Biomedical subjects

Ying Yang

Publications and source records attributed to Ying Yang.

9 recordsLinked to original sources

PubMed2026

Human m6A demethylase FTO modulates the flowering time of tomato plants under low-temperature stress.

N6-methyladenosine (m6A) RNA modification plays an important role in plant development and environmental stress responses. However, whether m6A demethylation modulates flowering under low-temperature (LT) stress in tomatoes remains unclear. Here, we investigated whether ectopic expression of FTO, a well-characterized human m6A demethylase, influences flowering and post-transcriptional behaviour in tomato (Solanum lycopersicum) under LT conditions. Flowering of transgenic tomato plants expressing FTO was analyzed under LT and normal conditions (NC), and the impacts of FTO on transcripts-specific m6A level, mRNA stability and splicing efficiency of flowering-related genes were evaluated using RT-qPCR, LC-MS/MS, m6A-IP-qPCR, and RNA decay and splicing analyses. FTO-expressing plants exhibited accelerated flowering specifically under LT, whereas no significant differences were observed under normal growth conditions. This phenotype was accompanied by increased expression of positive floral regulators (SlMC, SlFCA, and SlJ2) and decreased expression of negative regulators (SlSVP, SlSP, and SlTMF) under LT conditions. Notably, these expression changes were associated with altered mRNA stability, with positive regulators showing increased stability and negative regulators showing reduced stability under LT conditions. m6A-IP-qPCR analysis indicated reduced m6A enrichment in these selected transcripts in FTO-expressing plants. In addition to effects on mRNA stability, FTO expression was associated with changes in the splicing efficiency of SlMC transcripts. Collectively, our findings indicate that human FTO functions as an mRNA m6A demethylase in tomatoes and is associated with altered RNA regulatory processes under LT conditions. These findings suggest that m6A-mediated post-transcriptional regulation contributes to stress-induced flowering plasticity under LT conditions, rather than direct activation of canonical flowering pathways.

Abiotic stress↗

PubMed2026

Concurrence of antibiotic resistance genes in plasmid genomes shape environmental resistomes.

Horizontal transfer of plasmid-associated antibiotic resistance genes (ARGs) plays a pivotal role in environmental antibiotic resistance dissemination. Here, we characterized ARG concurrence patterns in plasmid genomes and examined plasmid-associated ARGs across 106 environmental metagenomes. Approximately half of known ARG subtypes (257) occurred in plasmid genomes, and nearly one-quarter of plasmids carried ARGs, including "super plasmids" harboring over 20 ARG subtypes spanning 10 antibiotic categories. Aminoglycoside resistance genes (AmRGs) exhibited the highest concurrence frequency (CF) with other ARGs in plasmid genomes, followed by beta-lactam and sulfonamide resistance genes. Many high-risk ARGs preferentially coexisted with AmRGs (45.6% of total AmRGs CF). Environmental metagenomes revealed distinct plasmid-associated ARG profiles between polluted and relatively pristine environments, with significantly greater diversity and abundance under anthropogenic pollution. Five widespread ARG subtypes occurred across all environmental media, whereas polluted environments contained more unique ARGs. Co-occurrence networks identified AmRGs as "hubs" linking multiple ARG subtypes in environmental resistomes. Plasmid-ARG interaction networks further showed more complex potential plasmid-mediated concurrent dissemination in polluted environments. Collectively, use of aminoglycosides is more likely to cause co-transmission of multiple plasmid-related ARGs than other antibiotics, and CF of ARGs is proposed as an important supplementary factor for evaluating ARG dissemination under anthropogenic antibiotic stress.

Antibiotic resistance genes (ARGs)↗

PubMed2026

Genetic evidence supports the combined targeting of lipoprotein(a) and LDL cholesterol to reduce coronary artery disease risk.

Distinct genetic mechanisms govern how lipoprotein(a) (Lp(a)) and low-density lipoprotein cholesterol (LDL-C) promote atherosclerosis. It remains unclear whether targeting both provides additive cardiovascular benefits. Here we use coding loss-of-function variants in LPA and PCSK9 and genetic scores associated with Lp(a) and LDL-C levels to evaluate the effects of lowering Lp(a) and LDL-C on coronary artery disease (CAD) risk. Among 408,039 individuals from the UK Biobank, LPA or PCSK9 loss-of-function carriers have lower CAD risk than noncarriers (odds ratio (OR) 0.91 and 0.81). Carriers of both variants have even lower CAD risk (OR 0.73). Genetic lowering of Lp(a) and LDL-C showed a stronger reduction of CAD risk (OR 0.70) than either trait individually (OR 0.85 and 0.81) in the two-factor genetic score analysis. Among statin users, Lp(a) reduction was linearly associated with CAD risk. A phenome-wide association study revealed that combined therapy was associated with cardiometabolic benefits without adverse effects. The additive benefits were replicated in 65,171 individuals from the Mass General Brigham Biobank.

