{"source":"biorxiv","name":"bioRxiv preprints","kind":"widget","records":[{"id":"10.64898/2026.05.25.727613","title":"The heritability of reinforcement learning parameters and their association with anxiety","subtitle":"Tim Kerr · SGDP · 2026-05-28","value":"genetics","href":"https://doi.org/10.64898/2026.05.25.727613","props":{"doi":"10.64898/2026.05.25.727613","authors":"Kerr, T.; Purves, K.; McGregor, T.; Barry, T. J.; Lester, K. J.; Robinson, O. J.; Eley, T. C.","institution":"SGDP","category":"genetics","date":"2026-05-28","abstract":"Impaired learning that both novel and previously dangerous stimuli are safe (safety and extinction learning, respectively) are long standing, robust, and heritable features of anxiety disorders, representing potential endophenotypes. The computational mechanisms underpinning them have demonstrated associations with anxiety severity in recent studies. We undertook a pre-registered replication in a tenfold larger independent sample of twins (n = 925). Extinction learning rates were associated with anxiety severity ({rho}replication = -0.14, BFr0 = 1189. 67) but safety learning rates were not. Conversely, although safety learning rates showed modest heritability (h2safety = 0.16), extinction learning rates were not heritable. Accordingly, we were unable to identify genetic overlap between anxiety and either learning rate. Although this suggests neither learning rate is an anxiety endophenotype, we confirmed a cognitive-behavioral mechanism underpinning a robust marker of anxiety severity. Furthermore, we demonstrated heritability of a computationally modelled learning parameter, a key step towards establishing its biological basis."}},{"id":"10.64898/2026.05.26.727846","title":"Draft genome assembly of the Woolly bottlebrush (Greyia radlkoferi) using Pacbio long-read sequencing technology.","subtitle":"Ntanganedzeni Mapholi · University of South Africa · 2026-05-28","value":"genomics","href":"https://doi.org/10.64898/2026.05.26.727846","props":{"doi":"10.64898/2026.05.26.727846","authors":"Molotsi, A. H.; Masebe, T.; Nesengani, L. T.; Mdyogolo, S.; Tshilate, T. S.; Smith, R. M.; Hlongwane, N.; Hadebe, S.; Mafokwane, T. M.; Mapholi, N.","institution":"University of South Africa","category":"genomics","date":"2026-05-28","abstract":"The Woolly bottlebrush (Greyia radlkoferi) is an indigenous South African plant known for its ornamental appeal and potential medicinal uses. It naturally grows on rocky hillsides and grasslands and highly resilient to drought, temperature fluctuations, and nutrient-poor soils. Its flavonoid-rich compounds with anti-tyrosinase activity support its traditional use to treat skin pigmentation disorders in humans. Despite its outstanding ecological and biochemical characteristics, no reference genome is available for Greyia radlkoferi. Therefore, this study aimed to generate the first draft genome of the Greyia Radlkofleri using PacBio Sequel IIe HiFi long read sequencing. A total of 56.07 Gb HiFi data was generated, providing a total genome coverage of 270X. The assembled genome size was 206Mb, with the longest scaffold being 13.9 Mb. The assembly statistics yielded a scaffold and contig N50 of 10.1 Mb, and an L50 of 9, and with an overall GC content of 34.9 %. The genome scope profile set at kmer = 17 indicated that the genome is triploid. The genome annotation predicted 17,804 protein-coding genes and 17,804 transcripts with an average gene length of 3,116.03 bp. This is the first draft genome of its kind for the Greyia genus and provides a foundation for future studies aimed at elucidating the genetic basis of its environmental resilience and the biosynthetic pathways underlying its medicinal properties."}},{"id":"10.64898/2026.05.22.727304","title":"Atg8 orchestrates stress-responsive chromatin programs across immunity and metabolism","subtitle":"Akhila Rajan · Fred Hutchinson Cancer Center · 2026-05-28","value":"genomics","href":"https://doi.org/10.64898/2026.05.22.727304","props":{"doi":"10.64898/2026.05.22.727304","authors":"Kelly, K. P.; Ramesh, N. A.; Ranganathan, S.; Madan, A.; Marschall, S. N.; Unckless, R.; Rajan, A.","institution":"Fred Hutchinson Cancer Center","category":"genomics","date":"2026-05-28","abstract":"Organisms must coordinate transcriptional responses to immune and metabolic stress, often within the same tissue. In Drosophila and mammals, adipose tissue integrates these signals by mounting antimicrobial defense during acute infection and remodeling lipid metabolism under chronic nutrient surplus. How one cell-biological system supports both functions, and through what molecular machinery, remains incompletely understood. Atg8/LC3, classically defined by canonical autophagy, has emerging non-canonical roles in nuclear gene regulation, raising the possibility that it contributes to stress-coordinated transcription beyond cargo turnover. Using unbiased CUT&RUN in adult Drosophila nuclei, we find that endogenous Atg8 exhibits broad chromatin occupancy at immune, metabolic, and autophagy loci, and accumulates in nuclei under prolonged high-sugar diet (HSD) and acute Gram-positive infection. We identify two conserved Atg8-interacting motifs (AIMs) within the Rel homology domain of NF-{kappa}B/Dif. Flies carrying CRISPR-engineered AIM-mutant Dif are highly susceptible to both infection and chronic HSD, establishing a physiological requirement for intact Dif AIMs. AIM-mutant Dif shows impaired infection-induced nuclear accumulation, suggesting that Atg8 contributes to both Dif cytoplasmic-to-nuclear shuttling and nuclear function. Unbiased comparison of Atg8 chromatin occupancy across HSD and infection further reveals shared and divergent motif grammar, positioning Atg8 as a stress-responsive chromatin cofactor for immune and metabolic transcription. Together, these findings expand the functional landscape of Atg8/LC3 beyond canonical autophagy and reveal that autophagy machinery contributes to stress-specific transcriptional complex assembly. AIM/LIR-mediated interactions, exemplified by Dif, represent one such interface, while additional mechanisms likely underlie Atg8s broader chromatin engagement at loci enriched for transcription factor motifs whose cognate factors lack known AIM/LIRs. We propose that Atg8/LC3-mediated coordination of immune and metabolic transcription is a general principle by which cells integrate diverse stress signals, with implications for obesity, chronic inflammation, and other disease states in which immune and metabolic dysregulation converge.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC=\"FIGDIR/small/727304v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@15c056dorg.highwire.dtl.DTLVardef@68493dorg.highwire.dtl.DTLVardef@a07c6corg.highwire.dtl.DTLVardef@4896c6_HPS_FORMAT_FIGEXP  M_FIG C_FIG O_LIStress drives Atg8 into nuclei, where it occupies immune and metabolic chromatin.\nC_LIO_LITwo conserved AIMs in NF-{kappa}B/Dif bind Atg8 and enable Dif nuclear entry.\nC_LIO_LIAIM-mutant Dif flies are highly susceptible to infection and chronic high-sugar diet.\nC_LIO_LIAtg8 occupies stress-related motifs on prolonged HSD and acute infection.\nC_LI"}},{"id":"10.64898/2026.04.22.720179","title":"Macrocyclization of Broad-Spectrum Kinase Inhibitor Bosutinib leads to Potent and Selective Quinoline-based HIPK4 Inhibitor AZ137","subtitle":"Thomas Hanke · Goethe University Frankfurt · 2026-05-28","value":"biochemistry","href":"https://doi.org/10.64898/2026.04.22.720179","props":{"doi":"10.64898/2026.04.22.720179","authors":"Zerva, A.; Raig, N. D.; Zhuang, Z.; Kraemer, A.; Dopfer, J.; Togashi, R.; Schwalm, M. P.; Elson, L.; Frischkorn, J. M.; Berger, B. T.; Mueller, S.; Chen, J. K.; Knapp, S.; Hanke, T.","institution":"Goethe University Frankfurt","category":"biochemistry","date":"2026-05-28","abstract":"Homeodomain-interacting protein kinase 4 (HIPK4) remains an understudied member of the dark kinome. While genetic knockout studies suggest roles for HIPK4 in spermiogenesis and cutaneous squamous cell carcinoma, whether these cellular functions can be recapitulated by pharmacological inhibition remains to be determined. However, such investigations have been hampered by a lack of high-quality chemical tools. To address this, we employed a rational design strategy utilizing macrocyclization of a bosutinib-based scaffold. Systematic optimization led to the discovery of AZ137 (28e), a potent and selective HIPK4 inhibitor (IC50 = 11 nM; cellular EC50 = 76 nM). AZ137 exhibits exceptional selectivity across three comprehensive orthogonal panels, high solubility, and no detectable cytotoxicity. Its cellular activity was confirmed in cell-based assays of HIPK4-dependent F-actin remodeling. Together with a negative control compound, this probe set provides a foundational framework for the validating HIPK4 as a therapeutic target and a high-quality resource to elucidate its roles in normal physiology and disease."