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Ning HY, Cai HJ, Ma TT, Fan CE, Wu DD, Gao FY, Kong F, Zhang FJ, Wang R, Guo HH, Ma RL, Zheng CY, Hao B, Wang HT, Zhang JJ, Zhang L, Wang XY. [Investigation and analysis of airborne allergenic pollen in 4 districts and 5 counties of Hohhot City]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1364-1372. [PMID: 37743296 DOI: 10.3760/cma.j.cn112150-20230116-00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Objective: To investigate the species, concentration and seasonal trends of main airborne allergenic pollen in 4 districts and 5 counties of Hohhot City. Methods: The Department of allergy, Beijing Shijitan Hospital Affiliated to Capital Medical University conducted a cross-sectional study about monitoring the airborne allergenic pollen from August 1, 2021 to July 31, 2022 by the gravitational method in 4 districts and 5 counties of Hohhot City, which include Yuquan District, Xincheng District, Huimin District, Saihan District, Tuoketuo County, Helingeer County, Tumotezuoqi County, Wuchuan County and Qingshuihe County. Daily pollens were counted and identified by optical microscopy, and the data were analyzed. Results: The airborne allergenic pollen was collected every month all year round in 4 districts and 5 counties of Hohhot city. Through the whole year of the total quantity of pollens ranged from 24 850 to 50 154 grains per 1 000 mm2 and two peaks of pollen concentration in air were observed,which happened in spring (from March to May) and in summer and autumn (from July to September). In spring, the main pollens were tree pollens, which principally distributed in Populus pollen (18.29%), Ulmus pollen (8.36%), Pinus pollen (6.20%), Cupressaceae pollen (5.23%), Betulaceae pollen (2.73%), Salix pollen (1.80%) and Quercus pollen (1.16%). In summer and autumn, the main pollens were weed pollens, which mainly included Artemisia pollen (42.73%), Chenopodiaceae pollen or Amaranthaceae pollen (7.46%), Poaceae pollen (2.26%), Humulus pollen or Cannabis pollen (0.60%). Conclusion: There were two peaks of main airborne allergenic pollen in 4 districts and 5 counties of Hohhot City. In the spring peak of pollen, the main airborne pollens were tree pollens. In the summer and autumn peak of pollen, the main airborne pollens were weed pollens. The Artemisia pollen was the most major airborne pollen in this area.
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Affiliation(s)
- H Y Ning
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China Allergy Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - H J Cai
- Allergy Center, Hohhot First Hospital, Hohhot 010030, China
| | - T T Ma
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China Allergy Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - C E Fan
- Allergy Center, Hohhot First Hospital, Hohhot 010030, China
| | - D D Wu
- Department of Primary Health Care, Hohhot Health Committee, Hohhot 010010, China
| | - F Y Gao
- Department of Allergy, Qingshuihe County Hospital, Hohhot 011600, China
| | - F Kong
- Department of Allergy, Hohhot Huimin District Hospital, Hohhot 010030, China
| | - F J Zhang
- Department of Clinical Laboratory, Ying Xin Road Office East Community Health Service Centre, Hohhot 010000, China
| | - R Wang
- Department of Clinical Laboratory, Daxuexi Road Community Health Service Centre, Hohhot 010018, China
| | - H H Guo
- Department of Allergy and Department of Clinical Laboratory, Tumotezuoqi People's Hospital, Hohhot 010100, China
| | - R L Ma
- Department of Allergy, Tuoketuo County Hospital, Hohhot 010200, China
| | - C Y Zheng
- Department of Allergy, Helingeer County Hospital, Hohhot 011500, China
| | - B Hao
- Department of Allergy, Wuchuan County Hospital, Hohhot 011700, China
| | - H T Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China Allergy Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - J J Zhang
- Allergy Center, Hohhot First Hospital, Hohhot 010030, China
| | - L Zhang
- Department of Otorhinolaryngology Head and Neck Surgery and Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China Beijing Key Laboratory of Allergic Diseases, Beijing Institute of Otorhinolaryngology, Beijing 100005, China
| | - X Y Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China Allergy Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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Hao B, Xu W, Gao W, Huang T, Lyu L, Lyu D, Xiao H, Li H, Qin J, Sheng L, Liu H. Association between Frailty Assessed Using Two Electronic Medical Record-Based Frailty Assessment Tools and Long-Term Adverse Prognosis in Older Critically Ill Survivors. J Nutr Health Aging 2023; 27:649-655. [PMID: 37702338 DOI: 10.1007/s12603-023-1961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVES Frailty has become an independent risk factor for adverse outcomes in critically ill patients. This study aimed to explore the predictive ability of two electronic medical record-based frailty assessment tools, the Hospital Frailty Risk Score (HFRS) and Frailty Index based on physiological and laboratory tests (FI-lab), for long-term adverse prognosis in older critically ill survivors. DESIGN Retrospective observational study. SETTING AND PARTICIPANTS 9,082 critically ill survivors aged ≥ 65 years. MEASUREMENTS The HFRS and the 33-item FI-lab were constructed based on the published literature. Cox and logistic regression models assessed the association between frailty and 1-year mortality and post-discharge care needs. RESULTS 2,586 patients died within 1 year of follow-up. In fully adjusted models, frailty assessed using both the HFRS (per point, hazard ratio [HR] 1.06, 95% confidential interval [CI] 1.05-1.06; intermediate frailty risk, HR 2.00, 95% CI 1.78-2.25; high frailty risk, HR 3.06, 95% CI 2.68-3.50) and FI-lab (per 0.01 points, HR 1.03, 95% CI 1.03-1.03; intermediate frailty risk, HR 1.59, 95% CI 1.44-1.76; high frailty risk, HR 2.30, 95% CI 2.06-2.57) was associated with mortality. Addition of frailty indicators improved the predictive validity of the Sequential Organ Failure Assessment score for mortality (HFRS alone ∆ C-index 0.034; FI-lab alone ∆ C-index 0.016; HFRS and FI-lab combined ∆ C-index 0.042). The HFRS but not the FI-lab was associated with higher probability of post-discharge care needs. CONCLUSION Both the HFRS and FI-lab could independently predict 1-year mortality in older critically ill survivors. Adding the HFRS to the SOFA score model improved it more than adding the FI-lab. The greatest improvement was achieved when both frailty indicators were used together. These findings suggest that electronic medical record-based frailty assessment methods can be useful tools for predicting long-term outcomes in older critically ill patients.
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Affiliation(s)
- B Hao
- Li Sheng, Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, China, ; Hongbin Liu, Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, China, e-mail:
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Jia J, Yuan Q, Hui JW, Liang JW, Wang X, Liu HH, Wang ZG, Dai XQ, Hao B, Gao RQ, Jiang FC, Ma HL. [Investigation of contamination of SARS-CoV-2 in imported frozen seafood from a foreign cargo ship and risk factors for infection in stevedores in Qingdao]. Zhonghua Liu Xing Bing Xue Za Zhi 2021; 42:1360-1364. [PMID: 34814554 DOI: 10.3760/cma.j.cn112338-20210209-00107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the contamination status of SARS-CoV-2 in imported frozen seafood from a Russia cargo ship in Qingdao and to analyze the risk factors for infection in local stevedores. Methods: The method of "two-stage, full coverage and mixed sampling" was used to collect the seafood packaging samples for the nucleic acid detection of SARS-CoV-2 by real-time fluorescent quantitative RT-PCR. A unified questionnaire was designed to investigate 71 stevedores in two shifts through telephone interview. The stevedores were divided into two groups, with 23 in the shit with two infections was group A and 48 in the shift without infection was group B. Software Epi Info7.2 was used to identify the risk factors for SARS-CoV-2 infections in the stevedores. Results: In the frozen seafood from a Russia cargo ship, the total positive rate of SARS-CoV-2 nucleic acid in the frozen seafood was 11.53% (106/919). The positive rate of SARS-CoV-2 nucleic acid in the frozen seafood unloaded by group A (14.29%,70/490) was significantly higher than that in the frozen seafood unloaded by group B (8.39%,36/429)(χ2=7.79,P=0.01) and the viral loads detected in the frozen seafood unloaded by group A were higher than those detected in the frozen seafood unloaded by group B. The scores of personal protection and behaviors in the stevedores in group A were significantly lower than those in group B (P<0.05), and toilet use, smoking and improper hand washing before meals were the risk factors for the infection. Conclusions: The imported frozen seafood was contaminated by SARS-CoV-2 and the contamination distribution was uneven. Supervision and management of personal occupational protection and behaviors of workers engaged in imported frozen food transportation should be strengthened. It is suggested that a closed-loop monitoring and management system for the whole process of "fishing-transport- loading/unloading" should be established by marine fishery authority.
