FEBS Lett. 2025 Aug 8. doi: 10.1002/1873-3468.70138. Online ahead of print.

ABSTRACT

Over the past few decades, research on polyextremophiles has revealed a diverse range of organisms adapted to multiple extreme conditions, such as combinations of high and low temperatures, acidity, pressure, salinity, and radiation. Under multiple extremes, a key survival mechanism is the production of exopolysaccharides (EPSs) via cell wall-associated or extracellular glycosyltransferases (GTs). EPSs not only protect cells against environmental extremes, desiccation, phage attacks, phagocytosis, and antibiotics; they also play important roles in inter- and intra-microbial interactions, quorum sensing, virulence, energy storage, and biofilm formation. Despite extensive studies on EPSs from extremophiles, knowledge on EPS production in polyextremophiles remains limited, particularly for psychrophiles, halophiles, and piezophiles. This review focuses on the adaptive strategies of polyextremophiles under multiple stress conditions, emphasizing the functional significance of EPS production. By providing an integrated perspective on polyextremophiles and their survival mechanisms, this work highlights the critical role of EPSs in their adaptation to extreme habitats and their potential biotechnological applications.

PMID:40779692 | DOI:10.1002/1873-3468.70138

Sci Immunol. 2025 Aug 8;10(110):eadt0688. doi: 10.1126/sciimmunol.adt0688. Epub 2025 Aug 8.

ABSTRACT

Pulmonary conventional dendritic cells (cDCs) are functionally and phenotypically heterogeneous antigen-presenting cells essential for orchestrating adaptive immune responses in the lung. Here, we define a cell-intrinsic role for granulocyte-macrophage colony-stimulating factor (GM-CSF) signaling in the development of a CD301b+ subset of terminally differentiated cDC2s, in addition to CD103+XCR1+ cDC1s. Unbiased single-cell transcriptomic profiling of CD11c+ cells identified both immature and differentiated lung cDC populations. GM-CSF deficiency disrupted antiapoptotic Bcl2a1 up-regulation and impaired progression to the CD301b+ transcriptional state. Despite the positioning of CD301b+ cDC2s in lymphoid cell-rich adventitial cuff areas, hematopoietic GM-CSF was dispensable for their development. Instead, alveolar epithelial type 2 cell-derived GM-CSF was required for CD301b+ cDC2 formation and pulmonary type 2 immune responses, highlighting the central role of GM-CSF signaling in shaping the pulmonary myeloid landscape.

PMID:40779647 | DOI:10.1126/sciimmunol.adt0688

Sci Adv. 2025 Aug 8;11(32):eadu3858. doi: 10.1126/sciadv.adu3858. Epub 2025 Aug 8.

ABSTRACT

Active restoration strategies targeting corals with elevated heat tolerance have the potential to enhance reef resistance under a warming climate. While stress-tolerant corals have been documented in extreme systems such as mangrove lagoons, it is critical to assess the ability of these corals to maintain tolerance when moved to a more benign habitat. Here, we translocated corals from a mangrove lagoon to an adjacent reef and evaluated the thermal thresholds of corals from both locations before translocation and after 1 year. We demonstrate that mangrove colonies have higher thermal tolerance than reef corals, and, critically, mangrove colonies exhibited no loss in thermal tolerance following 1-year translocation to a less extreme reef habitat. Up-regulation of genes associated with DNA repair, metabolism, and homeostasis indicates the importance of these pathways in helping mangrove corals mitigate thermal stress. Our findings suggest the use of heat tolerant corals from extreme systems holds promise as part of intervention strategies aiming to increase reef resistance.

PMID:40779617 | DOI:10.1126/sciadv.adu3858

Exp Physiol. 2025 Aug 8. doi: 10.1113/EP092677. Online ahead of print.

