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Journal Articles

Effective 3D data visualization in deep shaft construction

Inagaki, Daisuke*; Tsusaka, Kimikazu*; Aoyagi, Kazuhei; Nago, Makito*; Ijiri, Yuji*; Shigehiro, Michiko*

Proceedings of ITA-AITES World Tunnel Congress 2015 (WTC 2015)/41st General Assembly, 10 Pages, 2015/05

Journal Articles

An Application of three-dimensional geological information system to underground construction

Kato, Nobuyoshi*; Tsusaka, Kimikazu; Nago, Makito*; Yamagami, Masahito*; Matsubara, Makoto*; Shigehiro, Michiko*; Aizawa, Takao*; Kamemura, Katsumi*

Chishitsu To Chosa, (139), p.17 - 22, 2014/04

no abstracts in English

Journal Articles

Rock spalling and countermeasures in shaft sinking at the Horonobe Underground Research Laboratory

Tsusaka, Kimikazu; Inagaki, Daisuke; Nago, Makito*; Aoki, Tomoyuki*; Shigehiro, Michiko*

Proceedings of 6th International Symposium on In-situ Rock Stress (RS 2013) (CD-ROM), p.339 - 346, 2013/08

The Horonobe Underground Research Laboratory is planned to consist of the Ventilation Shaft (4.5 m in diameter), the East and West Access Shafts (6.5 m in diameter). The host rock of the URL site comprises Neogene sedimentary rocks. The unconfined compressive strength of the rocks is less than 20 MPa on average. Anisotropic stress distribution around the URL is also confirmed. Because several highly permeable fractures (hydraulic transmissivity: approximately 10$$^{-5}$$m$$^{2}$$/s) with the size greater than the shaft diameter develop under the condition of around 2 in competence factor (i.e., the ratio of the unconfined compressive strength of rock to the initial stress) below a depth of 250 m, shaft sinking is a challenging issue from the viewpoint of tunnel engineering in the Horonobe URL Project. In this paper, the construction of the Ventilation Shaft below a depth of 250 m at the Horonobe URL is reported. During shaft sinking, fracture mapping of the shaft wall was performed. The geometry of the shaft wall was also measured using a three-dimensional laser scanner in order to investigate the shape and volume of rock spalling in the shaft wall resulting from the excavation work. Rock spalling was predominantly observed on the south and north wall rock corresponding to the direction of the minimum horizontal initial stress. A large amount of rock spalling also developed along a large-scale fault. With respect to the lining span and the layout of rockbolts, several support patterns were designed and installed as the countermeasures to prevent the development of excessive rock spalling. A flowchart for selecting the optimum support design was then developed.

Journal Articles

Relationship between rock mass properties and damage of a concrete lining during shaft sinking in the Horonobe Underground Research Laboratory Project

Tsusaka, Kimikazu; Inagaki, Daisuke; Nago, Makito*; Kamemura, Katsumi*; Matsubara, Makoto*; Shigehiro, Michiko*

Proceedings of ITA-AITES World Tunnel Congress 2013 (WTC 2013)/39th General Assembly, p.2014 - 2021, 2013/05

Japan Atomic Energy Agency (JAEA) has been constructing three shafts to a depth of 500 m in the Horonobe Underground Research Laboratory Project. In this study, in consideration of support patterns installed, a relationship between the rock mass properties and mechanical response to excavation was investigated in detail during the construction of the East Access Shaft below a depth of 250 m. Since the shaft has intersected several faults with the size greater than the shaft diameter, some amounts of rock spalling have occurred and cracks have severely developed in a concrete lining in highly fractured zones. The results of pre-excavation grouting were compared with the results of fracture mapping in the shaft wall obtained during the shaft sinking. Applicability of several support patterns installed to control massive spalling during the shaft sinking was also analysed using the results of geometry profiling of shaft wall using a three-dimensional laser scanner and convergence measurements. As a result, based the empirical relationships among the characteristics of rocks, dimension of spalling, damage of a concrete lining and support patterns, a flow chart for selection of span of a concrete lining was proposed to control its severe damage prior to shaft excavation.