Humans↗

PubMed2026

The Impact of Baseline Negative Emotions on Postoperative Quality of Life in Adolescent Idiopathic Scoliosis Patients: A 2-Year Follow-Up Study.

OBJECTIVE: Adolescent idiopathic scoliosis (AIS) is a three-dimensional spinal deformity that develops during puberty without a clear etiology. Beyond physical manifestations, AIS severely impacts adolescents' psychological and social well-being, leading to anxiety, depression, and low self-esteem. While advancements in surgical techniques have enhanced objective outcomes, existing studies on AIS have primarily focused on objective indices, with limited attention to the long-term impact of preoperative negative emotions on patient-reported subjective quality of life. METHODS: This was a retrospective cohort study. A total of 112 eligible AIS patients who underwent posterior spinal correction surgery between April and August 2023 were enrolled. Inclusion criteria included confirmed AIS, completion of 2-year follow-up, and informed consent; exclusion criteria included missing imaging/questionnaire data, comorbid psychiatric/neurological diseases, or prior spinal surgery. Patients were grouped using the Hospital Anxiety and Depression Scale (HADS) administered on admission. Quality of life was assessed preoperatively and 2 years postoperatively using the Scoliosis Research Society-22 (SRS-22, evaluating self-image, mental health, pain, function, treatment satisfaction) and Short Form 36 Health Survey (SF-36, assessing 8 physical and mental health dimensions). Statistical analysis was performed via SPSS, using independent t-tests, paired t-tests, Mann-Whitney U test, and chi-square test. p < 0.05 was considered significant. RESULTS: There were no significant differences in baseline characteristics (age, gender, BMI, surgical parameters, scoliosis type, preoperative/postoperative Cobb angles) between the two groups (all p > 0.05). Preoperatively, SRS-22 and SF-36 scores showed no inter-group differences (all p > 0.05). Postoperatively, the Negative Emotion Group had significantly lower scores in SRS-22 mental health (3.9 ± 0.3 vs. 4.5 ± 0.2) and treatment satisfaction (4.0 ± 0.3 vs. 4.6 ± 0.7), as well as SF-36 general health (68.6 ± 6.4 vs. 79.7 ± 13.3), role-emotional (61.3 ± 9.3 vs. 70.8 ± 9.7), and mental health (61.8 ± 14.3 vs. 68.9 ± 10.7) (all p < 0.05); no inter-group differences were observed in physical function-related dimensions. Both groups showed significant improvements in physical function-related dimensions postoperatively. The Non-Negative Emotion Group also exhibited significant improvements in SRS-22 self-image/pain and SF-36 bodily pain (all p < 0.05), while the Negative Emotion Group showed no significant improvements in these dimensions. CONCLUSIONS: Preoperative anxiety and depression do not affect the recovery of physical function in AIS patients after spinal correction surgery but significantly impede improvements in subjective quality of life dimensions, including mental health and treatment satisfaction. These findings highlight the need to integrate psychological assessment and targeted interventions into the perioperative management of AIS. Such a patient-centered approach will help optimize both physical and psychological outcomes, ultimately achieving comprehensive rehabilitation for AIS adolescents.

Humans↗

PubMed2026

A black soybean yoghurt fermented with a reusable probiotic cellulose gel: beneficial effects and metabolic characteristics.

The demand for plant-based yoghurts is continuously increasing. However, achieving stable physicochemical properties and acceptable flavor of the plant-based yoghurts remains challenging. In our previous work, we encapsulated Lactiplantibacillus plantarum (L. plantarum) LCC-605 biofilm into bacterial cellulose (BC), obtaining a LP605@BC gel. LP605@BC gel exhibited excellent harsh-environment resistance abilities and storage stability, and is very suitable as a starter culture. In this work, we used LP605@BC as a starter culture to prepare the fermented plant-based yoghurt (e.g., black soybean yoghurt, BSY-LP605@BC). After fermentation, the inverted nonflowing yoghurt was formed due to the strong interaction between protein and exopolysaccharide (EPS) produced by LCC-605 during fermentation. In addition, the water holding capacity (67.2%) of BSY-LP605@BC was also greatly improved. The viable bacterial counts in BSY-LP605@BC reached 11.2 log CFU/mL after 21 days of storage. BSY-LP605@BC showed increased antioxidant, cholesterol-lowering abilities, and hypoglycemic potential compared with the unfermented black soybean milk. Interestingly, LP605@BC could be reused at least 5 times, demonstrating excellent sustainability. Significant metabolomic differences between BSY-LP605@BC and the black soybean milk were observed via untargeted metabolomic analysis, further proving the beneficial effects of BSY-LP605@BC. Overall, our work developed an effective reusable starter culture for preparing the plant-based yoghurt in a sustainable manner, providing a new design direction and form of starter culture.

