Biology subjects

Shan, W.

Publications and source records attributed to Shan, W..

8 recordsLinked to original sources

bioRxiv2026

Evaluating the added value of sequence models in noncoding RNA assays: a baseline-aware framework

Sequence models are evaluated against non-coding RNA assay read-outs, but prediction alone does not show what their features add to an explicit baseline. We estimated model-added-last changes in AUROC for lncRNA labels and cross-validated Spearman correlation for miRNA repression, fixing members and chromosome folds across available sources. In cross-cell CRISPRi (n = 2961), AlphaGenome increased AUROC from 0.6426 to 0.7551; adding K562 accessibility changed these values to 0.7282 and 0.7534. Corrected-source Cas13 increments ranged from -0.0161 to +0.0130 (n = 871). Separate post-audit comparisons tested fixed sequence composition, broader regularization and TargetScan aggregate identity. With expanded regularization, composition improved four baselines but reduced Cas13 AUROC by 0.0365. RNA-FM's increment was -0.0014 for CRISPRi and +0.000044 for HEK293FT after composition adjustment; small signs changed with regularization. On the same 1227 HeLa members, replacing a seed-family aggregate with an identity-supported mature-miRNA aggregate increased baseline Spearman from 0.4140 to 0.4799. RNA-FM then added 0.0170, or 0.0014 after composition adjustment. These source-row aggregates lack experimental transcript/site alignment. The results support testing baseline content, identity and regularization before interpreting residual model increments. Negative or near-zero increments do not establish absent information or equivalence. Resampling summaries remain conditional descriptions or non-joint sensitivities; calibrated confirmation, justified practical-size thresholds and pretraining-overlap verification were unavailable.

bioinformatics↗

bioRxiv2026

Symbiont effectors modulate plant signalling to increase host stress resilience

Plant colonizing mutualistic symbionts confer beneficial effects to their hosts, which often includes increased growth, and biotic and abiotic stress resilience. How these benefits are activated on a molecular level is mostly unknown. Here, we describe effector candidates of the fungal symbiont Serendipita indica (Si), which modulate plant stress signalling pathways. By analyzing the Si effector interactome, we reveal frequent targeting of stress related host proteins, which are linked to the identified effector signalling functions. Moreover, functional data indicate that Si effectors modulate abiotic stress response of Arabidopsis, as well as resistance to pathogen infection. Analysis of symbiont effectors might not only uncover previously unreported molecular mechanisms that increase plant fitness but might also be used to identify potential genetic traits for crop improvement under changing climates.

plant biology↗

bioRxiv2026

Adipose GPD2 Couples Glycolytic Signals to Epigenetic Control of Metabolic Homeostasis

The glycerol-3-phosphate shuttle (G3PS) is a classic reducing equivalent transferring system, yet its role in adipose metabolism remains poorly understood. Here, we identify mitochondrial glycerol-3-phosphate dehydrogenase (GPD2), the core enzyme of G3PS, as a critical orchestrator of adipose thermogenesis and systemic metabolic homeostasis. Adipocyte-specific GPD2 knockout mice exhibited impaired thermogenic capacity and energy expenditure, rendering them susceptible to obesity and metabolic dysfunction. Mechanistically, GPD2 deficiency elevated cytosolic NADH, which suppressed glycolysis and decreased the levels of key metabolites, such as acetyl-CoA, thereby diminishing H3K27ac at thermogenic gene loci and silencing these genes. NADH depletion with an NADH oxidase rescued both glycolysis and thermogenic gene expression. In support of this mechanism, we defined a previously undescribed enhancer of Ucp1 whose H3K27ac was tightly controlled by GPD2. Remarkably, replenishing the acetyl-CoA pool or directly restoring H3K27ac at the Ucp1 enhancer reversed UCP1 expression in GPD2-deficient adipocytes. Importantly, we find that human adipose GPD2 expression is inversely correlated with BMI, WHR, and HOMA-IR, underscoring its clinical relevance. Collectively, our findings establish GPD2 as an essential node in the metabolic-epigenetic axis that governs thermogenic activation and energy balance.

