Bioinformatic analysis of genes related to temporal epilepsy / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the genes associated with temporal epilepsy and explore the molecular mechanism of epilepsy.</p><p><b>METHODS</b>The microarray data of temporal epilepsy were downloaded from the Gene Expression Omnibus (GEO) database and analyzed by bioinformatics methods using String, KEGG and Panther databases.</p><p><b>RESULTS</b>Of all the 71 differentially expressed genes, 51 were found to encode proteins with interactions; the main biological pathways involved included neuroactive ligand-receptor interactions, MAPK signaling pathway, and calcium signaling pathway etc.</p><p><b>CONCLUSION</b>The pathogenesis of epilepsy involves multiple genes, and investigations of these genes may provide valuable insights into the mechanism of epilepsy.</p>

Analysis and verification of the interaction network of differentially expressed genes in invasive bladder cancer / 南方医科大学学报

<p><b>OBJECTIVE</b>To study the data of gene expression microarray by protein interaction network analysis, establish an interaction network of differentially expressed genes in invasive bladder cancer and verify the central nodes of the network.</p><p><b>METHODS</b>A total of 152 differentially expressed genes in invasive bladder cancer detected by gene expression microarray were inputted into STRING database online for analysis and establishment of the interaction network. The interaction data were imported into Cytoscape 2.6.2 software for screening the central nodes of the network. KEGG database was exploited for pathway analysis and functional study of the central node genes. Real-time RT-PCR was used for verification, and the genes with maximal differential expressions were screened for exploring the molecular mechanism of carcinogenesis of invasive bladder cancer.</p><p><b>RESULTS</b>The protein products of 103 differentially expressed genes in bladder cancer had interactions, forming a complicated interaction network. Twenty-six nodes involved in several signal pathways were confirmed by Cytoscape as the central nodes of the network, among which UBE2C, VEGF, TGFBR2, and CAV1 nodes were verified by real-time RT-PCR as the genes with maximal differential expressions between the bladder cancer and normal tissues, and the 2(-delta delta Ct) of these genes were 9.45, 4.17, 0.13 and 0.18 (GAPHD as the internal control), respectively.</p><p><b>CONCLUSION</b>The interaction network of the differentially expressed genes, especially the central nodes of this network, can provide clues to the carcinogenesis, early diagnosis and molecular targeted therapy of invasive bladder cancer.</p>

Effect of cinobufagin on nuclear factor-kappaB pathway in HepG2 cells / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the effect of cinobufagin on nuclear factor-kappaB (NF-kappaB) pathway of liver cancer cell line HepG2.</p><p><b>METHODS</b>Dual-luciferase cis-reporting system was used to detect the relative value of pNF-kappaB-TA-luc upon tumor necrosis factor-alpha (TNF-alpha) stimulation of NF-kappaB pathway. Western blotting was used to detect the protein level of NF-kappaB p65, and RT-PCR was used to detect the gene transcription level of intercellular adhesion molecule-1 (ICAM-1), a target downstream gene of NF-kappaB.</p><p><b>RESULTS</b>At the concentration of 0.25 and 0.5 microg/ml, cinobufagin significantly lowered the relative value of luciferase (P<0.05). The results of Western blotting showed that cinobufagin significantly suppressed the protein expression of NF-kappaB p65. The transcription level of ICAM-1 was reduced by different doses of cinobufagin.</p><p><b>CONCLUSION</b>The anti-cancer effect of cinobufagin may be related to its activity in inhibiting the activation of NF-kappaB pathway.</p>

Functional prediction of KIAA0101 gene in human non-small cell lung cancer / 南方医科大学学报

