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Sawa T, Hamaoka S, Kinoshita M, Kainuma A, Naito Y, Akiyama K, Kato H. Pseudomonas aeruginosa Type III Secretory Toxin ExoU and Its Predicted Homologs. Toxins (Basel) 2016; 8:toxins8110307. [PMID: 27792159 PMCID: PMC5127104 DOI: 10.3390/toxins8110307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa ExoU, a type III secretory toxin and major virulence factor with patatin-like phospholipase activity, is responsible for acute lung injury and sepsis in immunocompromised patients. Through use of a recently updated bacterial genome database, protein sequences predicted to be homologous to Ps. aeruginosa ExoU were identified in 17 other Pseudomonas species (Ps. fluorescens, Ps. lundensis, Ps. weihenstephanensis, Ps. marginalis, Ps. rhodesiae, Ps. synxantha, Ps. libanensis, Ps. extremaustralis, Ps. veronii, Ps. simiae, Ps. trivialis, Ps. tolaasii, Ps. orientalis, Ps. taetrolens, Ps. syringae, Ps. viridiflava, and Ps. cannabina) and 8 Gram-negative bacteria from three other genera (Photorhabdus, Aeromonas, and Paludibacterium). In the alignment of the predicted primary amino acid sequences used for the phylogenetic analyses, both highly conserved and nonconserved parts of the toxin were discovered among the various species. Further comparative studies of the predicted ExoU homologs should provide us with more detailed information about the unique characteristics of the Ps. aeruginosa ExoU toxin.
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Affiliation(s)
- Teiji Sawa
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Saeko Hamaoka
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Mao Kinoshita
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Atsushi Kainuma
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Yoshifumi Naito
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Koichi Akiyama
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Hideya Kato
- Department of Anesthesiology, School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
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Mashima J, Kodama Y, Fujisawa T, Katayama T, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T. DNA Data Bank of Japan. Nucleic Acids Res 2016; 45:D25-D31. [PMID: 27924010 PMCID: PMC5210514 DOI: 10.1093/nar/gkw1001] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 12/27/2022] Open
Abstract
The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.
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Affiliation(s)
- Jun Mashima
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | | | - Yoshihiro Okuda
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Eli Kaminuma
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Kousaku Okubo
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Toshihisa Takagi
- DDBJ Center, National Institute of Genetics, Shizuoka 411-8540, Japan .,National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-8666, Japan
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs. Sci Rep 2016; 6:30580. [PMID: 27466206 PMCID: PMC4964569 DOI: 10.1038/srep30580] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
The lung is an important organ for air breathing in tetrapods and originated well before the terrestrialization of vertebrates. Therefore, to better understand lung evolution, we investigated lung development in the extant basal actinopterygian fish Senegal bichir (Polypterus senegalus). First, we histologically confirmed that lung development in this species is very similar to that of tetrapods. We also found that the mesenchymal expression patterns of three genes that are known to play important roles in early lung development in tetrapods (Fgf10, Tbx4, and Tbx5) were quite similar to those of tetrapods. Moreover, we found a Tbx4 core lung mesenchyme-specific enhancer (C-LME) in the genomes of bichir and coelacanth (Latimeria chalumnae) and experimentally confirmed that these were functional in tetrapods. These findings provide the first molecular evidence that the developmental program for lung was already established in the common ancestor of actinopterygians and sarcopterygians.
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Kamal S, Ripon SH, Dey N, Ashour AS, Santhi V. A MapReduce approach to diminish imbalance parameters for big deoxyribonucleic acid dataset. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 131:191-206. [PMID: 27265059 DOI: 10.1016/j.cmpb.2016.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/18/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND In the age of information superhighway, big data play a significant role in information processing, extractions, retrieving and management. In computational biology, the continuous challenge is to manage the biological data. Data mining techniques are sometimes imperfect for new space and time requirements. Thus, it is critical to process massive amounts of data to retrieve knowledge. The existing software and automated tools to handle big data sets are not sufficient. As a result, an expandable mining technique that enfolds the large storage and processing capability of distributed or parallel processing platforms is essential. METHOD In this analysis, a contemporary distributed clustering methodology for imbalance data reduction using k-nearest neighbor (K-NN) classification approach has been introduced. The pivotal objective of this work is to illustrate real training data sets with reduced amount of elements or instances. These reduced amounts of data sets will ensure faster data classification and standard storage management with less sensitivity. However, general data reduction methods cannot manage very big data sets. To minimize these difficulties, a MapReduce-oriented framework is designed using various clusters of automated contents, comprising multiple algorithmic approaches. RESULTS To test the proposed approach, a real DNA (deoxyribonucleic acid) dataset that consists of 90 million pairs has been used. The proposed model reduces the imbalance data sets from large-scale data sets without loss of its accuracy. CONCLUSIONS The obtained results depict that MapReduce based K-NN classifier provided accurate results for big data of DNA.
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Affiliation(s)
- Sarwar Kamal
- Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | | | - Nilanjan Dey
- Techno India Institute of Technology, Kolkata, India
| | - Amira S Ashour
- Department of Electronics and Electrical Communications Engineering, Faculty of Engineering, Tanta University, Tanta, Egypt.
| | - V Santhi
- School of Computing Science and Engineering, VIT University, Vellore, Tamil Nadu, India
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