Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

CXCR3 on transferred T cells enables vaccine-boosted adoptive T-cell therapy in solid tumors

Adoptive T-cell therapy (ACT) has demonstrated marked clinical benefit in hematological malignancies but has limited efficacy against solid tumors. Cancer vaccines can improve ACT, but the mechanisms underlying this combination are poorly understood. Here, we combined ACT with chimpanzee adenovirus ChAdOx1 (ChAd) and modified vaccinia Ankara (MVA) encoding tumor antigens. Whereas PD1 blockade failed to improve ACT, the combination with ChAd/MVA vaccination drove durable regression of established tumors, correlating with expansion of tumor-reactive T cells in lymphoid organs and increased tumor infiltration by T cells. Mechanistically, ChAd priming induced CXCR3 ligands (CXCL10 and CXCL9) in the vaccine-draining lymph node, thereby recruiting transferred T cells to this node independently of cognate antigen. CXCR3 expression on the transferred T cells, but not on host cells, was required for the anti-tumor effect of the combination therapy and favored T-cell accumulation in the vaccine-draining lymph node and the tumor. These findings identify CXCR3 on the transferred T cells as a determinant of ACT plus vaccination synergy and provide a rationale for combining viral-vector vaccines with TCR-T therapies, and for selecting or engineering T cells to retain CXCR3 expression.

immunology↗

bioRxiv2026

Filling the Missing Puzzle: Integrating Interaction and Evolutionary Information to Enhance Protein Fitness Prediction in Inverse Folding

Protein inverse folding, which infers compatible amino acid sequences from a given backbone structure, is central to rational protein design. Current methods rely largely on sequence recovery rate as the evaluation metric, emphasizing structural compatibility but seldom addressing function. Yet functional activity depends on the proper network of non-covalent interactions-protein-ligand contacts being a prime example. We argue that function-oriented protein design is governed by three complementary constraints: structural, interaction, and evolutionary, none of which are handled in a unified manner by existing pretrained models. To bridge this gap, we introduce zPolaron, a graph neural network built on protein-ligand complexes for functional protein design. zPolaron represents residues and ligand atoms as a heterogeneous graph and jointly encodes structural, interaction, and evolutionary information by fusing physical-interaction-enhanced graph representations with ESM-2 embeddings. Across multiple fitness prediction benchmarks, zPolaron outperforms all baselines, with gains evident across structural, interaction, and evolutionary dimensions. Wet-lab experiments further confirm its utility in functional enzyme screening and design: the optimized CalA6-D205A-S160G mutant achieves a 17.84-fold improvement in activity, while the CalB-I121M mutant yields a 1.91-fold increase. Together, these results show that integrating interaction and evolutionary information fills the missing puzzle of inverse folding, enhancing protein fitness prediction beyond structural compatibility. zPolaron is available at https://github.com/zelixirSH/zPolaron.

bioinformatics↗

bioRxiv2026

A Hypothalamic Pathway for Energy Conservation

Many animals utilize a survival strategy of hypothermia, inactivity, and a dramatic decrease in their energy metabolism when faced with a shortfall in energy supplies. Mice, for example, show daily torpor that may last several hours to bridge the lack of energy availability in a cold environment. While our recent studies identified a population of neurons in the median preoptic nucleus (MnPO) necessary for fasting-induced torpor regulation, the specific brain circuits that trigger energy conservation in response to food restriction are unknown. We show here that the energy state of the animal is conveyed to preoptic neurons by inputs from the arcuate nucleus (ARC), a region known to be indispensable for driving metabolic and behavioral adaptations to the fasted state. We first found that the activity of ARC neurons expressing Agouti-Related Peptide (ARCAgRP) is required for the generation of fasting-induced torpor. Then, we showed that torpor-active ARCAgRP neurons innervate the preoptic area of the hypothalamus (POA), including the MnPO. Using optogenetic methods, we also found that activating the ARCAgRP-MnPO pathway induces key features of torpor: decreased body temperature, bradycardia, reduction of energy expenditure, and suppression of brown adipose tissue thermogenesis. Remarkably, we also show that inhibition of the ARCAgRP-MnPO brain circuit entirely prevents fasting-induced torpor. Furthermore, we identified that both NPY and GABA are neuromodulators used by ARCAgRP neurons to enable hypothermic responses during starvation. Our studies provide a detailed view of a hypothalamic pathway enabling energy conservation, a survival mechanism in conditions of low energy availability.

