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Search Results: 1 - 10 of 1180 matches for " Kentaro Yano "
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Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus
Hiromi Nishida,Reina Abe,Taishi Nagayama,Kentaro Yano
International Journal of Evolutionary Biology , 2012, DOI: 10.1155/2012/205274
Abstract: The extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common taxonomic group. Considering the distinct living environments of Deinococcus and Thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. Their guanine-cytosine (GC) contents are similar; however, we hypothesized that their genomic signatures would be different. Our findings indicated that the genomes of Deinococcus radiodurans and Thermus thermophilus have different tetranucleotide frequencies. This analysis showed that the genome signature of D. radiodurans is most similar to that of Pseudomonas aeruginosa, whereas the genome signature of T. thermophilus is most similar to that of Thermanaerovibrio acidaminovorans. This difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor. 1. Introduction In the present bacterial taxonomic system, the extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common lineage with remarkably different characteristics [1, 2]. Comparative genomic analyses have shown that after their divergence from a common ancestor, Deinococcus species seem to have acquired numerous genes from various other bacteria to survive different kinds of environmental stresses, whereas Thermus species have acquired genes from thermophilic archaea and bacteria to adapt to high-temperature environments [3]. For example, the aspartate kinase gene of Deinococcus radiodurans has a different evolutionary history from that of Thermus thermophilus [4]. In addition, D. radiodurans has several unique protein families [5] and genomic characters [6], and there is no genome-wide synteny between D. radiodurans and T. thermophilus [7]. However, phylogenetic analyses based on both orthologous protein sequence comparison and gene content comparison have shown that the genomes of Deinococcus and Thermus are most closely related with each other [3, 8]. The trinucleotide usage correlations have been used to predict the functional similarity between two RecA orthologs of bacteria including D. radiodurans and T. thermophilus [9]. If the genes acquired through horizontal gene transfers are different between Deinococcus and Thermus, then the genomic base composition (GC content) and/or genome signature can be hypothesized to also be different between these 2 genera. However, the GC content
Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions
Sota Fujii, Takushi Toda, Shunsuke Kikuchi, Ryutaro Suzuki, Koji Yokoyama, Hiroko Tsuchida, Kentaro Yano, Kinya Toriyama
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-279
Abstract: Whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria.The present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (Oryza sativa Mitochondrial rna Expression Server: OsMES) is publicly accessible at [http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search webcite].The obvious expansion of its genomic size indicates that higher plant mitochondria experienced a dramatic evolution. The common size of mitochondria genetic information is limited to approximately 16 kb in metazoans [1], whereas in higher plants the sequence length can be 200-2400 kb (Additional file 1) [2]. The principal role of mitochondria (i.e. oxidative phosphorylation) is undoubtedly shared between metazoans and higher plants. The presence of three genes encoding subunits of ATP synthase (atp6 and atp8), three genes encoding subunits of cytochrome oxidase (cox1-cox3), cytochrome b (cob), and seven genes for NADH dehydrogenase (nad1-nad4, nad4L, nad5 and nad6) is indeed conserved in mitochondria of both kingdoms. What is extra in plant mitochondria compared to that of metazoans are only a few more respiratory-related genes (including atp1, atp9, nad7 and nad9) and dozens of genes encoding ribosomal subunits (rps or rpl). Thus, usually a higher plant mitochondrion encodes about 40 genes with known functions, whereas in most cases there are 13 ti
L type Ca2+ channel blockers prevent oxaliplatin-induced cold hyperalgesia and TRPM8 overexpression in rats
Takehiro Kawashiri, Nobuaki Egashira, Kentaro Kurobe, Kuniaki Tsutsumi, Yuji Yamashita, Soichiro Ushio, Takahisa Yano, Ryozo Oishi
Molecular Pain , 2012, DOI: 10.1186/1744-8069-8-7
