Institution
National Institute of Technology and Evaluation
Government•Tokyo, Japan•
About: National Institute of Technology and Evaluation is a government organization based out in Tokyo, Japan. It is known for research contribution in the topics: Genome & Streptomyces. The organization has 400 authors who have published 853 publications receiving 28379 citations. The organization is also known as: NITE & Seihin Hyōka Gijutsu Kiban Kikō.
Papers published on a yearly basis
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
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TL;DR: Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve the understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.
2,020 citations
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TL;DR: The whole genome sequence of MW2, a strain of community-acquired MRSA, was ascertained by shotgun cloning and sequencing and found that it carried a range of virulence and resistance genes that was distinct from those displayed on the chromosomes of extant S aureus strains.
1,385 citations
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National Institute of Advanced Industrial Science and Technology1, National Institute of Technology and Evaluation2, Intec, Inc.3, Tohoku University4, University of Tokyo5, Nagoya University6, Tokyo University of Agriculture and Technology7, University of Manchester8, Broad Institute9, George Washington University10, Agricultural Research Service11, University of Nottingham12, Tulane University13, J. Craig Venter Institute14, Kikkoman15, Kyushu University16, Nara Institute of Science and Technology17
TL;DR: Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
Abstract: The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
1,149 citations
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TL;DR: There seems to be a slight bias against GC-rich transcripts in current gene prediction procedures in the “full-length long Japan” collection of sequenced human cDNAs.
Abstract: As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.
921 citations
Authors
Showing all 400 results
Name | H-index | Papers | Citations |
---|---|---|---|
Shigeaki Harayama | 78 | 291 | 19389 |
Takashi Tatsumi | 71 | 437 | 19993 |
Satoru Kuhara | 56 | 256 | 15905 |
Makoto Misono | 52 | 312 | 11712 |
Katsuya Gomi | 49 | 172 | 8629 |
Kazunobu Matsushita | 49 | 291 | 8747 |
Kiyoshi Asai | 46 | 192 | 10456 |
Ken-ichiro Suzuki | 45 | 171 | 8751 |
Masafumi Yohda | 42 | 256 | 6059 |
Ryuichi Hasegawa | 40 | 106 | 4165 |
Yutaka Kawarabayasi | 37 | 104 | 6417 |
Masayuki Machida | 35 | 145 | 7989 |
Shams Tabrez Khan | 31 | 93 | 2445 |
Nobuyuki Fujita | 30 | 107 | 2757 |
Mina Okochi | 28 | 132 | 2582 |