neuroscience↗

bioRxiv2026

Photobiocatalytic Diastereo- and Enantioselective Synthesis of Non-Canonical Amino Acids Bearing Challenging Stereochemical Dyads and Triads

Catalyst-controlled stereodivergent synthesis of acyclic molecules bearing multiple stereogenic centers remains a longstanding challenge in asymmetric catalysis, particularly through intermolecular radical C-C coupling. Here, we report the directed evolution of pyridoxal 5'-phosphate (PLP)-dependent biocatalysts for the stereodivergent synthesis of non canonical amino acids bearing either skipped , {gamma}-stereochemical dyads or contiguous , {beta}, {gamma}-stereochemical triads. Starting from a thermophilic tryptophan synthase {beta}-subunit, protein engineering generated complementary enzyme variants that selectively construct three of the four possible , {gamma}-stereoisomers through biocatalyst-controlled reversal of both remote {gamma}-stereochemistry and proximal -stereochemistry. These engineered enzymes catalyzed intermolecular radical C-C bond formation with a broad range of secondary alkyltrifluoroborates, affording , {gamma}-disubstituted amino acids in excellent yields and stereoselectivities. Furthermore, directed evolution enabled efficient {beta}-dehydroxylative radical coupling of the non-native threonine-derived aminoacrylate intermediate, providing amino acids bearing contiguous , {beta}, {gamma}-stereochemical triads with up to 96:4:<0.1:<0.1 d.r. and >99:1 e.r.. To further demonstrate the synthetic utility of this platform, the stereochemically enriched amino acids were transformed into valuable {gamma}-chiral amines through engineered PLP dependent tryptophan decarboxylases, establishing a dual PLP enzyme based biocatalytic cascade for the enantiodivergent synthesis of privileged amine scaffolds. Molecular dynamics simulations reveal that enzyme controlled {gamma}-stereoselectivity originates from active-site remodeling that modulates {pi}-{pi} interactions and steric contacts governing the facial selectivity of the radical addition step. This work expands the synthetic capabilities of radical biocatalysis by enabling catalyst-controlled stereodivergent assembly of complex acyclic stereochemical arrays and establishes engineered PLP enzymes as versatile catalysts for the synthesis of stereochemically complex amino acids and chiral amines.

biochemistry↗

bioRxiv2026

Monkeypox virus M2 rewires nucleocytoplasmic transport to coordinate host translation suppression and immune evasion

Host shutoff is a conserved viral strategy to dismantle cellular defenses, yet the molecular orchestrators in large DNA viruses remain poorly defined. Through a systematic functional screen of the monkeypox virus (MPXV) proteome, we identify M2 as a potent, multifunctional effector that executes a global blockade of host gene expression. Unlike its assembly-centric homologs across the orthopoxvirus genus, M2 localizes not only to the well-characterized endoplasmic reticulum but also to the nuclear envelope, where it may function as a molecular chokepoint, obstructing bidirectional nucleocytoplasmic transport. Concurrently, M2 expression is also associated with altered Akt/mTOR/4EBP1 signaling axis, which may contribute to reduced cap-dependent translation. Intriguingly, M2 may induce a 'transcriptional trap', triggering a robust but futile ERK-dependent activation of AP-1-mediated stress responses that are decoupled from translation. Using recombinant virus engineering, we provide evidence that M2 expression augments viral replication in cell culture. These findings suggest that M2 may contribute to MPXV-mediated host shutoff, although further studies under authentic infection conditions are required to establish causality and define the underlying mechanism. Our study preliminarily reveals an paradigm for viral niche adaptation, in which a single protein coordinates spatial sequestration and biochemical suppression to enact multi-layered host suppression, providing critical candidate targets for therapeutic intervention against emerging orthopoxviruses.

microbiology↗

bioRxiv2026

Passive Cell-Flux Partitioning Enables Single-Cell-Constrained Impedance Sensing From High-Density Microbial Cultures