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Affiliation(s)
- J Jia
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - Q Yuan
- Shandong Center for Disease Control and Prevention, Ji'nan 250014,China
| | - J W Hui
- Qingdao Shibei District Center for Disease Control and Prevention, Qingdao 266011, China
| | - J W Liang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - X Wang
- Qingdao Shibei District Center for Disease Control and Prevention, Qingdao 266011, China
| | - H H Liu
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z G Wang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - X Q Dai
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - B Hao
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - R Q Gao
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - F C Jiang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao 266033,China
| | - H L Ma
- Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Song HF, Deng X, Yang N, Hao B, Hu YB, Shi YW, Xue L, Zhao H. Impulse Control and ERP Characteristics of Patients with Mental Disorder Caused by Traumatic Brain Injury. Fa Yi Xue Za Zhi 2020; 36:326-332. [PMID: 32705844 DOI: 10.12116/j.issn.1004-5619.2020.03.006] [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] [Received: 11/12/2019] [Indexed: 11/30/2022]
Abstract
Abstract Objective To explore the impulse control and event-related potential (ERP) characteristics of patients with mental disorders caused by traumatic brain injury (TBI) in forensic psychiatry identification and to provide objective auxiliary indicators for forensic psychiatry identification. Methods Thirty patients (TBI group) with mental disorders caused by traumatic brain injury, who were identified as mild psychiatric impairment by judicial psychiatry, including 24 males and 6 females, as well as the thirty people in the control group participated in the study. All the participants completed Barratt Impulsiveness Scale-11 (BIS-11) and ERP induced by Go/NoGo tasks. BIS-11 and ERP data were collected and analyzed. Results The results of the BIS-11 showed that the total score and subscale scores of the TBI group were higher compared to the control group (P<0.05). Moreover, the TBI group exhibited significantly lower NoGo-N2 amplitude and lower NoGo-P3 amplitude than the control group. The NoGo-N2 amplitude was larger than the Go-N2 amplitude, and the NoGo-P3 amplitude was larger than the Go-P3 amplitude in both groups (P<0.05). Conclusion Traumatic brain injury could impair impulse control of mild psychiatric impairment patients, and the amplitudes of NoGo-N2 and NoGo-P3 could be important parameters to evaluate the impulse control of patients with mental disorders caused by traumatic brain injury.
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Affiliation(s)
- H F Song
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - X Deng
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - N Yang
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - B Hao
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Y B Hu
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Y W Shi
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Guangzhou 510080, China
| | - L Xue
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Guangzhou 510080, China
| | - H Zhao
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Guangzhou 510080, China
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Hao B, Chen Z, Zeng G, Huang L, Luan C, Xie Z, Chen J, Bao M, Tian X, Xu B, Wang Y, Wu J, Xia S, Yuan L, Huang J. Efficacy, safety and immunogenicity of live attenuated varicella vaccine in healthy children in China: double-blind, randomized, placebo-controlled clinical trial. Clin Microbiol Infect 2019; 25:1026-1031. [DOI: 10.1016/j.cmi.2018.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
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Yalla K, Elliott C, Day JP, Findlay J, Barratt S, Hughes ZA, Wilson L, Whiteley E, Popiolek M, Li Y, Dunlop J, Killick R, Adams DR, Brandon NJ, Houslay MD, Hao B, Baillie GS. FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system. Mol Psychiatry 2018; 23:1278-1286. [PMID: 28727686 PMCID: PMC5984089 DOI: 10.1038/mp.2017.138] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/27/2023]
Abstract
Disrupted in schizophrenia 1 (DISC1) is a multi-functional scaffolding protein that has been associated with neuropsychiatric disease. The role of DISC1 is to assemble protein complexes that promote neural development and signaling, hence tight control of the concentration of cellular DISC1 in neurons is vital to brain function. Using structural and biochemical techniques, we show for we believe the first time that not only is DISC1 turnover elicited by the ubiquitin proteasome system (UPS) but that it is orchestrated by the F-Box protein, FBXW7. We present the structure of FBXW7 bound to the DISC1 phosphodegron motif and exploit this information to prove that disruption of the FBXW7-DISC1 complex results in a stabilization of DISC1. This action can counteract DISC1 deficiencies observed in neural progenitor cells derived from induced pluripotent stem cells from schizophrenia patients with a DISC1 frameshift mutation. Thus manipulation of DISC1 levels via the UPS may provide a novel method to explore DISC1 function.
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Affiliation(s)
- K Yalla
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - C Elliott
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, UK
| | - J P Day
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J Findlay
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - S Barratt
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Z A Hughes
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - L Wilson
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - E Whiteley
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - M Popiolek
- Neuroscience Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - Y Li
- Department of Molecular Biology and Biophysics, University of Connecticut Health Centre, Farmington, CT, USA
| | - J Dunlop
- AstraZeneca, Neuroscience, Innovative Medicines & Early Development, Waltham, MA, USA
| | - R Killick
- Institute of Psychiatry, Psychology and Neuroscience, King’s College, London, UK
| | - D R Adams
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
| | - N J Brandon
- AstraZeneca, Neuroscience, Innovative Medicines & Early Development, Waltham, MA, USA
| | - M D Houslay
- Institute of Pharmaceutical Science, King’s College, London, UK
| | - B Hao
- Department of Molecular Biology and Biophysics, University of Connecticut Health Centre, Farmington, CT, USA
| | - G S Baillie
- College of Veterinary Medical and Life Sciences, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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Wu FY, Tang XH, Gai LL, Kong XP, Hao B, Huang EW, Shi H, Sheng LH, Quan L, Liu SP, Luo B. [Correlation between Genetic Variants and Polymorphism of Caveolin and Sudden Unexplained Death]. Fa Yi Xue Za Zhi 2017; 33:114-119. [PMID: 29231014 DOI: 10.3969/j.issn.1004-5619.2017.02.002] [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] [Received: 12/05/2016] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To explore the genetic variation sites of caveolin (CAV) and their correlation with sudden unexplained death (SUD). METHODS The blood samples were collected from SUD group (71 cases), coronary artery disease (CAD) group (62 cases) and control group (60 cases), respectively. The genome DNA were extracted and sequencing was performed directly by amplifying gene coding region and exon-intron splicing region of CAV1 and CAV3 using PCR. The type of heritable variation of CVA was confirmed and statistical analysis was performed. RESULTS A total of 4 variation sites that maybe significative were identified in SUD group, and two were newfound which were CAV1: c.45C>T (T15T) and CAV1:c.512G>A (R171H), and two were SNP loci which were CAV1:c.246C>T (rs35242077) and CAV3:c.99C>T (rs1008642) and had significant difference (P<0.05) in allele and genotype frequencies between SUD and control groups. Forementioned variation sites were not found in CAD group. CONCLUSIONS The variants of CAV1 and CAV3 may be correlated with a part of SUD group.
