Biology subjects

Shi, W.

Publications and source records attributed to Shi, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Targeting of the barley cell-surface receptor SRF3 by the Blumeria hordei effector AVRA13 overlaps with AVRA13 recognition by MLA and the induction of NLR-mediated cell death.

Pathogens secrete effector proteins to promote virulence. Despite their recognition by barley Mla resistance genes, the structurally-related Blumeria hordei (Bh) AVRA effectors are maintained in the Bh genome, suggesting virulence functions critical for fungal pathogenicity. Using proximity-dependent protein labelling in transgenic barley, we detected distinct host protein interactomes for five AVRAs despite their structural homology and convergence on MLAs. We report the specific interaction of the highly conserved AVRA13 effector with the barley cell-surface receptor SRF3. AVRA13 disrupts HvSRF3-HvBAK1 interaction and alters HvSRF3 plasma membrane levels. AVRa13-expression desensitizes iron-induced restriction of Bh growth, suggesting that AVRA13 facilitates fungal proliferation by manipulating SRF3-mediated iron homeostasis. Our results suggest that MLAs have diversified to specifically detect the residues that underly Bh effector neo-functionalization and intrinsic AVRA virulence functions. Together, these findings identify SRF3 as molecular link between pathogen virulence, immune recognition, and iron homeostasis.

plant biology↗

bioRxiv2025

Cortical microglia promote noradrenergic signaling to maintain wakefulness

Microglia are essential for maintaining brain homeostasis, including the sleep-wake cycle, but the underlying mechanisms remain unclear. Here, using in vivo two-photon imaging in both head-fixed and freely moving mice with simultaneous electroencephalogram-electromyogram (EEG-EMG) recording, we investigated microglial process dynamics and their interactions with locus coeruleus (LC) noradrenergic (NE) axons in the frontal cortex across sleep-wake states. During sleep or chemogenetic suppression of LC neurons, microglia enhanced their surveillance and increased interactions with NE axons. Correlative electron microscopy at nanometer resolution identified structural contacts between microglial process endings and NE boutons. Mechanistically, microglia-bouton interaction is primed by NE-{beta}2-adrenergic receptor ({beta}2AR) signaling, leading to enhanced Ca{superscript 2} activity in NE axons. These findings suggest that microglial interactions with NE axons promote cortical norepinephrine transmission and maintain stable wakefulness.

neuroscience↗

bioRxiv2025

Autolamellasomes: An Autophagy-Dependent Parallel Pathway for Bulk ER Degradation and Lysosome Biogenesis

Lysosomes containing multilamellar membrane whorls are a hallmark of cellular aging and storage disorders, yet the biogenesis of these structures has remained elusive for decades. Here, we identify a distinct form of endoplasmic reticulum (ER) remodeling, termed autolamellasomes, which mediates bulk ER degradation under chronic mTOR inhibition. Unlike canonical ER-phagy, autolamellasomes are concentric ER stacks that form via an autophagy-dependent but receptor-independent mechanism. Using Cryo-ET, CLEM, and a reconstituted cell-free system, we demonstrate that these structures arise from the cytosolic compaction of fragmented ER membranes, driven by the core autophagy machinery. We find that autolamellasomes accumulate in senescent cells and fibroblasts from patients with Hutchinson-Gilford progeria syndrome, linking sustained mTOR suppression to lysosomal membrane homeostasis. Our results resolve the origin of intralysosomal whorls and define a conserved pathway that couples nutrient sensing to membrane turnover and cellular aging.

