• BMB Reports
• /
• v.33 no.2
• /
• pp.162-165
• /
• 2000

Polymerase chain reaction (PCR) is well established as an indispensable tool of molecular biology; and yet a limitation for cloning applications continues to be that products often require subsequent restriction to be that products often require subsequent restriction digests, blunt-end ligation, or the use of special linear vectors. Here a rapid, PCR-based system is described for the simple, restriction enzyme-free generation of synthetic, 'restriction-like' DNA fragments with staggered ends. Any 3'- or 5'-protruding terminus, but also non-palindromic overhangs with an unrestricted single strand length are specifically created. With longer overhangs, "Restriction-PCR" does not even require a ligation step prior to transformation. Thereby the technique presents a powerful tool e.g. for a successive, authentic reconstitution of sub-fragments of long genes with no need to manipulate the sequence or to introduce restriction sites. Since restriction enzyme-free and thereby devoid the limitations of partial DNA digests, "Restriction-PCR" allows a straight one-step generation and cloning of difficult DNA fragments that internally carry additional sites for specific sequence insertions or deletions can be precisely engineered into genes of interest. With these properties "Restriction-PCR" has the potential to add significant speed and versatility to a wide variety of DNA cloning applications.

• BMB Reports
• /
• v.32 no.5
• /
• pp.456-460
• /
• 1999

The promoter of the HSV-1 VP16 gene contains binding sites for the cellular transcription factors such as USF, CTF, and Sp1, each of which affects basal level expression of the VP16 gene. Transcription of the VP16 gene was induced by viral immediate-early proteins, ICP0 and ICP4, in a synergistic manner but repressed by ICP22. To gain further insight into the role of ICP0 in the expression of the VP16 gene during virus infection, several mutants with deletions in each of their transcriptional regulatory elements were generated. According to transient gene expression assays of these mutants using the CAT gene as a reporter, the USF and CTF binding sites were necessary for efficient induction of the promoter in the presence of transfected ICP0 or during virus infection, whereas the Sp1 binding site had little effect on ICP0-mediated VP16 expression. These results indicate that the immediate early proteins of HSV-1 regulate expression of the VP16 gene during virus infection by modulating the activities of cellular transcription factors such as USF and CTF.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.3
• /
• pp.381-390
• /
• 2018

We have previously derived a novel antimicrobial peptide, LPcin-YK3(YK3), based on lactophoricin and have successfully studied and reported on the relationship between its structure and function. In this study, antimicrobial peptides with improved antimicrobial activity, less cytotoxicity, and shorter length were devised and characterized on the basis of YK3, and named YK5, YK8, and YK11. The peptide design was based on a variety of knowledge, and a total of nine analog peptides consisted of one to three amino acid substitutions and C-terminal deletions. In detail, tryptophan substitution improved the membrane perturbation, lysine substitution increased the net charge, and excessive amphipathicity decreased. The analog peptides were examined for structural characteristics through spectroscopic analytical techniques, and antimicrobial susceptibility tests were used to confirm their activity and safety. We expect that these studies will provide a platform for systematic engineering of new antibiotic peptides and generate libraries of various antibiotic peptides.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.8
• /
• pp.1109-1117
• /
• 2014

Chlorogenic acid and hydroxylcinnamoyl shikimates are major dietary phenolics as well as antioxidants, with recently discovered biological, activities including protection against chemotheraphy side effects and prevention of cardiovascular disease and cancer. Certain fruits and vegetables produce these compounds, although a microbial system can also be utilized for synthesis of chlorogenic acid and hydroxylcinnamoyl shikimates. In this study, we engineered Escherichia coli to produce chlorogenic acid and p-coumaroyl shikimates from glucose. For the synthesis of chlorogenic acid, two E. coli strains were used; one strain for the synthesis of caffeic acid from glucose and the other strain for the synthesis of chlorogenic acid from caffeic acid and quinic acid. The final yield of chlorogenic acid using this approach was approximately 78 mg/l. To synthesize p-coumaroyl shikimates, wild-type E. coli as well as several mutants were tested. Mutant E. coli carrying deletions in three genes (tyrR, pheA, and aroL) produced 236 mg/l of p-coumaroyl shikimates.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.9
• /
• pp.1473-1481
• /
• 2018

A cellulase hyperproducing mutant strain, JNDY-13, was obtained using the ARTP mutation system and with Trichoderma reesei RUT-C30 as the parent strain. Whole-genome sequencing of JNDY-13 confirmed that 105 of the 653 SNPs were point mutations, 336 mutations were deletions and 165 were insertions. Moreover, 99 mutations were insertions and duplications. Among all the mutations, the one that occurred in the galactokinase gene might be related to the production of cellulases in T. reesei JNDY-13. Moreover, the up-regulation of cellulase and hemicellulase genes in JNDY-13 might contribute to higher cellulases production. Under optimal conditions, the highest cellulase activity by batch fermentation reached 4.35 U/ml, and the highest activity of fed-batch fermentation achieved was 5.40 U/ml.

