{"messages":[{"status":"ok","category":"all","interval":"2025-01-01:2025-12-31","cursor":0,"count":30,"count_new_papers":"49318","total":"67211"}], "collection":[{"title":"Persistent DNA methylation and downregulation of homeostatic genes in astrocytes after pilocarpine-induced status epilepticus: Implications for epileptogenesis","authors":"Gomez Cuautle, D. D.; Rossi, A. R.; Villarreal, A.; D Alessio, L.; Ramos, A. J.","author_corresponding":"Alberto Javier Ramos","author_corresponding_institution":"CONICET","doi":"10.1101\/2024.12.31.630767","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630767.source.xml","abstract":"Epilepsy is a debilitating neurological disorder characterized by recurrent seizures, affecting millions of patients worldwide. Retrospective studies in Temporal lobe epilepsy (TLE) patients have shown a high incidence of an initial precipitating event (IPE) in early childhood followed by a silent period where epileptogenesis occurs to end up in chronic epilepsy. Epileptogenesis, the process through which a normal brain undergoes structural and functional changes leading to epilepsy, remains an enigmatic phenomenon. We hypothesized that epigenetics may be involved in epileptogenesis and specifically astrocytes could be affected by pathological remodeling. To study this process, we used three approaches: The lithium-pilocarpine model of TLE in rats, primary astroglial cultures exposed to epileptogenic DAMP named HMGB1, and brain tissue samples resected from TLE patients with drug-resistant epilepsy. We found that the IPE achieved by lithium- pilocarpine treatment (127\/30 mg\/kg IP) induced the hypermethylation of astrocytes at 7-, 21-, and 35 days post-IPE, indicating persistent epigenetic alterations in astrocytes during the epileptogenic period. In addition, we observed the downregulation of homeostatic astroglial genes AQP4; glutamine synthase (GS), and Kir4.1 with increased proinflammatory genes (C3, MAFG) and DNA methyl transferases (DNMT) expression. These alterations were mimicked in primary astrocyte cultures exposed to the epileptogenic HMGB1 (500 ng\/ml; 18 hours) that also induced the hypermethylation of homeostatic astroglial genes. Astrocytes from TLE patients brains showed reactive astrogliosis, increased DNA methylation, and downregulation of homeostatic genes Kir4.1 and GS. These findings show that astrocytes are pathologically altered during the epileptogenic period, combining the proinflammatory gain of function with the loss of homeostatic profile. This may sustain the long-term alterations underlining epileptogenesis.","published":"NA","server":"bioRxiv"},{"title":"CD44 and Ezrin restrict EGF receptor mobility to generate a novel spatial arrangement of cytoskeletal signaling modules driving bleb-based migration","authors":"Jha, A.; Chandra, A.; Farahani, P.; Toettcher, J. E.; Haugh, J. M.; Waterman, C. M.","author_corresponding":"Ankita Jha","author_corresponding_institution":"Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, United States.","doi":"10.1101\/2024.12.31.630838","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630838.source.xml","abstract":"Cells under high confinement form highly polarized hydrostatic pressure-driven, stable leader blebs that enable efficient migration in low adhesion, environments. Here we investigated the basis of the polarized bleb morphology of metastatic melanoma cells migrating in non-adhesive confinement. Using high-resolution time-lapse imaging and specific molecular perturbations, we found that EGF signaling via PI3K stabilizes and maintains a polarized leader bleb. Protein activity biosensors revealed a unique EGFR\/PI3K activity gradient decreasing from rear-to-front, promoting PIP3 and Rac1-GTP accumulation at the bleb rear, with its antagonists PIP2 and RhoA-GTP concentrated at the bleb tip, opposite to the front-to-rear organization of these signaling modules in integrin-mediated mesenchymal migration. Optogenetic experiments showed that disrupting this gradient caused bleb retraction, underscoring the role of this signaling gradient in bleb stability. Mathematical modeling and experiments identified a mechanism where, as the bleb initiates, CD44 and ERM proteins restrict EGFR mobility in a membrane-apposed cortical actin meshwork in the bleb rear, establishing a rear-to-front EGFR-PI3K-Rac activity gradient. Thus, our study reveals the biophysical and molecular underpinnings of cell polarity in bleb-based migration of metastatic cells in non-adhesive confinement, and underscores how alternative spatial arrangements of migration signaling modules can mediate different migration modes according to the local microenvironment.","published":"NA","server":"bioRxiv"},{"title":"Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment","authors":"Boulay, A.; Leprince, A.; Enault, F.; Rousseau, E.; Galiez, C.","author_corresponding":"Clovis Galiez","author_corresponding_institution":"Univ. Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France","doi":"10.1101\/2024.12.31.630607","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630607.source.xml","abstract":"Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner - from general functional categories such as \"structural\" and \"DNA-associated\" proteins to more specific ones including \"nucleases\", \"tail appendages\" and \"endolysins\" to name only a few. These categories were specifically tailored for phage protein functions and organized such that molecular-level functions are respected in each category, making it well suited for training machine learning classifiers based on protein embeddings. We show on a dataset of cultured phage genomes that Empathi significantly outperforms homology-based methods, tripling the number of annotated homologous groups. On the EnVhog database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. On complete genomes taken from new viromes, almost twice as many proteins are annotated using our method, predictions are consistent when compared to existing tools and Empathi predictions are highly colocalized. In addition, by leveraging Empathis ability to assign multiple labels to the same protein, it is possible to identify multifunctional proteins such as virion-associated lysins. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.","published":"10.1038\/s41467-025-64177-5","server":"bioRxiv"},{"title":"YX0798 Is a Highly Potent, Selective, and Orally Effective CDK9 Inhibitor for Treating Aggressive Lymphoma","authors":"Jiang, V.; Xue, Y.; Kim, H.; Cai, Q.; Zhang, T.; Nie, L.; McIntosh, J.; Liu, Y.; Chen, H.; Zhou, J.; Wang, M.","author_corresponding":"Vivian Jiang","author_corresponding_institution":"The University ot Texas MD Anderson Cancer Center","doi":"10.1101\/2024.12.31.629756","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.629756.source.xml","abstract":"Non-genetic transcription evolution has been increasingly explored and recognized to drive tumor cell progression and therapeutic resistance. As the regulation hub of transcription machinery, cyclin-dependent kinase 9 (CDK9) is the gatekeeper of RNA polymerase II (Pol II) transcription, and CDK9 dysfunction results in transcriptomic reprogramming and tumor cell progression. We recently reported that the HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma (MCL) through transcriptomic reprogramming. We also showed that targeting CDK9 by AZD4573 and enitociclib is a safe and effective treatment in preclinical MCL models, supporting CDK9 as a valid therapeutic target for MCL. However, current CDK9 inhibitors (CDK9i) under therapeutic development have room for improvement due to limited target selectivity and oral bioavailability. To this end, YX0798 was discovered to be a novel CDK9i through structural optimization. YX0798 demonstrated remarkable target selectivity and high affinity in binding to CDK9. Furthermore, YX0798 showed good oral bioavailability. YX0798, when administrated orally (5 mg\/kg, daily), led to an efficacious anti-tumor activity in vivo and showed the potency in overcoming therapeutic resistance. Mechanistically, YX0798 downregulated the short-lived oncoprotein c-MYC and pro-survival protein MCL-1 as a common mechanism of CDK9 inhibition. Moreover, YX0798 disrupted the cell cycle and resulted in transcriptomic reprogramming, eventually leading to cell death. Together, these data demonstrate that YX0798 has oral bioavailability, exquisite selectivity, and anti-tumor potency that results from driving transcription reprogramming towards tumor cell killing.