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Peng D, Jia D, Xia H, Zhang L, Huang P, Xue Y. Using bioinformatic resources for a systems-level understanding of phosphorylation. Sci Bull (Beijing) 2024; 69:989-992. [PMID: 38320898 DOI: 10.1016/j.scib.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Di Peng
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Luoying Zhang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengyu Huang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing 210031, China.
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Tian M, He L, Peng D, Fu M, Ma S, Mu J, Yu Q, Wang J, Yin H, Wang J. Characterizing NOx emissions from diesel trucks with tampered aftertreatment systems and its implications for identifying high emitters. Sci Total Environ 2024; 917:170378. [PMID: 38280581 DOI: 10.1016/j.scitotenv.2024.170378] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Reducing the differences between real-world and certificated NOx emission levels is an important element of in-use emission surveillance programs. Therefore, investigating the characteristics of the vehicles which have much higher NOx emissions (i.e., high-emitters) and determining a reasonable cut-off point to identify high-emitters with a low false detection rate is important. In this study, six diesel trucks were tested under different aftertreatment conditions. The results showed that the discrepancies of fuel-specific NOx emissions between vehicles with functioning and tampered selective catalytic reduction (SCR) systems occur mainly from medium- to high-speed modes. This is because the SCR systems were at low conversion efficiencies when the exhaust temperature was low, including cold-start and urban creep conditions. By using binary classification, we selected fuel-specific NOx cut-off points for high-emitters from China V and China VI diesel trucks. The false detection rate of high-emitters can decrease by 33 % and 95 %, if only NOx emissions from medium- to high-speed modes were used for the chosen cut-off points, respectively. This work highlights the importance of in-use emission compliance programs. It also suggests that high-emitters can be more accurately identified at medium- to high-speed modes if using instantaneous emission data.
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Affiliation(s)
- Miao Tian
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Liqiang He
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Di Peng
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Mingliang Fu
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Shuai Ma
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Jinsong Mu
- Xiamen Environment Protection Vehicle Emission Control Technology Center, Xiamen 361023, PR China
| | - Quanshun Yu
- CATARC Automotive Test Center (Tianjin) Company Limited, Tianjin 300300, PR China
| | - Jia Wang
- Jinan Automobile Testing Center Co, Ltd., Jinan 250102, PR China
| | - Hang Yin
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Junfang Wang
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
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Chen LC, Luo T, Cao ZY, Dalladay-Simpson P, Huang G, Peng D, Zhang LL, Gorelli FA, Zhong GH, Lin HQ, Chen XJ. Synthesis and superconductivity in yttrium-cerium hydrides at high pressures. Nat Commun 2024; 15:1809. [PMID: 38418489 PMCID: PMC10901869 DOI: 10.1038/s41467-024-46133-x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
Further increasing the critical temperature and/or decreasing the stabilized pressure are the general hopes for the hydride superconductors. Inspired by the low stabilized pressure associated with Ce 4f electrons in superconducting cerium superhydride and the high critical temperature in yttrium superhydride, we carry out seven independent runs to synthesize yttrium-cerium alloy hydrides. The synthetic process is examined by the Raman scattering and X-ray diffraction measurements. The superconductivity is obtained from the observed zero-resistance state with the detected onset critical temperatures in the range of 97-141 K. The upper critical field towards 0 K at pressure of 124 GPa is determined to be between 56 and 78 T by extrapolation of the results of the electrical transport measurements at applied magnetic fields. The analysis of the structural data and theoretical calculations suggest that the phase of Y0.5Ce0.5H9 in hexagonal structure with the space group of P63/mmc is stable in the studied pressure range. These results indicate that alloying superhydrides indeed can maintain relatively high critical temperature at relatively modest pressures accessible by laboratory conditions.
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Affiliation(s)
- Liu-Cheng Chen
- School of Science, Harbin Institute of Technology, Shenzhen, 518055, China
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
| | - Tao Luo
- School of Science, Harbin Institute of Technology, Shenzhen, 518055, China
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
| | - Zi-Yu Cao
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
- Center for Quantum Materials and Superconductivity (CQMS) and Department of Physics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | | | - Ge Huang
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
| | - Di Peng
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
| | - Li-Li Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Federico Aiace Gorelli
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China
- National Institute of Optics (INO-CNR) and European Laboratory for Non-Linear Spectroscopy (LENS), Via N. Carrara 1, 50019, Sesto Fiorentino (Florence), Italy
| | - Guo-Hua Zhong
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Qing Lin
- School of Physics, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Jia Chen
- Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX, 77204, USA.
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Chen J, Zeng M, Liang XF, Peng D, Xie R, Wu D. Dietary supplementation of VA enhances growth, feed utilization, glucose and lipid metabolism, appetite, and antioxidant capacity of Chinese perch (Siniperca chuatsi). Fish Physiol Biochem 2024; 50:225-237. [PMID: 37594622 DOI: 10.1007/s10695-023-01221-5] [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] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 08/19/2023]
Abstract
The aim of this study was to investigate the effect of dietary vitamin A on juvenile Chinese perch (Siniperca chuatsi). Chinese perch were fed with five experimental diets containing 0, 20, 40, 60, and 80 mg VA·kg-1 for 8 weeks. Results showed that dietary vitamin A significantly influenced the fish's growth, feed utilization, glucose and lipid metabolism, appetite, and antioxidant capacity. Vitamin A-supplemented groups had higher weight gain rate (WGR) and specific growth rate (SGR) compared to the control group. Feed conversion ratio (FCR) was also lower in the vitamin A-supplemented groups. Dietary vitamin A had no significant effect on the survival rate (SR). Compared to the control group, fish fed with vitamin A had increased feed intake (FI), and the expression of appetite-promoting genes (npy and agrp) was significantly higher in the 40 mg VA·kg-1 group. Vitamin A also enhanced the utilization of dietary protein by Chinese perch. The serum glucose content of the fish fed with 40 mg VA·kg-1 diet was significantly higher than that of the control group and 20 mg VA·kg-1 diet, indicating that the promoting effect of VA on gluconeogenesis was greater than that on glycolysis. Additionally, dietary vitamin A increased the expression of lipid metabolism-related genes (hl and fas) and antioxidant genes (nrf2 and gpx) in the fish. These results suggest that the optimal vitamin A requirement of juvenile Chinese perch bream was estimated to be 37.32 mg VA·kg-1 based on broken-line regression analysis of WGR. In conclusion, this study provides valuable insights into the potential benefits of dietary vitamin A on the growth, metabolism, and antioxidant capacity of Chinese perch.
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Affiliation(s)
- Junliang Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Ming Zeng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Di Peng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Ruipeng Xie
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Dongliang Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
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Bai X, Bao Y, Bei S, Bu C, Cao R, Cao Y, Cen H, Chao J, Chen F, Chen H, Chen K, Chen M, Chen M, Chen M, Chen Q, Chen R, Chen S, Chen T, Chen X, Chen X, Cheng Y, Chu Y, Cui Q, Dong L, Du Z, Duan G, Fan S, Fan Z, Fang X, Fang Z, Feng Z, Fu S, Gao F, Gao G, Gao H, Gao W, Gao X, Gao X, Gao X, Gong J, Gong J, Gou Y, Gu S, Guo AY, Guo G, Guo X, Han C, Hao D, Hao L, He Q, He S, He S, Hu W, Huang K, Huang T, Huang X, Huang Y, Jia P, Jia Y, Jiang C, Jiang M, Jiang S, Jiang T, Jiang X, Jin E, Jin W, Kang H, Kang H, Kong D, Lan L, Lei W, Li CY, Li C, Li C, Li H, Li J, Li J, Li L, Li P, Li R, Li X, Li Y, Li Y, Li Z, Liao X, Lin S, Lin Y, Ling Y, Liu B, Liu CJ, Liu D, Liu GH, Liu L, Liu S, Liu W, Liu X, Liu X, Liu Y, Liu Y, Lu M, Lu T, Luo H, Luo H, Luo M, Luo S, Luo X, Ma L, Ma Y, Mai J, Meng J, Meng X, Meng Y, Meng Y, Miao W, Miao YR, Ni L, Nie Z, Niu G, Niu X, Niu Y, Pan R, Pan S, Peng D, Peng J, Qi J, Qi Y, Qian Q, Qin Y, Qu H, Ren J, Ren J, Sang Z, Shang K, Shen WK, Shen Y, Shi Y, Song S, Song T, Su T, Sun J, Sun Y, Sun Y, Sun Y, Tang B, Tang D, Tang Q, Tang Z, Tian D, Tian F, Tian W, Tian Z, Wang A, Wang G, Wang G, Wang J, Wang J, Wang P, Wang P, Wang W, Wang Y, Wang Y, Wang Y, Wang Y, Wang Z, Wei H, Wei Y, Wei Z, Wu D, Wu G, Wu S, Wu S, Wu W, Wu W, Wu Z, Xia Z, Xiao J, Xiao L, Xiao Y, Xie G, Xie GY, Xie J, Xie Y, Xiong J, Xiong Z, Xu D, Xu S, Xu T, Xu T, Xue Y, Xue Y, Yan C, Yang D, Yang F, Yang F, Yang H, Yang J, Yang K, Yang N, Yang QY, Yang S, Yang X, Yang X, Yang X, Yang YG, Ye W, Yu C, Yu F, Yu S, Yuan C, Yuan H, Zeng J, Zhai S, Zhang C, Zhang F, Zhang G, Zhang M, Zhang P, Zhang Q, Zhang R, Zhang S, Zhang W, Zhang W, Zhang W, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang YE, Zhang Y, Zhang Z, Zhang Z, Zhao D, Zhao F, Zhao G, Zhao M, Zhao W, Zhao W, Zhao X, Zhao Y, Zhao Y, Zhao Z, Zheng X, Zheng Y, Zhou C, Zhou H, Zhou X, Zhou X, Zhou Y, Zhou Y, Zhu J, Zhu L, Zhu R, Zhu T, Zong W, Zou D, Zuo Z. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res 2024; 52:D18-D32. [PMID: 38018256 PMCID: PMC10767964 DOI: 10.1093/nar/gkad1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
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Yang D, Peng D, Zhou Y, Qiang Z, Wan L, Fan X, Meng Y, Xu G, Meng Y. Alpha-Momorcharin, a type I ribosome inactivating protein, induced apoptosis of hepatocellular carcinoma SK-HEP-1 cells through mitochondrial pathway. Nat Prod Res 2023:1-11. [PMID: 38126176 DOI: 10.1080/14786419.2023.2295915] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Alpha-Momorcharin (α-MMC), as one of the most important type I RIPs, has been reported to exert inhibitory effects against various tumour cells through its N-glycosidase activity. The present study was designed to propose an efficient purification strategy and explored its mechanism of apoptosis signalling pathway against human liver cancer cells SK-Hep-1. α-MMC can be successfully obtained by our purification strategy combining ion-exchange and gel-filtration chromatography. The functional studies revealed that α-MMC obviously increased the level of ROS and apoptosis rate, induced cell cycle arrest in the G1 phase, and depolarised MMP of SK-Hep-1 cells. To further confirm whether α-MMC could induce mitochondria involved apoptosis, we found that PARP-1, Caspase-3, Caspase-9, and BCL-2 were downregulated upon α-MMC. Taken together, these results suggested that this natural purified α-MMC can induce apoptosis involved mitochondria and may serve as a potential novel therapeutic drug in the treatment of human liver cancer in the future.
