1.Protein-protein interactions and their network analysis in bioinformatics
chao, XIE ; jin, GAO ; yun-sheng, YUAN ; yan, YU
Journal of Shanghai Jiaotong University(Medical Science) 2006;0(04):-
The ultimate goal of post-genome research is to understand a complete set of proteins in a living organism for their expression pattern and biological function,which is called proteomics.One of the major challenges in proteome research is to study the protein-protein interactions,and the emerging bioinformatics approaches present us tremendous advantages when dealing with protein interaction networking and data analysis.Useful bioinformatics tools include protein-protein interaction network mapping,topology of the network,structure of the module and comparison of the network.The technology advancement in this field brings further understandings to the structure and function of cells at the proteome level,which may eventually lead to the discovery of new drug targets and design methods.This paper attempts to review the current researches on protein-protein interaction with an emphasis on bioinformatics intervention,and also summarizes some widely used methods for network analysis.
2.Protective effect of BAG-1L mediated by lentivirus in human neuroblastoma cells induced by hypoxia
Yun WANG ; Qingshu LI ; Chao JIA ; Chunyu XIE ; Yankun SONG ; Nan ZHANG ; Yan QU
Chinese Critical Care Medicine 2017;29(3):239-243
Objective To investigate the protective effects of lentivirus mediated Bcl-2-associated athanogene 1L (BAG-1L) over-expression on human neuroblastoma cells (SH-SYSY) induced by hypoxia/re-oxygenation,and to study its effect on the phosphoinositide 3 kinase serine/threonine protein kinase (PI3K/AKT) pathway.Methods SH-SYSY cells were cultured in vitro,and the cells at logarithmic phase were collected,and they were divided into recombined lentiviral infection group [infected by lentivirus containing BAG-1L and green fluorescent protein (GFP) gene],vector control group (infected by lentivirus containing GFP without BAG-1L gene) and cell control group (non-infection).Western Blot was used to detect the expression of BAG-1L in target cells after infection for 48 hours.SH-SY5Y cells were subjected to hypoxia for 8 hours and re-oxygenation for 24 hours,then the cell counting kit-8(CCK-8) was used to detect the cell activity,and the apoptosis was detected by flow cytometry after allophycocyanin labeled annexin V/7-amino actinomycin D (Annexin V-APC/7-AAD) staining.Western Blot was used to detect the protein expressions of BAG-1L,heat shock protein 70 (HSP70),AKT and phosphorylated AKT (p-AKT).Results After infection for 48 hours,exogenous BAG-1L protein bands were observed in recombined lentiviral infection group,but not observed in cell control group and vector control group.After hypoxia/re-oxygenation treatment,the cell viability in recombined lentiviral infection group was significantly higher than that in cell control group and vector control group (A value:0.689 ± 0.036 vs.0.425 ± 0.013,0.400 ± 0.012),apoptosis was significantly decreased [apoptosis rate:(26.97 ± 1.82)% vs.(36.60± 1.45)%,(35.77 ± 3.74)%],the protein levels of BAG-1L,HSP70 and p-AKT were significantly increased [BAG-1L protein (gray value):2.405 ± 0.167 vs.0.529 ± 0.141,0.601 ± 0.099;HSP70protein (gray value):0.997±0.123 vs.0.634±0.091,0.584±0.106;p-AKT protein (gray value):1.234±0.118 vs.0.661 ± 0.210,0.712 ± 0.199,all P < 0.01],but the protein level of AKT was slightly increased (gray value:1.103 ± 0.269vs.0.646 ± 0.188,0.791 ± 0.326) without statistically significant differences (both P > 0.05).There was no significant difference in all parameters between cell control group and vector control group (all P > 0.05).Conclusion Lentivirus mediated BAG-1L gene over-expression can protect nerve cells against hypoxic injury and apoptosis,and the protective effect may be related to the activation increase of pathway on PI3K/AKT.
3.Discrimination of Pinellia ternata and Its Adulterants Based on Odour Fingerprints Analysis
Chao ZHANG ; Shilong YANG ; Min XU ; Dashuai XIE ; Yi LU ; Yun JIANG ; Chunjie WU
World Science and Technology-Modernization of Traditional Chinese Medicine 2015;(11):2300-2305
This study was aimed to establish a rapid discrimination method of Pinellia ternataand its adulterants based on the odour fingerprints analysis.Typhonium flagelliforme and Arisaema Rhizome,which were the common adulterants of Pinellia ternata,were collected.The adulterants were mixed with Pinellia ternatain different proportions.E-nose technology was used to obtain the odour fingerprints of Pinellia ternataand its adulterants of different types and proportions.Chemometrics methods,such as the analysis of variance (ANOVA),principal component analysis (PCA) and discriminant factor analysis (DFA) were used in the analysis and discrimination on sensors response data collected by sensors.The results showed that there were obvious differences on the odour characteristics between Pinellia ternateand its adulterants.PCA can obviously discriminate Pinellia ternateand its adulterants.And the odour difference became obvious along with the increasing of the adulteration proportion.There was a linear relationship between e-nose signal and the proportion of Typhonium flagelliforme.The cumulative proportion in ANOVA of the DFA model was 100%.The correct recognition rate was not less than 97%.It was concluded that e-nose can be used for rapid discrimination of Pinellia ternataand its adulterants.This study provided new technology and method for the discrimination of adulterants of Chinese materia medica.
