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Li Zhou

Publications and source records attributed to Li Zhou.

At least 19 recordsLinked to original sources
PubMed2026

Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa.

Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R2Y > 0.9, Q2 > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.

Evodia rutaecarpa↗
PubMed2026

Charting host structural variations in cervical cancer by long-read sequencing pinpoints a functional deletion in PIAS1.

Host structural variations (SVs) are critical in cancer development but their landscape and interaction with HPV integration in cervical carcinogenesis remain unclear. In this study, we performed Nanopore long-read sequencing on five HPV-positive cervical cancer tissues and two cell lines to profile host SVs. We identified thousands of SVs and statistically demonstrated their significant enrichment in genomic windows &#xb1;25 to &#xb1;50&#xa0;kb from HPV integration sites. Cross-sample analysis revealed 60 shared SVs, including a recurrent deletion within the PIAS1 gene. Multi-omics integration (Hi-C, H3K27ac ChIP-seq, and TCGA data) showed that this deletion is associated with reduced PIAS1 expression, disruption of local topologically associating domains, advanced pathological tumor stage, and poorer overall survival. Functional assays confirmed that PIAS1 deficiency inhibits cervical cancer cell proliferation and migration. Our findings identify a PIAS1 deletion as a candidate driver event, and underscore the pivotal role of host genomic instability in HPV-associated oncogenesis.

Cervical cancer↗
PubMed2026

Genomic and virulence characteristics of Staphylococcus aureus isolates from foodborne outbreak cases.

This study aimed to investigate the genomic characteristics, enterotoxin production, and antimicrobial resistance profiles of Staphylococcus aureus isolates associated with foodborne outbreaks. A total of 19 bacterial isolates were collected from foodborne outbreaks in Guizhou Province, China between 2014 and 2023. Following biochemical identification, all isolates were confirmed as S. aureus. Phylogenetic analysis divided the 19 strains into seven branches. Enterotoxin production was detected using standard microbiological techniques and immunoassays. Antimicrobial susceptibility was evaluated using the broth microdilution method. Whole-genome sequencing and subsequent bioinformatic analyses were conducted to characterize virulence genes, antimicrobial resistance genes, multilocus sequence typing (MLST) genotypes, and phylogenetic relationships among the isolates. This study found that all strains produced classical staphylococcal enterotoxins, with staphylococcal enterotoxin (SEA) showing the highest detection rate (63.16%). Virulence gene profiling revealed widespread presence of hlb, hlgA, nuc, clfB, spa, and set genes. All strains were resistant to penicillin, with high resistance rates for erythromycin and cefoxitin. Multidrug resistance occurred in 11 of the 19 strains, and 22 resistance genes were identified. MLST analysis showed that ST6 and ST59 were the dominant types, with ST59 methicillin-resistant S. aureus (MRSA) strains displaying stronger resistance and more virulence determinants. These findings provide insights into the virulence, resistance, and molecular epidemiology of S. aureus strains involved in foodborne outbreaks, and may provide useful information for future surveillance and risk assessment.

Staphylococcus aureus↗
PubMed2026

Development and validation of a plasma miRNA-CEA biomarker panel for early detection of lung cancer.

Lung cancer remains a leading cause of cancer-related mortality worldwide, underscoring the critical need for early detection to improve patient outcomes. This study aimed to develop and validate a plasma microRNA biomarker panel for the early detection of non-small cell lung cancer in a Japanese cohort. We enrolled 525 participants, comprising 261 LC cases and 264 non-LC controls, divided into optimization and validation cohorts. A 12-miRNA panel was optimized and further combined with CEA to enhance diagnostic performance. The miRNA-alone model demonstrated robust performance in both the optimization (AUC = 77.0%) and validation cohorts (AUC = 77.9%). Integration with CEA significantly improved accuracy, achieving AUCs of 86.2% in optimization and 84.9% in validation, with particularly high performance in late-stage cancers (AUC = 94.4%) and squamous cell carcinoma (AUC = 90.7%). Sensitivity and specificity thresholds were evaluated, enabling model customization for diverse clinical scenarios. These findings highlight the potential of the miRNA-CEA panel as a minimally invasive tool for early LC detection, especially in non-smoking populations.