}},{"id":"10.64898/2026.05.26.727630","title":"Nanostructured Zirconia thin films as neurogliomorphic interface for neural cells of central and peripheral nervous system","subtitle":"Valentina Benfenati · Consiglio Nazionale delle Ricerche · 2026-05-28","value":"bioengineering","href":"https://doi.org/10.64898/2026.05.26.727630","props":{"doi":"10.64898/2026.05.26.727630","authors":"Conte, G.; Borghi, F.; Lazzarini, C.; Piazzoni, C.; Konstantoulaki, A.; Fabbri, R.; Caprini, M.; Milani, P.; Benfenati, V.","institution":"Consiglio Nazionale delle Ricerche","category":"bioengineering","date":"2026-05-28","abstract":"Recent advances in neuroscience have highlighted the central role of glial cells, particularly astrocytes, in regulating neural network activity through calcium-dependent neuron-glia communication. In parallel, nanostructured cluster-assembled materials have emerged as promising candidates for developing brain-machine interfaces, because of their biomimetic morphology, mechanotransductive properties and neuromorphic behavior. Among these, nanostructured zirconium oxide (ns-ZrOx) thin films have recently demonstrated memristive and signal-processing capabilities compatible with biohybrid neural systems, yet their interaction with heterogeneous neuroglial networks remains poorly understood.\n\nHere, we investigate the biocompatibility and functional effects of ns-ZrOx interfaces on primary astrocytes and dorsal root ganglion (DRG) neuron-glia co-cultures, comparing nanostructured and flat zirconia substrates. Both substrates supported cellular adhesion, survival, and differentiation. However, ns-ZrOx selectively enhanced glial calcium signaling, increasing transient amplitude and accelerating response kinetics in both central and peripheral glial populations. Our findings identify ns-ZrOx as an active neurogliomorphic interface capable of modulating neuron-glia communication through nanoscale material properties. By bridging glial physiology with neuromorphic nanomaterials, this work supports the development of hybrid bioelectronic platforms integrating living neural networks with adaptive functional materials for brain-inspired computing and advanced neural interfaces."}},{"id":"10.64898/2025.12.05.692231","title":"Unimeth: A unified transformer framework for accurate DNA methylation detection from nanopore reads","subtitle":"Peng Ni · Central South University · 2026-05-28","value":"bioinformatics","href":"https://doi.org/10.64898/2025.12.05.692231","props":{"doi":"10.64898/2025.12.05.692231","authors":"Wang, S.; Xiao, Y.; Sheng, T.; Huang, N.; Shu, Y.; Zhai, J.; Luo, F.; Ni, P.","institution":"Central South University","category":"bioinformatics","date":"2026-05-28","abstract":"Nanopore sequencing enables direct detection of DNA modifications from native DNA. However, accurate methylation calling across species, sequence contexts, modification types and chemistries remains challenging. We present Unimeth, a transformer-based framework that jointly processes raw signals and basecalled sequences in read patches and predicts all target methylation sites within each patch. Unimeth uses a three-phase training strategy that combines signal pre-training, methylation fine-tuning and site-level calibration using methylation frequency information. We evaluated Unimeth for 5mC and 6mA detection using public and in-house datasets spanning 14 species, three nanopore chemistries and wild-type, mutant and enzyme-treated samples. Unimeth improved plant 5mC detection in non-CpG contexts, reduced false-positive calls in low-methylation samples and maintained high 5mCpG performance in mammalian datasets. For 6mA, Unimeth reduced background calls while preserving signals for Fiber-seq nucleosome and gene-level analyses. Unimeth provides a unified framework for nanopore-based methylation detection across methylation types and biological contexts."}},{"id":"10.64898/2026.05.26.727937","title":"Targeted mRNA restoration of ciliary function in DNAI1-related primary ciliary dyskinesia: ex vivo rescue in patient-derived nasal spheroids, A pilot study","subtitle":"Caroline Marie Torp Nygaard · National Danish PCD Centre, Paediatric Pulmonary Service, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital - Rigshospitalet, Co · 2026-05-28","value":"physiology","href":"https://doi.org/10.64898/2026.05.26.727937","props":{"doi":"10.64898/2026.05.26.727937","authors":"Nygaard, C. M. T.; Herrera-Cid, C. R.; Nedergaard, L.; Johansen, S. G.; Matthews, J. G.; Couch, J. A.; Qvist, T.; Nielsen, K. G.; Christensen, S. T.; Marthin, J. K.","institution":"National Danish PCD Centre, Paediatric Pulmonary Service, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital - Rigshospitalet, Co","category":"physiology","date":"2026-05-28","abstract":"RationalePrimary Ciliary Dyskinesia (PCD) is a genetic disorder characterized by impaired ciliary function, defective mucociliary clearance, and progressive lung disease. Pathogenic variants in the DNAI1 gene are a well-known cause of PCD. Currently, no approved therapies address the underlying genetic defect. RCT1100 is an inhaled mRNA therapy encoding DNAI1 currently under clinical development. This study evaluates the functional effects of RCT1100 using a fast three-dimensional explant spheroid (3DE-S) model consisting of apical-out undifferentiated nasal epithelial cells derived from patients with DNAI1 PCD.\n\nMethods3DE-S were generated from nasal brushings of five patients with confirmed biallelic DNAI1 variants. RCT1100 was administered from day 5 directly to culture wells three times weekly for two weeks. Spheroid motility was assessed throughout treatment by quantifying the proportion of moving spheroid rolling and their movement velocity. Following six doses, spheroids were harvested for high-speed video microscopy for assessment of ciliary beat frequency.\n\nResultsEvaluable data were obtained from three of five patient samples; two samples were excluded due to contamination. After six doses of RCT1100, ciliary beat frequency increased from a baseline range of 2.8-3.5 Hz to 6.7-6.8 Hz post-harvesting. Mean spheroid movement velocity increased from 0.11 {micro}m/sec to 3.87 {micro}m/sec following dosing with 10 {micro}g/mL RCT1100, with more than 80% of spheroids exhibiting coordinated rolling motion pattern.\n\nConclusionThe 3DE-S is a robust platform for evaluating targeted therapies. RCT1100 significantly restored ciliary function, supporting its therapeutic potential and highlighting the utility of spheroid-based systems for precision medicine approaches in DNAI1 PCD."}},{"id":"10.1101/2025.08.21.671439","title":"Ketone-body receptor GPR109A suppresses hepatic inflammation via gut-liver axis regulation","subtitle":"Akari Nishida · Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University · 2026-05-28","value":"physiology","href":"https://doi.org/10.1101/2025.08.21.671439","props":{"doi":"10.1101/2025.08.21.671439","authors":"Nishida, A.; Nishikawa, S.; Budau, R.; Yamano, M.; Ohue-Kitano, R.; Ikeda, T.; Sasaki, N.; Kimura, I.","institution":"Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University","category":"physiology","date":"2026-05-28","abstract":"The ketogenic diet (KD) promotes ketone body synthesis and has been used as an effective treatment for disorders such as epilepsy. Although elevated ketone bodies, including {beta}-hydroxybutyrate ({beta}HB) and acetoacetate, are thought to meditate the beneficial effects of the KD, the mechanisms underlying their metabolic actions remain incompletely understood. In this study, we focused on GPR109A, a receptor for {beta}HB with an unclear role in metabolic homeostasis. We employed KD and fasting models to examine metabolic changes under two distinct ketogenic conditions. Under KD conditions, Gpr109a-/- mice exhibited increased hepatic lipid accumulation, and subsequent hepatic inflammation and fibrosis. However, Gpr109a deletion did not exacerbate hepatic lipid accumulation or inflammation during short-term fasting, suggesting that GPR109A-mediated liver protection is specific to KD-induced metabolic stress rather than under fasting conditions. Mechanistic analysis revealed that GPR109A protects the liver from inflammation by maintaining intestinal barrier integrity. These findings highlight the novel protective mechanism of GPR109A, via the gut-liver axis, to sustain metabolic homeostasis during the KD. This study provides valuable insights into the physiological effects of ketone bodies."