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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

Structural characteristics of important daily movement corridors for waterbirds in urban areas: A case study on Black-headed Gulls

Landscape management facilitating animal movement is essential for sustaining urban wildlife populations and ecosystem services. Although linear vegetation corridors effectively conserve terrestrial animal movements, it remains unclear which landscape elements serve as pathways for aquatic organisms. Urban waterbirds frequently utilize rivers, but the specific characteristics that render certain river segments crucial as movement corridors have yet to be elucidated. This study aims to identify the characteristics of river segments functioning as critical corridors based on waterbird movement strategies. We tracked the movement behaviors of the Black-headed Gull (Chroicocephalus ridibundus), a river-dependent species in daily movements, and identified key movement corridors in highly urbanized Tokyo, Japan. Using GPS tracking data from gulls, we evaluated how river sinuosity and surrounding feature heights influenced tendencies to follow rivers across various temporal scales and perceptual ranges. Furthermore, we predicted and mapped these tendencies across individual river segments in central Tokyo. Gulls tended to fly along river segments with tall features during instantaneous to mid-term decision-making. In contrast, they utilized straight channels for long-term decisions. Although results varied slightly depending on the spatial scale they can perceive, this overarching trend remained consistent. Furthermore, our model predicted that the lower reaches of the Sumida River serve as critical movement corridors. This predictive tendency was also highly robust across all time scales. While straightened river segments with high feature heights may provide unsuitable habitats for diverse taxa, we emphasize their ecological value and argue that they should be conserved as essential movement corridors for waterbirds.

ecology↗

bioRxiv2026

Mapping Light-Induced Conformational Dynamics of Pigeon Cryptochrome 4 by HDX-MS: Structural Transitions from Spin Pair Formation to Activated Conformational States

The navigational prowess of migratory birds is thought to arise from light-dependent radical-pair chemistry in cryptochrome 4 (CRY4), yet the slow structural transitions that couple photochemistry to signaling remain elusive. Here, we combine temperature-controlled steady-state UV-visible spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to elucidate the photochemical and conformational dynamics of pigeon CRY4 (ClCRY4). Steady-state measurements at 5-25 {degrees}C reveal that lower temperatures slow FAD photoreduction and prolong the FAD neutral semiquinone signaling state. This occurs without a solvent kinetic isotope effect, implicating a conformational change rather than proton transfer as the rate determining step in FAD neutral semiquinone formation. Simultaneous HDX-MS under blue-light exposure identifies protection near the FAD-binding site and C-terminal region. To enhance sensitivity, we developed a pump-probe HDX-MS approach at 10 {degrees}C. This reveals eight peptides (within the phosphate-binding loop, protrusion motif, electron-transfer-chain loops and C-terminal tail) that exhibit rapid ([≤]10 s) and sustained light-induced protection, delineating early conformational rearrangements as a prerequisite for FAD neutral semiquinone accumulation. The findings of slower onset HDX protection as well as a bimodal pattern of deuterium uptake in the phosphate-binding loop further identify a local redistribution of conformational substates on the time scale of the accumulation of the signaling species. Site specific mutagenesis within the CTT supports the findings, which lead to a model in which blue light triggers rapid clamping down of protein near the two regions of spin pair separation, followed by a rate limiting closure of a surface loop. The resolution of time-dependent structural transitions that follow photoactivation of CRY4 resolves the interface between quantum radical-pair formation and classical conformational changes, while providing an enhanced structural framework for the molecular events that underlie avian magnetoreception.

biophysics↗

bioRxiv2026

Sensory-sleep dysfunction is a shared phenotype across genetically distinct neurodevelopmental disorder models

