Biomedical subjects

Xuan Li

Publications and source records attributed to Xuan Li.

3 recordsLinked to original sources

PubMed2026

CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.

CCCTC-binding factor (CTCF) is a key architectural protein in the three-dimensional (3D) genome, yet how its loss reshapes chromatin structure and transcription at single-cell resolution remains unclear. Using HiRES, which jointly profiles chromatin contacts and RNA from the same nucleus, we examined genome-wide effects of CTCF depletion. Topologically associating domain (TAD)-like domains (TLDs) across single cells remained largely unchanged in number and size after CTCF loss, but their boundaries became more variably positioned, and pseudobulk analyses revealed reduced interactions within A compartments. We also developed SALTAFinder to identify Spatially Aggregated Long-distance TLD Assemblies (SALTAs), clusters of TLDs occupying shared 3D space within single cells. A subset of SALTAs is enriched for highly expressed genes and super-enhancers and declines upon CTCF depletion. This structural reorganization coincided with a global reduction in per-cell RNA output, as indicated by HiRES and orthogonal measurements. Together, these findings suggest that CTCF contributes to the coordinated regulation of chromatin organization and transcriptional capacity and is associated with stabilization of long-range active chromatin clusters.

CCCTC-Binding Factor↗

PubMed2026

Simultaneous removal of nitrogen, Cu2+, and bisphenol A in a hydrogel-biochar-AQDS immobilized bioreactor with added bicarbonate: Performance and metagenomic insights.

As the complexity of industrial wastewater pollution continues to increase, the simultaneous removal of nitrogen, metal contaminants, and persistent organic pollutants under low carbon conditions has become a key challenge for biological treatment systems. To address the operational instability and dependence on carbon sources observed in immobilized systems when exposed to copper (Cu2+) and bisphenol A (BPA), the Pseudoalteromonas japonicus strain LY0623 was integrated into a hydrogel-biochar-AQDS composite carrier to construct a multifunctional immobilized biofilm system. Notably, under conditions containing only NaHCO3, the R4 system achieved an NH4+-N removal rate of 89%. Under conditions where Cu2+ and BPA coexist, the R4 system achieved removal of NH4+-N (89%), NO3--N (100%), Cu2+ (85%), and BPA (88%). Sediment characterization confirmed that Cu2+ was immobilized through adsorption, complexation, and microbiologically induced carbonate precipitation (MICP). Metagenomic analysis further indicated that the Pseudomonadota phylum remained the dominant phylum, while functional pathways associated with inorganic carbon assimilation, HNAD nitrogen metabolism, endogenous carbon transformation, biomineralization, electron transfer, and aromatic compound degradation were preserved. By combining ammonia oxidation driven energy production, inorganic carbon utilization, redox mediated processes, and biomineralization, this study provides a highly promising low carbon strategy for treating industrial wastewater containing mixed pollutants.

Bisphenol A Compounds↗

PubMed2025

A positive-sense single-stranded RNA virus acquired a negative-sense open reading frame through recombination.

Although positive- and negative-sense single-stranded RNA viruses are ubiquitous in nature, there is currently no evidence of recombination or reassortment between viruses with these two major forms of genome organization. Here, we describe the discovery of brine shrimp virga-like virus 1 (BSVV1), a novel positive-sense single-stranded RNA virus with a recombinant genome structure derived from two viral phyla with differing genome organizations. The genome of BSVV1 comprises three open reading frames (ORFs). ORF1 resembles the RNA-dependent RNA polymerase of Ips virga-like virus 1 (a positive-sense RNA virus), while ORF2, transcribed in the positive orientation, is related to the glycoprotein of Hubei bunya-like virus 10 and other negative-sense RNA viruses. The predicted ORF3 was unique to BSVV1 without known homologs identified. The presence of the three protein products was verified by mass spectrometry. Notably, our analysis also revealed that BSVV1 is geographically widespread and found in brine shrimp from at least eight countries on four continents. In addition, BSVV1 was successfully cultured and proliferated to high viral loads during brine shrimp development. In sum, we provide compelling evidence of an ancient recombination event between negative- and positive-sense single-stranded RNA viruses, enriching our understanding of the evolution of genome structures in RNA viruses.

Open Reading Frames↗