Biology subjects

Gu, Y.

Publications and source records attributed to Gu, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Aberrant medial entorhinal cortex dynamics link tau pathology to spatial memory impairment

Tau pathology in the entorhinal cortex (EC) is associated with spatial memory decline in aging and early-stage Alzheimers disease, but its impact on EC computations during learning is not well understood. We performed longitudinal two-photon calcium imaging of layer 2 excitatory neurons in the medial EC (MEC) of PS19 tauopathy mice over 10 days of an operant spatial learning task. Male PS19 mice showed marked learning impairments accompanied by dysregulated MEC activity and unstable spatial coding. Their activity also showed weakened representations in cue-poor relative to cue-rich regions, correlated with attenuated speed modulation. These changes suggest that impaired path integration destabilizes MEC spatial maps, leading to impaired spatial memory. In contrast, female PS19 mice exhibited only mild behavioral and neural deficits despite a comparable tau burden, suggesting sex-specific resilience. Among MEC cell types, pyramidal cells accumulated more phosphorylated tau than stellate cells and displayed the most severe functional disruption, linking cellular tau load to circuit dysfunction. Finally, general linear models of MEC activity reliably predicted learning performance, highlighted particularly strong contributions from non-grid and pyramidal cells, and accurately classified PS19 versus wild-type mice. These findings identify aberrant MEC dynamics as a key circuit mechanism underlying tau-related spatial memory deficits and point to early diagnostic and circuit-targeted therapeutic strategies.

neuroscience↗

bioRxiv2025

Activation of the medial entorhinal cortex drives memory-guided navigation behavior

The cognitive map in the medial entorhinal cortex (MEC) is essential for spatial memory and exhibits experience-dependent changes. Yet, it remains unclear whether MEC activation is sufficient to bias the network toward memory-guided navigation, precluding a causal link between the MEC and spatial memory. To address this gap, we examined and optogenetically manipulated MEC activity as mice navigated a virtual track for a water reward based on memory. During learning, spatial activity in the pre-reward region showed the highest consistency along the track and closely paralleled improvements in reward-predictive behaviors. This elevated pre-reward consistency was widespread across MEC neurons, rather than confined to a particular cell type, indicating a network-level representation supporting reward prediction. Strikingly, optogenetic activation of MEC at non-reward locations biased reward-predictive behaviors toward stimulation sites, but only when stimulation patterns were spatially consistent. Consistent stimulation also induced anticipatory reward-seeking before stimulation onset and this behavior gradually developed with repeated stimulation, reflecting memory formation for stimulation locations. Moreover, in animals that failed to learn the track well, consistent pre-reward activation, alone or combined with landmark activation, significantly enhanced their reward prediction. Thus, spatially consistent MEC activation underlies memory-guided reward prediction, supporting a causal role for the MEC in spatial memory.

neuroscience↗

bioRxiv2025

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

bioRxiv2025

Ser129 Phosphorylation Paradox: Non-phosphorylated α-Synuclein Drives Parkinson' s Disease-like Pathogenesis in Vivo

Accumulation of phosphorylated -synuclein at serine 129 is a hallmark of Parkinsons disease (PD), but its pathogenic role remains controversial. We conducted longitudinal studies using non-phosphorylatable S129A and phosphomimetic S129D -synuclein global knock-in mice. Unexpectedly, the S129A mice--rather than S129D mice--developed reproducible olfactory, motor, and cognitive deficits, dopaminergic dysfunction and neurodegeneration, -synuclein insolubility, and Lewy-like inclusions by 3 to 9 months, with progressive worsening up to 12 months of age. Spatial transcriptomics and electron microscopy revealed mitochondrial, synaptic, and protein ubiquitination abnormalities in the substantia nigra of S129A -synuclein mice. Viral vector-mediated nigral overexpression of S129D--synuclein or systemic administration of an anti--synuclein-aggregation drug partially alleviated the early neurological phenotypes of S129A mice. These results implicate non-phosphorylatable -synuclein as a direct pathogenic driver for PD.