Sensory abnormalities and sleep disruption frequently co-occur in neurodevelopmental disorders (NDDs), but how sensory input interacts with sleep regulation in NDDs remains poorly understood. Here, we examined vibration-induced sleep (VIS), in which prolonged gentle vibration promotes sleep in Drosophila, in three genetically distinct NDD models: dNf1, dNrx1, and dFmr1. Despite markedly different baseline sleep phenotypes, all three mutants exhibited impaired VIS, identifying disrupted sensory-sleep integration as a shared phenotype across these NDD models. Behavioral responses to vibration, activity-associated CRTC signaling in Nanchung-positive (Nan+) mechanosensory neurons, and thermogenetic activation of Nan+ neurons revealed distinct underlying abnormalities across the three models, indicating that disruption at different points along the sensory-sleep axis can converge on the same behavioral phenotype. The effect of mechanosensory stimulation was also strongly shaped by homeostatic sleep drive: following sleep deprivation, vibration promoted sleep in dNf1 mutants, remained ineffective in dNrx1 mutants, and opposed recovery sleep in dFmr1 mutants. Together, these findings identify impaired sensory regulation of sleep as a point of convergence across genetically distinct NDD models and demonstrate that the expression of this shared phenotype depends on internal state.

neuroscience↗

bioRxiv2026

PathFold: Predicting the Entire Protein Folding Pathway from Protein Sequence Alone

Recent advances in protein structure prediction, exemplified by AlphaFold, have largely addressed the determination of static structures, one aspect of the protein folding problem. However, predicting folding pathways, by which proteins reach their native states, remains a significant challenge. Here, we present PathFold, a deep learning framework that predicts protein folding pathways directly from sequence information. PathFold leverages an AlphaFold-based module to extract structural information from the sequence and generates a progressive folding trajectory from an extended conformation using a diffusion model. By modeling the full trajectory, it enables prediction of folding intermediates and transition pathways, analogous to those observed in steered molecular dynamics (SMD) simulations. The predicted pathways reveal well-defined intermediates and sequential folding events, and show agreement with experimental folding data, including measured {Phi}-values.

bioinformatics↗

bioRxiv2026

Beyond benchmark accuracy: machine-learning turnover-number predictors require system-level validation

Enzyme turnover numbers (kcat) are essential for kinetic models and enzyme-constrained genome-scale metabolic models (ecGEMs), but measured values are sparse and therefore increasingly estimated using machine learning (ML). Although these predictors are commonly evaluated by global regression metrics, their practical utility depends on how errors propagate through downstream models. We benchmarked six current kcat predictors on a curated BRENDA-derived dataset and five of them on EnzyExtract. To assess the influence of training-set proximity, we compared each benchmark dataset with the available training data for each predictor. We then used the predicted kcat values to parameterize ecGEMs of Saccharomyces cerevisiae and evaluated growth predictions across 19 conditions. We find that benchmark accuracy is moderate even on the BRENDA-derived dataset and drops sharply on EnzyExtract, where all predictors achieve R2 values of 0.20 or lower. This decline is accompanied by substantially lower overlap between the benchmark and training datasets, with exact sequence matches ranging from 24% to 78% for BRENDA, compared with 9% to 26% for EnzyExtract. However, that overlap alone does not explain differences in generalization across predictors. Moreover, downstream performance is also not explained by benchmark ranking. Across 19 conditions, none of the tool-specific ecGEMs consistently reproduces the experimentally observed variation in growth. In glucose minimal medium, the weakest benchmark performer yields the most accurate growth prediction in the downstream ecGEMs, whereas higher-ranked predictors produce larger deviations in growth. We trace this mismatch to localized errors at high-leverage positions in yeast's metabolic network, where underpredicted mitochondrial ADP/ATP carrier turnover numbers restrict adenine nucleotide exchange and impose an apparent limitation on cytosolic ATP supply. Relaxing this constraint shifts predicted growth toward the experimental reference. Thus, ML-derived kcat values can affect not only quantitative growth predictions but also the phenotype a mechanistic model appears to identify. These results argue for application-driven validation of biological parameter predictors in the downstream systems they are intended to support.

bioinformatics↗

bioRxiv2026

Paternal regulation of H3K4 methylation supports tumor suppressor networks in mammals intergenerationally