Journal Articles

An Observational construction management in the Horonobe Underground Research Laboratory Project

Tsusaka, Kimikazu; Inagaki, Daisuke; Tokiwa, Tetsuya; Yokota, Hideharu; Nago, Makito*; Matsubara, Makoto*; Shigehiro, Michiko*

Proceedings of ITA-AITES World Tunnel Congress 2012 (WTC 2012)/38th General Assembly (CD-ROM), 8 Pages, 2012/05

In the Horonobe URL Project, three shafts are planned to be excavated up to the depth of 500 m in the Neogene sedimentary rocks. The host rock of the URL site is comprised of diatomaceous and siliceous mudstones, which are the Koetoi and Wakkanai Formations, respectively. Approximately 100 m thick fracture zone with high hydraulic conductivity develops above about 400 m in depth in the Wakkanai Formation. The shaft sinking through the fracture zone is the most challenging issue from the aspect of tunnel engineering in the project. In the fracture zone, there is high possibility of severe breakout and spalling in shaft wall because the shafts might be intersecting faults with the size greater than shaft diameter in addition to low intact rock strength at great depth. In practice, prior to the construction of the Ventilation Shaft through the fracture zone below a depth of 250 m, the three dimensional fault distribution were predicted by integrating borehole investigation results and geological response to pre-excavation grouting operation. The countermeasure was also designed against massive spalling. During the shaft sinking, fracture mapping of shaft wall was carried out in order to evaluate the prediction of fault distribution. Roughness of shaft wall was also measured by three dimensional laser scanner in order to investigate the shape and volume of spalling resulting from the excavation work. Consequently, the Ventilation Shaft has successfully been constructed through the fracture zone. This is because the prediction of fault distribution was accurate, and the countermeasure against concrete lining damage due to spalling was promptly applied.

Journal Articles

The H-Invitational Database (H-InvDB); A Comprehensive annotation resource for human genes and transcripts

Yamasaki, Chisato*; Murakami, Katsuhiko*; Fujii, Yasuyuki*; Sato, Yoshiharu*; Harada, Erimi*; Takeda, Junichi*; Taniya, Takayuki*; Sakate, Ryuichi*; Kikugawa, Shingo*; Shimada, Makoto*; et al.

Nucleic Acids Research, 36(Database), p.D793 - D799, 2008/01

 Times Cited Count:51 Percentile:71.37(Biochemistry & Molecular Biology)

Here we report the new features and improvements in our latest release of the H-Invitational Database, a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of fulllength cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 protein-coding and 642 non-protein-coding loci; 858 transcribed loci overlapped with predicted pseudogenes.

Journal Articles

Contribution of computational biology and structural genomics to understand genome and transcriptome

Go, Michiko*; Yura, Kei; Shionyu, Masafumi*

Frontiers of Computational Science, p.75 - 80, 2007/00

Genome sequencing and structural genomics projects are both proceeded to gain a new perspective of life, that is global views on mechanisms of life with comprehensive and unbiased fashion. We now have genome sequences of human and other species, and are going to have a three-dimensional structure of whole proteins. Those massive pieces of information can only be deciphered with collaboration of computational biology. In this paper, we will discuss the amount of data we have at the moment and one of the new views on mechanisms of cellular function regulation obtained based on the computational analyses of those data.

Journal Articles

Alternative splicing in human transcriptome; Functional and structural influence on proteins

Yura, Kei; Shionyu, Masafumi*; Hagino, Kei*; Hijikata, Atsushi*; Hirashima, Yoshinori*; Nakahara, Taku*; Eguchi, Tatsuya*; Shinoda, Kazuki*; Yamaguchi, Akihiro*; Takahashi, Kenichi*; et al.

Gene, 380(2), p.63 - 71, 2006/10

 Times Cited Count:55 Percentile:72.39(Genetics & Heredity)

Alternative splicing is a molecular mechanism that produces multiple proteins from a single gene, and is thought to produce variety in proteins translated from a limited number of genes. Here we analyzed how alternative splicing produced variety in protein structure and function, by using human full-length cDNAs, on the assumption that all of the alternatively spliced mRNAs were translated to proteins. We found that the length of alternatively spliced amino acid sequences, in most cases, fell into a size shorter than that of average protein domain. We evaluated comprehensively the presumptive three-dimensional structures of the alternatively spliced products to assess the impact of alternative splicing on gene function. We found that more than half of the products encoded proteins which were involved in signal transduction, transcription and translation, and more than half of alternatively spliced regions comprised interaction sites between proteins and their binding partners, including substrates, DNA/RNA, and other proteins. Intriguingly, 67% of the alternatively spliced isoforms showed significant alterations to regions of the protein structural core, which likely resulted in large conformational change. Based on those findings, we speculate that there are a large number of cases that alternative splicing modulates protein networks through significant alteration in protein conformation.

