With the expanded application of heavy metal cadmium, soil cadmium pollution is more and more serious. In this study, using Salix matsudana as a phytoremediation candidate, we observed changes of gene expression and metabolic pathway after 1, 7 and 30 days under 2.5 mg/L and 50 mg/L cadmium stress. The result of transcriptome sequencing showed that we obtained 102 595 Unigenes; 26 623 and 32 154 differentially expressed genes (DEG) in the same concentration and different stress time; 8 550, 3 444 and 11 428 DEG with different concentrations at the same time; 25 genes closely related to cadmium stress response were screened. The changes of genes expression (such as metallothionein, ABC transporter, zinc and manganese transporter) depended on both concentration of cadmium and exposure time. The expression of several genes was obviously up-regulated after cadmium stress, for example 3,6-deoxyinosinone ketolase (ROT3) in brassinolide synthesis pathway and flavonoid synthase (FLS), flavanone-3-hydroxylase (F3H) in the synthesis pathway of brassinolide. In addition, GO analysis shows that GO entries were mainly enriched in metabolic processes including cellular processes, membranes, membrane fractions, cells, cellular fractions, catalytic activation and binding proteins in response to cadmium stress, whose number would increase along with cadmium concentration and exposure time. The reliability of transcriptome information was verified by qPCR and physiological experimental data. Response mechanisms of S. matsudana after cadmium stress were analyzed by transcriptome sequencing, which provided theoretical guidance for remediation of cadmium pollution in soil by S. matsudana.
Biodegradation, Environmental ; Cadmium ; toxicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; drug effects ; Plant Proteins ; genetics ; Reproducibility of Results ; Salix ; drug effects ; genetics ; Stress, Physiological ; genetics ; Transcriptome ; drug effects

OBJECTIVETo identify the genes differentially expressed among the steroid-resistant nephrotic syndrome (SRNS), steroid-sensitive nephrotic syndrome (SSNS) and normal children, and understand the molecular mechanism of SRNS.

METHODSAffymetrix microarray technology was used to obtain such a profile. The differentially expressed genes among these groups were identified based on signal-to-noise ratios by GCOS software; real-time PCR analysis was performed to confirm the microarray results.

RESULTSThere were 157 genes differentially expressed among these groups. The genes up-regulated both in SRNS and SSNS were involved primarily in ionic transportation, immuno-signal transduction and apoptosis. In particular, CLNS1A gene was down regulated in SRNS but up regulated in SSNS.

CONCLUSIONSeveral differentially expressed genes, such as CLNS1A and HLA-DRB4 were found to be closely related to the pathogenesis of SRNS and SSNS. This DNA microarray analysis has provided some important clue to the molecular mechanism of SRNS.

Child ; Gene Expression Profiling ; Gene Expression Regulation ; drug effects ; Humans ; Nephrotic Syndrome ; drug therapy ; genetics ; Steroids ; therapeutic use

OBJECTIVETo explore the pharmacologic mechanism of gardenin in treating cerebral ischemia, by studying its effect on gene expression profile in brain of rats with focal cerebral ischemia (FCI).

METHODSTotal RNAs were isolated from rats with FCI and those treated with gardenin. The mRNAs were reversely transcribed to cDNA with incorporation of fluorescent Cy5- or Cy3-dUTP to prepare hybridization probes. The PCR products of 4096 genes were spotted on the chip after a serial treatment. The mixed probes were hybridized to the cDNA microarray. Axon Genepix 4000B and GenePixPro 3.0 software were used to scan and analyze the fluorescent signals.

RESULTSIn the group treated with gardenin, there were 70 genes had expression profiles different to that in the model group in the focal cerebral ischemic brain tissue, in which 68 were up-regulated and 2 down-regulated.

CONCLUSIONGardenin has regulatory effect on the gene expression in rats with focal cerebral ischemia, which elucidates part of the pharmacologic mechanism of Qingkailing in molecular level.

Animals ; Brain Ischemia ; genetics ; metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; drug effects ; Male ; Pyridines ; pharmacology ; Rats ; Rats, Sprague-Dawley

