Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 397 records · Page 22Linked to original sources

bioRxiv2025

Underappreciated role of environmental enrichment in alleviating depression and anxiety: Quantitative evidence synthesis of rodent models

Environmental enrichment has long been recognized as a non-pharmacological intervention to mitigate mental health issues, yet its efficacy, and heterogeneity of treatment effects across experimental contexts remain underexplored. Heterogeneity of treatment effects, which reflects variability in individual responses to interventions, is a critical factor in determining the generalizability and personalization needs of treatments. Here, we conducted a registered meta-analysis of 62 studies and 1,112 comparisons in rodent models to evaluate the impact of environmental enrichment on depressive and anxiety-like behaviours. We found that environmental enrichment reduced these behaviours of animal models by 16% on average and decreased inter-individual variability by 12%, indicating not only effectiveness but also low heterogeneity of treatment effects, which suggests consistent effects across individuals. Environmental enrichment further nullified the adverse effects of stressors, demonstrating a significant antagonistic interaction. These effects were robust across multiple sensitivity analyses, including model-based predictions, post-stratification, multi-model inference, publication bias correction, and critical appraisal of study quality. Moderator analyses highlighted the importance of exposure timing and the inclusion of social enrichment components. Taken together, our pre-clinical evidence on rodent models supports environmental enrichment as a low-cost, scalable, and biologically grounded intervention with translational relevance for developing equitable and accessible treatments for depression and anxiety. Given the importance of innovation and personalization in mental health care, the low heterogeneity of treatment effects of environmental enrichment positions it as a promising avenue for non-pharmacological therapeutic strategies that can be broadly applied without extensive tailoring.

animal behavior and cognition↗

bioRxiv2025

Human microglia in brain assembloids display region-specific diversity and respond to hyperexcitable neurons carrying SCN2A mutation

Microglia critically shape neuronal circuit development and function, yet their region-specific properties and roles in distinct circuits of the human brain remain poorly understood. In this study, we generated region-specific brain organoids (cortical, striatal, and midbrain), each integrated with human microglia, to fill this critical gap. Single-cell RNA sequencing uncovered six distinct microglial subtypes exhibiting unique regional signatures, including a subtype highly enriched for the GABAB receptor gene within striatal organoids. To investigate the contributions of microglia to neural circuitry, we created microglia-incorporated midbrain-striatal assembloids, modeling a core circuit node for many neuropsychiatric disorders including autism. Using chemogenetics to activate this midbrain-striatal circuit, we observed increased calcium signaling in microglia involving GABAB receptors. Leveraging this model, we examined microglial responses within neural circuits harboring an SCN2A nonsense (C959X) mutation associated with profound autism. Remarkably, microglia displayed heightened calcium responses to SCN2A mutation-mediated neuronal hyperactivity, and engaged in excessive synaptic pruning. These pathological effects were reversed by pharmacological inhibition of microglial GABAB receptors. Collectively, our findings establish an advanced platform to dissect human neuroimmune interactions in sub-cortical regions, highlighting the important role of microglia in shaping critical circuitry related to neuropsychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/657874v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@125b36eorg.highwire.dtl.DTLVardef@270079org.highwire.dtl.DTLVardef@903525org.highwire.dtl.DTLVardef@19145c4_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserModeling regional microglial diversity in sub-cortical regions is challenging. We generated human organoid and assembloid models containing microglia that acquire region-specific heterogeneity. Our work shows dynamic responses of microglia when exposed to hyperexcitable midbrain-striatal circuits, providing an exciting platform to study neuroimmune interactions in human brain development and neuropsychiatric disorders, including SCN2A mutation-mediated monogenic autism. HighlightsO_LI* Single-cell RNA sequencing analyses reveal six distinct microglial subtypes that spontaneously attain unique specialization in human cortical, striatal, and midbrain organoids. C_LIO_LI* Microglia facilitate axonal projections across regional organoids, promoting assembloid formation. C_LIO_LI* Microglia respond to hyperexcitable neurons via calcium signaling and exhibit excessive pruning of neuronal synapses. C_LIO_LI* Blocking microglial GABAB receptors normalizes calcium activity and reduces synaptic pruning, suggesting a potential targeting strategy for synaptic deficits. C_LI

neuroscience↗

bioRxiv2025

A genetically encoded fluorescent sensor for monitoring spatiotemporal prostaglandin E2 dynamics in vivo

