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Wang Y, Wu S, Yan K, Zhang R, Liu S, Ye Q, Zhou F. Preparation of Hydrophilic Hyper-Cross-Linked Polystyrene Nanospheres with Antibacterial for Improved Water Lubrication Performance. Langmuir 2024; 40:8992-9000. [PMID: 38634657 DOI: 10.1021/acs.langmuir.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The present study utilizes styrene as a raw material to prepare hyper-cross-linked polystyrene nanospheres (HPSs) through the Friedel-Crafts reaction, establishing stable covalent bond structures within the polymer chains. The hydrophilic polystyrene nanospheres─TMA@SHPSs were successfully synthesized via sulfonation and ion exchange reactions, demonstrating exceptional properties in reducing friction and wear. Compared with pure water, the addition of 4.0 wt % TMA@SHPSs results in a 62.2% reduction in the friction coefficient, accompanied by a significant decrease to 1.17 × 105 μm3 in wear volume. The results demonstrate that TMA@SHPSs, as water-based lubrication additives, generate composite protective films (tribo-chemical protective films and physical protective films) during the friction process, which effectively prevents direct contact between the friction pairs and achieves remarkable antifriction and antiwear effects. The results of the antimicrobial activity test indicate that TMA@SHPSs demonstrate exceptional antibacterial efficacy due to the bacteriostatic effect induced by hydration and the bactericidal properties of quaternary ammonium cations.
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Affiliation(s)
- Yixin Wang
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Shihan Wu
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Kaige Yan
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Rui Zhang
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Shujuan Liu
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Qian Ye
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Feng Zhou
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
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Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Nat Plants 2024; 10:374-380. [PMID: 38413824 DOI: 10.1038/s41477-024-01640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhihui Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Wei Chen
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kaige Yan
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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Xin J, Zhou Y, Qiu Y, Geng H, Wang Y, Song Y, Liang J, Yan K. Structural insights into AtABCG25, an angiosperm-specific abscisic acid exporter. Plant Commun 2024; 5:100776. [PMID: 38050355 PMCID: PMC10811370 DOI: 10.1016/j.xplc.2023.100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/06/2023]
Abstract
Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and stress responses and confers fitness benefits over ecological and evolutionary timescales in terrestrial plants. Cellular ABA level is regulated by complex processes, including biosynthesis, catabolism, and transport. AtABCG25 is the first ABA exporter identified through genetic screening and affects diverse ABA responses. Resolving the structural basis of ABA export by ABCG25 is critical for further manipulations of ABA homeostasis and plant fitness. We used cryo-electron microscopy to elucidate the structural dynamics of AtABCG25 and successfully characterized different states, including apo AtABCG25, ABA-bound AtABCG25, and ATP-bound AtABCG25 (E232Q). Notably, AtABCG25 forms a homodimer that features a deep, slit-like cavity in the transmembrane domain, and we precisely characterized the critical residues in the cavity where ABA binds. ATP binding triggers closure of the nucleotide-binding domains and conformational transitions in the transmembrane domains. We show that AtABCG25 belongs to a conserved ABCG subfamily that originated during the evolution of angiosperms. This subfamily neofunctionalized to regulate seed germination via the endosperm, in concert with the evolution of this angiosperm-specific, embryo-nourishing tissue. Collectively, these findings provide valuable insights into the intricate substrate recognition and transport mechanisms of the ABA exporter AtABCG25, paving the way for genetic manipulation of ABA homeostasis and plant fitness.
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Affiliation(s)
- Jian Xin
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yeling Zhou
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yichun Qiu
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - He Geng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuzhu Wang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi Song
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Jiansheng Liang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Kaige Yan
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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Wang Y, Zhu J, Guo D, Yan K, Lu L, Wang S, Jin D, Ye X, Wang Q. Deep Learning for Automatic Prediction of Lymph Node Station Metastasis in Esophageal Cancer Patients from Contrast-Enhanced CT. Int J Radiat Oncol Biol Phys 2023; 117:S55. [PMID: 37784523 DOI: 10.1016/j.ijrobp.2023.06.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The diagnosis of lymph node (LN) metastasis in computed tomography (CT) is an essential yet challenging task in esophageal cancer staging and treatment planning. Although criteria (e.g., RECIST, morphological/texture features) are proposed to predict LN metastasis, the diagnostic accuracy remains low with sensitivity <50% and specificity <75%, as reported in previous studies. Deep learning (DL) has the potential to address this issue by learning from large-scale labeled data. However, due to the practical surgery procedure in lymph node dissection, it is difficult to pair the metastasis of individual LN reported in the pathology report to the LN instance found in the CT image. Hence, in this study, we first use pathology reports to determine the LNS metastasis, then develop a multiple instance deep learning (MIDL) model to predict lymph node station (LNS) metastasis. MATERIALS/METHODS We collected 1200 esophageal cancer patients with preoperative contrast-enhanced CT before surgery. A recently developed automatic mediastinal LNS segmentation model was first applied to segment LNS of 1 to 8 based on the IASLC protocol. For each LNS, the local CT region of interest (ROI) was cropped to generate a station-wise CT patch, where the LNS was labeled as metastatic if at least one metastatic LN was indicated in the pathology report. Using the station-wise CT patch and LNS label, we train a 3D MIDL model, MobileNetV3, to predict LNS metastasis. To better provide the LN position priors in MIDL, LN instances (with a short axis >4mm) were also segmented using an automatic LN detection algorithm and were added to the MIDL model as an auxiliary input. Five-fold cross-validation was conducted to evaluate the MIDL performance. RESULTS The MIDL model's performance is summarized in Table 1. The MIDL model incorporating an additional LN instance mask demonstrated a superior overall AUC of 0.7539, surpassing the model without the LN mask input by 2.93%. The specificity was evaluated at a threshold resulting in a recall of 0.7, and the best model outperformed the CT input model in terms of specificity by 2.11%. This highlights the value of including the LN position prior to the MIDL model. Notably, when a threshold was set to result in a specificity of 75%, the best MIDL model demonstrated a significantly higher recall compared to the previously reported clinical diagnostic recall (39.7% vs. 63.21%). CONCLUSION We developed a MIDL classification model to predict LNS metastasis using CT scans of 1200 patients. Our findings suggest that the MIDL model can substantially improve LNS metastasis prediction and has the potential to play an essential role in cancer staging, treatment planning, and prognostic analysis.
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Affiliation(s)
- Y Wang
- Alibaba Group (US) Inc., New York, NY
| | - J Zhu
- Department of Radiation Oncology, Sichuan Cancer Hospital and Institution, Sichuan Cancer Center, Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, China
| | - D Guo
- Alibaba Group (US) Inc., New York, NY
| | - K Yan
- Alibaba DAMO Academy, Beijing, China
| | - L Lu
- Alibaba Group (US) Inc., New York, NY
| | - S Wang
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, China
| | - D Jin
- Alibaba Group (US) Inc., New York, NY
| | - X Ye
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Q Wang
- Department of Radiation Oncology, Sichuan Cancer Hospital and Institution, Sichuan Cancer Center, Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, China
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Zhang XN, Yan K, You XD, Li JH, Zhang N, Wang GY, Liao MZ, Ma W. [Acceptance of pre-exposure prophylaxis and post-exposure prophylaxis against HIV and related factors in men who have sex with men in Shandong Province]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1352-1357. [PMID: 37743265 DOI: 10.3760/cma.j.cn112338-20230202-00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Objectives: To understand the use of pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) and related factors in men who have sex with men (MSM) in Shandong Province, and provide reference for the promotion of PrEP and PEP in MSM. Methods: From April to July in 2022, MSM were recruited from 7 sentinel surveillance sites in Shandong Province for a questionnaire survey, and the sample size of each city site was 400. The information about sociodemographic characteristics, sexual behaviors, the uses of PrEP and PEP and others were collected from the MSM, and blood samples were collected from them for HIV and syphilis testing. Results: A total of 2 815 MSM were investigated, the majority of them were aged less than 30 years (55.7%, 1 569/2 815), unmarried (68.6%, 1 931/2 815) and had education background of college and above (56.5%, 1 590/2 815). Only 9.2% (258/2 815) had used PrEP and 10.8% (305/2 815) had used PEP. Multivariate logistic regression showed that factors associated with high likelihood of PrEP use in MSM included age ≤30 years (aOR=4.04, 95%CI:1.25-13.01), self-perceived lower risk of HIV infection (aOR=1.76, 95%CI:1.16-2.68), group sex and commercial sex in the past six months (aOR=1.51, 95%CI: 1.10-2.09; aOR=1.69, 95%CI: 1.16-2.47), new-type drug use (aOR=1.53, 95%CI: 1.11-2.11), receiving peer education (aOR=1.56, 95%CI: 1.03-2.37), other people using PrEP (aOR=3.29, 95%CI: 2.48-4.36), and being HIV negative (aOR=8.40, 95%CI:1.12-63.12). Factor associated with low likelihood of PrEP use in MSM was anal sex with casual partner (aOR=0.67, 95%CI:0.49-0.90). Factors associated with high likelihood of PEP use in MSM included age under 50 years (≤30 years old: aOR=2.41, 95%CI:1.02-5.69; 31-49 years old: aOR=3.33, 95%CI:1.42-7.85), no self-perceived risk for HIV infection (aOR=1.87, 95%CI:1.12-3.11), group sex in the past six months (aOR=1.68, 95%CI:1.23-2.29), new-type drug use (aOR=3.86, 95%CI:2.94-5.07) and receiving no peer education (aOR=1.54, 95%CI:1.12-2.12). Conclusions: In Shandong, a higher proportion of MSM used PrEP and PEP. Peer education and self-perceived HIV infection risk education should be strengthened to increase the rates of PrEP and PEP use in MSM.