}},{"id":"10.64898/2026.05.22.727111","title":"Bark beetle protein elicitors trigger biphasic immune responses in Norway spruce seedlings","subtitle":"Carlos Trujillo Moya · Austrian Research Centre for Forests · 2026-05-28","value":"plant biology","href":"https://doi.org/10.64898/2026.05.22.727111","props":{"doi":"10.64898/2026.05.22.727111","authors":"Ramires, M. J.; Netherer, S.; Schebeck, M.; Ertl, R.; Ahmad, M.; Arc, E.; van Loo, M.; Trujillo Moya, C.","institution":"Austrian Research Centre for Forests","category":"plant biology","date":"2026-05-28","abstract":"Norway spruce (Picea abies) responds to attacks by the spruce bark beetle (Ips typographus) through the rapid activation of local defense mechanisms, but field studies can be difficult to standardize due to variable attack pressure and environmental heterogeneity. Here, we developed a phytotron-based assay that mimics early beetle-associated stress using insect-derived protein extracts, enabling reproducible molecular analyses under controlled conditions. Ten-week-old spruce seedlings were stem-treated with mock buffer or beetle protein extracts, followed by transcriptomic analyses of stem tissues and targeted metabolomic profiling of needles at 2 and 48 h post-inoculation. RT-qPCR analysis revealed rapid transcriptional activation of signaling and defense genes in Norway spruce, with NP-40-based protein extracts producing the most consistent early response. RNA-seq analysis revealed transcriptional dynamics, with 488 differentially expressed genes detected at 2 h and 84 at 48 h post-inoculation relative to mock-treated controls. Early responses at 2 h were characterized by activation of genes associated with immune perception and signal transduction. By 48 h, the response shifted toward accumulation of transcripts encoding defense proteins such as chitinases, defensins, proteinase inhibitors, and pathogenesis-related (PR) proteins. Importantly, a substantial proportion of differentially expressed genes overlapped with those previously identified in mature Norway spruce trees during pioneer bark beetle attack under field conditions, supporting the biological relevance of the assay. In contrast, targeted analyses of secondary metabolites performed in needle tissue revealed limited systemic changes across time points, suggesting that early induced defenses may remain largely localized to the stem. Together, these results demonstrate that beetle-derived proteins trigger a rapid and temporally structured defense response in Norway spruce seedlings and establish a reproducible elicitor-based platform that may provide a broadly applicable framework for investigating bark beetle-induced defenses across conifers.\n\nHighlightBark beetle protein elicitors trigger temporally structured immune responses in Norway spruce seedlings that overlap with responses observed in mature trees, with rapid immune signaling at 2 h followed by defense protein accumulation at 48 h."}},{"id":"10.64898/2026.05.14.725129","title":"A Root Foundation Model for Zero-Shot Segmentation","subtitle":"Abraham George Smith · Department of Computer Science, University of Copenhagen, Denmark · 2026-05-28","value":"plant biology","href":"https://doi.org/10.64898/2026.05.14.725129","props":{"doi":"10.64898/2026.05.14.725129","authors":"Smith, A. G.; Lamprinidis, S.; Wlaszczyk, A.; Petersen, J.","institution":"Department of Computer Science, University of Copenhagen, Denmark","category":"plant biology","date":"2026-05-28","abstract":"Foundation models pre-trained on massive datasets have demonstrated impressive performance, but in some specialised domains have been found to have lower accuracy. Domain-specific foundation models target a particular domain such as retinal or plant images. These domain-specific models have shown inconsistent results and the benefit to root segmentation is unknown. We train and evaluate the first domainspecific foundation model for root segmentation. Evaluation uses a leave-one-dataset-out design across nine diverse root datasets with two architectures. Applied zero-shot to unseen datasets, the root foundation model achieves 92% of fine-tuned Dice on average (0.636 versus 0.698), with 5 of 9 datasets above 90%. With 10 patches of few-shot fine-tuning, the root foundation model recovers 95% of its full-data Dice on average, versus 69% for a general pre-trained model. At low patch counts the general pre-trained model often failed to converge, with 5 of 9 datasets giving Dice below 0.05 at 3 patches, while the root foundation model produced Dice above 0.47 on every dataset and patch count. With full target-data fine-tuning, the two perform comparably, with mean improvements of +0.011 Dice for MobileSAM and +0.022 for M2F Swin-S, neither significant (Wilcoxon p = 0.150 and 0.064). We release our pre-trained MobileSAM root foundation model for use with RootPainter, enabling fully automatic root segmentation on new datasets with an ordinary laptop or desktop computer, with no need for annotation or training."}},{"id":"10.64898/2026.05.23.727417","title":"Metabolomics of Thermoregulatory Transitions in the Eastern Skunk Cabbage (Symplocarpus foetidus)","subtitle":"Alexander G Little · McMaster University · 2026-05-28","value":"plant biology","href":"https://doi.org/10.64898/2026.05.23.727417","props":{"doi":"10.64898/2026.05.23.727417","authors":"Toth, J.; Mantulak, R.; Bozzo-Rey, M.; Little, A. G.","institution":"McMaster University","category":"plant biology","date":"2026-05-28","abstract":"The Eastern skunk cabbage (Symplocarpus foetidus) is a thermogenic plant with remarkably precise thermoregulatory control. Its unique sexual dimorphism in thermogenic strategy, homeothermy in female-phase flowers versus diurnal heterothermy in male-phase flowers, offers a powerful natural framework to identify thermoregulatory signaling pathways. We used untargeted metabolomics and LC-MS/MS to compare metabolite profiles across four groups: homeothermic females sampled at midday and midnight, and diurnally heterothermic males sampled at midday and midnight. Pairwise comparisons and cross-filtering against circadian- and sex-specific metabolite changes yielded 190 candidate thermoregulatory metabolites. Principal component analysis revealed that thermogenic state (warm vs. cold) was the primary axis of metabolic variation, accounting for nearly 55% of variance. Metabolite set enrichment analysis identified significant enrichment for octadecanoid formation from linoleic acid, linoleic acid oxylipin metabolism, and eicosanoid metabolism via cyclooxygenases. Oxylipins including 9-oxoODE, 9(S)-HOT, 13(S)-HOT, and 15-OxoETE were among the compounds most strongly associated with low thermogenic activity. We propose that lipoxygenase-derived cyclopentenone oxylipins may suppress thermogenesis by inhibiting thioredoxin o (TRXo), thereby inactivating the alternative oxidase (AOX) pathway that drives heat production. These findings suggest convergence between plant and mammalian thermoregulatory pathways, with linoleic acid-derived oxylipins and prostaglandins emerging as conserved regulators of metabolic heat production across deeply divergent lineages."