Biology subjects

Gong, Z.

Publications and source records attributed to Gong, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Neural Representations of Visual Anagrams in Macaque Inferotemporal Cortex

Visual recognition requires stable representations of object identity despite large changes in the retinal image. Yet this stability must be selective: some transformations change not only how an image looks, but also what object it appears to depict. Visual anagrams highlight this challenge: a single image can resemble two different objects at different orientations, such as an elephant and a rabbit. Here, we asked how macaque inferotemporal (IT) cortex represents such transformations. We recorded large neuronal populations while presenting visual anagrams and unambiguous exemplars of their two interpretations across rotations. Neurons preferring one exemplar tended to prefer anagram orientations supporting the corresponding interpretation. At each of the two interpretation-relevant canonical angles, population responses more closely resembled those to the matching exemplar than those to the nonmatching exemplar. This matching advantage persisted when both exemplars were presented at the alternative canonical angle. Decoders trained exclusively on exemplars across rotations also tracked the shifts in anagram representations. Visual models showed anagram-exemplar alignment as well, with stronger alignment in models with greater relative shape preference. These findings suggest that transformation tolerance in IT is sensitive to what an image appears to depict, while relative shape preference is associated with similar representational organization in visual models.

neuroscience↗

bioRxiv2026

Pto evolved from malectin-like RLKs phosphorylates AvrPtoB to promote Prf-mediated immunity in Solanum pimpinellifolium

Bacterial speck, caused by Pseudomonas syringae pv. tomato (Pst), is a devastating disease of tomato that severely limits global tomato productivity. Understanding the molecular mechanisms underlying Pst and tomato is essential for developing disease resistant varieties. Here, we demonstrate that Pto, the first disease-resistance gene conferring recognition of a specific pathogen, phosphorylates Pst type III effector AvrPtoB at serine 335 site. This post-translational modification triggers the dissociation of the Prf immune complex, enhancing immune signaling and reducing bacterial pathogenicity. Furthermore, evolutionary analyses indicate that Pto-associated proteins originated from malectin-like receptor kinases (MLRs) through loss of the extracellular domain. Crucially, we identified two key amino acid substitutions, Arg158 and Glu258 in Pto, which replace the ancestral lysine residues in MLRs (SpHREK1-1, SpHERK1-2 and SpHERK1-3). These substitutions stabilize Pto by preventing degradation mediated by AvrPtoB's E3 ubiquitin ligase activity. Our findings reveal a novel mechanism, by which Pto phosphorylates a bacterial effector to trigger enhanced immunity and elucidate the key evolutionary adaptations that have shaped Pto into a stable resistance protein.

plant biology↗

bioRxiv2026

Pressure-induced membrane tension mechanically opens the germinant receptor GerA ion channel to trigger bacterial spore germination

High pressure (HP) can trigger bacterial spore germination, acting either through germinant receptors (GRs) or the SpoVA channel. However, the mechanism by which HP activates these membrane-embedded proteins remains elusive. Here, using Bacillus subtilis, we demonstrate that the GerA germinant receptor (GR) is the primary target of moderate HP (50-300 MPa). Mutagenesis reveals that pore-lining residues within the GerA ion channel are essential for the pressure response, whereas canonical ligand-binding and intramembrane signaling residues are dispensable. We then propose a s tretch- t o- o pen (STO) model, in which HP differentially compresses the more compliant inner membrane (IM) relative to the rigid spore core, generating lateral membrane tension that promotes opening of the GerA channel. In situ membrane tension measurements indicate HP-induced compression of IM phospholipids and elevated membrane tension. This tension-dependent gating is further supported by the pressure-dependent phenotypic rescue of GerA channel mutants. Consistently, HP increases IM permeability to water-soluble and membrane-impermeable agents (propidium iodide and formaldehyde), an effect potentiated by GerA, indicating concomitant opening of GerA by HP. Furthermore, modulating IM fluidity via heat activation or decoating altered membrane physical properties and delayed HP-induced germination, establishing the IM as the critical mechanical transducer. Additionally, computational modeling and calculations support faster compression of the IM than of the core under HP, rationalizing the source of tensile stress. Together, our findings establish a novel mechanism of HP-induced GerA activation via the STO model: HP compresses the IM, generates lateral tension, and promotes opening of the GerA ion channel to trigger bacterial spore germination.