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Affiliation(s)
- X N Zhang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, China
| | - K Yan
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - X D You
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - J H Li
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - N Zhang
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - G Y Wang
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - M Z Liao
- Department of AIDS/STD Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Ji'nan 250014, China
| | - W Ma
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, China
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Ma T, Wang L, Chai A, Liu C, Cui W, Yuan S, Wing Ngor Au S, Sun L, Zhang X, Zhang Z, Lu J, Gao Y, Wang P, Li Z, Liang Y, Vogel H, Wang YT, Wang D, Yan K, Zhang H. Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42. Nat Commun 2023; 14:3424. [PMID: 37296152 PMCID: PMC10256776 DOI: 10.1038/s41467-023-39218-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
ClC-2 transports chloride ions across plasma membranes and plays critical roles in cellular homeostasis. Its dysfunction is involved in diseases including leukodystrophy and primary aldosteronism. AK-42 was recently reported as a specific inhibitor of ClC-2. However, experimental structures are still missing to decipher its inhibition mechanism. Here, we present cryo-EM structures of apo ClC-2 and its complex with AK-42, both at 3.5 Å resolution. Residues S162, E205 and Y553 are involved in chloride binding and contribute to the ion selectivity. The side-chain of the gating glutamate E205 occupies the putative central chloride-binding site, indicating that our structure represents a closed state. Structural analysis, molecular dynamics and electrophysiological recordings identify key residues to interact with AK-42. Several AK-42 interacting residues are present in ClC-2 but not in other ClCs, providing a possible explanation for AK-42 specificity. Taken together, our results experimentally reveal the potential inhibition mechanism of ClC-2 inhibitor AK-42.
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Grants
- National Natural Science Foundation of China (National Science Foundation of China)
- National Science and Technology Innovation 2030 Major Program (No. 2022ZD0211900)
- the Science and Technology Innovation Committee of Shenzhen(No. JCYJ20200109150700942), the Key-Area Research and Development Program of Guangdong Province (2019B030335001), the Shenzhen Fund for Guangdong Provincial High Level Clinical Key Specialties (No. SZGSP013), and the Shenzhen Key Medical Discipline Construction Fund (No. SZXK042)
- The Shenzhen Key Laboratory of Computer Aided Drug Discovery, Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China, Funding number: ZDSYS20201230165400001. The Chinese Academy of Science President’s International Fellowship Initiative (PIFI) (No. 2020FSB0003), Guangdong Retired Expert (granted by Guangdong Province), National Overseas High Level Talent Introduction Plan-Foreign Expert from Organization Department of the CPC Central Committee (1000 talent project), Shenzhen Pengcheng Scientist, NSFC-SNSF Funding (No. 32161133022), AlphaMol & SIAT Joint Laboratory, Shenzhen Government Top-talent Working Funding and Guangdong Province Academician Work Funding.
- NSFC-Guangdong Joint Fund-U20A6005, Shenzhen Key Laboratory of Translational Research for Brain Diseases (ZDSYS20200828154800001)
- Shenzhen Science and Technology Program (No. JCYJ20220530115214033 and No. KQTD20210811090115021)
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Affiliation(s)
- Tao Ma
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Lei Wang
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Anping Chai
- Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, Shenzhen, Guangdong, China
| | - Chao Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Wenqiang Cui
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuguang Yuan
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Shannon Wing Ngor Au
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liang Sun
- Shenzhen Shuli Tech Co., Ltd, 518126, Shenzhen, Guangdong, China
| | - Xiaokang Zhang
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, Shenzhen, Guangdong, China
- Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China
| | - Zhenzhen Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Jianping Lu
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020, China
| | - Yuanzhu Gao
- Cryo-EM Facility Center, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Peiyi Wang
- Cryo-EM Facility Center, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Zhifang Li
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020, China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Yu Tian Wang
- Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China.
| | - Daping Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518000, Shenzhen, China.
| | - Kaige Yan
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Huawei Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China.
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7
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Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J. Molecular basis of the plant ROS1-mediated active DNA demethylation. Nat Plants 2023; 9:271-279. [PMID: 36624257 DOI: 10.1038/s41477-022-01322-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases.
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Affiliation(s)
- Xuan Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, China
| | - Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Kaige Yan
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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8
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Wijayawardena MAA, Yan K, Liu Y, Naidu R. Can the mouse model successfully predict mixed metal(loid)s bioavailability in humans from contaminated soils? Chemosphere 2023; 311:137113. [PMID: 36356801 DOI: 10.1016/j.chemosphere.2022.137113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Mouse models have been employed by many scientific research groups worldwide to predict the bioavailability of metal (loid)s and other chemicals in humans. Their suitability for predicting mixed metal (loid) bioavailability has been questioned and debated for decades by many research teams. In this study soils contaminated by lead (Pb) and arsenic (As), either in the field or by spiking in the laboratory, were used in bioavailability and bioaccessibility tests. The spiked soils were aged for more than a year prior to testing to achieve steady state and eliminate soil ageing effects, as reported in previous research. The bioavailability of, firstly, Pb in the presence of As and secondly, As in the presence of Pb was determined using mice. Furthermore, bioaccessibility was determined using a range of in vitro methods: relative bioaccessibility leaching procedure (RBALP), the Unified Bioaccessibility Research Group Europe (BARGE) method (UBM) gastric and intestinal phases, and the National Institute for Public Health and the Environment (RIVM) gastric and intestinal phases. The correlations between Pb and As bioavailability and their in vitro bioaccessibility when they were present in mixtures were analysed. The results indicated that the bioavailability of Pb in mice kidney tissues significantly correlated with bioaccessibility of Pb in RBALP (p < 0.01), UBM gastric (p < 0.01) and intestinal phases (p < 0.01) and RIVM gastric phases when Pb is present in metal (loid) mixtures. Results of the current study reveal that the RBALP, and UBM gastric and intestinal phase were by far the best methods for predicting the RB of Pb when it is present in metal (loid) mixtures. Consequently, the mouse model can successfully explain the in vivo in vitro correlation (IVIVC) of Pb when it is present in metal (loid) mixtures. However, we did find that a mouse model may not be the best one to explain the IVIVC of As when it is present in metal (loid) mixtures.
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Affiliation(s)
- M A A Wijayawardena
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - K Yan
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Y Liu
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building University of Newcastle, Callaghan, NSW, 2308, Australia
| | - R Naidu
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building University of Newcastle, Callaghan, NSW, 2308, Australia.
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Niu F, Liu Y, Sun K, Xu S, Dong J, Yu C, Yan K, Wei Z. Autoinhibition and activation mechanisms revealed by the triangular-shaped structure of myosin Va. Sci Adv 2022; 8:eadd4187. [PMID: 36490350 PMCID: PMC9733927 DOI: 10.1126/sciadv.add4187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and autoinhibited state, which can be relieved by cargo binding. The molecular mechanisms governing the autoinhibition and activation of MyoVa remain unclear. Here, we report the cryo-electron microscopy structure of the two full-length, closed MyoVa heavy chains in complex with 12 calmodulin light chains at 4.78-Å resolution. The MyoVa adopts a triangular structure with multiple intra- and interpolypeptide chain interactions in establishing the closed state with cargo binding and adenosine triphosphatase activity inhibited. Structural, biochemical, and cellular analyses uncover an asymmetric autoinhibition mechanism, in which the cargo-binding sites in the two MyoVa heavy chains are differently protected. Thus, specific and efficient MyoVa activation requires coincident binding of multiple cargo adaptors, revealing an intricate and elegant activity regulation of the motor in response to cargos.
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Affiliation(s)
- Fengfeng Niu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yong Liu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- SUSTech-HIT Joint PhD Program, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Kang Sun
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shun Xu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jiayuan Dong
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Cong Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China
| | - Kaige Yan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhiyi Wei
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Zhang K, Jiang SY, Yan K, Zhang P, Gao RW, Zhao J, Hu XJ, Liu Q, Ge YL, Wang XS, Chen WM, Shi Y, Zhai XW, Cao Y. [Clinical characteristics of 16 neonates infected with SARS-CoV-2 during Omicron variant outbreak]. Zhonghua Er Ke Za Zhi 2022; 60:1158-1162. [PMID: 36319150 DOI: 10.3760/cma.j.cn112140-20220617-00561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To analyze the clinical characteristics of the neonates infected with SARS-CoV-2 during the Omicron outbreak in Shanghai 2022. Methods: In this retrospective case series study, all the 16 neonates with SARS-CoV-2 Omicron infection who were admitted to the neonatal unit in Shanghai Public Health Clinical Center from March 1st to May 31st, 2022 were enrolled. Their epidemiological history, clinical manifestations, nucleic acid cycle threshold (Ct) value and outcomes were analyzed. Based on maternal vaccination, they were divided into vaccinated group and unvaccinated group. Rank sum test and Chi-square test were used for the comparison between the groups. Results: Among the 16 neonates, 10 were male, and 6 were female. All the infants were full-term. The infection was confirmed at the age of 12.5 (8.0, 20.5) days. All the neonates had a history of exposure to infected family members, and thus horizontal transmission was the primary mode. Four infants were asymptomatic, 12 were symptomatic, and there were no severe or critical cases. The most common clinical manifestation was fever (11 cases), with the highest temperature of 38.1 (37.9, 38.3) ℃ and a course of 1-5 days. Other clinical manifestations included nasal obstruction (3 cases), runny nose (2 cases), cough (2 cases), poor feeding (2 cases), vomiting (1 case), and mild tachypnea (1 case). The complete blood counts of all neonates were within the normal range, and the C-reactive protein increased slightly in 1 infant. Chest imaging was performed in 2 infants, showing mild focal exudative changes. Nucleic acid turned negative (Ct value ≥35) within 7-15 days after diagnosis. All neonates fully recovered after supportive treatment, and the length of hospitalization was 13 (10, 14) days. In the telephone follow-up 2 weeks after discharge for all 16 cases, no infant showed reoccurrence of clinical manifestations or nucleic acid reactivation. Maternal vaccination was not significantly correlated with symptomatic infection or the persistence of positive nucleic acid result in neonates (all P>0.05). Conclusions: Horizontal transmission is the primary mode for neonatal SARS-CoV-2 Omicron infection. Neonatal infections are usually mild or asymptomatic, with good short-term outcomes. And their clinical manifestations and laboratory examinations are nonspecific.