Paternally-inherited epigenetic information can influence phenotype in offspring (1). Here, we identify a critical mechanistic contribution of KDM6A (UTX), an X-linked histone modifier and tumor suppressor, in regulating transmissible epigenetic information in mammalian sperm. Paternal loss of KDM6A increases cancer risk in genetically wild type offspring, but how Kdm6a knockout sperm transmit this effect at the molecular level is unknown (2). We find that KDM6A functions in spermatogenesis to promote methylation of histone H3 lysine 4 (H3K4) via selective interaction with the COMPASS complex methyltransferase KMT2C (MLL3). KMT2C and KDM6A are coordinately recruited to promoters of active genes in spermatogenic cells, contrasting with recruitment to intergenic enhancers in other cell types (3, 4). Loss of KDM6A disrupts H3K4 methylation at promoters of tumor suppressor genes in spermatogonia, and some of these defects persist in epididymal sperm and correspond to impaired expression in preimplantation embryos. These genes are also misregulated in normal and malignant hematopoietic tissue of genetically wild type offspring, indicating that impaired H3K4 methylation in KDM6A-deficient male germ cells may preferentially alter regulation of tumor suppressor gene networks in development across generations.

genetics↗

bioRxiv2026

Snapshots from the Catalytic Landscape of Chalcone Isomerase

Chalcone isomerase (CHI) catalyzes the cyclization of 3-ring scaffolds of flavonoids, a class of plant-based natural products important for nutrition and disease prevention. A persistent question has been whether the enzyme uses dynamics to facilitate conformational rearrangements of substrates within the active site. To help resolve this question, CHI was crystallized with phloretin, a flexible substrate analogue that cannot undergo cyclization. The crystal structure possesses eight protein molecules per asymmetric unit, revealing different active site conformations that accommodate different bound conformers of phloretin. Together, the structural snapshots depict a series of coordinated, dynamic chemical interactions that lower barriers to substrate rearrangements approaching bond formation. Differential scanning fluorimetry combined with mutational analysis and enzyme kinetics further confirm that phloretin binds to the enzyme active site and that it acts as a competitive inhibitor of CHI. Together these findings answer outstanding questions about the flexibility and dynamics of CHI catalysis, information that may be useful for future biosynthetic design and enzyme engineering goals. Overall, this work supports a catalytic model in which the CHI enzyme operates as a dynamic ensemble of structures necessary to facilitate catalytic substrate rearrangements.

biochemistry↗

bioRxiv2026

GABAB Receptors Gate Sex-Specific Synaptic Plasticity in the Nucleus Accumbens

Excitatory synaptic plasticity within the nucleus accumbens (NAc) drives motivated behaviors, and dysregulation is implicated in several psychiatric disorders marked by impaired reward processing. The NAc integrates glutamatergic input, which conveys information about reward, context, and behavioral goals, with local GABAergic signaling that regulates excitatory transmission and medium spiny neuron (MSNs) output. However, little is known regarding GABA-dependent modulation of activity-dependent excitatory synaptic plasticity. Here, we investigated GABAB receptor (GABABR) regulation of plasticity at hippocampus (Hipp)-NAc synapses, at which plasticity is a key mediator of reward-related behaviors. Using whole-cell electrophysiological recordings in mouse brain slices, we found that pharmacological inhibition of GABABRs converts long-term potentiation (LTP) into long-term depression (LTD) selectively in females, identifying a sex-specific role for GABABRs in modulating long-term plasticity of Hipp-MSN synapses. This LTD required mGluR5 activation and estrogen receptor alpha (ER) in both D1- and D2-expressing MSN subtypes, while only D1-MSNs suggested that LTD was expressed presynaptically through a CB1 receptor-dependent mechanism. Notably, GABABR inhibition did not alter basal synaptic transmission, indicating a specific role for these receptors in gating plasticity beyond regulation of basal excitatory drive. Together, these findings identify a novel, sex-specific mechanism by which GABABRs control the direction of synaptic plasticity.

neuroscience↗

bioRxiv2026

RSV competes with the host for translational machinery without a host shutoff strategy