}},{"id":"10.64898/2026.05.24.727542","title":"A Stronger Association Between Screen Time and Externalizing Problems in Typically Developing Children than in Children with Autism Spectrum Disorder","subtitle":"Mitsuru Kikuchi · Kanazawa University Graduate School of Medical Sciences · 2026-05-28","value":"scientific communication and education","href":"https://doi.org/10.64898/2026.05.24.727542","props":{"doi":"10.64898/2026.05.24.727542","authors":"Miyashita, S.; Hirosawa, T.; Yoshimura, Y.; Hasegawa, C.; Tanaka, S.; Miyagishi, Y.; Naito, N.; Kikuchi, M.","institution":"Kanazawa University Graduate School of Medical Sciences","category":"scientific communication and education","date":"2026-05-28","abstract":"Excessive screen use is associated with childhood behavioral problems, but whether associations differ between typically developing (TD) children and those with autism spectrum disorder (ASD) is unclear. Our cross-sectional study included 108 children aged 5-9 years (61 TD, 47 ASD). ASD was diagnosed using standardized clinical instruments. Measures included parent-reported screen time (excluding TV/DVD), cognitive ability (K-ABC), and behavioral problems (Vineland-II). Screen time and externalizing problems were associated in the TD group (Spearmans {rho} = 0.361, p < 0.01), but not in the ASD group. In the regression model, screen time ({beta} = 0.40, t = 2.60, p < 0.05), ASD status ({beta} = 0.70, t = 8.30, p < 0.001), and their interaction ({beta} = -0.34, t = -2.06, p < 0.05) significantly predicted externalizing problems. Considering the diversity within the autism spectrum, future studies with larger sample sizes should consider individual heterogeneity when examining the association between behavioral outcomes and screen time."}},{"id":"10.1101/2025.05.16.653525","title":"Study on Liver Sinusoidal Endothelial Cell Fenestrations Based on Cellular Omics-Structure Integration Technology and Its Application in Metabolic Diseases","subtitle":"Richard D Leapman · National Institutes of Health · 2026-05-28","value":"systems biology","href":"https://doi.org/10.1101/2025.05.16.653525","props":{"doi":"10.1101/2025.05.16.653525","authors":"Wei, Z.; Chen, J.; Aronova, M. A.; Leapman, R. D.","institution":"National Institutes of Health","category":"systems biology","date":"2026-05-28","abstract":"This study developed a new Cellular Omics-Structural Integration (COSI) technology platform to address the limitation of traditional technologies in simultaneously obtaining gene expression profiles and super-resolution cellular structural information at the single-cell level. The platform comprises three core functional modules: (1) a single-cell transcriptomics and super-resolution fluorescence microscopy integration module that enables simultaneous acquisition of gene expression profiles and super-resolution fluorescence images at the single-cell level; (2) an electron microscopy and super-resolution fluorescence microscopy integration module with deep learning resolution enhancement that further gives fluorescence image high resolution features; and (3) a comprehensive analysis module that integrates transcriptomic data with enhanced super-resolution morphological data.\n\nApplication of this technology to primary liver sinusoidal endothelial cells successfully achieved efficient matching and analysis of ultrastructural information and gene transcription data at the single-cell level, revealing associations between specific genes and endothelial cell fenestration formation. Through correlation analysis and multivariate statistical methods, we identified specific gene sets associated with fenestration number and average area. Validation in published non-alcoholic steatohepatitis (NASH) and diabetic mouse models demonstrated that these gene sets can effectively assess disease status and drug intervention efficacy, with fenestration number-related gene sets showing significant reduction in NASH and time-dependent changes in response to diabetes treatments.\n\nThese findings not only expand our understanding of the mechanisms underlying liver and kidney endothelial cell fenestration formation but also provide novel molecular markers and potential therapeutic targets for early diagnosis and treatment evaluation of metabolic diseases. As a fundamental research tool, COSI technology fills critical gaps in existing spatial omics and cellular biology research, particularly for studying cellular structures lacking specific markers, and demonstrates significant potential for clinical applications in chronic metabolic diseases."}},{"id":"10.1101/2024.12.04.626803","title":"Uncovering the domain language of protein function and proteinnetworks using DANSy","subtitle":"Kristen M. Naegle · University of Virginia · 2026-05-28","value":"systems biology","href":"https://doi.org/10.1101/2024.12.04.626803","props":{"doi":"10.1101/2024.12.04.626803","authors":"Shimpi, A. A.; Naegle, K. M.","institution":"University of Virginia","category":"systems biology","date":"2026-05-28","abstract":"Protein-protein interaction networks can help identify co-regulated modules, emergent biology (such as pathways), disease-associated partners, and function through association. However, these networks are limited by the breadth of experimental data behind them, which is incomplete and uneven across the proteome. For example, the coverage of interactions driven by reversible post-translational modifications (acetylation, phosphorylation, etc.) or protein fusions in diseases are particularly difficult to establish. Protein domains, conserved structural and functional units, are a major component of what defines a proteins function and its interactions. Whereas protein interactions are sparsely understood at this time, domain identification and coverage is mature. In this work, we propose a language-based network that utilizes the domain as \"words\" that makes up protein \"sentences\" to cover an entire proteome. We first convert proteins into n-grams (a formalization of contiguous words in a sentence) and assemble n-grams into a comprehensive network. We then use information theory to reduce the complexity of the network, collapsing to a network and n-gram size that recovers the majority of the proteome complexity. Using network theoretic approaches, we explore the larger human proteome and subnetwork analysis to understand specific properties in two applications: reversible systems of post-translational modifications (PTMs) and cancer fusion genes. PTM analysis across species suggests that reversible PTM systems convergently evolved similar domain architectures - allowing higher interconnectivity between reader and writer domains, while eraser domains remained highly disconnected. Cancer fusion analysis finds that, despite the possibility that fusions may sample novel domain word combinations, creating new connections or altering the human protein network, most cancer fusion genes follow existing domain combination rules. Collectively, these results suggest that an n-gram based analysis of proteomes complements direct protein interaction approaches, but provides a more fully described network of interconnected protein function that can provide unique insights on signaling pathway analysis. We refer to this approach for converting proteomes into functional linguistic networks as Domain Architecture Network Syntax (DANSy).\n\nSignificanceHere, we develop a novel computational method that treats proteins as sentences made up of domain words. We integrate this linguistic representation with networks to uncover abstract functional relationships to more fully represent the proteome than traditional protein-protein interaction networks, which are limited by incomplete experimental data. Our findings show how this framework, which we term Domain Architecture Network Syntax (DANSy), uncovers common \"grammar\" governing protein functionality in the evolution of post-translational modification systems and demonstrates how cancer fusion genes maintain established principles of the natural proteome."