Prostaglandin E2 (PGE2) is an important lipid signaling molecule that regulates a wide range of physiological and pathological processes. However, its dynamics during these processes are largely unknown due to the lack of tools to directly visualize PGE2 with high spatiotemporal resolution. Here, we developed and characterized a genetically encoded PGE2 sensor, which we call GRABPGE2-1.0 (PGE2-1.0), that has high specificity for PGE2, nanomolar affinity, rapid kinetics, and high spatial resolution when expressed both in vitro and in vivo. Using fiber-photometry recordings, we found that PGE2-1.0 can reliably monitor endogenous PGE2 dynamics in the preoptic area in the brain during acute inflammation. The wide-field in vivo imaging with PGE2-1.0 reveals spatial heterogeneity in cortex-wide PGE2 dynamics during acute inflammation and seizure. Thus, our PGE2-1.0 sensor can be used to detect endogenous PGE2 dynamics with high spatiotemporal resolution, providing a robust tool for studying PGE2 under specific physiological and pathological conditions.

neuroscience↗

bioRxiv2025

Bazedoxifene rescues sexually dimorphic autistic-like abnormalities in mice carrying a biallelic MDGA1 mutation

In the accompanying study, we describe two pairs of MDGA1 missense mutations (Val116Met/Ala688Val and Tyr635Cys/Glu756Gln) from two patients with autism spectrum disorders (ASDs) and how these mutations exert distinct abnormalities in biological processes during central nervous system development. Here, we generated knockin (KI) mice harboring the murine version of Tyr635Cys/Glu756Gln MDGA1 (Mdga1Y636C/E751Q) and performed extensive behavioral analyses. Male KI mouse pups and adults exhibited impaired ultrasonic vocalizations and sensorimotor gating (ASD-relevant behavioral deficits), and thus exhibited phenotypes different from those of male Mdga1 conditional knockout (cKO) mice. In contrast, adult female KI mice did not exhibit a range of ASD-like behavioral abnormalities. Electrophysiological analyses performed using both juvenile and adult Mdga1Y636C/E751Q mice revealed sexually dimorphic and developmental stage-dependent compromises of GABAergic synaptic inhibition. In addition, proteomics analyses showed that the phospho-proteomic phenotypes differed between Mdga1Y636C/E751Q and Mdga1-cKO mice. Treatment of male Mdga1Y636C/E751Q KI mice with the FDA-approved estrogen receptor modulator, bazedoxifene, restores the KI-related molecular, GABAergic synapse, and behavioral changes. Collectively, our results suggest a novel treatment strategy for ASDs that present developmentally regulated and/or sexually dimorphic features.

neuroscience↗

bioRxiv2025

Autism-associated SCN2A deficiency disrupts cortico-striatal circuitry in human brain assembloids

Profound autism spectrum disorder (ASD) is frequently attributable to single-gene mutations, with SCN2A (voltage-gated sodium channel NaV1.2) protein-truncating variants (PTVs) being one of the most penetrant. Although cortico-striatal circuitry is implicated as a key node in ASD, the impact of SCN2A deficiency on human neural circuits is unknown. Using the human cortico-striatal assembloid model, we show that the autism-causing PTV SCN2A-C959X impairs long-range cortical axonal projections, reduces striatal spine density, and attenuates excitatory cortical-striatal synaptic transmission. Surprisingly, these assembloids carrying the heterozygous SCN2A nonsense mutation exhibited pronounced network hyperexcitability, a human cell-specific phenotype not observed in Scn2a+/- mice, highlighting a human-specific circuit vulnerability. Collectively, our study unveils human circuit-specific dysfunctions of SCN2A deficiency and SCN2A-mediated ASD. HighlightsO_LIAxonal projections facilitate synapse formation and functional connectivity in human brain assembloids. C_LIO_LINaV1.2 is expressed along neuronal axons, extending to soma and dendrites in human brain assembloids. C_LIO_LISCN2A-C959X disrupts axonal projection patterns, impairs excitatory synaptic transmission, reduces spine density, and results in elevated neuronal excitability. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/657036v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6d5b1forg.highwire.dtl.DTLVardef@1795ecdorg.highwire.dtl.DTLVardef@13f0d7eorg.highwire.dtl.DTLVardef@8ee059_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefO_ST_ABSSCN2A haploinsufficiency impairs cortico-striatal circuitry.C_ST_ABSSCN2A haploinsufficiency disrupts axon initial segment (AIS) integrity, leading to hyperexcitability (red arrow), reduced axon projections, and impaired synaptic transmission (decreased sEPSCs and altered network firing). These deficits result in dysfunction within the cortico-striatal circuitry.