\n\nKEY POINTSO_LIYX0798 showed high selectivity, target binding affinity, and anti-tumor efficacy in overcoming resistance to various therapies.\nC_LIO_LIYX0798 had good oral pharmacokinetics and anti-tumor effects that resulted from transcription reprogramming towards tumor cell killing.\nC_LI","published":"10.1182\/bloodadvances.2025016511","server":"bioRxiv"},{"title":"Tetralone-ABA enhances winter cold acclimation, reduces deacclimation, and delays budbreak in V. vinifera and V. hybrid grapevines","authors":"Wang, H.; Pan, Y.; Londo, J. P.","author_corresponding":"Jason Paul Londo","author_corresponding_institution":"School of Integrative Plant Science, Horticulture section, Cornell University-Cornell AgriTech, Geneva, NY, USA","doi":"10.1101\/2024.12.31.630556","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"plant biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630556.source.xml","abstract":"Climate change-related acute winter freezes and unseasonal false springs have become significant and predictable risks for grape growers across North America and Eurasia. Novel strategies to enhance resilience during the dormant season, particularly by improving bud cold hardiness and delaying budbreak, are urgently needed for the sustainability of grape and wine production. In this study, we evaluated a synthetic abscisic acid (ABA) analog, tetralone-ABA (ABA-1102), as a sprayable product for inducing these traits in three grapevine cultivars:  Riesling,  Cayuga White, and their progeny,  Aravelle. We determined that post-harvest foliar application of tetralone-ABA promoted early leaf senescence, induced cultivar-specific bud cold hardiness enhancement during cold acclimation, slowed deacclimation under controlled and field conditions, and delayed budbreak in spring without affecting growing season phenology, physiology or harvest yield. Transcriptomic analysis of during deacclimation assays suggests that tetralone-ABAs effect on delaying deacclimation may result from its suppression of the activation of growth-related pathways under growth-permissive conditions. Detailed investigations of these pathways indicate that tetralone-ABA may have modulated critical biological processes such as cell wall remodeling, sugar metabolism, and ABA signaling. Overall, this study provides novel insights into the genetic control of grapevine deacclimation, highlights ABAs role in grapevine dormant season physiology, and demonstrates tetralone-ABAs potential as a promising tool for improving dormant season viticulture resilience, offering a new strategy to protect grapevines against the increasing threats posed by climate change.","published":"10.1016\/j.stress.2025.100861","server":"bioRxiv"},{"title":"Circuit dynamics of approach-avoidance conflict in humans","authors":"Staveland, B. R.; Oberschulte, J.; Kim-McManus, O.; Willie, J. T.; Brunner, P.; Dastjerdi, M.; Lin, J. J.; Hsu, M.; Knight, R. T.","author_corresponding":"Robert T Knight","author_corresponding_institution":"University of California, Berkeley","doi":"10.1101\/2024.12.31.630927","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630927.source.xml","abstract":"Debilitating anxiety is pervasive in the modern world. Choices to approach or avoid are common in everyday life and excessive avoidance is a cardinal feature of anxiety disorders. Here, we used intracranial EEG to define a distributed prefrontal-limbic circuit supporting approach and avoidance. Presurgical epilepsy patients (n=20) performed a continuous-choice, approach-avoidance conflict decision-making task inspired by the arcade game Pac-Man, where patients trade-off harvesting rewards against potential losses from attack by the ghost. As patients approached increasing rewards and threats, we found evidence of a limbic circuit mediated by increased theta power in the hippocampus, amygdala, orbitofrontal cortex (OFC) and anterior cingulate cortex (ACC), that drops rapidly during avoidance. Theta band connectivity within this circuit and with the lateral prefrontal cortex increases during approach and falls during avoidance, and amygdala and lateral frontal activity granger-caused the theta oscillations in both the OFC and ACC. Importantly, the degree of network connectivity predicted how long patients approach, with enhanced network synchronicity extending approach times. Finally, when threat is imminent, the system dynamically switches to a sustained increase in high-frequency activity (70-150Hz) in the middle frontal gyrus (MFG), tracking the degree of threat. The results provide evidence for a distributed prefrontal-limbic circuit, mediated by theta oscillations and high frequency activity, underlying approach-avoidance conflict in humans.","published":"NA","server":"bioRxiv"},{"title":"Detection of HTTex1p by western blot and immunostaining of HD human and mouse brain using neo-epitope antibody P90 highlights impact of CAG repeat expansion on its size, solubility, and response to MSH3 silencing","authors":"Sapp, E.; Boudi, A.; Iwanowicz, A.; Belgrad, J.; Miller, R.; O'Reilly, D.; Yamada, K.; Deng, Y.; Joni, M.; Li, X.; Kegel-Gleason, K.; Khvorova, A.; Reiner, A.; Aronin, N.; DiFiglia, M.","author_corresponding":"Marian DiFiglia","author_corresponding_institution":"Massachusetts General Hospital","doi":"10.1101\/2024.12.31.630891","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630891.source.xml","abstract":"HTT1a was identified in human and mouse Huntingtons disease brain as the pathogenic exon 1 mRNA generated from aberrant splicing between exon 1 and 2 of HTT that contributes to aggregate formation and neuronal dysfunction.1 Detection of the huntingtin exon 1 protein (HTT1a) has been accomplished with fluorescence-based reporter assays (Meso Scale Discovery, Homogeneous Time Resolved Fluorescence) and immunoprecipitation assays in Huntingtons disease knock-in mice but direct detection in homogenates by gel electrophoresis and western blot assay has been lacking. Subcellular fractions prepared from mouse and human Huntingtons disease brain were separated by gel electrophoresis and probed by western blot with neo-epitope monoclonal antibodies 1B12 and 11G2 directed to the C-terminal eight residues of HTT1a. In caudate putamen of an allelic series of 6 month old Huntingtons disease knock-in mice (Q50, Q80, Q111, Q140 and Q175) HTT1a migration was inversely correlated with CAG repeat length and appeared as a SDS soluble high molecular mass smear in Q111, Q140 and Q175 mice but weakly in Q80 and not in WT mice or Q50 indicating a CAG repeat size threshold for detecting HTT1a. HTT1a immunoreactivity diminished if 1B12 and 11G2 antibodies were preincubated with an eight amino acid peptide containing the C-terminus of HTT1a but not with unrelated peptide sequence. Migration of HTT1a and its high molecular mass smear changed with age in caudate putamen of Q111, Q175 and YAC128 mice. Treating Q111 mice with siRNA to MSH3, a modifier of CAG repeat expansion, significantly reduced levels of the high molecular mass smear indicating that the effects of curbing CAG repeat expansion were quantifiable. A prominent 56-60 kDa doublet detected by 1B12 and 11G2 antibodies in lysates from human Huntingtons disease brain was not blocked by preincubation with C-terminal HTT1a blocking peptide and also appeared in brains of Parkinsons disease patients. 