cell biology↗

bioRxiv2025

Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site

Endemic human coronaviruses (HCoVs), such as HCoV-HKU1, account for [~]30% of common colds each year and can cause serious upper and lower respiratory infections, yet no licensed vaccines or therapeutic antibodies target HCoVs. Despite being endemic to the human population, little is known about the antigenic landscape of HCoV-HKU1. Here, we characterized key interactions between the HCoV-HKU1 spike (S) protein and monoclonal antibodies (mAbs) isolated from convalescent HCoV-HKU-1-positive peripheral blood mononuclear cells collected prior to the COVID-19 pandemic. We isolated 14 mAbs that bound distinct regions of S, including the receptor-binding domain (RBD), N-terminal domain, and S2 subunit. Structural and functional studies revealed three groups of RBD-specific mAbs targeting diverse footprints within and around the TMPRSS2 receptor-binding site: (1) H501-022, which recognizes the TMPRSS2-binding site and thereby blocks receptor engagement; (2) H501-008, which binds a distinct epitope outside the TMPRSS2-binding site that is shared with HCoV-OC43; and (3) H501-018, which recognizes both "up" and "down" RBD conformations at a distinct, non-overlapping epitope outside the TMPRSS2-binding site. H501-008 weakly neutralized live HCoV-OC43 in vitro and protected mice against lethal HCoV-OC43 challenge. Notably, the three RBD-specific mAbs potently neutralized HCoV-HKU1 pseudovirus in TMPRSS2-overexpressing cell lines, but exhibited limited neutralizing activity against authentic HCoV-HKU1 infection in primary human airway epithelial cells. Together, these findings structurally define the antigenic landscape within and around the HKU1 receptor-binding site and demonstrate that receptor-binding site recognition alone is insufficient to predict physiologically relevant antibody-mediated neutralization.

microbiology↗

bioRxiv2025

Canonical decision computations underlie behavioral and neural signatures of cooperation in primates

Successful cooperation requires dynamic integration of social cues. However, the neural mechanisms supporting this complex process remain unknown. Here, we reveal that the primate dorsomedial prefrontal cortex (dmPFC) implements a gaze-dependent social evidence accumulation process to guide cooperative decisions in freely moving marmoset dyads. A drift-diffusion process in which the partners action variability is accumulated by social gaze best explains the cooperative actions of the actor. Single-neuron recordings in dmPFC revealed a direct neural correlate: the slope of predictive ramping activity mapped directly onto the rate of evidence accumulation, while baseline firing, modulated by prior outcomes, mapped onto the initial bias. At the population level, the geometry of dmPFC neural trajectories reflected the strength of social evidence and was linked to cooperative success. Together, these findings establish a multi-level neural mechanism for transforming active sensing into a decision variable, linking a canonical computation to cooperative behavior in a naturalistic setting.

neuroscience↗

bioRxiv2025

Ordering from the edge: Chiral multicellular pattern formation directed by actin self-organisation in cells

The mechanisms underlying both the establishment of mirror symmetry and deviations from it in development of bilateral multicellular organisms remain insufficiently understood. Actin cytoskeletons of individual cells exhibit intrinsic chirality, and a strong correlation exists between single-cell actin fibres chiral organisation and the collective alignment of cells confined to rectangular adhesive islands (2D-microtissues). Here, we demonstrate how multicellular chiral patterns can be inferred from the chiral behaviour of actin fibres in individual cells. By analysing chiral actin systems in cells with elliptical and semi-circular shapes, representing inner and boundary positions within 2D-microtissues, we defined the rules of chiral motile behaviour and formulated two models of cell alignment: (i) chiral rotation of inner cells and (ii) chiral tilting of boundary cells relative to island edges. In both models, neighbouring cells are also mutually aligned. Systematic variation of island area and aspect ratio, combined with dynamic observations, revealed the primary role of boundary cells. Chiral order first emerged at tissue boundaries and then propagated inward. This outside-in mechanism also explains why mirror-symmetric cell groups are difficult to achieve with uniformly chiral cells, but can be obtained either by reversing chirality in one subgroup or by enlarging the microtissue to minimise boundary influence.

biophysics↗

bioRxiv2025

An SR45-dependent exonic splicing enhancer is essential for regulating alternative splicing in Arabidopsis