<p><b>OBJECTIVE</b>To predict the function of KIAA0101 gene over-expressed in human non-small cell lung cancer by bioinformatics methods.</p><p><b>METHODS</b>The gene expression profiles of the lung cancer tissues and the adjacent normal tissues were compared by dChip software analysis, and the differential genes coexpressed with KIAA0101 gene were identified. The biological functions of these genes were analyzed using the Database for Annotation, Visualization and Integrated Discovery (DAVID), Gene Ontology (GO) and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), and the common transcription factors of these genes were predicted using Gene Annotation Tool to Help Explain Relationships (GATHER).</p><p><b>RESULTS</b>Nine genes were found to have at least two-fold overexpressions in the lung cancer tissues in comparison with the expression level in the adjacent normal tissues, and showed similar pattern of expression variations in the lung cancer tissue. Most of these genes had the E2F1 binding sites in the promoter region.</p><p><b>CONCLUSION</b>KIAA0101 gene may participate in the cell cycle regulation of the non-small cell lung cancer, and the expression levels of the 9 genes identified may be regulated by the transcription factor E2F1.</p>

Time course of let-7a expression in the cell cycle of human cervical carcinoma HeLa cells / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the time course of let-7a microRNA expression in the cell cycle of HeLa cells.</p><p><b>METHODS</b>HeLa cells were synchronized in G(1), S and G(2)/M phases using double-thymidine block, and the cell cycle phases were defined by flow cytometry. Real-time quantitative RT-PCR was used to examine the expression of let-7a in HeLa cells in different cell cycle phases.</p><p><b>RESULTS</b>The synchronization rates of G(1), S and G(2)/M phases were 84.81%, 83.65% and 77.69%, respectively. Let-7a was constitutively expressed throughout the cell cycle in HeLa cells, but the expression levels in G(1) and S phases were lower than those in G(2)/M phase.</p><p><b>CONCLUSIONS</b>Cell cycle can significantly influence the expression level of let-7a, which may provide new clues to the understanding of the cell cycle control mechanisms.</p>

Bioinformatics analysis of mosquito densovirus nostructure protein NS1 / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To analyze and predict the structure and function of mosquito densovirus (MDV) nostructual protein1 (NS1).</p><p><b>METHODS</b>Using different bioinformatics software, the EXPASY pmtparam tool, ClustalX1.83, Bioedit, MEGA3.1, ScanProsite, and Motifscan, respectively to comparatively analyze and predict the physic-chemical parameters, homology, evolutionary relation, secondary structure and main functional motifs of NS1.</p><p><b>RESULTS</b>MDV NS1 protein was a unstable hydrophilic protein and the amino acid sequence was highly conserved which had a relatively closer evolutionary distance with infectious hypodermal and hematopoietic necrosis virus (IHHNV). MDV NS1 has a specific domain of superfamily 3 helicase of small DNA viruses. This domain contains the NTP-binding region with a metal ion-dependent ATPase activity. A virus replication roller rolling-circle replication(RCR) initiation domain was found near the N terminal of this protein. This protien has the biological function of single stranded incision enzyme.</p><p><b>CONCLUSION</b>The bioinformatics prediction results suggest that MDV NS1 protein plays a key role in viral replication, packaging, and the other stages of viral life.</p>

Preparation and application of Epstein-Barr virus genome-wide genechip / 南方医科大学学报

<p><b>OBJECTIVE</b>To prepare an Epstein-Barr virus (EBV) microarray using known and predicted EBV-coded genes as the cDNA probes to detect the EBV gene expression in nasopharyngeal carcinoma (NPC) tissues.</p><p><b>METHODS</b>The EBV gene probes were amplified by PCR using a pair of primers designed in both sides of the multiple clone site (MCS) of the T/A vector. After purification of the PCR products, 85 EBV genes and 8000 human genes were printed onto the same slide as the detection chip consisting of both EBV and human genes. This genechip was used to detect the differential gene expression in NPC and non-cancerous nasopharynx (NP) tissues.</p><p><b>RESULTS</b>Detection of the human gene expression profile using the prepared genechip resulted in the identification of numerous human genes in the tissue specimens. Some EBV genes were also detected in the tissues using the genechip, but the signals of the genes appeared rather weak without distinctly visible fluorescence, and were not comparable to the strong signal intensities of the human genes.</p><p><b>CONCLUSION</b>The EBV microarray, though constructed successfully, can not meet the needs for clinical application due to the limited detection sensitivity and the relative small quantity of EBV gene expression in NPC samples. Further improvements of the research methods are warranted.</p>