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Affiliation(s)
- F Y Wu
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - X H Tang
- Dongyuan Public Security Bureau, Dongyuan 517500, China
| | - L L Gai
- Huangpu Branch of Guangzhou Municipal Public Security Bureau, Guangzhou 510530, China
| | - X P Kong
- Panyu Branch of Guangzhou Municipal Public Security Bureau, Guangzhou 511430, China
| | - B Hao
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - E W Huang
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - H Shi
- Institute of Criminal Science and Technology, Guangzhou Municipal Public Security Bureau, Guangzhou 510030, China
| | - L H Sheng
- Institute of Criminal Science and Technology, Shenzhen Municipal Public Security Bureau, Shenzhen 518008, China
| | - L Quan
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - S P Liu
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - B Luo
- Department of Forensic Medicine, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
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Wu FY, Gai LL, Kong XP, Hao B, Huang EW, Shi H, Sheng LH, Quan L, Liu SP, Luo B. [Research Progress of the Correlation between Caveolin and Unexpected Sudden Cardiac Death]. Fa Yi Xue Za Zhi 2017; 33:284-288. [PMID: 29230996 DOI: 10.3969/j.issn.1004-5619.2017.03.015] [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] [Received: 04/14/2016] [Indexed: 11/18/2022]
Abstract
Due to the negative autopsy and without cardiac structural abnormalities, unexpected sudden cardiac death (USCD) is always a tough issue for forensic pathological expertise. USCD may be associated with parts of fatal arrhythmic diseases. These arrhythmic diseases may be caused by disorders of cardiac ion channels or channel-related proteins. Caveolin can combine with multiple myocardial ion channel proteins through its scaffolding regions and plays an important role in maintaining the depolarization and repolarization of cardiac action potential. When the structure and function of caveolin are affected by gene mutations or abnormal protein expression, the functions of the regulated ion channels are correspondingly impaired, which leads to the occurrence of multiple channelopathies, arrhythmia or even sudden cardiac death. It is important to study the effects of caveolin on the functions of ion channels for exploring the mechanisms of malignant arrhythmia and sudden cardiac death.
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Affiliation(s)
- F Y Wu
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - L L Gai
- Huangpu Branch of Guangzhou Municipal Public Security Bureau, Guangzhou 510530, China
| | - X P Kong
- Panyu Branch of Guangzhou Municipal Public Security Bureau, Guangzhou 511430, China
| | - B Hao
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - E W Huang
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - H Shi
- Guangzhou Institute of Criminal Science and Technology, Guangzhou 510030, China
| | - L H Sheng
- Institute of Criminal Science and Technology, Shenzhen Municipal Public Security Bureau, Shenzhen 518008, China
| | - L Quan
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - S P Liu
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
| | - B Luo
- Department of Forensic Pathology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, China
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Zuo G, Hao B. Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis. Int J Syst Evol Microbiol 2016; 66:2451. [DOI: 10.1099/ijsem.0.001047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Fudan University, Shanghai 200433, PR China
| | - Bailin Hao
- T-Life Research Center, Fudan University, Shanghai 200433, PR China
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Hao B, Caulfield JC, Hamilton ML, Pickett JA, Midega CAO, Khan ZR, Wang J, Hooper AM. Biosynthesis of natural and novel C-glycosylflavones utilising recombinant Oryza sativa C-glycosyltransferase (OsCGT) and Desmodium incanum root proteins. Phytochemistry 2016; 125:73-87. [PMID: 26923852 DOI: 10.1016/j.phytochem.2016.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/12/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
The rice C-glycosyltransferase (OsCGT) is one of only a small number of characterised plant C-glycosyltransferases (CGT) known. The enzyme C-glucosylates a 2-hydroxyflavanone substrate with UDP-glucose as the sugar donor to produce C-glucosyl-2-hydroxyflavanones. We tested substrate specificity of the enzyme, using synthetic 2-hydroxyflavanones, and showed it has the potential to generate known natural CGFs that have been isolated from rice and also other plants. In addition, we synthesised novel, unnatural 2-hydroxyflavanone substrates to test the B-ring chemical space of substrate accepted by the OsCGT and demonstrated the OsCGT capacity as a synthetic reagent to generate significant quantities of known and novel CGFs. Many B-ring analogues are tolerated within a confined steric limit. Finally the OsCGT was used to generate novel mono-C-glucosyl-2-hydroxyflavanones as putative biosynthetic intermediates to examine the potential of Desmodium incanum biosynthetic CGTs to produce novel di-C-glycosylflavones, compounds implicated in the allelopathic biological activity of Desmodium against parasitic weeds from the Striga genus.
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Affiliation(s)
- B Hao
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - J C Caulfield
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - M L Hamilton
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - J A Pickett
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - C A O Midega
- International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi, Kenya.
| | - Z R Khan
- International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi, Kenya.
| | - J Wang
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - A M Hooper
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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Zuo G, Zhi X, Xu Z, Hao B. LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics. Genomics Proteomics Bioinformatics 2016; 14:94-102. [PMID: 27018315 PMCID: PMC4880948 DOI: 10.1016/j.gpb.2015.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/04/2015] [Accepted: 12/21/2015] [Indexed: 11/18/2022]
Abstract
We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Xiaoyang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
| | - Zhao Xu
- Thermo Fisher Scientific, South San Francisco, CA 94080, USA
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
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12
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Zuo G, Hao B. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321-31. [PMID: 26563468 PMCID: PMC4678791 DOI: 10.1016/j.gpb.2015.08.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/10/2015] [Indexed: 01/15/2023]
Abstract
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
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Hooper AM, Caulfield JC, Hao B, Pickett JA, Midega CAO, Khan ZR. Isolation and identification of Desmodium root exudates from drought tolerant species used as intercrops against Striga hermonthica. Phytochemistry 2015; 117:380-387. [PMID: 26164239 PMCID: PMC4560159 DOI: 10.1016/j.phytochem.2015.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/16/2015] [Accepted: 06/25/2015] [Indexed: 05/04/2023]
Abstract
Plants from the genus Desmodium, in particular D. uncinatum, are used on sub-Saharan small-holder farms as intercrops to inhibit parasitism of cereal crops by Striga hermonthica and Striga asiatica via an allelopathic mechanism. The search for Desmodium species which are adapted to more arid conditions, and which show resilience to increased drought stress, previously identified D. intortum, D. incanum and D. ramosissimum as potential drought tolerant intercrops. Their potential as intercrops was assessed for resource poor areas of rain-fed cereal production where drought conditions can persist through normal meteorological activity, or where drought may have increasing impact through climate change. The chemical composition of the root exudates were characterised and the whole exudate biological activity was shown to be active in pot experiments for inhibition of Striga parasitism on maize. Furthermore, rain fed plot experiments showed the drought tolerant Desmodium intercrops to be effective for Striga inhibition. This work demonstrates the allelopathic nature of the new drought tolerant intercrops through activity of root exudates and the major compounds seen in the exudates are characterised as being C-glycosylflavonoid. In young plants, the exudates show large qualitative differences but as the plants mature, there is a high degree of convergence of the C-glycosylflavonoid exudate chemical profile amongst active Desmodium intercrops that confers biological activity. This defines the material for examining the mechanism for Striga inhibition.