}},{"id":"10.64898/2026.03.03.709377","title":"MORPHE: Bridging Image Generation and Spatial Omics for Tissue Synthesis","subtitle":"John W Hickey · Duke University · 2026-05-28","value":"systems biology","href":"https://doi.org/10.64898/2026.03.03.709377","props":{"doi":"10.64898/2026.03.03.709377","authors":"Feng, Y.; Robers, Z.; Rasheed, L.; Miao, Y.; Wen, S.; Lee, K.; Sohigian, J.; Brbic, M.; Hickey, J. W.","institution":"Duke University","category":"systems biology","date":"2026-05-28","abstract":"Spatially resolved omics technologies reveal tissue organization at single-cell resolution but remain limited by the cost of the assays, incomplete spatial coverage, 2D-only imaging, and experimental artifacts. These factors motivate the need for in silico methods that can reconstruct or extend tissue context beyond what current spatial measurements provide. We present MORPHE (MOdeling of stRuctured sPatial High-dimensional Embeddings), an AI framework that learns to synthesize biologically faithful tissue architecture directly from spatial-omics data. MORPHE introduces a graph-informed probabilistic embedding that maps discrete cell identities and their spatial relationships into a continuous RGB-like latent space compatible with diffusion modeling. This representational bridge enables spatial cellular maps to leverage large pre-trained image-generative models while preserving biological interpretability upon decoding. By modeling cells as the fundamental units of generation and learning how their identities and spatial relationships collectively give rise to large-scale tissue structure, MORPHE enables generation and reconstruction of tissue architecture at single-cell resolution. We applied the method across large-scale single-cell proteomic datasets from the intestine and single-cell transcriptomic datasets from the brain, showing computational scalability acrosss millions of cells. We used MORPHE on these datasets to outpaint beyond experimentally restricted fields of view, inpaint missing or experimentally damaged tissue regions, and perform cross-tissue imputation, connecting separated tissue regions into a single contiguous sample in both 2D and 3D. MORPHE represents a new class of tissue generation algorithms that will help solve current limitations and challenges with single-cell spatial-omics datasets."}},{"id":"10.64898/2026.05.26.728015","title":"Thalamic nuclei insights into Alzheimer's disease","subtitle":"Julie P Vidal · NZBRI/INSERM · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.64898/2026.05.26.728015","props":{"doi":"10.64898/2026.05.26.728015","authors":"Vidal, J. P.; Myall, D.; Pariente, J.; Pitcher, T.; Roberts, R. P.; Cawston, E.; Leheron, C.; Anderson, T.; Morgan, C.; Melzer, T.; Kirk, I.; Tippett, L.; Peran, P.; Dalrymple-alford, J.","institution":"NZBRI/INSERM","category":"neuroscience","date":"2026-05-28","abstract":"INTRODUCTIONThalamic nuclei support multiple cognitive processes, yet their integrity in biologically-defined Alzheimers disease (AD) remains unknown.\n\nMETHODAmyloid status was determined using PET Centiloids >24 in 1,327 participants from ADNI. Combined with clinical diagnosis, this yielded six groups: amyloid-negative or positive CN-MCI-dementia/AD. Thalamic nuclei volumes were extracted from T1-weighted MRI using the HIPS-THOMAS algorithm.\n\nRESULTSLarge volume reductions in the anteroventral, mediodorsal, and pulvinar nuclei were observed in amyloid-positive MCI and AD. Reduced volumes were also evident in amyloid-positive CN, supporting preclinical AD. Adding the anteroventral nucleus improved cognitive status classification in Random Forest analyses. A phenotypic model integrating thalamic nuclei clearly distinguished amyloid-positive groups from amyloid-negative CN and reclassified non-AD patients with 68% of amyloid-negative MCI subjects as CN-like, and 27% of amyloid-positive CN as MCI-like.\n\nDISCUSSIONThalamic volumetry from conventional T1-weighted MRI enhances clinical insight into AD and provides a practical biomarker for disease intervention."}},{"id":"10.1101/2024.10.29.620847","title":"Dynamic imbalances in cell-type-specific striatal ensembles reflect learned coupling between trajectory representations and locomotor dynamics","subtitle":"Mark Howe · Boston University · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.1101/2024.10.29.620847","props":{"doi":"10.1101/2024.10.29.620847","authors":"Tong, Y.; Fearey, B.; Xie, Z.; Alexander, A.; Bouabid, S.; Graham, B.; Howe, M.","institution":"Boston University","category":"neuroscience","date":"2026-05-28","abstract":"Basal ganglia models commonly propose that relative imbalances between direct and indirect pathway output shapes movement, but how such imbalances are expressed during behavior remains unclear. We simultaneously imaged identified direct-pathway and indirect-pathway spiny projection neurons (dSPNs and iSPNs) in dorsal striatum as mice locomoted through virtual visual environments for reward. Individual dSPNs and iSPNs encoded discrete locations within specific visual environments and, in a distance-based task, encoded distance traveled or elapsed time, revealing structured representations of goal-directed trajectories. At the population level, both pathways were broadly co-active and similarly correlated with locomotor speed, but their relative activity shifted systematically across learned trajectories: dSPNs dominated during early accelerating segments, and iSPNs dominated during later slowing segments. These imbalances were selectively expressed within ensembles tuned to spatial location or distance/time, depending on task structure, but were absent during comparable spontaneous locomotion outside the task context and during initial exposure to a novel environment. A computational model demonstrated that opponent plasticity driven by kinematics-linked teaching signals can reproduce the observed task-dependent imbalances through cell-type-specific plasticity of discrete trajectory-related inputs and can progressively organize locomotor kinematics over learning. Our findings indicate that direct/indirect pathway imbalances are not a general reflection of motor output, but are dynamic, state-dependent features of striatal activity that link structured trajectory representations to associated changes in behavioral vigor along repeated, goal-directed locomotor paths through learning."}},{"id":"10.64898/2026.02.17.706268","title":"Protocol Update: The Normative Modelling Paradigm for Computational Psychiatry","subtitle":"Andre F Marquand · Donders Institute for Brain, Cognition and Behaviour · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.64898/2026.02.17.706268","props":{"doi":"10.64898/2026.02.17.706268","authors":"de Boer, A. A. A.; Bayer, J. M. M.; Fraza, C.; Chavanne, A.; Rehak Buckova, B.; Tsilimparis, K.; Serin, E.; Bernas, A.; Cirstian, R.; Zabihi, M.; Rutherford, S.; Al Khaledi, A.; Wolfers, T.; Beckmann, C.; Marquand, A. F.","institution":"Donders Institute for Brain, Cognition and Behaviour","category":"neuroscience","date":"2026-05-28","abstract":"Normative Modelling ( brain growth charting) is now a well-established method for computational psychiatry and involves charting centiles of variation across a population in terms of mappings between biology and behavior, providing statistical inferences at the level of the individual. These models have helped the field to move away from case-control analysis toward individual-level analysis. Correspondingly, normative modelling has now been applied to chart brain development and ageing in many populations and has been used to quantify individual deviations across various neurological and psychiatric conditions. This has been supported by large-scale models that are openly accessible for diverse brain imaging modalities. As normative modelling continues to grow, several recent methodological developments, such as non-Gaussian models, longitudinal models, and federated learning, have been implemented in different software tools, including the Predictive Clinical Neuroscience toolkit (PCNtoolkit). In this protocol update, we provide: (i) a revised overview of this methodological landscape; (ii) an update to our 2022 standardised analytical protocol for normative modelling of neuroimaging data, including options for federated and longitudinal normative models; (iii) practical guidance suited to both novice and experienced practitioners supported by open-source code examples implemented in the refactored version of PCNtoolkit; and (iv) updated models for cortical thickness, surface area, volumetric data, functional connectivity and diffusion-weighted imaging for use by the community."