Biliary tract malignant tumours do not have any special symptom or physical sign in early stages.It is easy to be delayed for diagnosis and it is often very serious when the disease was diagnosised.With the development of technology of molecular biology,the biliary tract malignant tumours' diagnosis in molecular biology has been made some progresses,and it is expected to be possible to diagnose and treat the diseases in early stages.

Objective:To ascertain the optimized ultrasonic condition for extraction of flavone from Radix Astragali by orthogonal design. Methods: The contents of calycosin-7-O-?-D -glucoside and formononetin were taken as the indices and were determined. The ultrasonic time (10 min, 20 min, and 30 min), concentrations of methanol (50%, 75% and 100%) and times of extraction (1, 2, and 3) were analyzed by orthogonal design; the best ultrasonic condition was ascertained and compared with those of soak extraction and Soxhlet extraction. Results: Ultrasonic with 100% methanol twice (20 minutes each time) was the optimized condition for extraction of flavone from Radix Astragali. The efficiency of ultrasonic extraction was better than those of soak extraction and Soxhlet extraction. Conclusion: Compared with other methods, the ultrasonic extraction of flavone from Radix Astragali is efficient, quick and simple.

Objective:To re-establish the quality control standard for Weiling granules. Methods:The 4 chief herbs in the prepa-ration, radices paeoniae alba, licorice, rhizoma corydalis and hawthorn were identified by TLC qualitatively. The content of paeoniflor-in in radices paeoniae alba was determined by HPLC. The separation was performed on an Agilent XDB-C18 (250 mm × 4. 6 mm, 5μm)coulme with mobile phase consisting of acetonitrile-0. 1% phosphoric acid solution (10:90). The detection wavelength was 230 nm and the flow rate was 1. 0 ml·min-1 . Results:The spots in TLC were clear without any interference. The linear range for paeoni-florin was 0. 151-1. 212 μg(r=0. 999 9,n=5). The average recovery was 99. 63% and RSD was 2. 01%(n=9). Conclusion:The method is simple and accurate with high reproducibility, which can be used for the quality control of Weiling granules.

Objective To investigate the efficacy of regional lymphadenectomy for patients with T2 gallbladder cancer. Methods From January 1990 to December 2009, 48 patients with T2 gallbladder cancer received regional lymphadenectomy following radical surgery at the Xinhua Hospital of Shanghai Jiaotong University, and their clinical data were retrospectively analyzed. Patients were divided into two groups according to the range of lymphadenectomy. Standard group (23 patients): lymph nodes in the regions of bile duct, common bile duct and hepatoduodenal ligament were dissected; extended group (25 patients): lymph nodes in the regions of hepatoduodenal ligament, head of pancreas, duodenum, portal vein, common hepatic artery and celiac axis were dissected).The condition of patients in the two groups were compared after the treatment. The morbidity and survival rate were analyzed by using Fisher exact test and Kaplan-Meier method, respectively, and the survival rates between the two groups were compared by using Log-rank test. Results No perioperative death was found in the two groups. The morbidities was 17% (4/23) in the standard group and 24% (6/25) in the extended group, with no significant difference between the two groups ( P ＞ 0.05 ). The 5-year cumulative survival rate and median survival time were 40% and 29.8 months in the standard group, and 66% and 53.2 months in the extended group, with significant differences between the two groups ( x2 = 4. 687, P ＜ 0.05 ). Conclusion Extended regional lymphadenectomy should be performed on patients with T2 gallbladder cancer if the primary lesions can be dissected radically.

The large amount of repeats, especially high copy repeats, in the genomes of higher animals and plants makes whole genome assembly (WGA) quite difficult. In order to solve this problem, we tried to identify repeats and mask them prior to assembly even at the stage of genome survey. It is known that repeats of different copy number have different probabilities of appearance in shotgun data, so based on this principle, we constructed a statistical model and inferred criteria for mathematically defined repeats (MDRs) at different shotgun coverages. According to these criteria, we developed software MDRmasker to identify and mask MDRs in shotgun data. With repeats masked prior to assembly, the speed of assembly was increased with lower error probability. In addition, clone-insert size affect the accuracy of repeat assembly and scaffold construction, we also designed length distribution of clone-inserts using our model. In our simulated genomes of human and rice, the length distribution of repeats is different, so their optimal length distributions of clone-inserts were not the same. Thus with optimal length distribution of clone-inserts, a given genome could be assembled better at lower coverage.
Animals ; Cloning, Molecular ; Genome ; Genome, Human ; Genomics ; methods ; Humans ; Models, Genetic ; Models, Statistical ; Models, Theoretical ; Oryza ; genetics ; Sequence Analysis, DNA

Objective: To establish the HPLC fingerprints of compound Yinchen granules. Methods: The column was Agilent SB-C18(250 mm×4. 6 mm, 5 μm) and the mobile phase was acetonitrile (A)-0. 2% phosphoric acid solution (B) with gradient elution at a flow rate of 1. 0 ml·min-1. The column temperature was 25℃. The detection wavelength switching technology was used in 180-mi-nute elution time. Results: The HPLC fingerprints of compound Yinchen granules were established. Twenty-two common peaks were confirmed, of which five peaks were identified and 18 peaks were assigned to each crude drug. The overall similarity of the fingerprints of 10 batches of samples was 0. 9 or more when compared with the control map. Conclusion: The fingerprints of compound Yinchen granules can provide reference for the overall quality control of compound Yinchen granules.

Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.
Amino Acid Motifs ; Amino Acid Substitution ; Base Composition ; Codon ; genetics ; Computational Biology ; DNA Mutational Analysis ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Phylogeny ; SARS Virus ; genetics

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS.
Amino Acid Sequence ; Base Composition ; Base Sequence ; Cluster Analysis ; Computational Biology ; Conserved Sequence ; genetics ; Evolution, Molecular ; Gene Components ; Genome, Viral ; Molecular Sequence Data ; Mutation ; genetics ; Phylogeny ; Protein Structure, Tertiary ; RNA Replicase ; genetics ; SARS Virus ; genetics ; Sequence Analysis, DNA

Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves. Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions. The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs.
Amino Acid Substitution ; Base Composition ; Base Sequence ; Computational Biology ; methods ; Genome, Viral ; Isoelectric Point ; Models, Genetic ; Molecular Sequence Data ; Molecular Weight ; Open Reading Frames ; SARS Virus ; genetics ; Sequence Analysis ; Transcription, Genetic

The E (envelope) protein is the smallest structural protein in all coronaviruses and is the only viral structural protein in which no variation has been detected. We conducted genome sequencing and phylogenetic analyses of SARS-CoV. Based on genome sequencing, we predicted the E protein is a transmembrane (TM) protein characterized by a TM region with strong hydrophobicity and alpha-helix conformation. We identified a segment (NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH) in the carboxyl-terminal region of the E protein that appears to form three disulfide bonds with another segment of corresponding cysteines in the carboxyl-terminus of the S (spike) protein. These bonds point to a possible structural association between the E and S proteins. Our phylogenetic analyses of the E protein sequences in all published coronaviruses place SARS-CoV in an independent group in Coronaviridae and suggest a non-human animal origin.
Amino Acid Sequence ; Base Sequence ; Cluster Analysis ; Codon ; genetics ; Gene Components ; Genome, Viral ; Membrane Glycoproteins ; metabolism ; Membrane Proteins ; genetics ; metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; SARS Virus ; genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; genetics ; metabolism