microbiology↗

bioRxiv2026

Compartmental Profiling of PDE4B in Systemic Sclerosis

ObjectivesThe preferential phosphodiesterase 4B (PDE4B) inhibitor nerandomilast was recently approved for treatment of idiopathic pulmonary fibrosis (IPF) and progressive pulmonary fibrosis. Its proposed immunomodulatory, anti-fibrotic, and endothelial-stabilising actions target all three cardinal features of SSc, yet PDE4B expression has not been systematically characterised in SSc tissue. We aimed to define PDE4B expression across fibrotic organs and cellular compartments in SSc. MethodsPDE4B expression was profiled in SSc lung, peripheral blood mononuclear cells (PBMCs) and skin on the transcript level using single-cell RNA sequencing data and on the protein level using immunohistochemistry, immunofluorescence and multiplexed immunofluorescent stainings. ResultsPDE4B was consistently dysregulated in immune cells across SSc tissue and PBMCs, with compartment-specific direction and distribution. In SSc-ILD lung, expression was increased in CD8 and CD4 memory T-cells. In PBMCs, expression was increased in B cells, monocytes, and CD8 T-cells, and stratified patients into three endotypes (PDE4B//hi) not distinguishable by clinical variables. In skin, bulk RNA-seq showed a significant global increase, which localized to myeloid cells in scRNA-seq data. Approximately 90% of FAP activated fibroblasts co-expressed PDE4B at the protein level in SSc skin, identifying the activated fibroblast compartment as a candidate target for PDE4B inhibition. No PDE4B dysregulation was detected in vascular cell types. ConclusionsThis first cell-type-resolved characterisation of PDE4B in SSc demonstrates consistent immune-cell dysregulation across tissues and protein-level enrichment in activated fibroblasts. This provides a human-tissue rationale for the immunomodulatory and anti-fibrotic effects of PDE4B inhibition and supporting PDE4B as a disease-relevant therapeutic target in SSc. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LINerandomilast (BI 1015550), a PDE4B-preferential inhibitor, was approved for idiopathic pulmonary fibrosis and progressive pulmonary fibrosis. C_LIO_LIPre-clinical studies indicate that PDE4B inhibition may act on all cardinal features of SSc. C_LI What this study addsO_LIFirst cell-type-resolved characterization of PDE4B expression across SSc-affected lung, PBMCs, and skin. C_LIO_LIPBMC PDE4B expression is heterogeneous, stratifying patients into PDE4B// endotypes independent of standard clinical variables. C_LIO_LIscRNA-seq shows increased myeloid PDE4B expression in SSc skin, while [~]90% of FAP activated fibroblasts in SSc skin express PDE4B protein. C_LI How this study might affect research, practice or policyO_LIThe study strengthens the human-level evidence underpinning the target rationale for PDE4B inhibition in SSc. C_LI

molecular biology↗

bioRxiv2026

A glycoRNA switch for malignancy: SNORA73B activates TIAR-dependent oncogenic signaling in lung adenocarcinoma

Although glycosylated small non-coding RNAs are emerging players in cancer, their functions in lung adenocarcinoma (LUAD) are largely unknown. We identify SNORA73B as a glycosylated small nucleolar RNA (glycol-snoRNA) that carries sialic acid-capped O-glycans in both normal lung epithelial and LUAD cells. SNORA73B is markedly elevated in LUAD, and its plasma levels distinguish early-stage LUAD from healthy controls with an area under the curve (AUC) of 0.7903. Subcellular fractionation reveals predominant nuclear localization. Functional assays demonstrate that SNORA73B depletion curbs LUAD cell proliferation, migration, and invasion, whereas its overexpression fosters these malignant phenotypes and accelerates tumor growth. Mechanistically, SNORA73B directly binds the T-cell-restricted intracellular antigen-related protein (TIAR), thereby enhancing TIAR protein abundance without affecting its mRNA levels. TIAR then recognizes the 3-untranslated region (3-UTR) of MYC mRNA to upregulate c-Myc, which subsequently augments AKT phosphorylation. Importantly, c-Myc knockdown largely rescues the oncogenic phenotypes and tumorigenesis induced by SNORA73B overexpression. Collectively, our data unveil a glycoRNA-dependent oncogenic axis SNORA73B-TIAR-c-Myc-AKT that drives LUAD progression. These findings position SNORA73B as a promising early diagnostic biomarker and a candidate therapeutic target in LUAD.