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Affiliation(s)
- A M Hooper
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - J C Caulfield
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - B Hao
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - J A Pickett
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - C A O Midega
- International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi, Kenya.
| | - Z R Khan
- International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi, Kenya.
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Zuo G, Xu Z, Hao B. Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis. Life (Basel) 2015; 5:949-68. [PMID: 25789552 PMCID: PMC4390887 DOI: 10.3390/life5010949] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/29/2022] Open
Abstract
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey's Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.
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Affiliation(s)
- Guanghong Zuo
- Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Zhao Xu
- Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA.
| | - Bailin Hao
- Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
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Abstract
Using an enlarged alphabet of K-tuples is the way to carry out alignment-free comparison of genomes in the composition vector (CV) approach to prokaryotic phylogeny. We summarize the known aspects concerning the choice of K and examine the results of using CVs with subtraction of a statistical background for K=3-9 and using raw CVs without subtraction for K=1-12. The criterion for evaluation consists in direct comparison with taxonomy. For prokaryotes the best performances are obtained for K=5 and 6 with subtraction and for K=11, 12 or even more without subtraction. In general, CVs with subtractions are slightly better and less CPU consuming, but CVs without subtraction may provide complementary information.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Fudan University, Shanghai 200433, China
| | - Qiang Li
- CAS-MPG Partner Institute for Computational Biology, Shanghai 200032, China
| | - Bailin Hao
- T-Life Research Center, Fudan University, Shanghai 200433, China.
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Clancy C, Shields R, Potoski B, Hao B, Bermudez C, Pilewski J, Crespo M, Silveira F, Nguyen M. Identifying Optimal Treatment Regimens for Lung and Heart Transplant Patients (LTx, HTx pts) Infected With Extreme-Drug Resistant (XDR) Gram-Negative Bacteria. J Heart Lung Transplant 2014. [DOI: 10.1016/j.healun.2014.01.410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Clancy CJ, Chen L, Shields RK, Zhao Y, Cheng S, Chavda KD, Hao B, Hong JH, Doi Y, Kwak EJ, Silveira FP, Abdel-Massih R, Bogdanovich T, Humar A, Perlin DS, Kreiswirth BN, Hong Nguyen M. Epidemiology and molecular characterization of bacteremia due to carbapenem-resistant Klebsiella pneumoniae in transplant recipients. Am J Transplant 2013; 13:2619-33. [PMID: 24011185 PMCID: PMC3955300 DOI: 10.1111/ajt.12424] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [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: 03/06/2013] [Accepted: 06/28/2013] [Indexed: 01/25/2023]
Abstract
We conducted a retrospective study of 17 transplant recipients with carbapenem-resistant Klebsiella pneumoniae bacteremia, and described epidemiology, clinical characteristics and strain genotypes. Eighty-eight percent (15/17) of patients were liver or intestinal transplant recipients. Outcomes were death due to septic shock (18%), cure (24%) and persistent (>7 days) or recurrent bacteremia (29% each). Thirty- and 90-day mortality was 18% and 47%, respectively. Patients who were cured received at least one active antimicrobial agent and underwent source control interventions. Forty-one percent (7/17) of patients had intra-abdominal infections; all except one developed persistent/recurrent bacteremia despite drainage. Two patients tolerated persistent bacteremia for >300 days. All patients except one were infected with sequence type 258 (ST258), K. pneumoniae carbapenemase (KPC)-2-producing strains harboring a mutant ompK35 porin gene; the exception was infected with an ST37, KPC-3-producing strain. Seventy-one percent (12/17) of patients were infected with ST258 ompK36 mutant strains. In two patients, persistent bacteremia was caused by two strains with different ompK36 genotypes. Three ompK36 mutations were associated with significantly higher carbapenem minimum inhibitory concentrations than wild-type ompK36. Pulse-field gel electrophoresis identified a single ST258 lineage; serial strains from individual patients were indistinguishable. In conclusion, KPC-K. pneumoniae bacteremia exhibited highly diverse clinical courses following transplantation, and was caused by clonal ST258 strains with different ompK36 genotypes.
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Affiliation(s)
- C. J. Clancy
- University of Pittsburgh, Pittsburgh, PA,XDR Pathogen Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA,Pittsburgh VA Healthcare System, Pittsburgh, PA
| | - L. Chen
- Public Health Research Institute, New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, NJ
| | - R. K. Shields
- University of Pittsburgh, Pittsburgh, PA,XDR Pathogen Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Y. Zhao
- Public Health Research Institute, New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, NJ
| | - S. Cheng
- University of Pittsburgh, Pittsburgh, PA
| | - K. D. Chavda
- Public Health Research Institute, New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, NJ
| | - B. Hao
- University of Pittsburgh, Pittsburgh, PA,XDR Pathogen Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - J. H. Hong
- University of Pittsburgh, Pittsburgh, PA
| | - Y. Doi
- University of Pittsburgh, Pittsburgh, PA
| | - E. J. Kwak
- University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - A. Humar
- University of Pittsburgh, Pittsburgh, PA
| | - D. S. Perlin
- Public Health Research Institute, New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, NJ
| | - B. N. Kreiswirth
- Public Health Research Institute, New Jersey Medical School-University of Medicine and Dentistry of New Jersey, Newark, NJ
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, PA,XDR Pathogen Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA,Corresponding author: M. Hong Nguyen,
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Li GY, Mo ZL, Li J, Xiao P, Hao B, Guo YH. Development of a multiplex PCR for the identification of pathogenic Edwardsiella tarda and application to edwardsiellosis diagnostics. J Fish Dis 2013; 36:151-157. [PMID: 23126448 DOI: 10.1111/j.1365-2761.2012.01446.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 06/01/2023]
Affiliation(s)
- G Y Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Zuo G, Xu Z, Hao B. Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia. Genomics Proteomics Bioinformatics 2012; 11:61-5. [PMID: 23395177 PMCID: PMC4357666 DOI: 10.1016/j.gpb.2012.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 11/05/2012] [Indexed: 02/02/2023]
Abstract
Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Escherichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center and Department of Physics, Fudan University, Shanghai 200433, China
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20
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Nguyen MH, Wissel MC, Shields RK, Salomoni MA, Hao B, Press EG, Shields RM, Cheng S, Mitsani D, Vadnerkar A, Silveira FP, Kleiboeker SB, Clancy CJ. Performance of Candida Real-time Polymerase Chain Reaction, -D-Glucan Assay, and Blood Cultures in the Diagnosis of Invasive Candidiasis. Clin Infect Dis 2012; 54:1240-8. [DOI: 10.1093/cid/cis200] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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21
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Liu J, Ibrahim NM, Hao B, Chen L. Changes in left ventricular structure and function in patients with metabolic syndrome. Heart 2011. [DOI: 10.1136/heartjnl-2011-300867.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Composition vector trees (CVTrees) are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
- Shanghai Institute of Applied Physics, Chinese Acadamy of Sciences, Shanghai 201800, China
| | - Zhao Xu
- T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
- Applied Biosystems, Inc., Beijing 100027, China
| | - Hongjie Yu
- T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
- Fudan-VARI Center for Genetic Epidemiology, Fudan University, Shanghai 200433, China
| | - Bailin Hao
- T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
- Institute of Theoretical Physics, Chinese Acadamy of Sciences, Beijing 100190, China
- Santa Fe Institute, Santa Fe, NM 87505, USA
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Abstract
AIMS Genes uniquely expressed in vivo may contribute to the overall pathogenicity of an organism and are likely to serve as potential targets for the development of new vaccine. This study aims to screen the genes expressed in vivo after Vibrio anguillarum infection by in vivo-induced antigen technology (IVIAT). METHODS AND RESULTS The convalescent-phase sera were obtained from turbot (Scophthalmus maximus) survived after infection by the virulent V. anguillarum M3. The pooled sera were thoroughly adsorbed with M3 cells and Escherichia coli BL21 (DE3) cells. A genomic expression library of M3 was constructed and screened for the identification of immunogenic proteins by colony immunoblot analysis with the adsorbed sera. After three rounds of screening, 19 putative in vivo-induced (ivi) genes were obtained. These ivi genes were catalogued into four functional groups: regulator/signalling, metabolism, biological process and hypothetical proteins. Three ivi genes were insertion-mutated, and the growth and 50% lethal dose (LD(50) ) of these mutants were evaluated. CONCLUSIONS The identification of ivi genes in V. anguillarum M3 sheds light on understanding the bacterial pathogenesis and provides novel targets for the development of new vaccines and diagnostic reagents. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report describing in vivo-expressed genes of V. anguillarum using IVIAT. The screened ivi genes in this study could be new virulent factors and targets for the development of vaccine, which may have implications for the development of diagnostic regents.
