CURRENT MICROBIOLOGY
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2025
·Vol. 82
·期 4
·1-8
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IF 2.6
Bai Yameng,Liang Tianqi,Zhao Jie,Lin Yawen,Lu Qian,Zhou Xiujuan,Yang Menghua,Zhong Xiaojun
The marine bacterium Vibrio parahaemolyticus is responsible for the seafood-borne gastroenteritis in humans. Two-component system (TCS) TtrRS plays important roles in host colonization and works as an important regulator in V. parahaemolyticus . However, the mechanisms by which TtrRS regulates the downstream genes, as well as the function of their target genes, remain largely unknown. In this study, we performed a Find Individual Motif Occurrences (FIMO) analysis using the ttrR box to scan the V. parahaemolyticus genome and identified 68 potential binding sites harboring the ttrR box. Thereinto, a ttrR box exists in the promoter region of the 05890–05900 operon. We further demonstrated that TtrR directly regulates the expression of the 05890–05900 operon by binding to the ttrR box. In addition, another TCS, 05905/05910, could assist in the regulation of TtrR to the 05890 – 05900 operon. Subsequent study showed that the 05890–05900 operon promotes the sulfur metabolism of V. parahaemolyticus at the early growth stage. Our results suggested that TtrRS and their target genes generate a complex regulatory pathway to better control sulfur metabolism in V. parahaemolyticus .Please check and confirm the edit made in the article title and amend if necessary.It's OK.
研究领域:
微生物学
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分子生物学
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DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2022
·Vol. 50
·期 17
·9858-9872
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IF 19.16
You Xue-Jiao,Zhang Shan,Chen Juan-Juan,Tang Feng,He Jingang,Wang Jie,Qi Chu-Bo,Feng Yu-Qi,Yuan Bi-Feng
RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
研究领域:
分子生物学
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表观遗传学
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生物化学
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DOI
PubMed
高影响因子
ACS Applied Materials & Interfaces
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2025
·
IF 8.2
Yincheng Jin,Yu Zhang,Chenyang Xue,Shi Du,Jing Yao
Biofilm-associated bacterial infections pose significant therapeutic challenges due to their enhanced antibiotic resistance and complex extracellular matrix structure. To address this, we developed a carrier-free nanocomposite (named SPX-ICG) through self-assembling the antibiotic sparfloxacin (SPX) and the photosensitizer indocyanine green (ICG), creating a triple-mode antibacterial system that integrates photothermal, photodynamic, and antibiotic therapies. Upon near-infrared irradiation, SPX-ICG disassembled in the acidic biofilm environment, releasing bioactive components and initiating a therapeutic cascade: ICG generated mild photothermal effects that enhanced biofilm permeability, while simultaneously producing reactive oxygen species through photodynamic therapy, enabling efficient antibiotic penetration and bacterial eradication. The transcriptomic analysis revealed that SPX-ICG significantly downregulated genes involved in quorum sensing and two-component signal transduction systems, suggesting a fundamental reshaping of the biofilm microenvironment. Furthermore, SPX-ICG also demonstrated superior in vivo antibacterial effects in infected mouse models, effectively eradicating Staphylococcus aureus (S. aureus) and SPX-resistant S. aureus strains, with enhanced wound healing and minimal systemic toxicity. This approach, coupled with its minimalist design, presents a promising treatment option for the clinical management of biofilm-associated severe skin and soft tissue infections.
研究领域:
微生物学
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药理学
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分子生物学
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DOI
PubMed
高影响因子
WATER RESEARCH
·
2024
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IF 11.4
Yi Luo,Riji Qiu,Xingran Zhang,Fang Li
Reverse osmosis (RO) system has been increasingly applied for circulating cooling water (CCW) reclamation. Plasticizers, which may be dissolved into CCW system in plastic manufacturing industry, cannot be completely removed by the pretreatment prior to RO system, possibly leading to severe membrane biofouling. Deciphering the characteristics and mechanisms of RO membrane biofouling in the presence of trace plasticizers are of paramount importance to the development of effective fouling control strategies. Herein, we demonstrate that exposure to a low concentration (1 − 10 μg/L) of three typical plasticizers (Dibutyl phthalate (DBP), Tributyl phosphate (TBP) and 2,2,4-Trimethylpentane-1,3-diol (TMPD)) detected in pretreated real CCW promoted Escherichia coli biofilm formation. DBP, TBP and TMPD showed the highest stimulation at 5 or 10 μg/L with biomass increasing by 55.7 ± 8.2 %, 35.9 ± 9.5 % and 32.2 ± 14.7 % respectively, relative to the unexposed control. Accordingly, the bacteria upon exposure to trace plasticizers showed enhanced adenosine triphosphate (ATP) activity, stimulated extracellular polymeric substances (EPS) excretion and suppressed intracellular reactive oxygen species (ROS) induction, causing by upregulation of related genes. Long-term study further showed that the RO membranes flowing by the pretreated real CCW in a polypropylene plant exhibited a severer biofouling behavior than exposed control, and DBP and TBP parts played a key role in stimulation effects on bacterial proliferation. Overall, we demonstrate that RO membrane exposure to trace plasticizers in pretreated CCW can upregulate molecular processes and physiologic responses that accelerate membrane biofouling, which provides important implications for biofouling control strategies in membrane-based CCW treatment systems.
