OBJECTIVETo investigate the expression of immune-related genes during osteogenesis stimulated by simvastatin.

METHODSAfter treated with simvastatin, the expression of immune-related genes of mouse osteoblast was examined with gene chip (BiostarM-140s).

RESULTSThere were 16 differently expressed genes related to immune function, with nine down-regulated genes and seven up-regulated genes.

CONCLUSIONSAfter treated with simvastatin, expression of inflammation related genes is down-regulated and inflammation inhibitor genes is up-regulated in mouse osteoblasts.

Animals ; Down-Regulation ; Gene Expression Profiling ; Gene Expression Regulation ; Mice ; Osteoblasts ; drug effects ; immunology ; Osteogenesis ; drug effects ; Simvastatin ; pharmacology

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

The field of gene therapy has been increasingly studied in the last four decades, and its clinical application has become a reality in the last 15 years. Traditional Chinese medicine (TCM), an important component of complementary and alternative medicine, has evolved over thousands of years with its own unique system of theories, diagnostics and therapies. TCM is well-known for its various roles in preventing and treating infectious and chronic diseases, and its usage in other modern clinical practice. However, whether TCM can be applied alongside gene therapy is a topic that has not been systematically examined. Here we provide an overview of TCM theories in relation to gene therapy. We believe that TCM theories are congruent with some principles of gene therapy. TCM-derived drugs may also act as gene therapy vehicles, therapeutic genes, synergistic therapeutic treatments, and as co-administrated drugs to reduce side effects. We also discuss in this review some possible approaches to combine TCM and gene therapy.
Gene Expression ; drug effects ; Genes ; drug effects ; Genetic Therapy ; methods ; Humans ; Medicine, Chinese Traditional ; methods

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

Peptide nucleic acid(PNA) is a kind of artificial DNA mimic. PNA hybridizes with DNA or RNA by means of Watson-Crick's base-pairs complementary with high stability, affinity and selectivity. PNA not only regulates. DNA replication, but also adjusts DNA transcription (or reverse transcription) and translation. Many applications have been explored as a new kind of molecular biological tool and a gene-targeting strategy.
Gene Expression Regulation ; drug effects ; Peptide Nucleic Acids ; pharmacology ; Protein Biosynthesis ; drug effects ; Transcription, Genetic ; drug effects

Objective of this study was to perform bioinformatics analysis of the characteristics of gene expression profiling regulated by amifostine and predict its novel potential biological function to provide a direction for further exploring pharmacological actions of amifostine and study methods. Amifostine was used as a key word to search internet-based free gene expression database including GEO, affymetrix gene chip database, GenBank, SAGE, GeneCard, InterPro, ProtoNet, UniProt and BLOCKS and the sifted amifostine-regulated gene expression profiling data was subjected to validity testing, gene expression difference analysis and functional clustering and gene annotation. The results showed that only one data of gene expression profiling regulated by amifostine was sifted from GEO database (accession: GSE3212). Through validity testing and gene expression difference analysis, significant difference (p < 0.01) was only found in 2.14% of the whole genome (460/192000). Gene annotation analysis showed that 139 out of 460 genes were known genes, in which 77 genes were up-regulated and 62 genes were down-regulated. 13 out of 139 genes were newly expressed following amifostine treatment of K562 cells, however expression of 5 genes was completely inhibited. Functional clustering displayed that 139 genes were divided into 11 categories and their biological function was involved in hematopoietic and immunologic regulation, apoptosis and cell cycle. It is concluded that bioinformatics method can be applied to analysis of gene expression profiling regulated by amifostine. Amifostine has a regulatory effect on human gene expression profiling and this action is mainly presented in biological processes including hematopoiesis, immunologic regulation, apoptosis and cell cycle and so on. The effect of amifostine on human gene expression need to be further testified in experimental condition.
Amifostine ; pharmacology ; Computational Biology ; Gene Expression ; drug effects ; Gene Expression Profiling ; methods ; Humans ; Microarray Analysis ; Molecular Sequence Annotation

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

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

OBJECTIVESelecting an effective way to increase salt-resistance of Prunella vulgaris seed through seed priming technology.

METHODThe treatment of salt stress to P. vulgaris seeds was made by the different concentrations of NaCl solutions. Primed seeds germinated under 0.8% NaCl.

RESULTAs concentrations of NaCl increasing, seed germination percentage, germination index and vitality index reduced. Primed with 15%-35% PEG, 100-500 mg x L(-1) GA3 and 0.4%-2.0% KNO3-KH2PO4 could enhance seeds germination index and vitality index under salt stress while treated with NaCl seeds germination percentage reduced.

CONCLUSIONTreated with PEG, GA3, KNO3-KH2PO4 under proper concentration, the seed vigor, seed resistance under salt stress increased.

Gene Expression Regulation, Plant ; drug effects ; Germination ; drug effects ; Prunella ; drug effects ; physiology ; Salt-Tolerance ; drug effects ; Seeds ; drug effects ; physiology ; Sodium Chloride ; pharmacology