RNA viruses often enhance ribosome recruitment to their own mRNAs through non-canonical sequence elements or by degrading host mRNA. Respiratory syncytial virus (RSV) produces mRNAs with host-like features, including 5'-cap and poly(A) tail. Therefore, the virus lacks an obvious mechanism to preferentially protect its own mRNAs or recruit ribosomes. Furthermore, it remains unknown how RSV interacts with antiviral defense pathways that would reduce cap-dependent translation. Using spike-in normalized sequencing of total and ribosome-associated RNA, we found that RSV does not appear to evoke any host shutoff mechanisms to limit the expression of host genes. These findings show that RSV manages to make use of available ribosomes by competing effectively with host mRNAs and any translational shutoff mechanism would be detrimental. Consistent with this, we found that following activation of antiviral host pathways that reduce cap-dependent translation, translation of RSV mRNAs is decreased to the same extent as host mRNAs. Furthermore, we found that RSV infection does not trigger the dsRNA-activated kinase PKR (which initiates the ISR) and OAS (activates endonuclease RNase L) pathways. These data support a model in which RSV achieves viral protein production, not though inhibiting the host, but by successfully competing with host mRNAs and avoiding activation of antiviral pathways.

molecular biology↗

bioRxiv2026

An M-learner approach for heterogeneous mediation analysis with high-dimensional omics mediators

Causal mediation analysis is widely used to identify biological pathways linking exposures to outcomes, but most methods assume homogeneous mediation effects across individuals. In high-dimensional omics settings, this assumption can mask important heterogeneity driven by demographic, genetic, or environmental factors. We propose the M-high-learner, a flexible framework for detecting heterogeneous mediation effects with high-dimensional mediators. The method identifies mediators with subgroup-specific indirect effects while distinguishing them from null or homogeneous signals and controlling the type I error rate. It is computationally efficient, scalable, and yields interpretable sub-types. Simulation studies show that the proposed approach achieves high power while maintaining accurate error control. Applications to the Framingham Heart Study and the Multi-Ethnic Study of Atherosclerosis reveal that the mediation role of gene expression in sexs effect on high-density lipoprotein varies across subgroups defined by body mass index and age. Our framework provides a practical tool for uncovering heterogeneous biological mechanisms in high-dimensional genomic studies. Author SummaryBiological processes linking risk factors to disease often differ across individuals, but many existing methods assume these processes are the same for everyone. This can hide important differences between groups. We developed a powerful method to identify when these pathways vary across subgroups using large-scale molecular data. Our approach detects differences in how intermediate biological factors contribute to outcomes in populations defined by characteristics such as age and body mass index. Applying our method to population studies, we found that some biological pathways operate differently across groups, suggesting that key mechanisms may be missed when differences are ignored. Our work provides a tool to better understand how disease-related processes vary across individuals, which may support more targeted and personalized approaches to health research.

bioinformatics↗

bioRxiv2026

Starvation improves epithelial fitness by selectively extruding DNA damaged cells

During homeostasis, crowded cells with the lowest energy levels are eliminated by extrusion via Piezo1 signalling to maintain constant cell numbers. However, crowding-induced extrusion does not necessarily remove damaged or otherwise unfit cells. Here, we show that glucose or glutamine starvation triggers a rapid, regulated wave of extrusion, called starvation-induced cell extrusion (STICE), that selectively eliminates cells bearing DNA damage markers via a p53-dependent, Piezo1-independent pathway, improving monolayer fitness. Unlike non-extruding cells, which recycle contents through autophagy and lysosomal digestion, p53-activated cells instead use LC3 to drive lysosomal exocytosis, promoting extrusion signalling. By eliminating defective and transformed cells, STICE confers resistance to damage and apoptotic stimuli in the remaining monolayer. STICE thus acts as a tissue-level analogue of autophagy: rather than improving individual cells by digesting and recycling damaged components, it improves tissue fitness by eliminating substandard cells.

cell biology↗

bioRxiv2026

IKK2/β mediated phosphorylation of transcription factor Ets2 at site(s) distal to DNA binding domain negatively modulates its DNA binding activity

Transcription factor Ets2 coalesce with the NF-{kappa}B pathway to regulate gene expression in specific signaling contexts. IKK2/{beta}-mediated phosphorylation events critically regulate the NF-{kappa}B pathway. However, any link between Ets2 and IKK2 remains elusive. Here we report Ets2 as a direct substrate of IKK2. In-vitro kinase assays using deletion constructs, high resolution MS-MS and site directed mutagenesis identified S295 as a prominent phosphorylation site distal to the DNA binding domain, substitution of which to phosphor-mimetic Glutamate triggers further phosphorylation of Ets2. MD simulations clearly indicate conformational constriction of the otherwise disordered N-terminal region and inhibition of DNA binding activity upon phosphorylation, which was further confirmed by Electrophoretic mobility shift assays. Our results uncover a phosphoregulatory connection between Ets2 and IKK2.

