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>

The Epitope Recognized by Monoclonal Antibody 2B6 in the B/C Domains of Classical Swine Fever Virus Glycoprotein E2 Affects Viral Binding to Hyperimmune Sera and Replication

( Chao Tong ),( Ning Chen ),( Xun Liao ),( Wen Qi Xie ),( De Jiang Li ),( Xiao Liang Li ),( Wei Huan Fang ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.4

Classical swine fever (CSF) is a highly contagious disease of pigs caused by CSF virus (CSFV). E2 is the major viral envelope protein of immune dominance that induces neutralizing antibodies and confers protection against CSFV infection. The B/C domains of E2 are variable among CSFV isolates, which could affect immunogenicity and binding to antibodies. We attempted to characterize the epitope recognized by a monoclonal antibody 2B6 (mAb-2B6) raised against the E2 B/C domains of the vaccine C-strain and to examine if mutations in the epitope region would affect antibody binding and viral neutralization. The epitope specific for mAb-2B6 recognition is linear, spanning five residues 774DGXNP778 in the B/C domains. The residue N777 is indispensable for the specificity. The epitope exists only in group 1 strains, but not in those of group 2. The recombinant viruses containing individual mutations on the epitope region lost the reactivity to mAb-2B6. The mutant virus RecC-N777S had low replication potential, about 10-fold decrease in the yield of progeny virus particles, whereas the mutant virus RecC-P778A reverted to proline upon continuous passaging. The mutations on the mAb-2B6 epitope region did not affect neutralization by anti-C-strain polyclonal sera from pigs. Deletion from aa774 covering the mAb-2B6 epitope, but not that from aa781, also affected binding with the polyclonal antibodies from vaccinated pigs, although the major binding region for the vaccinated antibodies is aa690-773.

Continuous Passaging of a Recombinant C-Strain Virus in PK-15 Cells Selects Culture-Adapted Variants that Showed Enhanced Replication but Failed to Induce Fever in Rabbits

( Chao Tong ),( Ning Chen ),( Xun Liao ),( Xuemei Yuan ),( Mengjiao Sun ),( Xiaoliang Li ),( Weihuan Fang ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.9

Classical swine fever virus (CSFV) is the etiologic agent of classical swine fever, a highly contagious disease that causes significant economic losses to the swine industry. The lapinized C-strain, a widely used vaccine strain against CSFV, has low growth efficiency in cell culture, which limits the productivity in the vaccine industry. In this study, a recombinant virus derived from C-strain was constructed and subjected to continuous passaging in PK-15 cells with the goal of acquiring a high progeny virus yield. A cell-adapted virus variant, RecCpp80, had nearly 1,000-fold higher titer than its parent C-strain but lost the ability to induce fever in rabbits. Sequence analysis of cell-adapted RecC variants indicated that at least six nucleotide changes were fixed in RecCpp80. Further adaption of RecCpp80 variant in swine testicle cells led to a higher virus yield without additional mutations. Introduction of each of these residues into the wild-type RecC backbone showed that one mutation, M979R (T3310G), located in the C-terminal region of E2 might be closely related to the cell-adapted phenotype. Rabbit inoculation revealed that RecCpp80+10 failed to induce fever in rabbits, whereas RecCpp40₊₁₀ caused a fever response similar to the commercial C-strain vaccine. In conclusion, the C-strain can be adapted to cell culture by introducing specific mutations in its E2 protein. The mutations in RecCpp80 that led to the loss of fever response in rabbits require further investigation. Continuous passaging of the C-strain-based recombinant viruses in PK-15 cells could enhance its in vitro adaption. The non-synonymous mutations at 3310 and 3531 might play major roles in the enhanced capacity of general virus reproduction. Such findings may help design a modified C-strain for improved productivity of commercial vaccines at reduced production cost.

The Ubiquitin-Proteasome System and F-box Proteins in Pathogenic Fungi

( Tong Bao Liu ),( Chao Yang Xue ) 한국균학회 2011 Mycobiology Vol.39 No.4

The ubiquitin-proteasome system is one of the major protein turnover mechanisms that plays important roles in the regulation of a variety of cellular functions. It is composed of E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 ubiquitin ligases that transfer ubiquitin to the substrates that are subjected to degradation in the 26S proteasome. The Skp1, Cullin, F-box protein (SCF) E3 ligases are the largest E3 gene family, in which the F-box protein is the key component to determine substrate specificity. Although the SCF E3 ligase and its F-box proteins have been extensively studied in the model yeast Saccharomyces cerevisiae, only limited studies have been reported on the role of F-box proteins in other fungi. Recently, a number of studies revealed that F-box proteins are required for fungal pathogenicity. In this communication, we review the current understanding of F-box proteins in pathogenic fungi.