Journal Articles

Coverage of whole proteome by structural genomics observed through protein homology modeling database

Yura, Kei; Yamaguchi, Akihiro*; Go, Michiko*

Journal of Structural and Functional Genomics, 7(2), p.65 - 76, 2006/06

We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. Assuming that this rate would be maintained, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years.

Journal Articles

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Takeda, Junichi*; Suzuki, Yutaka*; Nakao, Mitsuteru*; Barrero, R. A.*; Koyanagi, Kanako*; Jin, L.*; Motono, Chie*; Hata, Hiroko*; Isogai, Takao*; Nagai, Keiichi*; et al.

Nucleic Acids Research, 34(14), p.3917 - 3928, 2006/00

 Times Cited Count:34 Percentile:54.48(Biochemistry & Molecular Biology)

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function which is mediated by the alternative splicing variants.

Journal Articles

Enlarged FAMSBAS; Protein 3D structure models of genome sequences for 41 species

Yamaguchi, Akihiro*; Iwadate, Mitsuo*; Suzuki, Eiichiro*; Yura, Kei; Kawakita, Shigetsune*; Umeyama, Hideaki*; Go, Michiko*

Nucleic Acids Research, 31(1), p.463 - 468, 2003/01

 Times Cited Count:15 Percentile:25.27(Biochemistry & Molecular Biology)

Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by FAMS, Full Automatic Modeling System. Enlarged FAMSBASE provides a wide range of query keys, such as name of ORF (open reading frame), ORF keywords, PDB ID, PDB heterogen atoms, and sequence similarity. Heterogen atoms in PDB include cofactors, ligands, and other factors that interact with proteins, and are a good starting point for analyzing interactions between proteins and other molecules. The data may also work as a template for drug design. The present number of ORFs with protein 3D models in FAMSBASE is 183,805, and the database includes an average of three models for each ORF. FAMSBASE is available at http://famsbase.bio.nagoya-u.ac.jp/famsbase/.

Journal Articles

3D-keynote; Genome function prediction based on protein module

Yura, Kei; Go, Michiko*

Tampakushitsu Kakusan Koso, 47(8), p.1090 - 1096, 2002/06

no abstracts in English

Oral presentation

Systematic detection of protein regions affected by alternative splicing

Shionyu, Masafumi*; Yura, Kei; Hijikata, Atsushi*; Nakahara, Taku*; Shinoda, Kazuki*; Yamaguchi, Akihiro*; Takahashi, Kenichi*; Go, Michiko*

no journal, , 

Alternative splicing (AS) is a cellular process where multiple mature mRNAs are produced from a single gene by different usage of exons. From computational and experimental approaches, it is estimated that 30-70% of human genes undergo alternative splicing. There are a number of reports on spliced mRNAs involved in biological processes, yet functional analyses of a large number of proteins produced by AS remain to be performed. Functional analyses of these proteins by experiments are time-consuming, and therefore, a computational approach that can estimate effect of AS on proteins is required. We have developed a pipeline that can systematically detect AS regions, which are defined as protein regions modified by alternatively spliced exon, using genomic sequences and full-length transcripts data. The pipeline further assigned AS regions to protein three-dimensional structures and can estimate effects of AS on protein conformation stability and functional sites. We analyzed human AS regions using our pipeline and found that about half of AS regions fell into a size shorter than 100 amino acid residues. We, then, assessed the relationship between AS regions and protein structural domains and found that about 40% of AS regions were placed within a domain and the ratio of AS regions corresponding to domains was only about 10%. This result suggests that AS regulates protein function through alteration of segments within a domain rather than through switching protein domains. We will discuss how AS regulates protein function through alteration of segments within a domain.