1B12 and 11G2 antibodies did not immunoprecipitate HTT proteins from either Huntingtons disease mouse or human brain lysates using conditions that pulled down full length HTT with anti-HTT antibody 2B7. Altogether these data show that 11G2 and 1B12 antibodies can be used in western blot assays to track and quantify immunoreactive HTT1a levels, solubility, and subcellular localization in Huntingtons disease mouse brain.\n\nAbbreviated SummarySapp et al., report that pathogenic exon 1 protein HTT1a is detected in brain of mouse models of Huntingtons disease by direct western blot assay using monoclonal antibodies 11G2 and 1B12. Lowering MSH3 mRNA in the caudate putamen to prevent CAG repeat expansion reduced levels of HTT1a.","published":"NA","server":"bioRxiv"},{"title":"Brain activation for language and its relationship to cognitive and linguistic measures","authors":"Balboni, I.; Rampinini, A.; Kepinska, O.; Berthele, R.; Golestani, N.","author_corresponding":"Irene Balboni","author_corresponding_institution":"University of Geneva","doi":"10.1101\/2024.12.31.630909","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630909.source.xml","abstract":"Language learning and use relies on both domain-specific and domain-general cognitive and sensory-motor functions. Evolutionary and developmental perspectives, as well as the use of language in interaction, suggest an overlap between language and other skills. Building on our previous behavioural findings, which outlined a consistent behavioural association between language and domain-general skills, we investigated brain-behavioural associations using story listening during fMRI and behavioural measures of language, reading, multilingual experience, cognition, musicality, arithmetic, and motor skills. Participants varied in multilingual language experience and reading aptitudes, including both typical (TRs) and dyslexic readers (DRs). Using multivariate Partial Least Squares correlation, we identified a main component linking cognitive, linguistic, and phonological measures to brain areas underlying lexico\/semantics, combinatorial processing, and amodal semantic processing. A second analysis excluding DRs showed closer associations between cognitive\/linguistic, literacy, phonological and memory processes within the same brain network as in the full sample. Here, we also isolated additional, complementary components, including one involving speed, automatization and lexical access, linked to auditory and motor brain areas. This suggests greater coherence and more integrated,  expert processing in TRs. This work is a first step in exploring complex relationships between language and non-linguistic functions that are important to it.","published":"10.1093\/cercor\/bhaf231","server":"bioRxiv"},{"title":"Different mechanisms link gain and loss of kinesin functions to axonal degeneration","authors":"Liew, Y.-T.; Voelzmann, A.; Owens, M.; Day, M.; Cairns, W.; Jones, E.; Dajas-Bailador, F.; McCann, S.; Murphy, T.; Tortoishell, H.; Parkin, J.; Bailey, D. M. D.; Landgraf, M.; Prokop, A.","author_corresponding":"Andreas Prokop","author_corresponding_institution":"The University of Manchester","doi":"10.1101\/2024.12.31.630930","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630930.source.xml","abstract":"Axons are the slender, often meter-long projections of neurons that form the biological cables wiring our bodies. Most of these delicate structures must survive for an organisms lifetime, meaning up to a century in humans. Long-term maintenance and sustained functionality of axons requires motor protein-driven transport distributing life-sustaining materials and organelles to places of need. It seems therefore plausible that loss of motor function would cause axon degeneration; however, also gain-of-function conditions were linked to disorders including motor neuron disease or spastic paraplegia. To understand this phenomenon, we studied [~]40 genetic manipulations of motor proteins, cargo linkers and regulators of reactive oxygen species in one standardised Drosophila primary neuron system. Using axonal microtubule bundle organisation as a relevant readout reflecting the state of axon integrity, we found that losses of Dynein heavy chain, KIF1A\/Unc-104 and KIF5\/Kinesin heavy chain (Khc) all cause bundle disintegration in the form of chaotically curled microtubules. Detailed functional studies of Khc and its adaptor proteins revealed that losses of mitochondrial or lysosomal transport cause ROS dyshomeostasis, which is a microtubule-curl-inducing condition in fly and mouse neurons alike. We find that hyper-activated Khc induces the same microtubule curling phenotype, not through ROS but likely more directly through enhanced mechanical forces. Studies with loss of Unc-104 or KIFBP and expression of an ALS-linked mutant form of the human Khc orthologue KIF5A suggest that loss or hyperactivation of different types of transport motors cause MT curling as a shared feature. We discuss a model which can explain our findings and their relevance for understanding motor-linked neurodegeneration.","published":"NA","server":"bioRxiv"},{"title":"Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer's disease neuropathology","authors":"Rodriguez-Rodriguez, P.; Wang, W.; Tsagkogianni, C.; Feng, I.; Morello-Megias, A.; Jain, K.; Alanko, V.; Kahvecioglu, H.; Mohammadi, E.; Li, X.; Flajolet, M.; Sandebring-Matton, A.; Maioli, S.; Vidal, N.; Milosevic, A.; Roussarie, J.-P.","author_corresponding":"Jean-Pierre Roussarie","author_corresponding_institution":"Boston University Chobanian & Avedisian School of Medicine","doi":"10.1101\/2024.12.31.630881","date":"2025-01-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630881.source.xml","abstract":"Neurons located in layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimers disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that curb the disease before symptom onset. Here we performed cell-type specific profiling of human EC at the onset of AD neuropathology. We identify an early response to amyloid pathology by microglia and oligodendrocytes. Importantly, we provide the first insight into neuronal alterations that coincide with incipient tau pathology: the signaling pathway for Reelin, recently shown to be a major AD resilience gene is dysregulated in ECII neurons, while the secreted synaptic organizer molecules NPTX2 and CBLN4, emerging AD biomarkers, are downregulated in surrounding neurons. By uncovering the complex multicellular landscape of EC at these early AD stages, this study paves the way for detailed characterization of the mechanisms governing NFT formation and opens long-needed novel therapeutic avenues.","published":"NA","server":"bioRxiv"},{"title":"Cortical responses to conflicting binocular stimuli in mouse primary visual cortex","authors":"Montgomery, D. P.; Bowen, D. A.; Wu, J.; Bear, M. F.; Gaier, E. D.","author_corresponding":"Eric D Gaier","author_corresponding_institution":"Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA","doi":"10.1101\/2024.12.31.630912","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630912.source.xml","abstract":"Binocular vision requires that the brain integrate input from both eyes to form a unified percept. Small interocular differences support depth perception (stereopsis), while larger disparities can cause diplopia or binocular rivalry. The neural mechanisms by which early visual circuits process concordant versus conflicting binocular signals remain incompletely understood, particularly in the case of large disparities. Here, we used visually evoked potential (VEP) recordings, unit recordings, and 2-photon calcium imaging in the binocular region of mouse primary visual cortex (bV1) to examine how distinct forms of binocular disparity engage local circuits. Using a dichoptic display, we found that interocular phase disparities reduced VEP magnitude through decreased neuronal firing early in the response (40-80 ms after stimulus onset). In contrast, orientation disparities also decreased VEP magnitude, but via increased firing later in the response (100-200 ms). This late activity was enhanced in both regular-spiking (putative excitatory) and fast-spiking (putative parvalbumin-positive inhibitory) units. In contrast, calcium imaging revealed that somatostatin-positive interneurons were suppressed during orientation conflict. These findings suggest that phase differences suppress bV1 responses via feedforward mechanisms, while orientation disparities prolong activity through disinhibition mediated by somatostatin-positive interneurons. Our results identify distinct circuit pathways recruited by different forms of binocular conflict, clarify how early visual cortex contributes to binocular integration, and provide a foundation for investigating perceptual suppression and rivalry.