Biology subjects

Ling, Q.

Publications and source records attributed to Ling, Q..

8 recordsLinked to original sources

bioRxiv2026

High-fat diet promotes exhaustion-associated T-cell remodeling across vascular and lymphoid tissues in atherosclerosis-prone mice

Background: Atherosclerosis is a chronic inflammatory disease driven by lipid accumulation and immune dysregulation. How chronic dietary lipid exposure reshapes T-cell states across vascular and lymphoid tissues, and whether these changes resolve after dietary normalization, remains incompletely defined. This study examined diet-associated T-cell remodeling and the contribution of macrophage-mediated stimulation. Methods: ApoE-deficient mice received a vegetarian diet (VD) or high-fat diet (HFD) for 12 or 24 weeks; a dietary reversal group received HFD for 12 weeks followed by VD for 12 weeks. CD45-positive cells from aorta, blood, spleen, lymph nodes, and bone marrow underwent single-cell RNA sequencing with matched T-cell receptor sequencing. T cell states were annotated using canonical markers, and exhaustion- and naive-associated programs were quantified using UCell scores. Analysis assessed T-cell composition, clonal expansion, and predicted macrophage-T cell communication, with splenic flow-cytometric validation. Results: HFD was associated with enrichment of exhaustion-associated states, with the highest exhaustion scores in the aorta. At 24 weeks, the pooled exhausted-cell proportion was 15.7% under HFD versus 10.6% under VD. Dietary reversal restored this proportion to 10.6%, while residual transcriptional changes persisted in a tissue-dependent manner. Flow cytometry corroborated increased inhibitory receptor expression and co-expression. Aortic macrophages exhibited inflammatory and antigen-presentation programs alongside increased predicted communication with T cells. Aortic T-cell activation and clonal expansion accompanied these changes, and clonotype size correlated with exhaustion score (Spearman correlation coefficient = 0.57, p = 0.029). Conclusion: Chronic HFD is associated with multicompartment T-cell remodeling, with prominent vascular exhaustion-associated programs and tissue-dependent recovery after dietary normalization. These findings suggest that dietary lipid exposure may leave a durable adaptive immune imprint across organs during atherosclerosis.

immunology↗

bioRxiv2026

Probiotic-Directed Fermentation Reprograms the Metabolic Profile of a Traditional Mongolian Whole-Wheat Diet and Modulates Escherichia coli-Induced Gut Microbiota Dysbiosis

Traditional Mongolian fermented foods have been extensively utilized for dietary regulation and the promotion of gastrointestinal health. However, spontaneous fermentation remains inherently unpredictable, leading to significant variations in microbial community dynamics, metabolite accumulation, and the consistency and quality of the final product. Drawing on the traditional preparation of Mongolian acidic foods, this study established a controlled production strategy for whole-wheat probiotic fermented soup (WWPFS) by combining enzymatic pretreatment with probiotic-directed fermentation. Physicochemical characterization, 16S rRNA gene-based microbial community profiling, LC-MS/MS-based untargeted metabolomics, safety evaluation, and an Escherichia coli-induced gut microbiota dysbiosis model were employed to optimize and comprehensively characterize the fermentation process of WWPFS. The optimized process established a reproducible fermentation system consistently dominated by Lactobacillus and Bacillus across independent fermentation batches. Compared with traditional spontaneous fermentation, probiotic-directed fermentation remodeled the physicochemical properties of the whole-wheat matrix, including carbon, nitrogen, phosphorus, sulfur, and mineral composition, and facilitated the accumulation of putatively annotated LC-MS/MS features, including DL-lactate, 1,4-D-xylobiose, diacetyl, and phenyllactic-acid-related features derivatives. Acute oral and 28-day repeated-dose toxicity evaluations showed no treatment-related adverse effects within the tested dose range and study duration. In the Escherichia coli-induced gut microbiota dysbiosis mouse model, microbial richness, diversity, and community structure differed among the experimental groups, and both low- and high-dose WWPFS groups showed significant shifts in overall gut microbial community composition relative to the model group after multiple-testing correction, together with directional recovery of selected model-responsive bacterial genera. Cross-system integration identified coordinated response patterns between fermentation-derived metabolite features and model-responsive gut bacterial taxa, supporting a potential metabolite-microbiota link in WWPFS-mediated gut microbiota modulation. In summary, probiotic-directed fermentation improved the controllability of the traditional Mongolian fermented food production process, reshaped its metabolic profile, and enhanced its potential to modulate the gut microbiota. These findings provide experimental evidence supporting the modernization of traditional Mongolian fermented foods and the development of probiotic-based functional foods.

