Transcriptome profile and its partly verification of human hepatocellular carcinoma cells exposed to Yuzhizi () seed extract.

OBJECTIVE: To investigate the efficacy of Yuzhizi seed extract (FAQSE) on inhibiting the proliferation of hepatocellular carcinoma (HCC) cells in vitro and to explore the anti-HCC action mechanism of FAQSE. METHODS: Human HCC HepG2 and Huh7 cells were used to investigate the anti-HCC effect of FAQSE. 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide (MTT) method was used to measure cell viability. Affymetrix microarray was adopted to detect the expression of transcriptome. The differentially expressed genes (DEGs) of each cell line were identified. For co-DEGs of both cell lines, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were enriched using the Database for Annotation, Visualization and Integrated Discovery (DAVID), and the network analysis of protein-protein interaction (PPI) was mapped using the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape software. Some important genes in the PPI network of co-DEGs were selected to verify by quantitative real-time reverse transcription-polymerase chain reaction, Western blot and enzyme-linked immunosorbent assay. RESULTS: FAQSE decreased the viability of HepG2 and Huh7 cells. There were 211 co-upregulated and 86 co-downregualted genes in both cell lines after FAQSE treatment. The enriched GO terms of co-upregulated DEGs were primarily involved cell-cell adhesion, viral process, transcription initiation from RNA polymerase II promoter, positive regulation of transcription from RNA polymerase II promoter and actin cytoskeleton organization. The GO terms of co-downregulated DEGs were mainly enriched in the processes of SRP-dependent cotranslational protein targeting to membrane, viral transcription, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, translational initiation and rRNA processing. Main KEGG pathways of co-upregulated DEGs were endocytosis, glutathione metabolism, protein processing in endoplasmic reticulum, synaptic vesicle cycle and lysosome. The major KEGG pathways of co-downregulated DEGs were ribosome, biosynthesis of amino acids, arginine and proline metabolism, systemic lupus erythematosus and complement and coagulation cascades. The top 10 co-DEGs with high hub nodes in STRING analysis were ribosomal protein S27a, transferrin, ribosomal protein S20, ribosomal protein L9, protein phosphatase 2 regulatory subunit B alpha, transthyretin, thioredoxin reductase 1, ribosomal protein L3, ribophorin I and ribosomal protein L24. Alpha-fetoprotein (AFP) was also co-downregulated and contained in the PPI network. The mRNA and protein expression of most verified genes was consistent with the results of co-DEGs analysis. And the AFP level was significantly reduced after FAQSE treatment. CONCLUSIONS: A series of genes and pathways of HepG2 and Huh7 cells were changed after FAQSE treatment, which might be the targets of FAQSE against HCC and worthy of further study. AFP might be important one of them.

Lung hypoplasia in rats with esophageal atresia and tracheo-esophageal fistula.

INTRODUCTION: Survivors of esophageal atresia and tracheo-esophageal fistula (EA-TEF) often suffer chronic respiratory tract disease. EA-TEF results from abnormal emergence of the trachea from the foregut. This study in a rat model tests the hypothesis that primary lung maldevelopment might be a downstream consequence of this defect. RESULTS: The lung was hypoplastic in rats with EA-TEF although the histological pattern was normal. Maturation and arteriolar wall thickness were unchanged, but mesenchymal control of airway branching was weakened. This branching was deficient from embryonal day (E13) on in adriamycin-treated explants. DISCUSSION: In conclusion, the lungs were hypoplastic in rats with experimental EA-TEF due to defective embryonal airway branching. However, arteriolar wall and respiratory epithelial patterns remained normal. These findings suggest that similarly defective lung development might contribute to chronic respiratory disease in EA-TEF patients. METHODS: Pregnant rats received either 1.75 mg/kg i.p. adriamycin or vehicle on E7, E8, and E9. Lungs were recovered at E15, E18, and E2. Lung weight/body weight ratio, total DNA and protein, radial alveolar count, arteriolar wall thickness, lung maturity, and mesenchymal control of airway branching were assessed. E13 lungs were cultured for 72 h and explant airway branching was measured daily. For comparisons, nonparametric tests (*P < 0.05) were used.

Microscopic magnetic resonance imaging of the thoracic venous system in rats with congenital diaphragmatic hernia.