neuroscience↗

bioRxiv2025

Concurrent saliency and intentional maps in posterior parietal cortex

AbstractThe goal for motor action represents the desired state of the individual when interacting with the world. Investigating how the goal is generated requires clarifying spatial extrapolation that involves perceptual and action processes. Here, we recorded neural activity from monkeys manually intercepting a circularly moving target being occluded. The saliency and intentional maps, which developed to locate the target of interest and the intended action goal, were thus distinguished in neural activity recorded from the lateral intraparietal cortex (LIP) and parietal reach region (PRR). Dynamic internal representations spanning from visual registration to state estimation were unveiled in both areas, with the goal for the interception being inferred as the visual consequence of the movement. The motion extrapolation was found to be an intrinsic part of movement planning, so that the continuous and stable spatial extrapolation from motion to action was prevalent in both areas. The goal estimation based on the sensory extrapolation rationalized the concurrency and correlation of saliency and intentional maps, which were found to switch their dominance by reorganizing the read-out dimensions of the spatial manifold. The extrapolation achieved at both the perceptual and motor stages not only bridged the saliency and intentional maps, but also revealed the form of the state estimation in guiding predictive sensorimotor control.

neuroscience↗

bioRxiv2025

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Serpentinization drives abiotic synthesis of organics (e.g., hydrocarbon) potentially conducive to the emergence of life, making serpentinite-hosted systems and associated microbial community key windows into nature of lifes origin. Although cultivation-independent studies uncovered the Candisdatus Bipolaricaulota widely distributed in serpentinizing environments, cultivation of this phylum has been unsuccessful. Here we cultured the first pure strain, J31, of Ca. Bipolaricaulota from the Lost City hydrothermal field, a well-characterized marine serpentinite system, using hydrocarbons as the primary nutrient source. As an early-branching bacterial lineage, strain J31 exhibits an unusual morphology composed of a central rod and elongated Toga-like extensions at both ends, and divides by binary fission. Strain J31 absorbs hexadecane through Toga ends via coordinated processes resembling inhalation and swallowing, after which hexadecane is efficiently transported to the central rod in the vesicle-like structures and subsequently converted into membrane lipids to support Toga synthesis and cellular growth. Hydrocarbon-degrading capability is widespread among the globally distributed members of Ca. Bipolaricaulota. Strain J31 colonizes serpentine minerals, facilitating the utilization of hydrocarbons derived from serpentines and promoting the release of soluble iron and silicon, thereby linking microbial activity to geochemical cycling. Thus, our study presents a novel strategy for cultivating deep-branching bacteria and offers insights into the metabolic foundations of early life on Earth--and potentially on other rocky planets undergoing serpentinization.

microbiology↗

bioRxiv2025

Phosphorylation remodels the mitotic centrosome matrix to generate bipartite gamma-tubulin complex docking sites

Mitotic centrosomes consist of centrioles surrounded by a proteinaceous matrix that docks and activates {gamma}-tubulin complexes ({gamma}TuCs) to nucleate microtubules for spindle assembly. During mitotic entry, phosphorylation at centrosomes remodels CDK5RAP2 family matrix proteins to generate {gamma}TuC docking sites. We address the mechanism of this conversion using C. elegans SPD-5 as a model. We show that SPD-5 contains two regions, PRGB1 and PRGB2, that are each sufficient for Polo-Like Kinase 1 (PLK1) phosphorylation-regulated {gamma}TuC binding. We define key phosphosites in each region and uncover autoinhibition mediated by interactions within and between them. PRGB2 is dimeric and requires {gamma}TuCs containing the Mozart family microprotein MZT-1 for binding, whereas PRGB1 is monomeric and binds independently of MZT-1. Our results support PLK1 phosphorylation inducing a conformational change that enables MZT-1-dependent PRGB2 binding, which in turn relieves PRGB1 inhibition. Such a multi-step mechanism would ensure robust spindle assembly by restricting microtubule nucleation in space and time.

