Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria

Tong, Tong,Chen, Si,Wang, Lianrong,Tang, You,Ryu, Jae Yong,Jiang, Susu,Wu, Xiaolin,Chen, Chao,Luo, Jie,Deng, Zixin,Li, Zhiqiang,Lee, Sang Yup,Chen, Shi National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.13

<P><B>Significance</B></P><P>Phosphorothioate (PT) modification of the DNA sugar-phosphate backbone is an important microbial epigenetic modification governed by DndABCDE, which together with DndFGH, constitutes a restriction-modification system. We show that up to 45% of 1,349 identified bacterial <I>dnd</I> systems exhibit the form of solitary <I>dndABCDE</I> without the restriction counterparts of <I>dndFGH</I>. The combination of epigenomics, transcriptome analysis, and metabolomics suggests that in addition to providing a genetic barrier against invasive DNA, PT modification is a versatile player involved in the epigenetic control of gene expression and the maintenance of cellular redox homeostasis. This finding provides evolutionary and functional insights into this unusual epigenetic modification. Our results imply that PT systems might evolve similar to other epigenetic modification systems with multiple cellular functions.</P><P>The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of <I>dnd</I> systems across a large number of bacterial genomes and their functions other than R-M are poorly understood. Here, a genomic survey revealed the prevalence of bacterial <I>dnd</I> systems: 1,349 bacterial <I>dnd</I> systems were observed to occur sporadically across diverse phylogenetic groups, and nearly half of these occur in the form of a solitary <I>dndBCDE</I> gene cluster that lacks the <I>dndFGH</I> restriction counterparts. A phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M and R components, despite the observation that several PT R-M pairs appeared to be assembled from M and R parts acquired from distantly related organisms. Concurrent epigenomic analysis, transcriptome analysis, and metabolome characterization showed that a solitary PT modification contributed to the overall cellular redox state, the loss of which perturbed the cellular redox balance and induced <I>Pseudomonas fluorescens</I> to reconfigure its metabolism to fend off oxidative stress. An in vitro transcriptional assay revealed altered transcriptional efficiency in the presence of PT DNA modification, implicating its function in epigenetic regulation. These data suggest the versatility of PT in addition to its involvement in R-M protection.</P>

Wnt/β-Catenin Promotes the Osteoblastic Potential of BMP9 Through Down-Regulating Cyp26b1 in Mesenchymal Stem Cells

Yao Xin-Tong,Li Pei-pei,Liu Jiang,Yang Yuan-Yuan,Luo Zhen-Ling,Jiang Hai-Tao,He Wen-Ge,Luo Hong-Hong,Deng Yi-Xuan,He Bai-Cheng 한국조직공학과 재생의학회 2023 조직공학과 재생의학 Vol.20 No.5

BACKGROUND: All-trans retinoic acid (ATRA) promotes the osteogenic differentiation induced by bone morphogenetic protein 9 (BMP9), but the intrinsic relationship between BMP9 and ATRA keeps unknown. Herein, we investigated the effect of Cyp26b1, a critical enzyme of ATRA degradation, on the BMP9-induced osteogenic differentiation in mesenchymal stem cells (MSCs), and unveiled possible mechanism through which BMP9 regulates the expression of Cyp26b1. METHODS: ATRA content was detected with ELISA and HPLC–MS/MS. PCR, Western blot, and histochemical staining were used to assay the osteogenic markers. Fetal limbs culture, cranial defect repair model, and micro–computed tomographic were used to evaluate the quality of bone formation. IP and ChIP assay were used to explore possible mechanism. RESULTS: We found that the protein level of Cyp26b1 was increased with age, whereas the ATRA content decreased. The osteogenic markers induced by BMP9 were increased by inhibiting or silencing Cyp26b1 but reduced by exogenous Cyp26b1. The BMP9-induced bone formation was enhanced by inhibiting Cyp26b1. The cranial defect repair was promoted by BMP9, which was strengthened by silencing Cyp26b1 and reduced by exogenous Cyp26b1. Mechanically, Cyp26b1 was reduced by BMP9, which was enhanced by activating Wnt/b-catenin, and reduced by inhibiting this pathway. b-catenin interacts with Smad1/5/9, and both were recruited at the promoter of Cyp26b1. CONCLUSIONS: Our findings suggested the BMP9-induced osteoblastic differentiation was mediated by activating retinoic acid signalling, viadown-regulating Cyp26b1. Meanwhile, Cyp26b1 may be a novel potential therapeutic target for the treatment of bone-related diseases or accelerating bone-tissue engineering.