Cancer Biology↗

bioRxiv2026

Humanin analogue promotes metabolic reprogramming to protect the ischemic heart

BackgroundMyocardial ischemia drives adverse cardiac remodeling, metabolic inflexibility, and progression to heart failure. Mitochondrial dysfunction and impaired substrate utilization contribute to cardiomyocyte death and fibrosis, particularly with aging. Humanin (HNG), a mitochondria-derived peptide, has been shown to reduce acute ischemic injury, but its role in chronic ischemia and cardiac remodeling remains unknown. MethodsWe investigated the effects of HNG treatment in young and aged murine models of myocardial ischemia without reperfusion. Cardiac function and structure were assessed by echocardiography and molecular markers of remodeling. Myocardial metabolism was interrogated using targeted metabolomics, gene expression, substrate uptake assays, and metabolic flux analyses. Mechanistic studies examined glucose transporter trafficking and protein-protein interactions. ResultsHNG treatment improved cardiac function and significantly attenuated adverse remodeling in both young and old mice. HNG treatment induced marked metabolic reprogramming characterized by reduced myocardial fatty acid content, downregulation of fatty acid uptake and oxidation pathways, and decreased oxidative stress. Importantly, these changes were accompanied by enhanced glucose oxidation, increased tricarboxylic acid cycle flux, improved coupling of glycolysis to mitochondrial oxidation, and increased ATP production. Time-course studies demonstrated that increased glucose oxidation preceded reductions in fatty acid oxidation, indicating a primary role for glucose metabolism in HNG-mediated cardioprotection. Mechanistically, we identified vesicle-associated membrane protein 7 (VAMP7) as a novel binding partner of HNG, and that this interaction is required for GLUT4 translocation to the plasma membrane and HNG-induced ATP generation. ConclusionsHNG protects the ischemic heart by promoting metabolic reprogramming that shifts substrate utilization from fatty acids to glucose and limiting maladaptive remodeling. These findings identify HNG as a novel regulator of cardiac metabolism and a potential therapeutic strategy for ischemic heart failure. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=65 SRC="FIGDIR/small/732776v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1929de8org.highwire.dtl.DTLVardef@bcf254org.highwire.dtl.DTLVardef@c99b70org.highwire.dtl.DTLVardef@1fc08bb_HPS_FORMAT_FIGEXP M_FIG C_FIG What are the clinical implications?Heart failure (HF) is a major global health concern, affecting over 6.7 million adults in the United States alone, with projections to exceed 11 million by 2050. Myocardial infarction (MI) is a leading cause of HF. Despite substantial advances in acute MI care, survivors remain at high risk for adverse cardiac remodeling and chronic HF, especially in the elderly. We report here that treatment with a potent analog of Humanin (HN), an endogenous mitochondria-associated peptide, decreases infarct size, decreases fibrosis and improves cardiac function following cardiac ischemia induced by permanent ligation of coronary artery in both young and aged mice. These effects are associated with changes in cardiac metabolism, oxidative stress, and remodeling. HN and analogs have been shown to be beneficial in many age-related diseases. The endogenous origin of Humanin, its favorable safety profile in preclinical studies and its pleiotropic effects support targeting HNG as a promising therapeutic strategy for ischemic heart disease and post-myocardial infarction heart failure in humans.

Systems Biology↗

bioRxiv2026

ATAD2 BRD mediates liquid-liquid phase separation of ATAD2 to promote histone acetylation

ATAD2 possesses a C-terminal bromodomain (BRD) that plays a critical role in recognizing and binding to acetylated lysine residues. However, because the native intracellular structure of ATAD2 remains poorly defined, the mechanisms by which the ATAD2 BRD recruits acetylated histones and the regulatory pathways involved are not yet understood. In this study, we report that the ATAD2 BRD mediates the formation of liquid-liquid phase separation (LLPS) of ATAD2 in cells. This phase separation promotes the process of histone H4 acetylation, leading to the up-regulation of C-MYC, CCND3, and ATF2 gene expression and the facilitation of chromatin remodeling. Our findings elucidate a vital function of ATAD2, wherein BRD-mediated LLPS drives histone acetylation to promote cellular chromatin remodeling.

molecular biology↗

bioRxiv2026

The Strehler-Mildvan mortality correlation arises from changes in the variability of ageing