\n\nIMPACT STATEMENTDistinct forms of binocular conflict engage separate circuit mechanisms in mouse primary visual cortex, revealing how interocular disparities shape population activity through feedforward and disinhibitory processes.","published":"NA","server":"bioRxiv"},{"title":"Nerve Growth Factor Signaling Tunes Axon Maintenance Protein Abundance and Kinetics of Wallerian Degeneration","authors":"Danos, J. A.; Addemir, M.; McGettigan, L.; Summers, D.","author_corresponding":"Daniel Summers","author_corresponding_institution":"University of Iowa","doi":"10.1101\/2024.12.31.630780","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630780.source.xml","abstract":"Neurotrophic factors are critical for establishing functional connectivity in the nervous system and sustaining neuronal survival through adulthood. As the first neurotrophic factor purified, nerve growth factor (NGF) is extensively studied for its prolific role in axon outgrowth, pruning, and survival. Applying NGF to diseased neuronal tissue is an exciting therapeutic option and understanding how NGF regulates local axon susceptibility to pathological degeneration is critical for exploiting its full potential. Our study identifies surprising connections between NGF signaling and proteostasis of axon maintenance factors. NGF deprivation increases Nmnat2 and Stmn2 protein levels in axon segments with a corresponding delay in Wallerian degeneration. Conversely, acute NGF stimulation reduces local abundance of these axon maintenance factors and accelerates Wallerian degeneration. Pharmacological studies implicate phospholipase C as the key effector in TrkA activation, which drives degradation of palmitoylated Stmn2. While seemingly opposed to neuroprotective activities well-documented for NGF, downregulating Nmnat2 and Stmn2 favors axonal outgrowth over transient hyper-susceptibility to Sarm1-dependent degeneration. This new facet of NGF biology has important implications for axonal remodeling during development and sustained integrity through adulthood.","published":"10.1091\/mbc.E25-01-0005","server":"bioRxiv"},{"title":"Nurr1 orchestrates claustrum development and functionality","authors":"Yan, K.; Newman, A. G.; Lange, P.; Mueller, S.; Marco Foddis, M.; Mantwill, M.; Finke, C.; Koch, S. P.; Boehm-Sturm, P.; Deng, P.; Long, M.; Tarabykin, V.","author_corresponding":"Victor Tarabykin","author_corresponding_institution":"Institute of Cell Biology and Neurobiology, Charite Universitaetsmedizin Berlin, Germany; Institute of Neurosciences, Lobachevsky State University of Nizhny Nov","doi":"10.1101\/2024.12.31.630879","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630879.source.xml","abstract":"Claustrum is the part of the forebrain known to be most widely interconnected tissue with almost all global regions. It is believed to be involved in coordinating multiple cognitive behaviors including consciousness formation. However, little is known about the molecular mechanisms underlying its development and involvement in behavioral control. Here we show that Nurr1 (Nr4a2) is the key transcription factor orchestrating claustral morphogenesis, functional connectivity and thus behaviors. Nurr1 deficient claustral cells aberrantly migrate into insular cortex, shaping claustrum into an abnormal wing-like structure, and ectopically turn on insular corticex genetic program. Accordingly, functional connectivity of the claustrum is not properly formed and relevant behaviors are dysregulated in Nurr1 deficient mice. We show that Nurr1 regulates claustral neuron positioning by suppressing G-protein signaling.","published":"10.1002\/advs.202508999","server":"bioRxiv"},{"title":"The limit of life at extremely low water activity:Lithium-concentration ponds in a solar saltern(Salar de Atacama, Chile)","authors":"Demergasso, C.; Avendano, P.; Escuti, C.; Veliz, R.; Chong Diaz, G.; Pedros Alio, C.","author_corresponding":"Cecilia Demergasso","author_corresponding_institution":"Biotechnology Center \"Profesor Alberto Ruiz\", Universidad Catolica del Norte","doi":"10.1101\/2024.12.31.629924","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.629924.source.xml","abstract":"Extremely hyper-saline ponds from an industrial lithium-concentration process in solar salterns in the Atacama Desert were studied to determine the limits of life at very low water activity. Water activity (aw) of 0.61 is the lowest aw value for growth of living beings recorded to date. Xerophilic (sometimes called osmophilic) filamentous fungi and yeasts are predominant in high-sugar foods with such low aw values. Some microorganisms are capable of growth at that water activity level. By contrast, high-salt environments are almost exclusively populated by prokaryotes, notably the Halobacteria class and some Bacteroidetes, capable of growing in saturated NaCl (aw 0.75). The lowest aw that can be achieved by the addition of NaCl is 0.75 (saturation point for NaCl). Crystallizer ponds in Li+ concentration plants reach down to water activity levels around 0.1. The aim of this study was to determine how far along the salinity gradient could life be found. Cell counts were attempted by epifluorescence microscopy and qPCR with bacterial and archaeal universal primers. Biomass for DNA extraction was obtained by an optimized protocol involving dialysis of brines previously fixed with ethanol. Prokaryotic diversity was studied by DNA extraction, PCR, qPCR and 16S rRNA amplicon sequencing in different ponds along the salinity gradient. Archaeal DNA was found in the lower salinity ponds, while bacterial DNA was found along the whole gradient. Bacterial cDNA was retrieved from ponds down to an aw of 0.2. Moreover, bacteria could be grown in enriched cultures from most ponds.","published":"NA","server":"bioRxiv"},{"title":"ZapA employs a two-pronged mechanism to facilitate Z ring formation in Escherichia coli","authors":"Cui, Y.; Gong, H.; Yan, D.; Li, H.; Yang, W.; Li, Y.; Chen, X.; Lutkenhaus, J.; Huang, S.-Y.; Yang, X.; Du, S.","author_corresponding":"Shishen Du","author_corresponding_institution":"Wuhan University","doi":"10.1101\/2024.12.31.629942","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.629942.source.xml","abstract":"The tubulin-like protein FtsZ assembles into the Z ring which leads to the assembly and activation of the division machinery in most bacteria. ZapA, a widely conserved protein that interacts with FtsZ, plays a pivotal role in organizing FtsZ filaments into a coherent Z ring. Previous studies revealed that ZapA forms a dumbbell-like tetramer that binds cooperatively to FtsZ filaments and aligns them in parallel, leading to the straightening and organization of FtsZ filament bundles. However, how ZapA interacts with FtsZ remains obscure. In this study, we uncover how ZapA interacts with FtsZ to facilitate Z ring formation in Escherichia coli. We find that mutations affecting surface exposed residues at the junction between adjacent FtsZ subunits in a filament as well as in an N-terminal motif of FtsZ weaken its interaction with ZapA in vivo and in vitro, indicating that ZapA binds to these regions of FtsZ. Consistent with this, ZapA prefers FtsZ polymers over monomeric FtsZ molecules and site-specific crosslinking confirmed that the dimer head domain of ZapA is in contact with the junction of FtsZ subunits. As a result, disruption of the putative interaction interfaces between FtsZ and ZapA abolishes the midcell localization of ZapA. Taken together, our results suggest that ZapA tetramers grab the N-terminal tails of FtsZ and then bind to the junctions between FtsZ subunits in the filament to straighten and crosslink parallel FtsZ filaments into the Z ring.