Computer-aided Diagnosis of Gastric Carcinoma B ased on Feature Selection and Probability Neural Network / 现代生物医学进展

Based on signal to noise ratio and probabilistic neural network method associated with experimental data,all analysis model in gastric carcinoma is presented.According to the available information,the samples of gastric carcinoma can be tested and ana.Lyzed.The signal to noise ratio is first calculated．Secondly,records in the database are chosen as a training set to build a probabilistie neural network model and the feature subset is selected according to accuracy.Finally,test set is to test accuracy of model．The model is implemented using MATLAB,and it can be generalized and applied to similar disease auxiliary diagnosis region.

Computer-aided Diagnosis of Gastric Carcinoma B ased on Feature Selection and Probability Neural Network / 现代生物医学进展

Based on signal to noise ratio and probabilistic neural network method associated with experimental data,all analysis model in gastric carcinoma is presented.According to the available information,the samples of gastric carcinoma can be tested and ana.Lyzed.The signal to noise ratio is first calculated．Secondly,records in the database are chosen as a training set to build a probabilistie neural network model and the feature subset is selected according to accuracy.Finally,test set is to test accuracy of model．The model is implemented using MATLAB,and it can be generalized and applied to similar disease auxiliary diagnosis region.

Screening for cervical cancer-related genes and their bioinformatics analysis / 南方医科大学学报

<p><b>OBJECTIVE</b>To better understand the molecular pathogenesis of cervical cancer, and provide novel means for clinical diagnosis and treatment of this malignancy.</p><p><b>METHODS</b>The gene chip data of cervical cancer were obtained from GEO database and statistically analyzed using BRB-ArrayTools to identify the genes related to cervical cancer with bioinformatics analysis using Panther software.</p><p><b>RESULTS</b>Thirty-seven differentially expressed genes were identified in cervical, cancer samples, including 23 up-regulated and 14 down-regulated genes. These genes were associated with the cell skeletons transporters and such processes as cell signal transduction, transcriptional control, cell adhesion, and cell apoptosis.</p><p><b>CONCLUSION</b>Bioinformatics analysis can help with effective analysis of the gene chip data. The pathogenesis of cervical cancer involves abnormal expression of multiple genes, and these data may benefit further investigations of the early diagnosis and treatment of the malignancy.</p>

Effect of Velcade on the gene expression profiles of K562 cells: study of its molecular mechanism / 南方医科大学学报

<p><b>OBJECTIVE</b>To analyze alterations in the gene expression profiles of Velcade-treated K562 cells using bioinformatics methods.</p><p><b>METHODS</b>The total RNAs of Velcade-treated and control K562 cells were amplified and labeled with fluorescent dyes. The labeled RNAs were hybridized to Agilent Human 1A Microarray, and the raw expression data were processed with Agilent Feature Extraction Software. GeneSifter and GATHER were used for data analysis of the differentially expressed genes to perform gene ontology classification, KEGG pathway analysis, functional protein association network construction and literature mining.</p><p><b>RESULTS</b>Totally 228 differentially expressed genes were identified in the Velcade-treated K562 cells. including 84 up-regulated and 144 down-regulated genes. Chymase 1 gene had the greatest down-regulation by 10.80 folds (log ratio), and interferon alpha-21 gene was also down-regulated by 2.31 folds. Gene ontology classification suggested enhanced aging and leukocyte activity. KEGG pathway analysis showed significant impact of Velcade on JAK-STAT signaling pathway, cytotoxicity mediated by natural killer cells, and antigen processing and presentation pathways. Protein-protein interaction analysis revealed that ubiquitin-dependent protein catabolism, antigen presentation and immune response, as well as JAK-STAT signaling pathway were the major elements of the protein network. Literature mining showed that the differentially expressed genes were strongly associated with terms such as leukemia, apoptosis, cell cycle, proteasome, inhibitor, aging and IkappaB, etc.</p><p><b>CONCLUSIONS</b>Velcade may inhibit the cell survival pathways such as NF-kappaB and JAK-STAT signaling pathways to enhance the cytotoxicity and inducing tumor cell apoptosis. Velcade might also be involved in antigen processing and presentation, immune response and inflammation. Chymase 1 gene is probably the key target of Velcade.</p>