Panax japonicus is a traditional Chinese medicine,and its principle components have shown certain pharmacological activities for cell damage,aging and cell apoptosis. In order to clarify the pharmacological mechanism and involved metabolic pathways of P. japonicas,the gene expression of Tetrahymena thermophila under P. japonicus treatment was analyzed through high-throughput transcriptome sequencing in this study. Based on the transcriptome analysis,3 544 differentially expressed genes were identified in control group,of which 1 945 genes showed up-regulated expression and 1 599 genes showed down-regulated expression. Under P. japonicas treatment in the experiment group,3 312 differentially expressed genes were screened,of which 1 `493 genes showed up-regulated expression and 1 819 genes showed down-regulated expression. GO enrichment analysis indicated that in control group,the genes in the cells in a series of fundamental biological process were down-regulated,such as DNA replication and protein synthesis; while the signal transduction process and fatty acids oxidizing process were enriched. Whereas in the experiment group,down-regulated genes were mainly enriched in oxidation-reduction,cofactor metabolic process and vitamin metabolic process; up-regulated genes were enriched in signal transduction process and protein modification process. In the analysis using KEGG database,cell cycle pathway was enhanced and autophagy pathway was inhibited under the condition of P. japonicas treatment. Real-time quantitative polymerase chain reaction( RT-qPCR) was used to detect the expression differences between 6 up-regulated and 4 down-regulated genes in related metabolic pathways. The RT-q PCR results and RNA-Seq data were highly correlated and consistent with each other. This study could provide important direction and basis for further study on the mechanism of cell growth regulation with the treatment of P. japonica.
Gene Expression ; Gene Expression Profiling ; Metabolic Networks and Pathways ; Panax ; chemistry ; Plants, Medicinal ; chemistry ; Tetrahymena thermophila ; drug effects ; genetics ; Transcriptome

OBJECTIVETo study the expression changes of apoptosis related genes induced by cerulenin in multiple myeloma cell line U266 and explore its molecular mechanism.

METHODSThe expression changes of 96 apoptosis related genes were analyzed by superArray cDNA in U266 cells treated with cerulenin (20 microg/ml) for 12 h. Semi-quantitative RT-PCR was used to confirm the representative expression changes genes, Rip2, caspase 9 and TRAF2.

RESULTSAfter treated with cerulenin for 12 h, 44 apoptosis related genes expression in the U266 cells were changed, among which 41 were over 2 fold increase and 3 over 2 fold decrease. The expression of caspase 9 was increased markedly, indicating that mitochondria pathway played a key role in cerulenin inducing apoptosis and TRAF2 expression change suggested that nuclear factor (NF) participates in cerulenin inducing apoptosis.

CONCLUSIONThe death acceptor signaling pathway and the death acceptor non-dependence signaling pathway co-regulate cerulenin inducing apoptosis in U266 cells. Mitochondria pathway played the key role and nuclear factor (NF) participates in the apoptosis process.

Apoptosis ; drug effects ; genetics ; Cell Line, Tumor ; Cerulenin ; pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Multiple Myeloma ; genetics ; metabolism ; pathology ; Signal Transduction ; drug effects

Chilling-sensitive rice varieties acquire chilling tolerance when their roots are exposed to water stress for short time. Caffeine-sensitive calcium signal was involved in this procedure. By using total RNA differential display, a chilling induced cDNA(ICT: induction of chilling treatment) was isolated from roots of chilling-sensitive rice variety. It was determined that it is a novel cDNA by homology searching. The transcript level of ict mRNA is up-regulated under chilling stress, it is decreased to low level when the samples were transferred to standard culture conditions. Pre-treated with mannitol for two hours is beneficial to inducing ICT level of expression. This chilling induction was inhibited by caffeine, suggesting that it may play a putative role in signal transduction of caffeine-sensitive calcium.
Cold Temperature ; DNA, Complementary ; genetics ; isolation & purification ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; drug effects ; Mannitol ; pharmacology ; Oryza ; drug effects ; genetics ; Plant Roots ; drug effects ; genetics ; RNA, Messenger ; drug effects ; genetics ; metabolism

Action mechanism and material base of compound Danshen dripping pills in treatment of carotid atherosclerosis were discussed based on gene expression profile and molecular fingerprint in this paper. First, gene expression profiles of atherosclerotic carotid artery tissues and histologically normal tissues in human body were collected, and were screened using significance analysis of microarray (SAM) to screen out differential gene expressions; then differential genes were analyzed by Gene Ontology (GO) analysis and KEGG pathway analysis; to avoid some genes with non-outstanding differential expression but biologically importance, Gene Set Enrichment Analysis (GSEA) were performed, and 7 chemical ingredients with higher negative enrichment score were obtained by Cmap method, implying that they could reversely regulate the gene expression profiles of pathological tissues; and last, based on the hypotheses that similar structures have similar activities, 336 ingredients of compound Danshen dripping pills were compared with 7 drug molecules in 2D molecular fingerprints method. The results showed that 147 differential genes including 60 up-regulated genes and 87 down regulated genes were screened out by SAM. And in GO analysis, Biological Process ( BP) is mainly concerned with biological adhesion, response to wounding and inflammatory response; Cellular Component (CC) is mainly concerned with extracellular region, extracellular space and plasma membrane; while Molecular Function (MF) is mainly concerned with antigen binding, metalloendopeptidase activity and peptide binding. KEGG pathway analysis is mainly concerned with JAK-STAT, RIG-I like receptor and PPAR signaling pathway. There were 10 compounds, such as hexadecane, with Tanimoto coefficients greater than 0.85, which implied that they may be the active ingredients (AIs) of compound Danshen dripping pills in treatment of carotid atherosclerosis (CAs). The present method can be applied to the research on material base and molecular action mechanism of TCM.
Carotid Artery Diseases ; drug therapy ; genetics ; metabolism ; Drugs, Chinese Herbal ; administration & dosage ; Gene Expression Profiling ; Gene Expression Regulation ; drug effects ; Humans ; Salvia miltiorrhiza ; chemistry ; Signal Transduction ; drug effects

