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Wang WJ, Xia B, Dong YM, He PP, Cheng ZW, Ma FQ, Wang CH, Liu FY, Hu WM, Wang FP, Zhao YF, Li HZ, Fu JL. [Correlation analysis between Pirani score and talo-navicular angle,calcaneo-cuboid angle and tibio-calcaneall angle of infant clubfoot under ultrasound]. Zhonghua Wai Ke Za Zhi 2024; 62:210-215. [PMID: 38291636 DOI: 10.3760/cma.j.cn112139-20230712-00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Objective: To explore the evaluation effect of ultrasonography and Pirani score on tarsal deformity, treatment effect and pseudo-correction of congenital clubfoot in infants and young children, and the correlation between the two methods. Methods: This is a retrospective case series study. The clinical data of 26 children (40 feet) with congenital clubfoot who were evaluated by ultrasonography in the Third Affiliated Hospital of Zhengzhou University from January 2020 to January 2023 were retrospectively collected. There were 16 males and 10 females. The age at the first ultrasound examination was (M(IQR)) 9.0 (18.0) days (range: 1 to 46 days). All patients were treated with Ponseti method by the same physician. The Pirani scores before and after treatment and at the last examination, and the talonavicular angle, calcaneocuboid angle and tibiocalcaneal angle measured by ultrasound were collected, and the treatment and follow-up were recorded. Paired sample t test, repeated measures analysis of variance or Kruskal-Wallis test were used for data comparison, and Spearman correlation analysis was used for correlation analysis. The receiver operating characteristic curve was used to calculate the efficacy of ultrasound in evaluating different Pirani scores. Results: The number of plaster fixation in 26 children was 4.0 (1.0) times (range: 2 to 8 times). The medial talonavicular angle and posterior tibiocalcaneal angle were significantly improved after treatment and at the last follow-up compared with those before treatment, and the differences were statistically significant (all P<0.01). There was no difference in lateral calcaneocuboid angle before and after treatment and at the last follow-up (F=1.971, P>0.05). Pseudo-correction occurred in 2 cases (2 feet) during the treatment, with an incidence of 5%. Correlation analysis showed that there was a moderate positive correlation between talonavicular angle and Pirani midfoot score (r=0.480, P<0.01). There was no correlation between calcaneocuboid angle and Pirani midfoot score (r=0.114, P=0.105). There was a moderate negative correlation between tibial heel angle and Pirani hindfoot score (r=-0.566, P<0.01). The cut-off point of Pirani midfoot score of 1.5 was 38.78°, the sensitivity was 0.90, the specificity was 0.56, and the area under the curve was 0.75. The cut-off value of angle was 27.51 °, the sensitivity was 0.16, the specificity was 0.92, and the area under the curve was 0.44.The cut-off points of Pirani midfoot score of 3.0 were 45.08°and 9.96°, the sensitivity was 0.94 and 0.91, the specificity was 0.37 and 0.42, and the area under the curve was 0.59 and 0.62, respectively. The cut-off values of Pirani hindfoot score of 2.0 and 3.0 were 167.46° and 160.15°, respectively. The sensitivity was 0.75 and 0.67, the specificity was 0.81 and 0.83, and the area under the curve was 0.78 and 0.71, respectively. Conclusion: Ultrasound can complement with Pirani score, visually and dynamically observe the morphology and position changes of talonavicular joint, calcaneocuboid joint and tibiotalocalcaneal joint, monitor the recovery and pseudo-correction of tarsal bones, and better evaluate the therapeutic effect.
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Affiliation(s)
- W J Wang
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - B Xia
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y M Dong
- Emergency Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - P P He
- Department of Ultrasound,the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Z W Cheng
- Medical Record Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - F Q Ma
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - C H Wang
- Department of Ultrasound,the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - F Y Liu
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - W M Hu
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - F P Wang
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y F Zhao
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - H Z Li
- Department of Ultrasound,the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - J L Fu
- Orthopaedic Department, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Xie YY, Qin XT, Zhang J, Sun MY, Wang FP, Huang M, Jia SR, Qi W, Wang Y, Zhong C. Self-assembly of peptide nanofibers with chirality-encoded antimicrobial activity. J Colloid Interface Sci 2022; 622:135-146. [DOI: 10.1016/j.jcis.2022.04.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/12/2022]
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Wang FP, Li B, Sun MY, Wahid F, Zhang HM, Wang SJ, Xie YY, Jia SR, Zhong C. In situ regulation of bacterial cellulose networks by starch from different sources or amylose/amylopectin content during fermentation. Int J Biol Macromol 2022; 195:59-66. [PMID: 34871660 DOI: 10.1016/j.ijbiomac.2021.11.198] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 11/05/2022]
Abstract
Bacterial cellulose (BC) is a promising biopolymer, but its three-dimensional structure needs to be controllable to be used in multiple fields. BC has some advantages over other types of cellulose, not only in terms of purity and properties but also in terms of modification (in situ modification) during the synthesis process. Here, starches from different sources or with amylose/amylopectin content were added to the growth medium to regulate the structural properties of BC in-situ. The obtained BC membranes were further modified by superhydrophobic treatment for oil-water separation. Starches alter the viscosity of the medium, thus affecting bacterial motility and cellulose synthesis, and adhere to the microfibers, limiting their further polymerization and ultimately altering the membrane porosity, pore size, and mechanical properties perpendicular to the BC fibril layer direction. The average pore diameter of the BC/PS membrane increased by 1.94 times compared to the initial BC membrane. The chemically modified BC/PS membrane exhibited super-hydrophobicity (water contact angle 167°), high oil-water separation flux (dichloromethane, 23,205 Lm-2 h-1 MPa-1), high separation efficiency (>97%). The study provides a foundation for developing methods to regulate the network structure of BC and broaden its application.
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Affiliation(s)
- Feng-Ping Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | - Bo Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | - Mei-Yan Sun
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | - Fazli Wahid
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | | | - Shu-Jun Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; School of Food Science and Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Yan-Yan Xie
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science and Technology, Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China.
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Wahid F, Zhao XJ, Zhao XQ, Ma XF, Xue N, Liu XZ, Wang FP, Jia SR, Zhong C. Fabrication of Bacterial Cellulose-Based Dressings for Promoting Infected Wound Healing. ACS Appl Mater Interfaces 2021; 13:32716-32728. [PMID: 34227797 DOI: 10.1021/acsami.1c06986] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial cellulose (BC) holds several unique properties such as high water retention capability, flexibility, biocompatibility, and high absorption capacity. All these features make it a potential material for wound healing applications. However, it lacks antibacterial properties, which hampers its applications for infectious wound healings. This study reported BC-based dressings containing ε-polylysine (ε-PL), cross-linked by a biocompatible and mussel-inspired polydopamine (PDA) for promoting infectious wound healing. BC membranes were coated with PDA by a simple self-polymerization process, followed by treating with different contents of ε-PL. The resulted membranes showed strong antibacterial properties against tested bacteria by both in vitro and in vivo evaluations. The membranes also exhibited hemocompatibility and cytocompatibility by in vitro investigations. Moreover, the functionalized membranes promoted infected wound healing using Sprague-Dawley rats as a model animal. A complete wound healing was observed in the group treated with functionalized membranes, while wounds were still open for control and pure BC groups in the same duration. Histological investigations indicated that the thickness of newborn skin was greater and smoother in the groups treated with modified membranes in comparison to neat BC or control groups. These results revealed that the functionalized membranes have great potential as a dressing material for infected wounds in future clinical applications.