Transcriptional regulation of genes involved in liver-selective cell communication / 南方医科大学学报

<p><b>OBJECTIVE</b>To explore the mechanism of transcription regulation of the liver-selective genes responsible for cell communication.</p><p><b>METHODS</b>Tissue-selective Affymetrix probe sets (3919 probes in total) were clustered by functional categories. Liver-selective cell communication (LSCC) genes were selected for further analysis. The 500-bp upstream sequences of all the LSCC genes were extracted for predicting the transcription factor binding sites (TFBS) of known transcription factors (TFs) using 3 programs; literature mining was then performed for these LSCC genes and TFs, and the transcription regulatory network were constructed.</p><p><b>RESULTS</b>The binding sites of 50 and 72 transcription factors were predicted from the upstream sequences of 23 LSCC genes by two programs respectively. Among them, 18 transcription factors were found in common. The top 10 TFBS sequences were basically consistent to the predicted TFs. Literature mining indicated that LSCC genes and TFs were closely related to such terms as albumin, diabetes, glucose, lipid, metabolism, and JNK, in addition to those associated with hepatic tissue and TFs. These observations suggested that LSCC genes and TFs were involved in the regulation of glucose and lipid metabolism, binding and transport, coagulation signal cascades, inflammatory response, etc. PPP2R1B, which was out of the network, showed a partial functional similarity to DUSP10 in the network.</p><p><b>CONCLUSIONS</b>LSCC genes and the predicted TFs may be involved in the regulation of many important functions of the liver, which are integrated into a sophisticated transcription regulatory network. JUN may be the key target for regulation, and PPP2R1B is presumed to participate in the regulation of JUN.</p>

Analysis of SOX4 gene mutation in non-small cell lung cancer tissues / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To investigate the mutation of SOX4 gene in the different tumor tissues with pathological stages and types of non-small cell lung cancer (NSCLC), and to explore its roles in the progression of lung carcinoma.</p><p><b>METHODS</b>The SOX4 gene HMG-box of lung cancer tissues and paracancerous tissues were amplified by PCR, 20 cases shown difference by single strand conformation polymorphyism analysis were sequenced. The DNA sequences were compared with normal sequences by software Clustal and DNAStar.</p><p><b>RESULTS</b>In the 90 NSCLCs, 18 cases were found with mutations of SOX4 gene and were sequenced, and there were 2 mutational points. Seven were detected from squamous cell carcinoma, five from adenocarcinoma and six from adeno-squamous. Three were obtained from tissues in stage I, five in stage II, six in stage III, and four in stage IV. The mutation rate in stage II, III and IV was significantly higher than that in stage I.</p><p><b>CONCLUSION</b>SOX4 gene mutation is not associated with pathology histological types of tumor, but it is significantly associated with pathological stages and the mutation rate increases gradually, which has relation with advanced pathological stages in NSCLC. The results indicate that the SOX4 gene mutations might be related in the lung carcinogenesis and tumor metastasis. The study also provides molecular data for study the links between the mutation of SOX gene and human oncogenesis.</p>