neuroscience↗

bioRxiv2025

Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning and increases cAMP-PKA signaling in a zebrafish model of Neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) is a neurogenetic disorder caused by loss of function mutations in the gene neurofibromin 1 (NF1). NF1 encodes neurofibromin, a multifunctional tumor suppressing protein that regulates Ras, cAMP, and dopamine signaling. NF1 predisposes patients to a wide range of symptoms, including peripheral nerve tumors, brain tumors, and cognitive dysfunction. Despite considerable work using animal models to investigate the role of neurofibromin in behavior, translating research into treatment for NF1-associated cognitive dysfunction has not yet been successful. Here, we identify Cxcr4 chemokine receptor signaling as a regulator of habituation learning and modulator of cAMP-PKA signaling in nf1 mutant larval zebrafish. Combining a small-molecule drug screen and RNAseq analysis, we show that cxcr4b expression is increased in nf1 mutants and that pharmacological inhibition of Cxcr4 with AMD3100 (Plerixafor) improves habituation learning in nf1 mutants. We further demonstrate that Plerixafor treatment activates cAMP-PKA pathway signaling but has limited effects on Ras-Raf-MEK-ERK pathway signaling in the nf1 mutant brain. CXCR4 was previously identified as a potential therapeutic target for neurofibromin-deficient tumorigenesis. Our results provide evidence that Cxcr4 signaling also regulates neurofibromin-dependent cognitive function.

neuroscience↗

bioRxiv2025

Distinct immunity protein families mediate compartment-specificneutralisation of a bacterial toxin

Staphylococcus aureus utilises a type VII secretion system (T7SS) to secrete antibacterial toxins that target competitor bacteria. EsxX is a T7SS substrate protein secreted by ST398 strains that has an LXG domain at its N-terminus. Here we show that the EsxX C-terminus is a membrane-depolarising toxin with a glycine zipper motif. EsxX is profoundly toxic to bacteria, displaying toxicity from both cytoplasmic and extracellular compartments. A pair of polytopic membrane proteins, ExiCD, protect cells from intoxication by extracellular EsxX. By contrast, a distinct soluble heterodimer, ExiAB, neutralises cytoplasmic EsxX by sequestration of its glycine zipper motif in a binding groove on ExiB. The exiA-exiB gene pair co-occur in staphylococcal genomes with esxX, invoking a model whereby ExiAB protects EsxX-producing cells from self-toxicity prior to EsxX secretion. By contrast ExiCD is encoded by both EsxX producers and in antitoxin islands of competitor strains that do not encode EsxX, consistent with providing immunity against the secreted form of the toxin. This work defines a new class of antibacterial toxin requiring two distinct types of immunity protein which follow different phylogenetic distributions.

microbiology↗

bioRxiv2025

Mitotic phosphorylation of ADAR1 regulates its centromeric localization and is required for faithful mitotic progression

