Cell-penetrating Effects and Repair of Cell Oxidative Damage of TAT-metallothionein Fusion Proteins / 中国生物化学与分子生物学报

The human Immunodeficiency Virus Transactivator (TAT) protein transduction peptide is a trans-transcription activator encoded by HIV-1. It is rich in basic amino acids, and capable of efficiently mediating the passage of exogenous macromolecules through a variety of membrane structures, such as the cytoplasmic membrane and the blood-brain barrier. Metallothionein (MT) is a protein with low molecular weights and rich cysteine contents. It plays important roles in maintaining the dynamic balance of metal contents in the body, in the detoxification of heavy metals and in defense against oxidative stress. Based on the full-length MT cDNA previously cloned from Sinopotamon henanense, we aim to prepare a TAT-mediated recombinant fusion protein that can cross the membrane and enter the cell by means of genetic engineering. The hydroxyl radical scavenging rate and total antioxidant capacity of TAT-MT were measured in vitro. An immunofluorescence technique was used to detect the transmembrane activity. An MTT assay was used to study the repair effect of H

Cloning,expression and characterization of chalcone isomerase from medicinal plant Chinese sumac (Rhus chinensis) / 中国中药杂志

Flavonoids are a group of secondary metabolites found in plants. They have many pharmacological functions and play an important role in Chinese sumac( Rhus chinensis),which is a well-known traditional Chinese medicinal plant. Chalcone isomerase( CHI,EC 5. 5. 1. 6) is one of the key enzymes in the flavonoids biosynthesis pathway. In this paper,the full-length c DNA sequence encoding the chalcone isomerase from R. chinensis( designated as Rc CHI) was cloned by RT-PCR and rapid-amplification of c DNA Ends( RACE). The Rc CHI c DNA sequence was 1 058 bp and the open reading frame( ORF) was 738 bp. The ORF predicted to encode a 245-amino acid polypeptide. Rc CHI gene contained an intron and two exons. The sequence alignments revealed Rc CHI shared47. 1%-71. 6% identity with the homologues in other plants. Real-time PCR analysis showed that the total flavonoid levels were positively correlated with tissue-specific expressions of Rc CHI mRNA in different tissues. The recombinant protein was successfully expressed in an Escherichia coli strain with the p GEX-6 P-1 vector. In this paper,the CHI gene was cloned and characterized in the family of Anacardiaceae and will help us to obtain better knowledge of the flavonoids biosynthesis of the flavonoid compounds in R. chinensis.

Research on chemotaxis response of Alternaria panax to amino acid of ginseng root exudates / 中国中药杂志

Plate assay and spore germination method were used to study the chemotaxis response of Alternaria panax to arginine, glutamic acid, aspartic acid and threonine. The result showed that the optimum temperature of A. panax chemotaxis response to four amino acids were all 25 ℃. And chemotaxis responses of A. panax were different under conditions of different concentration and pH value. The chemotaxin reached to the highest under the condition of 2 mg•L⁻¹ and pH value was 7 for arginine, glutamic acid and threonine while 20 mg•L⁻¹ and pH value was 6 for aspartic acid . The data of chemotactic migration index (CMI) were 1.24, 1.38, 1.27, 1.31 and chemotactic growth rates(CGR) were 0.451 0, 0.353 0, 0.381 3, 0.228 8 and spores germination rates(SGR) were 57.33%，63%，56.67%，58% and the dry weight of mycelial (DWM) were 372.9, 348.5, 314.4, 390.2 mg•L⁻¹ respectively. It indicated that the low and middle concentration of amino acid had significant promoting effect on chemotaxis response of A. panax. As important substances generated in ginseng root, amino acids exhibited an efficient chemotactic effect on A. panax, and some even show inhibition effect under high concentration.

Chemotaxis response of Erwinia carotovora on sugars and amino acids of root exudates of Panax ginseng / 中国中药杂志

The chemotaxis response of Erwinia carotovora to different sugars and amino acids in four kinds of chemotactic parameters (concentration, time, temperature and pH ) was determined by capillary method. The results showed that when pH was 8, concentration was 0.025 mg•L ⁻¹, culture temperature was 25 ℃ and the duration was 60 minutes, the optimal chemotaxis rate of lysine was 2.509,when pH was 6, concentration was 0.25 mg•L ⁻¹, culture temperature was 25 ℃ and the duration was 60 minutes, the optimal chemotaxis rate of arginine was 2.218 8,when pH was 7, concentration was 0.25 mg•L ⁻¹, culture temperature was 30 ℃ and the duration was 60 minutes, the optimal chemotaxis rate of L-rhamnose was 3.091 2, when pH was 6, concentration was 0.25 mg•L ⁻¹, culture temperature was 30 ℃ and the duration was 45 minutes, the optimal chemotaxis rate of D-arabinose was 3.026 3. Sugars and amino acids had obvious chemotaxis with E. carotovora,the high concentration of carbohydrate and amino acid exited an inhibitory effect on chemotaxis response of E. carotovora, and the chemotaxis response decreased with the increase of concentration of carbohydrates and amino acids.