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Affiliation(s)
- Fazli Wahid
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
| | - Xiang-Jun Zhao
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
| | - Xue-Qing Zhao
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
| | - Xiao-Fang Ma
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
| | - Na Xue
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
| | - Xiao-Zhi Liu
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, The Fifth Central Hospital of Tianjin, Tianjin 300222, PR China
| | - Feng-Ping Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300222, P.R. China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300222, P.R. China
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Huang KF, Chen QY, Sun C, Wang FP, Li SQ. [Significance of spinal sagittal balance for guiding acetabular prosthesis positioning]. Zhongguo Gu Shang 2021; 34:485-8. [PMID: 34032055 DOI: 10.12200/j.issn.1003-0034.2021.05.018] [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] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Since the concept of "safe area" put forward by Lewinnek, it has been widely recognized. While in recent years, many scholars have found that even if the acetabular prosthesis was placed on the "safe area", there were still many unexplained dislocation after total hip arthroplasty. And scholars began to question whether the "safe area" is really suitable for all patients. Spinal degeneration, deformity, lumbar fusion, etc. will lead to spine sagittal imbalance and changes in pelvic activity, which could lead to changes in acetabular orientation, and ultimately lead to edge loading, wear, impact, and even dislocation after total hip replacement. From the perspective of wear, impact and dislocation, it is determined by the functional positioning of the acetabular cup, not the anatomical positioning. The anatomical positioning and functional positioning of the neutral pelvic acetabular cup in the standing position can be considered equivalent. For pelvic rotation more than 20°, functional placement needs to be considered. In recent years, as the understanding of the internal relationship between the spine-pelvis-hip joint has become more and more profound, some scholars further classify the hip-spine relationship according to whether the spine is stiff or deformed, and propose corresponding acetabulums according to different types of hip-spine relationships The function of placement, so as to achieve a stable artificial hip joint. Therefore, it is of great significance to fully assess whether the patient's sagittal plane is balanced before surgery to guide artificial hip replacement surgery.
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Affiliation(s)
- Kai-Fu Huang
- Department of Joint Orthopaedics, No. 1 Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Qing-Yang Chen
- Department of Joint Orthopaedics, No. 1 Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Chao Sun
- Department of Joint Orthopaedics, No. 1 Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Feng-Ping Wang
- Department of Joint Orthopaedics, No. 1 Hospital of Jilin University, Changchun 130000, Jilin, China
| | - Shu-Qiang Li
- Department of Joint Orthopaedics, No. 1 Hospital of Jilin University, Changchun 130000, Jilin, China
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Zhang R, Zhong XM, Gong YZ, Ma X, Zhu D, Ning HJ, Wang FP, Zou JZ, Zhang YL. [Analysis of clinical characteristics and drug treatment of inflammatory bowel disease in children: a single center study]. Zhonghua Er Ke Za Zhi 2020; 58:570-575. [PMID: 32605341 DOI: 10.3760/cma.j.cn112140-20200504-00468] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the clinical characteristics and efficacy of drug treatment in children with inflammatory bowel disease (IBD) at different ages of onset. Methods: The clinical data of 87 children with IBD admitted to Department of Gastroenterology in Children's Hospital, Capital Institute of Pediatrics from January 2009 to December 2018 were collected. The patients were divided into four groups according to the age of onset: 0 -<2 years old group (36 cases), 2 -<6 years old group (10 cases), 6 -<10 years old group (12 cases) and 10 -<18 years old group (29 cases). The clinical manifestations, laboratory examination, endoscopic findings, pathologic and genetic changes, and treatment were compared among different age groups with chi-square test or Fisher's exact text. Results: (1) A total of 87 patients were diagnosed with IBD, including 50 Crohn's disease (CD) (57%), 25 ulcerative colitis (UC) (29%) and 12 unclassified inflammatory bowel disease (IBD-U) (14%). (2) Patients with fever accounted for 78% (28/36) and 8/10 in the 0 -<2 years old group and 2 -<6 years old group, respectively. Patients with abdominal pain and perianal diseases accounted for 6% (2/36) and 47% (17/36) in the 0 -<2 years old group, and their proportions were significantly different among the four groups (χ(2)=8.369, 40.317 and 13.130, all P<0.05). (3) Leukocytosis, thrombocytosis and anemia were more common in the 0-<2 years old group, seen in 72% (26/36), 31% (11/36) and 81% (29/36), respectively. There were significant differences in the changes of complete blood count among the four groups (χ(2)=21.919, 8.095 and 11.520, all P<0.05). (4) Colonic involvement accounted for 85% (17/20) in the 0 -<2 years old CD patients. While in the CD patients over 6 years old, 61% (14/23) had inflammation of ileum and colon, with a significant difference compared to that in patients under 6 years old (19% (5/27) , χ(2)=9.455, P=0.003). Also, the location of bowel inflammation among the four groups were significantly different (χ(2)=21.120, P<0.01). (5) Noncaseating granulomas were found in 15 (30%) CD patients, and crypt abscess was found in 11 (44%) UC patients. (6) Among the 24 patients whose genes were analyzed by high throughput sequencing, 12 had pathogenic single gene mutation. (7) There were 25 patients treated with total enteral nutrition. Among the 25 patients treated with thalidomide, 20 (80%) had clinical remission or partial remission. Among the 19 CD patients treated with infliximab (IFX), 14 had clinical remission at the 6(th) week of treatment, and the proportion of remission maintenance at the 30(th) week of treatment was 12/14. (8) The rate of clinical remission or partial remission was 64% (23/36) in the 0 -<2 years old group, 8/10 in the 2 -<6 years old group, 11/12 in the 6 -<10 years old group, and 83% (24/29) in the 10 -<18 years old group. Conclusions: The proportion of CD was higher than that of UC in this study. Infant onset inflammatory bowel disease was more likely to present with perianal lesions, and was usually associated with leukocytosis, thrombocytosis and anemia, and has high possibility of single gene mutation. IFX may be effective in treating CD.
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Affiliation(s)
- R Zhang
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - X M Zhong
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - Y Z Gong
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - X Ma
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - D Zhu
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - H J Ning
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - F P Wang
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - J Z Zou
- Department of Pathology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - Y L Zhang
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 6:136. [PMID: 33184503 PMCID: PMC7752755 DOI: 10.1038/s41564-020-00827-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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9
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Wahid F, Wang FP, Xie YY, Chu LQ, Jia SR, Duan YX, Zhang L, Zhong C. Reusable ternary PVA films containing bacterial cellulose fibers and ε-polylysine with improved mechanical and antibacterial properties. Colloids Surf B Biointerfaces 2019; 183:110486. [DOI: 10.1016/j.colsurfb.2019.110486] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/18/2019] [Accepted: 09/01/2019] [Indexed: 12/15/2022]
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10
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Gong YZ, Ning HJ, Ma X, Zhu D, Wang FP, Zhang R, Zhang YL, Zhong XM. [Clinical and genotypic characteristics of infantile inflammatory bowel disease]. Zhonghua Er Ke Za Zhi 2019; 57:520-525. [PMID: 31269551 DOI: 10.3760/cma.j.issn.0578-1310.2019.07.005] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Objective: To analyze the clinical and genotypic characteristics of infantile inflammatory bowel disease (IBD). Methods: The age of onset, family history, clinical manifestations, and treatment effect were retrospectively analyzed in 39 infants (male 23 cases, female 16 cases) with IBD who were admitted to the Department of Gastroenterology in Children's Hospital, Capital Institute of Pediatrics from January 2007 to December 2017. Next generation sequencing (NGS) based on target gene panel was used for gene analysis in 17 patients. Results: The median age of onset was 0.5 (0.5, 1.0) month. The most common clinical symptoms included diarrhea (39, 100%), malnutrition (38, 97%), hematochezia (34, 87%), fever (25, 64%), and perianal diseases (24, 61%). Four children had associated family history. Among the 17 patients whose gene was analyzed, 10 were found to have the pathogenic gene variation, within whom 7 had interleukin-10 receptor α subunit (IL-10RA) mutation, 2 had CYBB heterozygous mutation, 1 had interleukin-10 receptor β subunit (IL-10RB) mutation. The therapeutic medicine included mesalazine, steroids, and thalidomide. Eighteen children (46%) reached clinical remission (10 cases) or partial remission (8 cases). Conclusions: The incidence of single gene mutation in infants with IBD is high, with IL-10RA mutation as the most common. Refractory diarrhea and malnutrition may indicate infantile IBD.