biochemistry↗

bioRxiv2026

The Gordian Knot Enhances Ubiquitin Binding in UCH-L1

UCH-L1 is a monomeric deubiquitinating enzyme whose native structure embeds a shallow $5_2$ knot located near the N-terminus, placing the knotted topology in direct proximity to both the substrate-binding pocket and the catalytic site. While our previous work established that N-terminal integrity is critical for catalytic activity, the energetic cost of unknotting and its structural consequences remained unquantified. Here, we combine steered molecular dynamics with an umbrella sampling scheme to generate topologically modified variants of UCH-L1 and, for the first time, reconstruct the free-energy profile of UCH-L1 unknotting. The potential of mean force reveals a steep energetic barrier to knot disruption, consistent with knotting being a late, rate-limiting folding step that is effectively locked in once the native structure is established. Long unbiased MD simulations of fully unknotted variants in both apo and holo states show that knot removal increases local flexibility at the N-terminus without inducing significant global structural destabilization. Binding energy calculations indicate that the unknotted variant binds to ubiquitin less tightly than the wild-type ($\sim$-62~vs~$\sim$-76~kcal/mol), suggesting that topological integrity contributes to substrate affinity. Together, these results show that the $5_2$ knot in UCH-L1 is not a passive structural feature but a functional element that fine-tunes folding kinetics and contributes to substrate binding efficiency.

biophysics↗

bioRxiv2026

The pursuit of motivational goals reduces pain through an opioidergic mechanism

Pain promotes protective behavior but can interfere with other biologically important goals. Survival may require overcoming pain to obtain rewards, secure resources or escape danger, yet evidence for pain modulation by competing demands and endogenous modulatory systems during goal pursuit is lacking. We developed a paradigm in which participants chose whether to pursue monetary rewards despite painful heat stimulation during fMRI, under placebo or opioid receptor blockade with naloxone. Actively pursuing motivational goals during painful stimulation reduced perceived pain and increased fMRI signal in pain-modulatory cortical regions, including multiple subregions of the rostral anterior cingulate cortex (rACC) and dorsolateral prefrontal cortex, alongside enhanced rACC-periaqueductal gray coupling, consistent with recruitment of the descending pain modulatory system. Behavioral and neural effects were attenuated by naloxone, supporting a mediating role for endogenous opioids. These findings provide convergent evidence that active goal pursuit engages opioidergic pain modulatory mechanisms to reduce pain in humans.

neuroscience↗

bioRxiv2026

CREST: A Cortical Resting-State EEG Spatial Transformer for Chronic Pain Inference

Chronic pain mechanisms are complex, spanning multiple brain regions and networks. We ask whether resting brain activity carries a readout of that state. From a few minutes of resting-state electroencephalography (EEG), we generate a spectrogram to represent how each region of the cortex oscillates across frequency and time and pass it through CREST (Cortical Resting-state EEG Spatial Transformer): a frozen image-recognition network that reads each region as an image--here, a spectrogram--paired with a graph model that weighs the 56 cortical regions together to classify chronic-pain status. Across 125 people (74 with chronic pain, 51 healthy controls), evaluated through a leave-one-subject-out cross-validation, CREST separates the two groups with an area under the receiver operating characteristic curve (AUROC) = 0.782 (permutation p < 0.005). Control experiments implicate each persons individual alpha rhythm. Clinical relevanceA resting-state EEG readout of chronic MSK pain could clarify pathophysiology and inform treatment.