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>

Survey of the evolutionary characteristics of influenza H1N1 hemagglutinin gene HA1 in 2000-2009 / 南方医科大学学报

<p><b>OBJECTIVE</b>To study the global evolutionary characteristics of hemagglutinin gene HA1 of influenza H1N1 infecting different species during 2000-2009.</p><p><b>METHODS</b>The target sequences were downloaded from NCBI and analyzed using bioinformatic software to construct the phylogenetic tree.</p><p><b>RESULTS</b>The HA1 amino acid sequences of influenza H1N1 contained four mutated antigenic sites and receptor-binding sites, and the novel influenza virus shared most of the mutated amino acid sites with swine H1N1 influenza virus.</p><p><b>CONCLUSION</b>The HA1 gene of novel influenza virus might originate from the early swine H1N1 influenza virus from North America, and in the evolutionary process, a number of important sites of HA1 gene mutated to result in the outbreak of influenza.</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>

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>

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>

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>

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>

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>

Signal pathway in apoptosis of K562 cells induced by STI571 / 中国实验血液学杂志

This study was aimed to investigate the effect of tyrosine kinase inhibitor (STI571) on growth and proliferation of K562 cells by using microarray method, the changes of gene expression in the process of K562 cell apoptosis induced by STI571 and the mechanism of K562 cell apoptosis. The gene microarray probes were prepared by RD-PCR technique, then the microarray of gene expression map was constructed; the morphologic changes of K562 cells were observed under phase-contrast microscopy before and after treatment with STI571; the apoptosis of K562 cells treated with STI571 was assayed by MTT method; the expression level of genes was analyzed by self-made microarray. The results indicated that after the treatment of STI571 for 24 hours, in K562 cells appeared major morphological changes, which included nuclear shrinkage, membrane bleb and scattered apoptotic bodies. DNA gel electrophoresis also showed that the typical "DNA ladder" phenomena existed in the treated group. After hybridization, detection and analysis with microarray method, expression of 9 genes significantly down-regulated and expression of 4 genes up-regulated. These differentially expressed genes included cell cycle related genes, cell metabolizing pathway related genes, signal transduction and transcription regulation related genes and antiapoptosis genes. It is concluded that STI571 can effectively inhibit the K562 cell growth and induce K562 cell apoptosis. The genes screened from this microarray offer new information for exploration of pathogenesis of K562 cell malignant transformation and shows abundant potential targets for the treatment of CML.

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>

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>

Preparation and application of oligo microarrays for hepatitis virus detection and genotyping / 中华肝脏病杂志

<p><b>OBJECTIVE</b>To prepare oligo microarrays for hepatitis virus detection and genotyping.</p><p><b>METHODS</b>By analyzing the DNA or cDNA of HBV, HDV and 4 different genotypes of HCV with the BLAST program, a group of specific sequences for the candidate probes was specified. Array Designer 3.0 software was applied to analyze the candidates to select probes with high specificity, identical length and similar melting temperature (Tm). Altogether 16, 8 and 68 oligonucleotide probes were designed for diagnosis of HBV, HDV, and genotyping HCV. Following the synthesizing and purification, oligo probes were deposited on oligonucleotide chips as microarrays for hepatitis virus detection and genotyping. The samples were labeled by RD-PCR method. Hybridization results were analyzed to cross out those probes with low specificity and sensitivity, and those with signal to noise ratios (SNR) less than 4.0.</p><p><b>RESULTS</b>Two types of gene chips were successfully developed: microarrays for HBV and HDV simultaneous detection and for HCV genotyping.</p><p><b>CONCLUSION</b>Using oligo probes to construct gene chips for clinical diagnosis of hepatitis virus is a simple and effective method. It may be widely used in detecting hepatitis viruses and their genotyping in clinical settings.</p>