Gene expression profiles of K562 cells treated with total saponin of Panax ginseng / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the effect of the total saponin of Panax ginseng (TSPG) on gene expression profile of K562 cells using microarray technique.</p><p><b>METHODS</b>The total RNA were extracted and purified from K562 cells treated by 200 microg/ml TSPG for 3 days, and untreated K562 cells cultured in parallel served as the control. cRNAs were synthesized and labeled with Cy3 and Cy5 respectively. The labeled cRNA fragments were hybridized with Agilent human 1B 60 mer oligonucleotide microarray, which was then scanned to reveal the changes of gene expression profile in relation to TSPG treatment.</p><p><b>RESULTS</b>Totally 362 differentially expressed genes were identified in TSPG-treated K562 cells, including 20 up-regulated ones (consisting of metabolism-associated genes, signal transduction-associated genes and cell receptor-associated genes etc) and 342 down-regulated ones (consisting of immunity and defense-associated genes, DNA-binding and transcription genes, metabolism-associated genes and cell cycle-associated genes etc). Changes in expressions of FOSL1, E2F2, CCNE2 and ODZ1 were confirmed by semi-quantitative RT-PCR.</p><p><b>CONCLUSIONS</b>TSPG may induce changes in the gene expression profile in k562 cells possibly relevant to the anti-tumor mechanism of TSPG.</p>

Exogenous antizyme 1 gene transfection inhibits proliferation and promotes apoptosis of human neuroblastoma SH-SY5Y cells in vitro / 南方医科大学学报

<p><b>OBJECTIVE</b>To study the effect of antizyme 1 (ZA1) gene transfection on the cell proliferation, cell cycle and apoptosis of human neuroblastoma SH-SY5Y cells in vitro.</p><p><b>METHODS</b>The recombinant eukaryotic expression vector pAZ1m was constructed by cloning mutant AZ1 gene into the vector pEGFP-N1, and subsequently transfected in SH-SY5Y cells. The transfected cell proliferation was examined using MTT assay, and the changes in cell cycle and apoptosis were assayed using flow cytometry analysis. RT-PCR was performed to measure cyclin D1 and caspase-3 mRNA expressions, Western blotting carried out to examine cyclin D1 protein expression, and the changes in caspase-3 activity were detected using a caspase-3 detection kit.</p><p><b>RESULTS</b>AZ1 gene transfection significantly inhibited the proliferation of SH-SY5Y cells, causing cell cycle arrest at G0/G1 stage and down-regulated cyclin D1 and up-regulated caspase-3 expressions. Obviously increased caspase-3 activity was also observed in the transfected cells.</p><p><b>CONCLUSION</b>Exogenous AZ1 gene transfection can inhibit the proliferation and cause cell cycle arrest of SH-SY5Y cells by down-regulating cyclin D1 expression. Up-regulated caspase-3 expression resulting from AZ1 gene transfection may induce apoptosis of the neuroblastoma cells.</p>

Evaluation of Two Different Sample Labeling Methods on Background Signal Intensities for 60 mer Oligonucleotide Microarrays / 中国生物工程杂志

The effects of two different sample labeling methods on background signal intensities for high-density 60mer oligonucleotide microarray were investigated. Peripheral blood samples from five disease and five control subjects were collected. Total RNA targets from peripheral blood mononuclear cells were extracted and labeled with RD-PCR protocol, which were hybridized to Agilent Human 1B oligonucleotide microarrays in a two-color comparative format. The positive control targets were labeled with the directly incorporated fluorescently-labeled dNTP labeling. The SPSS program was performed to test normality of the dataset, variance homogeneity between the groups, coefficients of variation (CV) and analysis of variance. The results showed that the background signal intensities of Cy3 channel were higher than those of Cy5 channel. The differences of background signal intensities between the RD-PCR approach and the directly incorporated fluorescently-labeled dNTP labeling were extremely significant (P- Cy3

Phenotypic analysis of luxS gene deletion mutants and its application in virulence regulation research in group B Streptococcus / 南方医科大学学报