Evaluation of the effects of different freezing and thawing methods on the quality preservation of Pleurotus eryngii

Tong Li,이조원,Li Luo,김종기,문보경 한국응용생명화학회 2018 Applied Biological Chemistry (Appl Biol Chem) Vol.61 No.3

The individually quick-frozen (IQF) method is used to produce high-quality frozen food by freezing an individual piece of food separately from the remaining food. In this study, the effect of various freezing and thawing combinations on the quality preservation of Pleurotus eryngii (king oyster mushroom) was investigated. For this purpose, diced and mini P. eryngii mushrooms were frozen by natural freezing (NF, − 20 °C) or IQF (− 62.5 °C and speed 8.23 m/s) methods and thawed using three thawing methods—flowing water thawing (FT, 4 °C), microwave thawing (MT, 620 W), or natural air convection thawing (NT, 20 ± 5 °C). Quality characteristics, such as thawing loss, texture, water holding capacity, color, microstructure, and sensory quality, were evaluated. MT showed the most rapid thawing time, followed by FT and NT for all the samples. The results showed that thawing curve, water holding capacity, and hardness of IQF samples were better than those of NF samples after NT, FT, and MT. Scanning electron microscopy analysis revealed that cell integrity of the IQF sample was better than that of the NF sample. MT is the fastest of the thawing methods, but thawing after NF yielded a sample closest to the fresh mushroom sample. Therefore, when combined with NT, IQF minimized the quality changes in frozen diced and mini P. eryngii mushrooms. This study showed that the IQF technology can be used as a new preservation and distribution method of mushroom.

Initial fault diagnosis of bearing based on AVMD-SE and multiscale enhanced morphological top-hat filter

Tong Wang,Changzheng Chen,Yuanqing Luo,Siyu Zhao,Shaohui Huang 대한기계학회 2022 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.36 No.12

Early fault signature detection and background noise removal are essential for bearing fault diagnosis. A novel multiscale enhanced morphological top-hat filter fault diagnosis method, adaptive variational mode decomposition-sample entropy-multiscale enhanced top-hat filter (AVMD-SE-MEMTF), is proposed based on AVMD-SE noise reduction. First, gray wolf optimization algorithm is proposed to optimize the VMD to achieve the optimal decomposition parameters adaptively and combine with SE to eliminate the high noise components and improve the noise reduction effect. Then, based on the pulse extraction property of morphological operations, the concept of MEMTF is proposed. To enhance the multiscale index selection strategy, a synthesis method of eigenfrequency envelope coefficients is constructed to increase the accuracy of the operator during the vibration signal process. Finally, experimental and engineering results show that the proposed method has good diagnostic performance for weak faults in the presence of noise interference.

Performance Analysis of Co- and Cross-tier Device-to-Device Communication Underlaying Macro-small Cell Wireless Networks

( Tong Li ),( Zhu Xiao ),( Hassana Maigary Georges ),( Zhinian Luo ),( Dong Wang ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.4

Device-to-Device (D2D) communication underlaying macro-small cell networks, as one of the promising technologies in the era of 5G, is able to improve spectral efficiency and increase system capacity. In this paper, we model the cross- and co-tier D2D communications in two-tier macro-small cell networks. To avoid the complicated interference for cross-tier D2D, we propose a mode selection scheme with a dedicated resource sharing strategy. For co-tier D2D, we formulate a joint optimization problem of power control and resource reuse with the aim of maximizing the overall outage capacity. To solve this non-convex optimization problem, we devise a heuristic algorithm to obtain a suboptimal solution and reduce the computational complexity. System-level simulations demonstrate the effectiveness of the proposed method, which can provide enhanced system performance and guarantee the quality-of-service (QoS) of all devices in two-tier macro-small cell networks. In addition, our study reveals the high potential of introducing cross- and co-tier D2D in small cell networks: i) cross-tier D2D obtains better performance at low and medium small cell densities than co-tier D2D, and ii) co-tier D2D achieves a steady performance improvement with the increase of small cell density.