}},{"id":"10.64898/2026.02.03.703553","title":"Sensory adaptation and pupil-linked arousal support flexible evidence accumulation during perceptual decision making","subtitle":"Kara D McGaughey · University of Pennsylvania · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.64898/2026.02.03.703553","props":{"doi":"10.64898/2026.02.03.703553","authors":"McGaughey, K. D.; Gold, J. I.","institution":"University of Pennsylvania","category":"neuroscience","date":"2026-05-28","abstract":"Effective decision making in dynamic environments requires flexible evidence accumulation. Although models often express this flexibility as a property of the accumulator, its implementation in the brain may involve adaptive mechanisms operating at other stages of the decision process. We examined two such mechanisms: 1) stimulus-specific sensory adaptation at the level of evidence encoding; and 2) arousal-related neuromodulation, which could, in principle, affect both evidence encoding and accumulation. We measured single-unit activity in the middle temporal area (MT) and pupil-linked arousal while monkeys performed a modified random-dot motion direction-discrimination task in which an adapting stimulus with varied temporal stability preceded a behaviorally relevant test stimulus. The monkeys decisions reflected adaptive evidence accumulation that depended on temporal-context stability and corresponded to context-dependent changes in both stimulus-specific sensory adaptation in MT and task-evoked pupil responses. However, adaptation and pupil adjustments were not related to each other. Together, these findings suggest that multiple mechanisms contribute to flexible, context-dependent evidence accumulation, including changes in sensory adaptation that shape evidence encoding and changes in arousal that may shape the accumulation process itself."}},{"id":"10.1101/2025.09.09.675139","title":"Minimal mean-field gated parietal circuit model for flexible perceptual decisions","subtitle":"KongFatt Wong-Lin · Ulster University · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.1101/2025.09.09.675139","props":{"doi":"10.1101/2025.09.09.675139","authors":"Lenfesty, B.; Azimi, A.; Bhattacharyya, S.; Shushruth, S.; Wong-Lin, K.","institution":"Ulster University","category":"neuroscience","date":"2026-05-28","abstract":"Flexible perceptual decision-making requires rapid, context-dependent adjustments, yet the neural circuit mechanisms underlying its parsimonious representations remain unclear. Here, we propose a minimal mean-field neural circuit model that integrates sensory evidence and selects actions via distributed neuronal encoding, guided by data from a task that dissociates perceptual choice from motor response - abstract perceptual decision-making. The models nonlinear gating of action selective (AS) neurons replicates parietal cortical activity observed during task performance. Critically, recurrent excitation within the evidence integration (EI) population supports sensory evidence accumulation, working memory for sequential sampling, and reward rate optimisation. Moreover, the dynamics of EI and AS neuronal activities in the same model respectively mirror parietal neuronal activities related to sensory evidence encoding and ramping-to-threshold firing in a separate reaction-time task, while suggesting that decision readout engages both neuronal populations. The model also predicts decision interference in a novel two-stage decision version of the task, accounting for choice accuracy decrements observed in other experiments while predicting slower decisions. Together, these findings propose a minimal mean-field circuit-level mechanism unifying perceptual, memory-based, and abstract decision-making."}},{"id":"10.64898/2026.05.26.728058","title":"Modeling Prenatal Immune Activation in Human Brain Organoids Uncovers IL-6-Dependent Interneuron Dysmaturation","subtitle":"Peng Jiang · Rutgers University New Brunswick · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.64898/2026.05.26.728058","props":{"doi":"10.64898/2026.05.26.728058","authors":"Papetti, A. V.; Ma, Z.; NG, M.; Jin, M.; Levison, S. W.; Jiang, P.","institution":"Rutgers University New Brunswick","category":"neuroscience","date":"2026-05-28","abstract":"Prenatal inflammation has been associated with an increased likelihood of the child developing neurodevelopmental conditions, such as autism spectrum disorder (ASD). Several pro-inflammatory cytokines are significantly upregulated and play critical roles during immune activation, with interleukin-6 (IL-6) being particularly prominent. However, the specific impact of elevated IL-6 levels on human neural development remains to be elucidated. To address this, we established a human pluripotent stem cell-based forebrain organoid model enriched for multiple interneuron lineages, validated through immunohistochemistry and transcriptomic alignment with human fetal reference datasets. We showed IL-6 responsiveness via the activation of the JAK/STAT pathway and characterized downstream effects using bulk and single-nucleus RNA sequencing (RNA-seq). Bulk RNA-seq at the end of IL-6 exposure uncovered activation of inflammatory pathways, upregulation of MHC-I machinery, and early disruption of GABAergic signaling programs. Notably, single-nucleus RNA-sequencing performed one month after IL-6 withdrawal revealed a persistent inflammatory transcriptional signature across interneuron development, accompanied by accelerated progression through maturation stages and altered interneuron subtype output. Together, these findings demonstrate that transient prenatal IL-6 exposure is sufficient to reshape human interneuron fate specification and maturation trajectories, providing mechanistic insights into neuroimmune contributions to ASD."}},{"id":"10.64898/2026.05.27.727895","title":"Altering facial preferences with context","subtitle":"Asaf Madar · Tel Aviv University · 2026-05-28","value":"neuroscience","href":"https://doi.org/10.64898/2026.05.27.727895","props":{"doi":"10.64898/2026.05.27.727895","authors":"Madar, A.; Abudarham, N.; Yovel, G.; Tavor, I.; Levy, D. J.","institution":"Tel Aviv University","category":"neuroscience","date":"2026-05-28","abstract":"Facial features are known to play a key role in how we judge a persons traits. However, in many scenarios people do not evaluate a person in isolation but are required to compare and choose between multiple candidates. Yet, the principles that govern these decisions remain unknown. In economic literature, decisions are known to be influenced by the context of available options, but it is unclear to what extent these principles apply to social decisions about naturalistic stimuli such as human faces. Here, we bridged between these two fields of research - face evaluations and economic decisions - to investigate whether facial preferences can be systematically shifted by context, exhibiting a well-known choice context effect, the \"decoy effect\". We asked participants to choose the person they think is more trustworthy from either a set of two (\"target\" and \"competitor\") or three faces (including a \"decoy\"). Based on economic theory, we carefully selected face sets using their trustworthiness rankings and perceptual similarity, and tested them across several exploratory samples (n=100-400) and one large, preregistered experiment (n=1099). We found that adding a decoy face to the choice set increased participants choices of the target option by up to 7%, while the decoy face was rarely selected, consistent with a typical decoy effect. These results provide direct evidence that social judgements are affected by the same context-dependent principles known from economic choices, and that the decoy effect can be generalized to complex naturalistic stimuli such as human faces, relevant to various real-world applications."