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Affiliation(s)
- Di Yang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
| | - Di Peng
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
| | - Yiping Zhou
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Provincial People's Hospital Jinniu Hospital, Chengdu, Sichuan, China
| | - Zihao Qiang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
| | - Li Wan
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xiang Fan
- Key Laboratory of Bio-resources and Eco-environment Ministry of Education/Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yanfa Meng
- Key Laboratory of Bio-resources and Eco-environment Ministry of Education/Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Ge Xu
- The 3rd Affiliated Hospital of Chengdu Medical College, Pidu District People's Hospital, Chengdu, Sichuan, China
| | - Yao Meng
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
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Peng D, Mao Z, Zhang W, Yu J, Zhang S. In vivo knee biomechanics during badminton lunges at different distances and different foot positions by using the dual fluoroscopic imaging system. Front Bioeng Biotechnol 2023; 11:1320404. [PMID: 38188492 PMCID: PMC10768190 DOI: 10.3389/fbioe.2023.1320404] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background: Lunges are common in badminton. Distance and foot position affect knee joint loadings under lunges, which are closely related to knee injury incidence. Investigations involving dynamic knee motion in vivo, kinetics, and muscle activation in lunges, especially during lunges of different distances and foot positions, are instrumental for understanding knee performance and injury risks of players. Methods: A total of 10 experienced badminton athletes (10 females; height, 164.5 ± 5.0 cm; weight, 59.3 ± 6.0 kg; and age, 22 ± 1.0 years) were recruited. By using a high-speed dual fluoroscopic imaging system, Qualisys motion capture system, Kistler force plate, and Delsys electromyography simultaneously, data were collected during players' 1.5 times leg length lunge, the maximum lunge, and the maximum lunge while the foot rotated externally. Magnetic resonance and dual fluoroscopic imaging techniques were used to analyze the in vivo knee kinematics. Results: Compared with the 1.5 times leg length lunge, knee flexion for the maximum lunge increased significantly (p < 0.05). The anterior-posterior ground reaction force (GRF) and vertical GRF of the maximum lunge were significantly higher than those of the 1.5 times leg length lunge. During the two different foot position lunges with the maximum distance, the posterior translation of knee joint was larger (p < 0.05) when the foot rotated externally than the normal maximum lunge. Moreover, the anterior-posterior GRF and vertical GRF increased significantly when the foot rotated externally. Significant differences were observed in valgus-varus rotation torque and internal-external rotation torque of the knee joint under the two distance lunges and two foot position lunges (p < 0.05). No significant difference was found in knee muscle activation during the two distance lunges and during the two foot position lunges. Conclusion: High knee torque and compressive loadings with increasing lunge distance may cause knee injuries in badminton. When lunging in the external foot rotation under the maximum distance, high quadriceps force and posterior tibia translation force could result in knee injuries among badminton players.
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Affiliation(s)
| | | | | | | | - Shengnian Zhang
- Key Laboratory of Exercise and Health Sciences of Ministry of Education, School of Exercise and Health, Shanghai University of Sport, Shanghai, China
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Liu HH, Su CX, Li ZQ, Yue SJ, Cheng SH, Peng D. Assessment of consistency between peer-reviewed publications and clinical trial registrations in nursing journals. Worldviews Evid Based Nurs 2023; 20:574-581. [PMID: 37005350 DOI: 10.1111/wvn.12644] [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: 11/03/2022] [Revised: 02/15/2023] [Accepted: 03/04/2023] [Indexed: 04/04/2023]
Abstract
BACKGROUND The inconsistencies between randomized clinical trials (RCTs) registrations and peer-reviewed publications may distort trial results and threaten the validity of evidence-based medicine. Previous studies have found many inconsistencies between RCTs registrations and peer-reviewed publications, and outcome reporting bias is prevalent. AIMS The aims of this review were to assess whether the primary outcomes and other data reported in publications and registered records in RCTs of nursing journals were consistent and whether discrepancies in the reporting of primary outcomes favored statistically significant results. Moreover, we reviewed the proportion of RCTs for prospective registration. METHODS We systematically searched PubMed for RCTs published in the top 10 nursing journals between March 5, 2020, and March 5, 2022. Registration numbers were extracted from the publications, and registered records were identified from the registration platforms. The publications and registered records were compared to identify consistency. Inconsistencies were subdivided into discrepancies and omissions. RESULTS A total of 70 RCTs published in seven journals were included. The inconsistencies involved sample size estimation (71.4%), random sequence generation (75.7%), allocation concealment (97.1%), blinding (82.9%), primary outcomes (60.0%) and secondary outcomes (84.3%). Among the inconsistencies in the primary outcomes, 21.4% were due to discrepancies and 38.6% resulted from omissions. Fifty-three percent (8/15) presented discrepancies in the primary outcomes that favored statistically significant results. Additionally, although only 40.0% of the studies were prospective registrations, the number of prospectively registered trials has trended upward over time. LINKING EVIDENCE TO ACTION While not including all RCTs in the nursing field, our sample reflected a general trend: inconsistencies between publications and trial registrations were prevalent in the included nursing journals. Our research helps to provide a way to improve the transparency of research reports. Ensuring that clinical practice has access to transparent and reliable research results are essential to achieve the best possible evidence-based medicine.
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Affiliation(s)
- Hui-Hui Liu
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chun-Xiang Su
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
- Beijing University of Chinese Medicine Collaborating Center of Joanna Briggs Institute, Beijing, China
| | - Zhang-Qi Li
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shu-Jin Yue
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shu-Han Cheng
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Di Peng
- School of Nursing, Beijing University of Chinese Medicine, Beijing, 100029, China
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Wu D, Peng D, Liang XF, Xie R, Zeng M, Chen J, Lan J, Yang R, Hu J, Lu P. Dietary soybean lecithin promoted growth performance and feeding in juvenile Chinese perch (Siniperca chuatsi) could be by optimizing glucolipid metabolism. Fish Physiol Biochem 2023; 49:1097-1114. [PMID: 37855970 DOI: 10.1007/s10695-023-01241-1] [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: 04/18/2023] [Accepted: 09/16/2023] [Indexed: 10/20/2023]
Abstract
To explore the potential benefits of dietary phospholipids (PLs) in fish glucose metabolism and to promote feed culture of Chinese perch (Siniperca chuatsi), we set up six diets to feed Chinese perch (initial mean body weight 37.01 ± 0.20 g) for 86 days, including: Control diet (CT), 1% (SL1), 2% (SL2), 3% (SL3), 4% (SL4) soybean lecithin (SL) and 2% (KO2) krill oil (KO) supplemental diets (in triplicate, 20 fish each). Our study found that the SL2 significantly improved the weight gain rate and special growth rate, but the KO2 did not. In addition, the SL2 diet significantly improved feed intake, which is consistent with the mRNA levels of appetite-related genes (npy, agrp, leptin A). Additionally, in the CT and SL-added groups, leptin A expression levels were nearly synchronized with serum glucose levels. Besides, the SL2 significantly upregulated expression levels of glut2, gk, cs, fas and downregulated g6pase in the liver, suggesting that it may enhance glucose uptake, aerobic oxidation, and conversion to fatty acids. The SL2 also maintained the hepatic crude lipid content unchanged compared to the CT, possibly by significantly down-regulating the mRNA level of hepatic lipase gene (hl), and by elevating serum low-density lipoprotein (LDL) level and intraperitoneal fat ratio in significance. Moreover, the serum high-density lipoprotein levels were significantly increased by PL supplementation, and the SL2 further significantly increased serum total cholesterol and LDL levels, suggesting that dietary PLs promote lipid absorption and transport. Furthermore, dietary SL at 1% level could enhance non-specific immune capacity, with serum total protein level being markedly higher than that in the CT group. In conclusion, it is speculated that the promotion of glucose utilization and appetite by 2% dietary SL could be linked. We suggest a 1.91% supplementation of SL in the diet for the best growth performance in juvenile Chinese perch.
