Biology subjects

Xue, K.

Publications and source records attributed to Xue, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Efficient recovery of transgene-free edited tobacco using the transgene self-elimination system via de novo regeneration

Elimination of integrated editing constructs remains a major challenge for generating transgene-free progeny in plant genome editing based on Agrobacterium-mediated regeneration. Here, we adapted the Transgene Killer CRISPR (TKC) concept to tobacco and established the transgene self-elimination system, in which CRISPR/Cas9 is coupled with developmentally regulated BARNASE cassettes. Three pU3TR-derived vectors carrying DLL-, OsRP3- or PHAS-driven Barnase regenerated normally after leaf-disc transformation. The DLL construct pEB138 showed the highest T editing frequency, with 56 of 69 independent T plants (81.16%) carrying mutations at one or both NtDFR target loci. Under a stringent lineage-level screen in which up to 48 T progeny were tested per T line, 36 of 43 pEB138 lineages (83.72%) yielded uniformly marker-negative progeny for the three assayed T-DNA markers, compared with 0 of 7 lineages transformed with the parental pU3TR vector. The platform also supported recovery of dfr mutants with altered flower pigmentation and NtA622-edited lines with reduced nicotine accumulation. Moreover, introduction of DLL-iBarnase into the independent pDC45 editing backbone did not impair shoot regeneration, and representative NtBBL progeny showed markedly reduced nicotine content together with loss of the selectable cassette. These results demonstrate that BARNASE-assisted transgene elimination can be integrated with Agrobacterium-mediated de novo regeneration in a dicot, enabling one-step recovery of transgene-free edited tobacco progeny.

molecular biology↗

bioRxiv2026

Bilayer-bound structure of SARS-CoV-2 Envelope protein in complex with a host PDZ domain

Small multifunctional viral membrane proteins called viroporins are attractive drug targets but are difficult to structurally characterize in a lipid-bilayer environment. We have successfully reconstituted the full-length Envelope (E) protein from SARS-CoV-2 in a lipid-bilayer, co-assembled with a native host factor that binds to E, the PDZ domain 2 of ZO1. We have leveraged the enhancement afforded by dynamic nuclear polarization NMR to determine that the ensemble-averaged oligomer state of E is a pentamer. Complexing the protein with a host PDZ domain did not impact the oligomer state, but resulted in structuring of the last four residues of E, and immobilization of the PDZ domain near the lipid surface. Combined with secondary structure information derived from the chemical shifts, these data were used to model an E protein pentamer together with the PDZ protein dimer. Inclusion of a relevant host factor, as well as a complex lipid bilayer that mimics conditions in the ER-Golgi intermediate compartment, approaches native conditions, and addresses the ongoing controversy regarding the functional oligomer state in an infected cell.

biophysics↗

bioRxiv2026

Emergence of tunneling nanotube-like intervesicular connections

Tunneling nanotubes (TNTs) are actin-supported membrane bridges that mediate long-range intercellular communication and direct transfer of signaling molecules, organelles, and pathogenic cargo, yet the physicochemical mechanisms underlying their formation and organization remain poorly understood. Here we show that TNT-like intervesicular connections emerge from minimal physicochemical interactions between actin filaments and lipid membranes. Upon Mg2+ exposure, actin-encapsulating vesicles spontaneously generated actin bundle-embedded lipid nanotubes (AT-LNTs) that formed stable intervesicular networks. Mg2+ simultaneously induced actin polymerization, filament bundling, and electrostatic recruitment of F-actin to phosphatidylcholine membranes, enabling membrane tubulation without actin-binding proteins. Systematic perturbation of membrane phase, membrane tension, Mg2+ concentration, ionic strength, and actin concentration revealed that AT-LNT formation occurs only within a narrow physicochemical regime where membrane deformation and actin-membrane coupling are simultaneously permissive. The resulting AT-LNTs reproduced key structural and dynamic features of cellular TNTs, including bundled organization, helical unwinding, lumenal diffusion, and spontaneous bridging between synthetic vesicles and living cells. These findings establish a minimal biophysical framework for understanding the emergence of intercellular membrane connections in living systems and provide a foundation for engineering communication between synthetic and living cell.