cell biology↗

bioRxiv2025

Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes

The physicochemical properties of biological membranes must be maintained within a range compatible with cellular physiology. In the face of external perturbations, membrane lipid homeostasis mechanisms sense and control membrane features. How such mechanisms evolve to function in organisms with different cellular lipid make-up is unknown. Here, we address this fundamental question by exploiting the natural divergence in membrane lipid composition between the related fission yeasts S. pombe and S. japonicus. Using lipidomics and transcriptomics, we show that the activity of the membrane-bound transcriptional activator Mga2, which regulates the {Delta}-9 desaturase Ole1 expression, is set to sense distinct levels of membrane unsaturation in the two species. Through retro-engineering and physiological experiments, we identify an evolutionary divergent but functionally constrained element within the juxtamembrane region of Mga2, which fine-tunes its performance to species-specific lipid composition. Our experiments indicate that high baseline expression of ole1, set by cis-regulatory elements in its upstream non-coding region, has redefined the dynamic range of Mga2 activation in S. pombe, supporting high lipidome unsaturation. Our work explores an "experiment of nature" to highlight the broad principles underlying the organisation and evolution of membrane homeostasis, which should be applicable to other genetic networks supporting cellular homeostatic processes.

cell biology↗

bioRxiv2025

Mucoricin binding to β-glucan sites on germinating Mucorales spores disrupts neutrophil swarming to promote pathogenicity

Mucormycosis is an emerging, life-threatening infection caused by Mucorales fungi with incompletely understood immunopathogenesis. We found that unlike other fungal pathogens, Mucorales trigger coordinated neutrophil clustering (swarming) upon swelling of fungal spores. Neutrophil swarms efficiently eliminate germinating Mucorales via ROS production, upon sensing of {beta}-glucan by complement receptor 3 (CR3). Impaired neutrophil clustering in mucormycosis-predisposing conditions, allows for mucoricin toxin production by germinating Mucorales. Released mucoricin selectively binds to {beta}-glucan on the surface of Mucorales, creating a molecular trap that induces neutrophil apoptosis and swarming disruption, leading to invasive fungal disease. Suppression of mucoricin, either genetically or physiologically by albumin-bound free fatty acids, stabilizes neutrophil clusters leading to abrogation of fungal pathogenicity. Additionally, prophylactic GM-CSF administration prevents mucoricin-induced neutrophil death, and protects mice from mucormycosis. Our work identifies neutrophil swarming as the primary target of mucoricin and provides compelling evidence for therapeutic harnessing of this pathway to improve mucormycosis outcome.

immunology↗

bioRxiv2025

Single-particle multi-parametric microscopy reveals structural, size, and payload heterogeneity in mRNA-loaded lipid nanoparticles

Deciphering the heterogeneity of mRNA-containing lipid nanoparticles (LNPs) is essential for understanding the relationship between their microscopic properties and therapeutic function. Here, by combining alternating laser excitation (ALEX) with Convex Lens-induced Confinement (CLiC) microscopy, we simultaneously measure size, multi-color fluorescence, mRNA payload, and Forster resonance energy transfer (FRET) of individual suspended LNPs containing labeled lipid and mRNA molecules. By varying formulation parameters, including ionizable lipids, formulation buffers, and molecular ratios, we investigated and correlated key microscopic properties for relevant vaccine formulations. While the per-particle lipid fluorescence was lower for empty versus mRNA-loaded particles for all formulations, the relative size of empty versus mRNA-loaded particles depended upon the formulation and intraparticle structure. When comparing CLiC-ALEX to cryogenic transmission electron microscopy measurements (Cryo-TEM), for the LNP formulations that display blebs, the fraction of bleb LNPs is in close agreement with the fraction of mRNA-containing LNPs. CLiC-ALEX also enabled quantification of the per-particle mRNA fluorescence and FRET signals, and thus the heterogeneity in the mRNA copy number and mRNA-LNP structural arrangements, where the results were compared with biophysical estimates based on the LNP formulations. These rigorous biophysical insights are critical to inform our understanding of structure-activity relationships and inform rational design of nanomedicines.