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Affiliation(s)
- Dongliang Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Di Peng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Ruipeng Xie
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Ming Zeng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Junliang Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Jie Lan
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Ru Yang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Jiacheng Hu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Peisong Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
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10
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Xie RP, Liang XF, Peng D, Zhang QW, Wu DL, Chen JL, Zeng M. Dietary supplementation of pyridoxine can enhance the growth performance and improve the protein, lipid utilization efficiency of mandarin fish (Siniperca chuatsi). Fish Physiol Biochem 2023; 49:1063-1078. [PMID: 37542702 DOI: 10.1007/s10695-023-01223-3] [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: 04/11/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023]
Abstract
This study aimed to assess the effect of pyridoxine supplementation in the mandarin fish diet on growth performance, protein and lipid metabolism, and liver and intestinal histology. Mandarin fish were fed six diets with different levels of pyridoxine (2.67 mg/kg (control), 4.41 mg/kg, 6.57 mg/kg, 10.25 mg/kg, 17.93 mg/kg, 33.12 mg/kg diet) for 8 weeks, and samples were collected for analysis. The findings demonstrated that feeding mandarin fish a diet with 6.57 mg/kg pyridoxine led to a significant increase in weight gain rate (WGR), protein efficiency ratio (PER), whole-body crude protein, whole-body crude lipid, serum protein, cholesterol (CHO), triacylglycerol (TG), high-density lipoprotein-cholesterol (HDL-C), low-density lipoprotein-cholesterol (LDL-C), and alkaline phosphatase (ALP), as well as significantly lower serum glucose (GLU) and feed conversion ratio (FCR), compared to the control group (P < 0.05). Furthermore, we found a significant upregulation of the relative expression of genes associated with hepatic lipid oxidation and synthesis (hl, lpl, pparα, cpt1, cs, srebp1, and fas) and proteolysis (ast, alt, and gdh) in fish fed a diet containing 6.57 mg/kg pyridoxine (P < 0.05). Regarding the histological analysis, we observed a notable decrease in the quantity of intestinal mucus-secreting cells when the fish fed a diet containing 10.25 mg/kg pyridoxine (P < 0.05). These findings suggest that dietary pyridoxine supplementation promotes mandarin fish growth by improving the efficiency of protein and lipid utilization. Additionally, we used a broken-line regression analysis to estimate the optimal dietary pyridoxine requirement for mandarin fish in the range of 6.17-6.41 mg/kg based on WGR, FCR, and PER.
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Affiliation(s)
- Rui-Peng Xie
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| | - Di Peng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qi-Wei Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Dong-Liang Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Jun-Liang Chen
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Ming Zeng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, Hubei Province, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
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11
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Huang G, Peng D, Luo T, Chen LC, Dalladay-Simpson P, Cao ZY, Gorelli FA, Zhong GH, Lin HQ, Chen XJ. Synthesis of superconducting phase of La 0.5Ce 0.5H 10at high pressures. J Phys Condens Matter 2023; 36:075702. [PMID: 37918102 DOI: 10.1088/1361-648x/ad0915] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Clathrate hydrideFm3-m-LaH10has been proven as the most extraordinary superconductor with the critical temperatureTcabove 250 K upon compression of hundreds of GPa in recent years. A general hope is to reduce the stabilization pressure and maintain the highTcvalue of the specific phase in LaH10. However, strong structural instability distortsFm3-mstructure and leads to a rapid decrease ofTcat low pressures. Here, we investigate the phase stability and superconducting behaviors ofFm3-m-LaH10with enhanced chemical pre-compression through partly replacing La by Ce atoms from both experiments and calculations. For explicitly characterizing the synthesized hydride, we choose lanthanum-cerium alloy with stoichiometry composition of 1:1. X-ray diffraction and Raman scattering measurements reveal the stabilization ofFm3-m-La0.5Ce0.5H10in the pressure range of 140-160 GPa. Superconductivity withTcof 175 ± 2 K at 155 GPa is confirmed with the observation of the zero-resistivity state and supported by the theoretical calculations. These findings provide applicability in the future explorations for a large variety of hydrogen-rich hydrides.
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Affiliation(s)
- Ge Huang
- Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, People's Republic of China
| | - Di Peng
- Key Laboratory of Materials Physics, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, People's Republic of China
- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Tao Luo
- School of Science, Harbin Institute of Technology, Shenzhen 518055, People's Republic of China
| | - Liu-Cheng Chen
- Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, People's Republic of China
- School of Science, Harbin Institute of Technology, Shenzhen 518055, People's Republic of China
| | - Philip Dalladay-Simpson
- Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, People's Republic of China
| | - Zi-Yu Cao
- Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, People's Republic of China
- Center for Quantum Materials and Superconductivity (CQMS) and Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Federico A Gorelli
- Center for High Pressure Science and Technology Advanced Research, Shanghai 201203, People's Republic of China
- National Institute of Optics (INO-CNR) and European Laboratory for Non-Linear Spectroscopy (LENS), Via N. Carrara 1, 50019 Sesto Fiorentino (Florence), Italy
| | - Guo-Hua Zhong
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Shenzhen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hai-Qing Lin
- School of Physics, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiao-Jia Chen
- Department of Physics and Texas Center for Superconductivity, University of Houston, Houston TX 77204, United States of America
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12
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Ji S, Peng D, Sun F, You Q, Wang R, Yan N, Zhou Y, Wang W, Tang Q, Xia N, Zeng Z, Wu Z. Coexistent, Competing Tunnelling, and Hopping Charge Transport in Compressed Metal Nanocluster Crystals. J Am Chem Soc 2023; 145:24012-24020. [PMID: 37903430 DOI: 10.1021/jacs.3c07007] [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: 11/01/2023]
Abstract
Understanding charge transport among metal particles with sizes of approximately 1 nm poses a great challenge due to the ultrasmall nanosize, yet it holds great significance in the development of innovative materials as substitutes for traditional semiconductors, which are insulative and unstable in less than ∼10 nm thickness. Herein, atomically precise gold nanoclusters with well-defined compositions and structures were investigated to establish a mathematical relation between conductivity and interparticle distance. This was accomplished using high-pressure in situ resistance characterizations, synchrotron X-ray diffraction (XRD), and the Murnaghan equation of state. Based on this precise correlation, it was predicted that the conductivity of Au25(SNap)18 (SNap: 1-naphthalenethiolate) solid is comparable to that of bulk silver when the interparticle distance is reduced to approximately 3.6 Å. Furthermore, the study revealed the coexisting, competing tunneling, and incoherent hopping charge transport mechanisms, which differed from those previously reported. The introduction of conjugation-structured ligands, tuning of the structures of metal nanoclusters, and use of high-pressure techniques contributed to enhanced conductivity, and thus, the charge carrier types were determined using Hall measurements. Overall, this study provides valuable insight into the charge transport in gold nanocluster solids and represents an important advancement in metal nanocluster semiconductor research.
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Affiliation(s)
- Shiyu Ji
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- University of Science and Technology of China, Hefei 230601, P. R. China
| | - Di Peng
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- University of Science and Technology of China, Hefei 230601, P. R. China
| | - Fang Sun
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Qing You
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Runguo Wang
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- University of Science and Technology of China, Hefei 230601, P. R. China
| | - Nan Yan
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yue Zhou
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- University of Science and Technology of China, Hefei 230601, P. R. China
| | - Weiyi Wang
- University of Science and Technology of China, Hefei 230601, P. R. China
| | - Qing Tang
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 401331, China
| | - Nan Xia
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Zhi Zeng
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
| | - Zhikun Wu
- Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
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13
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Chen E, Yu H, He J, Peng D, Zhu P, Pan S, Wu X, Wang J, Ji C, Chao Z, Xu Z, Wu Y, Chao D, Wu Y, Zhang Z. The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize. Plant Cell 2023; 35:4066-4090. [PMID: 37542515 PMCID: PMC10615213 DOI: 10.1093/plcell/koad215] [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: 03/13/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/07/2023]
Abstract
Endosperm filling in maize (Zea mays), which involves nutrient uptake and biosynthesis of storage reserves, largely determines grain yield and quality. However, much remains unclear about the synchronization of these processes. Here, we comprehensively investigated the functions of duplicate NAM, ATAF1/2, and CUC2 (NAC)-type transcription factors, namely, ZmNAC128 and ZmNAC130, in endosperm filling. The gene-edited double mutant zmnac128 zmnac130 exhibits a poorly filled kernel phenotype such that the kernels have an inner cavity. RNA sequencing and protein abundance analysis revealed that the expression of many genes involved in the biosynthesis of zein and starch is reduced in the filling endosperm of zmnac128 zmnac130. Further, DNA affinity purification and sequencing combined with chromatin-immunoprecipitation quantitative PCR and promoter transactivation assays demonstrated that ZmNAC128 and ZmNAC130 are direct regulators of 3 (16-, 27-, and 50-kD) γ-zein genes and 6 important starch metabolism genes (Brittle2 [Bt2], pullulanase-type starch debranching enzyme [Zpu1], granule-bound starch synthase 1 [GBSS1], starch synthase 1 [SS1], starch synthase IIa [SSIIa], and sucrose synthase 1 [Sus1]). ZmNAC128 and ZmNAC130 recognize an additional cis-element in the Opaque2 (O2) promoter to regulate its expression. The triple mutant zmnac128 zmnac130 o2 exhibits extremely poor endosperm filling, which results in more than 70% of kernel weight loss. ZmNAC128 and ZmNAC130 regulate the expression of the transporter genes sugars that will eventually be exported transporter 4c (ZmSWEET4c), sucrose and glucose carrier 1 (ZmSUGCAR1), and yellow stripe-like2 (ZmYSL2) and in turn facilitate nutrient uptake, while O2 plays a supporting role. In conclusion, ZmNAC128 and ZmNAC130 cooperate with O2 to facilitate endosperm filling, which involves nutrient uptake in the basal endosperm transfer layer (BETL) and the synthesis of zeins and starch in the starchy endosperm (SE).
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Affiliation(s)
- Erwang Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Huiqin Yu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Di Peng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Panpan Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Shuxing Pan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Xu Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhuopin Xu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Yuejin Wu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Daiyin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
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14
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Lu C, Peng D, Erandani WCKU, Mitchell K, Martyniuk CJ, Trudeau VL. Simultaneous extraction and detection of peptides, steroids, and proteins in small tissue samples. Front Endocrinol (Lausanne) 2023; 14:1266985. [PMID: 37876537 PMCID: PMC10593444 DOI: 10.3389/fendo.2023.1266985] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
The detection and quantification of hormones are important to assess the reproductive and stress status of experimental models and for the diagnosis of diseases in human and veterinary clinics. Traditionally, steroid, peptide, and protein hormones are analyzed in individual experiments using different extraction methodologies. With the new advancement on HPLC sorbents, the simultaneous measurement of hormones from different categories becomes possible. In this study, we present a novel sample processing strategy for the simultaneous extraction and detection of peptides, steroids, and proteins using high-resolution liquid chromatography tandem mass spectrometry. We demonstrate the sensitivity of our method for small tissues by acquiring data from brain, pituitary gland, and gonads of single zebrafish samples. This approach promises to shed light on the hormonal pathways and their interrelationships, providing knowledge on the integration of hormone systems.