Oral presentation

Effect on protein three-dimensional structures of alternative splicing toward diversification of eukaryotic transcripts

Yura, Kei; Go, Michiko*

no journal, , 

Alternative splicing is a molecular mechanism that produces multiple proteins from a single gene, and is thought to produce variety in proteins translated from a limited number of genes. We evaluated comprehensively the presumptive three-dimensional structures of the alternatively spliced products to assess the impact of alternative splicing on gene function. We found that more than half of alternatively spliced regions comprised interaction sites between proteins and their binding partners, including substrates, DNA/RNA, and other proteins. Intriguingly, about 70% of the alternatively spliced isoforms showed significant alterations to regions of the protein structural core, which likely resulted in large conformational change. Based on those findings, we speculate that there are a large number of cases that alternative splicing modulates protein networks through significant alteration in protein conformation.

Oral presentation

Monitoring of rock behavior due to shaft excavation using tilt measurements

Nago, Makito*; Ijiri, Yuji*; Kinomura, Koji*; Sato, Masaru*; Shigehiro, Michiko*; Kunimaru, Takanori

no journal, , 

Since a geological disposal repository of nuclear waste will be constructed at depth of a few square kilometers and will be operated for a several tens years, it is crusial to develop a long-term monitoring technology of rock behavior of quite large area. For this purpose, a conventional monitoring method needs a number of deep boreholes and thus needs a huge amount of cost. In this paper, the results of tilt measurements for the shaft excavation at the Horonobe Underground Research Laboratory is presented.

Oral presentation

Development of technologies for monitoring rock behaviors using tiltmeter

Ijiri, Yuji*; Nago, Makito*; Kinomura, Koji*; Sugihara, Yutaka*; Shigehiro, Michiko*; Sato, Masaru*; Kunimaru, Takanori

no journal, , 

This paper presents the in-situ measurement data and the results of simulation analyses in order to develop technologies for monitoring rock behaviors using tiltmeters placed near ground surface. From the data, it is shown that the tiltmeters are able to capture the rock behaviors due to shaft excavations and concrete placements and are very sensitive to capture earthquakes, change in barometrical pressure and tide as well as the movements of heavy-construction-equipments. The applicability of inverse analysis for identifying the rock properties using tilting displacement data associated with construction activity is demonstrated by elastic analyses. In addition, the applicability of tiltmeters for monitoring high-permeable zones is also demonstrated by Hydro-Mechanical coupling analysis, because the groundwater flow toward the shaft along high-permeable zone cause an increase in the rate of tilting displacement and change in displacement mode.

Oral presentation

Correlation between RNA editing sites of plant organelle mRNAs and the three-dimensional structures of encoded proteins

Yura, Kei; Go, Michiko*

no journal, , 

DNAs of Plant Organelles undergo RNA editing, a transcript repair mechanisms. Those RNA editing sites seems to be located uniformly on pre-mature mRNA. This previous finding suggested that RNA editing has nothing to do with protein function. In this study, we challenged this idea based on our new database gathering all the known RNA editing sites combined with protein three-dimensional structures. We gathered 1923 RNA editing sites out of 365 pre-mature mRNAs. We have investigated and found a good correlation between the site undergoing RNA editing and protein three-dimensional structure. The finding may suggest mechanisms and evolution of RNA editing.

Oral presentation

Relationship between genome and protein structures in eukaryotes

Yura, Kei; Shionyu, Masafumi*; Go, Michiko*

no journal, , 

Open reading frames in eukaryotic genome is composed of introns and exons, and selection of appropirate exons is the mechanism of alternative splicing. In this lecture, we will discuss the correlation of intron/exon structures with protein three-dimensional structures and effect of alternative splicing in protein structures.

Oral presentation

Rapid analysis of radionuclides using porous polymer sheet functionalized by radiation-induced graft polymerization

Asai, Shiho; Magara, Masaaki; Suzuki, Daisuke; Shinohara, Nobuo; Saito, Kyoichi*; Sugo, Takanobu*; Takami, Michiko*; Shiraishi, Kunio*

no journal, , 

no abstracts in English

Oral presentation

Preparation of access-restricted separation material for analysis of bio-samples

Shibahara, Ryuji*; Asai, Shiho; Hagiwara, Kyohei*; Takami, Michiko*; Shiraishi, Kunio*; Umeno, Daisuke*; Shinohara, Nobuo; Sugo, Takanobu*; Saito, Kyoichi*

no journal, , 

no abstracts in English

21 (Records 1-20 displayed on this page)