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Affiliation(s)
- Y Z Gong
- Department of Gastroenterology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
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11
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Feng L, Chang CC, Song D, Jiang C, Song Y, Wang CF, Deng W, Zou YJ, Chen HF, Xiao X, Wang FP, Liu XP. The trimeric Hef-associated nuclease HAN is a 3'→5' exonuclease and is probably involved in DNA repair. Nucleic Acids Res 2019; 46:9027-9043. [PMID: 30102394 PMCID: PMC6158738 DOI: 10.1093/nar/gky707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Nucleases play important roles in nucleic acid metabolism. Some archaea encode a conserved protein known as Hef-associated nuclease (HAN). In addition to its C-terminal DHH nuclease domain, HAN also has three N-terminal domains, including a DnaJ-Zinc-finger, ribosomal protein S1-like, and oligonucleotide/oligosaccharide-binding fold. To further understand HAN’s function, we biochemically characterized the enzymatic properties of HAN from Pyrococcus furiosus (PfuHAN), solved the crystal structure of its DHH nuclease domain, and examined its role in DNA repair. Our results show that PfuHAN is a Mn2+-dependent 3′-exonuclease specific to ssDNA and ssRNA with no activity on blunt and 3′-recessive double-stranded DNA. Domain truncation confirmed that the intrinsic nuclease activity is dependent on the C-terminal DHH nuclease domain. The crystal structure of the DHH nuclease domain adopts a trimeric topology, with each subunit adopting a classical DHH phosphoesterase fold. Yeast two hybrid assay confirmed that the DHH domain interacts with the IDR peptide of Hef nuclease. Knockout of the han gene or its C-terminal DHH nuclease domain in Haloferax volcanii resulted in increased sensitivity to the DNA damage reagent MMS. Our results imply that HAN nuclease might be involved in repairing stalled replication forks in archaea.
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Affiliation(s)
- Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chen-Chen Chang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chuang Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Yang Song
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chao-Fan Wang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Wei Deng
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Ya-Juan Zou
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
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12
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Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP. The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Nucleic Acids Res 2019; 45:12551-12564. [PMID: 30053256 PMCID: PMC5716160 DOI: 10.1093/nar/gkx887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 04/10/2017] [Accepted: 10/01/2017] [Indexed: 12/27/2022] Open
Abstract
RecJ nucleases specifically degrade single-stranded (ss) DNA in the 5′ to 3′ direction. Archaeal RecJ is different from bacterial RecJ in sequence, domain organization, and substrate specificity. The RecJ from archaea Pyrococcus furiosus (PfuRecJ) also hydrolyzes RNA strands in the 3′ to 5′ direction. Like eukaryotic Cdc45 protein, archaeal RecJ forms a complex with MCM helicase and GINS. Here, we report the crystal structures of PfuRecJ and the complex of PfuRecJ and two CMPs. PfuRecJ bind one or two divalent metal ions in its crystal structure. A channel consisting of several positively charged residues is identified in the complex structure, and might be responsible for binding substrate ssDNA and/or releasing single nucleotide products. The deletion of the complex interaction domain (CID) increases the values of kcat/Km of 5′ exonuclease activity on ssDNA and 3′ exonuclease activity on ssRNA by 5- and 4-fold, respectively, indicating that the CID functions as a regulator of enzymatic activity. The DHH domain of PfuRecJ interacts with the C-terminal beta-sheet domain of the GINS51 subunit in the tetrameric GINS complex. The relationship of archaeal and bacterial RecJs, as well as eukaryotic Cdc45, is discussed based on biochemical and structural results.
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Affiliation(s)
- Min-Jun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Feng Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Jia-Nan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Chun-Yan Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
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13
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Wang FP, Wen YR, Tan JG, Wang MZ. [Functional and esthetic rehabilitation of a case with generalized severe tooth wear]. Zhonghua Kou Qiang Yi Xue Za Zhi 2019; 54:406-409. [PMID: 31177681 DOI: 10.3760/cma.j.issn.1002-0098.2019.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- F P Wang
- Department of Prosthodontics, Qingdao Stomatological Hospital, Qingdao 266001, China
| | - Y R Wen
- Jurgen Masterdental Co., Ltd., Beijing 100166, China
| | - J G Tan
- Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - M Z Wang
- Department of Prosthodontics, Qingdao Stomatological Hospital, Qingdao 266001, China
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14
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Han RL, Wang FP, Zhang PA, Zhou XY, Li Y. miR-383 inhibits ovarian cancer cell proliferation, invasion and aerobic glycolysis by targeting LDHA. Neoplasma 2019; 64:244-252. [PMID: 28043152 DOI: 10.4149/neo_2017_211] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
MicroRNAs (miRNAs) are differentially expressed in various cancers and act as oncogenes or tumor suppressors. MiR-383 has been characterized as a cancer suppressor in several cancers. However, the exact expression patterns of miR-383 and the precise molecular mechanisms underlying its role in ovarian cancer have not been investigated thoroughly. In this study, we found that the expression of miR-383 was significantly downregulated in ovarian cancer tissues and ovarian cancer cell lines. Ectopic expression of miR-383 remarkably suppressed the ovarian cancer cell proliferation by enhancing cell apoptosis and significantly inhibited the invasion of ovarian cancer cells, while low expression of miR-383 exhibited the opposite effect. Bioinformatics analysis suggested LDHA as a novel target of miR-383, and miR-383 suppressed the expression level of LDHA mRNA by direct binding to its 3'-untranslated region (3'UTR). Expression of miR-383 was negatively correlated with LDHA in ovarian cancer tissues. In addition, modulation of miR-383 expression could affect the aerobic glycolysis in the ovarian cancer cells. Furthermore, Silencing of LDHA counteracted the effects of miR-383 suppression, while its overexpression reversed tumor inhibitory effects of miR-383. In conclusion, our study demonstrated that miR-383 regulated LDHA expression in ovarian cancer cells, thereby stunting glycolysis, cell proliferation and invasion.
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15
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Wang WW, Zhou H, Xie JJ, Yi GS, He JH, Wang FP, Xiao X, Liu XP. Thermococcus Eurythermalis Endonuclease IV Can Cleave Various Apurinic/Apyrimidinic Site Analogues in ssDNA and dsDNA. Int J Mol Sci 2018; 20:ijms20010069. [PMID: 30586940 PMCID: PMC6341776 DOI: 10.3390/ijms20010069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022] Open
Abstract
Endonuclease IV (EndoIV) is a DNA damage-specific endonuclease that mainly hydrolyzes the phosphodiester bond located at 5' of an apurinic/apyrimidinic (AP) site in DNA. EndoIV also possesses 3'-exonuclease activity for removing 3'-blocking groups and normal nucleotides. Here, we report that Thermococcus eurythermalis EndoIV (TeuendoIV) shows AP endonuclease and 3'-exonuclease activities. The effect of AP site structures, positions and clustered patterns on the activity was characterized. The AP endonuclease activity of TeuendoIV can incise DNA 5' to various AP site analogues, including the alkane chain Spacer and polyethylene glycol Spacer. However, the short Spacer C2 strongly inhibits the AP endonuclease activity. The kinetic parameters also support its preference to various AP site analogues. In addition, the efficient cleavage at AP sites requires ≥2 normal nucleotides existing at the 5'-terminus. The 3'-exonuclease activity of TeuendoIV can remove one or more consecutive AP sites at the 3'-terminus. Mutations on the residues for substrate recognition show that binding AP site-containing or complementary strand plays a key role for the hydrolysis of phosphodiester bonds. Our results provide a comprehensive biochemical characterization of the cleavage/removal of AP site analogues and some insight for repairing AP sites in hyperthermophile cells.