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Affiliation(s)
- Y-X Zou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Li Q, Xu Z, Hao B. Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations. J Biotechnol 2009; 149:115-9. [PMID: 20036699 DOI: 10.1016/j.jbiotec.2009.12.015] [Citation(s) in RCA: 28] [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] [Received: 08/15/2009] [Revised: 12/08/2009] [Accepted: 12/21/2009] [Indexed: 11/18/2022]
Abstract
Composition vector approach to prokaryotic phylogeny provides an alignment-free and parameter-free method based on whole-genome data. It has also been applied to viruses and fungi. In all studied cases the inferred phylogenetic relationships agree well with taxonomic knowledge in major groupings and fine branchings. In this review article, after demonstrating its successful application to a collection of 892 genomes including 62 Archaea, 822 Bacteria and 8 Eukarya, we will outline some ongoing work towards the foundations of this new approach.
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Affiliation(s)
- Qiang Li
- T-Life Research Center, Fudan University, Shanghai 200433, China
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Wang H, Xu Z, Gao L, Hao B. A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol Biol 2009; 9:195. [PMID: 19664262 PMCID: PMC3087519 DOI: 10.1186/1471-2148-9-195] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 08/10/2009] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Molecular phylogenetics and phylogenomics have greatly revised and enriched the fungal systematics in the last two decades. Most of the analyses have been performed by comparing single or multiple orthologous gene regions. Sequence alignment has always been an essential element in tree construction. These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. The ever-increasing number of sequenced fungal genomes and the recent success of our newly proposed alignment-free composition vector tree (CVTree, see Methods) approach have made the verification feasible. RESULTS In all, 82 fungal genomes covering 5 phyla were obtained from the relevant genome sequencing centers. An unscaled phylogenetic tree with 3 outgroup species was constructed by using the CVTree method. Overall, the resultant phylogeny infers all major groups in accordance with standard methods. Furthermore, the CVTree provides information on the placement of several currently unsettled groups. Within the sub-phylum Pezizomycotina, our phylogeny places the Dothideomycetes and Eurotiomycetes as sister taxa. Within the Sordariomycetes, it infers that Magnaporthe grisea and the Plectosphaerellaceae are closely related to the Sordariales and Hypocreales, respectively. Within the Eurotiales, it supports that Aspergillus nidulans is the early-branching species among the 8 aspergilli. Within the Onygenales, it groups Histoplasma and Paracoccidioides together, supporting that the Ajellomycetaceae is a distinct clade from Onygenaceae. Within the sub-phylum Saccharomycotina, the CVTree clearly resolves two clades: (1) species that translate CTG as serine instead of leucine (the CTG clade) and (2) species that have undergone whole-genome duplication (the WGD clade). It places Candida glabrata at the base of the WGD clade. CONCLUSION Using different input data and methodology, the CVTree approach is a good complement to the standard methods. The remarkable consistency between them has brought about more confidence to the current understanding of the fungal branch of TOL.
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Affiliation(s)
- Hao Wang
- T-life Research Center, Department of Physics, Fudan University, Shanghai 200433, PR China.
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26
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Zhang H, Zhong Y, Hao B, Gu X. A simple method for phylogenomic inference using the information of gene content of genomes. Gene 2009; 441:163-8. [DOI: 10.1016/j.gene.2008.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 07/07/2008] [Accepted: 07/09/2008] [Indexed: 11/27/2022]
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Xu Z, Hao B. CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res 2009; 37:W174-8. [PMID: 19398429 PMCID: PMC2703908 DOI: 10.1093/nar/gkp278] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [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: 01/30/2009] [Revised: 04/10/2009] [Accepted: 04/14/2009] [Indexed: 11/21/2022] Open
Abstract
The CVTree web server (http://tlife.fudan.edu.cn/cvtree) presented here is a new implementation of the whole genome-based, alignment-free composition vector (CV) method for phylogenetic analysis. It is more efficient and user-friendly than the previously published version in the 2004 web server issue of Nucleic Acids Research. The development of whole genome-based alignment-free CV method has provided an independent verification to the traditional phylogenetic analysis based on a single gene or a few genes. This new implementation attempts to meet the challenge of ever increasing amount of genome data and includes in its database more than 850 prokaryotic genomes which will be updated monthly from NCBI, and more than 80 fungal genomes collected manually from several sequencing centers. This new CVTree web server provides a faster and stable research platform. Users can upload their own sequences to find their phylogenetic position among genomes selected from the server's; inbuilt database. All sequence data used in a session may be downloaded as a compressed file. In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels. This feature is particularly useful for comparing phylogeny with taxonomy when dealing with thousands of genomes.
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Affiliation(s)
- Zhao Xu
- T-Life Research Center, Fudan University, 220 Handan Road, Shanghai 200433, China.
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Abstract
BACKGROUND Bicyclol is a novel synthetic 'anti-hepatitis' drug, used in China for chronic hepatitis B. Until now, systematic reviews of bicyclol therapy have not been performed. OBJECTIVES To study the benefits and harms of bicyclol for patients with chronic hepatitis B. SEARCH STRATEGY We searched The Cochrane Hepato-Biliary Group Controlled Trials Register (July 2005), The Cochrane Central Register of Controlled Trials in The Cochrane Library (Issue 2, 2005), MEDLINE (1950 to July 2005), EMBASE (1980 to July 2005), Science Citation Index Expanded (1945 to July 2005), The Chinese Biomedical Database (1994 to August 2005), VIP Chinese Science and Technique Journals Database (1994 to August 2005), and China National Infrastructure (CNKI)(1994 to August 2005). We also contacted manufacturers and researchers in the field. SELECTION CRITERIA Randomised clinical trials with bicyclol versus no intervention, placebo, or other interventions were included, irrespective of blinding, publication status, or language. DATA COLLECTION AND ANALYSIS The primary outcome measures were mortality (total and liver-related) and liver-related morbidity (eg, cirrhosis and carcinoma). Secondary outcome measures were viral response and liver histology. MAIN RESULTS The search identified one randomised clinical trial comparing bicyclol with bifendate (biphenyldicarboxylate) for patients with hepatitis B. The follow-up was three months. There was no evidence that bicyclol was superior to bifendate for loss of HBeAg (RR 1.38, 95% CI 0.95 to 2.00), seroconversion of HBeAg to HBeAb (RR 1.44, 95% CI 0.90 to 2.29), loss of HBV DNA (RR 1.19, 95%CI 0.93 to 1.53), or number of patients with normalised alanine aminotransferase and aspartate aminotransferase activity (RR 0.88, 95% CI 0.70 to 1.11 and RR 0.97, 95% CI 0.79 to 1.20, respectively). AUTHORS' CONCLUSIONS Only one randomised clinical trial has examined the potential benefit of bicyclol for patients with chronic hepatitis B. This small, short-term trial found no evidence to support or refute its use. Large, randomised double-blind clinical trials with long-term follow-up are needed to examine the possible benefits and harms associated with bicyclol. Bicyclol can only be recommended for use in randomised trials.