Adenosine Deaminase Acting on RNA 1 p110 (ADAR1p110), the constitutively expressed nuclear isoform of the RNA-editing enzyme ADAR1, plays well-established roles in adenosine-to-inosine RNA editing, but its functions during mitosis remain poorly defined. Here, we identify ADAR1p110 as a chromatin-associated factor essential for mitotic chromosome segregation and cell viability. Depletion of ADAR1 caused metaphase arrest, DNA damage accumulation, and apoptosis. Co-immunoprecipitation experiments revealed that ADAR1p110 physically interacts with Structural Maintenance of Chromosome 3 (SMC3), a core component of the cohesin complex. Genome-wide DNA immunoprecipitation sequencing (DIP-seq) showed that ADAR1p110 selectively binds centromeric -satellite DNA during mitosis, a finding validated by DNA immunoprecipitation quantitative polymerase chain reaction (DIP-qPCR). Complementary DNA-RNA immunoprecipitation sequencing (DRIP-seq) revealed that RNA:DNA hybrids (R-loops) are enriched in centromeric regions during mitosis and are further augmented by ADAR1 overexpression. We identified serine 614 (S614) as a key mitosis-specific phosphorylation site on ADAR1p110, and demonstrated that this post-translational modification is essential for its chromatin recruitment, stability, and mitotic function. Rescue experiments using phospho-mimetic mutants (S614D and 3xD) successfully restored mitotic progression in ADAR1-deficient cells, whereas non-phosphorylatable variants failed to do so. These results reveal that ADAR1p110 is phosphorylated in a cell cycle-dependent manner and functions at the intersection of post-transcriptional and post-translational regulation. By coordinating R-loop recognition at centromeres with chromosome cohesion, ADAR1p110 safeguards genome integrity during mitosis. Our findings uncover a previously uncharacterized mechanism through which a canonical RNA-editing enzyme contributes to chromosomal dynamics independent of its deaminase activity.

molecular biology↗

bioRxiv2025

Establishing a Digital PCR-Based Reference Measurement Procedure for Monkeypox Virus: An Inter-laboratory Assessment and Standardization Study

The accurate detection of monkeypox virus (MPXV) is crucial for effective viral diagnosis and epidemic prevention. Currently, the field lacks standardized reference methods for MPXV quantification, as well as reliable pseudovirus reference materials (RMs) to ensure quality control throughout the detection process. To address this, we developed a droplet digital PCR (ddPCR) reference measurement procedure (RMP) for precise quantification of MPXV genes B6R, which demonstrates excellent performance with a wide dynamic range (11-1.24x104 copies/L), strong linearity (R2=0.9984), and a low limit of quantitation (11 copies/L, CV[≤]25%). Repeatability tests confirmed high precision, with inter-laboratory CVs <10% across nine labs using different dPCR platforms. recovery efficiencies for B6R and F3L were [~]69%, with uncertainties incorporated into final measurements. The homogeneity assessment showed good results (CV=2.94%), and stability studies confirmed the stability of the sample during -70 {degrees}C and short-term storage (4 {degrees}C/-20 {degrees}C). Mandels statistical data shows that the reproducibility between laboratories is consistent. This validated ddPCR RMP provides metrological traceability, ensuring reliable and comparable results for MPXV diagnosis and supporting public health efforts.

molecular biology↗

bioRxiv2025

Multifaceted brain representation of numerosity across the senses and presentation formats

Humans can extract numerosity from different senses and a variety of context. How and where the brain abstract numerical information from low-level sensory inputs remains debated. Using multivariate pattern decoding and representational similarity analysis applied to fMRI data, we comprehensively investigate how the brain represents numerical information (range 2-5) across different modalities (auditory, visual) and presentation formats (sequential, simultaneous; symbolic, non-symbolic). We identify a set of brain regions along the dorsal pathway-from early visual cortex to the intraparietal and frontal regions-that encode specific non-symbolic numerical information across formats and modalities. The numerical distance effect, a hallmark of magnitude encoding, was observed in most of these regions. We found aligned representation of numerical information across visual and auditory modalities in intraparietal and frontal regions, but only when they shared a sequential presentation format. Maintaining a distinction between spatial and temporal numerical representations may thus be a fundamental aspect of numerical processing. RSA further revealed a posterior-to-anterior gradient in the intraparietal sulcus (IPS) showing that the dominant factors influencing distributed numerical representations shifted from sensory modality in the posterior parietal regions to presentation format in the anterior parietal areas. Our study reveals a multifaceted brain representation of numerosity across the senses and presentation formats.

