Simple and sensitive detection of deoxyribonucleic acid using a RecA-GFP fusion protein-DNA filament as probe

A simple, rapid and highly sensitive method for detection of double-stranded DNA (dsDNA) was developed using a novel fluorescence probe composed of a RecA-GFP fusion protein that had specific recognition of ssDNA complexes (RecA-GFP-DNA filament). The RecA-GFP fusion protein not only had strong fluorescence, but could also occur by homologous recombination. In the presence of the target dsDNA, the complementary ssDNA of the RecA-GFP-DNA filaments invaded one end of the dsDNA chain. In addition, the other end of the ssDNA dissociated the RecA-GFP filaments. An assay of the probe showed a linear relationship with dsDNA concentration in the range 1-11 nM, with a correlation coefficient of 0.9923. The limit of detection for dsDNA was determined experimentally to be 0.3 nM (3δ). Compared with conventional methods, this method has the advantages of simple operation, high specificity, and high sensitivity.

Nitro Sulfonyl Fluorides are a new pharmacophore for the development of antibiotics

The development of antibiotics against Gram-negative bacteria is a central problem in drug discovery. In this report, we demonstrate that aromatic sulfonyl fluorides with a nitro group in their ortho position have remarkable antibacterial activity and are active against drug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), multidrug resistant Acinetobacter baumannii, and Pseudomonas aeruginosa.

Genetic Changes in Sporadic Keratocystic Odontogenic Tumors (Odontogenic Keratocysts)

Little is known about the genetic background of keratocystic odontogenic tumors (KCOT, odontogenic keratocysts). Our aim was to characterize genomic aberrations in sporadic KCOT using cDNA-expression arrays and array-comparative genomic hybridization. For cDNA-expression arrays, 10 KCOT specimens and 20 fetal tooth germs were studied. Quantitative real-time reverse-transcription/polymerase chain-reaction and immunohistochemical studies were also undertaken. Several genes were over-expressed in 12q13, including cytokeratin 6B ( KRT6B) (≈ 10-fold), epidermal growth factor receptor ERBB3 (~ 4.7-fold), and glioma-associated oncogene homologue 1 ( GLI1) (~ 5- to 12-fold). One amplicon (~ 0.7 Mega base pairs [Mbp]), covering several genes involved in the regulation of cell growth, was found in 12q13.2. Deletions were found in 3q13.1, 5p14.3, and 7q31.3, including the cell-adhesion-related gene cadherin 18 ( CDH18) and leukocyte cell adhesion molecule ( ALCAM, MEMD). Over-expressed and amplified genes in 12q13, also reported in several other tumors and cell lines, may contribute to the persistent growth characteristics of KCOT.

Microarray and quantitative RT-PCR analyses in calcium-channel blockers induced gingival overgrowth tissues of periodontitis patients

OBJECTIVES

The purpose of the present study was to analyse transcriptomes and mRNA expression levels for specific genes in calcium-channel blocker-induced gingival overgrowth (GO) tissues.

DESIGN

Eight gingival tissues samples (from both GO negative and positive sites) were harvested from four GO patients for microarray analyses. Twelve candidate genes were selected for further quantitative real time reverse transcription-polymerase chain reaction (qRT-PCR) analyses. Ten GO tissues from periodontitis patients and ten control gingival tissues from healthy subjects were compared by qRT-PCR. Mann-Whitney U-test was used for statistical evaluation.

RESULTS

In GO positive tissues, 163-1631 up-regulated and 100-695 down-regulated genes were identified with more than two-fold changes compared with GO negative tissues amongst patients by microarray experiments. No commonly expressed genes amongst the eight sets of microarray data were found. The clustering analysis confirmed that the entire transcriptome patterns showed similarities in individuals, but differences amongst the four patients. The qRT-PCR and statistical analyses for the candidate genes, though, revealed differential gene expressions between GO-positive and negative tissues. We found that matrix metalloproteinase (MMP)-1 and MMP-12 as well as cathepsin-L were significantly up-regulated whilst keratin-10 and transforming growth factor-β1 were significantly down-regulated in GO tissues of periodontitis patients compared with the control gingival tissues of healthy subjects.

