Anna Takahashi, Robert Nakayama, Nanako Ishibashi, Doi Ayano, Risa Ichinohe, Yoriko Ikuyo, Teruyoshi Takahashi, Shigetaka Marui, Koji Yasuhara, Tetsurō Nakamura, Shintaro Sugita, Hiromi Sakamoto, Teruhiko Yoshida, Tadashi Hasegawa, Hiro Takahashi,
The diagnosis and treatment of soft tissue sarcomas (STS) have been difficult. Of the diverse histological subtypes, undifferentiated pleomorphic sarcoma (UPS) is particularly difficult to diagnose accurately, and its classification per se is still controversial. Recent advances in genomic technologies provide an excellent way to address such problems. However, it is often difficult, if not impossible, to identify definitive disease-associated genes using genome-wide analysis alone, primarily because ...
Tópico(s): RNA modifications and cancer
2014 - Public Library of Science | PLoS ONE
Chiyoko Machida, Ayami Nakagawa, Shoko Kojima, Hiro Takahashi, Yasunori Machida,
Leaf primordia are born around meristem‐containing stem cells at shoot apices, grow along three axes (proximal–distal, adaxial–abaxial, medial–lateral), and develop into flat symmetric leaves with adaxial–abaxial polarity. Axis development and polarity specification of Arabidopsis leaves require a network of genes for transcription factor‐like proteins and small RNAs. Here, we summarize present understandings of adaxial‐specific genes, ASYMMETRIC LEAVES1 ( AS1 ) and AS2 . Their complex (AS1–AS2) functions ...
Tópico(s): Plant Gene Expression Analysis
2015 - Wiley | Wiley Interdisciplinary Reviews Developmental Biology
Aoi Jo, Sachiyo Mitani, Norio Shiba, Y Hayashi, Yusuke Hara, Hiro Takahashi, Ichiro Tsukimoto, Akio Tawa, Keizo Horibe, Daisuke Tomizawa, Takashi Taga, Souichi Adachi, Tetsuya Yoshida, Hitoshi Ichikawa,
EVI1 and MEL1 are homolog genes whose transcriptional activations by chromosomal translocations are known in small subsets of leukemia. From gene expression profiling data of 130 Japanese pediatric acute myeloid leukemia (AML) patients, we found that EVI1 and MEL1 were overexpressed in ~30% of patients without obvious translocations of these gene loci, and that their high expression was significantly associated with inferior survival. High EVI1 expression was detected mainly in myelomonocytic-lineage ( ...
Tópico(s): Genomics and Chromatin Dynamics
2015 - Springer Nature | Leukemia
Isao Ebina, Mariko Takemoto-Tsutsumi, Shun Watanabe, Hiroaki Koyama, Yayoi Endo, Kaori Kimata, Takuya Igarashi, K Murakami, Rin Kudo, Arisa Ohsumi, Abdul Latif Noh, Hiro Takahashi, Satoshi Naito, Hitoshi Onouchi,
Abstract Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with ...
Tópico(s): RNA modifications and cancer
2015 - Oxford University Press | Nucleic Acids Research
Peng Yang, Hiro Takahashi, Masataka Murase, Motoyuki Itoh,
Abstract In this work, we aim to construct a new behavior analysis method by using machine learning. We used two cameras to capture three-dimensional (3D) tracking data of zebrafish, which were analyzed using fuzzy adaptive resonance theory (FuzzyART), a type of machine learning algorithm, to identify specific behavioral features. The method was tested based on an experiment in which electric shocks were delivered to zebrafish and zebrafish swimming was tracked in 3D simultaneously to find electric ...
Tópico(s): Physiological and biochemical adaptations
2021 - Nature Portfolio | Scientific Reports
Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yui Yamashita, Satoshi Naito, Anna Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima, Hitoshi Onouchi,
Abstract Background Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, ...