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Affiliation(s)
- K Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - S Y Jiang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - K Yan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - P Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - R W Gao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - J Zhao
- Department of Neonatology, Shanghai Public Health Clinical Center, Shanghai 201508, China
| | - X J Hu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Q Liu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y L Ge
- Department of Infectious Diseases,Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X S Wang
- Department of Infectious Diseases,Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - W M Chen
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y Shi
- Department of Rheumatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X W Zhai
- Department of Hematology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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Li SJ, Zhang L, Yuan H, Zhang XB, Wang CQ, Liu GB, Gu Y, Yang TL, Zhu XT, Zhai XW, Shi Y, Jiang SY, Zhang K, Yan K, Zhang P, Hu XJ, Liu Q, Gao RW, Zhao J, Zhou JG, Cao Y, Li ZH. [Management and short-term outcomes of neonates born to mothers infected with SARS-CoV-2 Omicron variant]. Zhonghua Er Ke Za Zhi 2022; 60:1163-1167. [PMID: 36319151 DOI: 10.3760/cma.j.cn112140-20220613-00545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To summarize the management and short-term outcomes of neonates delivered by mothers infected with SARS-CoV-2 Omicron variant. Methods: A retrospective study was performed on 158 neonates born to mothers infected with SARS-CoV-2 Omicron variant admitted to the isolation ward of Children's Hospital of Fudan University from March 15th, 2022 to May 30th, 2022. The postnatal infection control measures for these neonates, and their clinical characteristics and short-term outcomes were analyzed. They were divided into maternal symptomatic group and maternal asymptomatic group according to whether their mothers had SARS-CoV-2 symptoms. The clinical outcomes were compared between the 2 groups using Rank sum test and Chi-square test. Results: All neonates were under strict infection control measures at birth and after birth. Of the 158 neonates, 75 (47.5%) were male. The gestational age was (38+3±1+3) weeks and the birth weight was (3 201±463)g. Of the neonates included, ten were preterm (6.3%) and the minimum gestational age was 30+1 weeks. Six neonates (3.8%) had respiratory difficulty and 4 of them were premature and required mechanical ventilation. All 158 neonates were tested negative for SARS-COV-2 nucleic acid by daily nasal swabs for the first 7 days. A total of 156 mothers (2 cases of twin pregnancy) infected with SARS-CoV-2 Omicron variant, the time from confirmed SARS-CoV-2 infection to delivery was 7 (3, 12) days. Among them, 88 cases (56.4%) showed clinical symptoms, but none needed intensive care treatment. The peripheral white blood cell count of the neonates in maternal symptomatic group was significantly higher than that in maternal symptomatic group (23.0 (18.7, 28.0) × 109 vs. 19.6 (15.4, 36.6) × 109/L, Z=2.44, P<0.05). Conclusions: Neonates of mothers infected with SARS-CoV-2 Omicron variant during third trimester have benign short-term outcomes, without intrauterine infection through vertical transmission. Strict infection control measures at birth and after birth can effectively protect these neonates from SARS-CoV-2 infection.
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Affiliation(s)
- S J Li
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - L Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - H Yuan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X B Zhang
- Department of Respiratory Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - C Q Wang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - G B Liu
- Department of Medical Affairs, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y Gu
- Department of Nursing, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - T L Yang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X T Zhu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X W Zhai
- Department of Hematology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y Shi
- Department of Rheumatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - S Y Jiang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - K Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - K Yan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - P Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - X J Hu
- Department of Nursing, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Q Liu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - R W Gao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - J Zhao
- Department of Neonatology, Shanghai Public Health Clinical Center, Shanghai 201508, China
| | - J G Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Y Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Z H Li
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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Wang LN, Yan K, Yu HY, Huang PX, Wang GY, Liao MZ, Ma W. [Analysis of related factors of new-type drug use and recent HIV infection among men who have sex with men in Shandong province]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:1632-1638. [PMID: 36456496 DOI: 10.3760/cma.j.cn112338-20220516-00421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Objective: To understand the related factors of new-type drug use and recent HIV infection among men who have sex with men (MSM), and provide a reference for formulating targeted strategies for HIV/AIDS prevention and control. Methods: MSM were recruited in sentinel surveillance sites of nine cities in Shandong province from April to July 2021, with a sample size of 400 in each city. A face-to-face questionnaire was conducted to collect demographic characteristics, high-risk behaviors, acceptance of HIV intervention services, etc. Blood samples were collected for HIV and syphilis antibodies detection. Limiting-antigen avidity enzyme immunoassay (LAg-Avidity EIA) was used to detect recent HIV infection, and the rate of recent HIV infection was calculated. Results: 3 624 MSM were under study with the following characteristics as: aged (32.70±9.33) years old, the aged 30 and above (59.52%, 2 157/3 624), with high school education or below (55.99%, 2 029/3 624), being unmarried/divorced/widowed (57.70%, 2 091/3 624) and as having homosexual orientation (86.26%, 3 126/3 624) accounted for the more mainly. Of 32.95% (1 194/3 624) had same-sex unprotected anal sex in recent six months; 27.48% (993/3 613) ever used new-type drugs, and the HIV antibody positive rate was 3.12% (113/3 624). The recent HIV infection rate appeared as 2.61% (95%CI: 1.73%-3.49%). The multivariable logistic regression analysis indicated that the related factors of new-type drug use were unmarried/divorced/widowed (compared with being married/cohabitating, aOR=1.43, 95%CI: 1.22-1.69), educational level of college or above (compared with educational level of high school or below, aOR=1.47, 95%CI: 1.25-1.72), mainly through the Internet/dating software to find male sex partners (compared with mainly through bars/baths/parks and other places to find male sex partners, aOR=1.76, 95%CI: 1.41-2.19). Those who had unprotected anal sex in the last six months (compared with no unprotected anal sex, aOR=1.33, 95%CI: 1.13-1.57), had sexually transmitted diseases in the past year (compared with no sexually transmitted disease, aOR=2.77, 95%CI: 2.04-3.76) were more likely to use new-type drugs. The multinominal logistic regression showed that MSM who had unprotected anal sex in the last six months (compared with no unprotected anal sex, aOR=2.51, 95%CI: 1.25-5.01) or did not receive HIV intervention services in the past year (compared with those who received HIV intervention services, aOR=3.89, 95%CI: 1.30-11.60), were syphilis positive (compared with syphilis negative, aOR=8.18, 95%CI: 2.98-22.48), used new-type drugs (compared with those who did not use new-type drugs, aOR=4.75, 95%CI: 2.32-9.70) had a higher risk of recent HIV infection. Conclusions: New-type drugs have been widely used in MSM in Shandong province. The abuse of new-type drugs increases the risk of recent HIV infection.