ABSTRACT

Electrical pulse stimulation (EPS) of skeletal muscle cells is increasingly used to model exercise In vitro. The murine C2C12 myotube system has become a common platform for such studies, yet wide variability in EPS protocols hampers reproducibility and cross-study comparisons. In this technical review, we analysed 54 peer-reviewed studies that employed EPS in C2C12 and extracted used EPS protocols to provide an overview of the most commonly used settings for the EPS parameters (pulse duration, frequency, voltage and stimulation duration). Additionally, we summarized the biological processes investigated in these studies to illustrate the range of research topics typically addressed using this model. The majority of studies used 2 ms pulses at 1 Hz and moderate voltages (10-20 V), often over 24 h of stimulation. Glucose uptake was the most commonly assessed endpoint, followed by AMPK activation, inflammation and mitochondrial adaptations. Correlation analyses revealed interdependence between pulse duration, voltage and EPS duration, indicating that these parameters are often balanced to avoid excessive or suboptimal stimulation. While frequency was largely standardized, voltage and pulse duration showed greater variation. Our findings underscore the need for more detailed parameter reporting and deliberate protocol design aligned with specific experimental objectives, such as mimicking endurance- or resistance-type exercise stimuli. This review serves as a resource for selecting EPS parameters tailored to specific biological processes and encourages standardization to improve translational relevance.

PMID:40779409 | DOI:10.1113/EP092677

Data Brief. 2025 Jul 10;61:111871. doi: 10.1016/j.dib.2025.111871. eCollection 2025 Aug.

ABSTRACT

Polygonum minus Huds., commonly referred to as kesum, is a traditional medicinal plant in Malaysia known for its unique fragrance attributed to its volatile compounds. The essential oil extracted from P. minus displayed various benefits, comprised of antioxidant, antimicrobial, and anticancer properties. Therefore, to identify volatile metabolites associated with such biological activities, we performed untargeted metabolite analysis on the essential oil extracted from P. minus leaf tissue. After the leaf samples were collected from the INBIOSIS experimental plot, a six-hour hydro-distillation procedure was performed to extract the essential oil, which was then subjected to GC-MS analysis. Thus, this data could provide a reference and benchmark for researchers conducting analyses on volatile compounds in P. minus.

PMID:40777556 | PMC:PMC12329244 | DOI:10.1016/j.dib.2025.111871

Front Immunol. 2025 Jul 24;16:1597862. doi: 10.3389/fimmu.2025.1597862. eCollection 2025.

ABSTRACT

INTRODUCTION: Mathematical models are powerful tools that can be used to advance our understanding of complex diseases. Autoimmune disorders such as systemic lupus erythematosus (SLE) are highly heterogeneous and require high-resolution mechanistic approaches. In this work, we present ONIDsc, a single-cell regulatory network inference model designed to elucidate immune-related disease mechanisms in SLE.

METHODS: ONIDsc enhances SINGE's Generalized Lasso Granger (GLG) causality model used in Single-cell Inference of Networks using Granger ensembles (SINGE) by finding the optimal lambda penalty with cyclical coordinate descent. We benchmarked ONIDsc against existing models and found it consistently outperforms SINGE and other methods when gold standards are generated from chromatin immunoprecipitation sequencing (ChIP-seq) and ChIP-chip experiments. We then applied ONIDsc to three large-scale datasets, one from control patients and the two from SLE patients, to reconstruct networks common to different immune cell types.

RESULTS: ONIDsc identified four gene transcripts: matrix remodelling-associated protein 8 (MXRA8), nicotinamide adenine dinucleotide kinase (NADK), RNA Polymerase III Subunit GL (POLR3GL) and Ultrabithorax Domain Protein 11 (UBXN11) in CD4+ T-lymphocytes, CD8+ Regulatory T-Lymphocytes, CD8+ T-lymphocytes 1 and Low Density Granulocytes that were present in SLE patients but absent in controls.

DISCUSSION: These genes were significantly related to nicotinate metabolism, ribonucleic acid (RNA) transcription, protein phosphorylation and the Rho family GTPase (RND) 1-3 signaling pathways, previously associated with immune regulation. Our results highlight ONIDsc's potential as a powerful tool for dissecting physiological and pathological processes in immune cells using high-dimensional single-cell data.

PMID:40777011 | PMC:PMC12328306 | DOI:10.3389/fimmu.2025.1597862

Chem Biodivers. 2025 Aug 8:e01727. doi: 10.1002/cbdv.202501727. Online ahead of print.

