A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. The method is based on calculating Cα distances between s...A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. The method is based on calculating Cα distances between selected pocket residues and subsequent analysis by multivariate methods. Five closely related serine proteases, the coagulation factors II, VII, IX, X, and XI, were studied and their pocket similarity was illustrated by PCA clustering. OPLS-DA was then applied to identify the residues responsible for the variation. By combining these two multivariate methods, we could successfully cluster the different proteases according to class and identify the important residues responsible for the observed variation.展开更多
BACKGROUND： Thrombus precursor protein （TpP） is the index of thrombus activity level, and it is also early referencing index in detecting thrombus diseases. OBJECTIVE： To dynamically observe the changes of TpP lev...BACKGROUND： Thrombus precursor protein （TpP） is the index of thrombus activity level, and it is also early referencing index in detecting thrombus diseases. OBJECTIVE： To dynamically observe the changes of TpP level in blood plasma of patients with acute cerebral infarction at different time after onset, and to compare the differences of plasma TpP level between patients with acute cerebral infarction and healthy persons who received health examination. DESIGN： Controlled observation SETTING： Department of Neurology, Affiliated Hospital of Xuzhou Medical College PARTICIPANTS： Totally 58 patients with acute cerebral infarction who received the treatment in the Department of Neurology, Affiliated Hospital of Xuzhou Medical College between September 2004 and March 2005 were recruited in this study. They all met the diagnostic criteria revised by the 4^th National Conference of Cerebrovascular Disorders in 1995 and were diagnosed by clinical and skull CT and （or） MRI examinations. The patients included 33 male and 25 female aged from 36 to 87 years. Time to onset 〈 6 hours, 6 to 11 hours, 12 to 23 hours, 24 to 48 hours and 〉 48 hours were found in 10,11,14,10 and 13 patients respectively. Another 51 persons who homeochronously received the health body examination in our hospital were recruited, including 34 male and 17 female, aged 38 to 85 years, serving as control group. Patients with cardio-cerebrovascualr diseases or liver and kidney diseases were excluded. All the involved subjects were informed of the detected items. METHODS： About 4 mL venous blood was respectively taken from patients admitted to the hospital within 6 hours, 6 toll hours, 12 to 23 hours, 24 to 48 hours and more then 48 hours after onset, and healthy persons when receiving health examination. The level of TpP in blood plasma was measured with enzymelinked immunosorbent assay. MAIN OUTCOME MEASURES： ① Comparison of the level of plasma TpP between patients and controls;② Comparison of the level of plasma TpP of patients with acute cerebral infarction at different time after onset. RESULTS： Totally 58 patients with acute cerebral infarction and 51 persons who received health examination participated in the result analysis. ①Comparison of plasma TpP level between patients and controls： The plasma TpP level of patients with acute cerebral infarction was significantly higher than that of control group [（16.12±3.28）vs （5.38±1.36） mg/L, t= 20.993, P〈 0.01 ]. ② Comparison of plasma TpP level of patients with acute cerebral infarction at different time after onset： The level of plasma TpP was （12.06±3.06） mg/L within 6 hours, （15.11±3.42） mg/L at 6 to 11 hours, （20.63±4.05） mg/L at 12 to 23 hours, （16.15±3.50） mg/L at 24 to 48 hours and （11.88±3.11） mg/L at more than 48 hours after onset. It increased from the 6^th hour, reached the peak at the 12^th to 23^rd hours, maintained at very high level at the 48= hour and then gradually decreased and recovered to the level within 6 hours after onset. The level of plasma TpP of patients with acute cerebral infarction was signiticantly higher at the 12^th to 23^rd hours after onset and the 24^th to 48^th hours after onset than within 6 hours after onset （t = 13.385, P 〈 0.05）. CONCLUSION： ①The level of plasma TpP of patients with acute cerebral infarction is significantly higher than that of persons who received health examination.② Plasma TpP levels of patients with acute cerebral infarction change in wave manner at the different time after onset.展开更多
We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using t...We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.展开更多
An isolate of PVS,HZ00P1,was obtained from nature infected Solanum tuberosum from Hangzhou,Zhejiang province.It was primarily identified by DAS-ELISA and host reaction tests.3’ end partial sequence of the virus isola...An isolate of PVS,HZ00P1,was obtained from nature infected Solanum tuberosum from Hangzhou,Zhejiang province.It was primarily identified by DAS-ELISA and host reaction tests.3’ end partial sequence of the virus isolate was cloned.Nucleic acid sequence of the cp gene and deduced cp amino acid sequence alignments were compared with 16 other isolates registered in GenBank.The results showed that the 17 PVS isolates were divided into two groups.Among them,two Andean isolates were classified to groupⅡ,HZ00P1 and the other 14 isolates were assigned to groupⅠ.Compared with other PVS isolates in group Ⅰ,PVS HZ00P1 had 93.1%-98.1% and 95.9%-99.3% homologies of nucleotide sequence and deduced amino acid sequence respectively,whereas its similarities to the groupⅡwere 81.4%-81.7% and 93.5%-93.9%.A survey of PVS occurrence in Zhejiang province was achieved by RNA spot hybridization(RSH).Among the 30 samples collected from different areas of the province,26.7% were found to have the infection of PVS.It is concluded that PVS has become a common virus in Zhejiang province.展开更多
文摘A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. The method is based on calculating Cα distances between selected pocket residues and subsequent analysis by multivariate methods. Five closely related serine proteases, the coagulation factors II, VII, IX, X, and XI, were studied and their pocket similarity was illustrated by PCA clustering. OPLS-DA was then applied to identify the residues responsible for the variation. By combining these two multivariate methods, we could successfully cluster the different proteases according to class and identify the important residues responsible for the observed variation.