Tópico(s): RNA modifications and cancer
2020 - BioMed Central | BMC Genomics
Kenji Kita, Koji Fukuda, Hiro Takahashi, Azusa Tanimoto, Akihiro Nishiyama, Sachiko Arai, Shinji Takeuchi, Kaname Yamashita, Koshiro Ohtsubo, Sakiko Otani, Naohiro Yanagimura, Chiaki Suzuki, Hiroko Ikeda, Masaya Tamura, Isao Matsumoto, Seiji Yano,
Abstract Patient‐derived xenograft ( PDX ) models are a useful tool in cancer biology research. However, the number of lung cancer PDX is limited. In the present study, we successfully established 10 PDX , including three adenocarcinoma ( AD ), six squamous cell carcinoma ( SQ ) and one large cell carcinoma ( LA ), from 30 patients with non‐small cell lung cancer ( NSCLC ) (18 AD , 10 SQ , and 2 LA ), mainly in SCID hairless outbred ( SHO ) mice (Crlj: SHO ‐Prkdc scid Hr hr ). Histology of SQ , advanced clinical stage ( III ‐ IV ), status of lymph ...
Tópico(s): Lung Cancer Treatments and Mutations
2019 - Wiley | Cancer Science
Simon Vial-Pradel, Sumie Keta, Mika Nomoto, Lilan Luo, Hiro Takahashi, Masataka G. Suzuki, Yuri Yokoyama, Michiko Sasabe, Shoko Kojima, Yasuomi Tada, Yasunori Machida, Chiyoko Machida,
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a critical role in leaf adaxial-abaxial partitioning by repressing expression of the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). We previously reported that six CpG dinucleotides in its exon 6 are thoroughly methylated by METHYLTRASFERASE1, that CpG methylation levels are inversely correlated with ETT/ARF3 transcript levels and that methylation levels at three out of the six CpG dinucleotides are decreased in as2-1. All these imply that ...
Tópico(s): Legume Nitrogen Fixing Symbiosis
2018 - Oxford University Press | Plant and Cell Physiology
Noriya Hayashi, Shun Sasaki, Hiro Takahashi, Yui Yamashita, Satoshi Naito, Hitoshi Onouchi,
Specific sequences of certain nascent peptides cause programmed ribosomal arrest during mRNA translation to control gene expression. In eukaryotes, most known regulatory arrest peptides are encoded by upstream open reading frames (uORFs) present in the 5'-untranslated region of mRNAs. However, to date, a limited number of eukaryotic uORFs encoding arrest peptides have been reported. Here, we searched for arrest peptide-encoding uORFs among Arabidopsis thaliana uORFs with evolutionarily conserved ...
Tópico(s): RNA Research and Splicing
2017 - Oxford University Press | Nucleic Acids Research
Yoko Matsumura, Iwai Ohbayashi, Hiro Takahashi, Shoko Kojima, Nanako Ishibashi, Sumie Keta, Ayami Nakagawa, Rika Hayashi, Julio Sáez‐Vásquez, Manuel Echeverrı́a, Munetaka Sugiyama, Kenzo Nakamura, Chiyoko Machida, Yasunori Machida,
ABSTRACT Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1) and AS2 (AS1-AS2) is critical to repress abaxial (ventral) genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal) development in leaf primordia at shoot apices. Double mutations ...
Tópico(s): Plant Gene Expression Analysis
2016 - The Company of Biologists | Biology Open
Takeshi Ueda, Hiro Takahashi, Ebru Uyar, Shu Ishikawa, Naotaka Ogasawara, Taku Oshima,
The Hha and YdgT proteins are suggested to modulate the expression of horizontally acquired genes by interacting with H-NS and StpA, which play central roles in the transcriptional silencing of such genes. However, it is also possible that Hha/YdgT repress gene expression independently of H-NS/StpA, as we have not fully understood the molecular mechanism through which Hha/YdgT modulate H-NS/StpA activity. To gain further insight into the basic functions of Hha/YdgT, we analysed the impact of hha/ ...