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Affiliation(s)
- Chunyu Lu
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Di Peng
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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15
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Chen K, Yang F, Shen H, Wang C, Li X, Chervova O, Wu S, Qiu F, Peng D, Zhu X, Chuai S, Beck S, Kanu N, Carbone D, Zhang Z, Wang J. Individualized tumor-informed circulating tumor DNA analysis for postoperative monitoring of non-small cell lung cancer. Cancer Cell 2023; 41:1749-1762.e6. [PMID: 37683638 DOI: 10.1016/j.ccell.2023.08.010] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
We report a personalized tumor-informed technology, Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) using deep sequencing of 50 patient-specific variants to detect molecular residual disease (MRD) with a limit of detection of 0.004%. PROPHET and state-of-the-art fixed-panel assays were applied to 760 plasma samples from 181 prospectively enrolled early stage non-small cell lung cancer patients. PROPHET shows higher sensitivity of 45% at baseline with circulating tumor DNA (ctDNA). It outperforms fixed-panel assays in prognostic analysis and demonstrates a median lead-time of 299 days to radiologically confirmed recurrence. Personalized non-canonical variants account for 98.2% with prognostic effects similar to canonical variants. The proposed tumor-node-metastasis-blood (TNMB) classification surpasses TNM staging for prognostic prediction at the decision point of adjuvant treatment. PROPHET shows potential to evaluate the effect of adjuvant therapy and serve as an arbiter of the equivocal radiological diagnosis. These findings highlight the potential advantages of personalized cancer techniques in MRD detection.
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Fan Yang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Haifeng Shen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | | | - Xi Li
- Burning Rock Biotech, Guangzhou 510300, China
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Shuailai Wu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Fujun Qiu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Di Peng
- Burning Rock Biotech, Guangzhou 510300, China
| | - Xin Zhu
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Nnennaya Kanu
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - David Carbone
- James Thoracic Oncology Center, Ohio State University, Columbus, OH 43026, USA
| | | | - Jun Wang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
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16
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Peng D, Yang L, Liang XF, Chai F. Dietary zinc levels affect growth, appetite, and lipid metabolism of Chinese perch (Siniperca chuatsi). Fish Physiol Biochem 2023; 49:1017-1030. [PMID: 37718352 DOI: 10.1007/s10695-023-01238-w] [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] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/27/2023] [Indexed: 09/19/2023]
Abstract
An 84-day feeding experiment was conducted to investigate the effects of dietary Zn (zinc) on growth performance, food intake, and lipid metabolism of Chinese perch (Siniperca chuatsi). Five isonitrogenous and isolipidic diets with differential Zn contents (67, 100, 149, 230, and 410 mg/kg) were fed to 270 fish (35.47 ± 0.49 g). Results showed that fish growth and food intake increased markedly with the dietary 149 mg/kg Zn levels. Meanwhile, the food intake of 149 mg/kg group was significantly higher than that of other treatment groups after feeding for 8 weeks (P < 0.05). The qRT-PCR results showed that the expression of center appetite regulation factors in the hypothalamus was significantly regulated, and 149 mg/kg significantly increased mRNA expression of npy (neuropeptide Y) and decreased pomc (anorexigenic proopiomelanocortin) and cart (cocaine- and amphetamine-regulated transcript) gene expression. Meanwhile, the expressions of the main genes (such as leptin A and ghrelin) involved in peripheral appetite regulation factors were significantly up-regulated firstly and then reduced with the dietary Zn level increased, whereas the expression of cck (cholecystokinin) was significantly up-regulated. Serum AST (aspartate transaminase) and ALT (alanine transaminase) activities in fish fed the diets containing 230 and 410 mg/kg were significantly higher than that in other groups (P < 0.05). The lipid content of liver in 67 and 100 mg/kg groups was significantly higher than other groups (P < 0.05). Furthermore, dietary Zn significantly elevated the serum TG (triglyceride) and TCHO (total cholesterol) content levels (P < 0.05). Fish fed a high Zn diet (149, 230, and 410 mg/kg) dramatically down-regulated expression of srebp1 (sterol regulatory element binding proteins1c) and fas (fatty acid synthetase), but up-regulated expression of pparα (peroxisome proliferators-activated receptor-α) and cpt1 (carnitine palmitoyl transferase I) in the liver. The optimal dietary Zn inclusion level ranged from 146.69 to 152.86 mg/kg diet, based on two-slope broken-line regression analysis of WGR (weight gain rate) and FCR (feed conversion rate) for Chinese perch.
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Affiliation(s)
- Di Peng
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Ministry of Education, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Wuhan, 430070, China
| | - Linwei Yang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Ministry of Education, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Wuhan, 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
- Ministry of Education, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Wuhan, 430070, China.
| | - Farui Chai
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
- Ministry of Education, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Wuhan, 430070, China
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Zong K, Peng D, Jiang P, Li Y, Cao Z, Wu Z, Mou T, Huang Z, Shen A, Wu Z, Zhou B. Derivation and validation of a novel preoperative risk prediction model for surgical site infection in pancreaticoduodenectomy and comparison of preoperative antibiotics with different risk stratifications in retrospective cohort. J Hosp Infect 2023; 139:228-237. [PMID: 37459915 DOI: 10.1016/j.jhin.2023.07.001] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Surgical site infections (SSIs) are common postoperative complications of pancreaticoduodenectomy. AIM To develop a model for preoperative identification of the risk of SSI that may improve outcomes and guide preoperative antibiotics. METHODS The prediction model was built by meta-analysis. After literature search and inclusion, data extraction, and quantitative synthesis, the prediction model was established based on the pooled odds ratio of predictors. A single-centre retrospective cohort was the validation cohort. Receiver operating characteristic curves and area under the curve were used to assess the model's ability. We also created a decision curve and a calibration plot to assess the nomogram. The effects of prophylactic antibiotics on SSI were compared between groups by multivariable logistic regression with different risk stratifications. FINDINGS Twenty-eight studies were included in the meta-analysis, 17 studies in the derivation cohort. Age, male gender, body mass index, pancreatic duct diameter, high-risk diagnosis, and preoperative biliary drainage were selected to build the prediction model. The model was validated in an external cohort. The cut-off value was 3.5 and area under the curve (AUC) was 0.76 in open pancreaticoduodenectomy (OPD). In laparoscopic pancreaticoduodenectomy, the cut-off value was 4.5 and AUC was 0.69. Decision curve and calibration plot showed good usability of the model, especially in OPD. Multivariable logistic regression did not indicate differences between broad- and narrow-spectrum antibiotics for SSI in different risk stratifications. CONCLUSION The model can identify patients with a high risk of SSI preoperatively. The choice of prophylactic antibiotics under different risk stratifications should be investigated further.
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Affiliation(s)
- K Zong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - D Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - P Jiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Y Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Z Cao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Z Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - T Mou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Z Huang
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing, China
| | - A Shen
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Z Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - B Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zhang X, Gao Y, Xing Z, Peng D, Han Y. Study on pressure-induced isostructural phase transition and electrical transport properties of BiOBr. Phys Chem Chem Phys 2023. [PMID: 37435704 DOI: 10.1039/d3cp02084c] [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: 07/13/2023]
Abstract
In this work, we prepared a BiOBr powder sample by the coprecipitation method for in situ high-pressure AC impedance spectroscopy tests, in situ high-pressure Raman measurements and in situ high-pressure X-ray diffraction experiments to explore its structural properties and electrical transport processes under compression. Two pressure-driven isostructural phase transitions, T-T' and T'-T'' (T - tetragonal, T' - tetragonal 1 and T'' - tetragonal 2), were discovered at around 10.0 and 15.0 GPa, respectively. The pressure-induced changes in the crystal structure and electrical transport of BiOBr can provide a reference for explaining the mechanism of the isostructural phase transition of other similar compounds after compression.
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Affiliation(s)
- Xiaotong Zhang
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, China.
| | - Yang Gao
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China.
- Shanghai Institute of Laser Plasma, Shanghai 200000, China
| | - Zhenfang Xing
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, China.
| | - Di Peng
- Center for High Pressure Science and Technology Advanced Research, Shanghai, 201203, China.
| | - Yonghao Han
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, China.
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Zou X, Zou S, Guo Y, Peng D, Min H, Zhang R, Qin R, Mai J, Wu Y, Sun X. Association of smoking status and nicotine dependence with multi-morbidity in China: A nationally representative crosssectional study. Tob Induc Dis 2023; 21:81. [PMID: 37333503 PMCID: PMC10273826 DOI: 10.18332/tid/166110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 05/12/2023] [Indexed: 06/20/2023] Open
Abstract
INTRODUCTION Multi-morbidity is a public health priority as it is associated with an increased risk of mortality and a substantial healthcare burden. Smoking is considered a predisposing factor for multi-morbidity, but evidence for an association between multi-morbidity and nicotine dependence is insufficient. This study aimed to explore the association between smoking status, nicotine dependence, and multi-morbidity in China. METHODS We recruited 11031 Chinese citizens from 31 provinces in 2021 using a multistage stratified cluster sampling strategy to ensure the study population represented national population characteristics. The association between smoking status and multi-morbidity was analyzed using binary logistic regression and multinomial logit regression models. We then analyzed the associations between four kinds of smoking status (age at smoking initiation, cigarette consumption per day, smoking when ill in bed, and inability to control smoking in public places), nicotine dependence, and multi-morbidity among participants who were current smokers. RESULTS Compared with non-smokers, the odds of multi-morbidity were higher among ex-smokers (adjusted odd ratio, AOR=1.40, 95% CI: 1.07-1.85). The risk of multi-morbidity was greater in participants who were underweight/overweight/obese (AOR=1.90; 95% CI: 1.60-2.26) compared with those who were normal weight. and also greater for drinkers (AOR=1.34; 95% CI: 1.09-1.63) than non-drinkers. Compared with children who began smoking at the age of <15 years, participants aged >18 years had a lower likelihood of multi-morbidity (AOR=0.52; 95% CI: 0.32-0.83). People who consumed ≥31 cigarettes per day (AOR=3.77; 95% CI: 1.47-9.68) and those who smoked when ill in bed (AOR=1.70; 95% CI: 1.10-2.64) were more likely to have multi-morbidity. CONCLUSIONS Our findings show that smoking behavior, including initiation age, frequency of daily smoking, and still smoking during illness or in public, is a critical risk factor for multi-morbidity, especially when combined with alcohol consumption, physical inactivity, and abnormal weight (underweight, overweight, or obese). This highlights the crucial effect of smoking cessation in the prevention and control of multi-morbidity, especially in patients with three or more diseases. Implementing smoking and lifestyle interventions to promote health would both benefit adults and prevent the next generation from initiating habits that increase the risk of multi-morbidity.
