{"messages":[{"status":"ok","category":"all","interval":"2026-05-01:2026-05-05","cursor":0,"count":30,"count_new_papers":"659","total":"896"}], "collection":[{"title":"Sex-specific organization and synaptic signaling in prefrontal-hypothalamic circuitry","authors":"Bouchet, C. A.; Pinsinski, E. C.; Cook, J. C.; Vaaga, C. E.; Myers, B.","author_corresponding":"Brent Myers","author_corresponding_institution":"Colorado State University","doi":"10.64898\/2026.04.29.721673","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721673.source.xml","abstract":"Top down signaling from the cortex to the hypothalamus is critical to link cognitive and emotional processing to homeostasis and motivation. This study investigates signaling from the medial prefrontal cortex (mPFC) to the posterior hypothalamus (PH), a region that modulates endocrine and autonomic stress responses and motivated behaviors. The function and anatomy of this circuit was examined with patch clamp electrophysiology and mapping studies in male and female rats. Spontaneous firing properties of PH neurons were determined in a cell-type specific manner by combining a transgenic glutamic acid decarboxylase-Cre rat with Cre-dependent colorswitch virus to determine postsynaptic cell-type identity. Overall, PH neurons were more excitable in females compared to males and, in both sexes, data indicated tonic inhibition within the PH, with significantly greater inhibition in males. Using Channelrhodopsin-assisted circuit mapping to query the mPFC-PH circuit, we found that a majority of PH neurons received input from the mPFC and mPFC synapses targeted glutamatergic cells over GABAergic PH cells. Retrograde tracing revealed more PH-projecting neurons in females, specifically within the tenia tecta and infralimbic regions of the mPFC, with significantly more stress-activated PH-projecting cells in the female prelimbic cortex. Anterograde tracing revealed, surprisingly, no sex differences in mPFC presynaptic terminal density in the PH, despite more PH-projecting cell bodies in the female mPFC. These data help to elucidate the sexual divergence in cortical-hypothalamic signaling and how cognitive and emotional information from the prefrontal cortex may differentially regulate homeostasis and motivation between sexes.\n\nSignificance StatementNeural signaling between the prefrontal cortex and the hypothalamus is important for maintaining homeostasis, particularly during contextual challenges such as stressors. Here we find multiple aspects of sex-specific organization and neurophysiology in this circuitry. Excitatory inputs from the medial prefrontal cortex target both excitatory and inhibitory neurons within the posterior hypothalamic nucleus in both sexes. However, there are sex differences in the number of stress-activated neurons in the prefrontal cortex that innervate the posterior hypothalamus, as well as differences in hypothalamic inhibitory signaling and estrous cycle-dependent effects on neuronal excitability. Altogether, these data suggest that organizational, synaptic, and hormonal factors may contribute to sex-specific behavioral and physiological integration.","published":"10.1523\/JNEUROSCI.0774-26.2026","server":"bioRxiv"},{"title":"Fiber-tract development contributes to functional specialization in the human hippocampus","authors":"Kember, J.; Tardif, C. L.; Baillet, S.; He, Y.; Audrain, S.; Barnett, A.; Riggins, T.; Chai, X.","author_corresponding":"Jonah Kember","author_corresponding_institution":"McGill University","doi":"10.64898\/2026.04.28.721442","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721442.source.xml","abstract":"Fiber-tracts exhibit distinct projection patterns along the anterior-posterior axis of the hippocampus, promoting a specialization in function. This specialization becomes increasingly pronounced throughout child development, with important implications for neurocognitive outcomes. Developmental changes in fiber-tract properties, including intra-axonal cross-sectional area and myelin content, may contribute to this anterior-posterior functional specialization. To test this, we developed a diffusion-MRI tractography pipeline to identify hippocampal fiber-tracts in single subjects, then examined whether age-related differences in total intra-axonal cross-sectional area and myelin content (T1w\/T2w) could predict functional specialization in a large cross-sectional sample (N=539, aged 5-21 years). With age, we found that the cross-sectional area of short-range medial-temporal tracts, which primarily target the anterior\/body of the hippocampus, exhibited rapid growth. Concomitantly, the cross-sectional area of long-range occipito-parietal tracts, which primarily target the posterior hippocampus, exhibited a modest pruning. Increases in myelin content were relatively homogenous across fiber-tracts. In support of our hypothesis, we found that the cross-sectional area of fiber-tracts significantly predicts the surface-area of an fMRI-defined posterior system; a sensitive marker of functional specialization in the hippocampus. Tracts targeting early visual cortex (V2, V3, V4) showed the strongest association, with statistical modeling indicating a mediating effect of early-visual tract development on the relation between age and functional specialization. These findings provide evidence consistent with a mechanism whereby anatomical neurodevelopment contributes to functional specialization in the human hippocampus.","published":"NA","server":"bioRxiv"},{"title":"Local translational repression and retention of SynGAP1 during synaptic plasticity","authors":"Livingstone, R. W.; Donlin-Asp, P. G.","author_corresponding":"Paul G Donlin-Asp","author_corresponding_institution":"Simons Initiative for the Developing Brain, Institute for Neuroscience and Cardiovascular Research, University of Edinburgh","doi":"10.64898\/2026.04.29.719691","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.719691.source.xml","abstract":"Synaptic plasticity depends on tightly controlled protein production, yet most locally synthesised synaptic proteins studied to date promote strengthening. Here, we investigate whether SynGAP1--a key negative regulator of Ras\/Rap signalling--undergoes local translation to constrain plasticity. We find highly regulated developmental distribution of SynGAP1 isoforms, with stable synaptic occupancy of 1, progressive enrichment of 2, and late dendritic accumulation of {beta}, with all isoforms positioned at the PSD. Despite abundant dendritic Syngap1 mRNA, nascent SynGAP1 translation is dynamically regulated, showing suppression during synaptic maturation. Contrary to the prevailing model, we find that activity-induced dispersion of SynGAP1 is an artefact of GFP overexpression, as the endogenous protein remains stably anchored at synapses following LTP induction. Instead, we uncover a transient, dendrite-specific suppression of SynGAP1 synthesis upon LTP induction. Our findings oppose the current model of SynGAP1 dispersion and identify translational repression as a key regulatory mechanism for synaptic SynGAP1. We propose that synapses transiently lift inhibitory constraints not by physically removing SynGAP1, but through its well reported inactivation and halting its local production.","published":"NA","server":"bioRxiv"},{"title":"Effects of bimodal divided attention on cortical representations of linguistic context during continuous speech perception in noise","authors":"Xie, Z.","author_corresponding":"Zilong Xie","author_corresponding_institution":"Florida State University","doi":"10.64898\/2026.04.28.721419","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721419.source.xml","abstract":"Speech perception often takes place in environments with competing sensory inputs, both within the auditory modality and across modalities; for example, following a conversation in a noisy cafe while simultaneously reading a menu. This study examined the extent to which dividing attention between auditory and visual modalities (bimodal divided attention) influences linguistic context processing across hierarchical levels during continuous speech perception in noise. Electroencephalographic (EEG) responses were recorded while