• Interdisciplinary Bio Central
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• v.3 no.1
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• pp.1.1-1.6
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• 2011

Recently, with the progress of genome sequencing, materials and information for research on tomato (Solanum lycopersicum) have been systematically organized. Tomato genomics tools including mutant collections, genome sequence information, full-length cDNA and metabolomic datasets have become available to the research community. In Japan, the National BioResource Project Tomato (NBRP Tomato) was launched in 2007, with aims to collect, propagate, maintain and distribute tomato bioresources to promote functional genomics studies in tomato. To this end, the dwarf variety Micro-Tom was chosen as a core genetic background, due to its many advantages as a model organism. In this project, a total of 12,000 mutagenized lines, consisting of 6000 EMS-mutagenized and 6000 gamma-ray irradiated M2 seeds, were produced, and the M3 offspring seeds derived from 2236 EMS-mutagenized M2 lines and 2700 gamma-ray irradiated M2 lines have been produced. Micro-Tom mutagenized lines in the M3 generation and monogenic Micro-Tom mutants are provided from NBRP tomato. Moreover, tomato cultivated varieties and its wild relatives, both of these are widely used for experimental study, are available. In addition to these bioresources, NBRP Tomato also provides 13,227 clones of full-length cDNA which represent individual transcripts non-redundantly. In this paper, we report the current status of NBRP Tomato and its future prospects.

• Ocean Science Journal
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• v.40 no.1
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• pp.55-59
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• 2005

We cloned the complete cDNA of the ${\beta}-bubulin$ from the soft coral, Scleronephthya gracillimum $(K\ddot{u}kenthal)$ (Alcyonacea, Octocorallia, Anthozoa, Cnidaria), via the random sequencing of a cDNA library and the 5'-rapid amplification of cDNA end (RACE) technique. The full-length cDNA of the S. gracillimum ${\beta}-tubulin$ comprised 1541 bp, not including the poly $A^+$ stretch, also contained a complete open reading frame, which codes for a total of 445 amino acids. The amino acid residues 16402 appeared to be in a state of conservation in a variety of animals. Northern blot analysis clearly demonstrated that the sequence we have obtained is, indeed, the full-length cDNA of the ${\beta}-bubulin$ gene in S. gracillimum.

• YAKHAK HOEJI
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• v.45 no.4
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• pp.426-430
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• 2001

Cells are eliminated in a variety of physiological settings by apoptosis, a genetically encoded process of cellular suicide. Bak, a member of the Bcl-2 protein family, accelerates apoptosis by an unknown mechanism. We have found a novel cDNA encoding a 101 amino acid protein possessing a Bak-like in our full-length cDNA bank. Bak-like shares the conserved domains BHI and 2 with other proapoptotic proteins but lacks the BH3 domain. Bak-like is expressed in a wide variety of tissues. Like Bak, Bak-like gene product primarily enhances apoptotic cell death following an appropriate stimulus.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• BMB Reports
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• v.35 no.3
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• pp.273-282
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• 2002

Sp3 is a bifunctional transcription factor that has been reported to stimulate or repress the transcription of numerous genes. Although the size of Sp3 mRNA is 4.0kb, the size of the known Sp3 cDNA sequence is 3.6kb. Thus, Sp3 functional studies have been performed with an artificially introduced start codon, and thus an amino-terminus that differs from the wild-type. Ideally, full-length cDNA expression vectors with the appropriate start codon should be utilized for these studies. Using 5'rapid amplification of cDNA ends, a full-length Sp3 cDNA clone was generated and the sequence verified in nine cell lines. No AUG initiation codon was present. However, stop codons were present in all three frames 5' to the known coding sequence. In vitro translation of this full-length cDNA clone produced the expected three isoforms-one at 100 kDa and two in the mid 60 kDa range. Electrophoretic mobility shift assays showed that the protein products had the ability to bind to the Sp1/3 consensus sequence. In vitro studies, using our Sp3 clone and site directed mutagenesis, identified the translation initiation site for the larger isoform as AUA. AUA has not been previously described as an endogenous initiation codon in eukaryotes.

• Proceedings of the Zoological Society Korea Conference
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• 1999.10b
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• pp.260.2-260
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• 1999

No Abstract, See Full Text

• Proceedings of the Microbiological Society of Korea Conference
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• 2003.05a
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• pp.83-86
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• 2003