Abstract: Cold hyperalgesia was assessed by the acetone test. Oxaliplatin (4 mg/kg), sodium oxalate (1.3 mg/kg) or vehicle was injected i.p. on days 1 and 2. Ca2+ (diltiazem, nifedipine and ethosuximide) and Na+ (mexiletine) channel blockers were administered p.o. simultaneously with oxaliplatin or oxalate on days 1 and 2.Oxaliplatin (4 mg/kg) induced cold hyperalgesia and increased in the transient receptor potential melastatin 8 (TRPM8) mRNA levels in the dorsal root ganglia (DRG). Furthermore, oxalate (1.3 mg/kg) significantly induced the increase in TRPM8 protein in the DRG. Treatment with oxaliplatin and oxalate (500 μM for each) also increased the TRPM8 mRNA levels and induced Ca2+ influx and nuclear factor of activated T-cell (NFAT) nuclear translocation in cultured DRG cells. These changes induced by oxalate were inhibited by nifedipine, diltiazem and mexiletine. Interestingly, co-administration with nifedipine, diltiazem or mexiletine prevented the oxaliplatin-induced cold hyperalgesia and increase in the TRPM8 mRNA levels in the DRG.These data suggest that the L type Ca2+ channels/NFAT/TRPM8 pathway is a downstream mediator for oxaliplatin-induced cold hyperalgesia, and that Ca2+ channel blockers have prophylactic potential for acute neuropathy.Oxaliplatin, a platinum-based chemotherapeutic agent, is widely used for treatment of colorectal cancer. However, oxaliplatin frequently causes severe acute and chronic peripheral neuropathies. Acute neuropathy is peculiar to oxaliplatin and includes acral paresthesias enhanced by exposure to cold [1-4]; the acute neuropathy is not attributed to morphological damage to the nerve [5,6]. On the other hand, the chronic neuropathy is characterized by loss of sensory and motor function after long-term oxaliplatin treatment, and it is similar to cisplatin-induced neurological symptoms [4]. Recently, we reported that repeated administration of oxaliplatin induced cold hyperalgesia in the early phase and mechanical allodynia in the l
The Effect of Eating Sea Cucumber Jelly on Candida Load in the Oral Cavity of Elderly Individuals in a Nursing Home
Akira Yano,Akiko Abe,Fumie Aizawa,Hidetoshi Yamada,Kentaro Minami,Miki Matsui,Mitsuo Kishi
Marine Drugs , 2013, DOI: 10.3390/md11124993
Abstract: We conducted a double-blind randomized controlled study of elderly individuals in a nursing home to investigate the effect of the consumption of jelly containing sea cucumber on their oral Candida load. The jelly contained a hydrolysate of the sea cucumber Stichopus japonicus, which contained triterpene glycosides called holotoxins. The holotoxins worked as a fungicide, and their minimum inhibitory concentrations for Candida albicans were 7 μg/mL. Eight individuals in the nursing home took the sea cucumber jelly for a week and their oral Candida were counted before and after the intervention. Nine individuals took a control jelly without S. japonicus. The sea cucumber jelly showed inhibitory effects on the oral Candida. Thus, daily consumption of the S. japonicus jelly has the potential to reduce the oral Candida load in the elderly in nursing homes.
Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms
Erika Asamizu,Kenta Shirasawa,Hideki Hirakawa,Shusei Sato,Satoshi Tabata,Kentaro Yano,Tohru Ariizumi,Daisuke Shibata,Hiroshi Ezura
International Journal of Plant Genomics , 2012, DOI: 10.1155/2012/437026
Abstract: A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423?bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565?bp) and 140,862 were found in heterochromatin (1 per 2,737?bp). The average polymorphism density in the genome was 1 polymorphism per 2,886?bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. 1. Introduction Tomato (Solanum lycopersicum) is one of the most important vegetable crops cultivated worldwide. Tomato has a diploid (2n = 2x = 24) and relatively compact genome of approximately 950?Mb [1]. Recently, its genome has been completely sequenced by the international genome sequencing consortium [2]. Genetic linkage maps of tomato have been created by crossing cultivated tomato (S. lycopersicum) with several wild relatives, S. pennellii, S. pimpinellifolium, S. cheesmaniae, S. neorickii, S. chmielewskii, S. habrochaites, and S. peruvianum [3]. Introgression lines generated from a cross between S. lycopersicum and S. pennellii have contributed to the isolation of important loci and quantitative trait loci (QTLs) related to fruit size by utilizing DNA markers on the Tomato-EXPEN 2000 genetic map [4–9]. Such interspecies genetic mapping is effective because the divergent genomes provide many polymorphic DNA markers. In contrast, intraspecies mapping is less popular in tomato because of the low genetic diversity within cultivated tomatoes that has resulted from the domestication process and subsequent modern breeding [10]. Recently, we developed SNP, simple sequence repeat (SSR), and intronic polymorphic markers using publicly
A New Omics Data Resource of Pleurocybella porrigens for Gene Discovery