microbiology↗

bioRxiv2026

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

bioRxiv2025

Long-term high throughput agitation culturing with real-time metabolic profiling

Cellular metabolism relies on the dynamic coordination between glycolytic flux in the cytosol and oxidative phosphorylation (OXPHOS) within the mitochondria. To study the metabolic profiles of cells, researchers apply a monitoring system for measurements of critical parameters, e.g., pH and dissolved oxygen (DO), to understand underlying energy production tendencies, dictating the performance, resilience and growth of cells. However, implementing sensitive, non-invasive sensors into long-term culturing environments remains a technical bottleneck. Here, we describe the DolphinQ bioanalyzer, a novel culturing platform designed for high-throughput, real-time monitoring of cellular metabolism states under physiologically relevant conditions. We validate the system across multiple cell types and experimental set-ups, demonstrating its ability to resolve subtle metabolic shifts that are typically obscured in end-point assays. Notably, we utilize the system to characterize the metabolic impact of heteroplasmy in a mitochondrial disease model with affected ATP synthase. Our results underscore the utility of continuous, minimally disruptive monitoring for revealing the complexities of cellular metabolic adaptation. The DolphinQ framework therefore offers a robust tool for optimizing culture conditions across a wide range of applications and advancing fundamental research into metabolic flux and mitochondrial dysfunction.

bioengineering↗

bioRxiv2022

Differential gene expression analysis and physiological response characteristics of passion fruit (Passiflora edulis) buds under high-temperature stress

High temperature in summer is an unfavorable factor for passion fruit (Passiflora edulis), which can lead to restricted growth, short flowering period, few flower buds, low fruit setting rate, severe fruit drop, and more deformed fruit. To explore the molecular physiology mechanism of passion fruit responding to high-temperature stress, we use Zhuangxiang Mibao, a hybrid passion fruit cultivar, as the test material. Several physiological indicators were measured and compared between high-temperature (average temperature 38{degrees}C) and nonmoral temperature (average temperature 25{degrees}C) conditions, including photosynthesis, chlorophyll fluorescence parameters, POD, SOD activity and malondialdehyde content. We performed RNA-seq analysis combined with biochemistry experiment to investigate the gene and molecular pathways that respond to high-temperature stress. The results showed that some physiological indicators in the high-temperature group, including the net photosynthetic rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, and the maximum chemical quantum yield of PS||, were significantly lower than those of the control group. Malondialdehyde content was substantially higher than the control group, while superoxide dismutase and superoxide dismutase activities decreased to different degrees. Transcriptome sequencing analysis showed that 140 genes were up-regulated and 75 genes were down-regulated under high-temperature stress. GO and KEGG annotation analysis of differentially expressed genes revealed many metabolic pathways related to high-temperature stress. Further investigation revealed that 30 genes might be related to high-temperature stress, such as CAO, GSH, WRKY, and HSP, which have also been reported in other species. The results of real-time fluorescence quantitative PCR and RNA-seq of randomly selected ten genes are consistent, which suggests that the transcriptome sequencing results were reliable. Our study provides a theoretical basis for the mechanism of passion fruit response to high-temperature stress. Also, it gives a theoretical basis for the subsequent breeding of new heat-resistant passion fruit varieties.

plant biology↗

bioRxiv2022

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double-membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated, and processed via the CHLORAD pathway: they are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically-derived chloroplasts, where it acts to regulate one of the most fundamental processes of life. One Sentence SummaryThe ubiquitin-proteasome system targets proteins inside chloroplasts, including chloroplast-encoded photosynthesis subunits.

plant biology↗

bioRxiv2021

Decoding the single-cell landscape and intercellular crosstalk in the transplanted liver: a 4-dimension mouse model

Graft remodeling after transplantation maintains graft functionality and determines graft survival. However, a comprehensive understanding of cellular diversity and interplay during graft remodeling remains to be fully characterized. In this study, we established a well tolerant C57BL/6 to C57BL/6 orthotopic liver transplantation (LT) mice model and observed two stages of graft recovery including an acute phase and a steady phase. We next performed single-cell RNA sequencing (scRNA-seq) and cytometry by time-of-flight (CyTOF) and recorded the cellular hierarchy in the transplanted liver during the two stages. Besides the dynamic change of cell proportion, it was notable that recipient-derived cells took over the transplanted liver in most cell types (e.g., B cells, T cells, dendritic cells, granulocytes and monocytes) except CD206+ MerTK+ macrophages and CD161+ CD49a+ CD49b-natural killer cells. We then focused on macrophages and captured 5 distinct transcriptional signatures to define novel subclusters. Using a ligand-receptor interaction strategy, we identified specific macrophage-hepatocyte interactions during the acute and stable phases, causing metabolic remodeling in the transplanted liver. Our results delineated a 4-dimension cell atlas (type-proportion-source-time) of the transplanted liver, which sheds light on the physiological process of liver graft maintenance and graft-recipient crosstalk.

immunology↗

bioRxiv2020

Crosstalk between chloroplast protein import and the SUMO system revealed through genetic and molecular investigation

The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation (CHLORAD) pathway. Here, we demonstrate that the stability of the TOC complex is also regulated by the SUMO system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale yellow mutant lacking the Toc33 protein. This suppression is linked to the increased stability of TOC proteins and improvements in chloroplast development. In addition, we demonstrate using molecular and biochemical experiments that the SUMO system directly targets TOC proteins. Thus, we have identified a regulatory link between the SUMO system and chloroplast protein import.

cell biology↗