4.Distribution and vicissitude of drug resistance of Acinetobacter baumannii in burn intensive care unit of Wuhan City Hospital No.3 in three years.
Hong WU ; Han-mei DING ; Li LI ; Chao-li ZHAO ; De-yun WANG ; Wei-guo XIE
Chinese Journal of Burns 2010;26(4):296-299
OBJECTIVETo study the clinical distribution characteristics and vicissitude of antibiotic resistance of Acinetobacter baumannii (AB), and to look for the risk factors of AB infection in order to provide reasonable reference for the prevention and treatment of its infection.
METHODSSpecimens of blood, venous catheters, sputum, wound exudates and pharyngeal swabs from 156 patients hospitalized in our burn ICU from January 2006 to December 2008 were collected and cultured. The clinical distribution and antibiotic resistance of AB were determined and analyzed. The risk factors related to AB infection were analyzed. Drug resistance rate data were processed with WHONET 5.3 software; the other data were processed with chi-square test and Logistic regression analysis.
RESULTSNinety-two strains of AB were identified during the three years from different kinds of specimens, with 41 (44.6%) from wound exudates, 14 (15.2%) from pharyngeal swabs and sputum respectively, 13 (14.1%) from blood, and 10 (10.9%) from venous catheters. AB accounted for 23.1% (30/130), 27.5% (25/91), 28.2% (37/131) respectively among the strains detected in 2006, 2007, and 2008. During the three years, except for imipenem and cefoperazone/sulbactam, the average resistance rates of AB to other ten commonly used antibiotics were all above 50.0%. Burn area (χ(2) = 24.374, P = 0.000), mechanical ventilation (χ(2) = 8.968, P = 0.003), duration of use of antibiotics (χ(2) = 3.981, P = 0.046), and deep venous catheterization (χ(2) = 9.170, P = 0.002) were the risk factors of AB infection, and the former two were independent risk factors.
CONCLUSIONSThere is a pan-drug resistance tendency of AB in our burn ICU, and the positive culture rates are increasing in recent years. Disinfection and isolation measures, appropriate use of antibiotics, avoidance of invasive performances such as deep venous catheterization and tracheostomy, or shortening their duration are important means to prevent and control infection of AB.
Acinetobacter Infections ; epidemiology ; Acinetobacter baumannii ; drug effects ; isolation & purification ; Adult ; Burns ; epidemiology ; microbiology ; China ; epidemiology ; Cross Infection ; microbiology ; Drug Resistance, Bacterial ; Female ; Humans ; Intensive Care Units ; statistics & numerical data ; Male ; Young Adult
5.Cognitive deficits in patients with brain tumor.
Chao SHEN ; Wei-Min BAO ; Bo-Jie YANG ; Rong XIE ; Xiao-Yun CAO ; Shi-Hai LUAN ; Ying MAO
Chinese Medical Journal 2012;125(14):2610-2617
OBJECTIVETo discuss the present status and progress of clinical research on the cognitive effects caused by different types of brain tumors and common treatments.
DATA SOURCESThe data used in this review were mainly from PubMed articles published in English from 1990 to Febuary 2012. Research terms were "cognitive deficits" or "cognitive dysfunction".
STUDY SELECTIONArticals including any information about brain tumor related cognitive deficits were selected.
RESULTSIt is widely accepted that brain tumors and related treatments can impair cognitive function across many domains, and can impact on patients' quality of life. Tumor localization, lateralization, surgery, drugs, radiotherapy and chemotherapy are all thought to be important factors in this process. However, some conflicting findings regarding brain tumor-related cognitive deficits have been reported. It can be difficult to determine the mechanism of these treatments, such as chemotherapy, antibiotics, antiepileptics, and steroids. Future research is needed to clarify these potential treatment effects.
CONCLUSIONSCognitive function is important for patients with brain tumor. Much more focus has been paid on this field. It should be regarded as an important prognostic index for the patients with brain tumor, and neuropsychological tests should be used in regular examinations.