Tópico(s): CRISPR and Genetic Engineering
2013 - University of Oxford | DNA Research
Hiro Takahashi, Hidekazu Iwakawa, Nanako Ishibashi, Shoko Kojima, Yoko Matsumura, Pratiwi Prananingrum, Mayumi Iwasaki, Anna Takahashi, Masaya Ikezaki, Lilan Luo, Takeshi Kobayashi, Yasunori Machida, Chiyoko Machida,
It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial–abaxial patterning ...
Tópico(s): Plant Gene Expression Analysis
2013 - Oxford University Press | Plant and Cell Physiology
Mayumi Iwasaki, Hiro Takahashi, Hidekazu Iwakawa, Ayami Nakagawa, Takaaki Ishikawa, Hirokazu Tanaka, Yoko Matsumura, Irena Pekker, Yuval Eshed, Simon Vial-Pradel, Toshiro Ito, Yuichiro Watanabe, Yoshihisa Ueno, Hiroshi Fukazawa, Shoko Kojima, Yasunori Machida, Chiyoko Machida,
Leaf primordia are generated at the periphery of the shoot apex, developing into flat symmetric organs with adaxial-abaxial polarity, in which the indeterminate state is repressed. Despite the crucial role of the ASYMMETRIC LEAVES1 (AS1)-AS2 nuclear-protein complex in leaf adaxial-abaxial polarity specification, information on mechanisms controlling their downstream genes has remained elusive. We systematically analyzed transcripts by microarray and chromatin immunoprecipitation assays and performed ...
Tópico(s): Plant Stress Responses and Tolerance
2013 - The Company of Biologists | Development
Hiro Takahashi, Anna Takahashi, Satoshi Naito, Hitoshi Onouchi,
Abstract Motivation: Upstream open reading frames (uORFs) are often found in the 5′-untranslated regions of eukaryotic messenger RNAs. Some uORFs have been shown to encode functional peptides involved in the translational regulation of the downstream main ORFs. Comparative genomic approaches have been used in genome-wide searches for uORFs encoding bioactive peptides, and by comparing uORF sequences between a few selected species or among a small group of species, uORFs with conserved amino acid ...
Tópico(s): Genomics and Phylogenetic Studies
2012 - Oxford University Press | Bioinformatics
Yukako Chiba, Katsuhiko Mineta, Masami Yokota Hirai, Yuya Suzuki, Shigehiko Kanaya, Hiro Takahashi, Hitoshi Onouchi, Junji Yamaguchi, Satoshi Naito,
Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. Half-lives of average transcripts were determined to be elongated ...
Tópico(s): RNA modifications and cancer
2012 - Oxford University Press | Plant and Cell Physiology
Hiro Takahashi, Ayami Nakagawa, Shoko Kojima, Anna Takahashi, Byung‐Yoon Cha, Je‐Tae Woo, Kazuo Nagai, Yasunori Machida, Chiyoko Machida,
The G-quadruplex is one of the most frequently studied secondary DNA structures and consists of 4 guanine residues that interact through Watson–Crick and Hoogsteen pairing. The G-quadruplex formation is thought to be a molecular switch for gene expression. Genome-wide analyses of G-quadruplexes have been published for many species; however, only one genome-wide analysis of G-quadruplexes in plants has been reported. Here, we propose a new approach involving a two-step procedure for identifying G- ...
Tópico(s): RNA and protein synthesis mechanisms
2012 - Elsevier BV | Journal of Bioscience and Bioengineering
Kazuya Yoshimura, Tatsuya Mori, Kunihiro Yokoyama, Yoshiyuki Koike, Noriaki Tanabe, Nobuo Sato, Hiro Takahashi, Takanori Maruta, Shigeru Shigeoka,
We have demonstrated that an Arabidopsis serine/arginine rich-like protein, atSR45a, interacts with other splicing factors and its expression is markedly induced by high-light stress, suggesting the involvement of atSR45a in the regulation of stress-responsive alternative splicing. A whole-genome tiling array identified the alternative splicing of genes regulated by atSR45a by comparing gene expression profiles in wild-type and knockout atSR45a (KO-sr45a) plants under high-light stress. The expression ...