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Affiliation(s)
- Wei-Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.
| | - Juan-Juan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
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16
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Fan JL, Wang FP, Wang S, Liu XL, Wu XN, Chen W, Chen LP, Li WX. [Phenotype and mechanism of inducible ppp2r1a knockout mouse model]. Zhonghua Yu Fang Yi Xue Za Zhi 2018; 52:530-537. [PMID: 29747346 DOI: 10.3760/cma.j.issn.0253-9624.2018.05.013] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: Investigate the effects of inducible ppp2r1a knockout on main physiological function in adult mice and study the mechanism. Methods: Ppp2r1a(flox/flox) mice and CAGG-CreER mice were hybridized to obtain 20 CAGG-CreER ppp2r1a(flox/flox) and 20 mice in homozygous group. Two groups of mice were divided into 4 groups respectively, finally we got 8 groups with 5 mice in each group. Tamoxifen was injected intraperitoneally to acquire inducible ppp2r1a knockout mice. The knockout efficiency of PP2A Aα in vital organs was measured by Western blot. At 0, 2, 4 and 6 days after injection, we measured body weight, histopathological change, peripheral blood cell counts and blood biochemical. Real-time PCR was performed to measure expression of liver glucolipid metabolism genes. Results: After tamoxifen injection for 6 days, the knockout efficiency of PP2A Aα in vital organs was 35%, 12%, 15%, 60%, 69% and 72%, respectively in heart, liver, spleen, lung, kidney and brain. After tamoxifen injection for 6 days, the weight of homozygous mice was lower than that of wild type mice, with values of (17.42±1.76) g and (21.69±1.82) g, respectively (P<0.05). Moreover, the activity level, abdominal and renal fat were significantly decreased in homozygous mice. Homozygous mice survived no more than 7 days. Compared with wild type mice, the organ coefficient of spleen of homozygous mice was decreased at the 6th day, with values of (0.59±0.10)% and (0.36±0.05)% respectively (P<0.05). Obvious spleen atrophy and marked decrease of nucleated cells were showed by performing HE staining. Tunel staining revealed increased apoptosis ratio of splenic lymphocytes in homozygous mice. The levels of alanine aminotransferase (ALT) and aspartate transaminase (AST) of homozygous mice were higher than wild type mice (P<0.05). The values of ALT and AST in homozygous mice were (153.68±62.80) U/L and (193.2±44.28) U/L. The corresponding values in wild type mice were (41.02±12.91) U/L and (69.40±9.55) U/L. The above results indicated that ppp2r1a knockout caused liver damage. Blood sugar level of homozygous mice was lower than in wild type mice (P<0.05), with values of (4.20±1.99) mmol/L and (8.88±0.65) mmol/L respectively. Plasma total cholesterol (TC), high density lipoprotein (HDL) and β-hydroxybutyric acid (β-HB) level of homozygous mice were higher than those of wild type mice (P<0.05). The values of TC, HDL and β-HB in homozygous mice were (3.12±0.39), (1.53±0.38) and (2.49±0.89) mmol/L. The corresponding values in wild type mice were (1.69±0.92), (0.78±0.50) and (0.45±0.30) mmol/L respectively. The above results indicated that ppp2r1a loss interfered glucose and cholesterol metabolism. In addition, we also found that the white blood cell count (WBC) and lymphocyte count (LYM) of homozygous mice were lower than in wild type mice (P<0.05). The values of WBC and LYM in homozygous mice were (1.88±0.89)×10(9)/L and (0.92±0.37)×10(9)/L respectively. The corresponding values in wild type mice were (3.91±0.80)×10(9)/L and (2.74±0.52)×10(9)/L respectively. The mRNA levels of glucose-6-phosphatase (G6P) and phosphoenolpyruvate carboxykinase (PEPCK) of homozygous were lower than wild type mice (P<0.05). The fold change of G6P and PEPCK in homozygous mice was 0.46±0.11 and 0.72±0.07 respectively. The corresponding fold change in wild type mice was 1.02±0.07 and 1.02±0.06 respectively. Conclusion: Whole body ppp2r1a is essential for the survival of adult mice, due to the important role in maintaining the metabolism of glucose and cholesterol of liver.
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Affiliation(s)
- J L Fan
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Guangzhou 510080, China
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Deng YJ, Feng L, Zhou H, Xiao X, Wang FP, Liu XP. NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA. DNA Repair (Amst) 2018; 65:54-63. [PMID: 29609115 DOI: 10.1016/j.dnarep.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/07/2018] [Accepted: 03/23/2018] [Indexed: 01/09/2023]
Abstract
In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3'-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3'-end in the presence of Mn2+. Interestingly, unlike bacterial Nrns, Ape0124 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads the 3'-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB.
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Affiliation(s)
- Yong-Jie Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
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Wang FP, Zhu XN, Zhang ZB, Chen LP, Fan JL, Li QY, Chen S, Chen W. [The relationship between histone H3Ser10 phosphorylation and DNA damage in periphery blood lymphocytes of polycyclic aromatic hydrocarbons exposed workers]. Zhonghua Yu Fang Yi Xue Za Zhi 2017; 51:421-426. [PMID: 28464593 DOI: 10.3760/cma.j.issn.0253-9624.2017.05.010] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the effect of polycyclic aromatic hydrocarbons (PAHs) exposure on the level of histone H3Ser10 phosphorylation (p-H3S10) and DNA damage degree in peripheral blood lymphocyte (PBLCs). Method: 75 coke oven workers from Benxi steel plant in Liaoning Province of China (PAHs-exposed group) and local 50 hot rolling workers (control group) were recruited in this study with age, working years, labor intensity and high temperature for matching factors using cluster sampling method in 2014. HPLC-fluorescence was performed to determine the level of urinary 1-hydroxypyrene (1-OHP), DNA damage and specific histone modification were measured in PBLCs of the subjects through comet assay and ELISA assay, respectively. Linear regression model analysis was used to analyze the differences among PAHs exposure, DNA damage and p-H3S10 level in two groups. The Mediation analysis was used to analyze the regulated relationships between urinary 1-OHP, DNA damage and histone modification through the bootstrap method. Results: Age of the control and the exposed group were (45.32±8.32) and (43.87±5.67) years old (P=0.284). The concentration of urinary 1-OHP, OTM value, Tail DNA% and p-H3S10 level in exposure group were higher than that in control group, while the M (P(5)-P(95)) of p-H3S10 levels in control and exposed group were 2.21 (0.68-4.71), 4.54 (1.85-23.91) (P<0.001). The degree p-H3S10 level was increased after the subgroups which were (2.59±1.19)%, (3.24±2.81)%, (5.55±3.25)%, (8.77±7.84)%, respectively, divided by quantitated 1-OHP concentration as P(0)-P(25), P(26)-P(50), P(51)-P(75) and P(76)-P(100) (P<0.001). We also found the correlations between urinary 1-OHP and p-H3S10 level or OTM value or Tail DNA%, β (95%CI) were 0.264 (0.167-0.360), 0.500 (0.299-0.702), and 0.510 (0.384-0.671), respectively (P<0.001). Similar result was also observed between p-H3S10 level and OTM value or Tail DNA%, β (95%CI) were 0.149 (0.073-0.226) and 0.220 (0.132-0.308) (P<0.001). Moreover, the mediation effect value of DNA damage on PAHs induced p-H3S10 alteration was 0.054(P=0.040). Conclusion: The results suggested that PAHs exposure could induce DNA damage and an increase in histone H3Ser10 phosphorylation in PBLCs. Particularly, the alteration of H3S10 phosphorylation may play an important role in regulating cell DNA damage repair.