ABSTRACT

Pulmonary tuberculosis (TB), caused by the Mycobacterium tuberculosis (MTB) bacterium, remains a significant health problem worldwide, intensified by the emergence of multidrug-resistant (MDR) and highly resistant (XDR) strains. The current treatment protocols, related side effects, and the increasing incidence of drug resistance limit the efficacy of conventional therapeutic strategies. Traditional medicinal constituents rich in diverse phytoconstituents offer multi-target action with reduced toxicity, minimal risk of resistance, and immunomodulatory properties. Network pharmacology (NP), an integrated approach merging systems biology and computational modeling, facilitates understanding complex interactions among phytochemicals, molecular targets, and signaling pathways. Integrating modern pharmacology principles with traditional wisdom, NP provides a logical framework for developing new plant-based anti-TB agents and advancing adjunctive therapies. Combining protein-protein interaction networks, pathway enrichment analyses, multi-combinational data, and molecular docking studies offers insights into how phytoconstituents affect the immune response, block efflux pumps, and reduce resistance. This review provides a detailed analysis of NP-based methods for the identification of active compounds (e.g., alkaloids, flavonoids, terpenoids, polyphenols) and their related molecular targets involved in the pathogenesis of TB, including tumor necrosis factor-alpha (TNF-α), Toll-like receptors (TLR), nucleotide-binding oligomerization domain (NOD)-like receptor, and Janus kinase/signal transducer and activator of transcription (JAK-STAT) pathway.

PMID:40776773 | DOI:10.1002/cbdv.202501727

Mol Nutr Food Res. 2025 Aug 8:e70195. doi: 10.1002/mnfr.70195. Online ahead of print.

ABSTRACT

Optimizing plant-based protein intake, such as pea protein hydrolysates (PPHs), may aid in obesity management. This study investigated whether PPHs with varying bitterness and degrees of hydrolysis (DH) differently affect satiety in healthy male participants. In a short-term randomized control trial, 19 moderately overweight men (BMI 25-30 kg/m2) consumed boluses of 75 g glucose plus 15 g PPH (control without PPH; PPH1: less bitter, DH = 35%; PPH2: more bitter, DH = 23%). Upon PPH administration, energy intake from an ad libitum breakfast was reduced by -126 ± 329 kcal (p < 0.05) in the PPH2 group compared to the control. PPH1 decreased plasma ghrelin and DPP-4 levels (AUC: -9.4 ± 19.6 and -12.5 ± 24.7, p < 0.05). Gastric emptying was delayed by a mean of 65% (p < 0.0001) after PPH2 consumption, assessed via 13C-Na-acetate breath test. Bitterness and DH of PPH influence satiety signals differently. PPH1 (less bitter, higher DH) reduces DPP-4 and ghrelin levels, promoting satiety. PPH2 (more bitter, lower DH) delays gastric emptying, enhancing satiation. These findings highlight the potential of PPHs as functional ingredients in weight management strategies.

PMID:40776629 | DOI:10.1002/mnfr.70195

Stud Health Technol Inform. 2025 Aug 7;329:32-36. doi: 10.3233/SHTI250796.

ABSTRACT

Despite the existence of ICD-O for tumor classification, the broader ICD-10 system is often used in practice. While OncoTree is significant in research and molecular tumor boards, it provides a more detailed classification based on molecular and histological characteristics, crucial for clinical trial enrollment and data comparison. Therefore, a mapping between ICD-10 and OncoTree was developed. The mapping uses SNOMED CT as an intermediary step because both ICD-10 and OncoTree are structured differently. During the mapping process, some challenges arose, such as differences in the structure of the coding systems and inaccurate mappings. Despite this, the approach achieved an accuracy rate of 86.18%, which is considered satisfactory. Future efforts will focus on refining the mapping process to enhance its integration into production systems.

PMID:40775814 | DOI:10.3233/SHTI250796

Plant Cell Rep. 2025 Aug 7;44(9):195. doi: 10.1007/s00299-025-03577-9.

