Visualization of the homology information is an important method to analyze the evolutionary and functional meanings of genes. With a database containing model genomes of Homo sapiens, Mus muculus, and Rattus norvegicus, we constructed a web-based comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale. The user interface has several features: it marks regions whose identity is greater than that specified, it shows or hides gaps from the result of global sequence alignment, and it inverts the graph when total identity is higher than the threshold specified.
Animals ; Genome ; Genomics* ; Humans ; Mice ; Rats ; Sequence Alignment

PURPOSE: Current treatment of glioblastoma after surgery consists of a combination of fractionated radiotherapy and temozolomide. However, it is difficult to completely remove glioblastoma because it has uncertain boundaries with surrounding tissues. Moreover, combination therapy is not always successful because glioblastoma has diverse resistances. To overcome these limitations, we examined the combined effects of chemotherapy and knockdown of mitogen-activated protein kinase phosphatase-1 (MKP-1). MATERIALS AND METHODS: We used ten different anti-cancer drugs (cisplatin, cyclophosphoamide, doxorubicin, epirubicin, etoposide, 5-fluorouracil, gemcitabine, irinotecan, mitomycin C, and vincristine) to treat glioblastoma multiforme (GBM) cells. Knockdown of MKP-1 was performed using siRNA and lipofectamine. The basal level of MKP-1 in GBM was analyzed based on cDNA microarray data obtained from the Gene Expression Omnibus (GEO) databases. RESULTS: Anti-cancer drug-induced cell death was significantly enhanced by knockdown of MKP-1, and this effect was most prominent in cells treated with irinotecan and etoposide. Treatment with these two drugs led to significantly increased phosphorylation of c-Jun N-terminal kinase (JNK) in a time-dependent manner, while pharmacological inhibition of JNK partially inhibited drug-induced cell death. Knockdown of MKP-1 also enhanced drug-induced phosphorylation of JNK. CONCLUSION: Increased MKP-1 expression levels could be the cause of the high resistance to conventional chemotherapeutics in human GBM. Therefore, MKP-1 is an attractive target for overcoming drug resistance in this highly refractory malignancy.
Apoptosis ; Camptothecin ; Cell Death ; Dacarbazine ; Deoxycytidine ; Doxorubicin ; Drug Resistance ; Drug Resistance, Multiple ; Dual Specificity Phosphatase 1 ; Epirubicin ; Etoposide ; Fluorouracil ; Gene Expression ; Glioblastoma ; Humans ; JNK Mitogen-Activated Protein Kinases ; Lipids ; Mitomycin ; Oligonucleotide Array Sequence Analysis ; Phosphorylation ; Phosphotransferases ; Protein Kinases ; RNA, Small Interfering

Background and purpose: The availability and promise of effective treatments for neurodegenerative disorders are increasing the importance of early diagnosis. Having molecular and biochemical markers of Alzheimer's disease (AD) would complement clinical approaches, and further the goals of early and accurate diagnosis. Combining multiple biomarkers in evaluations significantly increases the sensitivity and specificity of the biochemical tests. Methods: In this study, we used color-coded bead-based Luminex technology to test the potential of using chemokines and cytokines as biochemical markers of AD. We measured the levels of 22 chemokines and cytokines in the serum and cerebrospinal fluid (CSF) of 32 de novo patients (13 controls, 11 AD, and 8 Parkinson's disease [PD]). Results: MCP-1 was the only cytokine detectable in CSF, and its levels did not differ between control and disease groups. However, the serum concentration of eotaxin was significantly higher in AD patients than in the control group. Conclusions: The analysis of multiple inflammatory mediators revealed marginal differences in their CSF and serum concentrations for the differential diagnosis of AD and PD. These results provide evidence that immunological responses are not major contributors to the pathogenesis of AD and PD.
Alzheimer Disease ; Biomarkers ; Chemokines ; Complement System Proteins ; Cytokines ; Diagnosis, Differential ; Early Diagnosis ; Humans ; Neurodegenerative Diseases ; Parkinson Disease ; Sensitivity and Specificity