synthetic biology↗

bioRxiv2026

Learning Shapes the Energy Cost of Neural Tasks

The stark difference in energy use between AI systems and biological brains highlights both the remarkable efficiency of the brain and our limited understanding of the energetics underlying neural computation. Although efficiency is widely cited as a principle of neural design, direct measurement of the energy cost of specific neural tasks within their corresponding circuits has remained limited. Here, by simultaneously measuring intracellular glucose and calcium dynamics in the same behaving mice in vivo, we use neuronal glucose consumption to define circuit-level energy costs associated with learning-based behavioral tasks. We found that the post-learning fuel cost per task was significantly lower than pre-learning levels across multiple hippocampus- and cortex-dependent learning models, with or without changes in bulk calcium dynamics. This change in fuel cost was not mediated by extracellular glucose transport but instead reflected a reduction in intracellular glucose consumption and depended on canonical plasticity mechanisms, including NMDAR signaling and protein synthesis. Together, these findings suggest that attenuation of task-specific energy cost may represent a general bioenergetic trajectory of learning and plasticity. This "energy minimization" hypothesis provides insight into how the biological brain achieves efficiency and offers an orthogonal, complementary perspective to neural activity-centered frameworks.

neuroscience↗

bioRxiv2026

Fibroblast-encoded inflammatory memory orchestrates recurrent skin inflammation via NNMT-dependent metabolic remodeling

Chronic skin inflammation frequently recurs at the same anatomical sites after therapy withdrawal, implying stromal cells may encode local inflammatory memory. Here, we identified nicotinamide N-methyltransferase (NNMT) as a central metabolic-epigenetic regulator of fibroblast inflammatory memory enabling psoriasis relapse. Single-cell and spatial transcriptomics revealed that dermal fibroblasts acquire a persistent senescence-associated secretory phenotype (SASP) during inflammation, maintaining pro-inflammatory niche in resolved skin that supports CD 8+CD 103+ tissue-resident memory T cell (Trm) differentiation. Multi-omics profiling demonstrated that NNMT depletes S-adenosylmethionine (SAM), reduces H 3K 27me3 deposition, and permits sustained AP-1 occupancy at SASP gene promoters. Fibroblast-specific NNMT ablation or pharmacologic inhibition suppressed SASP activity, limited Trm accumulation, and prevented both initiation and relapse of skin inflammation in mice. These findings establish NNMT as a stromal regulator linking fibroblast metabolism to durable epigenetic memory and propose its targeting to erase inflammatory memory and achieve long-term remission in psoriasis and related immune-mediated diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/721223v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@34b2f4org.highwire.dtl.DTLVardef@1d0bb89org.highwire.dtl.DTLVardef@c8277borg.highwire.dtl.DTLVardef@9825ac_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic Abstract:C_FLOATNO Proposed mechanism through which NNMT-driven fibroblast SASP facilitates the initiation and recurrence of psoriasis C_FIG

immunology↗

bioRxiv2025

Single-cell and spatial transcriptomic analyses of gene therapy-associatedretinal inflammation in non-human primates

Adeno-associated viral (AAV) vectors are rapidly advancing as gene therapies for inherited and common retinal disorders, but gene therapy-associated uveitis (GTAU) limits their broader application. To investigate the primate ocular immune response, we administered subretinal AAV gene therapy to two non-human primates (NHPs): NHP1 received AAV2-CAG-hRPE65 (voretigene neparvovec) bilaterally at clinical dose; NHP2 received AAV8-GRK1-hRPGRco alongside an analogous mScarlet reporter vector in separate blebs. Longitudinal assessments over three months included multimodal imaging, electroretinography and cytokine profiling, followed by immunohistological, single-cell and spatial transcriptomic analyses of retinal punches. Both therapies were well-tolerated, with preserved retinal structure and function. Single-cell RNA-sequencing revealed that the AAV8 vector transduced 80% of cones/rods in treated areas, while AAV2 targeted 30% of retinal pigment epithelium (RPE)/rods. Transgene expression did not correlate with apoptotic markers. Persistent immune infiltration (dominated by myeloid and T cells) suggested a type 1 cell-mediated response. Adjunctive intravitreal anti-TNF (adalimumab) did not appear to mitigate this anti-viral response. Spatial analysis highlighted microglia migration to the subretinal space, consistent with upregulated cytokines (MCP-1/CCL2, IP-10/CXCL10, IL-8/CXCL8, IL-6), which implicate monocytic phagocytes in driving local inflammation. These findings elucidate the mechanism of GTAU and identify potential therapeutic targets to prevent immune-mediated complications in retinal gene therapy.