Fermentation is a process through which microorganisms are used to transform basic molecules into high value substances in various applications such as biopharma, food production, and biofuel generation. In such processes, monitoring the health of microbial cells is essential, as it is a key factor in the final product yield. Traditional methods of assessing the health of fermenter populations have involved manually extracting samples from the fermenter for benchtop testing, which lacked the accuracy and efficacy of real-time continuous measurements. This has opened the door for inline sensors to be integrated into fermenters for continuous measurement; including microfluidic based Electrochemical Impedance Spectroscopy (EIS). EIS utilizes a range of frequencies to gain insight into the characteristics of microbial populations, such as cell size and membrane capacitance. EIS cytometry, in particular, has emerged as a relevant tool, as it enables single-cell level detection in real-time. However, current EIS cytometry devices cannot be deployed directly within fermenters due to the high cell density conditions. This has limited EIS analysis in fermenters to bulk measurements averaged across a population. Here, we present a microfluidic chip that uses passive cell-flux-partitioning geometry to direct cells from high-density culture through a single-cell-constrained flow path containing integrated impedance-sensing electrodes. The proposed chip combines geometric channel design and embedded electrodes to enable continuous impedance measurements from cell-containing flow while operating at input cell densities on the scale of 10^9 CFU/mL. This work demonstrates a first step toward integrating single-cell-constrained microfluidic handling with impedance sensing for inline monitoring in industrial biomanufacturing.

bioengineering↗

bioRxiv2026

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

How perennial, postmitotic multinucleated tissues, such as skeletal myofibers, maintain their identity and transcriptional adaptation to homeostatic perturbations through adult life is an outstanding question. To address this issue, we investigated the consequences of loss of 3D-genome architecture in skeletal muscles by generating myofiber-specific Ctcf-deficient (CtcfmKO) mice. CtcfmKO mice did not exhibit muscular phenotype at birth but spontaneously developed a severe myopathy. Integrated analysis of snRNAseq, ATACseq and promoter-capture Hi-C revealed both common and fiber-type specific patterns of dysregulated gene expression associated with alterations in chromatin accessibility and promoter-based interactions in Ctcf-deficient myonuclei at distinct stages of myopathy development. Decreased chromatin accessibility at promoters and changes in their connectivity with distal elements were observed across all myonuclei as a direct consequence of Ctcf deficiency at early stages and associated with downregulation of genes implicated in myofiber contraction and anabolism, metabolism, adhesion and neuromuscular transmission. Conversely, at later stages, upregulation of genes leading to persistent activation of ER stress/UPR and catabolism resulted from global reconfiguration of chromatin structure and connectivity, partly as indirect consequence of Ctcf deficiency. Notably, type-IIB myonuclei exhibited specific alterations in gene expression that culminated in loss of fiber-type identity and ectopic expression of inflammatory genes. These results reveal a requirement of Ctcf for maintenance of fiber-type identity and transcriptional adaptation in vivo, through multilayered control of 3D genome integrity. They also indicate an unprecedented association between Ctcf deficiency in myofibers and susceptibility to develop myopathies, whereby Ctcf dispensability for developmental myogenesis confers vulnerability to develop myopathic syndromes.

molecular biology↗

bioRxiv2026

Anti-defense systems of viral communitie vary with genomic traits, host immunity and environmental stress

Abstract: Background Despite the ecological importance of viral anti-defense systems (ADS), yet how viral ADS repertoires vary across microbial ecosystems remains poorly understood. Here, we integrated global virus datasets with metagenomes from heavy metal-contaminated soils and chromium-stress microcosms to investigate ecological determinants of viral ADS. Results We found that ADS repertoires were constrained by viral genome capacity, with most ADS-carrying viruses encoded a single system, whereas multi-ADS occurred mainly in larger genomes. Viral lifestyle partitioned ADS, with temperate viruses enriched in ADS targeting early-stage defenses and virulent viruses preferentially encoding ADS against mid- and late-stage defense. ADS composition also varied by host lineage and across habitats, linking viral ADS repertoires to host immune landscapes and ecosystem-specific viral strategies. Moreover, along the heavy metal contamination gradient, changes in the prevalence of ADS-carrying viruses occurred alongside shifts in prokaryotic defense profiles. In addition, expanded ADS repertoires may further increase dissemination potential of MGE-borne adaptive genes, highlighting viral ADS as a potential contributor to the adaptive evolution of microbial community. Conclusions These findings reveal that viral ADS are shaped by genomic traits, host immunity and environmental stress, with implications for virus-host interaction and microbial adaptive evolution. More broadly, this study extends anti-defense research beyond individual virus-host systems, offering an integrative, community-level perspective to guide future studies testing whether and how virus-prokaryote immune interactions contribute to microbial community dynamics and evolution in changing environments.

microbiology↗

bioRxiv2026

Asymmetric assembly of congested contiguous stereocenters via photobiocatalytic three-component radical coupling