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Affiliation(s)
- L N Wang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, China
| | - K Yan
- Department of AIDS/STD Control and Prevention, Shandong Center for Disease Control and Prevention, Ji'nan 250014, China
| | - H Y Yu
- Department of AIDS/STD Control and Prevention, Shandong Center for Disease Control and Prevention, Ji'nan 250014, China
| | - P X Huang
- Department of AIDS/STD Control and Prevention, Shandong Center for Disease Control and Prevention, Ji'nan 250014, China
| | - G Y Wang
- Department of AIDS/STD Control and Prevention, Shandong Center for Disease Control and Prevention, Ji'nan 250014, China
| | - M Z Liao
- Department of AIDS/STD Control and Prevention, Shandong Center for Disease Control and Prevention, Ji'nan 250014, China
| | - Wei Ma
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, China
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del Angel Zuvirie C, van der Drift L, Yan K, Price L, Bange H. ePS6.03 Enabling RNA-based gene modification in high-throughput screenings using cystic fibrosis patient-derived organoids. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00330-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yan K, Yuan ZH, Zheng Y, Wang J. Clinical outcomes in patients with infrapopliteal arterial occlusive disease treated by lower extremity bypass surgery: a comparison of atherosclerosis and thromboangiitis obliterans. Eur Rev Med Pharmacol Sci 2022; 26:4228-4237. [PMID: 35776021 DOI: 10.26355/eurrev_202206_29059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE Surgical bypasses are commonly utilized for the treatment of infrapopliteal arterial occlusive disease resulting from atherosclerosis (ASO) and thromboangiitis obliterans (TAO), especially when endovascular procedures fail. The aim of this study is to compare the in-hospital and follow-up outcomes of ASO and TAO patients treated with infrapopliteal bypass surgery. PATIENTS AND METHODS A total of 32 infrapopliteal bypasses were analyzed in 18 TAO patients and 14 ASO patients. Preoperative and postoperative arterial Doppler ultrasonography was performed in all patients. The ankle-brachial index (ABI) was calculated preoperatively and postoperatively in all cases. All patients were followed-up for at least one year and clinical outcomes were recorded. RESULTS Within 1-7 days postoperatively, 4 grafts in TAO patients occluded; nevertheless, 1 graft occlusion occurred in ASO patients. Patency rates at in-hospital were 77.8% and 92.9% in TAO and ASO patients, respectively. In 27 patients with successful infrapopliteal bypass, ABIs and crural peak arterial flow velocities significantly increased at 1-7 days postoperatively. During the period of follow-up, 6 graft occlusions occurred in TAO patients, and one ASO patient died of myocardial infarction. Patency rates at follow-up were 44.5% and 85.7% in TAO and ASO patients. For TAO patients with graft failure, ABIs at follow-up did not statistically differ from those postoperatively; however, they were significantly higher than those preoperatively. CONCLUSIONS Infrapopliteal bypass surgery is a feasible and effective procedure for ASO and TAO patients. Patency rates are lower in TAO than those in ASO during the in-hospital and follow-up period. However, TAO patients had the ischemic symptom relief and the improvement in ABI despite graft occlusion one year postoperatively.
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Affiliation(s)
- K Yan
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Liu J, Yang Y, Yan K, Zhu C, Jiang M. [Development and validation of nomograms for predicting stroke recurrence after firstepisode ischemic stroke]. Nan Fang Yi Ke Da Xue Xue Bao 2022; 42:130-136. [PMID: 35249880 DOI: 10.12122/j.issn.1673-4254.2022.01.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To explore the risk factors for recurrence in first-episode ischemic stroke survivors and establish a model for predicting stroke recurrence using a nomogram. METHODS We collected the data from a total of 821 first-episode ischemic stroke survivors admitted in the Department of Neurology, West China Hospital, Sichuan University from January, 2010 to December, 2018. R software was used for random sampling of the patients, and 70% of the patients were included in the training set to establish the prediction model and 30% were included in the validation set. Cox proportional risk regression model was used to analyze the factors affecting stroke recurrence, and R software rms package was used to construct the histogram and establish the visual prediction model. C-index and calibration curve were used to evaluate the performance of the model for predicting stroke occurrence. RESULTS Among the 821 survivors, the recurrence rate was 16.81% at 3 years and 19.98% at 5 years. Multivariate analysis of the training set by Cox regression model showed that an age over 65 years (HR= 2.596, P=0.024), an age of 45-64 years (HR=2.510, P=0.006), a mRS score beyond 3 (HR=2.284, P=0.004) and a history of coronary heart disease (HR=1.353, P=0.034) were all risk factors for stroke recurrence. The C-indexes of the nomogram for the 3-and 5-year relapse prediction model were 0.640 and 0.671, respectively. CONCLUSION Age, mRS score and peripheral vascular disease are the factors affecting stroke recurrence in first-episode ischemic stroke survivors, and the nomogram has a high discrimination and predictive power for predicting ischemic stroke recurrence.
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Affiliation(s)
- J Liu
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Y Yang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - K Yan
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - C Zhu
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - M Jiang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
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Zhu Z, Ho T, Jin D, Yan K, Ye X, Guo D, Xiao J, Lu L, Hung T, Pai P, Tseng C. Deep Learning Based Lymph Node Gross Tumor Volume Detection via Distance-Guided Gating Using CT and 18F-FDG PET in Esophageal Cancer Radiotherapy. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Y, Ding X, Meng Z, Chen M, Zheng X, Cai M, Wu J, Chang Y, Zhang Q, Jin L, Qian D, Li X, Wu M, Yan K, Lu Y, Zhang X. A Genome-wide association study identified HLA-C associated with the effectiveness of methotrexate for psoriasis treatment. J Eur Acad Dermatol Venereol 2021; 35:e898-e900. [PMID: 34310775 DOI: 10.1111/jdv.17544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Y Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Ding
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Z Meng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Chen
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Zheng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Cai
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - J Wu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Y Chang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Q Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - L Jin
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - D Qian
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Li
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Wu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - K Yan
- Institute of Dermatology and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Y Lu
- Institute of Dermatology and Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - X Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
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18
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Yatskevich S, Kroonen JS, Alfieri C, Tischer T, Howes AC, Clijsters L, Yang J, Zhang Z, Yan K, Vertegaal ACO, Barford D. Molecular mechanisms of APC/C release from spindle assembly checkpoint inhibition by APC/C SUMOylation. Cell Rep 2021; 34:108929. [PMID: 33789095 PMCID: PMC8028313 DOI: 10.1016/j.celrep.2021.108929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls cell cycle transitions. Its regulation by the spindle assembly checkpoint (SAC) is coordinated with the attachment of sister chromatids to the mitotic spindle. APC/C SUMOylation on APC4 ensures timely anaphase onset and chromosome segregation. To understand the structural and functional consequences of APC/C SUMOylation, we reconstituted SUMOylated APC/C for electron cryo-microscopy and biochemical analyses. SUMOylation of the APC/C causes a substantial rearrangement of the WHB domain of APC/C's cullin subunit (APC2WHB). Although APC/CCdc20 SUMOylation results in a modest impact on normal APC/CCdc20 activity, repositioning APC2WHB reduces the affinity of APC/CCdc20 for the mitotic checkpoint complex (MCC), the effector of the SAC. This attenuates MCC-mediated suppression of APC/CCdc20 activity, allowing for more efficient ubiquitination of APC/CCdc20 substrates in the presence of the MCC. Thus, SUMOylation stimulates the reactivation of APC/CCdc20 when the SAC is silenced, contributing to timely anaphase onset.
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Affiliation(s)
- Stanislau Yatskevich
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jessie S Kroonen
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Claudio Alfieri
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas Tischer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anna C Howes
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Linda Clijsters
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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19
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Brüser R, Dlapa C, Henn JM, Yan K. Full Angle Dependence of the Four-Loop Cusp Anomalous Dimension in QED. Phys Rev Lett 2021; 126:021601. [PMID: 33512221 DOI: 10.1103/physrevlett.126.021601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/06/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The angle-dependent cusp anomalous dimension governs divergences coming from soft gluon exchanges between heavy particles, such as top quarks. We focus on the matter-dependent contributions and compute the first truly nonplanar terms. They appear at four loops and are proportional to a quartic Casimir operator in color space. Specializing our general gauge theory result to U(1), we obtain the full QED four-loop angle-dependent cusp anomalous dimension. While more complicated functions appear at intermediate steps, the analytic answer depends only on multiple polylogarithms with singularities at fourth roots of unity. It can be written in terms of four rational structures and contains functions of up to maximal transcendental weight seven. Despite this complexity, we find that numerically the answer is tantalizingly close to the appropriately rescaled one-loop formula, over most of the kinematic range. We take several limits of our analytic result, which serves as a check and allows us to obtain new, power-suppressed terms. In the antiparallel lines limit, which corresponds to production of two massive particles at threshold, we find that the subleading power correction vanishes. Finally, we compute the quartic Casimir contribution for scalars in the loop. Taking into account a supersymmetric decomposition, we derive the first nonplanar corrections to the quark antiquark potential in maximally supersymmetric gauge theory.
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Affiliation(s)
- R Brüser
- Theoretische Physik 1, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - C Dlapa
- Max-Planck-Institut für Physik, Werner-Heisenberg-Institut, 80805 München, Germany
| | - J M Henn
- Max-Planck-Institut für Physik, Werner-Heisenberg-Institut, 80805 München, Germany
| | - K Yan
- Max-Planck-Institut für Physik, Werner-Heisenberg-Institut, 80805 München, Germany
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20
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Zhu SC, Li QF, Zhang XY, Deng WZ, Song CY, Wang X, Yan K. [Clinical outcomes of different irradiation ranges in definitive intensity-modulated radiotherapy for esophageal cancer]. Zhonghua Zhong Liu Za Zhi 2020; 42:1040-1047. [PMID: 33342161 DOI: 10.3760/cma.j.cn112152-20191225-00842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the therapeutic efficacy and safety of elective nodal irradiation (ENI) and involved field irradiation (IFI) in intensity-modulated radiotherapy for esophageal cancer, screen the patients suitable to undergo ENI radiotherapy and provide evidences for individual treatment of esophageal cancer. Methods: A retrospective analysis was performed on the clinical data of 924 patients with esophageal cancer who received definitive intensity-modulated radiotherapy in our hospital from January 2006 to December 2015. Among them, 272 patients received ENI and the other 652 patients received IFI. The clinicopathologic characteristics of 272 cases in ENI group and 652 cases in IFI group, who were recruited according to the balance of propensity score matching method, were compared. The Kaplan-Meier method was used to calculate 1-year, 3-years and 5-years local-regional failure-free survival (LRFFS), progression-free survival (PFS) and overall survival (OS) rates. The univariate and multivariate analysis of prognostic factors were also determined by Cox proportional hazard model and Long-rank test. Results: The clinicopathologic characteristics of these two group were not significantly different (P>0.05). The median follow-up time was 85.9 months and the follow-up rate was 95.9%. The 1-year, 3-years, 5-years PFS rates of the ENI groups were 65.3%, 31.7%, 18.4%, respectively, higher than 54.0%, 20.9%, 12.7% of the IFI group (P=0.001). The 1-year, 3-years, 5-years OS rates of the ENI groups were 79.0%, 43.7%, 24.9%, respectively, higher than 75.0%, 31.8%, 17.2% of the IFI group (P=0.003). In multivariate analysis, the sex, tumor volume, N stage and radiation field were independent factors for PFS and OS (P<0.05). Subgroup analysis showed that patients with male, age≤66 year, cervical and upper-thoracic location, tumor length≤6 cm, T1-2 stage, N0-1 stage, Ⅰ-Ⅱ stage, tumor volume≤50 cm(3), dosage>60 Gy and≤2 cycles of chemotherapy in the ENI group had a better survival rate than those in the IFI group (P<0.05). The total failure rate, local-regional failure rate in ENI group were significantly lower than those of IFI group (P=0.001, P=0.004). The incidence of bone marrow depression≥ grade 2 and 3 in ENI group was higher than that of the IFI group (P<0.05). However, the incidences of radioactive esophagitis≥ grade 3, radioactive pneumonia and late adverse reactions were not significantly different between these two groups (P>0.05). Conclusion: Compared with IFI, ENI can significantly improve the long-term survival for young, early TN stage and cervical/upper-thoracic esophageal cancer patients underwent chemotherapy.