immunology↗

bioRxiv2025

The clinical drug candidate anle138b binds predominantly to the central cavity in lipidic Aβ fibrils and modulates fibril formation.

Alzheimers disease is a specific neurodegenerative disorder, distinct from normal aging, with a growing unmet medical need. It is characterized by the accumulation of amyloid plaques in the brain, primarily consisting of amyloid beta (A{beta}) fibrils. Therapeutic antibodies can slow down the disease, but are associated with potential severe side effects, motivating the development of small molecules to halt disease progression. This study investigates the interaction between the clinical drug candidate small molecule anle138b and lipidic A{beta}40 fibrils of type 1 (L1). L1 fibrils were previously shown to closely resemble fibrils from Alzheimers patients18. Using high-resolution structural biology techniques, including cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy enhanced by dynamic nuclear polarization (DNP), and molecular dynamics (MD) simulations, we find that anle138b selectively binds to a cavity within the fibril. This structural insight provides a deeper understanding of a potential drug-binding mechanism at the atomic level and may inform the development of novel therapies and diagnostic approaches. In addition, anle138b reduces fibril formation in the presence of lipids by approximately 75%. This may suggest a mechanistic connection to its previously reported activity in animal models of Alzheimers disease15.

biochemistry↗

bioRxiv2025

The coordinated regulatory roles of two LysR-Type Transcriptional Regulators balance chorismate and protocatechuate partition in Listeria organisms

Listeria monocytogenes is an economically deleterious foodborne pathogens that continually challenges the global food supply chain. Listeria species in general, synthesize protocatechuate from saprophytically-derived quinate and shikimate utilizing a novel class of bacterial dehydroshikimate dehydratase. Paradoxically, Listeria species are unable to metabolically utilize protocatechuate, as such, it was proposed that this compound is used as a currency to Listeria interactions with other microorganisms to improve their environmental proliferation. Therefore, an understanding of the regulatory mechanism for the metabolic pathway for protocatechuate biosynthesis is of great importance. Two LysR Type Transcriptional Regulators (LTTR), annotated QuiR and in this study QuiR2, are found upstream of genomic operons, qui1 and qui2, which transcribe genes for protocatechuate synthesis. QuiR, has been shown to activate the expression of genes from both operons with shikimate as a coinducer. However, the role of QuiR2, Lmo2233, is not clear. In this study, we conducted structural, biochemical and bioinformatics analyses of QuiR2 and demonstrated that it functions as a negative regulator of protocatechuate biosynthesis in Listeria species. Moreover, we determined that protocatechuate functions in modulating QuiR2 repressive properties through our mobility shift assay and LacZ reporter activity studies. Furthermore, phylogenetic analyses reveal that QuiR2 clusters closely but independently from QuiR thus supporting their distinct regulatory roles. We propose that QuiR2 prevents metabolic commitment of dehydroshikimate to protocatechuate when elevated and in limiting shikimate condition. In this study we revisited the biological role of the shikimate pathway in microbes and demonstrated that in addition to it producing chorismite for aromatic compound metabolism it is also important in allowing organisms to shuttle shikimate and quinate to produce protocatechuate which can be used as an energy source and more importantly in Listeria it is used to facilitate microbial interactions.

molecular biology↗

bioRxiv2025

Lower spatial turnover of rare fungal taxa dominantly shaped by stochastic processes in grassland soils

