Biomedical subjects

Lu Bai

Publications and source records attributed to Lu Bai.

3 recordsLinked to original sources

PubMed2026

Description of Dorea chungnamensis sp. nov., an Aerotolerant Anaerobe Isolated from Pig Feces.

A Gram-stain-positive, rod-shaped aerotolerant anaerobe was isolated from pig feces and designated as strain YH-dor228T. Phylogenetic analysis using 16 S rRNA gene sequence revealed that the strain was most closely related to Dorea hominis NSJ-36T, with 96.6% similarity. The phylogenomic tree revealed that the strain formed a distinct cluster within the genus Dorea. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between the strain and the most closely related strains within genus Dorea ranged from 73.4 to 74.9, 66.4-70.5, and 20.0-22.2%, respectively. The major fatty acids were C14:0, C16:0, and C16:1 ω9c DMA. The cell wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G + C content of the strain was 40.7%. The chemotaxonomic, phenotypic, and phylogenetic properties of YH-dor228T (= KCTC 25915T=NBRC 117235T) suggested that it represented a novel species of the genus Dorea, for which the name Dorea chungnamensis sp. nov. is proposed.

Animals↗

PubMed2026

Hi-C calibration by chemically induced chromosomal interactions.

The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within 10-60 kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in 5-10% of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

Chromosomes, Fungal↗

PubMed2026

Condensin accelerates long-range intra-chromosomal interactions.

The 3D genome organization plays a key role in regulating interactions among chromosomal loci. While Chromosome Conformation Capture (3C)-based methods have provided static snapshots of chromatin architecture, the kinetics of chromosomal encounters in live cells remain poorly characterized. In this study, we employ Chemically Induced Chromosomal Interaction (CICI) to measure encounter times between multiple loci pairs in G1-arrested budding yeast. Our results show that chromosome motion closely follows the Rouse polymer model, with similar diffusion parameters at all tested loci. Surprisingly, we find that long-range intra-chromosomal encounters occur significantly faster than inter-chromosomal encounters at similar 3D distances. Using targeted depletion experiments, we identify condensin, but not cohesin, as the complex mostly responsible for these rapid intra-chromosomal interactions. This is further supported by Hi-C analysis, which reveals that condensin promotes long-distance intra-chromosomal interactions in G1 yeast. Through polymer simulations, we estimate that condensin extrudes chromatin at ~2 kb/s with a density of one complex per 1-2 Mb and a processivity of 120-220 kb. These findings uncover a novel role for condensin in shaping the interphase genome organization and provide new insights into chromosomal search dynamics in vivo.

Saccharomyces cerevisiae↗