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Affiliation(s)
- T Wu
- West China Hospital, Sichuan University, Chinese Cochrane Centre, Chinese EBM Centre, No. 37, Guo Xue Xiang, Chengdu, Sichuan, China.
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Hao B, Miao X, Li Y, Zhang X, Sun T, Liang G, Zhao Y, Zhou Y, Wang H, Chen X, Zhang L, Tan W, Wei Q, Lin D, He F. A novel T-77C polymorphism in DNA repair gene XRCC1 contributes to diminished promoter activity and increased risk of non-small cell lung cancer. Oncogene 2006; 25:3613-20. [PMID: 16652158 DOI: 10.1038/sj.onc.1209355] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [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: 11/09/2022]
Abstract
X-ray repair cross-complementing 1 (XRCC1) plays a key role in DNA base excision repair and cells lacking its activity are hypersensitive to DNA damage. Recently, we reported a SNP (rs3213245, -77T>C) in the XRCC1 gene 5' untranslated region (UTR) was significantly associated with the risk of developing esophageal squamous-cell carcinoma. Computer analysis predicted that this SNP was in the core of Sp1-binding motif, which suggested its functional significance. Gel shift and super shift assays confirmed that -77T>C polymorphic site in the XRCC1 promoter was within the Sp1-binding motif and the T>C substitution greatly enhanced the binding affinity of Sp1 to this region. Luciferase assays indicated that the Sp1-high-affinity C-allelic XRCC1 promoter was associated with a reduced transcriptional activity. The association between -77T>C and three other amino-acid substitution-causing polymorphisms in XRCC1 and risk of lung cancer was examined in 1024 patients and 1118 controls and the results showed that only the -77T>C polymorphism was significantly associated with an increased risk of developing lung cancer. Multivariate logistic regression analysis found that an increased risk of lung cancer was associated with the variant XRCC1 -77 genotypes (TC and CC) compared with the TT genotype (OR=1.46, 95% CI=1.18-1.82; P=0.001) and the increased risk was more pronounced in smokers (OR=1.63, 95% CI=1.20-2.21) than in non-smokers (OR=1.28, 95% CI=0.94-1.76). Taken together, these results showed that the functional SNP -77T>C in XRCC1 5'UTR was associated with cancer development owing to the decreased transcriptional activity of C-allele-containing promoter with higher affinity to Sp1 binding.
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Affiliation(s)
- B Hao
- Department of Biology Sciences and Biotechnology, Tsinghua University, Beijing, China
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30
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Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJH, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GKS, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature 2006; 440:1194-8. [PMID: 16641997 DOI: 10.1038/nature04728] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 03/17/2006] [Indexed: 11/09/2022]
Abstract
After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
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Affiliation(s)
- Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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31
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Zhang G, Huang Z, Shi R, Lin Y, Hao B. Osteopontin regulation by protein kinase B (Akt) in HepG2 cells. Exp Oncol 2006; 28:36-9. [PMID: 16614705] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
AIM The mechanism responsible for osteopontin regulation is not understood in HepG2 cells. The aim of this study was to investigate the relationship between protein kinase B (Akt), a key gene in PI3K signal transduction pathway, and osteopontin expression. METHODS HepG2 cells were transfected with constitutively active Akt and dominant negative Akt using lipofectin. The Akt transfection was confirmed by Western blot analysis. Osteopontin expression was detected by both Northern blot and Western blot. RESULTS Overexpression of exogenous Akt was detected in HepG2 cells by Western blot, indicating that HepG2 cells were successfully transfected with the Akt genes. In serum-free condition, the expression of osteopontin was either low or undetectable in HepG2 cells transfected with vector only, however, the expression increased after transfection of cells with constitutively active Akt. Osteopontin expression decreased when HepG2 cells were transfected with dominant negative Akt. CONCLUSION Protein kinase B (Akt) gene regulated osteopontin expression in RNA level and protein level, suggesting that osteopontin synthesis can be blocked by inactivation of the Akt gene. This leads to a potential means of intervention for the inhibition of metastases in liver cancer.
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Affiliation(s)
- G Zhang
- Department of Gastroenterology, First Affiliated Hospital, Nanjing Medical University, China.
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32
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Shen J, Zhang S, Lee HC, Hao B. SeeDNA: a visualization tool for K-string content of long DNA sequences and their randomized counterparts. Genomics Proteomics Bioinformatics 2005; 2:192-6. [PMID: 15862120 PMCID: PMC5172470 DOI: 10.1016/s1672-0229(04)02025-x] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+ package is freely available.
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Affiliation(s)
- Junjie Shen
- Department of Computer Science, Zhejiang University, Hangzhou 310027, China
| | - Shuyu Zhang
- T-Life Research Center, Fudan University, Shanghai 200433, China
| | - Hoong-Chien Lee
- Department of Physics, National Central University, Chungli, Taiwan 320, China
| | - Bailin Hao
- T-Life Research Center, Fudan University, Shanghai 200433, China
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China
- Corresponding author.
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33
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Abstract
* Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. * Through analysing the 370 Mb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago. * Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30-65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization. * Together with other lines of evidence, we propose that polyploidization is still an ongoing process in grasses of polyploidy origins.
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Affiliation(s)
- Xiyin Wang
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
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Wang X, Shi X, Hao B, Ge S, Luo J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 2005. [PMID: 15720704 DOI: 10.1111/j.1469-8137.2004.01293] [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: 05/05/2023]
Abstract
* Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. * Through analysing the 370 Mb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago. * Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30-65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization. * Together with other lines of evidence, we propose that polyploidization is still an ongoing process in grasses of polyploidy origins.
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Affiliation(s)
- Xiyin Wang
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
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35
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Wong GKS, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RPMA, van der Poel JJ, Bovenhuis H, Groenen MAM, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 2004; 432:717-22. [PMID: 15592405 PMCID: PMC2263125 DOI: 10.1038/nature03156] [Citation(s) in RCA: 309] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Accepted: 11/01/2004] [Indexed: 11/09/2022]
Abstract
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
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Affiliation(s)
- Gane Ka-Shu Wong
- Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China
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36
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Wang H, Hao B, Zhou K, Chen X, Wu S, Zhou G, Zhu Y, He F. Linkage Disequilibrium and Haplotype Architecture for two ABC Transporter Genes (ABCC1 and ABCG2) in Chinese Population: Implications for Pharmacogenomic Association Studies. Ann Hum Genet 2004; 68:563-73. [PMID: 15598215 DOI: 10.1046/j.1529-8817.2003.00124.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [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: 11/20/2022]
Abstract
Information about linkage disequilibrium (LD) patterns and haplotype structures for candidate genes is instructive for the design and analysis of genetic association studies for complex diseases and drug response. ABCC1 and ABCG2 are genes coding for two multidrug resistance (MDR) associated transporters; they are also related to some pathophysiological traits. To pinpoint the LD profiles of these MDR genes in Chinese, we systemically screened 27 unrelated individuals for single nucleotide polymorphisms (SNPs) in the coding and regulatory regions of these genes, and thereby characterized their haplotype structures. Despite marked variations in haplotype diversity, LD pattern and intragenic recombination intensity between the two genes, both loci could be partitioned into several LD blocks, in which a modest number of haplotypes accounted for a high fraction of the sampled chromosomes. We concluded that each locus has its own genomic LD profile, but that they still share a common segmental LD architecture with low haplotype diversity. Our data will benefit genetic association studies of complex traits and drug response possibly related to these genes.