biophysics↗

bioRxiv2025

CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

Causal mediation analysis investigates whether the effect of an exposure on an outcome operates through intermediate variables known as mediators. Although progress has been made in high-dimensional mediation analysis, current methods do not reliably control the false discovery rate (FDR) in finite samples, especially when mediators are moderately to highly correlated or follow non-Gaussian distributions. These challenges frequently arise in DNA methylation studies. We introduce CoxMDS, a multiple data splitting method that uses Cox proportional hazards models to identify putative causal mediators for survival outcomes. CoxMDS ensures finite-sample FDR control even in the presence of correlated or non-Gaussian mediators. Through simulations, CoxMDS is shown to maintain FDR control and achieve higher statistical power compared with existing approaches. In applications to DNA methylation data with survival outcomes, CoxMDS identified eight CpG sites in The Cancer Genome Atlas (TCGA) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on lung cancer survival, and two CpG sites in the Alzheimers Disease Neuroimaging Initiative (ADNI) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on time to Alzheimers disease conversion.

bioinformatics↗

bioRxiv2025

Predictive in vitro profiling of LNP-induced innate immune response using an iPSC-derived monocyte model

Lipid nanoparticles (LNPs) are a powerful drug delivery platform advancing vaccines and gene therapies. While their efficacy and safety has been found to be closely linked to innate immune activation, current in vitro models are unable to predict immune responses reliably. Conventional models, such as PBMCs, are limited by donor variability and inconsistent sensitivity. To address this, we developed a cytokine profiling platform using induced pluripotent stem cell (iPSC)-derived monocytes (iMonocytes), a physiologically relevant innate immune cell type that plays a key role in immune surveillance and inflammation. iPSCs provide a renewable, uniform monocyte source for consistent, high-sensitivity LNP screening. When tested with LNPs of graded immunostimulatory potency, iMonocytes showed improved reproducibility and strong correlation with in vivo cytokine responses. This platform enables evaluation of cargo- and dose-dependent effects, providing a robust and scalable tool for preclinical assessment and rational design of LNP therapeutics.

bioengineering↗

bioRxiv2025

Repressed expression of nucleoporins and importins impairs plant defense against an infectious noncoding RNA

Plant pathogens threaten global food security and cause substantial annual economic losses. Of particular concern are host jumps, in which pathogens expand their host range to new species, often resulting in sudden and difficult-to-control disease outbreaks. However, the ability to anticipate such events remains limited by an incomplete understanding of pathogen adaptability and the mechanisms governing nonhost resistance. Here, we show that temperature modulates the infectivity and host range of potato spindle tuber viroid (PSTVd), a pathogenic noncoding RNA that severely impacts solanaceous crops such as potato and tomato. Using in vivo single-molecule RNA structure probing, we found that higher temperatures drive PSTVd into a more uniform RNA conformation associated with enhanced infectivity in tomato. Concurrently, elevated temperature suppresses key host defense pathways, including RNA silencing and NPR1-mediated immunity. Notably, these conditions enable PSTVd to overcome nonhost resistance and establish infection in Arabidopsis thaliana. Our findings reveal that elevated temperature promotes PSTVd host expansion through multiple coordinated mechanisms, linking changes in pathogen behavior with increased host susceptibility, and suggest that ongoing climate warming may heighten the risk of viroid host jumps.

plant biology↗

bioRxiv2025

Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo Randomization System to Model Cell Growth Behavior and Infer the Optimal Library Design for Growth-Based Double Knockout Screens

Advances in functional genomic technology, notably CRISPR using Cas9 or Cas12, now allow for large-scale double perturbation screens in which pairs of genes are inactivated, allowing for the experimental detection of genetic interactions (GIs). However, as it is not possible to validate GIs in high-throughput, there is no gold standard dataset where true interactions are known. Hence, we constructed a Double-CRISPR Knockout Simulation (DKOsim), which allows users to reproducibly generate synthetic simulation data where the single gene fitness effect of each gene and the interaction of each gene pair can be specified by the investigator. We adapted Monte-Carlo randomization methods to extend single knockout simulation methods to double knockout designs, which simulate the gene-gene interactions between all possible combinations of the input genes. Using DKOsim, we generated simulated datasets that closely resemble real double knockout CRISPR datasets in terms of Log Fold Change (LFC), GI distribution, and replicate correlation. We further inferred optimal CRISPR library designs by systematically investigating critical experimental parameters including depth of coverage, guide efficiency, and the variance of initial guide distribution. This simulation scheme will help to identify optimal computational methods for GI detection and aid in the design of future dual knockout CRISPR screens. Author SummaryWe designed DKOsim to simulate CRISPR double knockout screens by modeling cell division behavior with both single knockout (SKO) and double knockout (DKO) constructs via Monte-Carlo randomization samplers. Running DKOsim at large scale, we identified the asymptotic tuning points that optimize genetic interaction (GI) identification performance by the delta-LFC (dLFC) method compared to the simulated truth. We show that DKOsim is tunable to approximate actual dual-CRISPR knockout screening data. Comparing replicate correlation from DKOsim with experimentally generated data, DKOsim can be tuned based on users desires to reproduce a similar level of randomness to that observed in variety CRISPR screening conditions.