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Affiliation(s)
- Xinye Zou
- Faculty of Education, University of Cambridge, Cambridge, United Kingdom
- School of Public Health, Peking University, Beijing, China
| | - Siyu Zou
- School of Public Health, Peking University, Beijing, China
| | - Yi Guo
- School of Public Health, Peking University, Beijing, China
| | - Di Peng
- School of Education, Qingdao Hengxing University of Science and Technology, Qingdao, China
| | - Hewei Min
- School of Public Health, Peking University, Beijing, China
| | - Ruolin Zhang
- Department of Natural and Applied Science, Duke Kunshan University, Jiangsu, China
| | - Ruiwen Qin
- College of Foreign Languages, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Jianrong Mai
- School of Public Health, Peking University, Beijing, China
- School of Nursing, Guangzhou Xinhua University, Guangzhou, China
| | - Yibo Wu
- School of Public Health, Peking University, Beijing, China
| | - Xinying Sun
- School of Public Health, Peking University, Beijing, China
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Peng D, Ando K, Hußmann M, Gloger M, Skoczylas R, Mochizuki N, Betsholtz C, Fukuhara S, Schulte-Merker S, Lawson ND, Koltowska K. Correction: Proper migration of lymphatic endothelial cells requires survival and guidance cues from arterial mural cells. eLife 2023; 12:90048. [PMID: 37307048 DOI: 10.7554/elife.90048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
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21
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Shui K, Wang C, Zhang X, Ma S, Li Q, Ning W, Zhang W, Chen M, Peng D, Hu H, Fang Z, Guo A, Gao G, Ye M, Zhang L, Xue Y. Small-sample learning reveals propionylation in determining global protein homeostasis. Nat Commun 2023; 14:2813. [PMID: 37198164 DOI: 10.1038/s41467-023-38414-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7-16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.
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Affiliation(s)
- Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xuedi Zhang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qinyu Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Guanjun Gao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, Hubei, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, 210031, Jiangsu, China.
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Chen M, Zhang W, Gou Y, Xu D, Wei Y, Liu D, Han C, Huang X, Li C, Ning W, Peng D, Xue Y. GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. Nucleic Acids Res 2023:7157529. [PMID: 37158278 DOI: 10.1093/nar/gkad383] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/22/2023] [Accepted: 04/29/2023] [Indexed: 05/10/2023] Open
Abstract
Protein phosphorylation, catalyzed by protein kinases (PKs), is one of the most important post-translational modifications (PTMs), and involved in regulating almost all of biological processes. Here, we report an updated server, Group-based Prediction System (GPS) 6.0, for prediction of PK-specific phosphorylation sites (p-sites) in eukaryotes. First, we pre-trained a general model using penalized logistic regression (PLR), deep neural network (DNN), and Light Gradient Boosting Machine (LightGMB) on 490 762 non-redundant p-sites in 71 407 proteins. Then, transfer learning was conducted to obtain 577 PK-specific predictors at the group, family and single PK levels, using a well-curated data set of 30 043 known site-specific kinase-substrate relations in 7041 proteins. Together with the evolutionary information, GPS 6.0 could hierarchically predict PK-specific p-sites for 44046 PKs in 185 species. Besides the basic statistics, we also offered the knowledge from 22 public resources to annotate the prediction results, including the experimental evidence, physical interactions, sequence logos, and p-sites in sequences and 3D structures. The GPS 6.0 server is freely available at https://gps.biocuckoo.cn. We believe that GPS 6.0 could be a highly useful service for further analysis of phosphorylation.
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Affiliation(s)
- Miaomiao Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Weizhi Zhang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Yujie Gou
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Danyang Xu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Yuxiang Wei
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Dan Liu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Xinhe Huang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Chengzhi Li
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Wanshan Ning
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing210031, China
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Peng D, Zhao Z. Highly efficient ferric ion sensing and high resolution latent fingerprint imaging based on fluorescent silicon quantum dots. Spectrochim Acta A Mol Biomol Spectrosc 2023; 299:122827. [PMID: 37187149 DOI: 10.1016/j.saa.2023.122827] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
Expanding the application of silicon based luminescent materials is a fast-growing interdisciplinary field. Herein, a novel fluorescent bifunctional probe based on silicon quantum dots (SiQDs) for highly sensitive Fe3+ sensing and high-resolution latent fingerprint (LFP) imaging was subtly devised. The SiQD solution was mildly prepared using 3-aminopropyl trimethoxysilane as the silicon source and sodium ascorbate as the reductant, showing green emission at 515 nm under UV irradiation with a quantum yield of 19.8%. As a highly sensitive fluorescent sensor, the SiQD was demonstrated to have a highly selective quenching with Fe3+ in the concentration range of 2-1000 μM with the LOD of 0.086 μM in water. The quenching rate constant and association constant of the SiQDs-Fe3+ complex was calculated to be 1.05 × 1012 mol/s and 6.8 × 103 L/mol, respectively, suggesting a static quenching effect between them. Moreover, to achieve high-resolution LFP imaging, a novel SiO2@SiQDs composite powder was further fabricated. The SiQDs were covalently anchored on the surface of silica nanospheres to conquer aggregation-caused quenching for the high-solid fluorescence. In the demonstration of LFP imaging, this silicon based luminescent composite exhibited high developing sensitivity, high selectivity and high contrast, indicating its practical value as a fingerprint developer at crime scenes.
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Affiliation(s)
- Di Peng
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory, Criminal Investigation School, Southwest University of Political Science and Law, Chongqing 401102, China; Engineering Research Center of Intelligent Justice (Southwest University of Political Science and Law), Ministry of Education, Chongqing 401102, China.
| | - Zihe Zhao
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory, Criminal Investigation School, Southwest University of Political Science and Law, Chongqing 401102, China
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West C, Zhao H, Cantor R, Sood V, Lal A, Beaty C, Kirklin J, Peng D. Social Determinants of Heath and Outcomes after Pediatric Ventricular Assist Device Implantation. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.110] [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: 04/05/2023] Open
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Nandi D, Wright L, Sublett-Smith J, Brax A, Almond C, Bansal N, Azeka E, Butts R, Conway J, Chen C, Cunningham C, Fisher L, Hall E, Hunter T, Kobayashi R, Patterson D, Peng D, Simpson K, Ryan T, Spinner J, Wisotzkey B, Zangwill S, Gajarski R, O'Connor M. Suboptimal Titration of Heart Failure Medications in Pediatric Patients: Baseline Data from the ACTION Network. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1627] [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: 04/05/2023] Open
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McCormick A, Jarosz A, Lim H, Peng D, Schumacher K, Frame D, Cusick M. Daratumumab for Chronic Antibody Mediated Rejection and Subsequent Successful Pediatric Heart-Kidney Retransplantation. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1313] [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: 04/05/2023] Open
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Wang K, Zhang X, Zhou W, Peng D, Liu Y. Correction method for film cooling effectiveness measurement with temperature gradient using endoscopic PSP and TSP technique. J Vis (Tokyo) 2023. [DOI: 10.1007/s12650-023-00918-2] [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: 04/07/2023]
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Liu J, Zuo H, Wang Z, Wang W, Qian X, Xie Y, Peng D, Xie Y, Hong L, You W, Lou H, Luo G, Ren J, Shen B, Zheng J, Wang H, Ju Z. The m6A reader YTHDC1 regulates muscle stem cell proliferation via PI4K-Akt-mTOR signalling. Cell Prolif 2023:e13410. [PMID: 36722312 PMCID: PMC10392063 DOI: 10.1111/cpr.13410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/02/2023] Open
Abstract
Muscle stem cells are required for the homeostasis and regeneration of mammalian skeletal muscles. It has been reported that RNA N6-methyladenosine (m6A) modifications play a pivotal role in muscle development and regeneration. Nevertheless, we know little about which m6A reader regulates mammalian muscle stem cells. Here, we discovered that the m6A reader Ythdc1 is indispensable for mouse skeletal muscle regeneration and proliferation of muscle stem cells. In the absence of Ythdc1, Muscle stem cells in adult mice are unable to exit from quiescence. Mechanistically, Ythdc1 binds to m6A-modified Pi4k2a and Pi4kb mRNAs to regulate their alternative splicing and thus PI4K-Akt-mTOR signalling. Ythdc1-null muscle stem cells show a deficiency in phosphatidylinositol (PI) 3,4,5-trisphosphate, phospho-Akt and phospho-S6, which correlates with a failure in exit from quiescence. Our findings connect dynamic RNA methylation to the regulation of PI4K-Akt-mTOR signalling during stem cell proliferation and adult tissue regeneration.
