• The Plant Pathology Journal
• /
• v.32 no.2
• /
• pp.136-144
• /
• 2016

Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

• Journal of Plant Biotechnology
• /
• v.1 no.1
• /
• pp.13-19
• /
• 1999

The visco-elastic properties of gluten are major determinants of the processing properties of doughs. These visco-elastic properties are strongly influenced by the ratio of monomeric and polymeric proteins and the size distribution of the polymeric proteins, which make up the gluten fraction of the dough. Recent studies have revealed that other features, such as the number of the cysteine residues of the HMW-GS, also play an important role in determining the functional characteristics. To modify the processing properties at molecular level, the relationship between the structure of molecules and dough properties has to be understood. In order to explore the relationships between individual proteins and dough properties, we have developed procedures for incorporating bacterially expressed proteins into doughs, and measuring their functional properties in small-scale equipment. A major problem in investigating the structure/function relationships of individual seed storage proteins is to obtain sufficient amounts of pure polypeptides from the complex families of proteins expressed in the endosperm. Therefore, we have established a simplified model system in which we produce specific protein genes through bacterial expression and test their functional properties in smallscale apparatus after incorporation into base flour. An S poor protein gene has been chosen as a template gene. This template gene has been modified using standard recombinant DNA techniques in order to test the effects of varying the number and position of cysteine residues, and the size of the protein. Doughs have been mixed in small scale apparatus and characterized with respect to their polymeric composition and their functional properties, including dough mixing, extensibility and small scale bating. We conclude that dough characteristics can be manipulated in a predictable manner by altering the cysteine residues and the size of high molecular weight glutenins.

• Proceedings of the Botanical Society of Korea Conference
• /
• 1987.07a
• /
• pp.391-401
• /
• 1987

Plant chloroplast DNA exists as an unique circular structure in which large single copy(LSC) region and small single copy (SSC) region are separated by large inverted repeat sequences (IRS). It has been known that the unique existence of inverted repeat sequences in chloroplast DNA has no relation with the stability of the chloroplast DNA, but causes the inversion between inverted repeat its biological significance has not been understood so far. In rice, several gene clusters have been cloned and sequenced which contain ribulose-5-biophosphate car-boxylase large subunit (rbcL). Especially, one rbcL gene is linked with rp12 gene which is located in the IRS region in one of the gene clusters. By comparison of nucleotide sequence, the two genes are found to be linked through 151 bp repeat sequence which is homologous to the rp123 gene in IRS region. The repeat sequence is found to be located 3' downstream of rfcL gene and near psbA gene in LSC region. The existence of these repeat sequences and the presence of gene clusters caused by the gene rearrangement thorough the repeat sequence provide a possible which is found to be dispersed chloroplast DNA provide the model system to explaine the heterogeneity of the chloroplast DNA in rice in term of gene rearrangement.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.19
• /
• pp.8019-8026
• /
• 2014

The promyelocytic leukemia (PML) gene is a gene known to be a tumor suppressor, although recent data suggest that it has a dual function in tumorigenesis. It was initially discovered in acute promyelocytic leukemia (APL) in which a t(15; 17) chromosomal translocation fused it to the retinoic acid receptor alpha ($RAR{\alpha}$). It has been shown to be involved in various types of cancer. It has at least 6 nuclear isoforms and a cytoplasmic type with different characteristics. Its multiple functions in growth inhibition, apoptosis induction, replicative senescence, inhibition of oncogenic transformation, and suppression of migration and angiogenesis have made it a therapeutic target for cancer therapy. However, its dual role in the process of tumorigenesis has made this field challenging. In this review, we discuss PML structure, functions and expression in tumors.

• Journal of Microbiology
• /
• v.37 no.3
• /
• pp.175-179
• /
• 1999

To elucidate the role of vir-box in the expression of the virE gene, the vir-box was modified by site-directed mutagenesis and tested for ${\beta}$-galactosidase activities. A, C, T T, A, C substitutions at -62, -63, and -65 positions, destroying the 5'-region of the vir-box and A T at position -55, destroying the 3'-region of the vir-box respectively, showed only 17% promoter activity. When the vir-box was modified to contain perfect dyad symmetry structure (DSR) by the substitutions T, G A, T at -60 an d-61 positions, ${\beta}$-glactosidase activity increased 302%. These results indicate that the 5' and 3'-region of vir-box as well as the imperfect DSR of the vir-box itself may play a very important role in the regulation of virE gene expression.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.200-209
• /
• 2003