As global human life expectancy continues to rise, accompanying increases in healthspan that prevent morbidity expansion become increasingly imperative. Population lifespan can increase in distinct ways, for instance through rectangularization (steepening) or triangularization (flattening) of survival curves. These two demographic changes, particularly rectangularization, occur frequently across human and model organism populations, yet their biological determinants and effects on healthspan and morbidity are largely unknown. Notably, these modes of life-extension occur when parameters of the Gompertz mortality model (capturing exponential age-increases in mortality rate) change inversely, a widely-reported phenomenon known as the Strehler-Mildvan correlation - whose biological basis also remains unexplained. We therefore investigated longitudinal health, morbidity and lifespan in 30 Caenorhabditis elegans cohorts using multiple life-extension protocols. We report that survival curve rectangularization results from healthspan expansion in short-lived population members, whereas triangularization (which primarily extends the curve tail) from healthspan and morbidity expansion in long-lived population members. Interestingly, rectangularization and triangularization respectively decrease and increase inter-individual variation in the aging process, and the mode of life-extension that occurs depends on levels of existing variation. Notably, triangularization was more effective at extending lifespan without morbidity expansion. Analysis of fruit fly and mouse data show that these biodemographic dynamics are also largely evolutionarily conserved.

physiology↗

bioRxiv2026

Bidirectional allosteric ligand regulation in a central glycolytic enzyme

Allosteric regulation enables fine-tuned control of enzyme activity in response to cellular signals, yet its molecular basis often remains unclear. Phosphofructokinase-1 (PFK), the rate-limiting enzyme of glycolysis, is a paradigmatic, well-conserved system whose reaction kinetics conform to the Monod-Wyman-Changeux model of allostery. However, X-ray crystal structures of bacterial PFK orthologs in distinct ligand-bound states do not show the consistent, concerted structural rearrangements expected for classical "relaxed" and "tense" states, revealing a decades-long disconnect between structure and function. We resolve this paradox by integrating biophysical and computational approaches to show that activator and inhibitor binding to the same allosteric pocket differentially reweight the conformational ensemble of Escherichia coli PFK. Activator binding stabilizes conformational substates that preorganize the catalytic site, whereas inhibitor binding upweights apo-like, catalytically incompetent substates. These findings establish an ensemble-based mechanism for PFK regulation and provide an energetic framework for understanding the expanded allosteric architecture of higher PFK orthologs.

biophysics↗

bioRxiv2025

Reciprocal Homoeologous Replacement of MYB Factors Drives the Evolutionary Trade-off between Yield and Fiber Quality in Cotton

The long-standing phenotypic trade-off between Upland cotton (Gossypium hirsutum, high yield) and Sea Island cotton (G. barbadense, high quality) represents a major bottleneck in cotton breeding and industrialization. Despite rapid advances in genomics, the genomic structural variations driving the divergence of these two domestication strategies, and their subsequent impact on downstream transcriptional networks, remain unclear. This study integrates multi-tissue transcriptomic atlases spanning the full growth period with pan-genomic analyses of both Upland and Sea Island cotton, proposing a "Reciprocal Selective Retention (RSR)" strategy adopted by the two species during evolution. Transcriptomic analysis revealed that while the transcriptional chassis of the two species is highly conserved, a drastic "phase inversion" occurs during fiber development. Sea Island cotton appears to trade off for quality by specifically activating a "delayed elongation" module (at 20 DPA), whereas Upland cotton initiates a "precocious filling" program to pursue yield. Further Weighted Gene Co-expression Network Analysis (WGCNA), combined with genomic Presence/Absence Variation (PAV) analysis, identified a set of key transcription factors exhibiting a "3-vs-3" reciprocal loss pattern. Upland cotton specifically retained CRF10, WIND1, and MYB93, constructing a genetic foundation of "robust root system and strong regeneration" to support high yield. Conversely, Sea Island cotton specifically retained MYB111 and ERF105/017 to maintain long-staple characteristics and environmental buffering. Whole-genome structural variation and microsynteny analyses confirmed that these differences stem from asymmetric physical deletions (e.g., a 5 kb deletion in MYB111) or fragment sequence collapse (e.g., a 15.9 kb sequence divergence in MYB93) on homologous chromosomes. The RSR model proposed in this study not only offers a novel insight into the genetic roots of the negative correlation between yield and quality but also provides clear genomic targets for precision improvement using gene-editing technologies such as CRISPR.

genomics↗

bioRxiv2025

Small molecule inhibitor of PPARγ acetylation promotes insulin sensitization and browning of white adipose tissue with improved safety