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Affiliation(s)
- S C Zhu
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Q F Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang 050011, China
| | - X Y Zhang
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - W Z Deng
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - C Y Song
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - X Wang
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - K Yan
- Department of Radiation Oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
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21
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Goverse G, Beztsinna N, Visser B, Spanjaard E, Yan K, Price L, Daszkiewicz L. Visualization and quantification of anti-tumor immune responses in 3D cultures. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31245-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Beztsinna N, Grillet F, Jariani A, Overkamp J, van der Meer D, Daszkiewicz L, Yan K, Vader W, Price L. ‘In vitro clinical trials’ platform for drug testing in patient-derived ex vivo 3D cultured human tumor tissues. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31235-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Chen M, Chen W, Liu P, Yan K, Lv C, Zhang M, Lu Y, Qin Q, Kuang Y, Zhu W, Chen X. The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients. J Eur Acad Dermatol Venereol 2020; 34:2059-2065. [PMID: 32271961 DOI: 10.1111/jdv.16440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/24/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Methotrexate (MTX) is the first-line treatment for psoriasis in China. The metabolic processes of MTX include various proteins and genes. Previous studies have shown that gene polymorphisms had significant impacts on the efficacy of MTX. However, the influence of gene polymorphisms has not been reported in the Chinese psoriatic patients. OBJECTIVE The aim of this study was to verify the impacts of candidate genes polymorphisms on the effectiveness of MTX in a Chinese psoriatic population. METHODS In this study, we enrolled 259 psoriasis patients from two clinical centres. Each of them received MTX treatment at 7.5-15 mg/week for at least 8 weeks. Patients were stratified as responders and non-responders according to whether the Psoriasis Area and Severity Index score declined more than 75% (PASI75). According to previous reports, 16 single nucleotide polymorphisms (SNPs) were selected and genotyped for each patient using the Sequenom platform. Fisher's exact test, the chi-square test, Mann-Whitney tests and ANOVA analyses were used for statistical analysis. RESULTS Among 259 patients, there were 182 males and 77 females, 63 patients with psoriatic arthritis and 196 patients without arthritis phenotype, and the age of all patients ranged from 19 to 70 years (49.7 ± 13.6). The baseline PASI value of patients was 13.8 ± 8.5, and 33.2% of patients achieved a PASI75 response after MTX treatment. Patients carrying the ATP-binding cassette subfamily B member 1 gene (ABCB1) rs1045642 TT genotype were associated with more severe psoriasis skin lesion (P = 0.032). Furthermore, the ABCB1 rs1045642 TT genotype was found to be more frequent in non-responders (P = 0.017), especially in moderate-to-severe patients (P = 0.002) and patients without psoriatic arthritis (P = 0.026) after MTX treatment. CONCLUSION We have demonstrated for the first time that polymorphism of the ABCB1 rs1045642 TT genotype is predictive of a worse clinical response of skin lesions to MTX therapy in a Chinese psoriatic population.
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Affiliation(s)
- M Chen
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - W Chen
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - P Liu
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - K Yan
- Department of Dermatology, Dalian Dermatosis Hospital, Dalian, Liaoning, China
| | - C Lv
- Gerontology Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - M Zhang
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - Y Lu
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - Q Qin
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - Y Kuang
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - W Zhu
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
| | - X Chen
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,Department of Dermatology, Hua Shan Hospital, Fu dan University, Shanghai, China
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24
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Cao M, Li Y, Gao Z, Yan K, Zhong XX, Liu B, Zhang RY. [Malignant mesothelioma of intestinal: report of a case]. Zhonghua Bing Li Xue Za Zhi 2019; 48:897-899. [PMID: 31775444 DOI: 10.3760/cma.j.issn.0529-5807.2019.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- M Cao
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - Y Li
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - Z Gao
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - K Yan
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - X X Zhong
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - B Liu
- Department of Pathology, Yanzhou Area of Affiliated Hospital of Jining Medical College, Shandong Province, Yanzhou 272100, China
| | - R Y Zhang
- Department of Pathology, Affiliated Hospital of Jining Medical College, Shandong Province, Jining 272029, China
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25
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Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci D, Ehrenhofer-Murray AE, Heck AJR, Barford D. Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Nature 2019; 574:278-282. [PMID: 31578520 PMCID: PMC6859074 DOI: 10.1038/s41586-019-1609-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022]
Abstract
In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes1,2, function to connect centromeric chromatin to microtubules of the mitotic spindle3,4. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules5,6. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-ANuc), each of which is perfectly centred on its cognate centromere7-9. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-ANuc). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-ANuc to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-ANuc are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-ANuc. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
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Affiliation(s)
- Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Leifu Chang
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
| | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
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26
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Yan K, Zhang Z, Yang J, McLaughlin SH, Barford D. Architecture of the CBF3-centromere complex of the budding yeast kinetochore. Nat Struct Mol Biol 2018; 25:1103-1110. [PMID: 30478265 PMCID: PMC6292502 DOI: 10.1038/s41594-018-0154-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.
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Affiliation(s)
- Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, UK
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Peterson JA, Maroney SA, Zwifelhofer W, Wood JP, Yan K, Bercovitz RS, Woods RK, Mast AE. Heparin-protamine balance after neonatal cardiopulmonary bypass surgery. J Thromb Haemost 2018; 16:1973-1983. [PMID: 30016577 PMCID: PMC6173634 DOI: 10.1111/jth.14245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 12/18/2022]
Abstract
Essentials Heparin-protamine balance (HPB) modulates bleeding after neonatal cardiopulmonary bypass (CPB). HPB was examined in 44 neonates undergoing CPB. Post-operative bleeding occurred in 36% and heparin rebound in 73%. Thrombin-initiated fibrin clot kinetic assay and partial thromboplastin time best assessed HPB. SUMMARY Background Neonates undergoing cardiopulmonary bypass (CPB) are at risk of excessive bleeding. Blood is anticoagulated with heparin during CPB. Heparin activity is reversed with protamine at the end of CPB. Paradoxically, protamine also inhibits blood coagulation when it is dosed in excess of heparin. Objectives To evaluate heparin-protamine balance in neonates undergoing CPB by using research and clinical assays, and to determine its association with postoperative bleeding. Patients/Methods Neonates undergoing CPB in the first 30 days of life were studied. Blood samples were obtained during and after surgery. Heparin-protamine balance was assessed with calibrated automated thrombography, thrombin-initiated fibrin clot kinetic assay (TFCK), activated partial thromboplastin time (APTT), anti-FXa activity, and thromboelastometry. Excessive postoperative bleeding was determined by measurement of chest tube output or the development of cardiac tamponade. Results and Conclusions Of 44 neonates enrolled, 16 (36%) had excessive postoperative bleeding. The TFCK value was increased. By heparin in neonatal blood samples, but was only minimally altered by excess protamine. Therefore, it reliably measured heparin in samples containing a wide range of heparin and protamine concentrations. The APTT most closely correlated with TFCK results, whereas anti-FXa and thromboelastometry assays were less correlative. The TFCK and APTT assay also consistently detected postoperative heparin rebound, providing an important continued role for these long-established coagulation tests in the management of postoperative bleeding in neonates requiring cardiac surgical repair. None of the coagulation tests predicted the neonates who experienced postoperative bleeding, reflecting the multifactorial causes of bleeding in this population.