Alternative splicing (AS) is a critical gene regulatory mechanism that underpins developmental plasticity and environmental adaptation in eukaryotes. Although numerous cis-elements and trans-factors governing AS have been characterized in animals, their functional roles in plants remain largely unexplored. We previously identified the Arabidopsis sot5 mutant, which exhibits leaf virescence due to a mutation in the conserved 5 splice site (5ss) of intron 7. Here, through characterization of a suppressor of sot5 (E61), we found that E61 harbors a G to A mutation in exon 8 of the SOT5 gene. Interestingly, this mutation creates a synonymous codon but disrupts the exonic splicing enhancer (ESE) motif (AAGAAGA), thereby reducing the splicing efficiency of the adjacent intron 7. Retention of this intron produces a functional protein that rescues the sot5 virescent phenotype. We confirmed the causal role of this ESE by using a cytidine base editor (CBE) to convert the ESE sequence to AAGAAAA or AAAAAAA in sot5. The edited plants phenocopied the suppressor E61. Genetic analyses revealed that mutations of SR45 encoding an RNA-binding protein but not its paralog SR45a similarly rescues the sot5 phenotype by impairing intron 7 splicing. Furthermore, we demonstrated that SR45 directly binds to the ESE motif in vitro, and that mutating the proximal ESEs in intron 2 of another SR45 target, GPDHC1 (Glycerol-3-Phosphate Dehydrogenase C1), recapitulates the splicing defect observed in the sr45 mutant. These findings establish that SR45 specifically recognizes AAG-repeat ESEs to enhance the splicing of adjacent weak introns, revealing a potent strategy for fine-tuning gene expression through targeted editing of splicing regulatory elements for crop improvement.

molecular biology↗

bioRxiv2025

Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Formalin-fixed paraffin-embedded (FFPE) tissue-compatible spatial transcriptomics (ST) is transforming biology and histopathology, but achieving high sensitivity, genome-wide coverage, single-cell resolution and researcher-accessibility remains challenging. Here, we present a dendrimeric DNA coordinate-barcoding design for FFPE-adapted spatial RNA sequencing (Decoder-FFPE-seq), by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding. Decoder-FFPE-seq provides single-cell resolution with a 2.54-4.25-fold sensitivity increase in mouse brain transcriptomic profiling over similar assays with an available protocol, successfully mapping rare genes and sparse cell types. It robustly resolves tumor microenvironments (TMEs) in clinical archives preserved 6-20 years. With expanded probe libraries, Decoder-FFPE-seq captures long non-coding and viral RNAs, revealing spatial co-expression networks with mRNAs in oral squamous cell carcinomas (OSCCs). In an OSCC immunotherapy cohort, it delineates TME heterogeneity across pathology response groups and tracks spatial cellular dynamics pre- and post-immuno-chemotherapy. Decoder-FFPE-seq establishes a robust, high-resolution framework for sensitive ST profiling in fundamental and translational studies of archival tissues.

genomics↗

bioRxiv2025

Bidirectional translocation of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis

How epithelia perform a spatiotemporal heterogeneous force generating program to drive a sequential tissue morphogenesis remains unclear, particularly the underlying precise mechanical mechanisms. This study investigated dynamic actomyosin reorganization between apical and lateral membrane cortex regions during two sequentially invaginated stages during ascidian atrial siphon tube morphogenesis. At the initial invagination stage, the originally lateral-located actomyosin redistributed to the apical domains, while those actomyosin redistributed back to lateral domains at the accelerated invagination stage. Using genetic mutants to modulate myosin activities, the initial invagination was strengthened or abolished, indicating invagination is apical constriction dependent. Optogenetic inhibition of myosin activities in lateral domains after initial invagination stage blocked the further processes, suggesting lateral constriction of actomyosin is required for the accelerated invagination. Vertex model simulations uncovered a coupled mechanism underlying epithelial invagination driven by apicobasal tension imbalance and lateral contraction. We thus propose an actomyosin redistribution mechanical model: lateral actomyosin first redistributes apically to drive apical constriction and shape the initial invagination, then apical actomyosin redistributes laterally to promote lateral contractility and accelerate invagination. Our findings reveal a bidirectional reorganization of actomyosin network as a central mechanism driving epithelial invagination, providing insights on epithelial invagination and the organ morphogenesis during development.

developmental biology↗

bioRxiv2025

Cis-delivering releasable IL-15 superagonist enhances antitumor immunity in cold tumors by invigorating preexisting CD25+CD8+ T cells