研究领域:
环境科学
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微生物学
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产品关联
DOI
PubMed
高影响因子
Journal of Advanced Research
·
2025
·
IF 13
Yuepeng Yin,Mengfan Jia,Ping Li,Kaiwen Zhu,Min Nie,Xin Tang,Liqin He,Ting Li,Zhihong Guo,Zhigao Zhou,Lirong Li,Taolin Zhang,Xingxiang Wang,Changfeng Ding
Introduction Traditionally, Silicon (Si) fertilizers are applied externally to the soil or sprayed on the leaves to reduce rice’s arsenic (As) accumulation. However, in practical agricultural production, the economic benefits of lowering As in rice grains often fail to outweigh the production costs. Objectives This study investigated an innovative technology—Si-rich seedlings (endogenous Si)—that is simple to implement, cost-effective, and highly effective in reducing As accumulation in rice grains. Methods The effects of exogenous and endogenous Si supplementation on As dynamics in rice were investigated in hydroponics in field experiments. Results Both methods significantly reduced As accumulation in the rice grains (22.23 % and 17.70 %, respectively). There was no significant difference in the treatment effects. However, endogenous Si supplementation demonstrated a significantly lower cost per unit of As reduction (88.61 % decrease), and it was easier to implement when compared with exogenous Si supplementation. The main processes by which various Si treatment techniques decrease As accumulation in rice differed, even though Si was crucial to As absorption in rice through a combination of mechanisms, such as gene regulation, iron plaque inhibition, and node I sequestration. The fundamental mechanism was Si/As antagonism, which regulated Si absorption through gene regulation in both methods. Interestingly, the exogenous Si treatment improved the barrier function of the root surface iron plaque against As. At the same time, laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) demonstrated that endogenous Si had a more pronounced impact on rice node I. Furthermore, experiments conducted at multiple scales (including variety, pot, and field experiments) validated the stability and reliability of the Si-rich seedling technology under complex environmental conditions. Conclusion Si-rich seedlings provide a cost-effective, stable, and practical solution for mitigating As contamination in paddy fields. This approach holds significant potential for enhancing soil health and improving food safety, contributing to the sustainable development of rice cultivation.
研究领域:
植物学
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环境科学
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农业科学
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产品关联
DOI
PubMed
高影响因子
ACS Nano
·
2018
·
IF 13.709
Jie Feng,Zhen Xu,Feng Liu,Yun Zhao,Wenqian Yu,Min Pan,Fuan Wang,Xiaoqing Liu
Catalytic deoxyribozyme has great potential for gene regulation, but the poor efficiency of the cleavage of mRNA and the lack of versatile DNAzyme vehicles remain big challenges for potent gene therapy. By the rational designing of a diverse vehicle of polydopamine-Mn2+ nanoparticles (MnPDA), we demonstrate that MnPDA has integrated functions as an effective DNAzyme delivery vector, a self-generation source of DNAzyme cofactor for catalytic mRNA cleavage, and an inherent therapeutic photothermal agent as well as contrast agent for photoacoustic and magnetic resonance imaging. Specifically, the DNAzyme-MnPDA nanosystem protects catalytic deoxyribozyme from degradation and enhances cellular uptake efficiency. In the presence of intracellular glutathione, the nanoparticles are able to in situ generate free Mn2+ as a cofactor of DNAzyme to effectively trigger the catalytic cleavage of mRNA for gene silencing. In addition, the nanosystem shows high photothermal conversion efficiency and excellent stability against photothermal processing and degradation in complex environments. Unlike previous DNAzyme delivery vehicles, this vehicle exhibits diverse functionalities for potent gene regulation, allowing multimodal imaging-guided synergetic gene regulation and photothermal therapy both in vitro and in vivo.