ABSTRACT

The grapevine VviEPFL9-2 paralog is specifically expressed during leaf expansion and its knockout provide a phenotype with superior adaptation to environmental stresses via reduced stomatal density. In Arabidopsis stomatal initiation relies on the transcription factor SPEECHLESS, which is positively regulated by AtEPFL9, a peptide of the epidermal patterning factor family. In grapevine, two EPFL9 paralogs exist but despite a structural similarity, their specific function remains unclear. In this study, we investigated their distinct functional roles and the extent to which reduced stomatal density (SD) may be beneficial for grapevine in terms of water use. We combined expression analysis of the two paralogs in untreated and ABA-treated leaves with the functional characterization of the two genes using grapevine epfl9-1 and epfl9-2 mutants. A physiological analysis of epfl9-2 mutants under different environmental conditions was also performed. We showed that VviEPFL9-1 is exclusively expressed in leaf primordia, whereas VviEPFL9-2 plays a predominant role in fine-tuning SD during the leaf expansion. An epfl9-2 mutant line with 84% lower SD than wild type, exhibited a significant improvement in intrinsic water-use efficiency under both well-watered and water-stressed conditions, with little trade-off in photosynthesis. When the reduction in SD was close to 60%, photosynthetic rate and stomatal conductance were comparable to WT. Our results provide compelling evidence that VviEPFL9-2 knockout determines a significant reduction in stomatal density without a major impact on photosynthesis which may help optimize the adverse impacts of climate change on viticulture.

PMID:40775479 | DOI:10.1007/s00299-025-03577-9

Nat Commun. 2025 Aug 7;16(1):7291. doi: 10.1038/s41467-025-62101-5.

ABSTRACT

Diabetic kidney disease (DKD) progression is not well understood. Using high-throughput proteomics, biostatistical, pathway and machine learning tools, we examine the urinary Complement proteome in two prospective cohorts with type 1 or 2 diabetes and advanced DKD followed for 1,804 person-years. The top 5% urinary proteins representing multiple components of the Complement system (C2, C5a, CL-K1, C6, CFH and C7) are robustly associated with 10-year kidney failure risk, independent of clinical covariates. We confirm the top proteins in three early-to-moderate DKD cohorts (2,982 person-years). Associations are especially pronounced in advanced kidney disease stages, similar between the two diabetes types and far stronger for urinary than circulating proteins. We also observe increased Complement protein and single cell/spatial RNA expressions in diabetic kidney tissue. Here, our study shows Complement engagement in DKD progression and lays the groundwork for developing biomarker-guided treatments.

PMID:40775226 | DOI:10.1038/s41467-025-62101-5

Nat Methods. 2025 Aug 7. doi: 10.1038/s41592-025-02744-w. Online ahead of print.

ABSTRACT

Cellular interactions are of fundamental importance, orchestrating organismal development, tissue homeostasis and immunity. Recently, powerful methods that use single-cell genomic technologies to dissect physically interacting cells have been developed. However, these approaches are characterized by low cellular throughput, long processing times and high costs and are typically restricted to predefined cell types. Here we introduce Interact-omics, a cytometry-based framework to accurately map cellular landscapes and cellular interactions across all immune cell types at ultra-high resolution and scale. We demonstrate the utility of our approach to study kinetics, mode of action and personalized response prediction of immunotherapies, and organism-wide shifts in cellular composition and cellular interaction dynamics following infection in vivo. Our scalable framework can be applied a posteriori to existing cytometry datasets or incorporated into newly designed cytometry-based studies to map cellular interactions with a broad range of applications from fundamental biology to applied biomedicine.

PMID:40775086 | DOI:10.1038/s41592-025-02744-w

Nat Commun. 2025 Aug 7;16(1):7272. doi: 10.1038/s41467-025-62214-x.