Humans↗
PubMed2025

A deep-sea hydrothermal vent worm detoxifies arsenic and sulfur by intracellular biomineralization of orpiment (As2S3).

The alvinellid worm Paralvinella hessleri is the only animal that colonizes the hottest part of deep-sea hydrothermal vents in the west pacific. We found P. hessleri accumulates exceptionally high level of toxic element arsenic (>1% of wet weight) and tolerated elevated concentrations hydrogen sulphide. Using advanced microscopy, elementary analysis, and genomics and proteomics approaches, we identified a previously unrecognized arsenic-sulfide biomineralization process in P. hessleri. Our data suggest that arsenic accumulates within epithelial cell granules, where it likely reacts with sulphide diffused inward from the hydrothermal vent fluid, resulting in the intracellular formation of orpiment (As&#x2082;S&#x2083;) minerals. In this "fighting poison with poison" manner, the highly toxic arsenic and sulphide were simultaneously detoxified in the form of orpiment minerals within the intracellular granules of the single layer of epithelial cells. This process represents a remarkable adaptation to extreme chemical environments. Our study provides new insights into understanding animals' environment adaptation mechanisms and the diversity and plasticity of biomineralization.

Animals↗
PubMed2025

Chromosome-level genome assembly of Qihe gibel carp.

Qihe gibel carp (Carassius gibelio var. Qihe) is a local population of natural gynogenetic amphitriploid (AAABBB) Carassius gibelio, and has high nutritional and economic value. In this study, we assemble a high-quality chromosome-level genome of Qihe gibel carp through DNBSEQ, PacBio HiFi, and Hi-C sequencing data. The resulting assembly consisted of 350 contigs with the full length of 1.607&#x2009;Gb and 96.21% (1.515&#x2009;Gb) of the assembled genome was successfully anchored to 50 chromosomes, with a contig N50 of 28.97&#x2009;Mb and a scaffold N50 of 29.84&#x2009;Mb. Repeated sequences accounting for 43.72% (732.494&#x2009;Mb) of the total were also identified, and gene prediction revealed 46,131 protein-coding genes with an annotation ratio of 96.48%. Furthermore, Benchmarking Universal Single-Copy Orthologue (BUSCO) analysis demonstrated that the genome assembly achieved high completeness, with a score of 97.66%. This high-quality chromosome-level genome lays the foundation for molecular biology research as well as molecular breeding and evolutionary studies of Qihe gibel carp in the future.

Animals↗
PubMed2006

Adsorption of hydrogen isotopes on micro- and mesoporous adsorbents with orderly structure.

The equilibrium and dynamic adsorption data of H(2) and D(2) on different micro- and mesoporous adsorbents with orderly structure including 3A, 4A, 5A, Y, and 10X zeolites; carbon CMK-3; silica SBA-15; and so forth were collected. Critical effect of the nanodimension of adsorbents on the adsorption behavior of hydrogen and its isotopes is shown. The highest adsorption capacity was observed at pore size 0.7 nm, but equal or even larger isotope difference in the equilibrium adsorption was observed at larger pore sizes, whereas the largest isotope difference in the dynamic adsorption was observed at 0.5 nm. The adsorption rate of D(2) is larger than that of H(2) in microporous adsorbents, but the sequence could be switched over in mesoporous materials. Linear relationship was observed between the adsorption capacity for hydrogen and the specific surface area of adsorbents although the adsorbents are made of different material, which provides a convincing proof of the monolayer mechanism of hydrogen adsorption. The linear plot for microporous adsorbents has a larger slope than that for mesoporous adsorbents, which is attributed to the stronger adsorption potential in micropores.

Journal Article↗
PubMed2006

Differential and spermatogenic cell-specific expression of DMRT1 during sex reversal in protogynous hermaphroditic groupers.