Tópico(s): RNA and protein synthesis mechanisms
2011 - Oxford University Press | Plant and Cell Physiology
Shoko Kojima, Mayumi Iwasaki, Hiro Takahashi, Tomoya Imai, Yoko Matsumura, Delphine Fleury, Mieke Van Lijsebettens, Yasunori Machida, Chiyoko Machida,
Leaf primordia are generated around the shoot apical meristem. Mutation of the ASYMMETRIC LEAVES2 (AS2) gene of Arabidopsis thaliana results in defects in repression of the meristematic and indeterminate state, establishment of adaxial–abaxial polarity and left–right symmetry in leaves. AS2 represses transcription of meristem-specific class 1 KNOX homeobox genes and of the abaxial-determinant genes ETTIN/ARF3, KANADI2 and YABBY5. To clarify the role of AS2 in the establishment of leaf polarity, we ...
Tópico(s): Plant Gene Expression Analysis
2011 - Oxford University Press | Plant and Cell Physiology
Naoki Matsuo, Hiromi Mase, Miho Makino, Hiro Takahashi, Hiroharu Banno,
The Arabidopsis ENHANCER OF SHOOT REGENERATION 1 (ESR1) is thought to be a key gene for commitment to in vitro shoot regeneration in tissue culture. ESR1 encodes a member of the ETHYLENE RESPONSIVE FACTOR (ERF) family of transcription factors. Here, we report identification of genes downstream of ESR1 during in vitro shoot regeneration. We previously demonstrated that the ESR1 protein functions as a transcriptional activator; in the present study, genes upregulated after induction of ESR1 overexpression ...
Tópico(s): Light effects on plants
2009 - Japanese Society for Plant Biotechnology | Plant Biotechnology
Hiro Takahashi, Hidekazu Iwakawa, S. Nakao, Takahiro Ojio, Ryo Morishita, Satomi Morikawa, Yasunori Machida, Chiyoko Machida, Takeshi Kobayashi,
Gene expression data obtained from DNA microarrays are very useful in revealing the mechanisms that drive life. It is necessary to analyze these data through the use of algorithms, as in clustering and machine-learning. In a previous study, we developed fuzzy adaptive resonance theory (FuzzyART) and applied it to gene expression data, to identify genetic networks. FuzzyART was used as a clustering algorithm that is very suitable for the analysis of biological data; however, although FuzzyART is very ...
Tópico(s): Plant Reproductive Biology
2008 - Elsevier BV | Journal of Bioscience and Bioengineering
Robert Nakayama, T. Nemoto, Hiro Takahashi, Tsutomu Ohta, Akira Kawai, Kunihiko Seki, Teruhiko Yoshida, Yoshiaki Toyama, Hitoshi Ichikawa, Tadashi Hasegawa,
In soft tissue sarcomas, the diagnosis of malignant fibrous histiocytoma (MFH) has been a very controversial issue, and MFH is now considered to be reclassified into pleomorphic subtypes of other sarcomas. To characterize MFH genetically, we used an oligonucleotide microarray to analyze gene expression in 105 samples from 10 types of soft tissue tumors. Spindle cell and pleomorphic sarcomas, such as dedifferentiated liposarcoma, myxofibrosarcoma, leiomyosarcoma, malignant peripheral nerve sheath ...
Tópico(s): Cancer-related gene regulation
2007 - Elsevier BV | Modern Pathology
Hiro Takahashi, Yasuyuki Murase, Takeshi Kobayashi, Hiroyuki Honda,
Tópico(s): Face and Expression Recognition
2006 - Elsevier BV | Biochemical Engineering Journal
Chitta Baral, Juraj Dzifcak, Hiro Takahashi,
Currently, most knowledge representation using logic programming with answer set semantics (AnsProlog) is 'flat'. In this paper we elaborate on our thoughts about a modular structure for knowledge representation and declarative problem solving formalism using AnsProlog. We present language constructs that allow defining of modules and calling of such modules from programs. This allows one to write large knowledge bases or declarative problem solving programs by reusing existing modules instead of ...