Brain Neoplasms ; physiopathology ; Cognition ; physiology ; Cognition Disorders ; physiopathology ; Glioma ; physiopathology ; Humans
6.Lengthen-stem bipolar-femur prosthetic replacement for the treatment of old patients with intertrochanteric fracture osteoporosis
Wen-Wei XIE ; Sheng-Cheng LI ; Han-Gang YAO ; Bing-Gang XIONG ; De-Yun LIAO ; Chang-Yao SU ; Ming-Hua LI ; Run-Chao LI ;
Chinese Journal of Primary Medicine and Pharmacy 2006;0(07):-
Objective To evaluate the clinical application and significance of lengthen-stem bipolar-femur prosthetic replacement for the treatment of old-age patients with intertrochanteric fracture osteoporosis.Methods 28 cases of patients aging from 75 to 99 years old of intertrochanteric fracture osteoporosis treated with lengthen- stem cemented bipolar prosthesis were studicd from March 2000 to December 2006.After taking the blank margin, the bones of different sizes were replaced and the steel wire was fixed.After determining the depth of the front an- gle,the artificial bone was placed.Results After 28 examples attaining the following-up examination for 7 months to 3 years,with an average of 1.5 years,its function according to Harris standard was evaluated 3 months after the operation,8 examples were excellent,13 examples good,5 examples pass,2 examples inferior.The excellent or good rate reached 75% ,with no abnormal cases,no joint dislocation during the followed-up period.1 example had the phantom phenomenon 1 year after the operation.2 examples among the inferior had got more serious internal medicine disease which affected the restoring function.1 example died of the internal medicine disease 1 year after the operation.Conclusion By using the lengthen-stem bipolar-femur prosthetic replacement for the treatment of old patients with inrertrochanteric fracture osteoporosis,the patients will restore quickly after the operation and can carry a heavy load at an early time.The illness complication and the mortality rate will be redaced.But its related disease must be strictly dealt with and the surgery operating skill must be grasped.
7.Correlation between CT perfusion and vascular endothelial growth factor in neoplasm of head and neck
Zhi-Yun YANG ; Quan-Fei MENG ; Qiao-Lan XU ; Shu-Rong LI ; Chao-Gui YAN ; Hong-Bo XIE ; Xu-Feng YANG ; Qian PENG ; Ying-Rong LAI ;
Chinese Journal of Radiology 2001;0(09):-
Objective To investigate the correlation between the CT perfusion and microvessel density (MVD),expression of vascular endothelial growth factor(VEGF)in neoplasm of head and neck.Methods Eighty-eight lesions of head and neck were scanned by spiral CT.The largest axial surface of the mass was searched on unenhanced imaging,and at this level the dynamic contrast enhanced scan series was acquired.Time-density curves (TDC)were created from circular or oval regions of the interest drawn over the mass,target artery by Toshiba Xpress/SX spiral CT with perfusion functional software.The parameters were measured including:peak height (PH ),peak time (PT ),mean transit time (MTT), contrast enhancement ratio(RPH),and perfusion flow (PF).Histopathological slides of 35 masses were carefully prepared for the anti-CD34 and VEGF immunohistochemical staining and tumor microvessel density and calculation of VEGF expression scores.The parameters of CT perfusion were correlatively study with MVD and VEGF.Results(1)The TDC of CT perfusion imaging could be classified into 3 types.The TDC of 53/77 (68.9% )malignant tumors presented the type with rapid ascending and rapid descending after injecting contrast.The TDC of 6/9 malignant lymphomas showed low platform curve。(2)The PF median of thyroid carcinoma was 82.2(41.0,183.4)ml?min~(-1)?100 g~(-1).There was significantly difference in the parameters of CT perfusion among thyroid carcinoma and squamaous cell cancer (Median 23.8 (7.0, 108.4)ml?min~(-1)?100 g~(-1))and lymphomas (Median 24.5(13.2,78.6)ml?min~(-1)?100 g~(-1)).(3) MVD in benign tumors was (44.7?3.4),and in malignant tumors,it is (49.6?14.8 ).There was no significantly difference in MVD between benign and malignant tumors.High VEGF expression was found in 15 malignant tumors and 1 benign tumors,low VEGF expression was found in 9 malignant tumors and 10 benign tumors.(4)There were no significantly difference in VEGF expression and MVD.There was good correlation between MVD (M 40.0 )and PH (M 26.9 ),RPH (M 14.5 ),PF (M 46.8 )(r = 0.35,45.49, 0.41 ).There was correlation between VEGF(M 4.0)and MTT(M 16.7 )(r = -0.41 ).Conclusion The TDC and CT perfusion could be helpful to differentiate benign from malignant tumors. CT peffusion in neoplasm of head and neck is correlated with MVD and VEGF,and may reflect MVD and expression of VEGF.