The gene expression profile of Monochamus alternatus in response to deltamethrin exposure

Tong Lin,Huajun Wu,Linlin Luo 한국응용곤충학회 2014 Journal of Asia-Pacific Entomology Vol.17 No.4

To identify additional genes that are potentially associatedwith deltamethrin toxicology, differentially expressedgene (DGE) libraries of Monochamus alternatus after short-term exposure to a sub-lethal concentration of deltamethrinwere prepared. The transcripts were sequenced using the Illumina sequencing platform. After cleaningand quality checks, the total numbers of clean reads were 7.066 and 7.139 million in the control anddeltamethrin-exposed libraries, respectively. We found that 4886 and 2083 unique genes were significantlyup- and down-regulated, respectively. The gene ontology enrichment analysis identified that 4032, 3379 and8323 DEGs were involved in cellular components, molecular functions and biological processes, respectively,and showed that the genes were distributed among more than 50 categories. The Kyoto Encyclopedia of Genesand Genomes pathway enrichment analysis indicated that the top 20 enriched pathways included the glutathionemetabolismpathway and the antigen processing and presentation pathway. Therewere 42 DEGs enriched inthe antigen processing and presentation pathway, including those encoding the 70-kDa heat shock protein, proteindisulfide isomerase and calreticulin, all ofwhichwere up-regulated. There were 61 DEGs enriched in the glutathionemetabolism pathway, and these included the up-regulated DEGs encoding glutamate–cysteine ligase,glutathione synthase and glutathione reductase and the down-regulated DEGs encoding glutathione Stransferase,glutathione peroxidase and ornithine decarboxylase. This study is the first step toward achievingan understanding of the profile of the secondary targets of deltamethrin in M. alternatus, and the results may provideinsights to further explore the functions of the target genes in detoxification and resistance to deltamethrin.

Drift Error Calibration Method Based on Multi-MEMS Gyroscope Data Fusion

Tong Wang,Sheng Zhong,Hangzai Luo,Nailiang Kuang 한국정밀공학회 2023 International Journal of Precision Engineering and Vol.24 No.10

This article is concerned with the method of calibrating the temperature drift and random drift of Micro-Electro-Mechanical System (MEMS) gyroscope to improve the precision of MEMS gyroscope application. These methods include two steps. In the first step, the optimized BP neural network is used to establish the temperature drift error model of the MEMS gyroscope, and the B-spline method is used to improve the storage and calculation efficiency of the temperature drift calibration. In the second step, since the random drift error of a single sensor is difficult to reduce the data of multiple MEMS gyroscope sensors that have completed temperature drift calibration are fused.The error calibration evaluation indicators all use SSE (The sum of squares due to error) to compare the advantages of the proposed method.In the experimental part,the four most common MEMS chips MPU6050(including a three-axis gyroscope and accelerometer sensor) are used in the market to verify the effect of the proposed method in drift error calibration. Finally, it is proved that the data fusion of a Multi-sensor is not only significantly better than the random drift error of a single sensor. Moreover, with the increase in the number of fusion sensors, the calibration effect has a trend of gradual improvement.

Serum Insulin-Like Growth Factor Binding Protein 7 as a Potential Biomarker in the Diagnosis and Prognosis of Esophagogastric Junction Adenocarcinoma

Can-Tong Liu,Yi-Wei Xu,Hong Guo,Chao-Qun Hong,Xin-Yi Huang,Yu-Hao Luo,Shi-Han Yang,Ling-Yu Chu,En- Min Li,Yu-Hui Peng 거트앤리버 소화기연관학회협의회 2020 Gut and Liver Vol.14 No.6