CONCLUSION

The microarray analyses revealed that GO pathogenesis was complex and individually varied, though GO-affected gingival tissues were controlled at least by genes related to collagen metabolisms including regulated MMPs, cathepsin-L, growth factors, and keratins to maintain tissue homeostasis in vivo.

Gene expression analysis by cDNA microarray in oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) is common type of human cancer, but little is known about the molecular mechanisms deciding on this malignancy. Comprehensive gene expression profiling is essential for understanding OSCC.

METHODS

cDNA microarray was used to analyze expression patterns of 16 617 genes in nine OSCC patients.

RESULTS

Forty-seven genes with altered expression among all cases were extracted. The ontology of these 47 genes was classified into 10 categories. To validate the microarray data, the expression of genes, including TGFBI, FADD and DUSP1 was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR). By hierarchical clustering analysis, the nine cases were divided into two clusters.

CONCLUSIONS

The 47 genes are suggested as having a functional significance in oral squamous cell carcinogenesis. It is also suggested that the gene expression patterns by hierarchical clustering analysis can represent degrees of differentiation. The postoperative recovery was uneventful and patients free from tumor after surgery. In the future, on the occasion when the time comes that the number of cases accumulated for microarray increases and each case is observed more over a long-term, these data of 5-year survival rate will be added. Thereby, it will become possible to represent the malignancy of OSCC by these gene expression patterns.

Identification of potential biomarkers of lymph node metastasis in oral squamous cell carcinoma by cDNA microarray analysis

We surveyed the expression of 557 cancer-related genes in 15 cases of well-differentiated OSCC by cDNA microarray analysis. To identify potential biomarkers for lymph node metastasis, all microarray data were compared by the Mann-Whitney test and the significance analysis of microarrays between OSCCs with and those without lymph node metastasis. The tissues of OSCCs with lymph node metastasis exhibited increased expression levels of MMP-1, MMP-3, uPA, integrin-alpha3, paxillin, tenascin C and IL-6 transcripts. All of these genes were included in common clusters on the Cluster/TreeView analysis, implying that functional gene groups of proteolytic enzymes and integrin-related molecules are involved in cervical lymph node metastasis. The results of RTQ-PCR for differentially expressed genes were in accord with those of cDNA microarray analyses, suggesting that the data obtained by microarray gene expression analyses were valid. Consistent with cooperative expression patterns, immunohistochemical analyses demonstrated that products of MMP-1, MMP-3 and uPA were colocalized to components of the neoplastic stroma, particularly mononuclear inflammatory cells with well-developed eosinophilic cytoplasm. Our results suggest that expression levels of molecules involved in tissue remodeling and cell-ECM adhesion, especially MMP-1 and integrin-alpha3, can provide an accurate biomarker system for predicting the risk of cervical lymph node metastasis in OSCC.

Gene expression profiling of ameloblastoma and human tooth germ by means of a cDNA microarray

The molecular and genetic characteristics of ameloblastoma are still poorly understood. We analyzed gene expression in fresh-frozen ameloblastomas and human fetal tooth germs, using a cDNA microarray. Thirty-four genes exhibited significant changes in expression levels in the ameloblastoma. Eleven genes were overexpressed more than three-fold, and 23 genes were underexpressed to below 0.4 of the control level. The oncogene FOS was the most overexpressed gene (from eight- to 14-fold), followed by tumor-necrosis-factor-receptor 1 (TNFRSF1A). Genes for sonic hedgehog (SHH), TNF-receptor-associated-factor 3 (TRAF3), rhoGTP-ase-activating protein 4 (ARHGAP4), deleted in colorectal carcinoma (DCC), cadherins 12 and 13 (CDH12 and 13), teratocarcinoma-derived growth-factor-1 (TDGF1), and transforming growth-factor-beta1 (TGFB1) were underexpressed in all tumors. In selected genes, a comparison between cDNA microarray and real-time RT-PCR confirmed similar relative gene expression changes. The gene expression profile identifies candidate genes that may be involved in the origination of ameloblastoma and several genes previously unidentified in relation to human tooth development.