}},{"id":"10.64898/2026.05.18.725940","title":"Monoclonal anti-dsRNA antibody-based metagenomics (MADAM) reveal Pyricularia oryzae mycovirome","subtitle":"Philippe Roumagnac · CIRAD · 2026-05-28","value":"microbiology","href":"https://doi.org/10.64898/2026.05.18.725940","props":{"doi":"10.64898/2026.05.18.725940","authors":"Blondin, L.; Filloux, D.; Fernandez, E.; Adreit, H.; Huang, H.; Fournier, E.; Tharreau, D.; Roumagnac, P.","institution":"CIRAD","category":"microbiology","date":"2026-05-28","abstract":"This study introduces MADAM (Monoclonal Anti-dsRNA Antibody-Based Metagenomics), a novel approach that integrates multiple technical modules previously used independently in other protocols. MADAM combines monoclonal antibody-mediated double-stranded RNA (dsRNA) enrichment, sequence-independent RT-PCR, and Oxford Nanopore Technologies (ONT) sequencing. Applied to Pyricularia oryzae, the causal agent of rice blast disease, MADAM enabled the comprehensive characterization of mycovirus genomes from four fungal isolates collected in Yunnan, China. The approach achieved high viral read recovery rates (46.9-72.7%) and identified 18 P. oryzae-associated RNA viruses spanning seven families: Botourmiaviridae, Deltaormycoviridae, Mymonaviridae, Partitiviridae, Polymycoviridae, Splipalmiviridae, and Ambiguiviridae. Nearly complete to complete viral genomes (1,226-6,085 nucleotides) were recovered, with sequence coverage ranging from 88% to 100%. Co-infections were detected in three of the four isolates, with notable discoveries including the first deltaormycovirus reported in P. oryzae, a putative novel member of Botourmiaviridae, and an additional genomic segment of a polymycovirus. MADAM successfully detected positive-sense, negative-sense ssRNA, and dsRNA viruses, demonstrating its broad applicability. By uncovering novel viruses and resolving complex co-infections, this method proves invaluable for fungal virology, with potential applications in diagnostics, surveillance, and biological control. Ultimately, MADAM advances our understanding of fungal viral diversity and paves the way for further exploration of mycovirus ecology and evolution."}},{"id":"10.64898/2026.05.27.728125","title":"DORA: a dose-response autoencoder for interpretable transcriptome-to-viability prediction","subtitle":"Vaitea Opuu · Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France · 2026-05-28","value":"molecular biology","href":"https://doi.org/10.64898/2026.05.27.728125","props":{"doi":"10.64898/2026.05.27.728125","authors":"Wang, S.; Allauzen, A.; Opuu, V.; Nghe, P.","institution":"Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France","category":"molecular biology","date":"2026-05-28","abstract":"Predicting the effect of drugs on cell viability is a central challenge in drug discovery. Artificial intelligence holds the promise to considerably accelerate this process by leveraging rich cellular data such as transcriptomics. Current models focus on either transcriptomes or inhibitory concentrations, but they fall short in integrating these sources of information. Here, we propose DORA (Dose-Response Autoencoder), a deep learning model that predicts changes in transcriptomes and viability in a dose-dependent manner, knowing the unperturbed cell state. By enforcing a latent space consistent with cumulative dose effects, DORA matches other methods at predicting transcriptomes and substantially outperforms existing latent representations at viability prediction. The transcriptome-viability relationship provided by the model further allows the recovery of known biomarkers of cell viability while suggesting novel ones. Overall, DORA provides a unified framework delivering actionable biological insights for phenotypic drug screening and personalized medicine."}},{"id":"10.64898/2026.05.20.726462","title":"Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material","subtitle":"Thomas Braun · University of Basel · 2026-05-28","value":"molecular biology","href":"https://doi.org/10.64898/2026.05.20.726462","props":{"doi":"10.64898/2026.05.20.726462","authors":"Zimmermann, M.; Schneider, D. E.; Rima, L.; Clairfeuille, T.; Thoma, R.; Lauer, M.; Braun, T.","institution":"University of Basel","category":"molecular biology","date":"2026-05-28","abstract":"Cryo-EM is central to high-resolution structure determination, but conventional sample preparation consumes substantial amounts of protein and can destabilize sensitive complexes. Microfluidic approaches can miniaturize and accelerate these workflows while retaining the particle numbers required for single-particle analysis. Here, we present a generalized microfluidic isolation strategy that captures proteins directly from cell lysates or in vitro translation reactions using genetically encoded tags. The platform supports both affinitybased (ALFA-nanobody) and covalent (SpyTag3/SpyCatcher3) capture. Specificity derives from two sequential, orthogonal steps: (i) tag-mediated capture and concentration of the target protein on beads, and (ii) photoelution from the bead surface. By confining the sample to nanoliter volumes and minimizing transport, the approach suppresses non-specific carryover. Importantly, the isolation workflow is coupled to grid preparation, enabling preparation of three cryo-EM or negative-stain grids from a 25 nL eluate. Using this workflow, we isolated E. coli ferritin A, {beta}-galactosidase, and P. aeruginosa VgrG1 from cell lysate, obtaining reconstructions at 1.9-2.6 [A] resolution with B-factors comparable to optimized conventional workflows. We further isolated ferritin A from an in vitro translation reaction, yielding a 2.04 [A] reconstruction. A standardized 50 {micro}L starting volume enabled more than 16 independent microfluidic isolations. Tag-based microfluidic isolation thus provides a broadly applicable route to cryo-EM sample preparation, reducing sample volumes more than 1000-fold, reducing preparation times more than 3-fold for lysate-based workflows and up to 10-fold when combined with cell-free expression, and enabling high-throughput structural screening directly from in vitro translation reactions.\n\nSignificance StatementCryo-electron microscopy (cryo-EM) enables protein structure determination at atomic resolution, but conventional sample preparation requires large amounts of purified protein and laborious workflows that can damage fragile complexes. We present a microfluidic platform that captures tagged proteins directly from minute amounts of crude lysates or cell-free synthesis reactions and deposits them onto cryo-EM grids in a single integrated workflow. Using this approach, we determine three protein structures at high resolution. By reducing sample volumes by roughly three orders of magnitude, the platform expands cryo-EM to proteins inaccessible to conventional workflows and provides a foundation for automated, high-throughput structural analysis."}},{"id":"10.1101/2025.09.30.679618","title":"The tetraspanin disc proteins, peripherin-2 and ROM1, facilitate CNG channel localization to the rod outer segment","subtitle":"Jillian N Pearring · University of Michigan · 2026-05-28","value":"cell biology","href":"https://doi.org/10.1101/2025.09.30.679618","props":{"doi":"10.1101/2025.09.30.679618","authors":"Thorson, M. T.; Wei, S. E.; Park, J.; Martinez-Marquez, J. Y.; Ball, D. G.; Willer, J. R.; Spencer, W. J.; Pearring, J. N.","institution":"University of Michigan","category":"cell biology","date":"2026-05-28","abstract":"The light-responsive outer segment of rod photoreceptors is composed of two distinct membrane subdomains: discs and the plasma membrane. We investigate how the disc protein peripherin-2 is engaged in CNG channel delivery to the outer segment. Instead of forming outer segments, peripherin-2 knockout (Rds-/-) photoreceptors release ciliary ectosomes, in which CNG channel levels are markedly reduced relative to other outer segment proteins. This is intriguing as downregulation of the CNG channel is not a general feature of degenerative mouse models with dysmorphic outer segments. Overexpression of the {beta}1-subunit of CNG in Rds-/- rods reveals that the majority is trapped in intracellular membranes, but is restored to the outer segment by co-expressing peripherin-2. We test peripherin-2 chimeras containing either the N-terminus, tetraspanin core, or C-terminus and find that the tetraspanin domain is sufficient to localize CNG{beta}1 to the outer segment. We further show that the membrane remodeling function of the tetraspanin domain facilitates this process by the redundant action of the tetraspanin domain from ROM1 and the reemergence of the endogenous CNG channel in aged Rds-/- rods that have produced ciliary membrane protrusions."}},{"id":"10.1101/2025.03.20.644150","title":"A Critical Role for Neutral Sphingomyelinase-2 in Doxorubicin-induced Cardiotoxicity","subtitle":"Christopher J Clarke · Stony Brook University · 2026-05-28","value":"cell biology","href":"https://doi.org/10.1101/2025.03.20.644150","props":{"doi":"10.1101/2025.03.20.644150","authors":"Mohammed, S.; Alvarado, V.; Jiang, Y.