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Affiliation(s)
- H Wang
- Laboratory of Systems Biology, Beijing Institute of Radiation Medicine, Beijing 100850 PR China
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37
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Hao B, Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J Bioinform Comput Biol 2004; 2:1-19. [PMID: 15272430 DOI: 10.1142/s0219720004000442] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Revised: 11/17/2003] [Accepted: 11/24/2003] [Indexed: 11/18/2022]
Abstract
This is a review of a new and essentially simple method of inferring phylogenetic relationships from complete genome data without using sequence alignment. The method is based on counting the appearance frequency of oligopeptides of a fixed length (up to K = 6) in the collection of protein sequences of a species. It is a method without fine adjustment and choice of genes. Applied to prokaryotic genomes it has led to results comparable with the bacteriologists' systematics as reflected in the latest 2002 outline of the Bergey's Manual of Systematic Bacteriology. The method has also been used to compare chloroplast genomes and to the phylogeny of Coronaviruses including human SARS-CoV. A key point in our approach is subtraction of a random background from the original counts by using a Markov model of order K-2 in order to highlight the shaping role of natural selection. The implications of the subtraction procedure is specially analyzed and further development of the new approach is indicated.
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Affiliation(s)
- Bailin Hao
- T-Life Research Center, Fudan University, Shanghai 200433, China.
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38
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Qi J, Luo H, Hao B. CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 2004; 32:W45-7. [PMID: 15215347 PMCID: PMC441500 DOI: 10.1093/nar/gkh362] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.1] [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: 02/13/2004] [Revised: 03/03/2004] [Accepted: 03/03/2004] [Indexed: 11/14/2022] Open
Abstract
Composition Vector Tree (CVTree) implements a systematic method of inferring evolutionary relatedness of microbial organisms from the oligopeptide content of their complete proteomes (http://cvtree.cbi.pku.edu.cn). Since the first bacterial genomes were sequenced in 1995 there have been several attempts to infer prokaryote phylogeny from complete genomes. Most of them depend on sequence alignment directly or indirectly and, in some cases, need fine-tuning and adjustment. The composition vector method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. This new method does not contain 'free' parameter and 'fine-tuning'. A bootstrap test for a phylogenetic tree of 139 organisms has shown the stability of the branchings, which support the small subunit ribosomal RNA (SSU rRNA) tree of life in its overall structure and in many details. It may provide a quick reference in prokaryote phylogenetics whenever the proteome of an organism is available, a situation that will become commonplace in the near future.
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Affiliation(s)
- Ji Qi
- The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China.
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39
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Hao B, Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. Proc IEEE Comput Soc Bioinform Conf 2003; 2:375-84. [PMID: 16452813] [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: 05/06/2023]
Abstract
A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to K = 6) in their proteomes. This is a method without fine adjustment and choice of genes. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Bergey's Manual of Systematic Bacteriology [1, 2]. A key point in our approach is subtraction of a random background by using a Markovian model of order K - 1 from the composition vectors to highlight the shaping role of natural selection.
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Affiliation(s)
- Bailin Hao
- T-Life Research Center, Fudan University, Shanghai, 200433, China.
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40
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Abstract
Phylogenetic tree of coronaviruses (CoVs) including the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K-string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus genomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.
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Affiliation(s)
- Lei Gao
- 1Institute of Theoretical Physics, Chinese Academy of Sciences, 100080 Beijing, China
- 2T-Life Research Center, Fudan University, 200433 Shanghai, China
| | - Ji Qi
- 1Institute of Theoretical Physics, Chinese Academy of Sciences, 100080 Beijing, China
- 2T-Life Research Center, Fudan University, 200433 Shanghai, China
| | - Haibin Wei
- 3Graduate School, Zhejiang University, 310027 Hangzhou, China
- 4Hangzhou Branch, Beijing Genomics Institute, Chinese Academy of Sciences, 310008 Hangzhou, China
| | - Yigang Sun
- 3Graduate School, Zhejiang University, 310027 Hangzhou, China
- 4Hangzhou Branch, Beijing Genomics Institute, Chinese Academy of Sciences, 310008 Hangzhou, China
| | - Bailin Hao
- 2T-Life Research Center, Fudan University, 200433 Shanghai, China
- 4Hangzhou Branch, Beijing Genomics Institute, Chinese Academy of Sciences, 310008 Hangzhou, China
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41
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Yu J, Hu S, Wang J, Wong GKS, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002; 296:79-92. [PMID: 11935017 DOI: 10.1126/science.1068037] [Citation(s) in RCA: 1758] [Impact Index Per Article: 79.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
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MESH Headings
- Arabidopsis/genetics
- Base Composition
- Computational Biology
- Contig Mapping
- DNA Transposable Elements
- DNA, Intergenic
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Databases, Nucleic Acid
- Exons
- Gene Duplication
- Genes, Plant
- Genome, Plant
- Genomics
- Introns
- Molecular Sequence Data
- Oryza/genetics
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Polymorphism, Genetic
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Software
- Species Specificity
- Synteny
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Affiliation(s)
- Jun Yu
- Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China
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42
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Xie H, Hao B. Visualization of K-tuple distribution in procaryote complete genomes and their randomized counterparts. Proc IEEE Comput Soc Bioinform Conf 2002; 1:31-42. [PMID: 15838121] [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: 05/02/2023]
Abstract
A few years ago we developed a simple scheme to visualize the string composition of long DNA sequences in terms of two- and one-dimensional (2D and 1D) histograms. While the patterns in the 2D histograms have been well understood, the structure of the 1D histograms has not been analyzed in details. It turns out that the structure of the 1D histograms of the genomic sequences and their randomized counterparts varies significantly depending on the g+c content of the genomes. In particular, the 1D histograms of some randomized sequences may show rich structure, a seemingly anti-intuitive result. Three approaches are used to explain the phenomenon: (1) Monte Carlo simulation, (2) exact computation by using the Goulden-Jackson cluster method, and (3) a Poisson approximation method. The multi-modal phenomena in K-histograms are well elucidated by the last approach.
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Affiliation(s)
- Huimin Xie
- Department of Mathematics, Suzhou University, Suzhou, 215006, China.
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Yu J, Hu S, Wang J, Li S, Wong KSG, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Li G, Gao H, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Huang G, Tao M, Wang J, Zhu L, Yuan L, Yang H. A draft sequence of the rice (Oryza sativa ssp.indica) genome. ACTA ACUST UNITED AC 2001. [DOI: 10.1007/bf02901901] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hao B, Li Y, Yang Y, Wang Y, Huang F, Liao S, Wang Z, Si Y, Zhu W. [Genetic polymorphism of eight STR loci in the Han population in Henan province]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2001; 18:35-8. [PMID: 11172640] [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: 02/18/2023]
Abstract
OBJECTIVE To investigate the allele frequencies of eight short tandem repeats(STR) loci: TH01, FES, D19S400, D7S820, D16S539, D20S161, D3S1545 and D5S818 in Han population in Henan province. METHODS DNA was extracted with phenol-chloroform from EDTA-blood samples of the unrelated individuals in Henan province and amplified with PCR technique. The PCR product was analyzed with the undenatured PAGE vertical electrophoresis and silver-stain. RESULTS The authors got the frequencies of the eight loci. The heterozygosities of the eight loci are 0.66, 0.67, 0.80, 0.76, 0.79, 0.79, 0.78 and 0.78; the discrimination powers are 0.83, 0.83, 0.94, 0.91, 0.93, 0.93, 0.92 and 0.92. CONCLUSION The heterozygosities of the eight loci are high and the frequencies are in good agreement with Hardy-Weinberg equilibrium, so the eight loci can be used in individual identification testing.
