Biology subjects

zhang, W.

Publications and source records attributed to zhang, W..

4 recordsLinked to original sources

bioRxiv2026

Pre-existing antibiotic tolerance facilitates plasmid-mediated carbapenem resistance evolution in clinical Klebsiella pneumoniae

Antibiotic tolerance enables bacteria to survive bactericidal antibiotic exposure and has been linked to resistance evolution in laboratory systems and individual infections, but its role in plasmid-mediated resistance evolution in clinical populations remains unclear. Here, we analyzed a longitudinal collection of more than 800 clinical Klebsiella pneumoniae isolates spanning 1997-2020. Among 779 minimum inhibitory concentration (MIC)-defined ertapenem-susceptible isolates, 137 (17.6%) displayed hidden ertapenem tolerance, defined by enhanced survival after 6 h at 30 times the isolate-specific ertapenem MIC, mostly without extended lag time or reduced growth rate. Tolerance was detected before local ertapenem introduction and was enriched among ertapenem-resistant isolates, supporting a population-level association between pre-existing tolerance and the emergence of carbapenem resistance. Genomic and plasmid-curing analyses separated plasmid-mediated carbapenem resistance from plasmid-independent antibiotic tolerance. Moreover, tolerant recipient backgrounds enhanced resistance plasmid acquisition, preserved viable recipients following antibiotic exposure and accelerated ceftazidime-avibactam resistance evolution. A phylogeny-guided variant-enrichment analysis further identified the uhpABC regulatory operon as a candidate tolerance-associated locus, and coordinated expression of the complete operon increased ertapenem survival. Together, these findings identify clinical antibiotic tolerance as a pre-existing, MIC-hidden phenotype that can facilitate plasmid-mediated carbapenem resistance evolution in K. pneumoniae.

microbiology↗

bioRxiv2024

Effects of arbuscular mycorrhizal fungi on nitrogen uptake in cotton (Gossypium hirsutum L.) under low-nitrogen conditions

SummaryO_LICotton is an important global cash crop whose yield and quality are highly influenced by soil nitrogen. Therefore, examining the interactions between roots and arbuscular mycorrhizal fungi (AMF) under reduced nitrogen conditions is of great significance. C_LIO_LIWe investigated the effects of nitrogen application (0, 250, and 375 kg{middle dot} hm-2) on the AMF infection rate of cotton, the nitrogen content of each organ, root morphological characteristics and biomass, soil extracellular enzyme activity, and soil carbon and nitrogen content using a compartmentalized culture system. C_LIO_LIThe contribution of AMF to plant nitrogen was 10.40, 22.72, and 16.67% under high, low, and no nitrogen treatments, respectively. Under low-nitrogen conditions, the symbiosis between AMF and roots increased root surface area, tip number, branch number, mean diameter, and biomass; and increased soil extracellular enzyme activity (protease, NAG, PER, and PPO), the microbial biomass carbon-to-nitrogen ratio, active carbon content, and the soil nitrogen mineralization rate. Soil NO3--N, NH4+-N, and organic nitrogen content decreased, whereas the absorption of NO3--N by AMF hyphae was higher than that of NH4+-N. C_LIO_LIUnder low-nitrogen conditions, AMF promoted the decomposition of soil organic matter and the transformation of soil nitrogen through the action of hyphal microorganisms. C_LI

plant biology↗

bioRxiv2022

Mapping Multiple Factors Mediated Chromatin Interactions to Assess Regulatory Network and Dysregulation of Lung Cancer-Related Genes

Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, dysregulation of long-range chromatin interactions in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system. The generated high-resolution data revealed chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using specific antibodies and long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The EZH2/H3K27me3-mediated interactions further silenced target genes, either through loops or domains, and showed distributions along the genome distinct from and complementary to those associated with RNAPII. We found that cancer-related genes were highly enriched in chromatin interactions. We identified abnormal interactions associated with oncogenes and tumor suppressors, such as additional repressive interactions on FOXO4 and promoter - promoter interactions between NF1 and RNF135. Knockout of abnormal interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.

genomics↗

bioRxiv2018

Biolistic transformation of Haematococcus pluvialis with constructs based on the flanking sequences of its endogenous alpha tubulin gene

The complete sequence information of the alpha tubulin (tub) genes was obtained from both Haematococcus pluvialis NIES144 and SCCAP K0084., Putative transcriptional elements and polyadenylation signals were identified respectively in their 5 and 3 flanking regions. Three selection cassettes of tub/aadA, tub/hyr and tub/ble with 3 different antibiotic-resistant genes fused between the 5 and 3 flanking sequences of the tub gene were constructed and utilized for biolistic transformation of H.pluvialis. Antibiotic resistant transformants were obtained in the bombardments with the tub/aadA cassette in 2 strains. It was found that, the foreign tub/aadA DNA could be completely transferred and inherited in their genome through non-homologous recombination. Moreover, transcripts of the insert and spectinomycin resistance were identified. Transformation efficiencies up to 3x10-5 per g DNA could be obtained in H.pluvialis NIES144 or SCCAP K0084 through utilization of a culture with a high percentage of flagellate cells and by optimizing bombarding protocol. The presented selection marker and optimized transforming procedures in this report should strengthen the platform technology for genetical manipulation and modification of H.pluvialis.

molecular biology↗