Antibody-mediated cis-delivery and trans-delivery both direct cytokines to tumors and have been extensively investigated in clinical trials. However, a comparative analysis of their differential effects on cytokine activity is still lacking. In this study, we initially verify that cis-delivery of cytokine demonstrates a markedly stronger antitumor effect than trans-delivery, but it also exhibits certain drawbacks, including severe toxicity, insufficient activation of CD25+CD8+ T cells, and enhanced stimulation of intratumoral regulatory T cells (Tregs). To further address these issues, we developed a conditionally releasable and cis-delivering IL-15 immunocytokine (termed PMIS), which can selectively release a free IL-15 superagonist within tumors rather than immobilizing IL-15 to PD-1+ Tregs, thereby potently stimulating CD25+CD8+ T cells. Mice treated with PMIS showed significantly reduced systemic toxicities while achieving notably stronger antitumor effects. Administered either alone or in combination with other therapies, PMIS exhibits great potential for inhibiting orthotopic cold tumor and its metastases. Mechanistically, the significant activation of the pre-existing intratumoral CD25+CD8+ T cells and the improved CD25+CD8/Treg ratio contribute to the enhanced antitumor response of PMIS. These findings underscore the indispensable role of CD25+CD8+ T cells in cis-delivering IL-15 and provide a promising strategy for overcoming resistance to therapies and effectively controlling advanced cold tumors.

immunology↗

bioRxiv2025

HuiduRep: A Robust Self-Supervised Framework for Learning Neural Representations from Extracellular Recordings

Extracellular recordings are transient voltage fluctuations in the vicinity of neurons, serving as a fundamental modality in neuroscience for decoding brain activity at single-neuron resolution. Spike sorting, the process of attributing each detected spike to its corresponding neuron, is a pivotal step in brain sensing pipelines. However, it remains challenging under low signal-to-noise ratio (SNR), electrode drift, and cross-session variability. In this paper, we propose HuiduRep, a robust self-supervised representation learning framework that extracts discriminative and generalizable features from extra-cellular recordings. By integrating contrastive learning with a denoising autoencoder, HuiduRep learns latent representations robust to noise and drift. With HuiduRep, we develop a spike sorting pipeline that clusters spike representations without ground truth labels. Experiments on hybrid and real-world datasets demonstrate that HuiduRep achieves strong robustness. Furthermore, the pipeline outperforms state-of-the-art tools such as KiloSort4 and MountainSort5. These findings demonstrate the potential of self-supervised spike representation learning as a foundational tool for robust and generalizable processing of extracellular recordings.

bioinformatics↗

bioRxiv2025

Complexes between Netrin G Ligands and Chiral Nanoparticles Promote Axons Regeneration under Near-Infrared Illumination

Chiral nanoparticles combine functionalities of inorganic materials and large biomacromolecules enabling stimulation of neurons. However, multiple challenges remain in their use for central nervous system including identifying suitable cell signaling pathways and traversing the blood-brain barrier. In this study, we show that glutathione-coated Ni(OH)2 nanoparticles form nanoscale complexes with netrin-G1 ligands (NGL-1), critical for neuronal regeneration. NGL-1 features a semispherical pocket with a 2.5 nm radius of curvature, fitting well with nanoparticles sized 3 {+/-} 1.2 nm. D-NPs with D-glutathione surface ligands activate D-glutathione receptors on epithelial cells, facilitating their transport into the brain. When illuminated with 980 nm light, the nanoparticle-protein complex stimulates axon regeneration through localized IGF-1 production. This approach successfully regenerated (a) hippocampal neurons in Alzheimers disease mice and (b) dorsal root ganglion neurons in spinal cord-injured mice. The nanoparticles were thoroughly tested for safety and excreted intact. The local, rather than systemic, IGF-1 upregulation minimizes its side effects.

neuroscience↗

bioRxiv2025

Human Neural Synergy when combining Stevia with a Flavor Modifer and the Neural effects of Sucrose vs Stevia