Major advances in positive-sense RNA virus research have been facilitated by the development of reverse genetics systems. These systems consist of an infectious cDNA clone that encompasses the genome of the virus in question. This clone is then used as a template for the subsequent synthesis of infectious RNA for the generation of synthetic viruses. However, the construction of infectious cDNA for the Japanese encephalitis virus (JEV) has been repeatedly thwarted by the instability of its cDNA. As JEV is an important human pathogen that causes permanent neuropsychiatric sequelae and even fatal disease, a reliable reverse genetics system for this virus is highly desirable. The availability of this tool would greatly and the development of effective vaccines as well as facilitate studies into the basic biology of the virus, including the molecular mechanisms of viral replication, neurovirulence, and pathogenesis. We have successfully constructed a genetically stable infectious JEV cDNA containing full-length viral RNA genome. Synthetic RNA transcripts generated in vitro from the cDNA were highly infectious upon transfection into susceptible cells, and the cDNA remained stable after it had been propagated in E. coli for 180 generations. Using this infectious JEV cDNA, we have successfully expressed a variety of reporter genes from the full-length genomic and various subgenomic RNAs in vitro transcribed from functional JEV cDNAS. In summary, we have developed a reverse genetics system for JEV that will greatly facilitate the research on this virus in a variety of different fields. It will also be useful as a heterologous gene expression vector and aid the development of a vaccine against JEV.

• Animal cells and systems
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• v.16 no.6
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• pp.488-497
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• 2012

A DNA barcode based on 648 bp of cytochrome c oxidase I (COI) gene aims to build species-specific libraries for animal groups. However, it is hard to recover full-length (648 bp) barcode gene from environmental fecal samples due to DNA degradation. In this study, we designed a new primer set (K_Bird), which amplifies a 226 bp fragment targeted an inner position of full-length COI barcode based on 102 species of Korean birds to improve amplification success, and we attempted to identify bird species from 39 avian fecal samples collected during 4 months from Jinan, South Korea. Simultaneously, we conducted a dietary analysis using a universal DNA mini-barcode (Uni_Minibar) from same fecal samples. In silico analysis on newly designed mini-barcode represented that genetic distances were 0.5% in species and 9.1% in genera. Intraspecific variations of 149 species out of 174 species (86%) between Korea and North America were within the threshold (5.3% threshold in this study). From environmental fecal samples collected in Jinan, we identified seven avian species, which have high similarity (99-100%) with registered COI sequences in GenBank. Eight kinds of prey species, such as moth, spider, fly, and dragonfly, were identified in dietary analysis. We suppose that our strategy applying mini-barcode for environmental fecal samples, might be a useful and convenient tool for species identification and dietary analysis for birds.

• Microbiology and Biotechnology Letters
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• v.24 no.3
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• pp.290-298
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• 1996

In an effort to understand the role of the conserved domain and of the heterologous one-third part of the carboxy terminal domain of transglutaminase C (TGase II), attempts were made to express TGase II cDNA of human origin in yeast Saccharomyces cerevisiae as in a full-length form as well as in a form of C-terminal truncation. The 2$\mu$-based expression plasmids which contained the TGase II cDNA under the gal inducible promoter were introduced into yeast and the maintenance of the full-length and truncated form of the TGase II gene plasmids were confirmed by Southern blot. The expression of the TGase II gene was analysed by reverse transcription polymerase chain reaction (RT-PCR), and western blot analyses. As assayed by [1,4$^{14}$C]-putrescine incorporation into succinylated casein, the full-lenth as well as the truncated forms of recombinant TGase II showed some catalytic activity. These results indicate that the N-terminal homologous domain of human TGase II retains a catalytically active domain. The level of TGase II expressed in yeast, however, was far lower than satisfactory and other expression system should be sought further chracterization of the enzyme. The negative effect of TGase II on the growth of yeast is interesting with respect to the physiological effect of TGase II in cornification of epidermal keratinocytes.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.143.3-144
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• 2003

A Korean isolate of Pepper mild mottle virus (PMMoV-Kr) was isolated from a diseased pepper crop in Chunchon, Korea. The isolate was biologically purified on Nicoticaa tabacum cv. Xanthi-nc by successive single local transfer steps, and propagated on N. tabacum cv. Samsun. PMMoV-Kr could systemically infect on N. glauca, N. benthmiana, N. occidentalis and Lycopersicon esculentum, which is typical of known isolates of PMMoV. PMMoV-Kr belongs to the pathotype P1,2 based on pepper-tobamoviral indicator experiments; Capsicn chinone harboring L3 gene revealed resistant (necrotic local lesion on inoculated leaf, HR) whereas L+, L1 and L2 pepper plants expressed susceptible reactions of mosaic systemic symptoms for the isolate. To confirm the pathology and delineate symptom determinant of the isolate, full-length cDNAs of PMMoV-Kr were amplified by RT-PCR with a primer set corresponding to the 5'- and 3'-ends of PMMoV. The RT-PCR molecules amplified from genome RNA of the isolate was cloned into the pUC18 vector. Full-length cDNA clones constructed under the control of the T7 RNA promoter could be successfully transcribed to produce in vitro transcript RNA. Infectivity of the capped transcripts and its progeny virus was verified by Western blot and RT-PCR analyses.