neuroscience↗

bioRxiv2025

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

Cholesterol homeostasis is regulated by the sterol regulatory element-binding protein (SREBP) pathway, with the membrane-embedded SREBP-cleavage-activating protein (SCAP) and insulin-inducible gene protein (Insig)-1/2 acting as sterol sensors. Our previous studies unveiled a critical role of ammonia in activating the SREBP pathway. Here, we performed extensive molecular dynamics (MD) simulations to elucidate the structural mechanisms through which ammonia binding triggers SCAP/Insig dissociation and subsequently activate SREBP. The SCAP S4 helix exists in two distinct conformations: a partially unfolded S4 and an intact S4; the transition between these states may constitute a crucial aspect of SCAP activation. We first studied the binding of ammonia to SCAP in different S4 conformational states. We then explored how the binding of ammonia or 25-hydroxycholesterol (25-HC) affects the conformational transition of S4 using targeted MD simulations. Finally, we performed comparative analysis of the 25-HC-bound inactive SCAP and the ammonia-bound active SCAP. Collectively, our findings highlight the importance of S4 helix conformation in activating the SCAP protein. Our simulations suggest that ammonia and 25-HC act as an agonist and antagonist of SCAP activation, respectively. Specifically, ammonia binding facilitates the transition of S4 from the unfolded to the straight conformation, triggering subsequent conformational changes in the transmembrane domain of SCAP. These changes eventually promote the SCAP/Insig dissociation and alter the position of the MELADL motif at the membrane surface. Significant StatementCellular cholesterol homeostasis is tightly regulated by the SREBP pathway, which relies on the membrane proteins SCAP and Insig to sense sterol levels. While ammonia has recently been identified as a novel activator of this pathway, its structural mechanism of action remained unknown. Here, extensive molecular dynamics simulations reveal that ammonia binding promotes a critical conformational transition in the SCAP S4 helix, facilitating SCAP activation and its dissociation from Insig. Our findings show that ammonia and cholesterol act as opposing modulators--agonist and antagonist--of SCAP activity. This work uncovers a previously unrecognized structural switch in SCAP and provides new molecular insight into small-molecule regulation of cholesterol sensing.

molecular biology↗

bioRxiv2025

Clonal lineage tracing and parallel multiomics profiling reveal transcriptional diversification induced by ARID1A deficiency

Phenotypic heterogeneity among genetically identical cancer cells underpins tumor progression and therapy resistance. However, the mechanism of epigenetic dysregulation that drives such divergence remains unclear. This study introduces integrated multimodal experimental platform specialized in analyzing inter/intraclonal heterogeneity (IMPACH), a scalable platform that integrates lineage tracing, genetic perturbation, and multimodal single-cell analysis. Utilizing IMPACH, results revealed that loss of epigenetic regulators--particularly ARID1A--enhances transcriptomic and epigenetic heterogeneity under controlled conditions. ARID1A deficiency promotes stochastic chromatin opening and induces an atypical gene expression program associated with poor clinical outcomes. Despite increased epigenetic randomness, chromatin changes remain localized to regulatory elements, partially linked to SMARCA4 binding sites. These findings revealed that chromatin remodeling defects promote clonal diversification through both stochastic and constrained mechanisms. Thus, owing to its scalability and versatility, IMPACH provides a robust framework for elucidating how epigenetic perturbations shape cellular heterogeneity in cancer.

cancer biology↗

bioRxiv2025

TIP-seq: A Single-cell Multiomics Approach for Simultaneous Transcriptome and Intracellular Protein Profiling