Tomohiro Suzuki, Kaori Igarashi, Hideo Dohra, Takumi Someya, Tomoyuki Takano, Kiyonori Harada, Saori Omae, Hirofumi Hirai, Kentaro Yano, Hirokazu Kawagishi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069681
Abstract: Background Pleurocybella porrigens is a mushroom-forming fungus, which has been consumed as a traditional food in Japan. In 2004, 55 people were poisoned by eating the mushroom and 17 people among them died of acute encephalopathy. Since then, the Japanese government has been alerting Japanese people to take precautions against eating the P. porrigens mushroom. Unfortunately, despite efforts, the molecular mechanism of the encephalopathy remains elusive. The genome and transcriptome sequence data of P. porrigens and the related species, however, are not stored in the public database. To gain the omics data in P. porrigens, we sequenced genome and transcriptome of its fruiting bodies and mycelia by next generation sequencing. Methodology/Principal Findings Short read sequences of genomic DNAs and mRNAs in P. porrigens were generated by Illumina Genome Analyzer. Genome short reads were de novo assembled into scaffolds using Velvet. Comparisons of genome signatures among Agaricales showed that P. porrigens has a unique genome signature. Transcriptome sequences were assembled into contigs (unigenes). Biological functions of unigenes were predicted by Gene Ontology and KEGG pathway analyses. The majority of unigenes would be novel genes without significant counterparts in the public omics databases. Conclusions Functional analyses of unigenes present the existence of numerous novel genes in the basidiomycetes division. The results mean that the omics information such as genome, transcriptome and metabolome in basidiomycetes is short in the current databases. The large-scale omics information on P. porrigens, provided from this research, will give a new data resource for gene discovery in basidiomycetes.
An Algorithm for Global Optimization Using Formula Manupulation  [PDF]
Tsutomu Shohdohji, Fumihiko Yano
Applied Mathematics (AM) , 2012, DOI: 10.4236/am.2012.311221
Abstract: Constrained nonlinear optimization problems are well known as very difficult problems. In this paper, we present a new algorithm for solving such problems. Our proposed algorithm combines the Branch-and-Bound algorithm and Lipschitz constant to limit the search area effectively; this is essential for solving constrained nonlinear optimization problems. We obtain a more appropriate Lipschitz constant by applying the formula manipulation system of each divided area. Therefore, we obtain a better approximate solution without using a lot of searching points. The efficiency of our proposed algorithm has been shown by the results of some numerical experiments.
Interactive Fuzzy Approaches for Solving Multiobjective Two-Person Zero-Sum Games  [PDF]
Hitoshi Yano, Ichiro Nishizaki
Applied Mathematics (AM) , 2016, DOI: 10.4236/am.2016.75036
Abstract: In this paper, we consider multiobjective two-person zero-sum games with vector payoffs and vector fuzzy payoffs. We translate such games into the corresponding multiobjective programming problems and introduce the pessimistic Pareto optimal solution concept by assuming that a player supposes the opponent adopts the most disadvantage strategy for the self. It is shown that any pessimistic Pareto optimal solution can be obtained on the basis of linear programming techniques even if the membership functions for the objective functions are nonlinear. Moreover, we propose interactive algorithms based on the bisection method to obtain a pessimistic compromise solution from among the set of all pessimistic Pareto optimal solutions. In order to show the efficiency of the proposed method, we illustrate interactive processes of an application to a vegetable shipment problem.
Remarks on the density of the law of the occupation time for Bessel bridges and stable excursions
Kouji Yano,Yuko Yano
Mathematics , 2007,
Abstract: Smoothness and asymptotic behaviors are studied for the densities of the law of the occupation time on the positive line for Bessel bridges and the normalized excursion of strictly stable processes. The key role is played by these properties for functions defined by Riemann--Liouville fractional integrals.
On $ h $-transforms of one-dimensional diffusions stopped upon hitting zero
Kouji Yano,Yuko Yano
Mathematics , 2014,
Abstract: For a one-dimensional diffusion on an interval for which 0 is the regular-reflecting left boundary, three kinds of conditionings to avoid zero are studied. The limit processes are $ h $-transforms of the process stopped upon hitting zero, where $ h $'s are the ground state, the scale function, and the renormalized zero-resolvent. Several properties of the $ h $-transforms are investigated.
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