2  = 0.81), enables multi-state phenotype control in both Arabidopsis thaliana and Nicotiana benthamiana in response to chemical inducers. Our study achieves predictable design and application of synthetic circuits in plants, offering valuable tools for the rapid engineering of plant traits in biotechnology and agriculture., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome., Competing Interests: Declaration of interests J.T.L. is a cofounder of Fulcrum Therapeutics, an advisor to Skyhawk Therapeutics, and a non-executive director of GSK. P.L. is a cofounder of NuPhase Therapeutics., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Inflammatory diseases are often chronic and recurrent, and current treatments do not typically remove underlying disease drivers 1 . T cells participate in a wide range of inflammatory diseases such as psoriasis 2 , Crohn's disease 3 , oesophagitis 4 and multiple sclerosis 5,6 , and clonally expanded antigen-specific T cells may contribute to disease chronicity and recurrence, in part by forming persistent pathogenic memory. Chronic rhinosinusitis and asthma are inflammatory airway diseases that often present as comorbidities 7 . Chronic rhinosinusitis affects more than 10% of the general population 8 . Among these patients, 20-25% would develop nasal polyps, which often require repeated surgical resections owing to a high incidence of recurrence 9 . Whereas abundant T cells infiltrate the nasal polyps tissue 10,11 , T cell subsets that drive the disease pathology and promote recurrence are not fully understood. By comparing T cell repertoires in nasal polyp tissues obtained from consecutive surgeries, here we report that persistent CD8 + T cell clones carrying effector memory-like features colonize the mucosal tissue during disease recurrence, and these cells characteristically express the tryptase Granzyme K (GZMK). We find that GZMK cleaves many complement components, including C2, C3, C4 and C5, that collectively contribute to the activation of the complement cascade. GZMK-expressing CD8 + T cells participate in organized tertiary lymphoid structures, and tissue GZMK levels predict the disease severity and comorbidities better than well-established biomarkers such as eosinophilia and tissue interleukin-5. Using a mouse asthma model, we further show that GZMK-expressing CD8 + T cells exacerbate the disease in a manner dependent on the proteolytic activity of GZMK and complements. Genetic ablation or pharmacological inhibition of GZMK after the disease onset markedly alleviates tissue pathology and restores lung function. Our work identifies a pathogenic CD8 + memory T cell subset that promotes tissue inflammation and recurrent airway diseases by the effector molecule GZMK and suggests GZMK as a potential therapeutic target., Competing Interests: Competing interests: H.Q. is a cofounder of Emergent Biomed Solutions, Ltd., (© 2025. The Author(s).)

Circular RNAs (circRNA) lack 5' or 3' ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Human skin, as a sophisticated sensory organ, is able to detect subtle changes in ambient temperature. This thermosensory capability is primarily mediated by temperature-sensitive TRP channels expressed in both sensory neurons and keratinocytes. Among these, TRPV3, which responds to warm temperatures and plays a crucial role in various skin functions, is particularly notable. TRPV3 channels not only detect moderate warmth but are also sensitive to chemical ligands that evoke thermal sensations. The activation of TRPV3 by warm temperatures and compounds highlights its importance in the molecular mechanisms underlying skin thermosensation. This review mainly discusses the role of TRPV3, particularly its contribution to skin thermosensation and structural insights into its temperature sensitivity, providing an understanding of how TRPV3 modulates thermal perception at the molecular level., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier Inc.)

Several mesenchymal cell populations are known to regulate intestinal stem cell (ISC) self-renewal and differentiation. However, the influences of signaling mediators derived from mesenchymal cells other than ISC niche factors on epithelial homeostasis remain poorly understood. Here, we show that host and microbial metabolites, such as taurine and GABA, act on PDGFRαhigh Foxl1high sub-epithelial mesenchymal cells to regulate their transcription. In addition, we found that CXCL12 produced from Foxl1high sub-epithelial mesenchymal cells induces epithelial cell cycle arrest through modulation of the mevalonate-cholesterol synthesis pathway, which suppresses tumor progression in ApcMin/+ mice. We identified that Foxl1high sub-epithelial cells highly express CXCL12 among colonic mesenchymal cells. Foxl1-cre; Cxcl12f/f mice showed an increased number of Ki67+ colonic epithelial cells. CXCL12-induced Ca2+ mobilization facilitated phosphorylation of AMPK in intestinal epithelial cells, which inhibits the maturation of SREBPs that are responsible for mevalonate pathway activation. Furthermore, Cxcl12 deficiency in Foxl1-expressing cells promoted tumor development in the small and large intestines of ApcMin/+ mice. Collectively, these results demonstrate that CXCL12 secreted from Foxl1high mesenchymal cells manipulates intestinal epithelial cell metabolism, which links to the prevention of tumor progression in ApcMin/+ mice., (© The Author(s) 2025. Published by Oxford University Press on behalf of The Japanese Society for Immunology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)