Publications by authors named "Ye Chun"
Background: Systemic lupus erythematosus (SLE) has numerous symptoms across organs and an unpredictable flare-remittance pattern. This has made it challenging to understand drivers of long-term SLE outcomes. Our objective was to identify whether changes in DNA methylation over time, in an actively flaring SLE cohort, were associated with remission and whether these changes meaningfully subtype SLE patients.
View Article and Find Full Text PDFThe effects of electrical stimulation (ES) during the post-processing stage on NaCl diffusion, microstructure, and overall quality in the dry curing of pork tenderloin were investigated. ES treatment significantly increased the salt content in pork tenderloin, with the A2ES group (ES applied after 2 h of curing) showing a 28.32 % increase compared to the control group.
View Article and Find Full Text PDFDue to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake-terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities due to its bacteriostatic properties. To investigate the effects of long-term discharge of sewage containing low concentrations of SDS on microorganisms in the lake-terrestrial ecotone, alterations in bacterial community structure, functional genes, and biomass were examined using a simulated continuous pollutant input.
View Article and Find Full Text PDFArticle Synopsis
- - The study investigates how impaired signaling in naïve CD4+ T cells leads to the development of pathogenic autoreactive cells, which play a role in autoimmune arthritis, specifically using SKG mice with a mutated Zap70 gene.
- - Researchers found these pathogenic T cells had increased expression of activation and cytokine-related genes, but reduced expression of markers that usually promote tolerance compared to healthy cells.
- - The presence of specific TCR variable beta chains linked to superantigens from mouse retroviruses suggests that these viral elements may disrupt normal immune tolerance, fostering the development of self-reactive CD4+ T cells into harmful effector cells, with potential therapeutic implications.
Meckel's diverticulum, the most common congenital anomaly of the gastrointestinal tract, is often asymptomatic. Lack of complete resorption of the omphalomesenteric duct is an important cause of Meckel's diverticulum. Gastrointestinal (GI) bleeding is a major complication of Meckel's diverticulum.
View Article and Find Full Text PDFThe problem of lake pollution on the Tibetan Plateau has become prominent in recent years because of the warming climate and increased human activity. However, it is difficult to obtain effective indicators to explain the long-term eco-environmental changes in plateau lakes. In this study, a sediment core from Jinmucuo Lake was taken as the research object, and the Pb and Cs isotopes, diatom assemblages, and climatic and environmental factors were analyzed.
View Article and Find Full Text PDFThis study aims to detect the expression of phosphorylated PERK in breast cancer using immunohistochemistry and explore its significance. We examined 134 cases of formalin-fixed and paraffin-embedded breast cancer tissues. It was found that the expression of phosphorylated PERK in ductal carcinoma was higher than that in lobular carcinoma, and the difference between them was statistically significant, suggesting that phosphorylated PERK played different roles in the occurrence and development of different types of breast cancer.
View Article and Find Full Text PDFArticle Synopsis
- Physical activity improves symptoms in people with systemic lupus erythematosus (SLE), but the underlying mechanisms were unclear until this study explored immune cell differences among active vs. inactive patients.
- A cohort of 123 SLE patients underwent analysis of immune cells and gene expression through advanced RNA sequencing, revealing that sedentary patients had greater CD4+ T cell lymphopenia and an overall proinflammatory gene expression profile.
- The study indicates that increased physical activity could reduce levels of proinflammatory cytokines and improve immune function in SLE patients, suggesting potential therapeutic benefits of regular exercise for this condition.
Article Synopsis
- Researchers discovered that these atypical B cells provide valuable insights into antibody sequences, analyzing large-scale single-cell sequencing data that reveal widespread instances of light chain allelic inclusion.
- Machine learning models were developed to identify unique antibody sequences associated with properties like polyreactivity and mutation usage, outperforming previous antibody modeling techniques and highlighting the importance of allelic inclusion data.
Article Synopsis
- Differential expression analysis of single-cell RNA sequencing (scRNA-seq) helps understand gene expression variations due to experimental factors but is complicated by biological and technical variability.
- Memento is a new tool designed for efficient and reliable differential analysis of gene expression, scalability to large datasets, and the ability to assess mean expression, variability, and gene correlations.
- When applied to various large datasets, Memento outperformed existing methods by revealing more significant differences in gene expression and highlighting distinct transcriptional regulation mechanisms.
Microbial Biomarkers in Liquid Biopsy for Cancer: An Overview and Future Directions.
Cancer Control
October 2024
In recent years, the relationship between microbes and tumors has led to a new wave of scholarly pursuits. Due to the growing awareness of the importance of microbiota, including those within tumors, for cancer onset, progression, metastasis, and treatment, researchers have come to understand that microbiota and the tumor microenvironment together form a dynamic and complex ecosystem. Liquid biopsy technology, a non-invasive and easily repeatable method for sample collection, combined with emerging multi-omics techniques, allows for a more comprehensive and in-depth exploration of microbial signals and characteristics in bodily fluids.