biochemistry↗

bioRxiv2025

Stimuli-Expressed Protein Qubits for Quantum Quantification of Heavy Metals in Natural Water

Environmental heavy metal pollution poses a severe threat to ecological security and human health, necessitating the development of highly sensitive, specific, and rapid detection technologies. Traditional fluorescent biosensors are often constrained by high background interference and limited sensitivity, while single-target detection systems struggle to meet the demands of complex environmental monitoring. This study constructs a novel magnetically modulated photonic quantum biosensing system based on the CadC-T7 gene circuit, replacing the traditional fluorescent reporter gene EGFP with the magnetically modulated fluorescent protein MagLOV - a quantum biomaterial. To enhance its magnetic modulation performance, the mutant with the highest lock-in amplitude during the directed evolution (R10, MagLOV 2) was selected; Simultaneously, systematic parameter optimization was conducted to determine the optimal magnetic modulation frequency (0.05 Hz), the heavy metal stimulation duration (the 2-hour group exhibited the most significant intra-group variation), and the bacterial concentration at the onset of the heavy metal stimulation (controlled at OD600 = 1 to prevent fluorescence quenching due to culture turbidity). The system demonstrates excellent multi-analyte detection capabilities for lead chloride, lead nitrate, and cadmium chloride across a concentration range of 10-8 to 10-4 M. Compared to conventional steady-state photometric methods based on EGFP and MagLOV 2, the lock-in analysis of MagLOV 2 achieves detection sensitivities enhanced by 1[~]2 orders of magnitude, with detection limits as low as 2.4 nM for cadmium chloride, 4.8 nM for lead nitrate, and 9.9 nM for lead chloride. Langmuir isotherm fitting results demonstrate high quantitative accuracy (R2 > 0.950), with particularly outstanding fitting performance for cadmium chloride (R2 = 0.999) and lead nitrate (R2 = 0.995).

synthetic biology↗

bioRxiv2025

Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and intra-tumoral mucosal associated invariant T (MAIT) cell activation

The role of mucosal invariant T cells (MAITs), in the lung tumor microenvironment re-mains poorly understood, especially in the setting of immune checkpoint inhibitors. We identified intratumoral MAIT cells from paired single cell RNA and TCR sequencing datasets of tumor infil-trating CD3 T cells isolated from non-small cell lung cancer tumors in patients receiving neoadju-vant PD-1 blockade therapy. MAIT cells were subclustered to identify conventional MAIT-associ-ated TCR clonotypes predicted to recognize intratumoral bacteria, which we then tested for func-tional recognition using a MAIT TCR capture functional assay. Strikingly, although not directly recognized by MAIT cells, previously identified probiotic Enterococcus spp and detected in the intratumoral microbiome of lung cancer patients, selectively synergized with exogenous riboflavin biosynthesis-derived metabolites to induce expression of MR1 by antigen presenting cells, includ-ing dendritic cells, B cells and mononuclear phagocytes. Boosting of MR1 cell surface expression resulted from perturbation of endo-lysosomal vacuolar pathway by Enterococcus and recycling of early endosomal MR1 to the cytoplasmic membrane. Riboflavin auxotrophic Enterococcus spp may therefore exercise their beneficial immunomodulatory functions upon immune checkpoint blockade treatment, at least in part, by promoting intratumoral MR1 expression and innate like T cell activation. Our results indicate that composition of the intratumoral microbiome during im-mune checkpoint inhibitor treatment has the potential to impact the function of human intratumoral MAIT cells.

immunology↗

bioRxiv2023

The probiotic roles of Lactiplantibacillus plantarum E2 as a dietary supplement in growth promotion and disease resistance of juvenile large yellow croaker (Larimichthys crocea)