Single-cell multiomics technologies have significantly advanced our understanding of cellular heterogeneity; however, the concurrent profiling of mRNA transcripts and target proteins continues to pose a substantial challenge. To bridge the gap between single-cell sequencing and proteomic methods, we developed an innovative single-cell multiomics methodology, termed TIP-seq, which facilitates the simultaneous profiling of the transcriptome and intracellular proteins without prior cell manipulation. In TIP-seq, microfluidic technology is leveraged to integrate oligonucleotide-labeled antibodies with hydrogel beads, allowing for the capture of mRNAs and proteins from individual cells within droplets, thereby enabling high-throughput and precise dual-omics data acquisition. When applied to lung cell lines and non-small cell lung cancer (NSCLC) tissues, TIP-seq analysis revealed notable cellular heterogeneity and molecular dynamics, emphasizing the distinct immune cell interactions within NSCLC tissues. Key immune checkpoint interactions in NSCLC, such as SPP1-CD44, NECTIN2-TIGIT, and NECTIN2-CTLA4, along with functional alterations in tumor-associated dendritic cells (DCs) and T cells, were identified via TIP-seq, underscoring their pivotal roles in mediating immune suppression within the tumor microenvironment. Collectively, TIP-seq represents a powerful methodology for identifying novel therapeutic targets and biomarkers, thereby holding significant potential for the advancement of precision medicine in the treatment of lung cancer and other complex diseases.

biochemistry↗

bioRxiv2025

Advancing the Discovery of Phage-Host Interactions and Disease Classification from Metagenomic Profiles Using Deep Learning

Microbial communities are essential for sustaining ecosystem functions in diverse environments, including the human gut. Phages interact dynamically with their prokaryotic hosts and play a crucial role in shaping the structure and function of microbial communities. Previous approaches for inferring phage-host interactions (PHIs) from metagenomic data are constrained by low sensitivity and the inability to accurately capture ecological relationships. To overcome these limitations, we developed PHILM (Phage-Host Interaction Learning from Metagenomic profiles), a deep learning framework that predicts PHIs directly from the taxonomic profiles of metagenomic data. We validated PHILM on both synthetic datasets generated by ecological models and real-world data, finding that it consistently outperformed the co-abundance-based approach for inferring PHIs. When applied to a large-scale metagenomic dataset comprising 7,016 stool samples from healthy individuals, PHILM identified 90% more genus-level PHIs than the traditional assembly-based approach. In a longitudinal dataset tracking PHI dynamics, PHILMs latent representations recapitulated microbial succession patterns originally described using taxonomic abundances. Furthermore, we demonstrated that PHILMs latent representations served as more discriminative features than taxonomic abundance-based features for disease classifications. In summary, PHILM represents a novel computational framework for predicting phage-host interactions from metagenomic data, offering valuable insights for both microbiome science and translational medicine.

bioinformatics↗

bioRxiv2025

Alternating 2D and 3D Culture Reduces Cell Size and Extends the Lifespan of Placenta-Derived MSCs

Mesenchymal stem cells (MSCs) offer significant therapeutic potential, but traditional 2D culture on rigid substrates results in progressive cell enlargement and senescence, reducing proliferative capacity and therapeutic potency. This poses a major challenge for widespread clinical application. We explored a novel strategy for placenta-derived MSCs combining 2D expansion with 3D spheroid culture to address these limitations. Our research shows that culturing MSCs as 3D spheroids significantly reduces individual cell size and size distribution compared to 2D culture. Spheroid formation is feasible in chemically defined media with minimal cell death, and is enhanced by extracellular matrix protein supplementation. Although MSCs do not proliferate in 3D suspension, an alternating 2D/3D culture protocol, transitioning cells between 2D flasks and 3D spheroids after each passage, effectively slows MSC enlargement and senescence over long periods. This alternating method also preserves MSC immunomodulatory function, unlike continuous 2D culture which leads to its loss. For scalability, we developed an RGD-functionalized alginate hydrogel tube (AlgTube) system that mimics this alternating environment, supporting both adherent growth and chemically triggered spheroid formation. This alternating 2D/3D culture strategy and the scalable AlgTube platform provide a foundation for developing next-generation MSC manufacturing technologies to meet future clinical demands.

bioengineering↗

bioRxiv2025

Disturbed engram network caused by NPTXs downregulation underlies aging-related memory deficits