DMRT1 has been suggested to play different roles in sex determination and gonad differentiation, because different expression patterns have been reported among different vertebrates. The groupers, since their gonads first develop as ovary and then reverse into testis, have been thought as good models to study sex differentiation and determination. In this study, we cloned the full-length cDNAs of DMRT1 gene from orange-spotted grouper (Epinephelus coioides), and prepared corresponding anti-EcDMRT1 antiserum to study the relationship of DMRT1 to sex reversal. One important finding is that the grouper DMRT1 is not only differentially expressed in different stage gonads, but also restricted to specific stages and specific cells of spermatogenesis. Grouper DMRT1 protein exists only in spermatogonia, primary spermatocytes and secondary spermatocytes, but not in the supporting Sertoli cells. Moreover, we confirmed that EcSox3 is expressed not only in oogonia and different stage oocytes, but also in Sertoli cells and spermatogonia, and EcSox9 is expressed only in Sertoli cells. The data suggested that grouper DMRT1 might be a more specific sex differentiation gene for spermatogenesis, and play its role at the specific stages from spermatogonia to spermatocytes. In addition, no introns were found in the grouper DMRT1, and no duplicated DMRT1 genes were detected. The finding implicates that the intronless DMRT1 that is able to undergo rapid transcriptional turnover might be a significant gene for stimulating spermatogenesis in the protogynous hermaphroditic gonad.

Amino Acid Sequence↗
PubMed2006

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp.

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 aa, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein.

3' Untranslated Regions↗
PubMed2006

Inhibition of overactivated p38 MAPK can restore hematopoiesis in myelodysplastic syndrome progenitors.

The myelodysplastic syndromes (MDSs) are collections of heterogeneous hematologic diseases characterized by refractory cytopenias as a result of ineffective hematopoiesis. Development of effective treatments has been impeded by limited insights into any unifying pathogenic pathways. We provide evidence that the p38 MAP kinase is constitutively activated or phosphorylated in MDS bone marrows. Such activation is uniformly observed in varied morphologic subtypes of low-risk MDS and correlates with enhanced apoptosis observed in MDS hematopoietic progenitors. Most importantly, pharmacologic inhibition of p38alpha by a novel small molecule inhibitor, SCIO-469, decreases apoptosis in MDS CD34+ progenitors and leads to dose-dependant increases in erythroid and myeloid colony formation. Down-regulation of the dominant p38alpha isoform by siRNA also leads to enhancement of hematopoiesis in MDS bone marrow progenitors in vitro. These data implicate p38 MAPK in the pathobiology of ineffective hematopoiesis in lowrisk MDS and provide a strong rationale for clinical investigation of SCIO-469 in MDS.

Aged↗
PubMed2006

Antibody targeting of the insulin-like growth factor I receptor enhances the anti-tumor response of multiple myeloma to chemotherapy through inhibition of tumor proliferation and angiogenesis.

Although many multiple myeloma (MM) patients initially respond to cytotoxic therapy, most eventually relapse. Novel therapeutic strategies employing a combination of chemotherapy with targeted biologics may significantly enhance the response of tumor cells to treatment. We tested a fully human anti-IGF-IR antibody (A12) against MM, and showed specific inhibition of IGF-I or serum-induced IGF-IR signaling in MM cells in vitro. The A12 as a single agent was demonstrated to exert modest to significant inhibition of tumor growth in vivo in various subcutaneous xenograft MM models. The A12 was also evaluated in a disseminated xenograft MM.1S NOD/SCID model as monotherapy or in combination with other drugs (bortezomib, melphalan) currently in clinical use. The tumor burden, as determined by luciferase bioimaging, was sharply decreased, and overall survival significantly prolonged when the therapies were combined. Immunohistochemical analysis demonstrated that the A12 treated tumors had significantly decreased vascularization compared to control tumors. Furthermore, most MM lines constitutively secreted significant quantities of VEGF, and this was enhanced following IGF-I treatment. Inhibition of IGF-IR by the A12 in vitro suppressed both constitutive and IGF-I-induced secretion of VEGF, indicating that a putative anti-angiogenic mechanism associated with the A12 treatment may contribute to its anti-tumor effect.

Animals↗
PubMed2006

X-ray photoelectron spectroscopic and Raman analysis of silk fibroin-Cu(II) films.