neuroscience↗

bioRxiv2026

Using sequence-to-function models to interpret archaic hominin introgression

Understanding the functional impact of archaic hominin introgression remains challenging due to the poor representation of global introgression in publicly available genomics resources. Sequence-to-function models can predict the effects of any possible variant in the human genome and may fill this gap. Here, we used AlphaGenome to predict the effects of 144,139 introgressed SNPs segregating in present-day individuals of Papuan genetic ancestry. AlphaGenome's chromatin accessibility predictions recapitulate experimentally observed effects, but gene expression performs no better than chance. Predictions correlate more strongly with an independent reporter assay of single-variant activity than with the same variants' effects in live cells, indicating that AlphaGenome captures the regulatory potential of individual variants more reliably. Predictions carry tissue specificity, allowing us to predict specific tissues potentially impacted by introgressed haplotypes. We identify genes, including JAK1 and TAB2, that are associated with haplotypes that contain an excess of variants predicted by AlphaGenome to have large impacts on chromatin accessibility. Finally, we highlight the challenges and limitations associated with using sequence-to-function models for introgressed variant effect prediction, and show that while AlphaGenome's chromatin accessibility predictions can aid in prioritising candidate functional regions, expression predictions and the assignment of variants to target genes remain as open challenges.

genomics↗

bioRxiv2026

Behavioral signatures suggest distinct modes of suppressing irrelevant information during tactile temporal attention in human participants

To make adaptive perceptual judgments, the nervous system must selectively process behaviorally relevant sensory information while filtering out competing distractions. Although attentional control has been extensively studied in the visual domain, particularly in the context of spatial selection, considerably less is known about how attention operates in the tactile modality and across time rather than space. Here, we developed a paradigm to investigate temporal tactile attention in human participants, enabling the study of attentional behavior and underlying behavioral strategies in this sensory domain. Participants were instructed to categorize the intensity of a task-relevant tactile stimulus delivered to the fingertip while ignoring an irrelevant tactile stimulus. A visual cue indicated which of two sequentially presented stimuli was relevant on each trial. In addition, participants completed self-report questionnaires assessing autistic traits and aberrant salience (the tendency to assign significance to otherwise neutral stimuli or events). Across subjects, participants performed the task with high accuracy. However, clustering analyses based on behavioral features revealed distinct response profiles. One cluster did not exhibit biases induced by the irrelevant stimulus. In contrast, a third cluster displayed a repulsive effect of the irrelevant stimulus and showed lower overall performance. These behavioral phenotypes were also reflected, to some extent, in differences in learning trajectories across training sessions. We further explored participants' metacognitive awareness through a post-experiment questionnaire assessing subjective evaluations of task difficulty and performance. Although exploratory, the results suggest a relationship between metacognitive reports, behavioral strategies, and objective task performance. In contrast, neither autistic traits nor aberrant salience scores were associated with performance measures or behavioral phenotypes. Together, these findings support the view that attentional control is implemented through multiple, individualistic behavioral strategies rather than a single mechanism pertaining to all, suggesting that task structure interacts with individual predispositions to shape distinct modes of attentional control in human participants.

neuroscience↗

bioRxiv2026

X-inactivation escapee domains are CTCF-cohesin independent chromatin compartments

X-chromosome inactivation involves chromosome-wide gene silencing accompanied by extensive chromatin changes, as well the loss of topologically associating domains. Yet discrete regions of the inactive X chromosome retain activity within localised 3D domains, which contain active genes that variably escape from X inactivation. The transcription factor and architectural protein CTCF has been proposed to be implicated in escape by insulating escape domains or sustaining their topology via cohesin-mediated loop extrusion. Here, we test the role of CTCF and cohesin in escape using acute degron-mediated depletion of CTCF and RAD21 in neural progenitor cells with established escape profiles. Although CTCF occupancy correlates with escape status on the inactive X chromosome, its removal - together with loss of loop extrusion - does not disrupt escapee gene expression, or domain organization, nor does it result in spreading of silencing or activation of genes in cis. Rather, we show that facultative escape regions are self-sustaining compartments of active chromatin enriched in H3K27 acetylation and depleted in H3K27 methylation, with the magnitude of compartment strength scaling up with the degree of transcriptional activity on the inactive X chromosome. These active escapee compartments are propagated independently of CTCF and RAD21-dependent 3D architecture. Our findings identify chromatin compartmentalization as the primary feature of facultative escapee domains.

genetics↗