• Journal of KIISE:Computing Practices and Letters
• /
• v.14 no.7
• /
• pp.713-717
• /
• 2008

Recently, as the capacity of flash memory increases rapidly, efficient indexing methods become crucial for fast searching of a large volume of data stored in flash memory. Flash memory has its unique characteristics: the write operation is much more costly than the read operation and in-place updating is not allowed. In this paper, we propose a novel index structure that significantly reduces the number of write operations and thus supports efficient searches, insertions, and deletions. We verify the superiority of our method by performing extensive experiments.

• International Journal of Contents
• /
• v.3 no.2
• /
• pp.6-17
• /
• 2007

Emerging modem database applications require multi-dimensional index structures to provide high performance for data retrieval. In order for a multi-dimensional index structure to be integrated into a commercial database system, efficient techniques that provide transactional access to data through this index structure are necessary. The techniques must support all degrees of isolation offered by the database system. Especially degree 3 isolation, called "no phantom read," protects search ranges from concurrent insertions and the rollbacks of deletions. In this paper, we propose a new phantom protection method for multi-dimensional index structures that uses a multi-level grid technique. The proposed mechanism is independent of the type of the multi-dimensional index structure, i.e., it can be applied to all types of index structures such as tree-based, file-based, and hash-based index structures. In addition, it has a low development cost and achieves high concurrency with a low lock overhead. It is shown through various experiments that the proposed method outperforms existing phantom protection methods for multi-dimensional index structures.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.11
• /
• pp.1790-1798
• /
• 2019

Flock House virus (FHV), an insect RNA virus, has a bipartite genome. FHV RNA1 can be packaged in turnip yellow mosaic virus (TYMV) as long as the FHV RNA has a TYMV sequence at the 3'-end. The encapsidated FHV RNA1 has four additional nucleotides at the 5'-end. We investigated whether the recombinant FHV RNA1 could replicate in mammalian cells. To address this issue, we prepared in vitro transcribed FHV RNAs that mimicked the recombinant FHV RNA1, and introduced them into baby hamster kidney (BHK) cells. The result showed that the recombinant FHV RNA1 was capable of replication. An eGFP gene inserted into the frame with B2 gene of the FHV RNA1 was also successfully expressed. We also observed that eGFP expression at the protein level was strong at 28℃ but weak at 30℃. Sequence analysis showed that the 3'-ends of the RNA1 and RNA3 replication products were identical to those of the authentic FHV RNAs. This indicates that FHV replicase correctly recognized an internally-located replication signal. In contrast, the 5'-ends of recombinant FHV RNA1 frequently had deletions, indicating random initiation of (+)-strand synthesis.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.8
• /
• pp.3959-3962
• /
• 2016

The ten-eleven-translocation-2 (TET2) gene is a novel tumor suppressor gene involved in several hematological malignancies of myeloid and lymphoid origin. Besides loss-of-function mutations and deletions, hypermethylation of the CpG island at the TET2 promoter has been found in human cancers. The TET2 encoded protein regulates DNA methylation. The present study aimed to examine DNA promoter methylation of TET2 in 100 childhood acute lymphoblastic leukemia (ALL) cases and 120 healthy children in southeast Iran. In addition, mRNA expression levels were assessed in 30 new cases of ALL and 32 controls. Our ndings indicated that promoter methylation of TET2 signi cantly increases the risk of ALL (OR=2.60, 95% CI=1.31-5.12, p=0.0060) in comparison with absent methylation. Furthermore, the TET2 gene was signi cantly downregulated in childhood ALL compared to healthy children (p=0.0235). The results revealed that hypermethylation and downregulation of TET2 gene may play a role in predisposition to childhood ALL. Further studies with larger sample sizes and different ethnicities are needed to con rm our ndings.

• Molecules and Cells
• /
• v.26 no.6
• /
• pp.554-557
• /
• 2008

Double-stranded RNA (dsRNA) induces gene silencing in a sequence-specific manner by a process known as RNA interference (RNAi). The RNA-induced silencing complex (RISC) is a multi-subunit ribonucleoprotein complex that plays a key role in RNAi. VIG (Vasa intronic gene) has been identified as a component of Drosophila RISC; however, the role VIG plays in regulating RNAi is poorly understood. Here, we examined the spatial and temporal expression patterns of VIG-1, the C. elegans ortholog of Drosophila VIG, using a vig-1::gfp fusion construct. This construct contains the 908-bp region immediately upstream of vig-1 gene translation initiation site. Analysis by confocal microscopy demonstrated GFP-VIG-1 expression in a number of tissues including the pharynx, body wall muscle, hypodermis, intestine, reproductive system, and nervous system at the larval and adult stages. Furthermore, western blot analysis showed that VIG-1 is present in each developmental stage examined. To investigate regulatory sequences for vig-1 gene expression, we generated constructs containing deletions in the upstream region. It was determined that the GFP expression pattern of a deletion construct (${\Delta}-908$ to -597) was generally similar to that of the non-deletion construct. In contrast, removal of a larger segment (${\Delta}-908$ to -191) resulted in the loss of GFP expression in most cell types. Collectively, these results indicate that the 406-bp upstream region (-596 to -191) contains essential regulatory sequences required for VIG-1 expression.