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Affiliation(s)
- Jin Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Hongna Zuo
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Ziliu Wang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Wei Wang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Xuezhen Qian
- State Key Laboratory of Reproductive Medicine, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Yingyuan Xie
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Di Peng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Liquan Hong
- Department of Clinical Laboratory, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Wanling You
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Huiling Lou
- Department of Geriatrics, National Key Clinical Specialty, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guanzheng Luo
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, China
| | - Jinping Zheng
- Department of Public Health and Preventive Medicine, Changzhi Medical College, Changzhi, P. R. China
| | - Hu Wang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China.,Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Institute of Aging Research, Hangzhou Normal University, Hangzhou, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
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Ding G, Wang X, Ling-hu C, Fan Y, Zhou L, Luo D, Meng S, Meng J, Chen W, Liu Y, Gao G, Peng D. AIE-active light up probe for sensitive detection of amine vapors and its practical application in food spoilage monitoring. Tetrahedron 2023. [DOI: 10.1016/j.tet.2023.133306] [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: 02/11/2023]
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Chen Z, Su Y, Peng D, Wang W, Zhong J, Zhou A, Tan L. Circ_0124055 promotes the progression of thyroid cancer cells through the miR-486-3p/MTA1 axis. J Endocrinol Invest 2023:10.1007/s40618-022-01998-x. [PMID: 36604405 DOI: 10.1007/s40618-022-01998-x] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/08/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Thyroid cancer is one of the malignancy cancers. CircRNA, a non-coding RNA, plays an important role in the development of cancer. The relationship and roles of circ_0124055, miR-486-3p and MTA1 in thyroid cancer have not been reported. METHODS Real-time quantitative polymerase chain reaction (RT-qPCR) was performed to analyze the RNA levels of circ_0124055, miR-486-3p and MTA1. Western blot was conducted to analyze the protein levels of MTA1, Epithelial cadherin (E-cadherin) and Neuro cadherin (N-cadherin). Subcellular localization assay was used to analyze circ_0124055 location in thyroid cancer cells. Colony formation assay and 5-Ethynyl-2'-deoxyuridine (EdU) assay were carried out to analyze cell proliferation. Cell migration and invasion were analyzed by wound-healing assay and transwell assay. Flow cytometry assay was performed to investigate cell apoptosis. Dual-luciferase reporter assay and RIP assay were employed to analyze the interactions among circ_0124055, miR-486-3p and MTA1. Immunohistochemical (IHC) assay was performed to assess the expression of Ki67, MTA1 and E-cadherin in tumor tissues. Thyroid cancer tumor growth in vivo was evaluated by tumor xenograft mouse model assay. RESULTS The expression of circ_0124055 was up-regulated in tumor tissues and cells. Knockdown of circ_0124055 could inhibit thyroid cancer cell proliferation, migration and invasion and promote cell apoptosis, accompanied by the dysregulation of E-cadherin and N-cadherin expression. Circ_0124055 could target miR-486-3p, and miR-486-3p could target MTA1. MiR-486-3p inhibitor could restore the effect of circ_0124055 knockdown in the progression of thyroid cancer. Moreover, MTA1 overexpression weakened the inhibitory effects of miR-486-3p mimics on the progression of thyroid cancer. Further, circ_0124055 could influence tumor growth in vivo. CONCLUSION Circ_0124055 promoted the progression of thyroid cancer cells through the miR-486-3p /MTA1 axis.
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Affiliation(s)
- Z Chen
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - Y Su
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - D Peng
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - W Wang
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - J Zhong
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - A Zhou
- Department of Nuclear Medicine, Jiangxi Tumor Hospital, Nanchang, Jiangxi, China
| | - L Tan
- Department of Nuclear Medicine, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, China.
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Ji J, Zhang H, Peng D, Fu M, He C, Yi F, Yin H, Ding Y. Estimation of typical agricultural machinery emissions in China: Real-world emission factors and inventories. Chemosphere 2022; 307:136052. [PMID: 35977564 DOI: 10.1016/j.chemosphere.2022.136052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Jianglin Ji
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Mechanical and Traffic Engineering, Southwest Forestry University, Kunming, 650224, China; Key Lab of Vehicle Emission and Safety on Plateau Mountain, Yunnan Provincial Department of Education, Kunming, 650224, China
| | - Hefeng Zhang
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Di Peng
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Mingliang Fu
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Chao He
- School of Mechanical and Traffic Engineering, Southwest Forestry University, Kunming, 650224, China; Key Lab of Vehicle Emission and Safety on Plateau Mountain, Yunnan Provincial Department of Education, Kunming, 650224, China
| | - Fei Yi
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hang Yin
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Yan Ding
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Vehicle Emission Control Center of Ministry of Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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Peng D, Liu M, Tang B, Feng X, Liu Y, Li J, Wu F, Orlandini L. MR-Guided Boost Irradiation for Patients with Pelvic Recurrence of Gynecological Cancer. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1260] [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: 11/16/2022]
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Yuan W, Fu Z, Wu Y, Peng D, Zhang L, Zeng Z, Zhang Y, Zhang Z, Zhang S, Liu Y. Time-domain convolution model for studying oscillation dynamics in an injection-locked optoelectronic oscillator. Opt Express 2022; 30:40728-40738. [PMID: 36299002 DOI: 10.1364/oe.473268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
A time-domain convolution model is proposed to study the oscillation dynamics in the injection-locked optoelectronic oscillator (OEO). The model has the ability to calculate multiple characteristics of the oscillation signal, such as the spectrum and the phase noise. Based on the model, the injection locking, the frequency pulling and the asymmetrical spectrum generation phenomena are numerically simulated in success. The simulation results fit in with the experimental results, indicating that the proposed model accurately describes the oscillation dynamics in the injection-locked OEO. In addition, the building-up process of the oscillation signal in the OEO is simulated. Alternating appearance of the sidebands on both sides of the primary oscillation mode is observed for the first time in the asymmetrical spectrum generation. This model is a powerful tool to study the oscillation dynamics in the injection-locked OEO.
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Andelfinger G, Zenker M, Norrish G, Russell M, Meisner J, Peng D, Prendiville T, Kleinmahon J, Kantor P, Sen DG, Human D, Ewert P, Krueger M, Reber D, Donner B, Hart C, Odri-Komazec I, Rupp S, Hahn A, Hanser A, Hofbeck M, Draaisma J, Udink ten Cate F, Mussa A, Ferrero G, Vaujois L, Raboisson M, Delrue M, Marquis C, Théorêt Y, Kaski J, Gelb B, Wolf C. MAPK AND AKT/MTOR INHIBITION IMPROVES CHILDHOOD RASOPATHY-ASSOCIATED CARDIOMYOPATHY. Can J Cardiol 2022. [DOI: 10.1016/j.cjca.2022.08.056] [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: 11/25/2022] Open
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Rokui S, Peng D, Ye J. LONG-TERM OUTCOMES OF ISOLATED MECHANICAL VERSUS BIOPROSTHETIC MITRAL VALVE REPLACEMENT IN PROPENSITY MATCHED PATIENTS. Can J Cardiol 2022. [DOI: 10.1016/j.cjca.2022.08.192] [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: 11/28/2022] Open
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Li Y, Peng D. Hydrophobic‐Binding‐Driven and Fluoresence‐Free Development of Aged Fingerprints Based on Zinc Oxide Nanoparticles. ChemistrySelect 2022. [DOI: 10.1002/slct.202202252] [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: 11/10/2022]
Affiliation(s)
- Yayi Li
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory Criminal Investigation School Southwest University of Political Science and Law Chongqing 401120 P.R. China
| | - Di Peng
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory Criminal Investigation School Southwest University of Political Science and Law Chongqing 401120 P.R. China
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Abstract
The blood fingerprint enhancement is not so eye-catching as latent fingerprint development in forensic community, but it is indeed an important piece of evidence for personal identification, forensic analysis and even reconstruction of crime scenes. In over past ten years, novel reagents, advanced materials and emerging techniques have growingly participated in blood fingerprint enhancement, which not only leads to a higher level of developing sensitivity, selectivity and contrast, but also endows blood impressions with more forensic significance. This review summarizes recent advances in conventional chemical reagents targeting at heme, protein and amino acid as well as emerging enhancement techniques based on advanced materials, new equipment or methods. Some critical issues in forensic science are also discussed, including partial blood fingerprint enhancement, false positive of developing reagents, the compatibility of blood enhancement technique and DNA, fingerprint age determination, and so on. Finally, we have proposed several urgent problems to be solved and the prospects of some promising techniques were proposed in the field of blood fingerprint enhancement in future work.
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Affiliation(s)
- Zimin Zhang
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory, Criminal Investigation School, Southwest University of Political Science and Law, Chongqing, China
| | - Di Peng
- Chongqing Institutes of Higher Education Key Forensic Science Laboratory, Criminal Investigation School, Southwest University of Political Science and Law, Chongqing, China
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Zeng Z, Peng D, Yi Y, Zeng X, Liu S, Luo Y, Liu A. EP08.01-003 Efficacy of Immune Checkpoint Inhibitors in Pulmonary Sarcomatoid Carcinoma, A Multicenter Retrospective Study. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.575] [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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Liu L, Peng D, Fu S, Wang Y, Qin Y. Multi-band microwave signals generation based on a photonic sampling with a flexible ultra-short pulse source. Opt Express 2022; 30:32151-32161. [PMID: 36242283 DOI: 10.1364/oe.469085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
We propose and experimentally demonstrate a photonic sampling-enabled multi-band microwave signals generation scheme. The intermediate-frequency input signal is up-converted to high frequency output signals in multiple frequency bands, after being optically sampled by an ultra-short optical pulse train and subsequently being detected by a photodetector (PD). The ultra-short pulse source, realized by using an electro-optic modulation-based time lens with the chirp compensation, can be flexibly adjusted to enhance the performance of multi-band frequency up-conversion. In the experiment, after optimizing the optical ultra-short pulse source with a repetition frequency of 8 GHz, ten phase-coded up-converted microwave signals with a 13-bit Barker code were successfully generated within a frequency range from 7 GHz to 41 GHz. The power fluctuation among the generated microwave signals in multi-band is measured to be 5.9 dB. The experiment results indicate that, our proposed scheme can realize the multi-band up-conversion with a high fidelity.
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Liu L, Jiang H, Zhang X, Peng D. Biogeographic pattern and relevant environmental factors for rhizobial communities in the rhizosphere and root nodules of kudzu (Pueraria lobata). Environ Sci Pollut Res Int 2022; 29:49136-49146. [PMID: 35212898 DOI: 10.1007/s11356-022-19335-3] [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] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Kudzu (Pueraria lobata) is an important medicinal plant, which can associate with rhizobia for nitrogen fixation. The mutualistic symbiosis between rhizobium and kudzu is not well understood, but it is necessary to fully utilize kudzu. Nodules and rhizosphere soils collected from 16 sampling sites were characterized based on phylogenetic analyses of the rpoB gene; 16S rRNA gene; the housekeeping genes SMc00019, truA, and thrA; and the symbiotic genes nodA and nifH. The relationships between biogeographic pattern, nitrogenase activity, and environmental factors were studied. Results indicated that a clear biogeographic pattern of rhizobial communities in the kudzu rhizosphere existed in southern China; latitude and soil pH were found to be the most important factors affecting the biogeographic pattern. Bradyrhizobium diazoefficiens and Bradyrhizobium erythrophlei were the dominant species in kudzu rhizosphere. The symbiotic rhizobia in kudzu nodules mainly belonged to B. lablabi, B. elkanii, B. pachyrhizi, and B. japonicum. Nitrogenase activities in the nodules of kudzu in the Jiangxi sampling region were significantly higher than those in the Guangxi and Hunan sampling regions, and they were significantly negatively correlated to pH and exchangeable Ca. These results constitute the first report of the existence of symbiotic genes in kudzu bradyrhizobia, which are similar to those in B. elkanii and B. pachyrhizi. Our findings could improve the understanding of kudzu-rhizobium symbiosis and could advance the application of rhizobial inoculation in medicinal legumes in terms of increasing the content of active ingredients.