Bacterial diseases are the most important limiting factors for the development of large yellow croaker aquaculture. Probiotics are considered to be a promising alternative approach for the control of bacterial diseases in aquaculture. However, the studies on probiotics used in farmed large yellow croakers were very limited. In this study, we isolated and identified a Lactiplantibacillus plantarum E2 from the intestinal tract of large yellow croaker. L. plantarum E2 showed significant antibacterial activities against several aquaculture pathogenic bacteria, intestinal environmental tolerance, and biosafety. After 7 weeks of feeding, the E2 supplementation of dietary significantly improved the growth and the survival rates of large yellow croakers after Pseudomonas plecoglossicida PQLYC4 challenge. Further analysis showed that E2 effectively improved the intestinal integrity, and increased the intestinal -amylase, trypsin and lipase activities. Moreover, the E2 supplementation also significantly suppressed the mRNA expression of IL-10 and increased the mRNA expression of IL-1{beta}, IL-12, IL- 17D, IFN-{gamma}, and TNF--R. Gut microbiota analysis showed that E2 significantly affected gut microbial community composition by decreasing the relative abundance of Sphingomonas and increasing the relative abundance of Lactobacillus and Pseudomonas. Finally, E2 could improve resistance of large yellow croaker against P. plecoglossicida PQLYC4 infection. Therefore, our findings showed that L. plantarum E2 has potential application as a probiotic in large yellow croaker, which may provide a new strategy of preventing and controlling bacterial diseases in this species. HighlightsLactiplantibacillus plantarum E2 showed significant antibacterial activities against several aquaculture pathogenic bacteria, intestinal environmental tolerance, and biosafety. Lactiplantibacillus plantarum E2 supplementation improved growth rates, and intestinal health of large yellow croaker. Lactiplantibacillus plantarum E2 increased the abundance of potential probiotics in the intestine tract of large yellow croaker.

zoology↗

bioRxiv2023

MicroRNA-195-3p as a potential regulator of hypoxic injury in HUVECs

Coronary heart disease is the most common heart disease and is the leading cause of cardiovascular death worldwide. Revascularization methods are considered effective against coronary heart disease However, the mechanism of molecular revascularization remains largely unknown. Endothelial cells are the primary cells that initiate angiogenesis and arteriogenesis and require a hypoxic environment for induction. In this study, we aimed to determine the expression and role of microRNA-195-3p in hypoxia-treated HUVEs(human umbilical vein endothelial cells). Herein, we induced hypoxia in human umbilical vein endothelial cells using the "Anaerobic tank method." Hypoxia injured human umbilical vein endothelial cells showed upregulation of microRNA-195-3p; decreased cell proliferation, migration, and autophagy; and increased apoptosis. Furthermore, the microRNA-195-3p inhibitor partially reversed the effects of hypoxia-induced injury of human umbilical vein endothelial cells. Therapeutic intervention using microRNA-195-3p inhibitor could maintain endothelial cell function under hypoxic conditions, improve cell activity, and be considered a new treatment strategy for coronary heart diseases.

cell biology↗

bioRxiv2019

AUTS2 regulation of synapses for proper synaptic inputs and social communication.

Impairments in synapse development are thought to cause numerous psychiatric disorders. Autism susceptibility candidate 2 (AUTS2) gene has been associated with various psychiatric disorders, such as autism and intellectual disabilities. Although roles for AUTS2 in neuronal migration and neuritogenesis have been reported, its involvement in synapse regulation remains unclear. In this study, we found that excitatory synapses were specifically increased in the Auts2-deficient primary cultured neurons as well as Auts2 mutant forebrains. Electrophysiological recordings and immunostaining showed increases in excitatory synaptic inputs as well as c-fos expression in Auts2 mutant brains, suggesting that an altered balance of excitatory and inhibitory inputs enhances brain excitability. Auts2 mutant mice exhibited autistic-like behaviors including impairments in social interaction and altered vocal communication. Together, these findings suggest that AUTS2 regulates excitatory synapse number to coordinate E/I balance in the brain, whose impairment may underlie the pathology of psychiatric disorders in individuals with AUTS2 mutations.

neuroscience↗