The transcript assembly is essential for transcriptome studies trom next-generation sequencing data. However, there are still many faults of algorithms in the present assemblers, which should be largely improved in the future. According to the requirement of reference genome or not, the transcript assembly could be classified into the genome-guided and de novo methods. The two methods have different algorithms and implementation processes. The quality of assembled transcripts depends on a large number of factors, such as the PCR amplification, sequencing techniques, assembly algorithm and genome character. Here, we reviewed the present tools of transcript assembly and various indexes for assessing the quality of assembled transcripts, which would help biologists to determine which assembler should be used in their studies.
Algorithms ; Gene Expression Profiling ; Genome ; Genomics ; methods ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcriptome

Objective To study the relationship between the liver sinusoidal pathological changes and portal hypertension during the dimethylnitrosamine (DMN) induced liver fibrosis in rats. Methods The rat liver fibrosis model was established by peritoneal injection of DMN (at a dose of 10 mg/kg, 3 times a week, for 4 weeks) in 40 male Wister mice. In the control group of 24 healthy mice, saline solution was injected peritoneally. The dynamic changes of liver fibrosis were observed at different time points (1, 2, 3 day, 1, 2, 4, 6 and 8 week). The pressure of portal vein (Ppv) was directly measured by the intubation of mesentery anterior vein in 5 mice of the model and 3 of the control. The expressions of type Ⅳ collagen (Col Ⅳ), laminin (LM) and type Ⅰ collagen (Col Ⅰ) were detected by immunohistochemistry. Hepatic ultrastructure was observed by electron microscopy. Results Positive expression of Col Ⅳ was observed in the normal liver sinusoidal walls. The various intensities of positive staining of Col Ⅳ were observed in the liver sinusoidal walls of the fibrosis model. Positive expressions of LM and Col Ⅰ increased, and the strongest positive staining displayed in the 4 week model rats. Meanwhile, the fenestrae in the sinusoidal endothelial cells (SECs) were lost and the basal membrane was formed. There was a remarkable positive correlation between the Ppv and the expressions of LM in the DMN induced rat fibrosis( P

OBJECTIVE: To explore the significance of the combination of factor analysis and systematic cluster analysis in classification of traditional Chinese medical syndromes in patients with posthepatitic cirrhosis, and to provide a scientific basis for the criterion of the classification. METHODS: We designed a clinical questionnaire according to the clinical characteristics and the demands of traditional Chinese medical information collection for patients with posthepatitic cirrhosis. By means of clinical epidemiological research, with the four diagnosis methods for clinical information collection of traditional Chinese medicine, symptoms, physical signs, tongue conditions and pulse conditions in 310 patients with posthepatitic cirrhosis were collected, and the characteristics of traditional Chinese medical syndromes in these patients were explored with statistical methods, such as factor analysis, varimax and systematic cluster analysis. RESULTS: Analyzed by factor analysis and systematic cluster analysis with SPSS 11.0, the traditional Chinese medical syndromes in 287 of the 310 cases (92.58%) of posthepatitic cirrhosis could be classified. The syndromes could be divided into 7 categories, which were internal accumulation of damp-heat (55 cases), insufficiency of the spleen with overabundance of dampness (74 cases), accumulation of blood stasis plus deficiency of liver-yin and kidney-yin (73 cases), accumulation of blood stasis plus deficiency of both blood and qi (40 cases), deficiency of both blood and qi (16 cases), deficiency of yin and blood heat (6 cases) and stagnation of the liver-qi and deficiency of the spleen (23 cases). The traditional Chinese medical syndromes in the other 23 cases could not be classified. CONCLUSIONS: The clinical information collected with the four diagnostic methods of traditional Chinese medicine can be classified into different categories with the factor analysis and systematic cluster analysis. The factor analysis and systematic cluster analysis can reveal the characteristics and regularity of traditional Chinese medical syndromes in patients with posthepatitic cirrhosis in a way, and have value in researching the syndromes of traditional Chinese medicine.

Chronic severe hepatitis is a critical disease with high mortality. Currently, effective drugs and therapy still lack. Comprehensive and supportive treatment, artificial liver and liver transplantation are the main therapies. A great number of studies on traditional Chinese medicine (TCM) in many ways combined with Western medicine treatment for chronic severe hepatitis have been reported, but the efficacy and safety still lack systematic evaluation.

To study the effects of Cordyceps mycelia extract (CME) on portal hypertension in rats with dimethylnitrosamine (DMN) induced liver cirrhosis and probe into the mechanism of the action.