participants listened to audiobook stories in multitalker babble as a secondary task, concurrently performing a demanding primary visual task that imposed either low or high cognitive load. Behaviorally, speech comprehension accuracy was significantly lower under high-load than low-load dual-task conditions. Multivariate temporal response function (mTRF) encoding models were used to predict EEG responses from information-theoretic measures (entropy and surprisal) indexing linguistic context at sublexical, word-form, and sentence levels. Significant neutral tracking was observed at the word-form and sentence levels, but not the sublexical level. Critically, neutral tracking of sentence-level linguistic representations was significantly reduced under high compared to low load, with effects emerging at latencies beyond 200 ms. In contrast, neutral tracking of word-form-level representations was unaffected by dual-task load. mTRF analyses further revealed that neutral tracking of acoustic features was not modulated by dual-task load. These findings indicate that bimodal divided attention selectively disrupts cortical representations of sentence-level linguistic context, while lower-level processing remains relatively preserved. Such impairments in higher-level linguistic processing may contribute to reduced speech comprehension during multitasking in noisy environments.","published":"NA","server":"bioRxiv"},{"title":"Linking human brain functional connectivity to underlying neurotransmission","authors":"Lotter, L. D.; Shafiei, G.; Larabi, D.; Koushik, A.; Dipasquale, O.; Mehta, M.; Cercignani, M.; Sethi, A.; Harrison, N.; Holiga, S.; Umbricht, D.; Yakushev, I.; Muthukumaraswamy, S.; Forsyth, A.; Hipp, J. F.; Misic, B.; Caspers, S.; Koenig, J.; Patil, K. R.; Paquola, C.; Eickhoff, S. B.; Dukart, J.","author_corresponding":"Leon D. Lotter","author_corresponding_institution":"Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Centre Juelich; Juelich, Germany.","doi":"10.64898\/2026.04.28.721294","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721294.source.xml","abstract":"The human brain is organized into interacting functional systems. Their underlying neurobiological mechanisms remain difficult to study in vivo. Here, we adopt a topological framework to quantify the association between neurobiology and brain functional connectivity derived from both resting-state fMRI and MEG. Across six healthy adult cohorts (n = 19-112), regional variation in fMRI connectivity robustly aligns with the distribution of neurotransmitter receptors and transporters. These patterns are present in every single subject, replicate across all cohorts, and are mirrored in MEG. Most prominently, noradrenergic modulation of connectivity in a sensorimotor-insular network is consistently detected across individuals and linked to autonomic arousal. In pharmacological and clinical samples, associations are sensitive to neurotransmitter system manipulation and are altered in early psychosis, aligning with clinical symptomatology. These findings provide biological insight into typical and atypical functional organization of the human brain using a framework linking underlying neurobiology to the functional connectome (NEOFC).","published":"NA","server":"bioRxiv"},{"title":"Spectrotemporal signatures of driving and modulatory circuits across cortical and subcortical networks","authors":"O'Connell, M. N.; Barczak, A.; Mackey, C. A.; McGinnis, T.; Mackin, K.; Smiley, J.; Bleiwas, C.; Lakatos, P. A.; Schroeder, C. E.","author_corresponding":"Monica N O'Connell","author_corresponding_institution":"Nathan Kline Institute","doi":"10.64898\/2026.04.29.721627","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721627.source.xml","abstract":"Sensory processing depends on interactions between neural circuits that convey and regulate information across cortical and subcortical networks. Classical frameworks distinguish driving inputs, which transmit sensory content via suprathreshold activation, from modulatory inputs, which alter neuronal excitability without directly eliciting spiking. However, physiological signatures of these circuit types that generalize widely across distributed brain regions remain unclear. Here, we functionally differentiate driving and modulatory circuits in the awake macaque brain by jointly quantifying suprathreshold multiunit activity (MUA) and oscillatory phase coherence (inter-trial coherence, ITC) across eight cortical and thalamic structures during auditory, visual, and motor sampling conditions. Preferred sensory stimuli elicited broadband ITC increases accompanied by robust MUA, yielding relatively uniform spectral distributions across adjacent frequency bands, consistent with driving inputs. In contrast, non-preferred sensory and motor-related events produced narrowband, frequency-specific ITC modulation without concurrent firing, and was characterized by dominant peaks at stimulation or event rates, which is consistent with modulatory inputs. This narrowband ITC modulation is indicative of coordinated phase alignment, capable of dynamically regulating information transfer, mediated by driving inputs, across thalamocortical circuits. These response types were observed within individual regions, revealing two separable modes of neural activity. These findings identify distinct spectrotemporal signatures of driving and modulatory activity and demonstrate that subthreshold oscillatory modulation is a widespread mechanism for coordinating multisensory and motor influences on perception.","published":"10.3389\/fnhum.2026.1868940","server":"bioRxiv"},{"title":"Brain signatures of semantic activation for words that do not exist.","authors":"Bonandrini, R.; Amenta, S.; Sulpizio, S.; Basso, G.; Marelli, M.; Tettamanti, M.","author_corresponding":"Rolando Bonandrini","author_corresponding_institution":"Department of Psychology, University of Milano-Bicocca","doi":"10.64898\/2026.04.29.721646","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721646.source.xml","abstract":"The experience of making sense of novel words is ubiquitous in human communication. Still, novel words have traditionally been considered as meaningless by cognitive research. Here we combined behavioral, univariate and multivariate fMRI techniques, and computational modelling to explore whether and how novel words activate the neurocognitive hallmarks of semantic processing triggered by existing words, and whether this process is influenced by the presence of familiar functional linguistic elements, i.e., morphemes. We observed that semantic activation for novel words is comparable to that of existing words, provided that novel words contain a concatenation of identifiable morphemes. In addition, representational similarity analysis highlighted that existing words and novel words containing morphemes (but not novel words not containing morphemes) can activate fine-grained semantic representations. These results suggest that the difference in the neurocognitive underpinnings of semantic processing for existing and novel words might be quantitative rather than qualitative and based on how reliably linguistic form points to meaning.","published":"NA","server":"bioRxiv"},{"title":"A flexible cross-correlation based population model of interaural time difference coding in barn owl's midbrain","authors":"Fischer, B. J.; Syeda, R. F.; Pena, J. L.","author_corresponding":"Brian J Fischer","author_corresponding_institution":"Seattle University","doi":"10.64898\/2026.04.29.721697","date":"2026-05-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721697.source.xml","abstract":"The cross-correlation model has long served as the standard computational framework for describing interaural time difference (ITD) processing in the barn owls auditory system. While successful in explaining initial sinusoidal responses at the site of coincidence detection in the nucleus laminaris, this previous standard model fails to capture the full diversity of ITD tuning observed in the inferior colliculus (IC), where neurons exhibit sharper-than-sinusoidal ITD tuning, nonlinear frequency integration, level-dependent gain control, and interaural level difference (ILD)-dependent