The nuclear receptor PPAR{gamma} is a primary therapeutic target for insulin resistance and type 2 diabetes (T2D); however, its thiazolidinedione (TZD) class of PPAR{gamma} agonists have substantial safety concerns in clinical utilization. Genetic inhibition of PPAR{gamma} acetylation at K268 and K293 dissociates the major adverse effects of TZDs from insulin sensitization and other metabolic improvements. We therefore posit that chemical inhibition of PPAR{gamma} acetylation would elicit insulin sensitization with improved safety. Here we describe the identification of a synthetic thiopyrimidine derivative (TPMD) that acts as a small molecule inhibitor of PPAR{gamma} acetylation. TPMD improves insulin sensitivity, promotes brown remodeling of white adipose tissue (WAT), increases energy expenditure, and decreases adiposity in dietary and genetic mouse models of T2D. Importantly, TPMD is deprived of the major side effects of TZDs, including weight gain, fluid retention, cardiac hypertrophy, bone marrow adiposity, and bone loss. X-ray crystallography at 2.0 [A] resolution reveals a unique binding mode of TPMD molecules to the PPAR{gamma} ligand-binding domain and provides structural and molecular basis for the acetylation inhibitory activity of TPMD together with site-directed mutagenesis studies. These findings identify TPMD as a first-in-class compound that specifically targets PPAR{gamma} acetylation and possesses the potential of developing into a safe insulin sensitizer to treat and prevent T2D and obesity.

cell biology↗

bioRxiv2025

A Population-Scale Single-Cell Atlas of the Human Heart Reveals Cellular Remodeling and Cell-Cell Communication in Aging and Cardiac Disease

Previous single-cell and single-nucleus heart atlases, often limited by small sample sizes, lack the statistical power needed for phenotype association analysis, particularly for cardiovascular diseases and cardiac aging. To address this, we integrated data from 436 samples across 12 single-cell studies, harmonized the corresponding sample metadata, and constructed a comprehensive heart atlas comprising 355,762 cells and 1,436,719 nuclei. Consensus annotation identified 10 broad cell types and 54 fine-grained subsets. Associating gene expression patterns and cell type proportions with phenotypic data, we identified NRG1-expressing endocardial cells linked to multiple cardiac diseases and found that interferon (IFN) response signatures mark aging in multiple heart cell types. Importantly, we also developed PopComm, a novel computational method for inferring ligand-receptor (LR) interactions from population-scale single-cell data and quantifying interaction strength for individual samples. Using PopComm, we revealed a close association between the IFN response state and altered cell-cell communication during cardiac aging.

bioinformatics↗

bioRxiv2025

Evaluation of computational tools for predicting CRISPR gRNA on-target efficiency in plants.

CRISPR technologies has become an integral part of plant biotechnology, synthetic biology and basic plant research, routinely used by researchers for targeted genome modifications. CRISPR guide RNAs (gRNAs) undermines the highly programmable nature of CRISPR, enabling site-specific genome editing. However, different gRNA targets showed highly variable on-target effectiveness and poor gRNA design could amount to wasting valuable scientific resources. There has been broad development of computational and web-based tools for gRNA efficiency predictions but their performances in plant genome editing remains controversial or untested. Hence, in this study, we systematically evaluated over 20 accessible, web-based in silico gRNA on-target efficiency prediction tools using an experimental plant genome editing dataset. Excitingly, we identified multiple tools, mostly developed using machine learning, that were highly predictive of gRNA on-target genome editing efficiency in planta. The prediction scores assigned to gRNAs in the dataset by these tools were significantly correlated with the frequency of CRISPR-mediated InDels in plants. Furthermore, we evaluated efficiency prediction scores available on popular platforms such as CRISPOR and CRISPR-P which contain large numbers of non-model plant genomes. Our analysis showed that some prediction scores on CRISPOR performed quite well which allows efficient integration of on-target and off-target predictions. Overall, we believe that our study provided insights on improving gRNA design during conventional plant genome editing workflows and should also help unfamiliar researchers interested in CRISPR/SpCas9 genome editing.