Yogurt↗

PubMed2026

Bidirectional causal relationships between plasma proteins, neuroimaging metrics and risk of Alzheimer's disease.

BACKGROUND: Changes in neuroimaging metrics are among the first detectable pathophysiological alterations in Alzheimer's disease (AD). Proteins are closely linked to fluctuations in neuroimaging metrics. Therefore, the analysis of the proteomic signature associated with neuroimaging metrics holds significant promise for uncovering therapeutic targets that contribute to AD. METHODS: GWAS data concerning the Brain Imaging Data Structure (BIDs). The AD cohort comprised a total of 401,661 individuals diagnosed with AD, alongside 10,520 control participants. For a bidirectional MR analysis involving neuroimaging metrics, proteomics, and AD, the methods utilized included inverse variance weighted (IVW), MR Egger, weighted median, weighted mode, and the Wald ratio approaches. RESULTS: We identified 12 neuroimaging metrics that demonstrate significant relevance to AD (thickness of the left total hemisphere, volume of the right thalamus, and et al.). These metrics are structural magnetic resonance imaging (MRI) biomarkers that remain stable throughout the entire course of AD, from the preclinical stage through mild cognitive impairment (MCI) to dementia. Additionally, we found a substantial number of 1633 proteins that also show a noteworthy causal relationship with AD. Functional enrichment analysis indicated that these proteins were predominantly focused within various pathways linked to AD, encompassing those involved in the synaptic vesicle cycle, synaptic membranes, neurotransmitter release, and the activity of GABA receptors. In addition, our research indicates that the significant relationships observed between the identified proteins and AD are influenced by neuroimaging metrics. Notably, we found that these neuroimaging metrics play a crucial role in mediating a substantial 67% of the inverse relationship that exists between PTPRC and the phenotypic characteristics associated with AD. CONCLUSIONS: This study successfully establishes a connection between proteomic and neuroimaging metrics, as well as the AD that influence them. By creating this relationship, the research offers important information that aids in comprehending the intricate mechanisms involved in AD.

Alzheimer Disease↗

PubMed2025

MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.

Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.

Metagenomics↗

PubMed2025

The super-enhancer regulatory gene SH2D1A promotes the progression of T cell acute lymphoblastic leukemia by activating CHI3L2.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia subtype and a prevalent malignancy in children, with poor prognosis, high relapse rates, and drug resistance. Recent research has shown that super-enhancer-regulated genes play crucial roles in T-ALL progression. In this study, we identified SH2 domain containing 1 A (SH2D1A) as a gene regulated by super-enhancers, and is overexpressed, which correlates with unfavorable clinical outcomes in T-ALL. To investigate its role, we silenced SH2D1A expression in T-ALL cell models using RNA interference. This led to a significant reduction in cell proliferation, colony formation, and promoted apoptosis, as demonstrated by CCK-8 assays, soft agar colony formation, and flow cytometry analysis. In vivo, knockdown of SH2D1A significantly inhibited tumor growth and prolonged survival in mice bearing T-ALL. Mechanistically, we found that SH2D1A contributes to T-ALL progression by upregulating CHI3L2, a downstream effector that promotes cell proliferation and inhibits apoptosis. Using ChIP-Seq and RNA-seq technologies, we confirmed that SH2D1A regulates CHI3L2 expression through super-enhancer-mediated regulation in T-ALL cells. Our findings suggest that SH2D1A and CHI3L2 act as oncogenes in T-ALL, and may represent novel therapeutic targets. This research offers new insights into the molecular mechanisms of T-ALL and highlights potential avenues for therapeutic intervention.

Precursor T-Cell Lymphoblastic Leukemia-Lymphoma↗

PubMed2024

Brain glucose induces tolerance of Cryptococcus neoformans to amphotericin B during meningitis.

Antibiotic tolerance is the ability of a susceptible population to survive high doses of cidal drugs and has been shown to compromise therapeutic outcomes in bacterial infections. In comparison, whether fungicide tolerance can be induced by host-derived factors during fungal diseases remains largely unknown. Here, through a systematic evaluation of metabolite-drug-fungal interactions in the leading fungal meningitis pathogen, Cryptococcus neoformans, we found that brain glucose induces fungal tolerance to amphotericin B (AmB) in mouse brain tissue and patient cerebrospinal fluid via the fungal glucose repression activator Mig1. Mig1-mediated tolerance limits treatment efficacy for cryptococcal meningitis in mice via inhibiting the synthesis of ergosterol, the target of AmB, and promoting the production of inositolphosphorylceramide, which competes with AmB for ergosterol. Furthermore, AmB combined with an inhibitor of fungal-specific inositolphosphorylceramide synthase, aureobasidin A, shows better efficacy against cryptococcal meningitis in mice than do clinically recommended therapies.

Humans↗