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Affiliation(s)
- Lu Liu
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan, China
| | - Huidan Jiang
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan, China
| | - Xin Zhang
- Hunan Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan, China
| | - Di Peng
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan, China.
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Zhou J, Yang J, Zhang Z, Li Y, Yi B, Tang Y, Li D, Li X, Peng D, Li XI, Wang Y, Li H, Li B, Wang C, Zhu P, Chen L, Wu S, Fang S, Li C, Qiu F, Chuai S, Zhang Z. Abstract 5917: Patient-specific tumor-informed circulating tumor DNA (ctDNA) analysis for postoperative monitoring of patients with stages I-III colorectal cancer (CRC). Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5917] [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: 11/16/2022]
Abstract
Abstract
Background: Identifying molecular residual disease (MRD) with tailored tumor-informed ctDNA based next-generation sequencing (NGS) assays after curative surgery could facilitate the individualized management of resected CRC patients. Here, we investigated the clinical utility of tumor-informed ctDNA mutation analysis using a novel Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) approach for accessing MRD in resected CRC patients. Using the same set of baseline and post-operative blood samples, we compared the performance of PROPHET assay with tumor-naïve fixed panel for detecting MRD and predicting recurrence in resected CRC patients.
Methods: The prospective study recruited 42 patients diagnosed with stage I-III CRC from May 2019 to Jun 2020 at the First Affiliated Hospital of Soochow University. Tumor tissue samples were collected at surgery. Blood samples collected before surgery (baseline), 8-day post-operative time point before any adjuvant therapy were analyzed. The detection and quantification of ctDNA for MRD assessment was investigated using PROPHET, a personalized, tumor-informed ctDNA assay designed to track up to 50 top-ranked patient-specific somatic variants based on whole-exome sequencing (WES) of the tumor tissue and matched white blood cells (WBCs). Tumor- naïve fixed assay was performed using targeted NGS panel, containing 41 gastrointestinal cancer-related genes.
Results: Baseline ctDNA status was detected in 95.23% (40/42) of the patients with PROPHET assay, and 69.05% (29/42) of the patients with fixed panel. Of 42 patients included in the analysis, 1, 25, and 16 patients had pathological stages I, II, and III CRC with baseline ctDNA detected in 100% (1/1), 92% (23/25), 100% (16/16) patients with PROPHET assay, and 100% (1/1), 64% (16/25), 75% (12/16) patients with fixed panel. Post-operative ctDNA-positive status with PROPHET assay was associated with 3-year DFS, compared with ctDNA-negative group (hazard ratio [HR], 16.57, 95% confidence interval [CI]:3.01-91.36, p=0.014). 15% (6/40) patients were identified to be MRD- positive and 83.33% (5/6) patients eventually relapsed at 3-years follow-up. Although fixed panel also showed high performance in predicting relapse HR, 4.48, 95% CI:1.9-10.9; p< 0.001, 27.5% (11/40) patients were identified to be MRD-positive and only 45.45% (5/11) patients eventually relapsed. 3-year prognostication with PROPHET assay at 8-day post-operation yielded higher positive predictive value (83.33% vs 45.45%), negative predictive value (91.18% vs 89.66%), and specificity (96.88% vs 81.25%) as compared with tumor-naïve fixed panel.
Conclusion: Patient-specific PROPHET assay based on unique somatic mutation profiles detects patients with high-risk of recurrence, which achieved higher specificity than tumor-naïve fixed panel.
Citation Format: Jian Zhou, Jian Yang, Zixiang Zhang, Ye Li, Bin Yi, Yuchen Tang, Dechun Li, Xiaozhe Li, Di Peng, XI Li, Yang Wang, Haiyan Li, Bing Li, Chenyang Wang, Pengfei Zhu, Longfei Chen, Shuailai Wu, Shuai Fang, Chenxi Li, Fujun Qiu, Shannon Chuai, Zhihong Zhang. Patient-specific tumor-informed circulating tumor DNA (ctDNA) analysis for postoperative monitoring of patients with stages I-III colorectal cancer (CRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5917.
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Affiliation(s)
- Jian Zhou
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yang
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zixiang Zhang
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ye Li
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bin Yi
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuchen Tang
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Dechun Li
- 1the First Affiliated Hospital of Soochow University, Suzhou, China
| | | | - Di Peng
- 2Burning Rock Biotech, Guangzhou, China
| | - XI Li
- 2Burning Rock Biotech, Guangzhou, China
| | - Yang Wang
- 2Burning Rock Biotech, Guangzhou, China
| | - Haiyan Li
- 2Burning Rock Biotech, Guangzhou, China
| | - Bing Li
- 2Burning Rock Biotech, Guangzhou, China
| | | | | | | | | | | | - Chenxi Li
- 2Burning Rock Biotech, Guangzhou, China
| | - Fujun Qiu
- 2Burning Rock Biotech, Guangzhou, China
| | | | - Zhihong Zhang
- 3The First Affiliated Hospital of Soochow University, Suzhou, China
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Ning W, Wei Y, Gao L, Han C, Gou Y, Fu S, Liu D, Zhang C, Huang X, Wu S, Peng D, Wang C, Xue Y. HemI 2.0: an online service for heatmap illustration. Nucleic Acids Res 2022; 50:W405-W411. [PMID: 35670661 PMCID: PMC9252725 DOI: 10.1093/nar/gkac480] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 03/02/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Recent high-throughput omics techniques have produced a large amount of biological data. Visualization of big omics data is essential to answer a wide range of biological problems. As a concise but comprehensive strategy, a heatmap can analyze and visualize high-dimensional and heterogeneous biomolecular expression data in an attractive artwork. In 2014, we developed a stand-alone software package, Heat map Illustrator (HemI 1.0), which implemented three clustering methods and seven distance metrics for heatmap illustration. Here, we significantly improved 1.0 and released the online service of HemI 2.0, in which 7 clustering methods and 22 types of distance metrics were implemented. In HemI 2.0, the clustering results and publication-quality heatmaps can be exported directly. For an in-depth analysis of the data, we further added an option of enrichment analysis for 12 model organisms, with 15 types of functional annotations. The enrichment results can be visualized in five idioms, including bubble chart, bar graph, coxcomb chart, pie chart and word cloud. We anticipate that HemI 2.0 can be a helpful web server for visualization of biomolecular expression data, as well as the additional enrichment analysis. HemI 2.0 is freely available for all users at: https://hemi.biocuckoo.org/.
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Affiliation(s)
- Wanshan Ning
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China.,Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yuxiang Wei
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Letian Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Cheng Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yujie Gou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shanshan Fu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinhe Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Sicheng Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing 210031, China
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Zhang F, Peng D, Liu L, Jiang H, Bai L. Cultivar-dependent rhizobacteria community and cadmium accumulation in rice: Effects on cadmium availability in soils and iron-plaque formation. J Environ Sci (China) 2022; 116:90-102. [PMID: 35219428 DOI: 10.1016/j.jes.2021.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 06/14/2023]
Abstract
The association between the rhizospheric microbial community and Cd accumulation in rice is poorly understood. A field trial was conducted to investigate the different rhizobacterial communities of two rice cultivars with high Cd accumulation (HA) and low Cd accumulation (LA) at four growth stages. Results showed that the Cd content in the roots of the HA cultivar was 1.23 - 27.53 higher than that of the LA cultivar (0.08 - 10.5 µg/plant) at four stages. The LA cultivar had a significantly lower Cd availability in rhizosphere and a higher quantity of iron plaque (IP) on the root surface than the HA cultivar at four stages. This resulted in the reduction of Cd concentration in IPs and Cd translocation from IP-to-root. Microbial analysis indicated that the LA cultivar formed a distinct rhizobacterial community from the HA cultivar and had less α-diversity. The rhizosphere of the LA cultivar was enriched in specific bacterial taxa (e.g., Massilia and Bacillus) involved in Cd immobilization by phosphate precipitation and IP formation by iron oxidization. However, the rhizosphere in the HA cultivar assembled abundant sulfur-oxidizing bacteria (e.g., Sulfuricurvum) and iron reduction bacteria (Geobacter). They promoted Cd mobilization and reduced IP formation via the metal redox process. This study reveals a potential approach in which specific rhizobacteria decrease or increase Cd accumulation in rice on contaminated soil and provides a new perspective for secure rice production.
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Affiliation(s)
- Feng Zhang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Peng
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lu Liu
- Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Huidan Jiang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lianyang Bai
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Yang H, Wang S, Peng D, Qin Y, Fu S. Optically powered 5G WDM fronthaul network with weakly-coupled multicore fiber. Opt Express 2022; 30:19795-19804. [PMID: 36221746 DOI: 10.1364/oe.457347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/16/2023]
Abstract
The number of base stations (BSs) for the fifth generation (5G) wireless network is substantially increased, as each coverage is greatly reduced. Therefore, both the miniaturization and the densification of BSs suffer from the challenges of electrical power supply and deployment cost. Here, we present an optically powered 5G fronthaul network, in support of the co-propagation of spatial-division-multiplexing (SDM) energy light and wavelength-division-multiplexing (WDM) 5G new radio (NR) signals over the weakly-coupled multicore fiber (WC-MCF). When the 60-W energy light at 1064.8-nm is equally distributed among the outer six cores, and the 9-Gbit/s 5G NR WDM signals are transmitted over the central core of 1-km WC seven-core fiber (WC-7CF), we can collect total 11.9-W electrical power at the remote node, for the purpose of optically powered small cells. Meanwhile, the error-vector magnitude (EVM) values of 1.5-Gbit/s 5G NR 64-level quadrature amplitude modulation orthogonal frequency division multiplexing (64QAM-OFDM) signals at the central frequency of 3.5 GHz fluctuate within a range of 0.3%∼0.39%, under a received electrical power of -25 dBm, for all six-wavelength channels. Six optically powered small cells are equipped with the characteristics of centralized management and flexible access-rate.
