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Jong-In Han,
Hong-Kyu Choi, Seung-Won Lee,
Paul M Orwin,
Jina Kim,
Sarah L Laroe,
Tae-Gyu Kim,
Jennifer O'Neil,
Jared R Leadbetter,
Sang Yup Lee,
Cheol-Goo Hur,
Jim C Spain,
Galina Ovchinnikova,
Lynne Goodwin,
Cliff Han
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ABSTRACT: Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions.
Journal of bacteriology 03/2011; 193(5):1183-90. · 3.94 Impact Factor
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2010 International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2010, Wuhan, China, 8-11 December, 2010; 01/2010
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Haeyoung Jeong,
Valérie Barbe,
Choong Hoon Lee,
David Vallenet,
Dong Su Yu,
Sang-Haeng Choi,
Arnaud Couloux, Seung-Won Lee,
Sung Ho Yoon,
Laurence Cattolico,
Cheol-Goo Hur,
Hong-Seog Park,
Béatrice Ségurens,
Sun Chang Kim,
Tae Kwang Oh,
Richard E Lenski,
F William Studier,
Patrick Daegelen,
Jihyun F Kim
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ABSTRACT: Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
Journal of Molecular Biology 09/2009; 394(4):644-52. · 4.00 Impact Factor
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ABSTRACT: Alternative splicing is generally accepted as a mechanism that explains the discrepancy between the number of genes and proteins. We used peptide mass fingerprinting with a theoretical database and scoring method to discover and identify alternative splicing isoforms. Our theoretical database was built using published alternative splicing databases such as ECgene, H-DBAS, and TISA. According to our theoretical database of 190,529 isoforms, 37% of human genes have multiple isoforms. The isoforms produced from a gene partially share common peptide fragments because they have common exons, making it difficult to distinguish isoforms. Therefore, we developed a new method that effectively distinguishes a true isoform among multiple isoforms in a gene. In order to evaluate our algorithm, we made test sets for 4226 protein isoforms extracted from our theoretical database randomly. Consequently, 94% of true isoforms were identified by our scoring algorithm.
Biochemical and Biophysical Research Communications 11/2008; 377(1):253-6. · 2.48 Impact Factor
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ABSTRACT: There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses.
We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/.
The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.
BMC Plant Biology 11/2008; 8:101. · 3.45 Impact Factor
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Advances in Grid and Pervasive Computing, First International Conference, GPC 2006, Taichung, Taiwan, May 3-5, 2006, Proceedings; 01/2006
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Advances in Multimedia Information Processing - PCM 2004, 5th Pacific Rim Conference on Multimedia, Tokyo, Japan, November 30 - December 3, 2004, Proceedings, Part I; 01/2004
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Embedded and Ubiquitous Computing, International Conference EUC 2004, Aizu-Wakamatsu City, Japan, August 25-27, 2004, Proceedings; 01/2004
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Information Networking, Networking Technologies for Enhanced Internet Services International Conference, ICOIN 2003, Cheju Island, Korea, February 12-14, 2003, Revised Selected Papers; 01/2003
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Information Networking, Wireless Communications Technologies and Network Applications, International Conference, ICOIN 2002, Cheju Island, Korea, January 30 - February 1, 2002, Revised Papers, Part II; 01/2002
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Advances in Multimedia Information Processing - PCM 2002, Third IEEE Pacific Rim Conference on Multimedia, Hsinchu, Taiwan, December 16-18, 2002, Proceedings; 01/2002
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Proceedings of the 2001 IEEE International Conference on Multimedia and Expo, ICME 2001, August 22-25, 2001, Tokyo, Japan; 01/2001
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01/2001
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EUROSPEECH 2001 Scandinavia, 7th European Conference on Speech Communication and Technology, 2nd INTERSPEECH Event, Aalborg, Denmark, September 3-7, 2001; 01/2001
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Proceedings of the 2001 IEEE International Conference on Multimedia and Expo, ICME 2001, August 22-25, 2001, Tokyo, Japan; 01/2001