There is a drive to improve the acceptability of sweeteners like stevia by reducing their off-tastes. The main aim was to examine the synergistic neural effects of combining stevia with a flavor modifier and secondly to examine stevia vs. sucrose due to limited human neuroimaging data and concerns that sweeteners may be more addictive than sugar. In a within-subjects fMRI study, 34 healthy adults (Mean age = 25) tasted four conditions: stevia, stevia plus a flavor modifier, the modifier alone, and sucrose. We analyzed whole-brain responses and focused on regions of interest (ROIs) including the insula, postcentral gyrus, and hypothalamus (identified via meta-analysis of sweet taste processing), as well as the nucleus accumbens (NAcc) and amygdala due to their roles in reward and aversion. Stevia combined with the modifier evoked super-additive responses in the postcentral gyrus, parietal cortex, and occipital gyrus (p < 0.05, FWE-corrected). Compared to stevia alone, the stevia-modifier combination elicited reduced hypothalamic activity (p = 0.008) and the hypothalamus tracked pleasantness and mouth fullness only in this condition. The NAcc tracked mouth fullness more for the modified stevia than for stevia alone, and the amygdala tracked bitterness only in the plain stevia condition. Sucrose elicited higher postcentral gyrus activation than stevia (p = 0.01). We provide first evidence that combining stevia with a flavour modifier reveals synergistic neural activity associated with taste sensation, intensity and multisensory integration. Adding a modifier to stevia could increase unconscious desirability for stevia by masking its bitterness and increasing its mouth fullness.

neuroscience↗

bioRxiv2025

Kinesin drive meiotic chromosome dynamics via interaction with the KASH5-LINC complex

Telomere-led rapid prophase chromosome movements (RPMs) during meiotic prophase are critical for homologous chromosome pairing and proper meiotic progression. These movements are generated by the cytoskeleton and are transmitted to the telomeres via the LINC complex, yet the cytoplasmic components that generate these forces remain poorly defined. Among candidates of microtubule-associated motor proteins in mouse primary spermatocytes, we confirmed KIF5B as a specific interactor of the KASH5-LINC complex. Total internal reflection fluorescence microscopy and microtubule sedimentation assays performed with purified recombinant proteins suggest a direct interaction between KASH5 and KIF5B on microtubules, enhanced by MAP7, a known KIF5B-recruiting and activating cofactor. Mapping the KIF5B-binding surface of KASH5 revealed that KASH5 N-terminal EF-hand domains mediate the interaction. Further, in vivo KIF5B-KASH5 interaction and KIF5B role in RPMs are evidenced as (1) KIF5B is recruited by KASH5-SUN1 to the nuclear envelope in two different cultured somatic cell models, (2) KIF5B is telomere-associated and colocalizes with KASH5, and microtubules associated with the nuclear envelope in mouse spermatocytes, and (3) chemical inhibition of KIF5B reduces telomere-led chromosome motions. Altogether, our findings identify the KIF5B kinesin as a previously unrecognized component of the force-generating machinery that drives chromosome movement during meiotic prophase I, acting through KASH5 as a specific nuclear membrane adaptor.

cell biology↗

bioRxiv2025

Aptamer-Enabled Discovery and Clinical Analysis of Exosomal Surface Biomarkers in Hepatocellular Carcinoma

Exosomal membrane proteins hold promise as cancer biomarkers but face detection challenges due to low abundance and conformational sensitivity. We developed AptEx-ID, a microbead-displayed aptamer platform enabling high- throughput screening of hepatocellular carcinoma (HCC)-specific exosomal surface proteins. Aptamers, selected via competitive binding to tumor-derived versus healthy exosomes, demonstrated high affinity and specificity. Clinical validation using 50 HCC and 30 control plasma samples identified a 7-aptamer panel via machine learning, achieving 93.75% accuracy and 0.95 ROC-AUC. These aptamers further revealed HCC-associated biomarkers (e.g., IMPDH1, ASCC3, GTSE1), validated by siRNA knockdown and biophysical assays. Post-treatment monitoring showed aptamer signal reduction in responsive patients, highlighting their prognostic utility. This platform integrates biomarker discovery, diagnostics, and therapeutic monitoring, offering a robust approach for HCC management through exosomal surface proteome profiling.

molecular biology↗

bioRxiv2025

Data Heterogeneity Limits the Scaling Effect of Pretraining Neural Data Transformers