systems biology↗

bioRxiv2025

High-precision Biomedical Text Corpora for Multi-Entity Recognition: A CoDiet study

We present here five biomedical, multi-entity corpora that can be used as benchmarks for named-entity recognition (NER), targeted to literature on metabolic syndrome. The CoDiet-Gold corpus contains annotations for 500 full-text publications and 348,406 annotations. It is divided into CoDiet-Gold-public (450 documents) and CoDiet-Gold-private (50 documents). Each document was independently annotated by two human experts, with disagreements fully adjudicated by a third expert. The CoDiet-Electrum corpus (2,998,273 annotations) contains 4,423 publications that were annotated using case-insensitive matching of the surface forms with punctuation ignored, found in CoDiet-Gold-public. Finally, for the same 4,423 documents, two fully machine annotated corpora CoDiet-Bronze (2,938,738 annotations) and CoDiet-Silver (2,298,988 annotations), were created by utilising existing NER algorithms to annotate these. These corpora contain categories (organisms, disease, genes, proteins, metabolites) that add depth to existing corpora, as well as new categories that do not appear in other corpora (food, dietary methods, sample types, computational methods, study methodology, population characteristics, data types, and microbiome).

bioinformatics↗

bioRxiv2025

Transcriptional Readthrough at Atf4 Locus Suppresses Rps19bp1 and Impairs Heart Development

BACKGROUNDActivating Transcription Factor 4 (ATF4) functions as a transcriptional regulator in various cell types and tissues under both physiological and pathological conditions. While previous studies have linked ATF4 activation with promoting cardiomyocyte (CM) death in dilated cardiomyopathy (DCM), atrial fibrillation, and heart failure, its role in developing CMs remains unexplored. METHODSWe generated multiple distinct CM-specific (Atf4cKO(e2/3/pA) and Atf4cKO(e2)) and global Atf4 knockout (Atf47del/7del and Atf41ins/1ins) mouse models targeting different Atf4 regions, as well as cardiomyocyte-specific deletion of Rps19bp1 to study cardiac phenotypes. Detailed morphological and molecular analyses were performed. RESULTSAtf4cKO(e2/3/pA) (targeting exon 2-3 including the polyadenylation signal (polyA)) mice exhibited severe cardiac defects and died before E17.5, likely due to ectopic activation of p53 signaling pathway resulting from Rps19bp1 downregulation, a potent suppressor of p53. Further investigation revealed that deleting the polyA signal of Atf4 in Atf4cKO(e2/3/pA) mice led to transcriptional readthrough, resulting in the formation of an Atf4-Cacna1i fusion transcript and Rps19bp1 downregulation. To avoid readthrough while abolishing ATF4 function, we introduced small indels into exon 3 of Atf4 in mice (Atf47del/7del and Atf41ins/1ins), which showed normal Rps19bp1 expression and cardiac morphology. Importantly, CM-specific deletion of Rps19bp1 recapitulated the cardiac defects and transcriptional change seen in Atf4cKO(e2/3/pA) mice. CONCLUSIONSWe found that the downregulation of Rps19bp1, not loss of ATF4 function, underlying the cardiac phenotypes in Atf4cKO(e2/3/pA) mice. The reduced expression of Rps19bp1 in Atf4cKO(e2/3/pA) mice is likely due to the unintentional deletion of Atf4 polyA signal and subsequent transcriptional readthrough, underscoring the essential role of RPS19BP1, not ATF4, in cardiac development. Consistent Rps19bp1 downregulation has been observed in other tissue-specific Atf4 knockout models utilizing the Atf4fl(e2/3/pA) allele, suggesting that previously reported Atf4 KO phenotypes may result from Atf4 transcriptional readthrough effects. These findings reveal a locus-dependent transcriptional interference mechanism and emphasize the importance of avoiding confounding cis effects in genetically engineered models. TRANSLATIONAL PERSPECTIVEOur findings clarify ATF4s role in heart development by showing that cardiac defects in cardiomyocyte-specific ATF4 knockout mice--using a widely employed floxed ATF4 line--result from unintended downregulation of RPS19BP1 caused by transcriptional readthrough. This shifts the focus from ATF4 to RPS19BP1, a key regulator of p53 activity, as a potential driver of cardiac developmental abnormalities. Clinically, these insights caution against misinterpretation of genetic knockout models and highlight RPS19BP1 as a promising target for congenital heart disease and related cardiac dysfunctions, with potential implications for future therapies.