Despite rapid advances in new-to-nature biocatalysis, trimolecular enzymatic reactions that generate previously inaccessible molecular entities, particularly those bearing well-defined, congested stereochemical dyads, remain exceedingly rare. Here, we report a novel diastereo- and enantioselective photobiocatalytic three-component radical coupling unknown in both organic chemistry and enzymology, enabled by cooperative catalysis employing an evolved pyridoxal biocatalyst and a transition-metal photosensitizer. Directed evolution using high-throughput photobiocatalysis furnished two threonine aldolase variants, enabling the stereoselective assembly of contiguous tri- and tetrasubstituted stereocenters as well as vicinal tetrasubstituted stereocenters, which were long regarded as a challenging goal for stereoselective radical chemistry and asymmetric catalysis. Furthermore, a variety of radical precursors, including alpha-iodoesters, alpha-iodoamides, alpha-iodoketones, and alpha-iodonitriles, could be transformed into structurally diverse, densely substituted non-canonical amino acid derivatives via C-H functionalization with excellent stereocontrol. Leveraging the broad substrate compatibility of engineered pyridoxal biocatalysts, combinatorial biocatalysis was achieved by simultaneously varying all three coupling partners, delivering products with a 98% success rate. Collectively, this diversity-generating multicomponent photobiocatalytic radical coupling afforded a powerful strategy for addressing long-standing challenges in asymmetric catalysis while enabling access to valuable stereochemically complex small molecules with applications in medicinal chemistry.

biochemistry↗

bioRxiv2026

Forsythoside B attenuates neuropathic pain by suppressing USP7/HIF-1α-mediated microglial glycolytic reprogramming

Neuropathic pain involves spinal microglial activation and metabolic changes.Forsythoside B (FB) has anti-inflammatory effects, but its role in neuropathic pain and microglial glycolysis remains unclear. We investigated the effects and mechanisms of FB in mice with chronic constriction injury (CCI) and in LPS-stimulated BV2 microglia.FB reduced mechanical allodynia and thermal hyperalgesia in CCI mice. FB also reduced the spinal levels of HIF-1, HK2, PKM2, LDHA, and CD86. It decreased the proportion of IBA1+/CD86+ cells and the levels of IL-1{beta}, IL-6, and TNF-. In LPS20 stimulated BV2 microglia, FB reduced glycolysis-related proteins, proinflammatory markers, and cytokine release. FB also reduced glycolytic activity and partly restored basal mitochondrial respiration. FB did not change Hif1a mRNA levels. However, it Manuscript Click here to access/download;Manuscript;Manuscript.docx increased HIF-1 ubiquitination and promoted its proteasome-dependent degradation. HIF-1 overexpression partly reversed the effects of FB on glycolytic enzymes, CD86 expression, and proinflammatory cytokine production. Immunoprecipitation followed by mass spectrometry and UbiBrowser analysis identified USP7 as a candidate HIF27 1-associated deubiquitinase. Molecular docking and cellular thermal shift assays supported a possible interaction between FB and USP7. FB reduced the association between USP7 and HIF-1. USP7 knockdown produced effects similar to those of FB on HIF-1 ubiquitination and downstream glycolytic and inflammatory responses.Overall, FB alleviated neuropathic pain and reduced proinflammatory microglial responses. These effects may involve the promotion of HIF-1 degradation through modulation of the USP7-HIF-1 regulatory axis.

neuroscience↗

bioRxiv2026

Gap-free telomere-to-telomere haplotypes assembly of the hybrid grouper 'Yushuban' (Cromileptes altivelis female x Epinephelus fuscoguttatus male)

The hybrid grouper 'Yushuban' (Cromileptes altivelis [female] x Epinephelus fuscoguttatus [male]) has shown promising performance in aquaculture trials, yet no complete reference genome has been available for this hybrid. We generated two gapless, telomere-to-telomere (T2T) haplotype-resolved genome assemblies of a single individual by integrating short-read, PacBio HiFi, Oxford Nanopore ultralong-read and Hi-C data. The maternal (Yushu_Calti_1.0) and paternal (Yushu_Efusc_1.0) haplotypes are 1,077.33 Mb and 1,083.36 Mb in length, with N50 values of 45.46 Mb and 45.55 Mb, respectively. Across all platforms, over 99.4% of reads mapped to each assembly, and Merqury-based quality values reached 57.7413 and 59.2068 (PacBio). BUSCO recovered 99.78% and 99.75% of complete core genes. We predicted 27,248 and 27,566 protein-coding genes, of which 98.52% and 99.23% were functionally annotated, and annotated telomeric motifs and repetitive elements (46.12% and 47.18% of each genome). These assemblies fill a gap in grouper genomic resources and provide a foundation for genetic dissection, parental genome comparison and molecular breeding of this hybrid.