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Affiliation(s)
- J A Peterson
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA
| | - S A Maroney
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA
| | - W Zwifelhofer
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA
| | - J P Wood
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA
| | - K Yan
- Departments of Pathology and Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - R S Bercovitz
- Departments of Pathology and Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - R K Woods
- HermaHeart Center, Division of Pediatric Cardiothoracic Surgery, Children's Hospital of Wisconsin, Milwaukee, WI, USA
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A E Mast
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
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Yan K, Xu W, Huang Y, Zhang Z, Huang Q, Xin K, Ma Y, Han L. Methotrexate activated Tregs via the CD73/AMPK/mTOR pathway. Br J Dermatol 2018. [DOI: 10.1111/bjd.17165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yan K, Xu W, Huang Y, Zhang Z, Huang Q, Xin K, Ma Y, Han L. 甲氨蝶呤通过 CD73/AMPK/mTOR 通路激活 Treg. Br J Dermatol 2018. [DOI: 10.1111/bjd.17176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yan K, Xu W, Huang Y, Zhang Z, Huang Q, Xin KZ, Ma Y, Han L. Methotrexate restores the function of peripheral blood regulatory T cells in psoriasis vulgaris via the CD73/AMPK/mTOR pathway. Br J Dermatol 2018; 179:896-905. [PMID: 29572822 DOI: 10.1111/bjd.16560] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Methotrexate (MTX) is used to treat psoriasis, a chronic inflammatory skin disease. OBJECTIVES To investigate the molecular mechanism of MTX in the treatment of psoriasis. METHODS Regulatory T cells (Tregs) and effector T (Teff) cells were isolated from the blood of patients with psoriasis and healthy controls. The proliferation of Teff cells was detected by carboxyfluorescein succinimidyl ester assay. The interferon (IFN)-γ and interleukin (IL)-17 levels were analysed by enzyme-linked immunosorbent assay. The expression of CD73 and FoxP3 were determined by flow cytometry. The expression of proteins in the AMPK/mTOR pathway were detected by Western blot analysis. RESULTS The data suggested that patients with psoriasis have Tregs with decreased immune suppression function and reduced expression of CD73 compared with healthy controls. Moreover, MTX could significantly restore the immunosuppressive function of IL-17-secreting Tregs. This, in turn, inhibits aberrant proliferation of Teff cells in patients with psoriasis, reverses downregulation of CD73, upregulates phosphorylated AMPK and inhibits phosphorylated mTOR, and downregulates IL-17 and IFN-γ levels. CONCLUSIONS We speculate that MTX can restore the immunosuppressive function of Tregs through upregulating CD73, activating AMPK and inactivating the mTOR pathway. These findings may partly explain the mechanism by which MTX treats psoriasis.
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Affiliation(s)
- K Yan
- Department of Dermatology, Huashan Hospital, Shanghai, China
| | - W Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Y Huang
- Department of Dermatology, Huashan Hospital, Shanghai, China
| | - Z Zhang
- Department of Dermatology, Huashan Hospital, Shanghai, China
| | - Q Huang
- Department of Dermatology, Huashan Hospital, Shanghai, China
| | - K Z Xin
- Johns Hopkins University School of Medicin, 733 N Broadway, Baltimore, 21205, MD, U.S.A
| | - Y Ma
- Department of Dermatology, Huashan Hospital, Shanghai, China
| | - L Han
- Department of Dermatology, Huashan Hospital, Shanghai, China
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31
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Goverse G, Daszkiewicz L, Madej M, Yan K, Tleis M, Price L. PO-374 A 3D image-based quantification of organoid-immune cell interactions in the presence of immuno-modulators. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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32
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Price L, Basten S, Yan K, Giesemann T, Schueler J, Herpers B. PO-200 3D In vitro cultures of PDX-derived tumour for anti-cancer drug discovery. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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33
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Vader W, Brouwer T, Basten S, Sarasqueta AF, Overkamp J, Yan K, Price L, Morreau H, Bonsing B, Vahrmeijer A. PO-443 In vitro clinical trial for pancreatic cancer patients. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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34
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Zhang X, Medranda D, Borowiec J, Yan K, Zhang J, Wang S, Boi FS. On the morphological, structural and electrochemical properties of entangled Cu-filled carbon nano-onions. RSC Adv 2018; 8:6870-6877. [PMID: 35540343 PMCID: PMC9078305 DOI: 10.1039/c7ra12626c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/03/2018] [Indexed: 11/21/2022] Open
Abstract
We demonstrate an advanced CVS approach in which the synthesis of Cu-filled carbon nano-onions (CNOs) is achieved by direct sublimation and pyrolysis of a not previously used precursor, namely chloro(1,5-cyclooctadiene)copper(i) dimer.
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Affiliation(s)
- X. Zhang
- College of Physical Science and Technology
- Sichuan University
- Chengdu
- China
| | - D. Medranda
- College of Physical Science and Technology
- Sichuan University
- Chengdu
- China
| | - J. Borowiec
- College of Physical Science and Technology
- Sichuan University
- Chengdu
- China
| | - K. Yan
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan
- China
| | - J. Zhang
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan
- China
| | - S. Wang
- Analytical and Testing Centre
- Sichuan University
- Chengdu
- China
| | - F. S. Boi
- College of Physical Science and Technology
- Sichuan University
- Chengdu
- China
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35
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Medranda D, Borowiec J, Zhang X, Wang S, Yan K, Zhang J, He Y, Ivaturi S, Boi FS. Ferromagnetically filled carbon nano-onions: the key role of sulfur in dimensional, structural and electric control. R Soc Open Sci 2018; 5:170981. [PMID: 29410810 PMCID: PMC5792887 DOI: 10.1098/rsos.170981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/01/2017] [Indexed: 06/08/2023]
Abstract
A key challenge in the fabrication of ferromagnetically filled carbon nano-onions (CNOs) is the control of their thickness, dimensions and electric properties. Up to now literature works have mainly focused on the encapsulation of different types of ferromagnetic materials including α-Fe, Fe3C, Co, FeCo, FePd3 and others within CNOs. However, no report has yet shown a suitable method for controlling both the number of shells, diameter and electric properties of the produced CNOs. Here, we demonstrate an advanced chemical vapour deposition approach in which the use of small quantities of sulfur during the pyrolysis of ferrocene allows for the control of (i) the diameter of the CNOs, (ii) the number of shells and (iii) the electric properties. We demonstrate the morphological, structural, electric and magnetic properties of these new types of CNOs by using SEM, XRD, TEM, HRTEM, EIS and VSM techniques.
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Affiliation(s)
- D. Medranda
- College of Physical Science and Technology, Sichuan University, Chengdu, People's Republic of China
| | - J. Borowiec
- College of Physical Science and Technology, Sichuan University, Chengdu, People's Republic of China
| | - Xiao Zhang
- College of Physical Science and Technology, Sichuan University, Chengdu, People's Republic of China
| | - S. Wang
- Analytical and Testing Centre, Sichuan University, Chengdu, People's Republic of China
| | - K. Yan
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - J. Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Y. He
- Analytical and Testing Centre, Sichuan University, Chengdu, People's Republic of China
| | - S. Ivaturi
- College of Physical Science and Technology, Sichuan University, Chengdu, People's Republic of China
| | - F. S. Boi
- College of Physical Science and Technology, Sichuan University, Chengdu, People's Republic of China
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36
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Cvetkovski B, Yan K, Kritikos V, Bosnic-Anticevich S. P55: TELL ME ABOUT YOUR HAY FEVER: A QUALITATIVE INVESTIGATION OF THE PATIENT PERSPECTIVES OF ALLERGIC RHINITIS. Intern Med J 2017. [DOI: 10.1111/imj.55_13578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B Cvetkovski
- University of Sydney; Sydney Australia
- Woolcock Institute of Medical Research; Sydney Australia
| | - K Yan
- Royal Prince Alfred Hospital; Sydney Australia
| | - V Kritikos
- Woolcock Institute of Medical Research; Sydney Australia
- Royal Prince Alfred Hospital; Sydney Australia
| | - S Bosnic-Anticevich
- University of Sydney; Sydney Australia
- Woolcock Institute of Medical Research; Sydney Australia
- Central Sydney Local Area Health Network; Sydney Australia
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37
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Pang H, Ji J, Yan K, Leung C, Lam D. Malignant pleural mesothelioma: A systematic review of first-line chemotherapy and analysis of Hong Kong cohort. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx093.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Parsons LN, Gheorghe G, Yan K, Simpson P, Jarzembowski JA. An Evidence-based Recommendation for a Standardized Approach to Detecting Metastatic Neuroblastoma in Staging Bone Marrow Biopsies. Pediatr Dev Pathol 2017; 20:38-43. [PMID: 28276294 DOI: 10.1177/1093526616686253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neuroblastoma is a common malignant tumor of childhood. Accurate bone marrow (BM) evaluation for metastatic tumor is essential; however, no standardized pathologic workup exists for staging BMs. We examined the diagnostic yield of various BM components and optimal core biopsy (CB) length as part of developing evidence-based recommendations for BM evaluation. After obtaining institutional review board approval, 160 BM biopsies from 50 neuroblastoma patients were retrospectively selected. Hematoxylin and eosin-stained CB and Wright-stained aspirates were scored as positive, negative, or indeterminate. Total/trabecular CB lengths were measured using cellSens software and a DP71 camera (Olympus). Of the 160 BMs, 72 were positive for tumor in any component. Of these, 33 (45.8%) were positive in a single portion of the specimen: 19 CBs and 14 aspirates. Compared with overall diagnosis, sensitivities were as follows: CB 76.3%; aspirate 67.1%; core/aspirate combined 94.7%. Diagnostic CBs had significantly longer trabecular length than nondiagnostic CBs (6.74 mm vs 4.03 mm, P = .006). Positive CBs had longer trabecular space than negative marrows (7.91 mm vs 6.25 mm, P = .002). Nearly 50% of our positive specimens showed diagnostic discordance among the various components examined. However, combining CB and aspirate examination improved sensitivity for tumor detection. We therefore recommend bilateral CBs (>1 cm each) and aspirates for the optimal evaluation of BM for metastatic neuroblastoma.