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Affiliation(s)
- F P Wang
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Guangzhou 510080, China
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Liu XJ, Liu BY, Kong JY, Wang FP, Sun H, Xie WY, Wang HW, Shen B, Du YJ. Effect of P38MAPK inhibitor on endoplasmic reticulum stress-induced hepatocyte apoptosis in rats with acute liver failure. Shijie Huaren Xiaohua Zazhi 2014; 22:3625-3631. [DOI: 10.11569/wcjd.v22.i24.3625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To observe the effect of P38MAPK inhibitor SB203580 on Caspase12 protein expression and apoptosis of hepatocytes in rats with acute hepatic failure, and to explore the mechanism underlying its protective effect on acute hepatic failure.
METHODS: Seventy-two healthy Wistar rats were randomly divided into three groups: a control group (injected with normal saline), a model group (injected with D-galactosamine/lipopolysaccharide, D-Gal/LPS), and an inhibitor group (injected with D-Gal/LPS + SB203580). Each group was further divided into three subgroups for testing at different time points, with 8 rats in each subgroup. Blood samples were collected for the determination of alanine aminotransferase (ALT) and total bilirubin (TBIL). HE staining was performed to observe the liver pathological changes. Immunohistochemical assay was performed to detect the expression of Caspase12 protein. The diphenylamine method was used to detect the apoptosis rate.
RESULTS: The liver function, Caspase12 protein expression and apoptosis rate in the inhibitor group at 12 h were lower than those in the model group. Caspase12 protein expression at 18 h in the inhibitor group had no significant difference with that in the model group, while the apoptosis rate was significantly higher in the inhibitor group than in the model group. Necrosis occurred in the model group at 12 h, and in the inhibitor group at 18 h.
CONCLUSION: P38MAPK inhibitor SB203580 can reduce the expression of Caspase12 protein, inhibit the endoplasmic reticulum stress-mediated hepatocyte apoptosis, reduce the necrosis of liver cells and play a protective effect against acute hepatic failure.
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Chen Y, Li YL, Zhou GT, Li H, Lin YT, Xiao X, Wang FP. Biomineralization mediated by anaerobic methane-consuming cell consortia. Sci Rep 2014; 4:5696. [PMID: 25027246 PMCID: PMC4100016 DOI: 10.1038/srep05696] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/20/2014] [Indexed: 11/09/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME) play a significant role in global carbon cycles. These organisms consume more than 90% of ocean-derived methane and influence the landscape of the seafloor by stimulating the formation of carbonates. ANME frequently form cell consortia with sulfate-reducing bacteria (SRB) of the family Deltaproteobacteria. We investigated the mechanistic link between ANME and the natural consortium by examining anaerobic oxidation of methane (AOM) metabolism and the deposition of biogenetic minerals through high-resolution imaging analysis. All of the cell consortia found in a sample of marine sediment were encrusted by a thick siliceous envelope consisting of laminated and cementing substances, whereas carbonate minerals were not found attached to cells. Beside SRB cells, other bacteria (such as Betaproteobacteria) were found to link with the consortia by adhering to the siliceous crusts. Given the properties of siliceous minerals, we hypothesize that ANME cell consortia can interact with other microorganisms and their substrates via their siliceous envelope, and this mechanism of silicon accumulation may serve in clay mineral formation in marine sedimentary environments. A mechanism for biomineralization mediated by AOM consortia was suggested based on the above observations.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yi-Liang Li
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Gen-Tao Zhou
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Han Li
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yang-Ting Lin
- Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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Wu WF, Wang FP, Li JH, Yang XW, Xiao X, Pan YX. Iron reduction and mineralization of deep-sea iron reducing bacterium Shewanella piezotolerans WP3 at elevated hydrostatic pressures. Geobiology 2013; 11:593-601. [PMID: 24102974 DOI: 10.1111/gbi.12061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
Abstract
In this study, iron reduction and concomitant biomineralization of a deep-sea iron reducing bacterium (IRB), Shewanella piezotolerans WP3, were systematically examined at different hydrostatic pressures (0.1, 5, 20, and 50 MPa). Our results indicate that bacterial iron reduction and induced biomineralization are influenced by hydrostatic pressure. Specifically, the iron reduction rate and extent consistently decreases with the increase in hydrostatic pressure. By extrapolation, the iron reduction rate should drop to zero by ~68 MPa, which suggests a possible shut-off of enzymatic iron reduction of WP3 at this pressure. Nano-sized superparamagnetic magnetite minerals are formed under all the experimental pressures; nevertheless, even as magnetite production decreases, the crystallinity and grain size of magnetite minerals increase at higher pressure. These results imply that IRB may play an important role in iron reduction, biomineralization, and biogeochemical cycling in deep-sea environments.
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Affiliation(s)
- W F Wu
- Biogeomagnetism Group, Paleomagnetism and Geochronology Lab, Key Laboratory of the Earth's Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China; France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences, Beijing, China
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Yang XW, He Y, Xu J, Xiao X, Wang FP. The regulatory role of ferric uptake regulator (Fur) during anaerobic respiration of Shewanella piezotolerans WP3. PLoS One 2013; 8:e75588. [PMID: 24124499 PMCID: PMC3790847 DOI: 10.1371/journal.pone.0075588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/16/2013] [Indexed: 12/02/2022] Open
Abstract
Ferric uptake regulator (Fur) is a global regulator that controls bacterial iron homeostasis. In this study, a fur deletion mutant of the deep-sea bacterium Shewanella piezotolerans WP3 was constructed. Physiological studies revealed that the growth rate of this mutant under aerobic conditions was only slightly lower than that of wild type (WT), but severe growth defects were observed under anaerobic conditions when different electron acceptors (EAs) were provided. Comparative transcriptomic analysis demonstrated that Fur is involved not only in classical iron homeostasis but also in anaerobic respiration. Fur exerted pleiotropic effects on the regulation of anaerobic respiration by controlling anaerobic electron transport, the heme biosynthesis system, and the cytochrome c maturation system. Biochemical assays demonstrated that levels of c-type cytochromes were lower in the fur mutant, consistent with the transcriptional profiling. Transcriptomic analysis and electrophoretic mobility shift assays revealed a primary regulation network for Fur in WP3. These results suggest that Fur may act as a sensor for anoxic conditions to trigger and influence the anaerobic respiratory system.
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Affiliation(s)
- Xin-Wei Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Ying He
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Jiao Tong University, Shanghai, PR China
- * E-mail:
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Song ZQ, Wang L, Wang FP, Jiang HC, Chen JQ, Zhou EM, Liang F, Xiao X, Li WJ. Abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China. Extremophiles 2013; 17:871-9. [PMID: 23918087 DOI: 10.1007/s00792-013-0570-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/18/2013] [Indexed: 11/29/2022]
Abstract
It has been suggested that archaea carrying the accA gene, encoding the alpha subunit of the acetyl CoA carboxylase, autotrophically fix CO2 using the 3-hydroxypropionate/4-hydroxybutyrate pathway in low-temperature environments (e.g., soils, oceans). However, little new information has come to light regarding the occurrence of archaeal accA genes in high-temperature ecosystems. In this study, we investigated the abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China, using DNA- and RNA-based phylogenetic analyses and quantitative polymerase chain reaction. The results showed that archaeal accA genes were present and expressed in the investigated Yunnan hot springs with a wide range of temperatures (66-96 °C) and pH (4.3-9.0). The majority of the amplified archaeal accA gene sequences were affiliated with the ThAOA/HWCG III [thermophilic ammonia-oxidizing archaea (AOA)/hot water crenarchaeotic group III]. The archaeal accA gene abundance was very close to that of AOA amoA gene, encoding the alpha subunit of ammonia monooxygenase. These data suggest that AOA in terrestrial hot springs might acquire energy from ammonia oxidation coupled with CO2 fixation using the 3-hydroxypropionate/4-hydroxybutyrate pathway.
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Affiliation(s)
- Zhao-Qi Song
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
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Song ZQ, Wang FP, Zhi XY, Chen JQ, Zhou EM, Liang F, Xiao X, Tang SK, Jiang HC, Zhang CL, Dong H, Li WJ. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ Microbiol 2012; 15:1160-75. [PMID: 23126508 DOI: 10.1111/1462-2920.12025] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 09/17/2012] [Accepted: 10/09/2012] [Indexed: 11/27/2022]
Abstract
Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.