ABSTRACT

YKYY017 is a SARS-CoV-2 membrane fusion inhibitor. We report efficacy and safety of inhaled YKYY017 for COVID-19 patients with mild to moderate illness from a phase 2 trial (ChiCTR2300075467). 239 patients aged 18-75 years with mostly mild COVID-19 were randomly allocated to receive aerosol inhalation of 10 or 20 mg YKYY017 or placebo once daily. The primary endpoint is the change in SARS-CoV-2 viral load from baseline to Day 4. The mean (±SE) differences in viral load change from baseline were -0.48 ± 0.27 log10 copies/mL (95% CI, -1.01 to 0.06) for the 20 mg group and -0.27 ± 0.27 log10 copies/mL (95% CI, -0.79 to 0.26) for the 10 mg group, compared to the placebo group. Viral load changes at visits other than Day 4 did not differ significantly from placebo in either the 10 or 20 mg YKYY017 groups. The time to sustained symptom recovery was shorter in the 20 mg YKYY017 group (median 117.53, 95%CI 95.33 to 141.45 hours) than in the placebo group (median 143.00, 95%CI 139.17 to 186.87 hours; HR 1.552, 95%CI 1.089 to 2.214, p = 0.0151), whereas the 10 mg YKYY017 group showed a similar but not statistically significant trend compared to placebo (p = 0.0833). The time to sustained symptom alleviation was shorter in both the 20 and 10 mg YKYY017 groups than in the placebo group. The adverse events were mostly mild to moderate. The primary outcome was not met. Following a supplementary phase 1b trial, we are planning another phase 2/3 trial using a twice-daily 20 mg YKYY017 regimen to further assess efficacy and safety.

PMID:40775020 | DOI:10.1038/s41467-025-62214-x

Genome Res. 2025 Aug 7. doi: 10.1101/gr.280586.125. Online ahead of print.

ABSTRACT

Evolutionary rate covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been empirically validated, its predictive power has hitherto been limited by its inability to tackle the large numbers of species in contemporary comparative genomics data sets. This study introduces ERC2.0, an enhanced methodology for studying ERC across phylogenies with hundreds of species and tens of thousands of genes. ERC2.0 improves upon previous iterations of ERC in algorithm speed, normalizing for heteroskedasticity, and normalizing correlations via Fisher transformations. These improvements have resulted in greater statistical power to predict biological function. In exemplar yeast and mammalian data sets, we demonstrate that the predictive power of ERC2.0 is improved relative to the previous method, ERC1.0, and that further improvements are obtained by using larger yeast and mammalian phylogenies. We attribute the improvements to both the larger data sets and improved rate normalization. We demonstrate that ERC2.0 has high predictive accuracy for known annotations and can predict the functions of genes in nonmodel systems. Our findings underscore the potential for ERC2.0 to be used as a single-pass computational tool in candidate gene screening and functional predictions.

PMID:40774815 | DOI:10.1101/gr.280586.125

Biochim Biophys Acta Rev Cancer. 2025 Aug 5:189408. doi: 10.1016/j.bbcan.2025.189408. Online ahead of print.

ABSTRACT

DNA repair is involved in the cellular response to alkylating agents used for the treatment of various cancers, decreasing the damages induced by the compounds and thus limiting the efficacy of the drugs. The inhibition of DNA repair should therefore increase the cytotoxic effect of alkylating agents, and this has been suggested as a therapeutic approach to increase clinical success. In this review, we focus on proteins involved in Nucleotide Excision Repair (NER) with a particular emphasis on the heterodimer ERCC1/XPF, and give an overview of preclinical and clinical studies underlying this therapeutic approach, as well as details on studies and compounds with notable activities. We also discuss the use of computer-aided methods to develop small molecule inhibitors targeting NER-related proteins, with a focus on structure-based virtual screening, and reflect on future perspectives on this topic. Although interesting results are obtained on cell models with various molecules, we believe new efforts are needed in order to validate the proof of concept in vivo and to translate the use of NER inhibitors in cancer patients.

PMID:40774469 | DOI:10.1016/j.bbcan.2025.189408

Cell Syst. 2025 Aug 1:101367. doi: 10.1016/j.cels.2025.101367. Online ahead of print.

ABSTRACT

Clostridioides difficile (C. difficile) colonizes up to 40% of community-dwelling adults without causing disease but can eventually lead to infection (C. difficile infection [CDI]). There has been a lack of focus on how to prevent colonization and facilitate the successful clearance of C. difficile prior to the emergence of CDI. We show that microbial community-scale metabolic models (MCMMs) accurately predict C. difficile colonization susceptibility in vitro and in vivo, offering mechanistic insights into microbiota-specific interactions involving metabolites like succinate, trehalose, and ornithine. MCMMs reveal distinct C. difficile metabolic niches-two growth-associated and one non-growth-associated-observed across 15,204 individuals from five cohorts. We further demonstrate that MCMMs can predict personalized C. difficile growth suppression by a probiotic cocktail designed to replace fecal microbiota transplants (FMTs) for the treatment of recurrent CDI, and we identify new probiotic targets for future validation. MCMMs represent a powerful framework for predicting pathogen colonization and assessing probiotic efficacy across diverse microbiota contexts. A record of this paper's transparent peer review process is included in the supplemental information.