The spatial pattern and community assembly of soil microbial taxa have notable meanings for biodiversity shaping and maintaining mechanisms. Rare fungal taxa may exhibit distinct patterns and assembly mechanisms compared to abundant taxa, but such information is limited, especially at large scales. Here, we investigated distance-decay patterns and underlying assembly mechanisms for abundant and rare fungal taxa in 129 soil samples collected across 4,000 km in Chinese Northern grasslands, based on high-throughput sequencing data. A total of 208 abundant OTUs (relative abundance > 0.1%, 2.73% of entire OTUs) and 5,779 rare OTUs (relative abundance < 0.01%, 75.85% of entire OTUs) were identified. Both abundant and rare fungal taxa showed significant distance-decay relationships (P < 0.001), but the turnover rate for rare taxa (0.0024 per 100 km) was nearly half that of abundant taxa (0.0054 per 100 km) based on the binary Bray-Curtis distance. The lower turnover of rare fungal taxa was likely due to their community assembly mechanism dominated by stochastic processes, which were less influenced by environmental gradients. In contrast, abundant taxa assembly was dominated by deterministic factors like soil variables and plant traits, which varied significantly along the geographic distance. Consistently, rare fungal taxa were also less sensitive to environmental changes, with a lower turnover rate by environmental distance (0.0027 vs. 0.0099) than abundant taxa. In summary, our findings revealed that rare fungal taxa, shaped mainly by stochastic processes, had lower spatial turnover compared to abundant taxa, dominated by deterministic processes, enhancing our understanding of rare microbial biogeography.

ecology↗

bioRxiv2024

Extracellular electron transfer drives efficient H2-independent methylotrophic methanogenesis by Methanomassiliicoccus, a seventh order methanogen

Methylotrophic methanogenesis is achieved via methyl group dismutation or H2 reduction. This study reports extracellular electron droving efficient methylotrophic methanogenesis. The 7th order methanogen Methanomassiliicoccus luminyensis exclusively implements H2-dependent methylotrophic methanogenesis, but strain CZDD1 isolated from paddy soil possessed a higher methane-producing rate in coculture with Clostridium malenominatum CZB5 or the electrogenic Geobacter metallireducens. Chronoamperometry detected current production from CZB5, and current consumption accompanied CH4 production in a methanol-containing electrochemical culture of CZDD1. This demonstrated that M. luminyensis was capable of both direct species electron transfer (DIET) and extracellular electron transfer (EET) in methylotrophic methanogenesis. EET and DIET also enabled CZDD1 to produce methane from dimethyl arsenate. Differential transcriptomic analysis on H2-versus EET- and DIET-cocultures suggested that a membrane-bound Fpo-like complex and archaella of M. luminyensis CZDD1 could accept extracellular electrons. Given the ubiquitous environmental distribution of Methanomassiliicoccus strains, EET driven methylotrophic methanogenesis may contribute significantly to methane emission.

microbiology↗

bioRxiv2024

Feather degradation in Stenotrophomonas maltophilia relies on conversion and internalization of keratin monomer

Feather keratin is the most abundant nitrogen source waste in nature. This insoluble material cannot be directly utilized as nutrition by most organisms, especially animals and plants. While feathers are naturally decomposed by some microorganisms through keratinase-based degradation which remains mechanistically not fully understood. In this study, we find that when feathers serve as the only nutrient source for Stenotrophomonas maltophilia culture, keratin monomer of about 10 kDa is present in the medium as a predominant hydrolyzed product. We further show that keratin monomers bind to cells and in turn enter cells via an undetermined pathway. The cell entry of keratin monomer elicits keratinase activity to promote the forward reaction in keratin hydrolysis. This study highlights the importance of keratin monomer production as the first step in feather biodegradation, in which the insoluble feather is converted into soluble intermediate to facilitate its internalization and complete hydrolysis. ImportanceA large amount of feathers have been produced in poultry breeding, which could cause environmental pollution if not processed in time. On the other hand, amino acids degraded from feathers can be used in many fields, such as feed, fertilizer, daily chemicals and other fields. Biodegradable feathers have the advantages of low energy consumption, mild conditions and no destruction of the amino acids obtained from degradation. We previously isolated and identified a highly efficient feather-degrading bacterium, Stenotrophomonas maltophilia DHHJ, which can grow well on the medium with feathers as the only nutrient and completely degrade feathers. We know, feather particles are much larger than bacterial cells. In what form and how they are absorbed into cells by bacteria are interesting and critical questions for feather degradation. In our research, feathers had been first degraded extracellularly by basically expressed keratinase into keratin monomers. The keratin monomers bound to cells and enter across the membrane and can induce further expression of keratinase. The understanding of keratin monomers provides new clues for the study of feather degradation mechanisms.