modulation of ITD selectivity. Here we present a modified cross-correlation model that addresses these limitations through the addition of parameterized gain control, linear filters with inhibitory surround structure, static nonlinearities, and ILD-dependent modulation of the cross-correlation computation. We show that divisive gain control produces realistic rate-level functions, including non-monotonic responses. Furthermore, inhibitory weights in the linear filter, combined with a threshold or expansive nonlinearity, generate sharper-than-sinusoidal ITD tuning consistent with experimental observations. This model reproduces both linear and nonlinear two-tone frequency integration and demonstrates that independent variation of filter bandwidth and nonlinearity shape accounts for the experimentally observed lack of correlation between side-peak suppression and frequency tuning width across the neuronal population. In addition, ILD-dependent modifications to the model produce shifts in best ITD and reductions in ITD tuning strength, as observed in the lateral shell of the central nucleus of the IC. The model parameters can be efficiently determined using simulation-based inference, enabling generation of realistic neuronal populations. Thus, this flexible, analytically tractable framework provides a foundation for investigating population coding of auditory space in the owls midbrain.","published":"NA","server":"bioRxiv"},{"title":"Dorsal and ventral premotor cortices differentially influence contralateral motor cortex excitability","authors":"Allahverdloo, E.; Chiu, L. K.; O'Farrell, A.; Harroum, N.; Dancause, N.; Neva, J. L.","author_corresponding":"Jason L Neva","author_corresponding_institution":"Universite de Montreal","doi":"10.64898\/2026.04.29.721139","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721139.source.xml","abstract":"Dorsal (PMd) and ventral (PMv) premotor cortices can modulate contralateral primary motor cortex (M1) excitability, but their distinct interhemispheric influence via transcranial magnetic stimulation (TMS) remains unclear. Single-pulse TMS over PMd, PMv and M1 assessed transcallosal inhibition via the ipsilateral silent period (iSP). Dual-site TMS examined short-(10 ms inter-stimulus interval [ISI]), long-(50 ms ISI) and non-callosal-(0 ms ISI) interhemispheric inhibition (IHI). An iSP was elicited from PMd, PMv, and M1, with distinctly evoked iSP parameters. The iSP magnitude was greatest from M1, followed by PMd and then PMv, while iSP duration was greatest for M1 and showed no differences between PMd and PMv. Dual-site TMS revealed that PMd and M1 inhibited contralateral M1 excitability across all ISIs, while PMv showed inhibition at 0-and 50-ms ISIs. PMd and M1 demonstrated greater short-IHI compared to PMv, all demonstrating similar long-IHI, and PMd demonstrating greater non-callosal-IHI than M1. PMv displayed distinct IHI across ISIs, PMd showed differences across most ISIs and M1 demonstrated the fewest differences across ISIs. Longer iSP duration related to greater long-IHI magnitude elicited from PMd and PMv. Our findings demonstrate differential IHI from PMd and PMv on contralateral M1, which may inform neuromodulation strategies in rehabilitation contexts.","published":"NA","server":"bioRxiv"},{"title":"Melatonin Partially Attenuates Oxycodone-Induced Placental Stress Signaling and Fetal Brain Apoptosis in a Sex-Specific Manner.","authors":"Adediji, I. O.; Kamra, K.; Kowash, H. M.; Nouri Mousa, P.; Aloba, C. O.; Schaal, V. L.; Davis, J. S.; Peeples, E. S.; Pendyala, G. N.; Harris, L. K.","author_corresponding":"Lynda K Harris","author_corresponding_institution":"University of Nebraska Medical Center, Omaha","doi":"10.64898\/2026.04.29.721662","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721662.source.xml","abstract":"BackgroundMaternal oxycodone (oxy) exposure can disrupt placental function and fetal neurodevelopment, but the molecular mechanisms remain unclear. We investigated whether prenatal oxy exposure activates inflammation and stress response pathways in the placenta and fetal brain, and if maternal melatonin supplementation attenuates these effects.\n\nMethodsFemale Sprague-Dawley rats received either saline or oxy via oral gavage for 15 days before mating (10-15mg\/kg\/day dose escalation) and throughout pregnancy (15mg\/kg\/day). From gestational day (GD) 12.5, half of the dams received melatonin (10mg\/kg\/day). On GD 19.5, placental and fetal brain tissues were collected. Changes in expression of markers of oxidative stress, antioxidant defense signaling, inflammation, ER stress, and apoptosis were assessed by western blotting. Data were analyzed by two-way ANOVA with Tukeys post hoc test.\n\nResultsNeither oxy exposure nor melatonin treatment increased markers of oxidative stress or antioxidant defenses in the placenta and fetal brain. Oxy exposure increased placental IL-1{beta} expression but did not alter expression of the other inflammatory markers examined. Oxy increased phosphorylation of eIF2 and increased the phospho-eIF2:eIF2 ratio in the placentas of male fetuses, and fetal brains of both sexes. CHOP expression was increased in the placentas and brains of female, but not male fetuses after oxy exposure. Oxy exposure increased levels of cleaved caspase-3 and cleaved caspase-9 in the fetal brain, but not the placenta; melatonin treatment attenuated the oxy-induced increase in cleaved caspase-9, but not cleaved caspase-3.\n\nConclusionPrenatal oxy exposure induced a modest inflammatory response in the placenta and activated the integrated stress response and intrinsic apoptotic signaling in the fetal brain. Maternal melatonin supplementation partially mitigated the oxy-induced upregulation of caspase-9 but did not prevent stress signaling in either tissue. These findings demonstrate the presence of sex-specific placental and fetal brain responses to prenatal oxy exposure but suggest that melatonin may not provide complete protection against oxy-induced neurodevelopmental impairment.","published":"NA","server":"bioRxiv"},{"title":"HERVs as building blocks of RNA regulatory architecture in the human genome","authors":"Montserrat-Ayuso, T.; Pujol, A.; Esteve-Codina, A.","author_corresponding":"Anna Esteve-Codina","author_corresponding_institution":"CNAG","doi":"10.64898\/2026.04.29.721355","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721355.source.xml","abstract":"Human endogenous retroviruses (HERVs) comprise nearly 8% of the human genome and have contributed extensively to gene regulatory evolution. However, their roles in RNA-centered regulatory processes remain poorly characterized. Here, we present a genome-wide annotation of RNA regulatory features embedded within HERV internal regions and long terminal repeats (LTRs), revealing that HERV sequences act as pervasive components of the human transcriptome. Systematic analysis of RNA-binding protein (RBP) motifs uncovers structured, family-specific regulatory architectures, with distinct RBP signatures distinguishing major HERV subfamilies. Notably, HERVH elements are enriched for RBPs associated with developmentally regulated RNA processing, whereas HERVK (HML-2) elements preferentially harbor motifs linked to canonical splicing and mRNA maturation. Integration with gene annotations reveals widespread incorporation of HERV sequences into transcript structures, including more than 4,000 long non-coding RNAs. Conserved retroviral protein domains within predicted open reading frames are strongly enriched in terminal exons and 3' untranslated regions, consistent with potential micropeptide-encoding capacity. In addition, we identify a subclass of lncRNAs largely composed of HERV sequence, indicating that endogenous retroviral loci have been extensively captured within annotated transcripts. Finally, we detect more than 6,500 antisense LTR insertions in transcript termini, defining widespread SPARCS-like (stimulated 3 prime antisense retroviral coding sequences) configurations with potential for double-stranded RNA formation and preferential association with immune-related genes. Together, these results establish HERV sequences as a pervasive layer of RNA regulatory potential embedded