Tópico(s): Topic Modeling
2006 - Springer Science+Business Media | Lecture notes in computer science
Hiro Takahashi, T. Nemoto, Teruhiko Yoshida, Hiroyuki Honda, Tadashi Hasegawa,
Abstract Background Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis and selection of treatment. To accomplish this objective, it is important to establish a sophisticated algorithm that can deal with large quantities of data such as gene expression profiles obtained by DNA microarray analysis. Results Previously, we developed the projective adaptive resonance ...
Tópico(s): Genomics and Chromatin Dynamics
2006 - BioMed Central | BMC Bioinformatics
Hiro Takahashi, Hiroyuki Honda,
Tópico(s): Immunotherapy and Immune Responses
2006 - Elsevier BV | Journal of Bioscience and Bioengineering
Hiro Takahashi, Hiroyuki Honda,
For the adequate treatment of patients, it is important to have an accurate and reliable algorithm developed for construction of a diagnosis system that can deal with gene expression data of DNA microarray, or proteomic data obtained by means of mass spectrometry (MS). It is also necessary that this algorithm is fast because these data consist of thousands of attributes (genes or proteins).We have developed a boosted fuzzy classifier with a SWEEP operator (BFCS) method on the basis of the fuzzy theory ...
Tópico(s): Bioinformatics and Genomic Networks
2005 - Society of Chemical Engineers, Japan | JOURNAL OF CHEMICAL ENGINEERING OF JAPAN
Hiro Takahashi, Takeshi Kobayashi, Hiroyuki Honda,
Abstract Motivation: For establishing prognostic predictors of various diseases using DNA microarray analysis technology, it is desired to find selectively significant genes for constructing the prognostic model and it is also necessary to eliminate non-specific genes or genes with error before constructing the model. Results: We applied projective adaptive resonance theory (PART) to gene screening for DNA microarray data. Genes selected by PART were subjected to our FNN-SWEEP modeling method for ...
Tópico(s): Genomics and Chromatin Dynamics
2004 - Oxford University Press | Bioinformatics
Hiro Takahashi, Kayoko Masuda, Tatsuya Ando, Takeshi Kobayashi, Hiroyuki Honda,
Gene expression profiling data from DNA microarray were analyzed using the fuzzy neural network (FNN) modeling method for predicting the distant metastases of breast cancer. The best model consisting of five genes was able to predict metastases of breast cancer with 94% accuracy. Furthermore, 100% accuracy was achieved by majoritarian decision using only 25 genes from five noninferior models which were constructed independently. From the constructed model, gene expression rules, which may cause distant ...
Tópico(s): AI in cancer detection
2004 - Elsevier BV | Journal of Bioscience and Bioengineering
Hiro Takahashi, Shuta Tomida, Takeshi Kobayashi, Hiroyuki Honda,
Inferring genetic networks from gene expression data is the most challenging work in the post-genomic era. However, most studies tend to show their genetic network inference ability by using artificial data. Here, we developed the fuzzy adaptive resonance theory associated matrix (F-ART matrix) method to infer genetic networks and applied it to experimental time series data, which are gene expression profiles of Saccharomyces cerevisiae responding under oxidative stresses such as diamide, heat shock ...
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2003 - Elsevier BV | Journal of Bioscience and Bioengineering
K. Uchimura, Hiro Takahashi, Takeshi Saito,
An advanced public transportation system called the local initiative for neighborhood circulation (LINC) is proposed and the realization of its usage is investigated. LINC effectiveness and efficiency comes from its utilization of a transit-station-oriented system with elimination of present bus stops. LINC has three levels of services. Level 1 is the regional trunk line service with high-speed and high-capacity service provided by the regional transit authority. Level 2 is the intercommunity express ...
Tópico(s): Smart Parking Systems Research
2002 - Institute of Electrical and Electronics Engineers | IEEE Transactions on Vehicular Technology