研究领域:
生物化学
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分子生物学
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诊疗学
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纳米医学
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产品关联
DOI
PubMed
高影响因子
Cell Reports Medicine
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2024
·
IF 11.7
Chengyu Li,Xin Shao,Shujing Zhang,Yingchao Wang,Kaiyu Jin,Penghui Yang,Xiaoyan Lu,Xiaohui Fan,Yi Wang
Cells respond divergently to drugs due to the heterogeneity among cell populations. Thus, it is crucial to identify drug-responsive cell populations in order to accurately elucidate the mechanism of drug action, which is still a great challenge. Here, we address this problem with scRank, which employs a target-perturbed gene regulatory network to rank drug-responsive cell populations via in silico drug perturbations using untreated single-cell transcriptomic data. We benchmark scRank on simulated and real datasets, which shows the superior performance of scRank over existing methods. When applied to medulloblastoma and major depressive disorder datasets, scRank identifies drug-responsive cell types that are consistent with the literature. Moreover, scRank accurately uncovers the macrophage subpopulation responsive to tanshinone IIA and its potential targets in myocardial infarction, with experimental validation. In conclusion, scRank enables the inference of drug-responsive cell types using untreated single-cell data, thus providing insights into the cellular-level impacts of therapeutic interventions.
研究领域:
生物信息学
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系统生物学
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医学
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DOI
PubMed
高影响因子
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
·
2025
·Vol. 122
·期 14
·e2424112122
·
IF 9.1
Pan Chu,Jingwen Zhu,Zhixin Ma,Xiongfei Fu
Microbial colony development hinges upon a myriad of factors, including mechanical, biochemical, and environmental niches, which collectively shape spatial patterns governed by intricate gene regulatory networks. The inherent complexity of this phenomenon necessitates innovative approaches to comprehend and compare the mechanisms driving pattern formation. Here, we unveil the multistability of bacterial colony patterns, where bacterial colony patterns can stabilize into multiple distinct types including ring-like patterns and sector-like patterns on hard agar, orchestrated by a simple synthetic bistable switch. Utilizing quantitative imaging and spatially resolved transcriptome approaches, we explore the deterministic process of a ring-like colony pattern formation from a single cell. This process is primarily driven by bifurcation events programmed by the gene regulatory network and microenvironmental cues. Additionally, we observe a noise-induced process amplified by the founder effect, leading to patterns of symmetry-break during range expansion. The degrees of asymmetry are profoundly influenced by the initial conditions of single progenitor cells during the nascent stages of colony development. These findings underscore how the process of range expansion enables individual cells, exposed to a uniform growth-promoting environment, to exhibit inherent capabilities in generating emergent, self-organized behavior.
研究领域:
微生物学
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系统生物学
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合成生物学
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产品关联
DOI
PubMed
高影响因子
BIORESOURCE TECHNOLOGY
·
2021
·
IF 9.642
Jingyang Luo,Le Zhang,Wei Du,Xiaoshi Cheng,Fang Fang,Jiashun Cao,Yang Wu,Yinglong Su
T his work revealed the impacts of exogeneous allicins on the antibiotic resistance genes (ARGs) variations during waste activated sludge (WAS) fermentation process. The overall abundance of ARGs was respectively reduced by 4.84 and 9.42% in presence of 0.01 and 0.05 g allicin/g TSS. Allicins disrupted the EPS structure and increased the permeability of cell membranes, which resulted in the release of ARGs for subsequent removal. Allicins also reduced intracellular ATP levels, which was disadvantageous to ARGs dissemination. Besides, allicins affected the microbial community and decreased the abundance of potential hosts based on bacterial taxa-ARGs network analysis. Moreover, the metabolic pathways and genetic expressions ( i.e., two-component system, quorum sensing, and SOS response) involved in ARGs propagation were down-regulated, which caused the ARGs alleviation in allicins-stressed reactors. Overall, the simultaneous responses of cellular status, bacterial host, and genetic regulation accounted for the effective ARGs reduction induced by allicins during WAS fermentation.