within human transcripts, highlighting previously underappreciated roles in post-transcriptional gene regulation.","published":"NA","server":"bioRxiv"},{"title":"The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications","authors":"Tsepilov, Y. A.; Suveges, D.; Considine, D.; Szyszkowski, S.; Ge, X. J.; Lopez Santiago, I.; Rusina, P.; Alegbe, T.; Ho, V. W.; Tsukanov, K.; Roldan-Romero, J. M.; Smit, I. A.; Cornu, H.; Harris, L.; Alasoo, K.; Predeus, A.; Lessard, S.; Chatelain, C.; Khader, S.; Yang, S.; O'Carroll, A.; Aulchenko, Y. S.; Seaton, D.; Buniello, A.; Birney, E.; Fauman, E. B.; McCarthy, M. I.; Hulcoop, D. G.; Trynka, G.; McDonagh, E. M.; Ochoa, D.","author_corresponding":"Yakov A. Tsepilov","author_corresponding_institution":"Wellcome Sanger Institute","doi":"10.64898\/2026.04.28.721048","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721048.source.xml","abstract":"Genetic support for drug targets substantially increases clinical success rates, establishing genome-wide association studies (GWAS) as central to therapeutic hypothesis generation. However, the same genetic evidence that reveals causal gene-disease relationships simultaneously exposes organism-level safety liabilities--a dimension requiring principled, genome-wide quantification. Here we systematically analyse 100,526 GWAS to yield 789,453 credible sets and gene prioritisations for 15,641 genes, with discovery showing no saturation as GWAS expand and increase diversity. We find that 64% of GWAS-implicated genes are pleiotropic, associated with traits across multiple diseases and showing a non-linear relationship between the degree of pleiotropy and clinical success. Highly pleiotropic genes--concentrated in immune, inflammatory, and oncogenic signalling programmes--are enriched in safety-terminated clinical programmes, mouse lethal knockouts, and cancer driver genes, establishing gene-level pleiotropy as a potential measure of genetically-informed organism-level safety liability. Protein-altering variant (PAV) support amplifies therapeutic signal (OR = 6.0), yet PAV targets show higher average pleiotropy, introducing a competing safety liability. Combining PAV support with intermediate pleiotropy (2-5 therapeutic areas) resolves this tension, yielding OR = 10.3 and relative success = 4.8--a profile already satisfied by 52 approved therapies. As GWAS continue to expand in scale and resolution, these findings lay the groundwork for increasingly sophisticated target discovery strategies that yield safer and more effective therapeutic hypotheses.","published":"NA","server":"bioRxiv"},{"title":"Improved sensors for fructose-1,6-bisphosphate enable in vivo imaging of glycolysis","authors":"Tyler, J.; Amrapali Vishwanath, A.; Menon, T.; Duarah, T.; Adhikari, R.; Koberstein, J. N.; Feliciano, D.; Espinosa-Medina, I.; Colon-Ramos, D.; Tebo, A. G.","author_corresponding":"Alison G. Tebo","author_corresponding_institution":"HHMI - Janelia Research Campus","doi":"10.64898\/2026.04.29.721630","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721630.source.xml","abstract":"Fructose-1,6-bisphosphate (FBP) is the product of the first committed step of glycolysis, and its concentration is tightly correlated with glycolytic flux. Glycolytic activity varies across tissues and cell types: some tissues, such as the brain, dynamically regulate glycolysis in response to demand, while others, such as the liver have characterized spatial heterogeneity. Here, we report HYlight2, an improved sensor for FBP developed through random whole-gene mutagenesis in E. coli lysate. After four rounds of screening, we isolated HYlight2, which retains its binding affinity while displaying a {Delta}R\/R [~]9 in vitro, a three-fold improvement in mammalian cells, and a two-fold improvement in detecting glycolytic responses during stimulated neuronal activity. We further demonstrate its use in vivo to detect altered glycolytic activity in C. elegans neurons, zebrafish pancreatic islets, and mouse liver.","published":"NA","server":"bioRxiv"},{"title":"Myo1e\/f regulate phagocytic podosomes to promote efficient cup closure in macrophages","authors":"Paul, T. C.; Loyd, Y. M.; Chase, S. E.; O'Connor, T. W.; Hobson, C. M.; Lee, R. M.; Vorselen, D.; Krendel, M.","author_corresponding":"Mira Krendel","author_corresponding_institution":"SUNY Upstate Medical University","doi":"10.64898\/2026.04.30.721640","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.30.721640.source.xml","abstract":"Phagocytosis requires coordinated remodeling of the actin cytoskeleton to generate protrusive and contractile forces that drive target engulfment. Class I myosins Myo1e and Myo1f (Myo1e\/f) have been implicated in linking the plasma membrane to the actin network, but their specific roles during Fc-receptor-mediated phagocytosis remain unclear. Using CRISPR-edited RAW 264.7 macrophages lacking Myo1e and Myo1f, we show that double knockout (dKO) cells exhibit markedly reduced uptake of IgG-coated beads, a phenotype that is partially rescued by re-expression of either myosin. Lattice-light-sheet and confocal imaging revealed distinct F-actin architectures corresponding to the various stages of cup progression, including basal podosome-like adhesions, individual phagocytic podosomes (actin teeth) along the rim of the cup, and a contractile phagocytic ring formed by the reorganization of podosomes into a higher-order network. In Myo1e\/f- deficient cells, podosome formation was diminished, actin teeth were largely absent, and the phagocytic ring formed prematurely, which was often accompanied by stalled cup progression and repeated engulfment attempts. Myo1e\/f localized both to podosomes and to the inner surface of the phagocytic ring, non-muscle myosin II (NM2) localized to the outer surface, and the absence of Myo1e\/f correlated with the diffuse distribution of NM2. In addition, Myo1e\/f-deficient macrophages exhibited increased trogocytosis of antibody-opsonized HL-60 cells, indicating a shift from whole-target engulfment toward partial target ingestion. These results suggest that Myo1e\/f coordinate spatial and temporal transitions between protrusive and contractile actin networks, thereby ensuring efficient phagocytic cup progression. Our findings highlight a dual role for Myo1e\/f in adhesion regulation and force balance during macrophage phagocytosis.","published":"NA","server":"bioRxiv"},{"title":"Multi-omics Characterization of Duck Embryonic Stem Cells for Cultivated Meat","authors":"Kusters, R.; Mathieu, T.; Kamgang Nzekoue, F.; Manzati, M.; Palma, J.; Chun, B.; Lester, H.","author_corresponding":"Remy Kusters","author_corresponding_institution":"Gourmey (SUPERME)","doi":"10.64898\/2026.04.27.720974","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.27.720974.source.xml","abstract":"Industrializing cultivated meat requires cell lines with high proliferative capacity, genetic stability, and suspension adaptability. We present a comprehensive multi-omics framework, integrating genomics, transcriptomics, and proteomics, to characterize a commercial duck Embryonic Stem Cell (dESC) line. Our analysis demonstrates continuous proliferation in protein-free suspension media while maintaining a stable genome and a functional conserved transcriptome. Broad-scale transcriptomics confirms the absence of hazardous pathway activation, and targeted assays verify sustained pluripotency marker expression during scale-up. Compositional analysis reveals a low-fat biomass containing all nine essential amino acids with an amino acid profile comparable to conventional duck meat. Furthermore, proteomic profiling demonstrates inter-batch reproducibility and protein distributions comparable to duck breast and liver. This study provides the first detailed molecular characterization of a commercial cultivated meat cell line, establishing a reference for the stability and safety assessment of future cultivated meat cell lines.","published":"NA","server":"bioRxiv"},{"title":"Phosphoproteomics identifies the DYRK1B protein kinase as a regulator of processing bodies","authors":"Ashford, A. L.; Ber, S.; Ems, M. S.; Duncan, E.; Balmanno, K.; Reeves, H.; Huntly, R.; Cassidy, M. A.; Johnston, H. E.; Oxley, D.; Nthiga, T. M.; Johansen, T.; Kluge, M.; Jacob, R.; Lauth, M.; Cook, S. J.","author_corresponding":"Simon