microbiology↗

bioRxiv2023

Common computations in automatic cue combination and metacognitive confidence reports

It is well known that sensory information from one modality can automatically affect judgments from a different sensory modality. However, it remains unclear what determines the strength of the influence of an irrelevant sensory cue from one modality on a perceptual judgment for a different modality. Here we test whether the strength of multisensory impact by an irrelevant sensory cue depends on participants objective accuracy or subjective confidence for that cue. We created visual motion stimuli with low vs. high overall motion energy, where high-energy stimuli yielded higher confidence but lower accuracy in a visual-only task. We then tested the impact of the low- and high-energy visual stimuli on auditory motion perception. We found that the high-energy visual stimuli influenced the auditory motion judgments more strongly than the low-energy visual stimuli, consistent with their higher confidence but contrary to their lower accuracy. A computational model assuming common principles underlying confidence reports and multisensory integration captured these effects. Our findings show that automatic multisensory integration follows subjective confidence rather than objective performance and suggest the existence of common computations across vastly different stages of perceptual decision making.

neuroscience↗

bioRxiv2023

The timing of confidence computations in human prefrontal cortex

Knowing when confidence computations take place is critical for building mechanistic understanding of the neural and computational bases of metacognition. Yet, even though substantial amount of research has focused on revealing the neural correlates and computations underlying human confidence judgments, very little is known about the timing of confidence computations. Subjects judged the orientation of a briefly presented visual stimulus and provided a confidence rating regarding the accuracy of their decision. We delivered single pulses of transcranial magnetic stimulation (TMS) at different times after stimulus presentation. TMS was delivered to either dorsolateral prefrontal cortex (DLPFC) in the experimental group or to vertex in the control group. We found that TMS to DLPFC, but not to vertex, led to increased confidence in the absence of changes to accuracy or metacognitive ability. Critically, equivalent levels of confidence increase occurred for TMS delivered between 200 and 500 ms after stimulus presentation. These results suggest that confidence computations occur during a broad window that begins before the perceptual decision has been fully made and thus provide important constraints for theories of confidence generation.

neuroscience↗

bioRxiv2023

Mechanism of sensor kinase CitA transmembrane signaling

Membrane bound histidine kinases (HKs) are ubiquitous sensors of extracellular stimuli in bacteria. Here, we used solid-state NMR in conjunction with crystallography, solution NMR and distance measurements to investigate the transmembrane signaling mechanism of a paradigmatic citrate sensing membrane embedded HK, CitA. Citrate binding in the sensory extracytoplasmic PAS domain (PASp) causes the linker to transmembrane helix 2 (TM2) to adopt a helical conformation. This triggers a piston-like pulling of TM2 and a quaternary structure rearrangement in the cytosolic PAS domain (PASc). Crystal structures of PASc reveal both anti-parallel and parallel dimer conformations. An anti-parallel to parallel transition upon citrate binding agrees with interdimer distances measured in the lipid embedded protein using a site-specific 19F label in PASc. These data show how Angstrom scale structural changes in the sensor domain are transmitted across the membrane to be converted and amplified into a nm scale shift in the linker to the phosphorylation subdomain of the kinase. One-Sentence SummaryTransmembrane signal transduction of a PAS-domain containing histidine kinase occurs via a piston-like pulling of a transmembrane helix, and amplification by cytoplasmic PAS domain dimer rearrangement.

molecular biology↗

bioRxiv2023

Single-cell transcriptomic landscape deciphers novel olfactory neuroblastoma subtypes and intratumoral heterogeneity

