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251.
252.
The identification of novel miRNAs has significant biological and clinical importance. However, none of the known miRNA features alone is sufficient for accurately detecting novel miRNAs. The aim of this paper is to integrate these features in a straightforward manner for detecting miRNAs with better accuracy. Since most miRNA regions are highly conserved among vertebrates for the ability to form stable hairpin structures, we implemented a hidden Markov model that outputs multidimensional feature vectors composed of both evolutionary features and secondary structural ones. The proposed method, called miRRim, outperformed existing ones in terms of detection/prediction performance: The total number of predictions was smaller than with existing methods when the number of miRNAs detected was adjusted to be the same. Moreover, there were several candidates predicted only by our method that are clustered with the known miRNAs, suggesting that our method is able to detect novel miRNAs. Genomic coordinates of predicted miRNA can be obtained from http://mirrim.ncrna.org/. 相似文献
253.
Using gene cloning and in silico cloning, we analyzed the structures of hatching enzyme gene orthologs of vertebrates. Comparison led to a hypothesis that hatching enzyme genes of Japanese eel conserve an ancestral structure of the genes of fishes, amphibians, birds and mammals. However, the exon-intron structure of the genes was different from species to species in Teleostei: Japanese eel hatching enzyme genes were 9-exon-8-intron genes, and zebrafish genes were 5-exon-4-intron genes. In the present study, we further analyzed the gene structures of fishes belonging to Acanthopterygii. In the species of Teleostei we examined, diversification of hatching enzyme gene into two paralogous genes for HCE (high choriolytic enzyme) and LCE (low choriolytic enzyme) was found only in the acanthopterygian fishes such as medaka Oryzias latipes, Fundulus heteroclitus, Takifugu rubripes and Tetraodon nigroviridis. In addition, the HCE gene had no intron, while the LCE gene consisted of 8 exons and 7 introns. Phylogenetic analysis revealed that HCE and LCE genes were paralogous to each other, and diverged during the evolutionary lineage to Acanthopterygii. Analysis of gene synteny and cluster structure showed that the syntenic genes around the HCE and LCE genes were highly conserved between medaka and Teraodon, but such synteny was not found around the zebrafish hatching enzyme genes. We hypothesize that the zebrafish hatching enzyme genes were translocated from chromosome to chromosome, and lost some of their introns during evolution. 相似文献
254.
Kato S Shimizu-Ibuka A Mura K Takeuchi A Tokue C Arai S 《Bioscience, biotechnology, and biochemistry》2007,71(12):3007-3013
An alpha-amylase secreted by Pichia burtonii 15-1 isolated from a traditional starter murcha of Nepal, named Pichia burtonii alpha-amylase (PBA), was studied. The gene was cloned and its nucleotide sequence was determined. PBA was deduced to consist of 494 amino acid residues. It shared certain degrees of amino acid sequence identity with other homologous proteins: 60% with Schwanniomyces occidentalis alpha-amylase, 58% with Saccharomycopsis sp. alpha-amylase, and 47% with Taka-amylase A from Aspergillus oryzae. A three-dimensional structural model of PBA generated using the known three-dimensional structure of Taka-amylase A as a template suggested high structural similarity between them. Kinetic analysis revealed that the K(m) values of PBA were lower than those of Taka-amylase A for the oligosaccharides. Although the k(cat) values of PBA were lower than those of Taka-amylase A for the oligosaccharide substrates, the k(cat)/K(m) values of PBA were higher. 相似文献
255.
Sato E Niwano Y Matsuyama Y Kim D Nakashima T Oda T Kohno M 《Bioscience, biotechnology, and biochemistry》2007,71(3):704-710
Recent studies indicate that some raphidophycean red tide flagellates produce substances able to scavenge superoxide, whereas there have been no reports on superoxide scavenger production by dinophycean red tide flagellates. In this study, we examined the superoxide-scavenging activity of aqueous extracts from dinophycean red tide flagellates, Gymnodinium spp., Scrippsiella trochoidea, and Karenia sp., by a luminol analog L-012-dependent chemiluminescence (CL) method and an electron spin resonance (ESR)-spin trapping method, and compared the activity to that of raphidophycean red tide flagellates, Chattonella spp., Heterosigma akashiwo, and Fibrocapsa japonica. In the experiment applying the L-012-dependent CL method, only the aqueous extracts from raphidophycean red tide flagellates showed superoxide-scavenging activity. On the other hand, applying the ESR-spin trapping method, we found that the aqueous extracts from dinophycean red tide flagellates also showed superoxide-scavenging activity. This is the first report on the production of a superoxide-scavenger by dinophycean red tide flagellates. 相似文献
256.
257.