Effect of Coagulating Agents on Lignin and Sugar Contents in Acid Prehydrolysis Liquor

Chao-Jun Wu,Dong-Mei Yu,Shu-Ping Li,Li-Juan Bing,Rui-Ping Tong 한국펄프·종이공학회 2016 한국펄프·종이공학회 학술발표논문집 Vol.2016 No.10

중국군사후동제도사적시대구분

동초 중국사학회 1999 中國史硏究 Vol.6 No.-

Elastostatic Stiffness Analysis of a 2PUR-PSR Overconstrained Parallel Mechanism

Chao Yang,Qiaohong Chen,Junhua Tong,Qinchuan Li 한국정밀공학회 2019 International Journal of Precision Engineering and Vol.20 No.4

The elastostatic stiffness performance of a 2PUR-PSR (S: spherical joint; U: universal joint; R: revolute joint; P: prismatic pair) overconstrained parallel mechanism with two rotational and one translational (2R1T) degrees of freedom was studied based on screw theory and strain energy. First, the actuator and constraint wrenches of the mechanism were obtained based on screw theory. Second, by considering the space composite elastic deformation of the rod (including axial tension, and shear, torsional and bending deformation), compact limb stiffness matrixes were obtained in terms of strain energy and Castigliano’s second theorem. Finally, analytic expressions for the overall stiffness matrix of the mechanism and the amplitudes of the actuator and constrained wrenches were obtained based on the virtual-work principle and the balance equation for a moving platform. The relative error between results from the analytical model and the Workbench finite element model is approximately 1.3%, which validates the effectiveness of the proposed elastostatic stiffness model. Unlike traditional stiffness evaluation index, a regional stiffness index was proposed to measure the mechanism’s stiffness performance at various working heights. Using the index, it is possible to determine the optimum stiffness region of a moving platform with known external wrenches.

Cosmogenic nuclides (10Be and 26Al) erosion rate constraints in the Badain Jaran Desert, northwest China: implications for surface erosion mechanisms and landform evolution

Tong Zhao,Wenjing Liu,Zhifang Xu,Taoze Liu,Sheng Xu,Lifeng Cui,Chao Shi 한국지질과학협의회 2019 Geosciences Journal Vol.23 No.1

Both tectonics and climate affect surface erosion and change the landform. Long-term surface erosion rates determined by in situ produced cosmogenic nuclides are useful quantitative constraints for landform evolution in geological time scale. Measurements of cosmogenic 10Be and 26Al in the granitic rocks exposed in the Badain Jaran Desert, give a mean erosion rate of 7.3 ± 2.6 m/Ma, which is an order of magnitude higher than those reported in other extremely arid regions. Tectonic activity is supposed to be the first order control on regional erosion rate by comparing the 10Be erosion rates of arid regions with different precipitation ranges and tectonic activities worldwide. However the higher erosion rates in the Badain Jaran Desert compared with other arid regions within the stable tectonic background were attributed to the wind erosion and periodically warmer and wetter climate since late Pleistocene. Besides, the estimated eroded mass flux of 7.8 × 104 t/y suggests that erosion products of bedrocks in the Badian Jaran Desert only contribute minor desert deposits, which indicates massive exogenous materials input to the desert.

Application of advanced biomaterials in photothermal therapy for malignant bone tumors

Bo Chao,Jianhang Jiao,Lili Yang,Yang Wang,Weibo Jiang,Tong Yu,Linfeng Wang,He Liu,Han Zhang,Zhonghan Wang,Minfei Wu 한국생체재료학회 2023 생체재료학회지 Vol.27 No.00

Malignant bone tumors are characterized by severe disability rate, mortality rate, and heavy recurrence rate owing to the complex pathogenesis and insidious disease progression, which seriously affect the terminal quality of patients' lives. Photothermal therapy (PTT) has emerged as an attractive adjunctive treatment offering prominent hyperthermal therapeutic effects to enhance the effectiveness of surgical treatment and avoid recurrence. Simultaneously, various advanced biomaterials with photothermal capacity are currently created to address malignant bone tumors, performing distinctive biological functions, including nanomaterials, bioceramics (BC), polymers, and hydrogels et al. Furthermore, PTT-related combination therapeutic strategies can provide more significant curative benefits by reducing drug toxicity, improving tumor-killing efficiency, stimulating anti-cancer immunity, and improving immune sensitivity relative to monotherapy, even in complex tumor microenvironments (TME). This review summarizes the current advanced biomaterials applicable in PTT and relevant combination therapies on malignant bone tumors for the first time. The multiple choices of advanced biomaterials, treatment methods, and new prospects for future research in treating malignant bone tumors with PTT are generalized to provide guidance.

Performance analysis and experimental verification of hydraulic driven axial flow pumps

Zhiting Tong,Ye Yuan,Chao Zhang,Zhimin Zhang,Yue Zhang 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.6

To investigate axial flow pumps’ performance characteristics, NUMECA software is selected to perform numerical simulation at four rotating speeds (1380, 1840, 2300, and 2530 r/min) based on the Spalart-Allmaras turbulence model. The relationship curves of flowhead and flow-pump efficiency, static pressure distribution on blade surfaces, velocity variation near the hub, and total pressure distribution at different blade heights are obtained. Results indicate that with the improvement of the rotating speed, the curves of the head and the efficiency rise and shift to the right, the pressure difference on both sides of the blade ascends, and the moment acting on the blade induced by the water flow also increases, resulting in higher head. At the rated speed of 2300 r/min, the pressure difference between the pressure side and the suction side at low flowrates increases, the minimum pressure is lower, and the anticavitation performance decreases, whereas the velocity distribution near the hub is the same at different flowrates. Moreover, the velocity is lower near the hub’s leading edge, and no influence is observed. To guarantee the reliability and comparability, experimental data are contrasted with the simulated results at the speed of 2182 r/min. At the near design condition (Q = 534.4-567 m 3 /h), the relative deviation of efficiency and head is less than 4.5 %, which is a small gap. These conclusions provide valuable reference for axial flow pumps to operate under variable speed conditions.