Olfactory neuroblastoma (ONB) is an uncommon malignant tumor known to originate from the olfactory epithelial. The complex tumor ecosystem of this pathology remained unclear. Here, we explored the cellular components with ONB tumors based on scRNA profiles of 96,325 single-cells derived from 10 tumors and 1 olfactory mucosa sample. We discovered 11 major cell types, including 6 immune cell, 3 stromal cell subtypes and epithelial cluster in the tumor microenvironment (TME), and identified 5 common expression programs from malignant epithelial cells. We analyzed subclusters of TME and the interactions among different cell types in the TME. An innovative three-classification of ONB was established via scRNA analysis. Markers for categorizing tumor samples into new subtypes were elucidated. Different responses towards certain chemotherapy regimens could be inferred according to the molecular features of three tumor types. Relative abundance of immunosuppressive TAMs indicated the benefits of immunotherapies targeting myeloid cells.

cancer biology↗

bioRxiv2022

Idiosyncratic relation between human brain activity and behavior

Research in neuroscience often assumes universal neural mechanisms, but increasing evidence points towards sizeable individual differences in brain activations. What remains unclear is the extent of the idiosyncrasy and whether different types of analyses are associated with different levels of idiosyncrasy. Here we develop a new method for addressing these questions. The method consists of computing the within-subject reliability and subject-to-group similarity of brain activations and submitting these values to a computational model that quantifies the relative strength of group- and subject-level factors. We apply this method to a perceptual decision-making task (N=50) and find that activations related to task, reaction time (RT), and confidence are influenced equally strongly by group- and subject-level factors. Both group- and subject-level factors are dwarfed by a noise factor, though higher levels of smoothing increases their contributions relative to noise. Overall, our method allows for the quantification of group- and subject-level factors of brain activations and thus provides a more detailed understanding of the idiosyncrasy levels in brain activations.

neuroscience↗

bioRxiv2021

Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Dextran Sodium Sulfate-Induced Ulcerative Colitis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease caused by multi-factors including colonic inflammation and microbiota dysbiosis. Previous studies have indicated that Celastrol (CSR) has strong anti-inflammatory and immune-inhibitory effects. Here, we investigated the effects of CSR on colonic inflammation and the mucosal immunity in an experimental colitis model, and addressed the mechanism by which CSR preforms the protective effect. We characterized the therapeutic effects and the potential mechanism of CSR in treating UC using histological staining, intestinal permeability assay, cytokine assay, flow cytometry, fecal microbiota transplantation (FMT), 16S rRNA sequencing, untargeted metabolomics, and cell differentiation approaches. CSR administration significantly ameliorated DSS-induced colitis, as evidenced by the recovery of body weight and colon length, decreased disease activity index (DAI) score, as well as decreased intestinal permeability. CSR down-regulated the secretion of proinflammatory cytokines, upregulated the anti-inflammatory mediators, and improved the balances of Treg/Th1 and Treg/Th17 to maintain colonic immune homeostasis. However, the protective effects of CSR disappeared when the antibiotic cocktail was applied to deplete the gut microbiota, and the gut microbiota-mediated effect was confirmed by FMT. Furthermore, CSR treatment increased the gut microbiota diversity and composition, and raised the metabolic productions of pyruvate and adenosine, which probably involve in gut microbiota mediated protective effect. In conclusion, CSR ameliorates colonic inflammation in a gut microbiota-dependent manner. The underlying protective mechanism is associated with the rectified Treg/Th1 and Treg/Th17 balance, and increased pyruvate and adenosine production. The study provided the solid evidence that CSR might be a promising therapeutic drug for UC.

microbiology↗

bioRxiv2021

Homogeneous environmental selection overturns distance-decay relationship of soil prokaryotic community

Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biomes on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4,000 km in both alpine and temperate biomes. Surprisingly, prokaryotic similarities increased with geographic distance after tipping points of 1,760 - 1,920 km, overturning the well-accepted distance-decay relationship and generating a significant U-shape pattern. Such U-shape pattern was likely due to decreased disparities in environmental heterogeneity along with geographic distance when across biomes, as homogeneous environmental selection dominated prokaryotic assembly based on {beta}NTI analysis. Consistently, short-term environmental heterogeneity also followed the U-shape pattern spatially, mainly attributed to dissolved nutrients. In sum, these results demonstrate that homogeneous environmental selection via dissolved nutrients overwhelmed the "distance" effect when across biomes, subverting the previously well-accepted geographic pattern for microbes on a large scale.

ecology↗