PMID:40774255 | DOI:10.1016/j.cels.2025.101367

Cell. 2025 Jul 29:S0092-8674(25)00803-7. doi: 10.1016/j.cell.2025.07.014. Online ahead of print.

ABSTRACT

Discrete genomic units can recombine into composite transposons that transcribe and transpose as single units, but their regulation and function are not fully understood. We report that composite transposons harbor bivalent histone marks, with activating and repressive marks in distinct regions. Genome-wide CRISPR-Cas9 screening, using a reporter driven by the hominid-specific composite transposon SVA (SINE [short interspersed nuclear element]-VNTR [variable number of tandem repeats]-Alu) in human cells, identified diverse genes that modify bivalent histone marks to regulate SVA transcription. SVA transcripts are critical for SVA's cis-regulatory function in selectively contacting and activating long-range gene expression. Remarkably, a subset of bivalent SVAs is activated during erythropoiesis to boost multiple erythroid gene expression, and knocking down these SVAs leads to deficient erythropoiesis. The RNA-dependent cis-regulatory function of SVA activates genes for myelopoiesis and can contribute to aging-associated myeloid-biased hematopoiesis. These results reveal that the cis-regulatory functions of composite transposons are bivalently regulated to control cell fate transitions in development and aging.

PMID:40774253 | DOI:10.1016/j.cell.2025.07.014

Science. 2025 Aug 7;389(6760):594-599. doi: 10.1126/science.adx4380. Epub 2025 Aug 7.

ABSTRACT

The immune system's central function is to maintain homeostasis by guarding the organism against dangerous external and internal stressors. Immunity's operational toolbox contains diverse processes, such as phagocytosis, antigen recognition, cell killing, and secretion of cytokines and antibodies. Although immune cells interact with each other, they also communicate with cells typically associated with other organ systems, including the nervous, circulatory, metabolic, musculoskeletal, endocrine, and hematopoietic. This abundant cross-talk shows that immunity transcends defense and homeostasis: It is a network that participates in many physiological processes necessary for life. By accessing the circulation and inhabiting every tissue, leukocytes sense, interpret, and regulate biological processes. In this Review, we highlight recent studies that illustrate the often bidirectional and symbiotic relationships through which the immune system regulates physiology.

PMID:40773571 | DOI:10.1126/science.adx4380

Mol Plant Pathol. 2025 Aug;26(8):e70135. doi: 10.1111/mpp.70135.

ABSTRACT

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, was first reported in the continental United States of America (USA) in 2004 and over the years has been of concern to soybean production in the United States. The prevailing hypothesis is that P. pachyrhizi spores were introduced into the United States via hurricanes originating from South America, particularly hurricane Ivan. To investigate the genetic diversity and global population structure of P. pachyrhizi, we employed exome-capture based sequencing on 84 field isolates collected from different geographic regions worldwide. We compared the gene-encoding regions from all these field isolates and found that four major mitochondrial haplotypes are prevalent worldwide. Here, we provide genetic evidence supporting multiple incursions that have led to the currently established P. pachyrhizi population of the United States. Phylogenetic analysis of mitochondrial genes further supports this hypothesis. We observed limited genetic diversity in P. pachyrhizi populations across different geographic regions, suggesting a clonal population structure. Additionally, this study is the first to report the F129L mutation in the Cytb gene outside South America, which is associated with strobilurin tolerance. This study provides the first comprehensive characterisation of P. pachyrhizi population structures defined by genetic evidence from populations across major soybean-growing regions.

PMID:40773485 | DOI:10.1111/mpp.70135

Proc Natl Acad Sci U S A. 2025 Aug 12;122(32):e2504578122. doi: 10.1073/pnas.2504578122. Epub 2025 Aug 7.

ABSTRACT

DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of total internal reflection fluorescence microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic and kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and three-dimensional (3D) imaging.

PMID:40773232 | DOI:10.1073/pnas.2504578122