We designed and constructed an antibiotic screening system by using antibiotic responsive genes as reporters. Plasmid pCS26 carrying a promoterless luminescence reporter, luxCDABE, was used as the vector and the promoter regions of antibiotic responsive genes/operons from Escherichia coli were cloned upstream of the lux reporter to form the first part of the screening reporter array. Random promoter library of Salmonella enterica and Pseudomonas aeruginosa were screened for antibiotic responsive clones which consist of the second part of the screening array. The selected final reporter array responded to different antibiotics in distinct patterns and enabled in vivo high-throughput screening for antibiotics. Unknown antibiotics could, in general, be classified by analyzing the response patterns. This screening system is both sensitive and efficient and should prove to be a useful tool for screening new antibiotic compounds.
Anti-Bacterial Agents ; pharmacology ; Drug Evaluation, Preclinical ; methods ; Gene Expression Regulation, Bacterial ; drug effects ; Promoter Regions, Genetic ; genetics ; Pseudomonas aeruginosa ; drug effects ; genetics ; Salmonella enterica ; drug effects ; genetics

OBJECTIVETo investigate the molecular mechanisms and effective target points of lipid-lowering drug, Rhizoma Curcumae Longae, and study the effect of curcumin on the expression of low density lipoprotein (LDL) receptors in macrophages in mice.

METHODSMacrophages in mice were treated with curcumin, which was purified from the ethanolly extraction of Rhizoma Curcumae Longae for 24 h. The LDL receptors expressed in the macrophages were determined by enzyme-linked immunosorbent assay (ELISA) and assay of DiI labeled LDL uptake by flow cytometer.

RESULTSIt was found for the first time that 10 micromol/L-50 micromol/L curcumin could obviously up-regulate the expression of LDL receptor in macrophages in mice, and a dose-effect relationship was demonstrated.

CONCLUSIONOne of the lipid-lowering mechanisms of traditional Chinese medicine, Rhizoma Curcumae Longae, was completed by the effect of curcumin through the up-regulation of the expression of LDL receptor.

Animals ; Cell Line ; Curcumin ; pharmacology ; Gene Expression ; drug effects ; Hypolipidemic Agents ; pharmacology ; Macrophages ; drug effects ; Mice ; Receptors, LDL ; drug effects ; genetics ; Up-Regulation ; drug effects ; genetics

This study investigated the effect of etoposide, an anticancer chemotherapy drug, on B7-H1 expression in retinoblastoma (Rb) cells and the role of miR-513a-5p in the process. Rb cells were divided into control and etoposide groups. In the etoposide group, cells were treated with etoposide at different concentrations (2.5, 5, 10, 20 and 40 μg/mL) for 24 h. Those given no treatment of etopside served as controls. Reverse transcription polymerase chain reaction (RT-PCR), fluorescence quantitative PCR and flow cytometry were performed to measure the mRNA and protein expression of B7-H1 in Rb cells. The mRNA expression of miR-513a-5p in Rb cells before and after etoposide treatment was also detected by fluorescence quantitative PCR. The miR-513a-5p mimics and the miR-513a-5p inhibitor were transfected into Rb cells separately, and fluorescence quantitative PCR and flow cytometry were used to detect the effect of the miR-513a-5p mimics or inhibitor on B7-H1 expression. TargetScan5.2 was employed to predict the miR-513a-5p binding sites in the 3'-untranslated region of B7-H1 mRNA. Luciferase reporter plasmids carrying this site were prepared and transfected into Rb cells and luciferase activity analyzed. The results showed that etoposide stimulated the mRNA and protein expression of B7-H1 in Rb cells, which reached a maximal level after treatment with 5 μg/mL etoposide (P<0.05). However, miR-513a-5p expression was decreased in Rb cells after etoposide treatment. When the miR-513a-5p inhibitor was added, B7-H1 expression was increased with the concentration of the miR-513a-5p inhibitor (P<0.05). Moreover, B7-H1 expression was decreased gradually with the concentration of the miR-513a-5p mimics increased (P<0.01). Additionally, the miR-513a-5p mimics were found to inhibit the luciferase activity. It was concluded that etoposide can promote B7-H1 expression in Rb cells, which may be associated with chemoresistance. The promoting effect of etoposide on B7-H1 expression can be reversed by miR-513a-5p mimics. MiR-513a-5p inhibits the mRNA and protein expression of B7-H1 via binding to the 3'-UTR of B7-H1 mRNA.
B7-H1 Antigen ; genetics ; Cell Line, Tumor ; Etoposide ; pharmacology ; Gene Expression ; drug effects ; genetics ; Humans ; MicroRNAs ; genetics ; Retinoblastoma ; genetics