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Affiliation(s)
- Zhao-Qi Song
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
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Javed Q, Wang FP, Rafique MY, Toufiq AM, Li QS, Mahmood H, Khan W. Diameter-controlled synthesis of α-Mn2O3 nanorods and nanowires with enhanced surface morphology and optical properties. Nanotechnology 2012; 23:415603. [PMID: 23011093 DOI: 10.1088/0957-4484/23/41/415603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single crystalline α-Mn(2)O(3) nanorods, and nanowires with and without nanoparticles on them have been successfully synthesized by a template-free hydrothermal route. The variation in hydrothermal temperature has not only affected the diameter of the nanostructure but also noticeably affected the morphology and optical properties of the α-Mn(2)O(3) nanostructure. The influence of temperature on the diameter, crystallinity, surface morphology and optical properties of the α-Mn(2)O(3) nanostructure have been characterized by x-ray diffraction, scanning electron microscopy, energy dispersive x-ray analysis, transmission electron microscopy, high resolution transmission electron microscopy, Raman spectroscopy and UV-visible spectroscopy and photoluminescent (PL) spectroscopy. The results showed in our experimental conditions that single crystalline nanorods of the α-Mn(2)O(3) were obtained at a temperature of 180 °C, while single crystalline nanowires were obtained by increasing the temperature to 240 and 300 °C. Nanowires with nanoparticles on them were obtained by increasing the temperature to 240 °C and nanowires without nanoparticles on them were obtained by increasing the temperature to 300 °C. The nanorods and nanowires obtained had a well-defined morphology. The nanowires synthesized at 300 °C exhibited an intense orange band PL spectrum.
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Affiliation(s)
- Q Javed
- Department of Physics, School of Applied Sciences, University of Science and Technology Beijing, Beijing 100083, People's Republic of China
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Kong JY, Wang TQ, Jiang GH, Li L, Wang FP. Urinary trypsin inhibitor reduced inflammatory response after stent injury in minipig. Pathol Res Pract 2012; 208:344-9. [PMID: 22537506 DOI: 10.1016/j.prp.2012.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/01/2012] [Accepted: 03/06/2012] [Indexed: 11/28/2022]
Abstract
This study investigated whether urinary trypsin inhibitor (UTI) inhibits neointimal formation by reducing inflammatory response after stent injury. Twenty minipigs having undergone oversized bare material stent implantation in the left anterior descending artery were randomly subdivided into two groups: a UTI group (n=10) and a control group (n=10). Two systemic markers of inflammation (serum macrophage chemoattractant protein-1 and interleukin-6 levels measured by ELISA) were increased after stent implantation, and two days after stem implantation, their levels were positively correlated with the maximal percentage of area stenosis on day 28 (r(2)=0.889 and 0.743, respectively). This effect was abolished by UTI administration. Twenty-eight days after implantation, morphometric analysis of the stented arteries revealed significantly reduced luminal stenosis (38±6% vs. 64±12%, P<0.05), a neointimal area (3.22±0.57 mm(2) vs. 5.21±1.04 mm(2), P<0.05), neointimal thickness (0.31±0.13 mm vs. 0.46±0.16 mm, P<0.05), and an inflammatory score of 1.02±0.05 vs. 1.30±0.08 in UTI-treated animals as compared with controls. Twenty-eight days after stenting, arterial nuclear factor-κB expression was 36.93±7.16% in all of the cells in controls and 23.32±4.54% in UTI-treated minipigs. UTI could reduce neointimal formation after stenting by inhibiting the local and the systemic inflammatory response. Percutaneous coronary intervention could benefit from precocious anti-inflammatory treatment.
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Affiliation(s)
- J Y Kong
- Department of Emergency, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Hei Long Jiang, China.
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Li DH, Cai SX, Zhu TJ, Wang FP, Xiao X, Gu QQ. New Cytotoxic Metabolites from a Deep-Sea-Derived Fungus, Phialocephala sp., Strain FL30r. Chem Biodivers 2011; 8:895-901. [DOI: 10.1002/cbdv.201000134] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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29
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Xie XS, Liu HC, Wang FP, Zhang CL, Zuo C, Deng Y, Fan JM. Ginsenoside Rg1 modulation on thrombospondin-1 and vascular endothelial growth factor expression in early renal fibrogenesis in unilateral obstruction. Phytother Res 2010; 24:1581-7. [DOI: 10.1002/ptr.3190] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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30
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Liu C, Wang L, Xie XS, Xie LS, Li FY, Wang FP, Zhang L, Zhang HP, Fan JM. [Leukemia inhibitory factor suppresses renal interstitial fibroblast activation induced by transforming growth factor]. Sichuan Da Xue Xue Bao Yi Xue Ban 2010; 41:448-452. [PMID: 20629319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
OBJECTIVE To investigate the effects of leukemia inhibitory factor (LIF) on renal interstitial fibroblast activation following induction by transforming growth factor beta 1 (TGF-beta1). METHODS Normal rat interstitial fibroblast cells (NRK/49F) were treated with TGF-beta1 and TGF-beta1, combining with LIF respectively for different duration with different concentration. Changes in cell morphology and expression of alpha-SMA were evaluated with electronic microscope and Western blot respectively. The collagen I in the supernatant was detected with ABC-ELISA. RESULTS TGF-beta1 induced renal interstitial fibroblast activation, and this was accompanied by significant morphological transformations and secretion of collagen I. Co-culturing of cells with LIF blocked the morphological transformation. In addition, LIF inhibited TGF-beta1-induced expression of alpha-SMA mRNA and protein (P < 0.01), and decreased the levels of collagen I (P < 0.01) in a dose-dependent manner. CONCLUSION LIF suppresses TGF-beta1-induced activation and collagen I secretion of cultured renal interstitial fibroblasts.
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Affiliation(s)
- Chang Liu
- Department of Nephrology, West China Hospital, Sichuan University, Chengdu 610041, China
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31
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Liu SS, Wei QN, Feng WW, Zhan K, Wang FP. [A method for resolving spectra shift in the urban air quality monitoring system (DOAS)]. Guang Pu Xue Yu Guang Pu Fen Xi 2009; 29:1450-1453. [PMID: 19810506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In the urban air quality monitoring system, there is spectra shift which is caused by environment factors on the optical part (temperature and optic fiber position), or by the self-change of Xe-lamp. Relative spectra shift will occur if the shift of lamp-spectrum and air-spectrum is inconsistent which has direct influences on the accuracy of the measurement results. So the match of wavelength between lamp-spectrum and air-spectrum should be considered when we retrieve pollutants concentration measurement of trace gas in the atmosphere through DOAS method. Based on the study of the unique structures for Xe-lamp emitting spectrum, a method for the calibration of two signal spectra using Xe-lamp emitting peak and least square fitting is given. The results show that, the impact of spectrum shift can be reduced by this method for retrieving results.
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Affiliation(s)
- Shi-Sheng Liu
- Key Laboratory of Environmental Optics & Technology, Anhui Institute of Optics and Fine Mechanic, Chinese Academy of Sciences, Hefei 230031, China.
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33
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Long YY, Hu LF, Jiang CJ, Fang CR, Wang FP, Shen DS. Releasing behavior of copper in recirculated bioreactor landfill. Bioresour Technol 2009; 100:2419-2424. [PMID: 19119001 DOI: 10.1016/j.biortech.2008.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 11/09/2008] [Accepted: 11/11/2008] [Indexed: 05/27/2023]
Abstract
The purpose of this study was to determine the releasing behavior of copper in municipal solid waste (MSW) in landfill with respect to refuse and leachate as an inseparable system. Two simulated bioreactor landfills, one with leachate recirculation and the other without, were operated in room temperature for 320 days. Copper in refuse showed behaviors of staggered migration and retention, which corresponded with the degradation process of landfill obviously. The significant different amounts of Cu2+ leached out from refuse into leachate of two landfills were 24.74 mg and 118.53 mg after 320 days' operation, respectively. It also reflected the releasing behavior of copper in landfill refuse at different stage accordingly. The results confirmed that the refuse in landfill had high potential of secondary pollution after closure.