plant biology↗

bioRxiv2025

Force loading on molecular clutches governs the stability of cell lamellipodia

Cells can utilize the lamellipodia, a thin actin-rich membrane protrusion, to probe the mechanical properties of microenvironments. During the mechanosensing process, the lamellipodium usually exhibits instability in dynamics, i.e., protrusion-retraction cycles. However, how mechanical instability arises in lamellipodia, along with the functional role of dynamic instability in mechanosensing, is poorly understood. Here, we develop a minimal mechanochemical model for lamellipodia dynamics that integrates membrane deformation, myosin contractility, and binding kinetics of adhesion molecules (molecular clutches). Through stochastic simulations and analytical mean-field analysis, we demonstrate that both force-loading rate and magnitude applied by myosin-driven retrograde flow mediate the clutch binding kinetics, governing lamellipodial stability and hence the mechanosensing. Specifically, a slow force loading rate allows the clutches to bind and traction to accumulate, while a high loading magnitude collapses the bound clutches, causing protrusion-retraction cycles (instability) in lamellipodia. Our model predicts that a stiffer substrate stabilizes the lamellipodia by increasing the force loading rate, consistence with previous experiments. Furthermore, our model predictions on the biphasic regulation effect of myosin perturbations have been quantitatively validated by experimental results. Overall, the theoretical framework highlights the force loading as the key mechanical input driving lamellipodial instability and cell mechanosensing, advancing our understanding of mechanotransductions role in cell behaviors. SignificanceCell behavior can be highly dynamic, showing periodic protrusion and retraction at the leading edge, and this dynamic instability is key to migration, immune response, and cancer invasion. How such instability arises from mechanotransduction between intercellular components and extracellular matrices remains unclear. Here, through theoretical modeling, we identify the rate and magnitude of force loading on adhesion molecules (molecular clutches) as the key factors for controlling lamellipodial stability. We find that a slow loading rate enables more clutches to bind and traction to accumulate, while a high loading magnitude collapses the bound clutches, causing protrusion-retraction cycles in lamellipodia. This work reveals a physical mechanism of how cells sense mechanical cues and adapt their dynamics, offering insights into diverse biological processes.

biophysics↗

bioRxiv2025

Recapitulating apicobasal tissue polarity in extracellular matrix incorporated airway organoids

The airway epithelium is a dynamic barrier that interfaces with the external environment and internal matrix along its apicobasal axis. To recapitulate this tissue arrangement in an organoid format, we present the decellularized ExtraCellular Matrix-incorporated Apical-out Airway Organoid (dECM-AoAO) that integrates basolateral matrix cues through incorporation of human lung dECM microparticles, while maintaining direct apical exposure to the exterior. Compared to the ECM-free AoAO, dECM incorporation effectively diversifies lineage distribution that better recapitulates native epithelial composition. Harnessing dECM-AoAO locomotion powered by its outward-facing ciliary beating, we developed an experimental and computational pipeline for swarm analysis of organoid group motility as a functional readout of ciliary function. Lastly, dECM-AoAO withstood cryopreservation and revival with sustained viability, lineage composition, and ciliary function, enabling future scalability and broad distribution. Together, this work establishes dECM-AoAO as a more physiologically relevant model system for investigating epithelial-ECM crosstalk during airway homeostasis, pathogenesis, and injury responses.

cell biology↗

bioRxiv2025

Mycobacterium tuberculosis m4C DNA methyltransferase Rv3204 promotes mycobacteria survival under oxidative stress

Reactive oxygen species (ROS) inflict cellular damage yet are pivotal mediators of signaling pathways. Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), persists as a major global health threat, partly due to its capacity to neutralize host-derived ROS toxicity. While DNA methylation deficiency is known to attenuate Mtb virulence, the specific role of DNA methyltransferases in mycobacterial survival under oxidative stress remains poorly defined. Here, we demonstrate that the mycobacterial protein Rv3204 functions as an N4-methylcytosine (m4C) DNA methyltransferase. Deletion of the Rv3204 homolog (Ms_1939) in Mycobacterium smegmatis significantly impaired bacterial survival upon rifampicin exposure. This phenotype was associated with heightened intracellular ROS accumulation and a failure to upregulate transcription of ROS detoxification genes. Furthermore, the mutant exhibited downregulated expression of DNA repair genes and increased susceptibility to fluoroquinolone antibiotics (norfloxacin, ofloxacin). Crucially, the Ms_1939 deletion strain displayed elevated levels of DNA damage. To our knowledge, this is the first study establishing a direct link between an m4C DNA methyltransferase and ROS homeostasis in mycobacteria. Our findings identify Rv3204 as a potential novel therapeutic target for modulating ROS sensitivity in M. tuberculosis. ImportanceMycobacterium tuberculosis, the causative agent of tuberculosis, remains a major global health threat due in part to its ability to withstand host-derived oxidative stress. This study identifies Rv3204 as a novel N4-methylcytosine DNA methyltransferase essential for mycobacterial survival under oxidative stress. We demonstrate that deletion of Rv3204 homolog in M. smegmatis leads to elevated intracellular ROS, impaired transcriptional activation of antioxidant and DNA repair genes, increased DNA damage, and heightened susceptibility to fluoroquinolone antibiotics. Our findings establish a critical link between epigenetic regulation via m4C methylation and ROS homeostasis in mycobacteria--a relationship previously unexplored. This work not only advances our understanding of bacterial epigenetic mechanisms in stress adaptation but also positions Rv3204 as a promising target for novel anti-tuberculosis strategies aimed at disrupting redox balance and enhancing antibiotic efficacy. DATA summaryRaw data files have been deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) under accession number GSE139646 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139646).