BACKGROUND/AIM: Infants and rats with congenital diaphragmatic hernia (CDH) have malformations of the heart and the great arteries caused by neural crest (NC) dysregulation during embryogenesis. Abnormally narrow jugular veins have been found in babies during cannulation for ECMO. However, the venous system has not been examined in depth so far. We hypothesized that abnormal patterning and/or size of the thoracic veins could occur in rats with CDH. This hypothesis was tested by microscopic magnetic resonance imaging (MMRI), a high-resolution tool able to detect subtle changes of vessels in small animals. MATERIAL/METHODS: Fetuses from pregnant rats fed either 100 mg i.g. nitrofen or vehicle on E9.5 were recovered near term. A 7 T MMRI system with a coronal multislice fast spin echo sequence allowed diagnosis of CDH (n = 19), and T2 SE high-resolution sequences made assessment of the pattern and width of cervico-thoracic veins possible. Values were corrected for body size by dividing them by the length of thoracic vertebrae T3-T5. The results in nitrofen and control (n = 11) groups were compared by non-parametric tests (*p < 0.05). RESULTS: Congenital diaphragmatic hernia fetuses were smaller than controls (4.5 ± 0.26 vs. 5.3 ± 0.2 g*). The widths (corrected for body size) of left external, both innominate, right superior vena cava and azygos veins were significantly smaller in CDH rats than in controls. CONCLUSIONS: The cervico-thoracic veins are normally patterned but abnormally narrow (except the internal jugulars) in rats with CDH. The same embryonic NC dysregulation that accounts for cardiovascular malformations could also explain these venous anomalies in CDH.

Abnormal development of the enteric nervous system in rat embryos and fetuses with congenital diaphragmatic hernia.

BACKGROUND/AIM: Esophageal dilatation, gastroesophageal reflux, and intestinal obstruction have been demonstrated in CDH survivors. Abnormal esophageal and intestinal innervations were recently found in rats and babies with this disease. Our aim was to further characterize these malformations in embryos and fetal rats exposed to nitrofen. METHODS: Pregnant rats received either 100 mg nitrofen or vehicle on E9.5. Fetuses were recovered at E15, E18, and E21. Sections of esophagus and small bowel were histochemically stained with acetylcholinesterase (AChE) and immunostained for PGP9.5. PGP9.5 gen protein were measured on E21 and PGP9.5 mRNA on E15, E18 and E21. Comparisons between groups were made with non-parametrics tests. RESULTS: Histochemistry and immunohistochemistry showed deficient innervation in all anatomical areas studied at E15, E18, and E21, and WB confirmed this decrease in E21 fetuses. PGP9.5 messenger was decreased in nitrofen-exposed animals on E18 (esophagus) or E15 (small bowel), and increased on E21 in the esophagus and E18 in small bowel. CONCLUSIONS: Development of the enteric nervous system of the esophagus, stomach, and small bowel is deficient in rat embryos and fetuses exposed to nitrofen. These anomalies could account in part for the long-term gastrointestinal morbidity observed in CDH survivors.

Phytoextraction of Zn and Cu from sewage sludge and impact on agronomic characteristics.

The presence of elevated concentrations of heavy metals limits the usage of sewage sludge as a fertilizer and soil amendment. Experiments were carried out to examine the extent to which seven plant species phytoextracted Zn and Cu from dewatered sludge. The hyperaccumulators Thlaspi caerulescens and Sedum alfredii showed the greatest removal of Zn, while shoots and tubers of two species of Alocasia showed the greatest Cu removal. Cultivation of plants in the sludge resulted in significant decreases in total Zn and changes in the partitioning of Zn between soil pools. However, Cu levels were largely unchanged and remained associated predominantly with the organic matter pool. Agronomic characteristics of the sludge material, such as pH, organic matter content, and nitrogen, phosphorus, and potassium concentrations, did not change significantly during the four-month growth period, indicating that subsequent crops could be sustained by this material. These results suggest that Zn can be phytoextracted from sludge material, provided the rate of metal uptake exceeds the rate of mobilization to the exchangeable fraction. Since there was no appreciable accumulation of Zn and Cu in seeds of Zea mays in this study, some tissues from sludge-grown plants could potentially be used as animal fodder.

On Temporal Generalization of Simple Recurrent Networks.

Simple recurrent networks (Elman networks) have been widely used in temporal processing applications. In this study we investigate temporal generalization of simple recurrent networks, drawing comparisons between network capabilities and human performance. Elman networks are trained to generate temporal trajectories sampled at different rates. The networks are then tested with trajectories at the trained rates and other sampling rates, including trajectories representing mixtures of different sampling rates. It is found that for simple trajectories the networks show interval invariance, but not rate invariance. However, for complex trajectories which require greater contextural information, these networks do not seem to show any temporal generalization. Similar results are also obtained using measured speech data. These results suggest that this class of recurrent networks exhibits severe limitations in temporal generalization. Discussions are provided regarding rate invariance and possible ways to achieve it in neural networks. Copyright 1996 Elsevier Science Ltd