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Affiliation(s)
- Yu-Yang Long
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, China
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34
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Chen GY, Somesfalean G, Zhang ZG, Sun Q, Wang FP. Ultraviolet upconversion fluorescence in rare-earth-ion-doped Y2O3 induced by infrared diode laser excitation. Opt Lett 2007; 32:87-9. [PMID: 17167593 DOI: 10.1364/ol.32.000087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Room-temperature ultraviolet emission of Tm(3+) ions at 298 ((1)I(6)-->(3)H(6)), 364 ((1)D(2)-->(3)H(6)), and 391 nm ((1)I(6)-->(3)H(5)) was obtained in Y(2)O(3):Yb(3+)-Tm(3+) by continuous-wave diode laser excitation of 980 nm. Power dependence analysis demonstrates that five- and six-photon upconversion processes populate the (1)D(2) and (1)I(6) states, respectively. We believe that the (1)D(2) population originates from the cross relaxation (1)G(4)+(3)F(4)-->(3)H(4)+(1)D(2) of the Tm(3+) ions, while subsequent energy transfer from Yb(3+) to Tm(3+) excites the (1)D(2) state to the upper (1)I(6) state. High multiphoton-induced ultraviolet emission is also expected for other trivalent rare-earth ions similar to Tm(3+).
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Affiliation(s)
- G Y Chen
- Department of Physics, Harbin Institute of Technology, Harbin, China
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35
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Wang FP, Li Q, Zhou Y, Li MG, Xiao X. The C-terminal module of Chi1 fromAeromonas caviae CB101 has a function in substrate binding and hydrolysis. Proteins 2003; 53:908-16. [PMID: 14635132 DOI: 10.1002/prot.10501] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The chitinase gene chi1 of Aeromonas caviae CB101 encodes an 865-amino-acid protein (with signal peptide) composed of four domains named from the N-terminal as an all-beta-sheet domain ChiN, a triosephosphate isomerase (TIM) catalytic domain, a function-unknown A region, and a putative chitin-binding domain (ChBD) composed of two repeated sequences. The N-terminal 563-amino-acid segment of Chi1 (Chi1DeltaADeltaChBD) shares 74% identity with ChiA of Serratia marcescens. By the homology modeling method, the three-dimensional (3D) structure of Chi1DeltaADeltaChBD was constructed. It fit the structure of ChiA very well. To understand fully the function of the C-terminal module of Chi1 (from 564 to 865 amino acids), two different C-terminal truncates, Chi1DeltaChBD and Chi1DeltaADeltaChBD, were constructed, based on polymerase chain reaction (PCR). Comparison studies of the substrate binding, hydrolysis capacity, and specificity among Chi1 and its two truncates showed that the C-terminal putative ChBD contributed to the insoluble substrate-protein binding and hydrolysis; the A region did not have any function in the insoluble substrate-protein binding, but it did have a role in the chitin hydrolysis: Deletion of the A region caused the enzyme to lose 30-40% of its activity toward amorphous colloidal chitin and soluble chitin, and around 50% toward p-nitrophenyl (pNP)-chitobiose pNP-chitotriose, and its activity toward low-molecular-weight chitooligomers (GlcNAc)3-6 also dropped, as shown by analysis of its digestion processes. This is the first clear demonstration that a domain or segment without a function in insoluble substrate-chitinase binding has a role in the digestion of a broad range of chitin substrates, including low-molecular-weight chitin oligomers. The reaction mode of Chi1 is also described and discussed.
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Affiliation(s)
- F P Wang
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, and Third Institute of Oceanography, State Oceanic Administration, China
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36
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Xiao X, Wang FP, Schrempf H. [Purification and kinetic parameters of a Streptomyces olivaceoviridis protein which binds N-acetylglucosamine and chitin oligomers]. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 2002; 34:253-7. [PMID: 12523352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
A specific substrate binding protein is located within the membrane of Streptomyces olivaceoviridis mycelia. After Triton extraction of the membrane, two forms of the protein (46.0 kD and 47.5 kD) were purified to apparent homogeneity by consecutive anionic exchange chromatographies. The results of competition interacted with N-acetylglucosamine and chitin oligomers (C2 to C6), but not with cellobiose nor glucose. Using surface plasmon resonance, the kinetic parameters of the 46 kD form of the binding protein were determined. This protein showed a very high affinity for N-acetylglucosamine (K(d) = 8.29 x 10(-9) mol/L) and for chitobiose (K(d) = 3.81 X 10(-6) mol/L), and the lowest one was for chitotriose (K(d) = 1.95 X 10(-5) mol/L). Comparisons of the dissociation and association rate constants indicated that the interaction of this protein with each ligand was controlled by the association rate. N terminal sequence indicated that this protein might belong to an ABC transporter system.
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Affiliation(s)
- Xiang Xiao
- The Applied Genetics of Microorganisms, Faculty of Biology, University of Osnabrueck, Barbarastr, Germany
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Liu N, Shan Y, Wang FP, Xu CG, Peng KM, Li XH, Zhang Q. Identification of an 85-kb DNA fragment containing pms1, a locus for photoperiod-sensitive genic male sterility in rice. Mol Genet Genomics 2001; 266:271-5. [PMID: 11683269 DOI: 10.1007/s004380100553] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Photoperiod-sensitive genic male-sterile rice has a number of desirable characteristics for hybrid rice production. Previous studies identified pms1, located on chromosome 7, as a major locus for photoperiod-sensitive genic male sterility. The objective of this study was to localize the pms1 locus to a specific DNA fragment by genetic and physical mapping. Using 240 highly sterile individuals and a random sample of 599 individuals from an F2 population of over 5000 individuals from a cross between Minghui 63 and 32001S, we localized the pms1 locus by molecular marker analysis to a genetic interval of about 4 cM, 0.25 cM from RG477 on one side and 3.8 cM from R1807 on the other side. A contig map composed of seven BAC clones spanning approximate 500 kb in length was constructed for the pms1 region by screening a BAC library of Minghui 63 DNA using RFLP markers and chromosomal walking. Analysis of recombination events in the pms1 region among the highly sterile individuals reduced the length of the contig map to three BAC clones. Sequencing of one BAC clone, 2109, identified two SSR markers located 85 kb apart in the clone that flanked the pms1 locus on both sides, as indicated by the distribution of recombination events. We thus concluded that the pms1 locus was located on the fragment bounded by the two SSR markers.
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Affiliation(s)
- N Liu
- National Key Laboratory of Genetic Crop Improvement, Huazhong Agricultural University, Wuhan, China
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Abstract
Oxidation of pseudaconine 8, a norditerpenoid alkaloid, with HIO4 led to a series of novel interesting products, depending greatly on reaction medium and work-up conditions. Treatment of 8 in MeOH-H2O (1:1) with NaIO4 gave compounds 10 and 11, but compound 12 was obtained quantitatively when the final reaction solution was alkalized with conc. NH4OH. The imine 12 was also obtained in 100% yield by treating 8 in 5% HCl solution with NaIO4 followed by alkalizing the reaction products to pH>9 with conc. NH4OH. When the work up pH was 7-8, only N,O-mixed acetal-ketal 13 was formed in 96% yield, which was converted quantitatively to 12 by further alkalizing. When the reaction mixture was alkalized to pH 7-8 with Na2CO3, a hemiacetalketal 14 was afforded quantitatively, which was converted to 15 in 87% yield by further treatment with Na2CO3 or 5% NaOH methanol. Compound 15 could be converted back to 14 by treatment with 10% HCl solution. Acetylation of the imine 12 gave the compounds 16 and 17 in 15% and 19% yields, respectively. All of the new compounds were isolated and fully characterized.