\n\nSignificanceZapA is a widely conserved FtsZ-associated protein that promotes the organization of the Z ring, the key cytoskeletal element in the bacterial divisome. Although ZapA is known to crosslink FtsZ filaments, how it interacts with FtsZ remains enigmatic. In this study, we find that E. coli ZapA utilizes a dual binding mode in which it binds the junction between FtsZ subunits in a filament and to an N-terminal motif in FtsZ so that it can straighten and crosslink parallel FtsZ filaments simultaneously. Since the junction is formed when FtsZ polymerizes and falls apart when FtsZ depolymerizes, this interaction mode indicates that ZapA employs the polymerization dynamics of FtsZ to organize the filaments into the Z ring.","published":"NA","server":"bioRxiv"},{"title":"Dynamic balance of H3K9me2 heterochromatin by CoREST-2 and RE-1 in growing neurons","authors":"Drube, J. F.; Cardozo-Gizzi, A.; Rozes-Salvador, V.; Martinez, I.; Ceschin, D. G.; Giordano, L.; Serniotti, L.; Gastaldi, L.; Remedi, M.; Moyano, A. L.; Caceres, A.; Wilson, C.","author_corresponding":"Carlos Wilson","author_corresponding_institution":"Centro de Investigacion en Medicina Traslacional Severo R. Amuchastegui (CIMETSA), Instituto Universitario de Ciencias Biomedicas de Cordoba; Consejo Nacional d","doi":"10.1101\/2024.12.31.629745","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.629745.source.xml","abstract":"A well-balanced chromatin dynamic is vital for the survival and physiology of all cells, including brain neurons. Heterochromatin, commonly associated with transcriptional silencing, also plays significant roles in maintaining genomic stability and facilitating DNA-repair processes. Notably, the bimethylation of histone H3 at lysine 9 (H3K9me2), a hallmark of repressive heterochromatin, supports the axonal specification of neurons. However, neuronal maintenance of H3K9me2 equilibrium remains understudied.\n\nIn this work, we unveil a dynamic equilibrium of H3K9me2 regulated by the epigenetic factor CoREST-2 and RE-1 DNA motifs, sustaining axonal and dendritic outgrowth. Using primary cultures of rat hippocampal neurons and a combination of advanced imaging techniques, we observed an enriched nuclear accumulation of CoREST-2 and H3K9me2 along neuronal development. Genetic silencing of CoREST-2 induced axon-dendrite retraction, accompanied by an increase in nuclear levels of H3K9me2. To further investigate heterochromatin structure at the nanoscale, we employed STED nanoscopy and discovered that H3K9me2 is organized into small nanodomains, which were notably enlarged following the suppression of CoREST-2. In contrast, the genetic blockade of RE-1 DNA motifs led to axon-dendrite retraction alongside the disassembly of H3K9me2 nanodomains.\n\nThese findings highlight that CoREST-2 and RE-1 sites actively shape neuronal H3K9me2 heterochromatin. Moreover, they uncover that maintaining a precise balance of H3K9me2 is essential for the extension of axons and dendrites, underpinning the connectivity and plasticity of brain neurons.","published":"NA","server":"bioRxiv"},{"title":"Argonaute proteins regulate the timing of the spermatogenic transcriptional program","authors":"Carro, M. d. l. M.; Dziubek, A.; Touey, A.; Popkowski, E.; Abdelmassih, M.; Simon, L. E.; Tanis, S. L.; Ahmed, F.; Grenier, J. K.; Grimson, A.; Cohen, P. E.","author_corresponding":"Paula E Cohen","author_corresponding_institution":"Cornell University","doi":"10.1101\/2024.12.31.630913","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630913.source.xml","abstract":"Argonaute proteins are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we show that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes where they are required for transcriptional silencing of XY-linked genes, known as Meiotic Sex Chromosome Inactivation (MSCI). Using an Ago413-\/- mouse, we show that AGO3 and AGO4 are key regulators of spermatogenesis, orchestrating expression of meiosis-related genes during prophase I while maintaining silencing of spermiogenesis genes. Premature overexpression of spermiogenesis genes during prophase I in Ago413-\/- mice results in subfertility, altered sperm morphology and reduced fertilization capability. We also identify BRG1, a BAF complex subunit, as an AGO3 interactor. Loss of AGO3 and AGO4 results in increased BRG1 in spermatocytes, suggesting that AGO3 aids in removing BRG1 from the XY chromatin to achieve MSCI and demonstrating a meiotic role for AGO3 in transcriptional control through the chromatin remodeling machinery.","published":"NA","server":"bioRxiv"},{"title":"Single-cell and spatial transcriptomics uncover the role of B chromosomes in driving plant invasiveness","authors":"Wang, C.; Ord, J.; Yan, M.; Shao, H.; Lin, L.; Salojarvi, J.; Liu, L.; Guo, W.","author_corresponding":"Cui Wang","author_corresponding_institution":"University of Helsinki","doi":"10.1101\/2024.12.31.630906","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630906.source.xml","abstract":"Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the common reed (Phragmites australis), a grass species that became invasive in North America after introduction from Europe, to unravel the molecular mechanisms of its invasiveness. By integrating single-cell RNA sequencing, spatial transcriptomics, and comparative genomics, we constructed a single-cell atlas of P. australis and identified 19 transcriptionally distinct cell types, including shoot apical meristem, epidermal, and vascular tissues. Comparative analysis of common garden-grown native (European) and invasive (North American) populations revealed a significant proportion of differentially expressed genes (DEGs) located on B chromosomes, which underwent copy number expansion in invasive genomes. The proportion of B chromosome genes in DEGs varies across cell types, with the highest proportions observed in the epidermis and mesophyll, and lower proportions in the vascular tissues. Gene IMPA-3, a B chromosome gene likely derived from transposable element activity, exhibited an elevated mutation rate compared to its ancestral counterparts, potentially enhancing adaptive evolution in invasive populations. Invasive individuals also displayed molecular regulatory networks related to photosynthetic efficiency, stress tolerance, and growth-defense trade-offs. Together, our findings provide a cell-type-resolved molecular atlas of a non-model invasive plant and offer key insights into the cellular and genomic architecture of plant invasiveness, with implications for ecological management.","published":"NA","server":"bioRxiv"},{"title":"40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion","authors":"Wakabayashi, H.; Zhu, M.; Grayhack, E.; Mathews, D.; Ermolenko, D.","author_corresponding":"Dmitri Ermolenko","author_corresponding_institution":"University of Rochester","doi":"10.1101\/2024.12.30.630811","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"genetics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630811.source.xml","abstract":"During eukaryotic translation initiation, the small (40S) ribosomal subunit is recruited to the 5' cap and subsequently scans the 5' untranslated region (5' UTR) of mRNA in search of the start codon. The molecular mechanism of mRNA scanning remains unclear. Here, using GFP reporters in Saccharomyces cerevisiae cells, we show that order-of-magnitude variations in the lengths of unstructured 5' UTRs have a modest effect on protein synthesis. These observations indicate that mRNA scanning is not rate limiting in yeast cells. Conversely, the presence of secondary structures in the 5' UTR strongly inhibits translation. Loss-of-function mutations in translational