genetics↗

bioRxiv2025

Correctness is its own reward: bootstrapping error signals in self-guided reinforcement learning

Reinforcement learning (RL) offers a compelling account of how agents learn complex behaviors by trial and error, yet RL is predicated on the existence of a reward function provided by the agents environment. By contrast, many skills are learned without external guidance, posing a challenge to RLs ability to account for self-directed learning. For instance, juvenile male zebra finches first memorize and then train themselves to reproduce the song of an adult male tutor through extensive practice. This process is believed to be guided by an internally computed assessment of performance quality, though the mechanism and development of this signal remain unknown. Here, we propose that, contrary to prevailing assumptions, tutor song memorization and performance assessment are subserved by the same neural circuit, one trained to predictively cancel tutor song. To test this hypothesis, we built models of a local forebrain circuit that uses contextual premotor signals to cancel tutor song auditory input via synaptic plasticity. After learning, excitatory projection neurons signaled mismatches between the tutor song and birds own performance, best matching experimental data when learning involved anti-Hebbian plasticity in recurrent interneurons. We also found that learning proceeds by both sharpening error sensitivity and minimizing responses to the tutor song. Finally, the error signals produced by this model can train a simple RL agent to replicate the spectrograms of adult bird songs. These results suggest that local learning via predictive cancellation suffices for bootstrapping error signals capable of guiding self-directed learning of natural behaviors. SignificanceMany species, including humans, learn new skills by trial and error. But in the absence of external rewards and punishments, individuals need a means of assessing the quality of their performance. Here, we model the process by which juvenile male zebra finches memorize the song of an adult tutor, showing how local changes in brain circuits responsible for hearing can give rise during this process to an internal error signal that later allows for self-guided learning.

neuroscience↗

bioRxiv2025

Triple-N Dataset: Non-human Primate Neural Responses to Natural Scenes

Understanding the neural mechanisms of visual perception requires data that encompass both large-scale cortical activity and the fine-grained dynamics of individual neurons. While the Natural Scenes Dataset (NSD) has provided substantial insights into visual processing in humans (Allen et al., 2022), its reliance on functional magnetic resonance imaging (fMRI) limits the exploration of individual neuron contributions. To bridge this gap, we present a new dataset: the Triple-N (Non-human Primate Neural Responses to Natural Scenes) dataset, which extends the NSD framework to non-human primates, incorporating single-neuron activity and fMRI recorded from the inferotemporal (IT) cortex. Using Neuropixels probes, we recorded neural responses from five macaques as they passively viewed 1,000 shared NSD images. The dataset includes 59 sessions across 27 sub-regions, capturing over 30,000 visual responsive units. Many recordings were obtained from fMRI-defined category-selective regions, such as face-, body-, scene-, and color-selective areas. Our dataset enables in-depth exploration of neural responses at multiple levels - from population dynamics to single-neuron activity, providing new insights into various aspects of visual processing, including the heterogeneity of object selectivity within functional regions and the temporal dynamics of responses to natural images. Furthermore, the dataset enables joint cross-species analyses, by integrating the macaque neural recordings with human fMRI data, offering a framework for comparing and aligning visual representations across primate species. Overall, our dataset provides a valuable resource for advancing our understanding of visual perception, bridging the gap between large-scale neuroimaging and fine-grained electrophysiological signals, while also facilitating the development of computational models of the high-level visual system.

neuroscience↗