genomics↗

bioRxiv2026

Gene therapy with doxycycline-controlled expression of human Kv1.1 reduces neuronal excitability and increases sociability of Scn2a-deficient mice

Genetic loss-of-function (LoF) variants in SCN2A, a gene encoding the voltage-gated sodium channel Nav1.2, have been identified as one of the foremost monogenic causes of autism spectrum disorder (ASD). ASD encompasses a broad spectrum of behavioral phenotypes, with impaired sociability as a core characteristic. We have established Scn2a-deficient mice (Scn2agt/gt) to model Scn2a-related ASD and found that this model recapitulates social impairment, exhibiting severe social deficits. Scn2agt/gt mice exhibit neuronal hyperexcitability and a marked global reduction in potassium channel expression, which plays a crucial role in maintaining the resting membrane potential and repolarizing neurons after an action potential. Among these downregulated potassium channels, potassium voltage-gated channel subfamily A member 1 (Kv1.1) was one of the most affected. To explore whether Kv1.1 could be a potential therapeutic target in SCN2A-related ASD, we evaluated the in vivo efficacy of a genetic construct driven by the CaMKII promoter that allows for exogenous expression of human Kv1.1 (hKv1.1) in principal neurons. In Scn2agt/gt mice, we found that hKv1.1 expression normalizes neuronal hyperexcitability. Importantly, doxycycline-induced hKv1.1 expression enhances sociability in Scn2a-deficient mice without influencing social behavior in wild-type mice, and this effect was reversed upon doxycycline withdrawal. Overall, we demonstrate the successful use of an inducible AAV-mediated gene delivery system to supplement hKv1.1 expression to mitigate neuronal hyperexcitability and ameliorate social impairments in a mouse model of SCN2A-related ASD. These findings highlight the contribution of Kv1.1 to SCN2A-associated pathophysiology and its potential as a therapeutic target for severe social deficits.

neuroscience↗

bioRxiv2026

Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants

The gut microbiome develops from birth and is associated with cognition and mental health, but its relationship with early brain maturation remains unclear. We studied 223 typically developing infants aged 0-3 years using multimodal MRI and paired fecal shotgun metagenomics. Microbiome-wide association analysis linked microbial features to cortical morphology, white-matter microstructure, and functional networks. Regularized canonical correlation analysis identified structural-metabolic and functional-taxonomic covariance patterns. Sparse partial least-squares analysis recapitulated both full-sample CCA patterns and their defining structural and functional phenotypes, providing cross-method corroboration. Longitudinal canonical-score slopes did not significantly covary, whereas earlier neuroimaging CCA1 scores predicted microbiome CCA1 scores 1-6 months later in bidirectional autoregressive cross-lag models. These observational results identify coordinated developmental patterns and temporal ordering without establishing causality.

developmental biology↗

bioRxiv2026

Temporal TOC1-CLV3-WUS cascade controls organogenesis and rhythmic stem development

Coordinated organogenesis and rhythmic stem development determine shoot morphogenesis, which governs distinct plant architecture and crop yield. The shoot apical meristem (SAM) drives organ initiation and stem growth, with its activity sustained by the spatially defined CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback loop. However, how the temporal CLV3-WUS module modulates SAM activity remains elusive. Here, we demonstrate that both CLV3 and WUS are required for circadian stem elongation. The clock component TIMING OF CAB EXPRESSION1 (TOC1) directly activates and sustains the circadian expression of CLV3, and this regulatory process is controlled by the APETALA1-CIRCADIAN CLOCK-ASSOCIATED1 module. Notably, the rhythmic expression pattern of CLV3, rather than its transcript abundance, plays a more important role in regulating WUS expression and sustaining SAM activity, and CLV3 confers circadian rhythmicity to WUS protein accumulation. Transcriptome and ChIP seq analyses reveal that WUS modulates multiple developmental programs, including meristem homeostasis, phytohormone responses, and cell wall remodeling. Mechanistically, WUS directly activates PECTIN METHYLESTERASE5 expression to promote stem elongation. Collectively, our findings uncover a spatiotemporal regulatory cascade that fine-tunes SAM activity to coordinate rhythmic organogenesis and stem development, thereby establishing optimal phyllotactic patterning in plants.