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Affiliation(s)
- L N Parsons
- 1 Department of Pathology, Medical College of Wisconsin, Wisconsin, USA
| | - G Gheorghe
- 1 Department of Pathology, Medical College of Wisconsin, Wisconsin, USA.,2 Children's Hospital of Wisconsin, Wisconsin, USA
| | - K Yan
- 3 Division of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - P Simpson
- 3 Division of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - J A Jarzembowski
- 1 Department of Pathology, Medical College of Wisconsin, Wisconsin, USA.,2 Children's Hospital of Wisconsin, Wisconsin, USA
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39
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Suzuki T, Miyake N, Tsurusaki Y, Okamoto N, Alkindy A, Inaba A, Sato M, Ito S, Muramatsu K, Kimura S, Ieda D, Saitoh S, Hiyane M, Suzumura H, Yagyu K, Shiraishi H, Nakajima M, Fueki N, Habata Y, Ueda Y, Komatsu Y, Yan K, Shimoda K, Shitara Y, Mizuno S, Ichinomiya K, Sameshima K, Tsuyusaki Y, Kurosawa K, Sakai Y, Haginoya K, Kobayashi Y, Yoshizawa C, Hisano M, Nakashima M, Saitsu H, Takeda S, Matsumoto N. Molecular genetic analysis of 30 families with Joubert syndrome. Clin Genet 2016; 90:526-535. [PMID: 27434533 DOI: 10.1111/cge.12836] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 02/02/2023]
Abstract
Joubert syndrome (JS) is rare recessive disorders characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles, and a deep interpeduncular fossa which is defined by neuroimaging and is termed the 'molar tooth sign'. JS is genetically highly heterogeneous, with at least 29 disease genes being involved. To further understand the genetic causes of JS, we performed whole-exome sequencing in 24 newly recruited JS families. Together with six previously reported families, we identified causative mutations in 25 out of 30 (24 + 6) families (83.3%). We identified eight mutated genes in 27 (21 + 6) Japanese families, TMEM67 (7/27, 25.9%) and CEP290 (6/27, 22.2%) were the most commonly mutated. Interestingly, 9 of 12 CEP290 disease alleles were c.6012-12T>A (75.0%), an allele that has not been reported in non-Japanese populations. Therefore c.6012-12T>A is a common allele in the Japanese population. Importantly, one Japanese and one Omani families carried compound biallelic mutations in two distinct genes (TMEM67/RPGRIP1L and TMEM138/BBS1, respectively). BBS1 is the causative gene in Bardet-Biedl syndrome. These concomitant mutations led to severe and/or complex clinical features in the patients, suggesting combined effects of different mutant genes.
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Affiliation(s)
- T Suzuki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - N Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Y Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - N Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - A Alkindy
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - A Inaba
- Yokohama City University Medical Center, Children's Medical Center, Yokohama, Japan
| | - M Sato
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - S Ito
- Department of Pediatrics, Graduate school of Medicine, Yokohama City University, Yokohama, Japan
| | - K Muramatsu
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - S Kimura
- Kumamoto City Child Development Support Center, Kumamoto, Japan
| | - D Ieda
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - S Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - M Hiyane
- Division of Child Neurology, Okinawa Prefectural Southern Medical Center & Children's Medical Center, Okinawa, Japan
| | - H Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - K Yagyu
- Department of Child and Adolescent Psychiatry, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - H Shiraishi
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - M Nakajima
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - N Fueki
- Division of Rehabilitation, Nagano Children's Hospital, Nagano, Japan
| | - Y Habata
- Department of Pediatric Rehabilitation, Hokkaido Medical Center for Child Health and Rehabilitation, Hokkaido, Japan
| | - Y Ueda
- Nire-no-kai Children's Clinic, Hokkaido, Japan
| | - Y Komatsu
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - K Yan
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - K Shimoda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Y Shitara
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - S Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - K Ichinomiya
- Department of Neonatology, Gunma Children's Medical Center, Gunma, Japan
| | - K Sameshima
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Y Tsuyusaki
- Division of Neurology, Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - K Kurosawa
- Division of Medical Genetics, Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Y Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - K Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Y Kobayashi
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan.,Academic Renal Unit, School of Clinical Science, University of Bristol, Bristol, UK
| | - C Yoshizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - M Hisano
- Department of Nephrology, Chiba Children's Hospital, Chiba, Japan
| | - M Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - H Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - S Takeda
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - N Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Able C, Zakikhani R, Yan K, Sha D, Chopra A. SU-F-T-491: Photon Beam Matching Analysis at Multiple Sites Up to Twelve Years Post Installation. Med Phys 2016. [DOI: 10.1118/1.4956676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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41
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Huh MS, Ivanochko D, Hashem LE, Curtin M, Delorme M, Goodall E, Yan K, Picketts DJ. Stalled replication forks within heterochromatin require ATRX for protection. Cell Death Dis 2016; 7:e2220. [PMID: 27171262 PMCID: PMC4917659 DOI: 10.1038/cddis.2016.121] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 01/04/2023]
Abstract
Expansive growth of neural progenitor cells (NPCs) is a prerequisite to the temporal waves of neuronal differentiation that generate the six-layered neocortex, while also placing a heavy burden on proteins that regulate chromatin packaging and genome integrity. This problem is further reflected by the growing number of developmental disorders caused by mutations in chromatin regulators. ATRX gene mutations cause a severe intellectual disability disorder (α-thalassemia mental retardation X-linked (ATRX) syndrome; OMIM no. 301040), characterized by microcephaly, urogenital abnormalities and α-thalassemia. Although the ATRX protein is required for the maintenance of repetitive DNA within heterochromatin, how this translates to disease pathogenesis remain poorly understood and was a focus of this study. We demonstrate that Atrx(FoxG1Cre) forebrain-specific conditional knockout mice display poly(ADP-ribose) polymerase-1 (Parp-1) hyperactivation during neurogenesis and generate fewer late-born Cux1- and Brn2-positive neurons that accounts for the reduced cortical size. Moreover, DNA damage, induced Parp-1 and Atm activation is elevated in progenitor cells and contributes to their increased level of cell death. ATRX-null HeLa cells are similarly sensitive to hydroxyurea-induced replication stress, accumulate DNA damage and proliferate poorly. Impaired BRCA1-RAD51 colocalization and PARP-1 hyperactivation indicated that stalled replication forks are not efficiently protected. DNA fiber assays confirmed that MRE11 degradation of stalled replication forks was rampant in the absence of ATRX or DAXX. Indeed, fork degradation in ATRX-null cells could be attenuated by treatment with the MRE11 inhibitor mirin, or exacerbated by inhibiting PARP-1 activity. Taken together, these results suggest that ATRX is required to limit replication stress during cellular proliferation, whereas upregulation of PARP-1 activity functions as a compensatory mechanism to protect stalled forks, limiting genomic damage, and facilitating late-born neuron production.
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Affiliation(s)
- M S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - D Ivanochko
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - L E Hashem
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - M Curtin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - M Delorme
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - E Goodall
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - K Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - D J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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42
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Fu JJ, Wang S, Guan RH, Yang W, Yan K, Chen MH. [Effect of thermo-sensitive Matrigel on minimization of thermal injury to the nearby structures in radiofrequency ablation of subcapsular hepatic tumors in a rat model]. Zhonghua Yi Xue Za Zhi 2016; 96:43-7. [PMID: 26792607 DOI: 10.3760/cma.j.issn.0376-2491.2016.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To evaluate the effect and safety of using thermo-sensitive Matrigel as artificial ascites on minimizing thermal injury to the nearby structures in a rat model of radiofrequency (RF) ablation of the liver. METHODS In this research, the morphological characterization of Matrigel was observed at different temperatures in vitro. In vivo study was conducted by using 42 SD rats in Matrigel, Saline and control groups of 14 rats each. Artificial ascites with 10 ml of Matrigel or saline was produced under ultrasound guidance before RF in the experimental groups. Using a 0.7 cm exposed 17 G RF electrode for 5 minutes (90 ± 2) ℃, 41 hepatic ablations was performed abutting the diaphragm, abdominal wall and stomach. The 41 rats were sacrificed at 24 h, and necropsy was performed.Gross and histopathologic examinations were performed to compare the frequency and extent of thermal injury to the nearby organs.The animal status was followed up to achieve long term safety evaluation of Matrigel. RESULTS Matrigel was in liquid formation at 0-4 ℃, but was not moving in vials at temperature 37 ℃ in 1 min, presenting gel formation.In vivo experiment, the artificial fluid thickness of Matrigel in site was significant larger than that of saline group, especially at 5 min of ablation ((8.1 ± 1.1) mm vs (2.4 ± 0.8)mm, P<0.01). Thermal injury to the nearby structures was found in 12 of 13 cases in control group, 8 of 14 cases (P=0.037) in saline group, and 1 of 14 cases (P<0.01) in Matrigel group. The sizes of the ablation zone of the liver did not differ among the three groups. There was no difference in the incidence of operation related complications among the three groups. There was no significant difference in body weight and health related parameters between Matrigel and saline group during 60 days of follow up. CONCLUSIONS Using thermo-sensitive Matrigel as artificial ascites may be a safe and useful technique and help to further reduce the frequency and severity of collateral thermal injury to the nearby structures compare to conventional saline, during RF ablation of subcapsular hepatic tumors.