RNA helicases eIF4A and Ded1, as well as mutations in other initiation factors implicated in mRNA scanning, namely eIF4G, eIF4B, eIF3g and eIF3i, produced a similar decrease in translation of GFP reporters with short and long unstructured 5' UTRs. As expected, mutations in Ded1, eIF4B and eIF3i severely diminished translation of the reporters with structured 5' UTRs. Evidently, while RNA helicases eIF4A and Ded1 facilitate 40S recruitment and secondary structure unwinding, they are not rate-limiting for the 40S movement along the 5' UTR. Hence, our data indicate that, instead of helicase-driven translocation, one-dimensional diffusion predominately drives mRNA scanning by the 40S subunits in yeast cells.","published":"10.1261\/rna.080493.125","server":"bioRxiv"},{"title":"Iris Crypts Could Reduce the Chance of Angle Closure: A Computational Biomechanics Study Derived from Clinical and Human Iris Data","authors":"Tan, R. K. Y.; Tun, T. A.; Braeu, F. A.; Perera, S. A.; Girard, M. J. A.","author_corresponding":"Michael J.A. Girard","author_corresponding_institution":"Ophthalmic Engineering & Innovation Laboratory (OEIL)","doi":"10.1101\/2024.12.30.630843","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630843.source.xml","abstract":"PurposeTo investigate the effect of crypts during pupil constriction and dilation on the potential for angle closure by performing finite element analysis using clinical and experimental data on human tissues.\n\nMethodsA computational model was developed to determine the influence of small crypts (surface area of [~]0.015 mm2) and large crypts (surface area of 0.300 mm2) on the anterior chamber angles during pupil dilation. The model needed permeability data from human subjects, hence 21 enucleated human eyes (72 hours post-mortem) were procured and subjected to a flow set-up previously reported. Finally, 66 subjects were recruited to measure pupil constriction and dilation levels from optical coherence tomography (OCT) videos.\n\nResultsThe hydraulic permeability of the human iris stroma was determined to be 2.55 {+\/-} 1.93 x 10-5 mm2\/Pa{middle dot}s. The average iris constriction and dilation durations were 0.710 {+\/-} 0.213 seconds and 1.24 {+\/-} 0.401 seconds, respectively, with pupil diameter changes of 1.16 {+\/-} 0.39 mm and 0.75 {+\/-} 0.27 mm, respectively. The computational models had starting anterior chamber angles of 51.30{degrees} and final anterior chamber angles of 26.81{degrees} once steady state has been reached. In an extreme case with decreased anterior border layer (ABL) permeability, the anterior chamber angle narrowed to 12.37{degrees}, but the presence of crypts kept the angle above 20.36{degrees}, highlighting the potential of crypts in preventing angle closure.\n\nConclusionsOur findings on the biomechanics of crypts in the iris may drive the development of novel treatments by altering ABL morphology, providing an alternative bypass for angle closure prevention in high-risk patients.","published":"10.1167\/iovs.66.5.36","server":"bioRxiv"},{"title":"Wavefront estimation through structured detection in laser scanning microscopy","authors":"Fersini, F.; Zunino, A.; Morerio, P.; Baldini, F.; Booth, M. J.; Del Bue, A.; Vicidomini, G.","author_corresponding":"Giuseppe Vicidomini","author_corresponding_institution":"Istituto Italiano di Tecnologia","doi":"10.1101\/2024.12.31.630574","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630574.source.xml","abstract":"Laser scanning microscopy (LSM) is the base of numerous advanced imaging techniques, including confocal laser scanning microscopy (CLSM), a widely used tool in life sciences research. However, its effective resolution is often compromised by optical aberrations, a common challenge in all optical systems. While adaptive optics (AO) can correct these aberrations, current methods face significant limitations: Aberration estimation, which is central to any AO approach, typically requires specialized hardware or prolonged sample exposure, rendering these methods sample-invasive, and less user-friendly. In this study, we introduce a simple and efficient AO approach for CLSM systems equipped with a detector array - the same of super-resolved image-scanning microscopy - and an AO element for beam shaping. We demonstrate that imaging datasets acquired with a detector array inherently encode aberration information. Leveraging this property, we developed a custom convolutional neural network capable of decoding aberrations, up to the 11th Zernike coefficient, directly from a single acquisition. This method enables a new generation of AO implementations for LSM, offering an accessible solution that minimizes sample stress while achieving high-resolution, and aberration-free imaging.","published":"10.1364\/BOE.559899","server":"bioRxiv"},{"title":"Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump","authors":"Sim, A. D.; Ling, M. H.; Chen, Y.; Lu, H.; See, Y. X.; Perrin, A.; Leng Agnes, O. B.; Cao, E. Y.; Chia, B.; Liu, J.; Wu\u0308stefeld, T.; Shin, J.; Go\u0308ke, J.","author_corresponding":"Jonathan G\u00f6ke","author_corresponding_institution":"Genome Institute of Singapore","doi":"10.1101\/2024.12.30.630828","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630828.source.xml","abstract":"Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth.\n\nHere we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5 and 3 selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.","published":"NA","server":"bioRxiv"},{"title":"Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data","authors":"Wang, X.; Shi, D.; Xue, F.; Liu, Y.; Yang, H.; Jiang, L.","author_corresponding":"Xiaotao Wang","author_corresponding_institution":"Fudan University","doi":"10.1101\/2024.12.30.630839","date":"2025-01-01","version":"1","type":"new results","license":"cc_no","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630839.source.xml","abstract":"Accurately detecting enhancer-promoter loops from genome-wide interaction data, such as Hi-C, is crucial for understanding gene regulation. Current normalization methods, such as Iterative Correction and Eigenvector decomposition (ICE), are commonly used to remove biases in Hi-C data prior to chromatin loop detection. However, while structural or CTCF-associated loop signals are retained, enhancer-promoter interaction signals are often greatly diminished after ICE normalization and similar methods, making these regulatory loops harder to detect. To address this limitation, we developed Raichu, a novel method for normalizing chromatin contact data. Raichu identifies nearly twice as many chromatin loops as ICE, recovering almost all loops detected by ICE and revealing thousands of additional enhancer-promoter loops missed by ICE. With its enhanced sensitivity for regulatory loops, Raichu detects more biologically meaningful differential loops between conditions in the same cell type. Furthermore, Raichu performs consistently across different sequencing depths and platforms, including Hi-C, HiChIP, and single-cell Hi-C, making it a versatile tool for uncovering new insights into three- dimensional (3D) genomic organization and transcriptional regulation.","published":"10.1038\/s41467-026-69082-z","server":"bioRxiv"},{"title":"Microbial general model: Leveraging large language model for contextualized microbiome analysis","authors":"Zhang, H.; Kang, Z.; Zhang, Y.; Song, L.; Ning, K.; Yang, R.","author_corresponding":"Kang Ning","author_corresponding_institution":"Huazhong University of Science and Technology","doi":"10.1101\/2024.12.30.630825","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630825.source.xml","abstract":"Microbial communities significantly impact medicine, biotechnology, and agriculture. Advanced sequencing technologies have generated extensive microbiome data, enabling the discovery of substantial evolutionary and ecological patterns. However, traditional supervised learning methods struggle to capture universal patterns in microbial community data, largely due