-P.; Velazquez, F. N.; Alexander, M. E.; Alvarez, F. A.; Chiappone, S. B.; Ostermeyer-Fay, A. G.; Zhang, L.; Shamseddine, A. A.; Canals, D.; Snider, A. J.; Lin, R. Z.; Hannun, Y. A.; Clarke, C. J.","institution":"Stony Brook University","category":"cell biology","date":"2026-05-28","abstract":"Cardiotoxicity is a major side effect of Doxorubicin (Dox) that has hampered its clinical utility, and strategies to mitigate this cardiotoxicity are limited. Sphingolipids (SL) are central to the chemotherapy response in cancer but their role in normal tissue is less clear. Here, we identified the SL enzyme neutral sphingomyelinase-2 (nSMase2) as a critical mediator of chronic Dox-induced cardiotoxicity, establishing nSMase2 as a key downstream effector of Dox in cardiomyocytes (CM) and showing that in vivo loss of nSMase2 activity is protecting against chronic Dox-induced cardiac damage and dysfunction. Biologically, these studies link nSMase2 with Dox-induced CM senescence both in vitro and in vivo and identify the dual specificity phosphatase DUSP4 as a novel effector of nSMase2 in the Dox response. In addition to cementing a role for SL metabolism in Dox effects in normal tissue, this study advances nSMase2 as a target of interest for cardioprotection."}},{"id":"10.1101/2025.11.25.690431","title":"Mitochondrial pull-outs are a distinct type of dynamic tubulation events regulated by mitochondrial activity","subtitle":"Marc Germain · UQTR · 2026-05-28","value":"cell biology","href":"https://doi.org/10.1101/2025.11.25.690431","props":{"doi":"10.1101/2025.11.25.690431","authors":"Kasmaie, A.; Gatti, P.; Ilamathi, H. S.; Gueye, S. M.; Brown, A. I.; Manor, U.; Germain, M.","institution":"UQTR","category":"cell biology","date":"2026-05-28","abstract":"Mitochondrial networks undergo continuous remodeling through fusion and fission, processes that are essential for maintaining energy production and cellular homeostasis. Rapid elongation of the tip of mitochondrial tubules, a process termed dynamic tubulation, also participates in mitochondrial network formation. However, these mechanisms alone cannot fully account for the formation of highly interconnected mitochondrial networks that are required for rapid distribution of mitochondria material. Here, we identify a distinct type of dynamic tubulation, mitochondrial pull-outs characterized by the lateral extrusion from pre-existing mitochondrial tubules, as metabolically regulated determinants of mitochondrial network formation. Pull-outs are distinct from the tip elongation form of dynamic tubulation as they are modulated by the mitochondrial dynamins MFN1 and DRP1 and are stimulated by conditions favoring oxidative phosphorylation. Pull-outs also depend on mitochondrial actin polymerization and are required to increase mitochondrial connectivity and respiratory activity. Together, these findings establish mitochondrial pull-out as a metabolically sensitive mechanism that promotes mitochondrial network connectivity and links organelle architecture to cellular energy demands."}},{"id":"10.1101/2025.11.11.687834","title":"Simple Methods to Acutely Measure Multiple Timing Metrics among Sexual Repertoire of Male Drosophila","subtitle":"Woo Jae Kim · Harbin Institute of Technology · 2026-05-28","value":"developmental biology","href":"https://doi.org/10.1101/2025.11.11.687834","props":{"doi":"10.1101/2025.11.11.687834","authors":"Song, Y.; Miao, H.; Sun, D.; Liu, X.; Jiang, F.; Yang, X.; Kim, W. J.","institution":"Harbin Institute of Technology","category":"developmental biology","date":"2026-05-28","abstract":"Male Drosophila courtship behavior is a key model for studying temporal decision-making. While courtship index (CI) is widely used to quantify mating activity, other timing metrics like courtship latency, copulation latency (CL), and mating duration (MD) remain understudied. Traditional methods for quantifying these behaviors are often labor-intensive and prone to human error.\n\nIn this study, we present a protocol combining a modular chamber system and automated software (DrosoMating) to quantify 6 key timing metrics during male courtship. Our image-based video analysis enables precise identification of courtship and copulation events, as well as quantification of their timing and duration under controlled conditions. Validation shows <0.05% error rates and 98-99% agreement with manual scoring for CL, CI, and MD. The protocol supports genetic and neural circuit manipulations, detecting subtle genetic, social, and environmental behavioral variations.\n\nBy minimizing manual effort and standardizing data collection, this approach facilitates scalable, reproducible studies on adaptive trade-offs, learning, and neural mechanisms in mating behavior. This method streamlines timing analysis in male courtship, offering reproducible metrics for behavioral genetics.\n\nHighlightA high-throughput software pipeline for automated temporal profiling of Drosophila melanogaster mating behavior after brief user-guided calibration.\n\nAn accompanying, open-hardware platform that can be assembled at minimal cost while maintaining experimental rigor.\n\nThe system attains near-manual accuracy and outputs Temporal Measurement Parameters data that are readily adaptable to--and quantifiable within--diverse behavioral paradigms."}},{"id":"10.64898/2026.05.25.727670","title":"Is the winter survival area of Empoasca fabae continuously expanding?","subtitle":"Edel Pérez-López Sr. · Université Laval · 2026-05-28","value":"ecology","href":"https://doi.org/10.64898/2026.05.25.727670","props":{"doi":"10.64898/2026.05.25.727670","authors":"Almeida Santos, A.; Perez-Lopez, E.","institution":"Université Laval","category":"ecology","date":"2026-05-28","abstract":"O_LIEmpoasca fabae is a migratory pest that overwinters in the Southeastern United States (US) and damages crops throughout its summer range in North America. Its spring arrival has advanced by 9.7 days between 1951 and 2012, and increased damage is linked to warmer conditions that accelerate host and pest development. Yet whether this advance is also associated with a northward expansion of its winter survival area remains an open question.\nC_LIO_LIHere, we analyzed 126 years of minimum temperature data across the contiguous US to address this question. Using its winter survival threshold (-9{degrees}C), we calculated the annual winter survival area for E. fabae (temperature-only) and tested for time-series trends. We also mapped the potential overwintering area (temperature + winter hosts) under evergreen and pine-only forest scenarios.\nC_LIO_LIThe estimated winter survival area varies over 126 years, showing a nonlinear pattern. However, we found no significant trend, change-point year, or rate of change. This lack of significance was also observed when considering the 1951-2012 period.\nC_LIO_LIThe Southeastern US remained consistently suitable for winter survival, while the northern edge varied latitudinally, especially within the range of 35{degrees}-40{degrees}N, with no clear trend.\nC_LIO_LIPotential overwintering areas extend into Central Florida and the Texas Gulf Coastal Plain but exclude parts of Tennessee. In the pine-only scenario, the area in Mississippi and Alabama would be smaller.\nC_LIO_LIThe winter survival area for E. fabae has not continually expanded. The Southeastern US area remains suitable for over 126 years, whereas the northern range varies dynamically.\nC_LI\n\nGRAPHICAL ABSTRACT AND HIGHLIGHTS\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC=\"FIGDIR/small/727670v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@150ac82org.highwire.dtl.DTLVardef@16dc3e6org.highwire.dtl.DTLVardef@1583e14org.highwire.dtl.DTLVardef@53cf3b_HPS_FORMAT_FIGEXP  M_FIG C_FIG O_LIThe winter survival zone (temperature only) of Empoasca fabae has not expanded continuously over the past 126 years.\nC_LIO_LIThe Southeastern United States remained suitable over this period, with the maximum northward extent of potential survival reaching 45{degrees}N and high variation within the range of 35{degrees}-40{degrees}N.\nC_LIO_LIUpdated potential overwintering zones (temperature + winter hosts) extend into Central Florida and the Texas Gulf Coastal Plain.\nC_LI"}}],"count":30,"generated_at":"2026-06-04T06:43:13.912Z","cached":true}