주어진 염기서열에서 유전자 영역을 예측하는 유전자 구조 예측은 유전체 프로젝트의 중요한 과정 중 하나이며 유전체 프로젝트 전체에 큰 영향을 준다. 진핵생물의 유전체가 원핵생물의 유전체에 비해 더 복잡한 구조를 가지기 때문에 진핵생물의 유전자 구조 예측 모델 역시원핵생물에 비해 다양한 모델이 제안되었다. 본 연구팀은 duration hidden markov model을 기본형태로 하여 EGSP(Eukaryotic Gene Structure Prediction)프로그램을 개발하였다. 현재 개발된 진핵생물의 유전자 구조 예측 알고리즘 중에서 GenScan이 가장 정교한 젓으로 보고 되고 있는데, EGSP의 결과분석을 위해 Genscan과 함께 GeneID, Morgan의 예측결과를 여러 가지 기준에서 비교하였다. EGSP는 정교한 예측모델을 가지고 있음에도 각 구성모듈에 대한 파라메터의 정교함에서 부족한 면이 나타나므로, 모델의 개선과 각 모듈의 조율을 통해 더욱 개선된 결과를 가지게 될 것이다.

• Journal of Microbiology and Biotechnology
• /
• v.13 no.4
• /
• pp.483-486
• /
• 2003

3'-[S-Methyl-cysteinyl]-3'-amino-3'-deoxy-N,N- dimethyl adenosine, cystocin, is a biosynthesized antibiotic material newly identified from Streptomyces sp. GCA0001. Its structure was found to be similar to puromycin, where the terminal tyrosine is replaced by a methyl cysteine. NMR data prove that the 3-ammo ribose is connected to dimethylaminopurine through the anomeric carbon at 1'-carbon. The methyl cysteinyl unit is connected to the amino unit of ribose by peptide bond. The verification of the structure was performed by comparing the puromycin nucleosides resulted from the hydrolysis of cystocin and puromycin, respectively. Antibiotic activity of cystocin against Streptococcus was found to be two times more potent than that of puromycin.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.1
• /
• pp.18-23
• /
• 1997

Data from structure/activity studies in vir gene induction system have led to evaluate the working hypothesis of interaction between phenolic inducers and phenol binding proteins. The primary specificity in the association of a phenolic inducer with its receptor in our system is hypothesized to be the hydrogen bonding interactions through the ortho methoxy substituents as well as the proton transfer between the inducer and the binding protein. In this paper the proposed working model for phenol-mediating signal transduction was evaluated in several ways. The importance of the general acid-base catalysis was first addressed by the presence of an acidic residue and a basic residue in the phenol binding protein. Series of compounds were tested for vir gene expression activity to confirm the generation of a strong nucleophile by an acidic residue and an involvement of a basic residue as a proton acceptor. An attempt was made to correlate the pKa values of the phenolic compounds with vir gene induction activities as inducers to further support the proposed proton transfer mechanism. Finally, it was also observed that the regioselectively attached methoxy group on phenol compounds is required as the proper hydrogen bond acceptor.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.24 no.1
• /
• pp.41-47
• /
• 2012

The Scarites aterrimus (Coleoptera: Carabidae) dwells exclusively on coastal sandy dunes. Previously, we investigated the nation-wide magnitude and nature of genetic diversity of the species using mitochondrial COI gene and found moderate to low magnitude of sequence diversity, the presence of closely related haplotypes, and relatively high gene flow estimate. Based on these observations we concluded that the species had no historical barriers that bolster genetic subdivision and possible population decline. In this study, we additionally sequenced mitochondrial COII gene from 23 individuals collected from 9 Korean localities to confirm previous findings. Sequencing of 688 bp COII gene provided 5 haplotypes ranging in sequence divergence from 0.145% to 0.291% (1 ~ 2 bp), further confirming low sequence divergence of the species. Gene flow estimates and genetic diversity estimates also support the previous findings that there had been no historical barriers that bolster genetic subdivision.

• Genomics & Informatics
• /
• v.1 no.1
• /
• pp.32-39
• /
• 2003

We present a latent variable model-based approach to the analysis of gene expression patterns, coupled with topographic clustering. Aspect model, a latent variable model for dyadic data, is applied to extract latent patterns underlying complex variations of gene expression levels. Then a topographic clustering is performed to find coherent groups of genes, based on the extracted latent patterns as well as individual gene expression behaviors. Applied to cell cycle­regulated genes of the yeast Saccharomyces cerevisiae, the proposed method could discover biologically meaningful patterns related with characteristic expression behavior in particular cell cycle phases. In addition, the display of the variation in the composition of these latent patterns on the cluster map provided more facilitated interpretation of the resulting cluster structure. From this, we argue that latent variable models, coupled with topographic clustering, are a promising tool for explorative analysis of gene expression data.