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Affiliation(s)
- B Hao
- Medical Genetic Institute of Henan Province, the People's Hospital of Henan Province, Zhengzhou, Henan, 450003 P.R. China.
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Xie J, Wang X, Zhuang G, Xu H, Hao B, Tang X, Wu Q. [Relationship between interleukin-2, interleukin-2 receptor and the non-and hypo-responsiveness to hepatitis B vaccine]. Zhonghua Gan Zang Bing Za Zhi 2000; 8:332-4. [PMID: 11135687] [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: 02/18/2023]
Abstract
OBJECTIVE To study the relationship between interleukin-2 (IL-2), soluble interleukin-2 receptor (sIL-2R) and the non-and-hypo-responsiveness to hepatitis B vaccine. METHODS Peripheral blood mononuclear cells (PBMC) isolated from 21 non-and -hypo-responders, 22 hyperresponders and 21 chronic HBsAg carriers were incubated in the presence of HBsAg and phytohaemagglutinin (PHA). The levels of IL-2 and sIL-2R in the supernatants of activated cells were measured by an enzyme-linked immunosorbent assay. RESULTS The average level of IL-2 in the non-and-hypo-responders was significantly lower than that in the hyperresponders (t=8.80, P<0.001), but was comparable to that in chronic HBsAg carriers (q=0.06, P>0.5). Between the hyperresponders and the non-and-hypo-responders, the average sIL-2R levels showed no noticeable difference. CONCLUSION The results suggest that low level of IL-2 may be one of the causes and mechanisms of non-and-hypo-responsiveness to hepatitis B vaccine.
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Affiliation(s)
- J Xie
- Department of Epidemiology Xi'an Medical University, Xi'an 710061, China
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Hao B, Luo J, Yin G, Zheng C, Zheng Y. [Study on statistical method of distribution for erythrocyte morphological features by computerized image processing]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2000; 17:429-32, 443. [PMID: 11211832] [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: 02/19/2023]
Abstract
This study sought to develop a new statistic method for the semiautomatic analysis and classification of erythrocyte morphology based on the morphological features and shape analysis of erythrocytes by computer image processing. Shape factor as the description of the erythrocyte morphological features was used for the shape classification of erythrocytes. And the models and algorithms of erythrocytes image segmentation, cell body shape recognition and measure can be implemented through the VC++. The present method can efficiently and semi-automatically provide the statistical analysis of erythrocyte morphology, and can give the distribution of erythrocyte morphological features. The result showed that there was a significant difference between the distribution curves of the normal erythrocyte morphology (one apex) and hemolytic anemia's (two apices). By this way, it can be obtained the proportion data of different cell bodies' shapes. This method could provide some information for the study and diagnosis of the diseases (e.g. hemolytic anemia, pre-leukemia) related to erythrocyte morphology.
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Affiliation(s)
- B Hao
- Southwest Nationalities College, Chengdu 610041
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Hao B, Qiao W, Dong H. [The influence of conception of time - space - orientation in pre - Qin society on traditional Chinese medicine theories]. Zhonghua Yi Shi Za Zhi 2000; 30:243-6. [PMID: 11871439] [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: 02/23/2023]
Abstract
The article discusses the views of the time - space - orientation of Wuxing (Five - Evolutive Phase), Yin - yang and Sifeng (Four - Wind), and its influence on traditional Chinese medical theories. It is shown that traditional Chinese medical theories are developed and established on the basis of the science and technology and social thought of the pre - Qin period, with some contents to be further discussed, and bias would be resulted if the issue is interpreted by concepts of post - Qin period.
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Affiliation(s)
- B Hao
- Shaanxi College of Traditional Chinese Medicine, Xianyang 713083
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Abstract
The FixL heme domain serves as the dioxygen switch in the FixL/FixJ two-component system of Rhizobia. Recent structural studies of the Bradyrhizobium japonicum FixL heme domain (BjFixLH) have suggested an allosteric mechanism that is distinct from the classical hemoglobin model. To gain further insight into the FixL sensing mechanism, structures of BjFixLH bound to dioxygen, imidazole, and nitric oxide have been determined. These structures, particularly the structure of BjFixLH bound to its physiological ligand, dioxygen, have helped to address a number of important issues relevant to the BjFixLH sensing mechanism. On the basis of the oxy-BjFixLH structure, a conserved arginine is found to stabilize the dioxygen ligand in a mode reminiscent of the distal histidine in classical myoglobins and hemoglobins. The structure of BjFixLH bound to imidazole elucidates the structural requirements for accommodating sterically bulky ligands. Finally, the structure of BjFixLH bound to nitric oxide provides evidence for a structural intermediate in the heme-driven conformational change.
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Affiliation(s)
- W Gong
- Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA
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Abstract
While protein synthesis in bacteria begins with a formylated methionine, the formyl group of the nascent polypeptide is removed by peptide deformylase. Since eukaryotic protein synthesis does not involve formylation and deformylation at the N-terminus, there has been increasing interest in peptide deformylase as a potential target for antibacterial chemotherapy. Toward this end and to aid in the design of effective antibiotics targeting peptide deformylase, the structures of the protein-inhibitor complexes of both the cobalt and the zinc containing Escherichia coli peptide deformylase bound to the transition-state analogue, (S)-2-O-(H-phosphonoxy)-L-caproyl-L-leucyl-p-nitroanilide (PCLNA), have been determined. The proteins for both deformylase-inhibitor complexes show basically the same fold as for the native enzyme. The PCLNA inhibitor adopts an extended conformation and fits nicely into a hydrophobic cavity located near the metal site. On the basis of these structures, guidelines for the design of high-affinity deformylase inhibitors are suggested. As our results show that the protein residues which interact with the PCLNA inhibitor are conserved over a wide variety of species, we suggest that antibiotics targeting deformylase could have wide applicability.
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Affiliation(s)
- B Hao
- Departments of Biochemistry and Chemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA
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Gong W, Hao B, Mansy SS, Gonzalez G, Gilles-Gonzalez MA, Chan MK. Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci U S A 1998; 95:15177-82. [PMID: 9860942 PMCID: PMC28016 DOI: 10.1073/pnas.95.26.15177] [Citation(s) in RCA: 264] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The FixL proteins are biological oxygen sensors that restrict the expression of specific genes to hypoxic conditions. FixL's oxygen-detecting domain is a heme binding region that controls the activity of an attached histidine kinase. The FixL switch is regulated by binding of oxygen and other strong-field ligands. In the absence of bound ligand, the heme domain permits kinase activity. In the presence of bound ligand, this domain turns off kinase activity. Comparison of the structures of two forms of the Bradyrhizobium japonicum FixL heme domain, one in the "on" state without bound ligand and one in the "off" state with bound cyanide, reveals a mechanism of regulation by a heme that is distinct from the classical hemoglobin models. The close structural resemblance of the FixL heme domain to the photoactive yellow protein confirms the existence of a PAS structural motif but reveals the presence of an alternative regulatory gateway.
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Affiliation(s)
- W Gong
- Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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