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Affiliation(s)
- J J Fu
- Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education), Department of Ultrasound, Peking University Cancer Hospital and Institute, Beijing 100142, China
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Ma C, Yan K, Tan D, Li N, Zhang Y, Yuan Y, Li Z, Dong MQ, Lei J, Gao N. Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation. Protein Cell 2016; 7:187-200. [PMID: 26850260 PMCID: PMC4791427 DOI: 10.1007/s13238-015-0242-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 12/16/2022] Open
Abstract
The human Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease caused by mutations in a highly conserved ribosome assembly factor SBDS. The functional role of SBDS is to cooperate with another assembly factor, elongation factor 1-like (Efl1), to promote the release of eukaryotic initiation factor 6 (eIF6) from the late-stage cytoplasmic 60S precursors. In the present work, we characterized, both biochemically and structurally, the interaction between the 60S subunit and SBDS protein (Sdo1p) from yeast. Our data show that Sdo1p interacts tightly with the mature 60S subunit in vitro through its domain I and II, and is capable of bridging two 60S subunits to form a stable 2:2 dimer. Structural analysis indicates that Sdo1p bind to the ribosomal P-site, in the proximity of uL16 and uL5, and with direct contact to H69 and H38. The dynamic nature of Sdo1p on the 60S subunit, together with its strategic binding position, suggests a surveillance role of Sdo1p in monitoring the conformational maturation of the ribosomal P-site. Altogether, our data support a conformational signal-relay cascade during late-stage 60S maturation, involving uL16, Sdo1p, and Efl1p, which interrogates the functional P-site to control the departure of the anti-association factor eIF6.
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Affiliation(s)
- Chengying Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kaige Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China.,Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ningning Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yixiao Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifei Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China.,Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jianlin Lei
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ning Gao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Abstract
Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling. However, the underlying molecular mechanism is still not clear at the atomic level. Here, we present two cryo-EM structures of the SecM-stalled ribosomes at 3.3–3.7 Å resolution, which reveal two different stalling mechanisms at distinct elongation steps of the translation cycle: one is due to the inactivation of ribosomal peptidyl-transferase center which inhibits peptide bond formation with the incoming prolyl-tRNA; the other is the prolonged residence of the peptidyl-RNA at the hybrid A/P site which inhibits the full-scale tRNA translocation. These results demonstrate an elegant control of translation cycle by regulatory peptides through a continuous, dynamic reshaping of the functional center of the ribosome. DOI:http://dx.doi.org/10.7554/eLife.09684.001 Many genes code for proteins that carry out essential tasks. The instructions in a gene are first copied into a messenger RNA (mRNA), and a molecular machine known as a ribosome reads the copied instructions in groups of three letters at a time (called codons). The ribosome translates the order of the codons into a sequence of amino acids; each amino acid is carried into the ribosome by a transfer RNA (tRNA) molecule. As it translates, the ribosome joins each new amino acid to the one before it, like the links in a chain. Finally, the newly built protein chain passes through a tunnel to exit the ribosome. Ribosomes do not build all proteins at a constant rate; there are many examples of proteins that stall when they are in the ribosome exit tunnel. It is thought that this stalling is an important way for cells to control the expression of proteins. SecM is a bacterial protein that stalls while it is being made. Previous research has shown that a sequence of amino acids in SecM (called the arrest sequence) interacts with components of the ribosome tunnel. This interaction leads to stalling, and regulates the translation of another important bacterial protein (called SecA) that is encoded downstream on the same mRNA as SecM. If SecM-induced stalling takes place, the translation of SecA actually increases. Nevertheless, it remains poorly understood how SecM stalls in the ribosome. Zhang et al. have now solved the structures of SecM proteins stalled inside ribosomes using a method called cryo-electron microscopy. This approach identified two different states of SecM present in the ribosome, which corresponded to two different stalling mechanisms. The addition of an amino acid to a growing protein occurs in stages. First, the tRNA that carries the amino acid to the ribosome and bind to it in a region known as the A-site. After this, the tRNA moves to the P-site where the attached amino acid is incorporated into the elongating protein chain. Zhang et al. observed that the arrest sequence of SecM and the ribosome tunnel interact extensively. These interactions are strong and alter the configuration of both the A-site and P-site of the ribosome. This has two major consequences for translation. First, the tRNA cannot be stably accommodated in the A-site and secondly, its passage to the P-site is slowed down. Both these mechanisms contribute to stalling. This study provides a detailed analysis of how the ribosome can adjust to control translation. It also highlights that codon-specific control of translation constitutes an important component of how gene expression is regulated. DOI:http://dx.doi.org/10.7554/eLife.09684.002
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xijiang Pan
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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46
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Yan K, Campbell L, Rashid A, Wu B, Pang D, Gurka M, Collins S, Unger K. Patient Specific Model Predictive of Gastrointestinal Toxicity Following Stereotactic Body Radiation Therapy (SBRT) for Pancreatic Cancer: Preliminary Factor Study. Int J Radiat Oncol Biol Phys 2015. [DOI: 10.1016/j.ijrobp.2015.07.2076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Zhang D, Yan K, Zhang Y, Liu G, Cao X, Song G, Xie Q, Gao N, Qin Y. New insights into the enzymatic role of EF-G in ribosome recycling. Nucleic Acids Res 2015; 43:10525-33. [PMID: 26432831 PMCID: PMC4666400 DOI: 10.1093/nar/gkv995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/19/2015] [Indexed: 12/30/2022] Open
Abstract
During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ribosome recycling factor (RRF), EF-G was hypothesized to induce the domain rotations of RRF, which subsequently performs the function of splitting the major intersubunit bridges and thus separates the ribosome into subunits for recycling. Here, with systematic mutagenesis, FRET analysis and cryo-EM single particle approach, we analyzed the interplay between EF-G/RRF and post termination complex (PoTC). Our data reveal that the two conserved loops (loop I and II) at the tip region of EF-G domain IV possess distinct roles in tRNA translocation and ribosome recycling. Specifically, loop II might be directly involved in disrupting the main intersubunit bridge B2a between helix 44 (h44 from the 30S subunit) and helix 69 (H69 from the 50S subunit) in PoTC. Therefore, our data suggest a new ribosome recycling mechanism which requires an active involvement of EF-G. In addition to supporting RRF, EF-G plays an enzymatic role in destabilizing B2a via its loop II.
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Affiliation(s)
- Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiwei Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guangqiao Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xintao Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangtao Song
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Xie
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
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48
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Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y, Xu Y, Lei J, Gao N. Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Nucleic Acids Res 2014; 42:13430-9. [PMID: 25389271 PMCID: PMC4245960 DOI: 10.1093/nar/gku1135] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.
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Affiliation(s)
- Xiaoxiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yixiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chengying Ma
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhifei Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Boya Feng
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Liu
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yadong Sun
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanji Xu
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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49
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Zhu B, Yan K, Li L, Lin M, Zhang S, He Q, Zheng D, Yang H, Shao G. K63-linked ubiquitination of FANCG is required for its association with the Rap80-BRCA1 complex to modulate homologous recombination repair of DNA interstand crosslinks. Oncogene 2014; 34:2867-78. [PMID: 25132264 DOI: 10.1038/onc.2014.229] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 05/21/2014] [Accepted: 06/23/2014] [Indexed: 11/09/2022]
Abstract
DNA interstrand crosslinks (ICLs) are extremely deleterious lesions that are repaired by homologous recombination (HR) through coordination of Fanconi anemia (FA) proteins and breast cancer susceptibility gene 1 (BRCA1) product, but the exact role these proteins have remains unclear. Here we report that FANCG was modified by the addition of lysine63-linked polyubiquitin chains (K63Ub) in response to DNA damage. We show that FANCG K63Ub was dispensable for monoubiquitination of FANCD2, but was required for FANCG to interact with the Rap80-BRCA1 (receptor-associated protein 80-BRCA1) complex for subsequent modulation of HR repair of ICLs induced by mitomycin C. Mutation of three lysine residues within FANCG to arginine (K182, K258 and K347, 3KR) reduced FANCG K63Ub modification, as well as its interaction with the Rap80-BRCA1 complex, and therefore impeded HR repair. In addition, we demonstrated that K63Ub-modified FANCG was deubiquitinated by BRCC36 complex in vitro and in vivo. Inhibition of BRCC36 resulted in increased K63Ub modification of FANCG. Taken together, our results identify a new role of FANCG in HR repair of ICL through K63Ub-mediated interaction with the Rap80-BRCA1 complex.
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Affiliation(s)
- B Zhu
- 1] Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China [2] Institute of Systems Biology, Peking University, Beijing, China
| | - K Yan
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - L Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - M Lin
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - S Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Q He
- Center of Medical and Health Analysis, Peking University, Beijing, China
| | - D Zheng
- School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
| | - H Yang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - G Shao
- 1] Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China [2] Institute of Systems Biology, Peking University, Beijing, China
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50
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Yang Z, Guo Q, Goto S, Chen Y, Li N, Yan K, Zhang Y, Muto A, Deng H, Himeno H, Lei J, Gao N. Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence. Protein Cell 2014; 5:394-407. [PMID: 24671761 PMCID: PMC3996153 DOI: 10.1007/s13238-014-0044-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/26/2014] [Indexed: 12/20/2022] Open
Abstract
The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.
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Affiliation(s)
- Zhixiu Yang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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