Background/Aims: Esophagogastric junction adenocarcinoma (EJA) is a malignant tumor associated with high morbidity and has attracted increasing attention due to a rising incidence and low survival rate. Pathological biopsy is the gold standard for diagnosis, but noninvasive and effective tests are lacking, resulting in diagnoses at advanced stages. This study explored the diagnostic value of insulin-like growth factor binding protein 7 (IGFBP7) in EJA. Methods: A total of 120 EJA patients and 88 normal controls were recruited, and their serum levels of IGFBP7 were measured by enzymelinked immunosorbent assay. Receiver operating characteristic (ROC) curve analysis was used to assess the diagnostic value, and Pearson chi-square analysis was used to evaluate the correlation between IGFBP7 and clinical parameters. Kaplan- Meier survival analysis was carried out to assess the effect of IGFBP7 on overall survival (OS). Results: The levels of IGFBP7 were higher in both early- and late-stage EJA patients than in normal controls (p<0.001). The area under the ROC curve for EJA patients was 0.794 (95% confidence interval [CI], 0.733 to 0.854), with a cutoff value of 2.716 ng/mL, a sensitivity of 63.3% (95% CI, 54.0% to 71.8%) and a specificity of 90.9% (95% CI, 82.4% to 95.7%). For the diagnosis of early-stage EJA, the same cutoff value and specificity were obtained, but the sensitivity of IGFBP7 was 54.3% (95% CI, 36.9% to 70.8%). Patients with low IGFBP7 protein expression had lower OS than those with high expression (p=0.034). The multivariate analysis showed that IGFBP7 is an independent prognostic factor for EJA (p=0.011). Conclusions: Serum IGFBP7 acts as a potential diagnostic and prognostic marker for EJA.

원자력발전소의 직무 스트레스 측정방법에 대한 비교 연구

Meiling Luo,Yeon Ju Oh,Tong Il Jang,Yong Hee Lee 대한인간공학회 2012 대한인간공학회 학술대회논문집 Vol.2012 No.11

고신뢰도 체계인 원자력발전소(이하 원전)에서는 스트레스로 인한 인적오류는 중대한 사고를 초래할 수 있다. 따라서 직무 관련 스트레스에 대한 보다 정확한 평가가 필요하다. 스트레스 측정 사례를 살펴보면 설문, 인터뷰, 생리학적 실험, 혈액 및 타액 채취 등 다양한 평가방법들이 사용되고 있다. 원전에서의 스트레스 측정은 주로 설문기반의 주관적인 방법이 사용되고 있지만, 그 적합성에 대한 연구는 미흡하다. 본 논문에서는 기존의 직무스트레스 측정방법을 비교하고, 원전의 직무 스트레스 평가에 적합한 측정방법을 모색하였다. 새로운 방법으로 원전에서 수행되는 직무의 유형을 분류하고 유사한 타 산업에서의 직무에 적용되는 스트레스 측정법을 검토하였다. 원전 직무의 특성상 추가적인 고려사항을 합산하거나, 직무요소의 분할을 통해 원전 직무에 적용 가능한 스트레스 측정법을 제안하였다. 또한 이들을 종합하여 원전 종사자의 스트레스를 보다 정확하게 평가할 수 있도록 단계적 접근 방안을 제시하였다.

The Antibacterial Mechanism of Zn(II) Frame Supported on Alginate Membrane

Dan Luo,Ruo-Wei Lu,Cui-Juan Wang,Yan Tong,Cheng Liu,Yu-Mei Xiao,Yan-Xia Chen 대한화학회 2020 Bulletin of the Korean Chemical Society Vol.41 No.11

In order to solve the problem of antibiotic-resistant bacteria caused by excessive use of antibiotics, herein, an antibacterial membrane composed of natural sodium alginate (ALG), zeolite imidazolate skeleton (ZIF-8) and niflumic acid (NIF) was reported. The membrane serves as a versatile platform for local antibacterial. This report carried out in-depth research on the physical properties and antibacterial mechanism of the synthesized sodium alginate composite film. The data shows that the sodium alginate-based antibacterial film has a continuous antibacterial effect, and the release of antibacterial molecules can be controlled according to changes in the external environment. The results show that the complex has stronger mechanical and bacteriostatic properties. Niflumic acid and Zn(II) have synergistic antibacterial effect. The complex promotes bacterial death by hindering bacterial respiratory metabolism and destroying cell membrane structure.