A key challenge in analyzing neuroscience datasets is the profound variability they exhibit across sessions, animals, and data modalities-i.e., heterogeneity. Several recent studies have demonstrated performance gains from pretraining neural foundation models on multi-session datasets, seemingly overcoming this challenge. However, these studies typically lack finegrained data scaling analyses. It remains unclear how different sources of heterogeneity influence model performance as the amount of pretraining data increases, and whether all sessions contribute equally to downstream performance gains. In this work, we systematically investigate how data heterogeneity impacts the scaling behavior of neural data transformers (NDTs) in neural activity prediction. We found that explicit sources of heterogeneity, such as brain region mismatches among sessions, reduced scaling benefits of neuron-level and region-level activity prediction performances. For tasks that do exhibit consistent scaling, we identified implicit data heterogeneity arising from cross-session variability. Through our proposed session-selection procedure, models pretrained on as few as five selected sessions outperformed those pretrained on the entire dataset of 84 sessions. Our findings challenge the direct applicability of traditional scaling laws to neural data and suggest that prior reports of multi-session scaling benefits may need to be re-examined in the light of data heterogeneity. This work both highlights the importance of incremental data scaling analyses and suggests new avenues toward optimally selecting pretraining data when developing foundation models on large-scale neuroscience datasets.

neuroscience↗

bioRxiv2025

Changes in slow oscillations and sleep spindles by auditory stimulation positively correlate with memory consolidation in children with epilepsy and controls

BackgroundSleep-dependent memory consolidation is supported by sleep spindles during stages 2 and 3 non-rapid eye movement sleep. Sleep spindles and sleep-dependent memory consolidation are both decreased in Rolandic epilepsy (RE). Non-invasive auditory stimulation evokes SOs and SO-spindle complexes in healthy adults but the impact on memory consolidation has been inconsistent. ObjectiveWe investigated the effects of auditory stimulation during sleep on SOs, SO-spindle complexes, and sleep-dependent memory consolidation in children with RE and controls. MethodsA prospective cross-over study was conducted in children with RE and control. Children completed two nap visits with auditory or sham stimulation. SOs and SO-spindle complexes rates were measured offline using validated detectors. Sleep-dependent memory consolidation was assessed using the motor sequence typing task. ResultsAuditory stimulation evoked SOs and SO-spindle complexes broadly with maximal effect over frontal electrodes. Compared to sham, stimulation delivered during background activity evoked SOs (29.8% increase, p<0.001) and SO-spindle complexes (16.8% increase, p<0.001) and stimulations delivered near the peak of an ongoing SO upstate maximally evoked SOs (51.3% increase, p<0.001) and SO-spindle complexes (32.3% increase, p<0.001). Changes in frontal SO (1.9% improvement per increase in SO/min; p<0.001) and SO-spindle complexes (9.5% improvement per increase in SO-spindle/min) event rates due to auditory stimulation positively predicted changes in sleep-dependent memory consolidation. ConclusionAuditory stimulation reliably modulates sleep oscillations when delivered on background activity and during the upstate of SOs. As increased event rates improve memory consolidation, stimulation paradigms to increase SO and SO-spindle complex rates are required to enhance memory.

neuroscience↗

bioRxiv2025

A hierarchical cascade of sleep rhythms drive memory consolidation in humans and are disrupted in epilepsy.

The cross-regional interplay of slow oscillations, sleep spindles, and ripples during sleep is believed to support systems memory consolidation but is understudied in humans. Using a validated behavioral task and intracranial neural recordings from orbitofrontal cortex, thalamus, and hippocampus in 19 epilepsy patients, we examined the cross-regional interplay of sleep-oscillations and their role in memory consolidation. Orbitofrontal slow oscillations robustly modulate sleep rhythms both within and across regions. Most combinations of oscillation rates predict overnight memory consolidation, but hippocampal ripple rate and coupled hippocampal-orbitofrontal ripples were the strongest positive predictors of memory consolidation. In contrast, epileptic spikes coupled to sleep oscillations strongly predicted reduced memory consolidation, with the strongest negative effect observed when epileptic spikes were coupled to slow oscillations. These findings provide direct evidence of the hierarchical cascade of sleep oscillations in human memory processing and reveal how epileptic spikes disrupt this process in patients with epilepsy.

neuroscience↗