genetics↗

bioRxiv2025

A fully-open structure-guided RNA foundation model for robust structural and functional inference

RNA language models have achieved strong performances across diverse downstream tasks by leveraging large-scale sequence data. However, RNA function is fundamentally shaped by its hierarchical structure, making the integration of structural information into pre-training essential. Existing methods often depend on noisy structural annotations or introduce task-specific biases, limiting model generalizability. Here, we propose structRFM, a structure-guided RNA foundation model that is pre-trained on millions of RNA sequences and secondary structures data by integrating base pairing interactions into masked language modeling through a novel pair matching operation. We further introduce MUSES (multi-source ensemble of secondary structures) to mitigate model bias, and a dynamic masking ratio to balance the structure-guided mask and nucleotide-level mask. structRFM learns joint knowledge of sequential and structural data, producing versatile representations, including classification-level, sequence-level, and pairwise matrix features, that support a broad spectrum of downstream adaptations. structRFM ranks among the top models in zero-shot homology classification across seventeen biological language models, and sets new benchmarks for secondary structure prediction. structRFM further derives Zfold, which enables robust and reliable tertiary structure prediction, with consistent improvements in estimating 3D structures and their accordingly extracted 2D structures, achieving a pronounced about 20% performance gain compared with baselines and comparable performances with AlphaFold3 on CASP15-natural, CASP16, and RNA-Puzzles datasets. In functional tasks such as internal ribosome entry site identification, structRFM achieves a whopping 48% performance gain in F1 score. Furthermore, state-of-the-art performances in extensive experiments across novel RNA families and long non-coding RNAs indicate the robustness and generalizability of structRFM. These results demonstrate the effectiveness of structure-guided pre-training and highlight a promising direction for developing multi-modal RNA language models in computational biology. To support the broader scientific community, we have made the 21-million sequence-structure dataset and the pre-trained structRFM model fully open-source, facilitating the development of multimodal foundation models in biology.

bioinformatics↗

bioRxiv2025

Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally imaged calcium dynamics of grid cells over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting slow plasticity. The backward shifts partially reset daily, reflecting a slower consolidation timescale. While individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics on the same two-dimensional torus. Spatial learning leads to systematic changes and stabilization of their population phase trajectory, including lateral shift, rotation, and phase resets at landmarks, forming a landmark-fragmented representation for the environment. Next, we build an entorhinal-hippocampal model that provides a mechanistic explanation of the diverse phenomena - grid field shifts, increasing fidelity, and fragmentation of the spatial map - and predicts slow Hebbian plasticity in the hippocampus-to-entorhinal pathway. Supporting this, electrophysiology demonstrates that learning-performance-correlated weakening of local inhibition facilitates potentiation of indirect hippocampal inputs to superficial MEC. Together, our study provides multifaceted evidence of slow hippocampus-to-MEC plasticity, elucidating the formation of stable and fragmented cognitive maps that combine internal and cue-driven positional estimates in rich environments during learning. This mechanism may extend to broader memory processes involving this circuit.

neuroscience↗