<p><b>OBJECTIVE</b>To explore the mechanism of virulence regulation in group B streptococcus (BGS) by studying LuxS-related AI-2 quorum-sensing pathway in GBS.</p><p><b>METHODS</b>luxS gene deletion mutants of GBS (Delta lusX) were characterized by reverse transcription (RT)-PCR, colony immunoblot analysis, growth curve measurement, and cAMP determination. Functional analysis of luxS in the deletion mutants was conducted by bioluminescence assay.</p><p><b>RESULTS</b>Genetic analysis results showed that the luxS deletion in the mutant 515-Delta lusX caused upregulation of scpB gene expression. Phenotypic analysis revealed that, in comparison with the wild strain, 515-Delta lusX mutant grew slowly in DCM media but quickly in THY media. An approximately two-fold decrement in bioluminescence was detected in the luxS deletion mutants as compared with the wild strain.</p><p><b>CONCLUSION</b>This study confirms the importance of LuxS molecule in the AI-2 quorum-sensing pathway in GBS and provides new insights into the virulence regulation mechanism of GBS.</p>

Construction of a eukaryotic expression plasmid containing gp120 gene of HIV-1 subtype B and its expression in HepG2 cells / 南方医科大学学报

<p><b>OBJECTIVE</b>To construct an eukaryotic expression plasmid containing gp120 gene of HIV-1 subtype B and obtain gp120 gene expression in HepG2 cells.</p><p><b>METHODS</b>According to the published gp120 gene sequence in Genbank, a pair of primers was designed and synthesized. The PCR amplification product of gp120 gene was cloned into pMD-18T vector using TA cloning followed by BamHI and XhoI digestion and sequence analysis. The target gene was then subcloned into a highly efficient eukaryotic expression vector pcDNA3.1 (+). The recombinant plasmid was sequenced and identified by restrictive endonuclease digestion, and transfected into HepG2 cells via liposome. The expression of gp120 gene was analyzed by RT-PCR and Western blotting, respectively.</p><p><b>RESULTS</b>Restriction endonuclease digestion and sequence analysis verified successful construction of the recombinant vector pcDNA3.1(+)/gp120. The target fragment gp120 was identical with U26942 in Genbank, and the expression of gp120 gene was detected in the lysate of the transfected HepG2 cells by RT-PCR and Western blotting.</p><p><b>CONCLUSION</b>The eukaryotic expression plasmid for gp120 has been constructed successfully, which is capable of stable expression in HepG2 cells.</p>

Human cytomegalovirus induces apoptosis of ECV304 endothelial-like cells / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the mechanisms for the cytopathic effect (CPE) of human cytomegalovirus (HCMV) in ECV304 endothelial-like cells.</p><p><b>METHODS</b>PCR and indirect immunofluorescence were used to detect HCMV infection by examining immediate-early (IE) gene and protein expression of the virus in ECV304 cells. Phase-contrast and electron microscopies were performed to observe the morphological changes of the infected and uninfected cells, and DNA ladder analysis and flow cytometry were carried out to study HCMV-induced cell apoptosis.</p><p><b>RESULTS</b>In HCMV-infected ECV304 cells, cytopathic effects were first observed at approximately 72 h post-infection. The cells with CPE changes exhibited detachment from the monolayer, cell rounding and shrinkage. The expression of the IE gene was detected. Chromatin condensation and nuclear fragmentation along with dramatic changes of the mitochondria were observed by electron microscopy at 96 h post-infection. Cellular DNA fragmentation was observed in the infected cells, which had cells apoptotic rates of 4.1% and 45.7% at 96 h and 144 h post-infection, respectively.</p><p><b>CONCLUSION</b>HCMV can induce apoptosis of ECV304 endothelial-like cells.</p>

Effect of S-bioallethrin on human lymphocyte / 南方医科大学学报

<p><b>OBJECTIVE</b>To study the effect of the S-bioallethrin on human lymphocytes by microarray technique.</p><p><b>METHODS</b>The changes of normal human lymphocytes treated with S-bioallethrin were examined with light microscope, flow cytometry, electron microscope, DNA ladder and microarray techniques.</p><p><b>RESULTS</b>Morphological study showed that the lymphocytes underwent apoptosis after S-bioallethrin exposure, which as further confirmed by the expression changes of 346 genes.</p><p><b>CONCLUSION</b>S-bioallethrin can induce apoptosis of normal human lymphocytes and changes in their gene expression profiles.</p>