J Cook","author_corresponding_institution":"The Babraham Institute","doi":"10.64898\/2026.04.29.721300","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721300.source.xml","abstract":"Dual-specificity tyrosine-phosphorylation-regulated kinase 1B (DYRK1B) modulates the cell cycle, cell fate during development, and is deregulated in cancer and metabolic syndrome. However, only a few DYRK1B substrates have been defined, so we undertook a phosphoproteomics screen in cells that exhibit inducible DYRK1B expression. Motif analysis revealed enrichment for proline-directed serine or threonine phosphorylation sites (pSer\/pThr-Pro), consistent with the consensus motif of class I DYRKs. Gene ontology analysis revealed enrichment of proteins involved in mRNA binding, mRNA processing and ribonucleoprotein complexes. Several processing body (PB) components, including DCP1A, PATL1(PAT1B), EDC3 and 4E-T, were identified as DYRK1B-inducible phosphoproteins. DYRK1B also co-immunoprecipitated with DCP1A, PAT1B, EDC3, EDC4, DDX6 and XRN1. Super-resolution microscopy demonstrated that DYRK1B co-localised with DCP1A, DCP1B and DDX6 in PBs. Activation of DYRK1B increased PB abundance, whereas inhibition, depletion or knockout of DYRK1B reduced phosphorylation of DCP1A and 4E-T and decreased PB number. Re-expression of wild type, but not kinase-dead, DYRK1B restored PB numbers in knockout cells. These findings reveal novel DYRK1B targets and establish DYRK1B as a regulator of processing body abundance.\n\nHighlightsO_LIDYRK1B induces phosphorylation of a cluster of RNA binding and processing body associated proteins.\nC_LIO_LIDYRK1B localises to PBs and associates with multiple PB components.\nC_LIO_LIDYRK1B controls P-body abundance in a kinase-dependent manner.\nC_LI","published":"10.1242\/jcs.265054","server":"bioRxiv"},{"title":"TORC1 spatial segregation and hysteresis are regulated by the small GTPase Arf1","authors":"Enkler, L.; Nuredini, T.; Mironov, A.; Ritz, D.; Wang, C.; Zavolan, M.; Spang, A.","author_corresponding":"Anne Spang","author_corresponding_institution":"Biozentrum, University of Basel","doi":"10.64898\/2026.04.29.721593","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721593.source.xml","abstract":"TORC1 is a central regulator of growth, integrating inputs from kinases and signaling proteins. How TORC1 activity is regulated, is still not completely understood. The small GTPase Arf1 has been implicated in TORC1 regulation, but the underlying mechanism remains elusive. Here, we show that Arf1 controls TORC1 in an allele-specific manner under nutrient and heat stress in yeast. Unexpectedly, both the hyperactive mutant arf1-11 and the loss-of-function mutant arf1-18 reduce TORC1 activity, while other loss-of-function alleles did not. We reveal two distinct functions of Arf1: first, it ensures Golgi-to-vacuole\/lysosome transport for the functional maintenance of these organelles; second, it regulates TORC1 activity at the ER-Golgi-vacuole interface. Hyperactive Arf1-11 drives sequestration of Kog1 and Tor1 into cytoplasmic foci, to which Arf1-11 can be equally recruited. Importantly, Arf1 also promotes TORC1 re-activation during stress recovery - so-called hysteresis. Our data reveal an unexpected dual function for Arf1 as a negative and a positive regulator of TORC1 activity in a context-dependent manner.\n\nTeaserThe small GPTase Arf1 acts as a dual switch for the key cellular growth regulator TORC1 by increasing or decreasing TORC1 activity depending on nutritional status and stress.","published":"NA","server":"bioRxiv"},{"title":"LAT condensation gates PLC\u03b31 activation via bimodal LAT phosphorylation","authors":"Ren, H.; Lee, H.-R.; Omar, Y. A. D.; DeGrandchamp, J. B.; Hung, C.-L.; Eisen, T. J.; Stamou, D.; Kuriyan, J.; Chakraborty, A. K.; Groves, J. T.","author_corresponding":"Jay T Groves","author_corresponding_institution":"University of California Berkeley","doi":"10.64898\/2026.04.29.721478","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721478.source.xml","abstract":"T cells can respond to even a single molecular binding event of antigen to a TCR. A key step in the TCR signaling pathway that definitively exhibits this single molecule response is the initiation of calcium influx by activation of PLC{gamma}1 in the LAT protein condensate. Here, we describe detailed kinetic measurements examining how protein condensation of LAT regulates activation of PLC{gamma}1 using a reconstituted membrane system. The results reveal that membrane recruitment of PLC{gamma}1 is tightly controlled by the LAT phosphorylation state, with no measurable independent recruitment to PIP2 or PIP3 lipids via the PLC{gamma}1 PH domains. We further observe PLC{gamma}1 is rapidly activated by membrane-associated kinase upon recruitment, irrespective of the LAT condensation state. These studies also revealed a crosstalk mechanism in which the TEC family kinases responsible for PLC{gamma}1 activation also phosphorylate LAT. This interaction establishes a positive feedback loop in LAT phosphorylation, mediated through LAT condensation, which drives a bimodal LAT phosphorylation response to TCR activation. Kinetic modeling reveals how this LAT phosphorylation response can cooperatively gate PLC{gamma}1 activation from a single TCR. These results suggest the LAT condensate facilitates both signal amplification and noise suppression in PLC{gamma}1 activation through a bimodal switch affecting LAT phosphorylation.\n\nSignificance StatementT cells are sensitive sensors capable of detecting and responding to trace amounts of foreign antigen. Understanding how they achieve such sensitivity while maintaining accurate antigen discrimination remains a key challenge. Here, through detailed kinetic measurements of PLC{gamma}1 activation, we identify a cross reactivity in which kinases responsible for PLC{gamma}1 phosphorylation also phosphorylate LAT. This creates a bimodal switch controlling LAT phosphorylation levels, which gates PLC{gamma}1 activation from single TCR signals. We suggest this mechanism plays a key role in the signal amplification and noise suppression required for T cells to detect single antigen molecules.","published":"NA","server":"bioRxiv"},{"title":"A unified photosensitizer platform for in situ DNA, RNA, and protein directed proximity labeling","authors":"Biletch, E. B.; Herlihy, C. P.; Li, L.; Krebs, M.; Kelly, C. J.; Longhi, N. J.; Weissenfels, O.; Goldberg, H.; Brandt, K.; Grimm, J. B.; Lavis, L. D.; Huttlin, E. L.; Schweppe, D. K.; Backus, K. M.; Beliveau, B. J.","author_corresponding":"Brian J Beliveau","author_corresponding_institution":"University of Washington","doi":"10.64898\/2026.04.30.721698","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.30.721698.source.xml","abstract":"Cells depend on the spatial organization of proteins, RNA, and DNA into discrete subcellular compartments. Previous methods have largely centered on measuring spatial organization based on only one of these biomolecular classes at a time. Here, we demonstrate that POCA photocatalytic proximity labeling can serve as a unified photosensitizer-based platform for profiling the proximal proteomes of protein, RNA, and DNA targets within a single experimental framework. We show that POCA can harness standard immunofluorescence or in situ hybridization workflows to specifically target organic fluorophore photosensitizers to intracellular targets for proximity labeling in fixed cells. POCA-targeted proximity labeling requires minimal cellular input and does not require genetic engineering. Additionally, POCA photosensitizers are selected to also be fluorescent, enabling direct confirmation of on-target localization by imaging prior to proteomic analysis. To demonstrate broad utility, we apply POCA across multiple molecular targets spanning protein, RNA, and genomic DNA, including components of the nuclear pore complex, nucleolus, nuclear speckles, telomeres, and pericentromeric heterochromatin. By anchoring proximity labeling to both a protein and an RNA within the same nuclear compartment, we resolve shared and distinct