View Article and Find Full Text PDFArticle Synopsis
- The text discusses how different cell types work together in biological processes, and recent single-cell assays allow researchers to understand variations in these cells across individuals.
- It introduces a method called single-cell interpretable tensor decomposition (scITD), which combines cell type data to uncover patterns of variation and interaction.
- By applying scITD to data from individuals with lupus and COVID-19, researchers found connections between cellular activity and disease severity, providing insights into potential signaling pathways and the complexities of disease stratification.
Clostridium perfringens (C. perfringens) causes avian necrotic enteritis, leading to huge economic losses to the poultry industry. This pathogen induces host immunosuppression; however, the molecular mechanism is still unclear.
View Article and Find Full Text PDFArticle Synopsis
- - Kidney failure significantly impacts health, prompting a large-scale study of 406,504 participants to uncover genetic factors affecting kidney function, identifying 430 key genetic loci.
- - The research revealed that 56% of inherited differences in kidney function are linked to regulatory elements in kidney tubule epithelial cells, while 7% relate to podocyte cells, suggesting these are crucial for gene expression.
- - Further analysis using advanced techniques like enhancer assays and CRISPRi identified specific genes (NDRG1, CCNB1, and STC1) regulated by these genetic loci, shedding light on their roles in kidney function.
Article Synopsis
- The study investigates the connection between interferon and systemic lupus erythematosus (SLE), focusing on how transposable elements (TEs) might influence SLE symptoms, particularly autoantibody production.
- Researchers analyzed RNA-sequencing data from immune cells in 120 SLE patients, identifying over 27,000 TEs and observing 731 that were differentially expressed among various SLE phenotypes.
- Results indicate that specific TEs are linked to genes responsible for antiviral responses and IFN signaling, highlighting their potential role in understanding and treating SLE.
Article Synopsis
- Deep learning models are used to predict epigenetic features, but their performance varies, especially in cell type-specific regions crucial for gene regulation.
- The study compares general-purpose models and tissue-specific models, finding that tailored models can enhance accuracy in predicting chromatin accessibility in specific cells.
- It emphasizes the need for novel strategies to improve predictions on genetic variants, as high reference sequence accuracy does not guarantee better variant effect predictions.
Glaesserella parasuis (G. parasuis) induces vascular damage and systemic inflammation. However, the mechanism by which it causes vascular damage is currently unclear.
View Article and Find Full Text PDFEnterotoxigenic (ETEC) is the main bacterial cause of diarrhea in weaned piglets. Baicalin-aluminum (BA) complex is the main active ingredient of Georgi extracted-aluminum complex, which has been used to treat diarrhea in weaning piglets, however the underlying mechanism remains unclear. To investigate the effects of the BA complex on the regulation of porcine intestinal epithelial (IPEC-1) cells infected with ETEC, IPEC-1 cells were incubated with an ETEC bacterial strain at a multiplicity of infection of 1 for 6 h and then treated with different concentrations of the BA complex for 6 h.
View Article and Find Full Text PDFArticle Synopsis
- A variety of deep learning models are being developed to predict chromatin accessibility from DNA sequences, but evaluation results often overlook the significance of cell type specific regulatory elements (CREs), which are crucial for gene regulation and complex disease heritability.
- The study evaluates the accuracy of these genomic models, revealing that general purpose models like Enformer and Sei perform worse in regions that are specifically accessible to certain cell types.
- The research highlights that tailoring models for specific tissues and enhancing their capacity for cell type specific regulation can boost performance, but improving predictions of reference sequences doesn't necessarily translate to better predictions of variant effects, suggesting the need for new approaches in the field.
Article Synopsis
- Poultry necrotic enteritis is a serious disease in chickens that can be controlled with antibiotics, but rising antibiotic resistance is a concern.
- Anemoside B4 has anti-inflammatory and immunomodulatory properties and was tested for its effects on this disease, showing it inhibited harmful processes in Caco-2 cells without exhibiting antibacterial activity.
- The study found that Anemoside B4 improved health markers in infected chickens, reduced tissue damage, and enhanced protective proteins in the intestines, demonstrating its potential as an alternative treatment.
Article Synopsis
- This study focused on managing rheumatoid arthritis (RA) by analyzing blood cells from patients and healthy individuals to identify specific cell types and their roles in disease activity.
- Researchers discovered 18 distinct types of immune cells, noting that patients with more severe RA had an increase in certain T cells, while those in remission showed fewer nonclassical monocytes.
- The study also highlighted key gene expressions related to inflammation and disease, providing insights into the complex biological processes that contribute to RA's variability in severity.
Article Synopsis
- Kidney disease is largely influenced by genetics, yet the specific genes and mechanisms involved are still not fully understood; a recent GWAS identified 462 genetic loci associated with kidney function.
- Researchers used single-cell ATAC-seq maps to explore chromatin accessibility in the kidney, finding that regulatory elements in kidney tubule epithelial cells accounted for the majority of genetic heritability related to kidney function.
- The study further utilized CRISPR interference to demonstrate how inherited variations in regulatory elements impact gene expression in tubule epithelial cells, ultimately linking these differences to a predisposition for kidney disease in humans.