Engram cells storing specific memories are allocated to separate neuronal ensembles, which preferentially recruit either excitatory or inhibitory inputs to drive precise memory expression. However, how these formed neuronal ensembles maintain their stability, and whether the disturbed stability contributes to aging-related memory deficits remain elusive. Here, we show that neuronal pentraxin1 (NPTX1) facilitates Kv7.2-mediated inhibition of Fos+ensemble hyperexcitability, thereby restricting its response to excitatory inputs from medial entorhinal cortex (MEC) and promoting memory expression in the fear context. Meanwhile, NPTX2 facilitates the perisomatic inhibition of the Npas4+ ensemble by parvalbumin+ (PV+) interneurons, thus preventing fear memory overgeneralization. Pharmacological activation of Kv7.2 or chemogenetic activation of PV+ interneurons repaired memory deficits caused by engram specific NPTXs depletion. Contextual fear memory precision and NPTXs expression in dentate gyrus (DG) engram cells are decreased in aged mice. Overexpression of NPTX1 in Fos+ensemble or AMPAR binding domain of NPTX2 in Npas4+ ensemble rescued memory imprecision. These findings elucidate that the coordination of NPTXs prevents engram ensembles from becoming hyperactive and provide a causal link between engram network destabilization and aging-associated memory deficits.

neuroscience↗

bioRxiv2025

A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies

Single-domain antibodies (sdAbs) have emerged as powerful therapeutic agents due to their small size, high stability, and superior tissue penetration. However, unlike conventional monoclonal antibodies (mAbs), sdAbs lack an Fc domain, limiting their functional versatility and manufacturability. To address this challenge, we developed TFDesign-sdAb, a deep learning-based generative-ranking framework that enables rational engineering of sdAbs with tailored functionalities. Our framework integrates a structure-aware diffusion model (IgGM) for large-scale candidate generation and a fine-tuned sorter (A2binder) that evaluates and prioritizes them based on predicted functionality. Unlike traditional CDR-focused approaches, TFDesign-sdAb optimizes both complementarity-determining regions (CDRs) and framework regions (FRs), allowing sdAbs to acquire new functional properties while maintaining antigen specificity. We validated our approach by conferring Protein A binding to human VHs and nanobodies that originally lacked this feature, achieving high expression rates, strong binding affinities, and successful purification via industry-standard Protein A affinity chromatography. High-resolution structural characterization (1.49 [A] and 2.0 [A]) of the redesigned sdAb-Protein A complexes revealed conserved FR-mediated binding motifs that recapitulate natural Fc-Protein A interactions, validating the accuracy of our model. Furthermore, our pipeline streamlined the antibody engineering process, achieving a 100% success rate in generating Protein A-binding sdAbs while maintaining their original antigen-binding affinity. This work demonstrates the power of AI-driven design in overcoming long-standing limitations in antibody engineering and presents a scalable, generalizable solution for enhancing sdAb functionality.

bioinformatics↗

bioRxiv2025

Neural sampling from cognitive maps supportsgoal-directed planning and imagination

AI systems are becoming more intelligent, but at a very high cost in terms of energy consumption and training requirements. In contrast, our brains only require 20W of energy, they learn online, and they can instantly adjust to changing contingencies. This begs the question what data structures, algorithms, and learning methods enable brains to achieve that, and whether these can be ported into artificial devices. We are addressing this question for a core feature of intelligence: The capacity to plan and solve problems, including new problems that involve states which were never encountered before. We examine three tools that brains are likely to employ for achieving that: Cognitive maps, stochastic computing, and compositional coding. We integrate these tools into a transparent neural network model, and demonstrate its power for flexible planning and problem solving. Importantly, this approach is suitable for implementation by in-memory computing and other energy-efficient neuromorphic hardware. In particular, it only requires self-supervised local synaptic plasticity that is suited for on-chip learning. Hence a core feature of brain intelligence, the capacity to generate solutions to problems that were never encountered before, does not require deep neural networks or large language models, and can be implemented in energy-efficient edge devices.

neuroscience↗