proximal proteomes from orthogonal molecular perspectives.","published":"NA","server":"bioRxiv"},{"title":"Loss of nuclear-cytoplasmic compartmentalization is a hallmark of aging in podocytes","authors":"Hamed, M.; Gao, Y.; Stein, F.; Vijay, G.; Stausberg, T.; Juehlen, R.; Martin, I. V.; Raffetseder, U.; Stamellou, E.; Kramann, R.; Ostendorf, T.; Antonin, W.","author_corresponding":"Wolfram Antonin","author_corresponding_institution":"Institute of Biochemistry and Molecular Cell Biology, RWTH University Clinic, Aachen, Germany","doi":"10.64898\/2026.04.29.721580","date":"2026-05-01","version":"1","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721580.source.xml","abstract":"The nuclear envelope, with its nuclear pore complexes, establishes a selective barrier that maintains the spatial organization of the cellular proteome. Whether this barrier remains intact in long-lived postmitotic cells during aging is largely unknown. Here, we show that aging podocytes experience a progressive loss of nuclear-cytoplasmic compartmentalization. Using subcellular proteomics and quantitative imaging, we identify a global redistribution of proteins between the nucleus and cytoplasm, affecting key regulators of RNA processing, chromatin organization, and cellular metabolism. Loss of compartmentalization is accompanied by mitochondrial dysfunction, increased reactive oxygen species production, and aberrant nuclear accumulation of YAP1, linking nuclear barrier failure to metabolic and transcriptional dysregulation. These findings identify nuclear envelope dysfunction as a driver of proteome disorganization and cellular decline in aging podocytes and suggest that loss of nuclear-cytoplasmic compartmentalization represents a general mechanism contributing to dysfunction in long-lived cells.","published":"NA","server":"bioRxiv"},{"title":"Oxidative DNA lesions destabilize centromeres and drive chromosome instability","authors":"Thompson, L.; Nassar, R.; Angrisani, A.; Hsiu, O. O. N.; Yang, Y.; Kedziora, K. M.; Muoio, D.; Fachinetti, D.; Stallaert, w.; Fouquerel, E.","author_corresponding":"Elise Fouquerel","author_corresponding_institution":"University of Pittsburgh","doi":"10.64898\/2026.04.28.717272","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.717272.source.xml","abstract":"Centromeres are essential regions of the genome that ensure chromosome segregation during mitosis. Yet, they are also hotspots for chromosome breaks and rearrangements in cancer. The mechanisms underlying this fragility is not fully elucidated. Here we show that oxidative DNA damage destabilizes centromeres and promotes chromosome instability. Using a chemoptogenetic system to generate singlet oxygen locally at centromeres, we uncouple centromeric oxidative damage from global oxidative stress. We find that oxidative base lesions activate base excision repair at centromeres but slow DNA synthesis, destabilize CENP-A chromatin, and are converted into DNA breaks that can persist into subsequent cell cycles. Single cell time lapse imaging reveals that the cellular fate of centromeric DNA damage depends on the cell cycle phase during which the oxidative lesions occur. Lesions induced before and during replication primarily induce cell cycle delays and often drive the cells into a state of quiescence, whereas lesions arising after replication allow mitotic progression but compromise the proliferative capacity of daughter cells. Finally, in pre-tumorigenic cells, centromeric oxidative lesions lead to mitotic defects, aneuploidy, and whole-arm chromosome translocations. Collectively, we identify centromeres as cell cycle-sensitive DNA damage sensors and oxidative stress as a direct driver of centromere fragility and chromosome instability\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC=\"FIGDIR\/small\/717272v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@71f4e6org.highwire.dtl.DTLVardef@1853dcforg.highwire.dtl.DTLVardef@9cf133org.highwire.dtl.DTLVardef@19f7edf_HPS_FORMAT_FIGEXP  M_FIG C_FIG","published":"NA","server":"bioRxiv"},{"title":"CD4+ T cell activation is dependent on a novel form of ULK1\/2-independent autophagy","authors":"Coffer, P. J.; Corrigan, E.; van Beek, J.; Raud, B.; Oliverira Lima, J.; de Maziere, A.; Knol, A.; Pals, C.; Amsen, D.; Klumperman, J.; Mocholi, E.","author_corresponding":"Paul J Coffer","author_corresponding_institution":"UMC Utrecht","doi":"10.64898\/2026.04.29.721097","date":"2026-05-01","version":"1","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721097.source.xml","abstract":"Autophagy is essential for CD4+ T cell activation and immune regulation. However, during activation both autophagy and anabolic signaling must be simultaneously sustained, challenging established models of pathway antagonism. Here, we show that T cell receptor signaling and co-stimulation induce a non-canonical form of autophagy required for proliferation and cytokine production. Pharmacological and genetic analyses reveal that this pathway is activated concurrently with mTORC1, and is dependent on PIK3C3, but occurs independently of the canonical regulators ULK1\/2, AMPK, ATG13, and Beclin 1. Furthermore, immuno-electron microscopy demonstrates that activation generates smaller autophagic structures that associate with multivesicular bodies and exhibit a unique morphology. These findings uncover a fundamental rewiring of autophagy control in CD4+ T cells and identify a novel form of mechanistically and morphologically distinct non-canonical autophagy.","published":"NA","server":"bioRxiv"},{"title":"A sterol-binding pocket in iRhom1 underlies paralog-specific regulation of the sheddase ADAM17","authors":"Lu, F.; Zhao, H.; Dai, Y.; Lee, C.-H.; Freeman, M.","author_corresponding":"Matthew Freeman","author_corresponding_institution":"University of Oxford","doi":"10.64898\/2026.04.28.721421","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721421.source.xml","abstract":"ADAM17, the major sheddase in mammalian cells, releases membrane-tethered EGFR ligands and inflammatory cytokines, and is a central regulator of cell signalling. The rhomboid pseudoproteases, iRhom1 and iRhom2, function as essential cofactors of ADAM17, controlling its maturation and activation. In contrast to the well-characterized iRhom2, the mechanism and regulation of its ubiquitously expressed paralog iRhom1 remain undefined. Here, we present a 2.5 [A] cryo-EM structure of the full-length human iRhom1\/ADAM17 complex, revealing a previously unrecognized sterol-binding pocket located between TMD2 and TMD5. Structure-guided mutagenesis and pharmacological perturbation of sterol binding demonstrate that sterol binding is required to stabilize the iRhom1\/ADAM17 complex and sustain its shedding activity. Strikingly, this regulation is paralog-specific: iRhom2 precludes sterol binding and instead stabilizes ADAM17 through direct intramolecular interactions. Furthermore, two human iRhom1 variants associated with cardiac disease localize adjacent to the sterol-binding pocket and disrupt ADAM17 maturation and activity. Together, these findings uncover mechanistic divergence between iRhom paralogs and establish a sterol-binding pocket in iRhom1 as a critical determinant of ADAM17 stability, revealing a potential avenue for paralog-selective therapeutic targeting.","published":"NA","server":"bioRxiv"},{"title":"The Nuclear Pore Complex Facilitates Centriole-Nuclear Attachment in Spermatids","authors":"Buglak, D. B.; Galletta, B. J.; Rusan, N. M.","author_corresponding":"Nasser M Rusan","author_corresponding_institution":"National Heart, Lung, and Blood Institute - NIH","doi":"10.64898\/2026.04.28.721503","date":"2026-05-01","version":"1","type":"new results","license":"cc0","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721503.source.xml","abstract":"Proper connection between the sperm head and tail is critical for fertility and is mediated by the head-tail coupling apparatus (HTCA). Recent evidence suggests that the nuclear pore complex (NPC) may be important in male fertility, though a specific role at the HTCA has not been described. To investigate this, we performed a testis-specific RNAi screen targeting nucleoporins of the NPC. We identified Nup133 