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Search Results: 1 - 10 of 4515 matches for " Hiroshi Ezura "
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Systematic Development of Tomato BioResources in Japan
Tohru Ariizumi,Koh Aoki,Hiroshi Ezura
Interdisciplinary Bio Central , 2011,
Abstract: Recently, with the progress of genome sequencing, materials and information for research on tomato (Solanum lycopersicum) have been systematically organized. Tomato genomics tools including mutant collections, genome sequence information, full-length cDNA and metabolomic datasets have become available to the research community. In Japan, the National BioResource Project Tomato (NBRP Tomato) was launched in 2007, with aims to collect, propagate, maintain and distribute tomato bioresources to promote functional genomics studies in tomato. To this end, the dwarf variety Micro-Tom was chosen as a core genetic background, due to its many advantages as a model organism. In this project, a total of 12 000 mutagenized lines, consisting of 6000 EMS-mutagenized and 6000 gamma-ray irradiated M2 seeds, were produced, and the M3 offspring seeds derived from 2236 EMS-mutagenized M2 lines and 2700 gamma-ray irradiated M2 lines have been produced. Micro-Tom mutagenized lines in the M3 generation and monogenic Micro-Tom mutants are provided from NBRP tomato. Moreover, tomato cultivated varieties and its wild relatives, both of these are widely used for experimental study, are available. In addition to these bioresources, NBRP Tomato also provides 13 227 clones of full-length cDNA which represent individual transcripts non-redundantly. In this paper, we report the current status of NBRP Tomato and its future prospects.
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
Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment
Miyako Kusano,Henning Redestig,Tadayoshi Hirai,Akira Oikawa,Fumio Matsuda,Atsushi Fukushima,Masanori Arita,Shin Watanabe,Megumu Yano,Kyoko Hiwasa-Tanase,Hiroshi Ezura,Kazuki Saito
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016989
Abstract: As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms.
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
Koh Aoki, Kentaro Yano, Ayako Suzuki, Shingo Kawamura, Nozomu Sakurai, Kunihiro Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Taneaki Tsugane, Manabu Watanabe, Kazuhide Ooga, Maiko Torii, Takanori Narita, Tadasu Shin-i, Yuji Kohara, Naoki Yamamoto, Hideki Takahashi, Yuichiro Watanabe, Mayumi Egusa, Motoichiro Kodama, Yuki Ichinose, Mari Kikuchi, Sumire Fukushima, Akiko Okabe, Tsutomu Arie, Yuko Sato, Katsumi Yazawa, Shinobu Satoh, Toshikazu Omura, Hiroshi Ezura, Daisuke Shibata
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-210
Abstract: To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%.The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ webcite via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp webcite.The Solanaceae family comprises 1000-2000 species that show wide morphological variability and ecological adaptability [1]. This taxon includes a number of vegetable crops including fruit-bearing vegetables, tuber-bearing vegetables, and ornamental plants, many of which have economic importan
Distribution of Aeromonas spp. Emphasizing on a Newly Identified Species Aeromonas sp. T8 Isolated from Fish and Aquatic Animals in Southeast Asia
M.M. Rahman,T. Somsiri,K. Tajima,Y. Ezura
Pakistan Journal of Biological Sciences , 2004,
Abstract: Distribution pattern of a collection of 106 Aeromonas strains isolated from both healthy and epizootic ulcerative syndrome (EUS)-affected fish, septicaemic disease affected frog and turtle in Bangladesh, Japan, Malaysia, Philippines and Thailand was investigated. The study was conducted through the physio-biochemical characterization of the strains and subsequent confirmation by analysis of the 16S rDNA sequences of some randomly chosen representative strains from all identified phenotype. Special emphasis was given to confirm a group of strains, which belonged to a newly identified species Aeromonas sp. T8 by DNA-DNA hybridization method. The newly identified species Aeromonas sp. T8 group was particularly found in different species of EUS-affected fish in Philippines and Thailand. A. hydrophila subsp. hydrophila and A. hydrophila subsp. ranae was recovered from EUS of fish and septicaemic diseases of frog and turtle. A. hydrophila subsp. hydrophila was distributed in Bangladesh and Thailand while A. hydrophila subsp. ranae was found only in Thailand. A. veronii biotype sobria and A. veronii biotype veronii was found to be dispersed mostly in EUS-affected fish in different countries. A. jandaei was obtained from EUS-positive fish in Bangladesh and Malaysia but A. media from healthy fish in Bangladesh.
Behaviour of Ru(bpy)2+3 on the Surface of Water-Soluble Single-Walled Carbon Nanotubes on Adding Other Cations  [PDF]
Hiroshi Shioyama
Journal of Surface Engineered Materials and Advanced Technology (JSEMAT) , 2012, DOI: 10.4236/jsemat.2012.22015
Abstract: Behaviour of excited Ru(bpy)2+3 bound to the surface of water-soluble single-walled carbon nanotubes on addition of other cations have been investigated by measuring Ru(bpy) luminescence. In contrast to what was observed with a solution containing rod-like aggregation particles of Nafion, we found that Ru(bpy)2+3 has a stronger attraction than that of other cations to the sulfonic groups on the carbon nanotubes. Such a difference is attributed to the unique micro-environmental characteristics of the molecular assemblies.