to the large data heterogeneity and profound batch effects among samples, rendering it difficult to classify samples as well as detect biomarkers from millions of samples, not to say the intricate but important dynamic patterns from a variety of contextualized sceneries. In this study, we introduce the Microbial General Model (MGM), the first microbiome community foundation model pre-trained on a dataset of 263,302 microbiome samples using language modeling techniques. MGM demonstrated significant improvements in microbial community classification compared to traditional machine learning methods. Additionally, MGM has enabled contextualized classification, effectively overcomes cross-regional limitations, showing enhanced performance on intercontinental datasets through transfer learning. Furthermore, fine-tuning MGM on a longitudinal infant dataset revealed distinct keystone genera during development, with Bacteroides and Bifidobacterium exhibiting higher attention weights in vaginal deliveries, and Haemophilus in cesarean deliveries. Finally, through in silico modeling, the model also uncovered novel microbial dynamic patterns in a Crohns disease cohort following antibiotic treatment. In conclusion, by leveraging self-attention and autoregressive pre-training, MGM serves as a versatile model for various downstream microbiome tasks and holds significant potential for achieving contextualized aims.\n\nKey pointsO_LIThe Microbial General Model (MGM) is a foundation model with millions of parameters pre-trained on sub-million microbial community data.\nC_LIO_LIMGM outperforms traditional methods in various microbiome classification and prediction tasks, such as microbial community classification.\nC_LIO_LIMGM effectively captures the spatial and temporal dynamics of microbial communities.\nC_LIO_LIMGM could detect the effects of perturbation on microbial community through in silico experiments.\nC_LI","published":"10.1002\/advs.202513333","server":"bioRxiv"},{"title":"Directionality of two-photon absorption in representative fluorescent proteins","authors":"Lazar, J.; Timr, S.; Rybakova, O.; Khoroshyy, P.; Brynda, J.; Thuen, A.; Drobizhev, M.; Myskova, J.","author_corresponding":"Jitka Myskova","author_corresponding_institution":"1st Faculty of Medicine, Charles University, Czechia","doi":"10.1101\/2024.12.31.630429","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630429.source.xml","abstract":"Molecules of fluorescent proteins (FPs) exhibit anisotropic optical properties. While the directionality of single-photon (1P) absorption and emission in the most commonly used FPs has already been characterized, directionality of their two-photon (2P) excitation remains poorly understood, even though it offers higher sensitivity to molecular orientation and promises to yield more information on molecular orientational distributions than the 1P processes. By measuring optical properties of FP crystals, we have now determined the two-photon absorptivity tensors (2PATs) of the FPs mTurquoise2, eGFP and mCherry. Our results demonstrate the feasibility of experimental 2PAT determinations, provide new insights into molecular mechanisms of 2P absorption in FPs, open a new avenue to rational development of novel biosensors and allow detailed structural interpretation of results obtained with such biosensors.","published":"NA","server":"bioRxiv"},{"title":"Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer.","authors":"Yoffe, L.; Bhinder, B.; Kang, S. W.; Zhang, H.; Singh, A.; Ravichandran, H.; Markowitz, G. J.; Martin, M.; Kim, J.; Zhang, C.; Elemento, O.; Tansey, W.; Bates, S.; McGraw, T. E.; Borczuk, A.; Lee, H.-S.; Altorki, N. K.; Mittal, V.","author_corresponding":"Vivek Mittal","author_corresponding_institution":"Weill Cornell Medicine","doi":"10.1101\/2024.12.31.630523","date":"2025-01-01","version":"1","type":"new results","license":"cc_by","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630523.source.xml","abstract":"Computerized chest tomography (CT)-guided screening in populations at risk for lung cancer has increased the detection of preinvasive subsolid nodules, which progress to solid invasive adenocarcinoma. Despite the clinical significance, there is a lack of effective therapies for intercepting the progression of preinvasive to invasive adenocarcinoma. To uncover determinants of early disease emergence and progression, we used integrated single-cell approaches, including scRNA-seq, multiplexed imaging mass cytometry and spatial transcriptomics, to construct the first high-resolution map of the composition, lineage\/functional states, developmental trajectories and multicellular crosstalk networks from microdissected non-solid (preinvasive) and solid compartments (invasive) of individual part-solid nodules. We found that early disease initiation and subsequent progression are associated with the evolution of immune-suppressive cellular phenotypes characterized by decreased cytotoxic CD8 T and NK cells, increased T cell exhaustion and accumulation of immunosuppressive regulatory T cells (Tregs) and M2-like macrophages expressing TREM2. Within Tregs, we identified a unique population of 4-1BB+ Treg subset enriched for the IL2-STAT5 suppressive pathway with transcription profiles supporting discrete metabolic alterations. Spatial analysis showed increased density of suppressive immune cells around tumor cells, increased exhaustion phenotype of both CD4 and CD8 T cells expressing chemokine CXCL13, and spatial micro-complex of endothelial and lymphocyte interactions within tertiary lymphoid structures. The single-cell architecture identifies determinants of early disease emergence and progression, which may be developed not only as diagnostic\/prognostic biomarkers but also as targets for disease interception. Additionally, our dataset constitutes a valuable resource for the preinvasive lung cancer research community.","published":"NA","server":"bioRxiv"},{"title":"MaiZaic: a robust end-to-end pipeline for mosaicking freely flown aerial video of agricultural fields","authors":"Kharismawati, D. E.; Kazic, T.","author_corresponding":"Dewi E Kharismawati","author_corresponding_institution":"University of Missouri","doi":"10.1101\/2024.12.31.630534","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc","category":"plant biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630534.source.xml","abstract":"Unmanned aerial vehicles (UAVs) are increasingly used for high throughput phenotyping. In principle, freely flown vehicles would permit real-time flexibility in identifying and scouting regions of interest. Mosaicking multiple images provides a high resolution global image and consumer-grade UAVs offer low cost, ease of flying, and excellent RGB cameras. The vehicles inaccurate telemetry complicates estimating the homographies between pairs of frames, the standard mosaicking approach. Moreover, errors accumulate during computation, distorting later portions of the mosaic. Finally, crop fields are particularly challenging to mosaic because their planting is so regular and the plants are so similar, eliminating distinctive features that could guide mosaicking. We propose MaiZaic, an end-to-end pipeline that dynamically samples video frames using optical flow, automates camera and gimbal calibration, estimates homographies with an unsupervised convolutional neural network, detects shots among frames, and generates mini-mosaics. Together, these techniques significantly reduce errors in the output mosaics. Our deep learning model is trained on a comprehensive video dataset comprising different flight trajectories, maize lines, growth stages, and augmented illumination data. MaiZaic is more accurate and faster than ASIFT and more robust than our earlier CorNet and CorNetv2. We demonstrate MaiZaics effectiveness in generating accurate mosaics of imagery captured by freely-flown UAVs and explore its generalizability.\n\nCore ideasO_LIMaiZaic is an end-to-end pipeline to mosaic freely flown agricultural imagery captured with consumer-grade UAVs.