and Nup107 as regulators of HTCA development. We found that Nup133 and Nup107 were required to form the initial connection between the nucleus and centriole during HTCA establishment. We determined that failure to build the HTCA following Nup133 and Nup107 depletion was due to loss of nuclear envelope dynein\/dynactin. Finally, we showed that loss of the NPC cytoplasmic filament component Nup358 results in the most severe centriole detachment phenotype, thus potentially functioning as the dynein anchor. Together, our data indicate that NPCs are critical regulators of early HTCA establishment and are required to recruit dynein to the nuclear envelope to bring the nucleus and centriole together during spermiogenesis.","published":"NA","server":"bioRxiv"},{"title":"Hidden Dynamical Canalization at the Onset of Hydra Morphogenesis","authors":"Agam, O.; Braun, E.","author_corresponding":"Erez Braun","author_corresponding_institution":"Technion","doi":"10.64898\/2026.04.28.721438","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721438.source.xml","abstract":"The primary morphological transition in Hydra regeneration, from a quasi-spherical fragment to an elongated body, is preceded by a prolonged period during which its average form changes only modestly, while its instantaneous shape continues to fluctuate. We asked whether this preparatory stage contains signatures of dynamical organization. Using principal component analysis, we calculated the effective dimension of shape fluctuations, which characterizes how broadly they are distributed across PCA directions. Across all five conditions, spanning differences in tissue fragment size, axial origin and GdCl exposure, the effective dimension decreased progressively before overt tissue elongation. Total fluctuation variance increased about 2.8-fold, whereas the leading eigenvalue increased about fourfold. Late intervals had lower effective dimension than early intervals at similar coarse shapes. Calcium analysis in GdCl-treated tissues distinguished mean level, fast events and spatial heterogeneity. Fast events were associated with short-timescale shape changes. After accounting for temporal trends, mean Ca2+ and coarse morphology, higher spatial heterogeneity of Ca2+ activity was associated with lower effective dimension. The progressive concentration of morphological fluctuations along fewer dominant directions characterizes dynamical canalization associated with spatial Ca2+ heterogeneity.","published":"NA","server":"bioRxiv"},{"title":"Confronting global eradication of TB head on: Uncovering the root of drug resistance and bacterial survival strategies through a comprehensive computational study of first-line TB drug resistant mutations","authors":"Pawar, P.; Samarasinghe, S.","author_corresponding":"Sandhya Samarasinghe","author_corresponding_institution":"Lincoln University","doi":"10.64898\/2026.04.28.721232","date":"2026-05-01","version":"1","type":"new results","license":"cc_no","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721232.source.xml","abstract":"Tuberculosis (TB) is fast becoming incurable affecting millions globally. Mycobacterium tuberculosis (Mtb), causative agent of TB, has evolved elusive survival strategies through point mutations in the drug targets leading to a daunting scenario of resistance towards first-line TB drugs, exacerbated by global differences in mutation patterns. Drug resistance studies have focussed only on few mutations; however, hundreds of mutations have been reported in the last three decades. WHOs goal of global eradication of TB therefore now requires a deep understanding of mechanisms of drug resistance, involving many mutations, addressed in a global context. This study addresses bacterial survival strategies by following bacteria-drug interaction to probe into how bacteria evolve drug resistance mechanisms through mutations. We hypothesise that bacteria favour mutations that protect them from a drug while making the drug ineffective. To test the hypothesis, we quantify the impact of mutations on both bacterial function and drug binding affinity to get to the root of drug resistance revealing how bacteria may evolve an arsenal of mutations towards an optimal survival strategy. This first comprehensive and systematic in-depth study global patterns of mutation and drug resistance mechanisms from mutation data for Mtb reported over the last 30 years. These were collected for 31,073 drug-resistant Mtb isolates from 149 published studies for the four first line drugs isoniazid (INH), pyrazinamide (PZA), rifampicin (RIF), and ethambutol (EMB). We found 821 single frequency non-synonymous mutations for INH (n= 202), RIF (n=120), EMB (n=226) and PZA (n=273). We then investigated the prevalence and diversity of these mutations in the drug targets across the globe. We found S315T in the target katG (60%) to be the most prevalent mutation in INH resistance followed by S450L in rpoB (56%) and M306V in embB (29%) associated with RIF and EMB resistance, respectively; these were also the highly occurring mutations across the six WHO regions, except for the most common mutation Q10P in pncA (1.4%) (PZA resistance; with shorter exposure to drug) showing a variable pattern of occurrence globally. We found the highest mutational burden in the Western Pacific and South-East Asia regions for INH and RIF resistance. Frequent mutations had also undergone frequent amino acid substitutions. Accordingly, we developed a comprehensive atlas of mutation spread across the globe and their evolution over the last 30 years. We then probed into the impact of mutations on TB bacteria and drug binding with a comprehensive bioinformatics analysis for understanding crucial changes caused by mutation at the molecular level affecting function and structural stability of bacteria and the drug binding affinity. We found that the most prevalent mutations occur in non-conserved areas in the drug binding region indicating a choice of a less dramatic level of change in target protein function and stability. All mutations reduced drug binding affnity. For characterising drug resistance mechanisms, we introduced a new concept of ranking drug-resistant TB mutations into lethal, moderate, mild and neutral considering the combined effect on Mtb viability and drug binding. We identified 340 mutations as  lethal, 284 as  moderate, 185 as  mild and 12 as  neutral. We observed that frequently occurring mutations occur in non-conserved regions causing a mild effect on target proteins (such as S315T of katG, S450L of rpoB and M306V in embB), while reducing drug binding affinity. With these we uncovered a universal strategy of drug resistance and bacterial survival: Mtb favours less harmful mutations in the drug binding region without compromising conservancy while destabilising the drugs, thus striking a balance between fitness and drug resistance. This ingenuous strategy seems successful and reasonable persisting globally over three decades and provides a holistic understanding of drug resistance and a strong foundation for designing efficacious drugs and therapies towards global eradication of TB.","published":"NA","server":"bioRxiv"},{"title":"Layer-specific wide-field calcium imaging of neocortical activity","authors":"Lorenzo, D. A.; Gallero-Salas, Y.; Panzeri, M.; Wahl, A.