Extension of Smoothed Particle Hydrodynamics (SPH), Mathematical Background of Vortex Blob Method (VBM) and Moving Particle Semi-Implicit (MPS)  [PDF]
Hiroshi Isshiki
American Journal of Computational Mathematics (AJCM) , 2014, DOI: 10.4236/ajcm.2014.45036
Abstract: SPH has a reasonable mathematical background. Although VBM and MPS are similar to SPH, their ma-thematical backgrounds seem fragile. VBM has some problems in treating the viscous diffusion of vortices but is known as a practical method for calculating viscous flows. The mathematical background of MPS is also not sufficient. Not with standing, the numerical results seem reasonable in many cases. The problem common in both VBM and MPS is that the space derivatives necessary for calculating viscous diffusion are not estimated reasonably, although the treatment of advection is mathematically correct. This paper discusses a method to estimate the above mentioned problem of how to treat the space derivatives. The numerical results show the comparison among FDM (Finite Difference Method), SPH and MPS in detail. In some cases, there are big differences among them. An extension of SPH is also given.
The Effective Chiral Model of Quantum Hadrodynamics Applied to Nuclear Matter and Neutron Stars  [PDF]
Hiroshi Uechi
Journal of Applied Mathematics and Physics (JAMP) , 2015, DOI: 10.4236/jamp.2015.32017
Abstract:

We review theoretical relations between macroscopic properties of neutron stars and microscopic quantities of nuclear matter, such as consistency of hadronic nuclear models and observed masses of neutron stars. The relativistic hadronic field theory, quantum hadrodynamics (QHD), and mean-field approximations of the theory are applied to saturation properties of symmetric nuclear and neutron matter. The equivalence between mean-field approximations and Hartree approximation is emphasized in terms of renormalized effective masses and effective coupling constants of hadrons. This is important to prove that the direct application of mean-field (Hartree) approximation to nuclear and neutron matter is inadequate to examine physical observables. The equations of state (EOS), binding energies of nuclear matter, self-consistency of nuclear matter, are reviewed, and the result of chiral Hartree-Fock \"\"approximation is shown. Neutron stars and history of nuclear astrophysics, nuclear model and nuclear matter, possibility of hadron and hadron-quark neutron stars are briefly reviewed. The hadronic models are very useful and practical for understanding astrophysical phenomena, nuclear

Patterns in Stroke Occurrence on Warm Days in Winter by Associations Analysis  [PDF]
Hiroshi Morimoto
Open Journal of Applied Sciences (OJAppS) , 2015, DOI: 10.4236/ojapps.2015.512074
Abstract: There is increasing interest in the effects of meteorological factors on stroke occurrence. A number of studies have found that cold exposure was a trigger to the onset of cerebral infarction in winter. It was believed that the case of stroke occurrence on warm days in winterwas just a coincidence and negligible. The main objective of this study was to offer the evidence against the above belief. We aimed to find typical patterns among stroke occurrences in case the weather became warmer in winter. Associations analysis was conducted using daily data of emergency transport at Nagoya City in Japan. Typical patterns were identified among risky stroke occurrences even for the case that the weather became warmer in winter. These findings will contribute to an accurate forecast of stroke occurrence in winter.
Hidden Markov Models and Self-Organizing Maps Applied to Stroke Incidence  [PDF]
Hiroshi Morimoto
Open Journal of Applied Sciences (OJAppS) , 2016, DOI: 10.4236/ojapps.2016.63017
Abstract: Several studies were devoted to investigate the effects of meteorological factors on the occurrence of stroke. Regression models had been mostly used to assess the correlation between weather and stroke incidence. However, these methods could not describe the process proceeding in the back-ground of stroke incidence. The purpose of this study was to provide a new approach based on Hidden Markov Models (HMMs) and self-organizing maps (SOM), interpreting the background from the viewpoint of weather variability. Based on meteorological data, SOM was performed to classify weather patterns. Using these classes by SOM as randomly changing “states”, our Hidden Markov Models were constructed with “observation data” that were extracted from the daily data of emergency transport at Nagoya City in Japan. We showed that SOM was an effective method to get weather patterns that would serve as “states” of Hidden Markov Models. Our Hidden Markov Models provided effective models to clarify background process for stroke incidence. The effectiveness of these Hidden Markov Models was estimated by stochastic test for root mean square errors (RMSE). “HMMs with states by SOM” would serve as a description of the background process of stroke incidence and were useful to show the influence of weather on stroke onset. This finding will contribute to an improvement of our understanding for links between weather variability and stroke incidence.
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