plant biology↗

bioRxiv2026

An N-Terminally Acetylated Degron Specifically Recognized by the CTLHMKLN1-FAM72A E3 Ubiquitin Ligase for Regulatory Protein Degradation

N-terminal acetylation of cellular proteins has been implicated in their proteasomal degradation through the Ac/N-degron pathway. Despite representing a major branch of the N-degron system, only a limited number of degrons and their motifs have been identified and characterized in this pathway, and the mechanism underpinning the recognition of N-terminal acetylation has remained largely elusive. Here, by interrogating FAM72A-mediated degradation of UNG2, we pinpointed the N-terminally acetylated sequence of UNG2 as a bona fide Ac/N-degron specifically recognized by the CTLHMKLN1-FAM72A E3 ubiquitin ligase. Rather than relying solely on a single acetylated N-terminal residue, this degron features a consensus Nt-AcM1-[ILV]2-G3 motif that governs both E3 targeting and the intracellular stability of the neo-substrates uncovered through proteomic screenings. Cryo-EM structure of the UNG2-FAM72A-MKLN1 complex further elucidated the molecular details supporting the high specificity of degron recognition. Notably, this degron pathway is subject to multilayered regulation, highlighting the characteristic conditionality of degron system. Our findings thus define a distinct AcM-[ILV]-G/N-degron pathway and provide mechanistic insights into degron recognition dictated by both N-terminal acetylation and sequence motif context.

biochemistry↗

bioRxiv2026

A binuclear copper enzyme platform for enantioconvergent radical (pseudo)halogenation

Despite their intriguing native metalloenzymology, naturally occurring copper enzymes remain largely underexploited for new-to-nature biocatalytic reactions. Herein, we report the systematic investigation and reprogramming of natural copper enzymes to catalyze unnatural free radical (pseudo)halogenation reaction in a highly enantioselective fashion. Evaluating Cu enzymes in the decarboxylative azidation of redox-active esters revealed activity across multiple Cu enzyme families, with type III binuclear Cu enzymes, particularly the Bacillus megaterium tyrosinase (BmTyr), exhibiting superior activity and enantioselectivity across both stabilized and unstabilized alkyl radicals upon further engineering. The strong halide binding affinity of the binuclear Cu system also enabled challenging enantioconvergent bromination, chlorination and isothiocyanation reactions, which remained inaccessible to repurposed nonheme Fe enzymes. Further EPR and UV-visible spectroscopic analyses confirmed the coupled binuclear nature of wild-type and engineered bacterial tyrosinases and provided insights into the origin of their enhanced activity. Collectively, this study establishes binuclear copper enzymes as a powerful platform for new-to-nature stereoselective radical reactions, expanding the scope of metalloenzyme catalysis beyond mononuclear systems.

biochemistry↗

bioRxiv2026

Head-level lesion-symptom mapping of picture naming in vision-language models

Researchers in artificial intelligence increasingly intervene on language models to study how their functions are organized, silencing weights and attention components in ways reminiscent of the brain lesions long used to map language in post-stroke aphasia. Under this program of mechanistic interpretability, a common move is to ablate an attention head and read the resulting drop in a behavior as evidence that the head implements it. How much that move can establish about where a behavior is computed remains unclear, because a head whose removal disrupts a behavior is necessary for it but need not be the site where it is computed. We examined this question for the picture naming task, taking the loss of naming (anomia) that defines aphasia as the behavior of interest. Across six vision-language models, spanning three language backbones and a range of parameter scales, we ablated each attention head in turn during single-word picture naming and measured accuracy before and after. The degree of localization varied widely across models. In LLaVA-1.6-Vicuna-13B, a single early head (layer 0, head 20) was necessary: removing it alone reduced naming accuracy from 0.99 to 0.006. The same head was not sufficient, because retaining it while ablating the other 1{,}599 heads also produced 0\% accuracy. Two Mistral-backbone models (LLaVA-Mistral-7B and Idefics2-8B) had no critical head. An early-layer dependence was present in every model but varied in strength, whereas dependence on any single head ranged from dominant to absent. Within Qwen2.5-VL, a dominant head was present in the 7B model but not the 3B model, indicating that this concentration emerged with scale rather than being fixed across a model family, and it was not explained by attention type. These results show that ablating the head whose removal disrupts naming does not establish that the head computes the behavior, that the result generalizes across models, or that the behavior localizes to a head at all.

neuroscience↗

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