-S.; Gilad, A.; Lewis, C. M.; Helmchen, F.","author_corresponding":"Fritjof Helmchen","author_corresponding_institution":"University of Zurich","doi":"10.64898\/2026.04.28.721258","date":"2026-05-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.28.721258.source.xml","abstract":"The mammalian neocortex is highly organized in local microcircuits and through long-range projection patterns between different regions. Since various features of local and long-range connectivity are determined by the cortical layer in which the respective neurons reside, understanding the flow of cortical information within and across layers is essential. Wide-field calcium imaging enables mesoscale functional mapping of genetically identified neurons across cortical areas. However, it has been applied primarily to superficial cortical layers, and systematic comparisons of wide-field signals across cortical layers are scarce. Here, we apply wide-field calcium imaging to different cortical layers using transgenic mouse lines with selective expression of GCaMP6f in layers 2\/3, 5, and 6. We address several challenges of layer-specific wide-field imaging and provide possible solutions. First, to improve the registration of functional data to standard atlases, we demonstrate the benefit of layer-specific registration maps that are warped on the basis of the depth-dependent surface projections of the labeled cell populations. These maps help to assign the imaged calcium signals to the specific regions from which they originate. Second, we measure the depth-dependent blurring of wide-field fluorescence signals induced by light scattering and reveal stronger blurring in deep vs. superficial layers, in line with previous theoretical predictions from simulations. We used measured point spread functions to deconvolve single-whisker-evoked calcium signals in the barrel cortex and demonstrate improved signal confinement to individual barrel columns across layers. Finally, we investigate cross-regional functional connectivity during awake resting state periods for distinct layers. We find that mesoscopic functional connectivity is largely conserved between the cortical layers, with subtle differences for key regions of the default mode network (retrosplenial cortex and medial prefrontal cortex). Our approaches facilitate the comprehensive characterization of layer-specific cortico-cortical interactions, expanding wide-field calcium imaging as a powerful tool to investigate the layered organization of distributed brain dynamics.","published":"NA","server":"bioRxiv"},{"title":"Rational Design of an Arid Plant-Derived Endophytic Consortium Improves Crop Performance under Controlled Conditions","authors":"Mouhib, S.; Ait Si Mhand, K.; khatour, I.; Radouane, N.; Hijri, M.","author_corresponding":"Mohamed Hijri","author_corresponding_institution":"Universite Mohammed VI Polytechnique","doi":"10.64898\/2026.04.29.721730","date":"2026-05-01","version":"1","type":"new results","license":"cc_no","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721730.source.xml","abstract":"Endophytic bacteria from arid medicinal plants represent a promising source of stress-adapted, plant growth-promoting (PGP) microorganisms. Here, we investigated the cultivable endophytic microbiota of Peganum harmala using both nutrient-rich and diluted media to maximize taxonomic recovery. Isolates were dominated by Bacillota and Gammaproteobacteria, with higher diversity in roots than in shoots. Venn analysis revealed a shared core fraction between compartments, forming the basis for consortium assembly. Nine representative strains belonging to Phyllobacterium, Bacillus, Brevibacillus, Burkholderia, Ralstonia, and Amycolatopsis were selected for functional screening. Pairwise antagonism assays showed high compatibility among Bacillus-related strains, whereas certain taxa exhibited inhibitory interactions, guiding rational consortium design. Functional characterization demonstrated complementary PGP traits, including nitrogen-related activity, phosphate, potassium, and silicate solubilization, siderophore and indole-3-acetic acid production, and ammonia production. No single isolate performed optimally across all traits, supporting a consortium-based strategy. A synthetic bacterial consortium (C2), reconstructed from the core endophytic microbiota using compatibility-guided selection, was evaluated in two crop systems. In vitro flax germination assays showed accelerated radicle emergence and improved vigor index, particularly with C2. Under greenhouse conditions, C2 significantly enhanced flax shoot and root biomass, root architecture, leaf area expansion, and photosystem II performance in sterile soil. In faba bean under natural soil, C2 increased leaf number (p = 0.02) relative to the control. These results indicate that consortia derived from core endophytes of arid medicinal plants can promote plant growth across diverse crops and soil contexts, although effects remain context-dependent and require rigorous field validation.\n\nIMPORTANCEEndophytic bacteria can serve as sustainable bioinoculants to enhance crop performance under stress conditions. This study demonstrates that the core microbiota of the arid medicinal plant Peganum harmala can be rationally assembled into a functionally complementary consortium that improves germination, nutrient acquisition, and whole-plant physiological performance in flax and faba bean. By combining compatibility-guided assembly with functional screening, we show that consortium-based strategies may outperform single-strain inoculants. These findings provide insight into the development of scalable, plant growth-promoting microbial consortia and highlight the importance of testing microbial inoculants under multiple environmental contexts to ensure consistent benefits.","published":"NA","server":"bioRxiv"},{"title":"Average local nucleosome motion remains constant during interphase in living human cells","authors":"Nagata, Y.; Iida, S.; Shimazoe, M. A.; Tamura, S.; Nakazato, K.; Shimizu, K.; Hatoyama, Y.; Kanemaki, M.; Maeshima, K.","author_corresponding":"Kazuhiro Maeshima","author_corresponding_institution":"National Institute of Genetics","doi":"10.64898\/2026.04.29.721002","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.29.721002.source.xml","abstract":"Dynamic chromatin behavior, which is related to chromatin accessibility, plays a critical role in various genome functions such as RNA transcription and DNA replication\/repair. Previous studies using highly synchronized cells showed that average local chromatin motion, captured by single-nucleosome imaging on a subsecond time scale, remained nearly constant throughout G1, S, and G2 phases in living human cells. Here, we combined single-nucleosome imaging with Fucci cell-cycle probes to test this finding in asynchronous living human cells. Using HeLa and HCT116 cells expressing H2B-HaloTag and Fucci probes, we found that local nucleosome motion remained similar on average throughout interphase. Consistently, H3.3-Halo-labeled nucleosomes, which are enriched in Hi-C A compartments (euchromatin), also showed near-constant motion throughout interphase. Transcription inhibition increased nucleosome motion throughout interphase. Local nucleosome motion also increased following cellular perturbations, such as replication stress or DNA damage. Our findings suggest that near-constant chromatin motion supports housekeeping functions under similar physical conditions during interphase. They also suggest that cells can transiently change chromatin motion to perform ad hoc tasks in response to intra- and extracellular signals, such as DNA damage.","published":"NA","server":"bioRxiv"},{"title":"Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina","authors":"Corre, E.; Morin, E.; Sperschneider, J.; Abdalrahem, A.; Pernaci, M.; Grigoriev, I. V.; Frey, P.; Duplessis, S.; Lorrain, C.","author_corresponding":"C\u00e9cile Lorrain","author_corresponding_institution":"Eidgenossische Technische Hochschule Zurich","doi":"10.64898\/2026.04.23.720444","date":"2026-05-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2026\/05\/01\/2026.04.23.720444.source.xml","abstract":"Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolved 18 chromosomes per haplotype, providing the first near chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ~203 Mb, while M. allii-populina reaches ~416 Mb, with high completeness and strong collinearity between haplotypes. Compared with previous fragmented or collapsed references, these assemblies greatly improve contiguity, recover centromeric and telomeric features, and support the transposable element-driven genome size expansion in M. allii-populina. The haplotype-aware annotations of genes and predicted effectors derived from these resources will enable detailed analyses of genome architecture, repeat dynamics, and key loci such as avirulence genes. Together, these assemblies provide a robust genomic resource for investigating host adaptation, virulence evolution, and population diversity in poplar rust fungi.","published":"NA","server":"bioRxiv"}]}