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Ando K, Tong L, Peng D, Vázquez-Liébanas E, Chiyoda H, He L, Liu J, Kawakami K, Mochizuki N, Fukuhara S, Grutzendler J, Betsholtz C. KCNJ8/ABCC9-containing K-ATP channel modulates brain vascular smooth muscle development and neurovascular coupling. Dev Cell 2022; 57:1383-1399.e7. [PMID: 35588738 DOI: 10.1016/j.devcel.2022.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/24/2021] [Revised: 12/22/2021] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
Loss- or gain-of-function mutations in ATP-sensitive potassium channel (K-ATP)-encoding genes, KCNJ8 and ABCC9, cause human central nervous system disorders with unknown pathogenesis. Here, using mice, zebrafish, and cell culture models, we investigated cellular and molecular causes of brain dysfunctions derived from altered K-ATP channel function. We show that genetic/chemical inhibition or activation of KCNJ8/ABCC9-containing K-ATP channel function leads to brain-selective suppression or promotion of arterial/arteriolar vascular smooth muscle cell (VSMC) differentiation, respectively. We further show that brain VSMCs develop from KCNJ8/ABCC9-containing K-ATP channel-expressing mural cell progenitor and that K-ATP channel cell autonomously regulates VSMC differentiation through modulation of intracellular Ca2+ oscillation via voltage-dependent calcium channels. Consistent with defective VSMC development, Kcnj8 knockout mice showed deficiency in vasoconstrictive capacity and neuronal-evoked vasodilation leading to local hyperemia. Our results demonstrate a role for KCNJ8/ABCC9-containing K-ATP channels in the differentiation of brain VSMC, which in turn is necessary for fine-tuning of cerebral blood flow.
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Affiliation(s)
- Koji Ando
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden; Department of Molecular Pathophysiology, Institute of Advanced Medical Science, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan; Department of Regenerative Medicine and Tissue Engineering, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-Shinmachi, Suita, Osaka 564-8565, Japan.
| | - Lei Tong
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Di Peng
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Elisa Vázquez-Liébanas
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Hirohisa Chiyoda
- Department of Molecular Pathophysiology, Institute of Advanced Medical Science, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan; Department of Regenerative Medicine and Tissue Engineering, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-Shinmachi, Suita, Osaka 564-8565, Japan
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Jianping Liu
- Department of Medicine Huddinge (MedH), Karolinska Institute, Campus Flemingsburg, Neo, Blickagången 16, 141 57 Huddinge, Sweden
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-Shinmachi, Suita, Osaka 564-8565, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute of Advanced Medical Science, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan
| | - Jaime Grutzendler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden; Department of Medicine Huddinge (MedH), Karolinska Institute, Campus Flemingsburg, Neo, Blickagången 16, 141 57 Huddinge, Sweden.
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Yang J, Tsai T, Chang Y, Chen C, Hung Y, Peng D, Wu C. Mesenchymal Stem/Stromal Cells: STUDY THE MECHANISM OF ACTION OF ELIXCYTE®, AN ALLOGENIC STEM CELL PRODUCT, ON OSTEOARTRITIS. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00216-x] [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: 11/27/2022]
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Deng Y, Wang W, Zheng Q, Feng Y, Zou Y, Dong H, Tan Z, Zeng X, Zhao Y, Peng D, Yang X, Sun A. Menopausal hormone therapy: what are the problems in the perception of Chinese physicians? Climacteric 2022; 25:413-420. [PMID: 35438051 DOI: 10.1080/13697137.2022.2058391] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE This study aimed to investigate Chinese physicians' perception and attitudes toward menopausal hormone therapy (MHT). METHODS This nationwide online survey was conducted in China. Physicians registered in the WeChat groups of the Gynecological Endocrinology Committee of China's Maternal and Child Health Care Association received a message invitation to complete this anonymous online survey from April 2020 to July 2020. Physicians' knowledge of and attitudes toward MHT were surveyed. RESULTS In total, 4672 questionnaires were submitted; only completed questionnaires could be submitted. The message was sent to 6021 doctors, so the response rate was 77.6%. Overall, 77.9-92.9% of physicians knew the common indications and contraindications to MHT. Additionally, 90.6%, 85.4%, 80.7% and 37.5% of physicians thought that MHT would increase the risk of venous thrombosis, breast cancer, endometrial cancer and weight gain, respectively. In total, 58.1% of the physicians mistakenly believed that a sex hormone test was one of the necessary examinations to reassess MHT prescription during follow-up visits. We found that 68.5% of physicians would consider using MHT themselves or recommend MHT to their partners in the future, and 11.4% were currently using MHT. CONCLUSIONS Most Chinese physicians have basic knowledge of MHT. Their misunderstandings about MHT mainly centered on the risks of endometrial cancer, weight gain and the necessary examinations during follow-up visits. These misunderstandings need to be clarified in future professional training programs.
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Affiliation(s)
- Y Deng
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - W Wang
- Department of Reproductive Medicine, The Second Hospital of Hebei Medical University, Hebei, China
| | - Q Zheng
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Shandong, China
| | - Y Feng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, JiangXi, China
| | - Y Zou
- Department of Obstetrics and Gynecology, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China
| | - H Dong
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Jinzhou, Liaoning, China
| | - Z Tan
- Department of Obstetrics and Gynecology, Xinhui Maternity and Children's Hospital, Guangxi, China
| | - X Zeng
- Department of Gynecology, Guangzhou Women and Children's Medical Centre, Guangdong, China
| | - Y Zhao
- Department of Obstetrics and Gynecology, Xinhui Maternity and Children's Hospital, Guangxi, China
| | - D Peng
- Department of Obstetrics and Gynecology, Zhongda Hospital Southeast Univeisity, Jiangsu, China
| | - X Yang
- Department of Obstetrics and Gynecology, Liuzhou Maternity and Child Healthcare Hospital, GuangXi, China
| | - A Sun
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
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Huang Q, Wang X, Dong J, Zheng Z, Xu O, Fu S, Peng D, Li J, Qin Y. Ultra-broadband LP 11 mode converter with high purity based on long-period fiber grating and an integrated Y-junction. Opt Express 2022; 30:12751-12759. [PMID: 35472905 DOI: 10.1364/oe.454537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
We report an ultra-broadband LP11 mode converter with high purity based on integrated two shunt-wound long-period fiber gratings (LPFGs) and an adiabatic Y-junction, together with a high-order-mode bandpass filter. Two shunt-wound LPFGs are inscribed by CO2 laser in a two-mode fiber to achieve a 10 dB bandwidth of 50 nm and 51 nm at resonance wavelengths of 1530 nm and 1570 nm, respectively. Meanwhile, the Y-junction fabricated by lithography can be operated over S + C+L band to combine the converted LP11 mode. The presented ultra-broadband mode converter is able to achieve a mode conversion efficiency of 95%, together with a wavelength-dependent loss of less than 3 dB over the S + C+L band. This device has low modal crosstalk of 17 dB between the LP01 and LP11 modes, because most of the residual LP01 mode is further filtered by a high-order-mode bandpass filter at the output port of the Y-junction. The insertion loss of mode converter is estimated to be lower than 2.7 dB, due to the use of low loss polymer material during the fabrication. The proposed ultra-broadband LP11 mode converter with high purity is promising for the application of ultra-broadband mode-division-multiplexing transmission systems.
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Machado D, Vazquez-Colon Z, Lopez-Colon D, Joong A, Waldman E, Jaudon A, Lukich S, Cousino M, Peng D. End of Life in Children on Mechanical Circulatory Support. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.254] [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] Open
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Peng D, Ando K, Hußmann M, Gloger M, Skoczylas R, Mochizuki N, Betsholtz C, Fukuhara S, Schulte-Merker S, Lawson ND, Koltowska K. Proper migration of lymphatic endothelial cells requires survival and guidance cues from arterial mural cells. eLife 2022; 11:e74094. [PMID: 35316177 PMCID: PMC9042226 DOI: 10.7554/elife.74094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The migration of lymphatic endothelial cells (LECs) is key for the development of the complex and vast lymphatic vascular network that pervades most tissues in an organism. In zebrafish, arterial intersegmental vessels together with chemokines have been shown to promote lymphatic cell migration from the horizontal myoseptum (HM). We observed that emergence of mural cells around the intersegmental arteries coincides with lymphatic departure from HM which raised the possibility that arterial mural cells promote LEC migration. Our live imaging and cell ablation experiments revealed that LECs migrate slower and fail to establish the lymphatic vascular network in the absence of arterial mural cells. We determined that mural cells are a source for the C-X-C motif chemokine 12 (Cxcl12a and Cxcl12b), vascular endothelial growth factor C (Vegfc) and collagen and calcium-binding EGF domain-containing protein 1 (Ccbe1). We showed that chemokine and growth factor signalling function cooperatively to induce robust LEC migration. Specifically, Vegfc-Vegfr3 signalling, but not chemokines, induces extracellular signal-regulated kinase (ERK) activation in LECs, and has an additional pro-survival role in LECs during the migration. Together, the identification of mural cells as a source for signals that guide LEC migration and survival will be important in the future design for rebuilding lymphatic vessels in disease contexts.
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Affiliation(s)
- Di Peng
- Uppsala University, Immunology Genetics and PathologyUppsalaSweden
| | - Koji Ando
- Department of Molecular Pathophysiology, Institute of Advanced Medical Sciences, Nippon Medical SchoolTokyoJapan
| | - Melina Hußmann
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU MünsterMünsterGermany
| | - Marleen Gloger
- Uppsala University, Immunology Genetics and PathologyUppsalaSweden
| | - Renae Skoczylas
- Uppsala University, Immunology Genetics and PathologyUppsalaSweden
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research InstituteSuitaJapan
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala UniversityUppsalaSweden
- Department of Medicine Huddinge (MedH), Karolinska Institutet, Campus FlemingsbergHuddingeSweden
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute of Advanced Medical Sciences, Nippon Medical SchoolTokyoJapan
| | - Stefan Schulte-Merker
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU MünsterMünsterGermany
| | - Nathan D Lawson
- Department of Molecular, Cellular, and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
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