Objective To compare the efficacies of anatomic and nonanatomic mesohepatectomy for central type hepatocellular carcinoma.Methods The clinical data of 85 patients with central type hepatocellular carcinoma undergoing hepatectomies were retrospectively analysed.36 patients underwent anatomic mesohepatectomy and the other 49 patients did nonanatomic mesohepatectomy.The operative time,intraoperative blood loss,incidence of postoperative complications,postoperative drainage volume,time to flatus and length of postoperative stay between the two groups were compared.Results There were no significant differences in the general condition,organ function,tumor size and location between the two groups before operation (P ＞ 0.05).The intraoperative blood loss,incidence of postoperative complications,drainage volume were significantly less but the operative time longer in anatomic mesohepatectomy group than nonanatomic hepatectomy group (P ＜ 0.05).No differences between the two groups were found in regard to the time for flatus and length of postoperative hospital stay (P ＞ 0.05).Tumor recurrence developed in 7 cases in group A and 20 cases in group B (P ＜ 0.05).Conclusions Anatomic mesohepatectomy has the advantages of less surgical trauma,less exudation and complications in patients with central type hepatocellular carcinoma.

Accumulating evidence has shown that neutrophil-lymphocyte ratio (NLR), as an assessment index for inflammatory response, is closely related to the prognosis of various malignant tumors. This article summarizes the research advances in the relationship of NLR with overall survival, disease-free survival, and pathological features of hepatocellular carcinoma and related mechanisms of action, and points out that NLR is a convenient, economic, and effective predictor for the prognosis of patients with hepatocellular carcinoma.

AIM: To study the role of injury and phenotype shift of liver sinusoidal endothelial cells in the development of portal hypertension of liver cirrhosis in rats. METHODS: The rat liver cirrhosis model was established by peritoneal injection of dimethylnitrosamine (DMN) (at a dose of 10 mg?kg~(-1), 3 times a week, for 4 weeks). The dynamic changes of liver cirrhosis were observed at different time points (1 day, 2 days, 3 days, 1 week, 2 weeks, 4 weeks, 6 weeks and 8 weeks). The pressure of portal vein (Ppv), the expression of CD44, von Willebrand factor (vWF), endothelin-1 (ET-1) mRNA and endothelial nitric oxide synthase (eNOS) mRNA, the serum hyaluronic acid (HA) content and liver ET-1 content were measured. RESULTS: Compared with the normal control rats, CD44 positive staining was weak in the 1 day model rats, and the numbers of fenestrae of sinusoidal endothelial cells (SECs) rapidly decreased, but serum HA content rapidly increased (P

Primary biliary cholangitis (PBC) is an immune-mediated chronic and progressive intrahepatic cholestasis disease. Treatment with ursodeoxycholic acid (UDCA) can significantly improve the prognosis of patients with PBC, but some patients still have poor response to UDCA, which is the main risk factor for disease progression. Several evaluation models and scoring systems based on biochemical response have been applied to screen out patients with poor response in clinical practice. Integrated traditional Chinese and Western medicine therapy for PBC has certain advantages in improving the symptoms, liver biochemistry, fibrosis indices, and biochemical response rate of PBC patients and thus holds promise for clinical application; however, further improvement is needed for experimental design and efficacy evaluation.

OBJECTIVETo study the role of hepatic sinusoidal endothelium injury during hepatic fibrogenesis induced by dimethylnitrosamine (DMN) in rats.

METHODSHepatic fibrosis of rats was induced by administration of DMN intraperitoneally three times a week for 4 weeks. The animals were harvested on day 2 and week 1, 2, 3, 4, 5, 6, 8, 12, and 24. The formation of liver fibrosis and hepatic sinusoid capillarization were successively observed by morphological observation and other methods.

RESULTSTwo days after treated with DMN, there was no obvious changes in the liver, but the fenestration of the sinusoidal endothelial cells decreased, and it became more obvious after one week. After four weeks, there was a large necrotic area and a number of pseudolobes appeared. The HA in the serum was lower than that of control (231.30 ng/ml +/- 143.80 ng/ml vs 56.50 ng/ml +/- 18.10 ng/ml; t=3.14, P<0.05), but the hydroxyproline content was obviously higher than that of control (223.04 microg/g +/- 37.09 microg/g vs 61.55 microg/g +/- 20.85 microg/g; t=8.28, P<0.05). Hepatic sinusoid capillarization was gradually formed and defenestration of the hepatic sinusoidal endothelium preceded the appearance of serious hepatocellular damage, hepatic fibrosis and basement membrane.

CONCLUSIONSThe damage and phenotypic alteration of the hepatic sinusoidal endothelium may be a vital issue triggering the liver fibrosis induced by DMN.

Actins ; analysis ; Animals ; Dimethylnitrosamine ; toxicity ; Endothelium, Vascular ; pathology ; physiopathology ; Fibrosis ; chemically induced ; Immunohistochemistry ; Liver ; blood supply ; chemistry ; pathology ; Male ; Muscle, Smooth ; chemistry ; Rats ; Rats, Wistar ; Time Factors ; von Willebrand Factor ; analysis