8.Epidemiological characteristics of notifiable respiratory infectious diseases in Beijing from 2015 to 2018
Yun-ping SHI ; Gang LI ; Yang LIU ; Chao WANG ; Chun-yan XIE ; Yan-lin GAO
Chinese Journal of Disease Control & Prevention 2020;24(1):97-100,113
Objective To explore the epidemiological characteristics of notifiable respiratory infectious diseases in Beijing from 2015 to 2018. Methods Descriptive epidemiological method was used to analyze the monitoring data of notifiable respiratory infectious diseases, and to describe the main characteristics of the diseases. Results Average annual reported incidence was 227.64/100 000, accounting for 36.24% of the total reports and deaths of notifiable infectious diseases. Class B and C respiratory infectious diseases showed a downward and upward trend respectively. The epidemic trend and risk population of the six major infectious diseases were different. Conclusions The incidence and mortality of legal respiratory infectious diseases in Beijing increases year by year due to the sharp increase of influenza from 2015 to 2018, and the responsibility of prevention and control is great. Respiratory infectious diseases have different epidemic season and predisposing population. Different prevention and control measures should be taken according to the different epidemic characteristics of different diseases.
9.Factors Related to Tympanic Membrane Perforation in Children with Acute Suppurative Otitis Media.
Chao-Yun XIE ; Dong CHEN ; Fu-Xiang LIU
Acta Academiae Medicinae Sinicae 2021;43(4):531-535
Objective To explore the factors related to tympanic membrane perforation in children with acute suppurative otitis media,and to provide reference for clinical practice. Methods We reviewed the clinical data of 1274 children with acute suppurative otitis media from February 2017 to May 2020,and analyzed the factors related to tympanic membrane perforation. Results Tympanic membrane perforation occurred in 67 out of the 1274 children with acute suppurative otitis media,with the incidence of 5.27%.The univariate analysis showed that 11 factors including the duration of onset(
Child
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Chronic Disease
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Humans
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Otitis Media, Suppurative/complications*
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Procalcitonin
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Risk Factors
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Tympanic Membrane Perforation/etiology*
10.Cardiac protection from myocardial ischemic postconditioning and remote postconditioning during myocardial ischemia/reperfusion injury in rabbits.
Guang-Yun CAO ; Rui-Qin XIE ; Wei CUI ; Fan LIU ; Jing LIU ; Jing-Chao LU ; Hui-Min REN ; Hai-Juan HU
Chinese Journal of Applied Physiology 2012;28(5):476-480
OBJECTIVETo observe whether there are some differences between myocardial postconditioning and remote postconditioning, and whether there is additional cardiac protection when they are used combined during myocardial ischemia/reperfusion injury in rabbits.
METHODSThirty healthy New Zealand rabbits which were randomly divided into 5 groups (n = 5): ischemic control group (CON), sham operation group (Sham), myocardial postconditioning group (MPostC), remote postconditioning group (RPostC), myocardial postconditioning plus remote postconditioning group (MPostC + RPostC). Acute myocardial infarction was induced by 45 minutes occlusion on left circumflex coronary artery (LCX) and 2 hours reperfusion in all anesthetized open-chest rabbits except the Sham, the coronary occlusion and reperfusion were determined by changes of ECG and cardiac color. Skeletal muscle ischemia model was induced by extrinsic iliac arteries occlusion and reperfusion with artery clamps. The condition that the extrinsic iliac arteries were occluded or reperfused could be tested by according to the distal arterial pulse. Plasma creatine kinase (CPK) activity and lactate dehydrogenase (LDH) activity were measured at baseline, the end of ischemia, after 1 hour and 2 hours of reperfusion respectively. The extent of myocardial infarction was assessed by triphenyltetrazolium (TTC) staining and measured by area ratio of AN/AAR.
RESULTSCompared with the Con, myocardial infarct size was significantly reduced in MPostC and RpostC group (P < 0.05). But there was no significant difference between MPostC and RPostC group. Combined MPostC and RPostC markedly enhanced myocardial protection (P < 0.05). The trend of CPK and LDH release was similar to the trend of myocardial infarct size.
CONCLUSIONBoth MPostC and RPostC induced cardiac protection. There was no significant difference between MPostC and RPostC. Combined MPostC and RPostC induced markedly additive effect on myocardial protection.
Animals ; Disease Models, Animal ; Ischemic Postconditioning ; Muscle, Skeletal ; blood supply ; Myocardial Reperfusion Injury ; prevention & control ; Myocardium ; metabolism ; Rabbits