Niwano Y Sato E Kohno M Matsuyama Y Kim D Oda T 《Bioscience, biotechnology, and biochemistry》2007,71(5):1145-1153
The antioxidant properties of aqueous extracts from the dinophycean flagellates Gymnodinium impudicum and Alexandrium affine and the raphidophycean flagellate Chattonella ovata were examined. An electron spin resonance (ESR)-spin trapping method coupled with steady state kinetic analysis showed that all of the extracts directly scavenge superoxide, and that the superoxide scavenging potential of any of the extracts was comparable to that of L-ascorbic acid. As for hydroxyl radical scavenging, the Fenton reaction and the method of ultraviolet radiation to hydrogen peroxide were used as hydroxyl radical generation systems. All of extracts reduced the level of hydroxyl radicals in both of the systems, indicating that the extracts also directly scavenge hydroxyl radicals. Since the levels of phenolic compounds did not correlate with the antioxidant activities of the extracts, substances other than phenolic compounds also appeared to be attributable to the activities. It is of our interest that the scavenging activities of extract from G. impudicum against superoxide and hydroxyl radicals were increased by heat exposure at 100 degrees C and 200 degrees C respectively. Although the reason for the increased activities of the aqueous extract from G. impudicum is not clear, the heat-resistance of the extract from G. impudicum might make it a desirable antioxidant. 相似文献
258.
Ko-ichiro Miyamoto Parida Yamada Ryo-taro Yamaguchi Takami Muto Ayumi Hirano Yasuo Kimura Michio Niwano Hiroko Isoda 《Cytotechnology》2007,55(2-3):143-149
In this study, we report on an in situ monitoring system of living cultured cells using infrared absorption spectroscopy in
the geometry of multiple internal reflections (MIR-IRAS). In order to observe living cultured cells, the temperature in the
sample chamber of a FT-IR spectrometer was maintained at 37 °C and a humidified gas mixture containing 5% CO2 was introduced into the sample chamber. Human breast cell line MCF-7 cultured on Si MIR prisms were placed in the sample
chamber and infrared spectra of MCF-7 cells were collected for 5 h. It was found that the adhesion and metabolism of MCF-7
cells could be monitored by the absorption intensity of amide-II protein band (1,545 cm−1) and also by the absorption intensities of CH
x
bands (2,700–3,100 cm−1). These results suggest that our system is useful for a nondestructive and non-label monitoring of cell viability. Our method
based on infrared absorption spectroscopy has a potential for bioscreening application. 相似文献
259.
Enzymatic activities of uridine and thymidine phosphorylase in normal and cancerous uterine cervical tissues 总被引:1,自引:0,他引:1
Kobayashi Y Wada Y Ohara T Okuda Y Suzuki N Hasegawa K Kiguchi K Ishizuka B 《Human cell》2007,20(4):107-110
In this study, the preliminary analyses were conducted of enzymatic activities of uridine phosphorylase (UP) and thymidine phosphorylase (TP) in normal tissues and cancer tissues of the uterine cervix. The study was performed on 27 patients of cervical cancer, treated first in our hospital. Normal cervical tissues obtained from 15 patients undergoing hysterectomy for benign diseases were used as controls. The supernatant of the homogenated cervical tissues and the stroma (5-FU and ribose-1-P or deoxyribose-1-P) were analyzed by high performance liquid chromatography, and then the UP and TP activities calculated. TP activity was significantly greater than UP activity (P < 0.0001). Both UP and TP showed significantly greater activity in cancer tissues than in normal tissues (P < 0.0001). In the TP activity of the cancer tissues, there was no significant difference among the histological types, while the TP activity tended to be significantly higher in the cases with lymph node metastasis. These results showed that the TP-mediated route seemed important as the 5FU metabolic pathway in the uterine cervical tissues, and TP enzymatic activity might be associated with lymph node metastasis. 相似文献
260.
The phosphatidylinositol 3-kinase-Akt (PI3K-Akt) pathway and the mitogen activated protein kinase (MAPK) pathway are important in the development and proliferation of various human cancers. It has been found recently that ursolic acid treatment affects growth and apoptosis in cancer cells. We sought to determine whether prominent signaling pathways, including the PI3K-Akt pathway and the MAPK (JNK, P38, and P44/42) pathway mediate these effects. Endometrial cancer cells often have high levels of phosphorylated Akt seen in conjunction with a PTEN mutation or deletion. Elevation in Akt protects the cancer cell from apoptosis. Ursolic acid treatment moderately decreased PI3K levels in SNG-II cells. Treatment also decreased phospho-Akt and phospho-P44/42 in a dose- and time-dependent fashion, dramatically in SNG-II cells and moderately in HEC108 cells. This effect was most pronounced following treatment with 50 mum ursolic acid for 72 h. Our study found inhibition of both the PI3K-Akt pathway and the MAPK pathway in two endometrial cancer cell lines, SNG-II and the poorly differentiated HEC108 cell line. 相似文献