文摘BACKGROUND： Thrombus precursor protein （TpP） is the index of thrombus activity level, and it is also early referencing index in detecting thrombus diseases. OBJECTIVE： To dynamically observe the changes of TpP level in blood plasma of patients with acute cerebral infarction at different time after onset, and to compare the differences of plasma TpP level between patients with acute cerebral infarction and healthy persons who received health examination. DESIGN： Controlled observation SETTING： Department of Neurology, Affiliated Hospital of Xuzhou Medical College PARTICIPANTS： Totally 58 patients with acute cerebral infarction who received the treatment in the Department of Neurology, Affiliated Hospital of Xuzhou Medical College between September 2004 and March 2005 were recruited in this study. They all met the diagnostic criteria revised by the 4^th National Conference of Cerebrovascular Disorders in 1995 and were diagnosed by clinical and skull CT and （or） MRI examinations. The patients included 33 male and 25 female aged from 36 to 87 years. Time to onset 〈 6 hours, 6 to 11 hours, 12 to 23 hours, 24 to 48 hours and 〉 48 hours were found in 10,11,14,10 and 13 patients respectively. Another 51 persons who homeochronously received the health body examination in our hospital were recruited, including 34 male and 17 female, aged 38 to 85 years, serving as control group. Patients with cardio-cerebrovascualr diseases or liver and kidney diseases were excluded. All the involved subjects were informed of the detected items. METHODS： About 4 mL venous blood was respectively taken from patients admitted to the hospital within 6 hours, 6 toll hours, 12 to 23 hours, 24 to 48 hours and more then 48 hours after onset, and healthy persons when receiving health examination. The level of TpP in blood plasma was measured with enzymelinked immunosorbent assay. MAIN OUTCOME MEASURES： ① Comparison of the level of plasma TpP between patients and controls;② Comparison of the level of plasma TpP of patients with acute cerebral infarction at different time after onset. RESULTS： Totally 58 patients with acute cerebral infarction and 51 persons who received health examination participated in the result analysis. ①Comparison of plasma TpP level between patients and controls： The plasma TpP level of patients with acute cerebral infarction was significantly higher than that of control group [（16.12±3.28）vs （5.38±1.36） mg/L, t= 20.993, P〈 0.01 ]. ② Comparison of plasma TpP level of patients with acute cerebral infarction at different time after onset： The level of plasma TpP was （12.06±3.06） mg/L within 6 hours, （15.11±3.42） mg/L at 6 to 11 hours, （20.63±4.05） mg/L at 12 to 23 hours, （16.15±3.50） mg/L at 24 to 48 hours and （11.88±3.11） mg/L at more than 48 hours after onset. It increased from the 6^th hour, reached the peak at the 12^th to 23^rd hours, maintained at very high level at the 48= hour and then gradually decreased and recovered to the level within 6 hours after onset. The level of plasma TpP of patients with acute cerebral infarction was signiticantly higher at the 12^th to 23^rd hours after onset and the 24^th to 48^th hours after onset than within 6 hours after onset （t = 13.385, P 〈 0.05）. CONCLUSION： ①The level of plasma TpP of patients with acute cerebral infarction is significantly higher than that of persons who received health examination.② Plasma TpP levels of patients with acute cerebral infarction change in wave manner at the different time after onset.
基金supported by the grants from the Ministry of Science and Technology of China (No.2006AA02Z331 and 2004CB117404)the Key Project of Chinese Academy of Sciences (No.KSCX2-YW-N-020) to Liangbiao ChenNSF OPP 0636696 to C-H CC
文摘We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.
文摘An isolate of PVS,HZ00P1,was obtained from nature infected Solanum tuberosum from Hangzhou,Zhejiang province.It was primarily identified by DAS-ELISA and host reaction tests.3’ end partial sequence of the virus isolate was cloned.Nucleic acid sequence of the cp gene and deduced cp amino acid sequence alignments were compared with 16 other isolates registered in GenBank.The results showed that the 17 PVS isolates were divided into two groups.Among them,two Andean isolates were classified to groupⅡ,HZ00P1 and the other 14 isolates were assigned to groupⅠ.Compared with other PVS isolates in group Ⅰ,PVS HZ00P1 had 93.1%-98.1% and 95.9%-99.3% homologies of nucleotide sequence and deduced amino acid sequence respectively,whereas its similarities to the groupⅡwere 81.4%-81.7% and 93.5%-93.9%.A survey of PVS occurrence in Zhejiang province was achieved by RNA spot hybridization(RSH).Among the 30 samples collected from different areas of the province,26.7% were found to have the infection of PVS.It is concluded that PVS has become a common virus in Zhejiang province.