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Affiliation(s)
- F P Wang
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu, Peoples Republic of China.
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39
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Shi YQ, Fukai T, Sakagami H, Chang WJ, Yang PQ, Wang FP, Nomura T. Cytotoxic flavonoids with isoprenoid groups from Morus mongolica. J Nat Prod 2001; 64:181-188. [PMID: 11429996 DOI: 10.1021/np000317c] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new pyranoflavanone, sanggenol L (1), a Diels-Alder type adduct regarded as a cycloaddition product of a dehydrogeranylflavanone and a prenylchalcone, sanggenol M (2), along with four new 2-arylbenzofurans with isoprenoid units, mulberrofurans W-Z (3-6), were isolated together with 10 known flavonoids from Chinese Morus mongolica. The structures of these novel compounds were elucidated by spectroscopic methods. All flavanones investigated here showed higher cytotoxicity against human oral tumor cell lines (HSC-2 and HSG) than against normal human gingival fibroblasts (HGF). Among them, the cytotoxicity of compound 2 and the Diels-Alder type flavanone sanggenon C (7) isolated from Morus cathayana were the most potent. On the other hand, seven 2-arylbenzofurans exhibited lower cytotoxicity and tumor specificity as compared with flavanones.
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Affiliation(s)
- Y Q Shi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Abstract
A new diterpenoid alkaloid, racemulotine (1), was isolated from the whole plants of Aconitum racemulosum Franch var. pengzhouense, and its structure was elucidated by 1D- and 2D-NMR spectra.
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Affiliation(s)
- C S Peng
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu
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41
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Abstract
Four new norditerpenoid alkaloids, geniculatines A (1), B (4), C (7) and D (8), were isolated from the roots of Aconitum geniculatum Fletcher, and their structures were elucidated by spectral methods.
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Affiliation(s)
- Z B Li
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu
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Abstract
From the roots of Aconitum sinomontanum, five new norditerpenoid alkaloids, sinomontanitines A (1) and B (2), sinomontanines A (3), B (4) and C (5), were isolated together with the known alkaloids lappaconitine (6) and ranaconitine (7), The structures of the new alkaloids were determined by spectral analysis.
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Affiliation(s)
- F P Wang
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu.
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43
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Peng CS, Wang FP. [Advances in chemistry of norditerpenoid alkaloids]. Yao Xue Xue Bao 2000; 35:932-8. [PMID: 12567919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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Wang FP, Yang JS, Chen QH, Yu L, Li BG. New access to 7,17-seco norditerpenoid alkaloids via reduction of the corresponding 8-chloro derivatives. Chem Pharm Bull (Tokyo) 2000; 48:1912-6. [PMID: 11145143 DOI: 10.1248/cpb.48.1912] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
New access to the 7, 17-seco norditerpenoid alkaloids 9 (60%) from yunnaconitine (5), as well as 14 (46%) and 15 (22%) from isotalatizidine (10), via selective hydrolysis, chlorination and reduction with NaBH4 is described.
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Affiliation(s)
- F P Wang
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu.
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Abstract
Two new norditerpenoid alkaloids, 13-deoxyludaconitine (1) and 8-deacetylsungpaconitine (3), were isolated from the roots of Aconitum hemsleyanum Pritz var. pengzhouense and their structures were elucidated by spectral data.
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Affiliation(s)
- C S Peng
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu
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Abstract
A novel norditerpenoid alkaloid, beiwudine (1), was isolated from the roots of Aconitum kusnezoffii. Its structure was established on the basis of chemical and NMR spectral studies.
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Affiliation(s)
- FP Wang
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu 610041, China, and Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong
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Abstract
Two new atisine-type diterpenoid alkaloids, beiwusine A (1) and B (2), have been isolated from the roots of Aconitum kusnezoffii Reichb. Their structures were established on the basis of spectroscopic data. Beiwusines A and B are the first examples of atisine-type diterpenoid alkaloids having a hydroxyl group at C-1. In addition, one known diterpenoid alkaloid spiramine H (3) has been isolated.
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Affiliation(s)
- Z B Li
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu 610041, China
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Abstract
An unsaturated lactone, 10-epi-olguine (1), has been isolated from Rabdosia ternifolia (D. Don) Hara. The structure was established by spectroscopic and X-ray crystallographic analyses. The compound displayed modest cytotoxicity in several human cancer cell lines.
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Affiliation(s)
- G H Lu
- Department of Chemistry of Medicinal Natural Products, School of Pharmacy, West China University of Medical Sciences, Chengdu
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Liu Y, Wang FP. [Impact on the development of extrinsic asthma caused by dust mites exposure, and its sensitization in Jiangsu]. Zhonghua Liu Xing Bing Xue Za Zhi 1996; 17:157-9. [PMID: 9208514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To obtain information on the relationship between dust mites exposure, dust mite sensitization, and the development of extrinsic asthma in Jiangsu province between 1992-1993, a case-control study was carried out. Unconditional logistic regression method was conducted. The results showed that the history of allergy in parents, dust mites exposure, dust mite sensitization, and birth in months with high mite densities were factors which played important roles in the development of extrinsic asthma. The population attributable rate of dust mites exposure was 70.29%. Based on the results, some practical preventive measures were put forward.
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Affiliation(s)
- Y Liu
- Nanjing Railway Medical College
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Benari B, Kiat H, Erel J, Hyun M, Wang FP, Williams C, Friedman JD, Germano G, Van Train KF, Berman D. Repeatability of treadmill exercise ejection fraction and wall motion using technetium 99m-labeled sestamibi first-pass radionuclide ventriculography. J Nucl Cardiol 1995; 2:478-84. [PMID: 9420829 DOI: 10.1016/s1071-3581(05)80039-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Peak treadmill exercise radionuclide ventriculography (RVG) with technetium 99m has recently been validated for determination of left ventricular ejection fraction (LVEF). However, the repeatability of this technique for determination of both LVEF and regional wall motion has not been reported. METHODS AND RESULTS Each of 27 clinically stable patients underwent two treadmill exercise RVG studies within 40 +/- 51 days. The level of exercise achieved in the two tests was similar (double product: 26,357 +/- 3877 vs 26,621 +/- 4287), and there was no change in clinical or treatment status between the studies. Acquisition and processing were accomplished with a mobile multicrystal camera and a new version of a commercial software (Scinticor SIM 400 V. 4.1 BETA, Milwaukee, Wis.) that uses two left ventricular regions of interest. The two tests were compared to assess agreement (repeatability) on both an automatically calculated LVEF and wall motion in five left ventricular segments (basal anterior, distal anterior, apical, distal inferior, and basal inferior), with a 3-point semiquantitative visual score. Intraobserver and interobserver agreements (reproducibility) also were assessed on quantitative exercise LVEF derived from the same RVG test from a separate group of 20 patients with a broad range of exercise LVEF. The first and second treadmill exercise LVEFs were highly correlated (r = 0.92, SEE = 3.96, y = 0.97x + 0.58; and r = 0.99, SEE = 1.32, y = 0.99x + 0.25, respectively). Results of segmental visual score agreement between the first and the second treadmill first-pass studies were as follows: overall, 86% (116/135, kappa = 0.74); basal anterior, 85% (23/27, kappa = 0.72); distal anterior, 85% (23/27, kappa = 0.84); apical, 93% (25/27, kappa = 0.85); distal inferior, 93% (25/27, kappa = 0.80); and basal inferior, 67% (18/27, kappa = 0.64). CONCLUSION Treadmill exercise first-pass RVG is a highly repeatable and reproducible test for quantitative LVEF and visual regional wall motion analysis. Our results imply the procedure may be useful for serial follow-up of patients with coronary artery disease and for the evaluation of the efficacy of medical or interventional treatment.
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Affiliation(s)
- B Benari
- Department of Medicine (Division of Cardiology), Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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