There is evidence to suggest that Cu(II) is involved in the natural spinning process of a silkworm helping to convert the concentrated silk fibroin (SF) solution (or dope) into tough insoluble threads. To investigate the interaction between SF and Cu(II), a series of regenerated SF (RSF) films with different mass ratios of Cu(II) to SF were prepared. X-ray photoelectron spectroscopy (XPS) was employed to study the chemical interaction between Cu(II) and SF in these Cu(II)-RSF films. A significant change in the binding energy of Cu 2p(3/2) demonstrated that the chemical state of Cu(II) in the Cu(II)-RSF films was affected by the interaction between Cu(II) and SF. Moreover, chemical shifts of N 1s and O 1s of SF were also detected, implying that Cu(II) may coordinate with both N and O atoms in the SF. In addition, Raman spectra of the same series of Cu(II)-RSF films recorded the conformation transition of SF that may occur by the coordination of Cu(II) and SF macromolecular chains.

Animals↗
PubMed2006

New interface plate for microspray ionization mass spectrometry.

A new interface plate was employed in microspray ionization mass spectrometry (microESI-MS) to improve ion transmission from the sprayer into the sampling nozzle of the mass spectrometer at atmospheric pressure. Using a time-of-flight mass spectrometer (TOFMS), a fivefold increase in ion intensity and a sevenfold reduction in method detection limit were observed. The interface plate attenuated the dependence of the ion intensity on the sprayer position. Even when the distance between the sprayer tip and sampling nozzle was 15.0 mm, ion signals were still stronger than when the sprayer tip was positioned 3.0 mm in front of the sampling nozzle with the original interface plate. This enhancement in the performance of microESI-MS was due to the improved shapes of the equipotential lines near the sprayer tip and the long desolvation distance between the sprayer and the sampling nozzle of the MS.

Journal Article↗
PubMed2006

The autoimmune regulator (Aire) controls iNKT cell development and maturation.

The mechanism underlying the autoimmune polyglandular syndrome type-1 (APS1) has been attributed to defective T-cell negative selection resulting from reduced expression and presentation of autoantigens in thymic medullary epithelial cells (MECs). It has also been postulated that Aire is involved in development of regulatory T cells, although supporting evidence is lacking. Here we show that expression of Aire in MECs is required for development of iNKT cells, suggesting a role for iNKT cells in APS1.

Animals↗
PubMed2006

Using discordance to improve classification in narrative clinical databases: an application to community-acquired pneumonia.

Data mining in electronic medical records may facilitate clinical research, but much of the structured data may be miscoded, incomplete, or non-specific. The exploitation of narrative data using natural language processing may help, although nesting, varying granularity, and repetition remain challenges. In a study of community-acquired pneumonia using electronic records, these issues led to poor classification. Limiting queries to accurate, complete records led to vastly reduced, possibly biased samples. We exploited knowledge latent in the electronic records to improve classification. A similarity metric was used to cluster cases. We defined discordance as the degree to which cases within a cluster give different answers for some query that addresses a classification task of interest. Cases with higher discordance are more likely to be incorrectly classified, and can be reviewed manually to adjust the classification, improve the query, or estimate the likely accuracy of the query. In a study of pneumonia--in which the ICD9-CM coding was found to be very poor--the discordance measure was statistically significantly correlated with classification correctness (.45; 95% CI .15-.62).

Adult↗
PubMed2006

Improvement of cell viability and hirudin production by ascorbic acid in Pichia pastoris fermentation.

In recombinant Pichia pastoris fermentation for hirudin production, copious cells were not viable and most of the secreted hirudin molecules were C-terminally truncated at the end of fermentation. In this work, the influences of reactive oxygen species (ROS) on cell viability and hirudin production were subsequently studied. In contrast to the untreated control condition, the addition of ascorbic acid at the methanol fed-batch phase could obviously relieve the damage of intracellular ROS to cell membranes. As a result, the cell viability could be increased to 91% from 74% in control at the end of fermentation and the extracellular proteolysis of hirudin reduced. Intact and total hirudin production, by supplying ascorbic acid, could reach 2.90 and 5.03 g/l, respectively, in contrast to 1.75 and 4.70 g/l at the control condition. Ascorbic acid, 4 mmol/l or more, in the fermentation broth increased markedly the production of the intact hirudin, despite a little effect on total hirudin production.

Ascorbic Acid↗