\nC_LIO_LIMaiZaic introduces novel algorithms that efficiently choose video frames, calibrate, and mosaic the imagery.\nC_LIO_LIOur unsupervised deep homography estimator, CorNetv3, is 14 times faster and 8.59% more accurare than ASIFT.\nC_LIO_LIMaiZaic generalizes well and mosaicks maize at different growth stages, objects, trajectories, cameras, and pilots.\nC_LIO_LIThe mini-mosaicking algorithm improves mosaic accuracy by interrupting error accumulation.\nC_LI","published":"NA","server":"bioRxiv"},{"title":"Rotationally Stable Dynamics Over Long Timescales Emerge in Neuronal Development","authors":"Burrows, D. R.; Rosch, R. E.","author_corresponding":"Richard E Rosch","author_corresponding_institution":"King's College London","doi":"10.1101\/2024.12.31.630917","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.31.630917.source.xml","abstract":"Neuronal networks must balance the need for stable yet flexible dynamics. This is evident during brain development, when synaptic plasticity during critical windows enables adaptability to changing environments whilst ensuring the stability of population dynamics. The emergence of population dynamics that balance stability and flexibility during development is poorly understood. Here, we investigated developmental brain dynamics in larval zebrafish, using in vivo 2-photon imaging to record single-cell activity across major brain regions from 3-8 days post-fertilisation, a highly plastic period in which hunting behaviours are established. Our findings revealed region-specific trajectories in the development of such dynamic regimes: the telencephalon exhibited increased neuronal excitability and long-range correlations, alongside the emergence of scale invariant avalanche dynamics indicative of enhanced flexibility. Conversely, while other regions showed increased state transitions over development, the telencephalon demonstrated a surprising rise in state stability, characterized by slightly longer dwell times and drastically reduced angular velocity in state space. Remarkably, such rotationally stable dynamics persisted up to 5 seconds into the future, indicating the emergence of strong attractors supporting stability over long timescales. Notably, we observed that telencephalon dynamics were maintained near to but not at a phase transition, thus allowing for robust responses while remaining adaptable to novel inputs. Our results highlight regionally-specific trajectories in the relationship between flexibility and stability, illustrating how developing neuronal populations can self-organize to balance these competing demands.\n\nSignificance StatementBrain networks must balance the flexibility to adapt to new stimuli with the need for stability. This trade-off is particularly important during periods of high plasticity in brain development. Our study investigates this balance by recording single-cell activity across the entire brain of developing larval zebrafish. We discovered that brain dynamics become increasingly diverse, characterized by both short and long bursts of activity, reflecting increased flexibility. Simultaneously, we observed the emergence of stable dynamics, linked to consistent activity patterns over time. Using a modelling approach, we showed that this stability was driven by the formation of stable attractors that shape the dynamic trajectories. These findings highlight how population mechanisms can shape the dynamic interplay between flexibility and stability in regional networks in the developing brain.","published":"NA","server":"bioRxiv"},{"title":"Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer","authors":"Queen, J.; Cing, Z.; Minsky, H.; Nandi, A.; Southward, T.; Ferri, J.; McMann, M.; Iyadorai, T.; Vadivelu, J.; Roslani, A.; Loke, M. F.; Wanyiri, J.; White, J. R.; Drewes, J. L.; Sears, C. L.","author_corresponding":"Cynthia L. Sears","author_corresponding_institution":"Johns Hopkins University School of Medicine","doi":"10.1101\/2024.12.30.630810","date":"2025-01-01","version":"1","type":"new results","license":"cc_by","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630810.source.xml","abstract":"Fusobacterium nucleatum is an oral bacterium known to colonize colorectal tumors, where it is thought to play an important role in cancer progression. Recent advances in sequencing and phenotyping of F. nucleatum have revealed important differences at the subspecies level, but whether these differences impact the overall tumor ecology, and tumorigenesis itself, remain poorly understood. In this study, we sought to characterize Fusobacteria in the tumor microbiome of a cohort of individuals with CRC through a combination of molecular, spatial, and microbiologic analyses. We assessed for relative abundance of F. nucleatum in tumors compared to paired normal tissue, and correlated abundance with clinical and pathological features. We demonstrate striking enrichment of F. nucleatum and the recently discovered subspecies animalis clade 2 (Fna C2) specifically in colon tumors that have biofilms, highlighting the importance of complex community partnerships in the pathogenesis of this important organism.","published":"10.1038\/s41522-025-00717-7","server":"bioRxiv"},{"title":"Single-nucleus RNA sequencing revealed the impact of post-mortem interval on the cellular component and gene expression analysis of mouse brains","authors":"yunxia, G.; Junjie, M.; xiaoying, M.; Hao, H.; Zhao, X.","author_corresponding":"Xiangwei Zhao","author_corresponding_institution":"State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China","doi":"10.1101\/2024.12.30.630832","date":"2025-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2025\/01\/01\/2024.12.30.630832.source.xml","abstract":"Accurate analysis of cell atlas and gene expression in biological tissues using single-nucleus RNA sequencing (snRNA-seq) is dependent on the quality of source material, and post-mortem interval (PMI) is one of the major sources of variation in RNA quality. Although the use of RNA-degraded tissues in transcriptome analysis remains controversial, such samples are sometimes the sole means to address specific questions. Current studies on the impact of PMI on transcriptome data are limited to large-scale RNA-seq, which ignores cellular heterogeneity. Thus, deciphering the non-cell- autonomous effects caused by PMI is imperative for understanding the cellular and molecular disruption it elicits. Here, we investigated the impact of PMI on cellular components and gene expression using snRNA-seq data from mouse brain tissues of post-mortem. We collected samples that were allowed to decay for varying amounts of time at 25{degrees}C prior to snRNA-seq, covering the entire range of RIN values. The different effects on the PMI to the degradation rate of mRNA and rRNA within nuclei, and the mRNA presented a more stable state. Multi-channel analysis revealed the preferential transient depletion oligodendrocytes and OPCs with increasing PMI. In addition, a rapid widespread overregulation of ribosomal transient recruitment to protein (RP) genes in various cells, and reached a plateau at PMI of 36h. Although state depletion of neuronal cells was not detected, we reported significant upregulation of PMI-dependent RP genes in its subpopulations and their cell loss. Moreover, RP genes showed the greatest differential expression in the subpopulations with greater cell perturbation, and we speculated that aberrant expression of these genes might be associated with cell death. In this study, we systematically investigated the changes in the transcriptome profile of brain tissue induced by PMI at single-cell resolution, and revealed one of the important factors that might be responsible for the changes. In addition, our data complemented a possible explanation for the changes in the cellular state of brain tissue induced by postmortem hypoxia-ischemia, and provided a reference for transcriptome studies of RNA degradation samples.","published":"NA","server":"bioRxiv"}]}