研究领域:
环境科学
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微生物学
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DOI
PubMed
高影响因子
ANALYST
·
2019
·Vol. 144
·期 17
·5098-5107
·
IF 4.019
Shengfeng Wang,Jinsong Ding,Wenhu Zhou
Simultaneous detection and regulation of tumor-related genes presents a promising strategy for early diagnosis and treatment of cancer, but achieving this has been a huge challenge for both chemical and biomedical communities. Towards this objective, we have devised a novel aptamer-tethered, DNAzyme-embedded molecular beacon (MB) for multiple functions in cancer cells. In this design, a tumor targeting aptamer was employed to specifically deliver the sensor into cancer cells for target gene detection, and an RNA-cleaving DNAzyme was embedded to realize gene regulation. Both aptamer-tethering and DNAzyme-embedding had little influence on the sensor performance, with a detection limit of ∼2 nM and high specificity. After delivering into tumor cells, our device could monitor the tumor-related genes by producing detectable fluorescence signals, and regulate the gene expression at both mRNA and protein levels as evidenced by the RT-PCR and western blot analyses. This study provides a simple and efficient strategy to rationally combine various functional nucleic acids for multi-functional applications in living cells, which hold great potential for cancer diagnosis and therapy.
研究领域:
生物技术
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分子生物学
·
癌症研究
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产品关联
DOI
PubMed
高影响因子
ANALYTICA CHIMICA ACTA
·
2024
·
IF 5.7
Jihua Wei,Jiayi Zhang,Wei Wang,Haidong Zhou,Huade Ma,Yuanxun Gong,Qianli Tang,Kai Zhang,Xianjiu Liao
The article details a groundbreaking platform for detecting microRNAs (miRNAs), crucial biomolecules involved in gene regulation and linked to various diseases. This innovative platform combines the CRISPR-Cas13a system's precise ability to specifically target and cleave RNA molecules with the amplification capabilities of the hybridization chain reaction (HCR). HCR aids in signal enhancement by creating branched DNA structures. Additionally, the platform employs electrochemiluminescence (ECL) for detection, noted for its high sensitivity and low background noise, making it particularly effective. A key application of this technology is in the detection of miR-17, a biomarker associated with multiple cancer types. It exhibits remarkable detection capabilities, characterized by low detection limits (14.38 aM) and high specificity. Furthermore, the platform's ability to distinguish between similar miRNA sequences and accurately quantify miR-17 in cell lysates underscores its significant potential in clinical and biomedical fields. This combination of precise targeting, signal amplification, and sensitive detection positions the platform as a powerful tool for miRNA analysis in medical diagnostics and research.
研究领域:
生物技术
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分子生物学
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医学诊断
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癌症研究
✓ 已验证
DOI
PubMed
高影响因子
ENVIRONMENTAL POLLUTION
·
2023
·
IF 8.9
Yu-Xi Feng,Peng Tian,Yu-Juan Lin,Dan-Yang Cao,Cheng-Zhi Li,Abid Ullah
The induction of disruption in the electronic transport chain by thiocyanate (SCN − ) leads to an excessive generation of reactive oxygen species (ROS) within rice ( Oryza sativa ). Hydrogen sulfide (H 2 S) assumes a crucial role as a gaseous signaling molecule, holding significant potential in alleviating SCN − -related stress. Nevertheless, there remains a dearth of understanding regarding the intricate interplay between H 2 S and ROS in Oryza sativa amidst SCN − pollution. In this investigation, a hydroponics-based experiment was meticulously devised to explore how H 2 S-mediated modifications influence the genetic feedback network governing ROS metabolism within the subcellular organelles of Oryza sativa when exposed to varying effective concentrations (EC 20 : 24 mg SCN/L; EC 50 : 96 mg SCN/L; EC 75 : 300 mg SCN/L) of SCN − . The findings unveiled the enhanced capacity of Oryza sativa to uptake SCN − under H 2 S + SCN − treatments in comparison to SCN − treatments alone. Notably, the relative growth rate (RGR) of seedlings subjected to H 2 S + SCN − exhibited a superior performance when contrasted with seedlings exposed solely to SCN − . Furthermore, the application of exogenous H 2 S yielded a significant reduction in ROS levels within Oryza sativa tissues during SCN − exposure. To elucidate the intricacies of gene regulation governing ROS metabolism at the mRNA level, the 52 targeted genes were categorized into four distinct types, namely: initial regulatory ROS generation genes (ROS-I), direct ROS scavenging genes (ROS-II), indirect ROS scavenging genes (ROS-III), and lipid oxidation genes (ROS-IV). On the whole, exogenous H 2 S exhibited the capacity to activate the majority of ROS-I ∼ ROS-IV genes within both Oryza sativa tissues at the EC 20 concentration of SCN − . However, genetic positive/negative feedback networks emphasized the pivotal role of ROS-II genes in governing ROS metabolism within Oryza sativa . Notably, these genes were predominantly activated within the cytoplasm, chloroplasts, mitochondria, peroxisomes, and the cell wall.
研究领域:
植物生理学
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分子生物学
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环境科学
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农学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）