• The Journal of the Korean Society for Microbiology
• /
• v.34 no.6
• /
• pp.519-532
• /
• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Korean Journal of Soil Science and Fertilizer
• /
• v.41 no.6
• /
• pp.415-418
• /
• 2008

The application of sludge wastes into agricultural fields has been increasing annually in Korea. In particular, sewage sludge application has been widely accepted in decades. Sewage sludge application aid in the recycling of essential nutrients and act as a source of organic matter improving the structure and water-holding properties of the soil. The efficient use of sludge wastes, however, requires an individual assessment of waste products. This study assessed the biological characteristics of organic waste-treated lysimeter soils and develop its indicator to assess the soil health of organic waste-treated lysimeter soils. Several analytical techniques more recently developed such as restriction fragment length polymorphism (RFLP), phospholipid fatty acid (PLFA), and community level substrate utilization (CLSU) fingerprints allow for detailed analyses of soil microbial communities. PLFA and RFLP was, therefore, used in the study to characterize the microbial communities in soil without the need to isolate individual fungi and bacteria. PLFA, RFLP and CLSU have been utilized to assess microbial characteristics of the lysimeter soils with four different sludge wastes for eight consecutive years. Each of these methods was analyzed for a different aspect of soil microbial characteristics. The study would disclose those methods yielded highly reproductive results for each soil and allow distinguishing the soils based on the structures of specific geneand PLFA-pools more than CLSU fingerprints. PLFA methods, especially, revealed the same relative similarities of the treated soils based on cluster analysis of the biological characteristics. Pig manure compost-treated soil, however, was only the same relative resemblance among the three methods. These results indicated that PLFA easily assessed the biological soil characterization.

• The Korean Journal of Pesticide Science
• /
• v.4 no.1
• /
• pp.32-37
• /
• 2000

A series of transition metal complexes of 3,6-bis(6'-methyl-2'-pyridyl)pyridazine ($L^{1}$) and 3,6-bis(2'-pyridyl)pyridazine ($L^{2}$) as artificial nuclease, $1{\sim}8$ were synthesized. After determining of X-ray crystal structure, hydrolysis rate constants of phosphates, as DNA model compound and biological activities were confirmed. $L^{2}$-Zn(II) complex, 8 was shown the best hydrolysis rate constant. The $L^{2}$-Ni(II) complex, 5 and $L^{2}$-Co(II) complex, 6 showed the highest herbicidal activity against SCP (Scriptus Juncoids) with excellent tolerance to rice, ORY (Oryzae sativa L.). And the $L^{1}$-Co(II) complex, 2, $L^{1}$-Zn(II) complex, 4 and ligand ($L^{1}$ amp; $L^{2}$) displayed above 90% fungicidal activity against MAG (Magnaporthe grisea).

• Asian-Australasian Journal of Animal Sciences
• /
• v.27 no.9
• /
• pp.1345-1354
• /
• 2014

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

• Journal of Microbiology and Biotechnology
• /
• v.12 no.1
• /
• pp.157-161
• /
• 2002

A lactic acid bacteria with ${\beta}$-gal activity was isolated from Kimchi, a traditional fermented vegetable food in Korea. The isolate was identified as a Lactococcus lactis strain and named L. lactis A2. The gene encoding ${\beta}$-gal of L. lactis A2 was cloned as a 5.8 kb PstI fragment. DNA sequencing identified the complete lacA (galactoside acetyltransferase)-lacZ (${\beta}$-galactosidase) genes together with the 3' part of upstream galT (galactose-1-phosphate uridyltransferase), and the 5'region of downstream galE (UDP-galactose-4-epimerase) genes. L. lactis A2 had the same gal/lac operon structure as in L. lactis subsp. lactis 7962. Other genes of the Leloir pathway are most likely to be located in the 5'upstream of the 5.8 kb fragment on the A2 chromosome. Sequences downstream of galE were different from those of L. lactis subsp. lactis 7962.

• Microbiology and Biotechnology Letters
• /
• v.48 no.3
• /
• pp.287-295
• /
• 2020

Lactobacillus zymae GU240 was previously isolated from Kimchi, a Korean fermented vegetable, as a strong GABA producer. The strain showed β-galactosidase (β-Gal) activity on MRS agar plates with X-gal. When growth and β-Gal activities of GU240 were measured using MRS (glucose, 2%, w/v) and MRSL (lactose, 2%, w/v) broths, cells were found to grow slowly in MRSL, and the β-Gal activity (36 units at 4 h) was lower than that of cells grown in MRS (94 units at 16 h). The highest OD₆₀₀ value of the culture in MRS was 1.6 at 24 h at 37℃, whereas that of the culture in MRSL was 0.6 at 16 h. β-Gal activity of the culture in MRS reached the maximum (95.6 u/ml) at 16 h, decreased thereafter, and was not detected at 48 h. β-Gal activity for culture in MRSL reached its highest (36 u/ml) at 4 h and decreased gradually, but some activity (11.05 u/ml) still remained at 72 h. The structural gene encoding β-Gal in L. zymae GU240 was cloned as a 3.1 kb fragment, and DNA sequencing confirmed the presence of complete lacLM genes. lacLM genes from L. zymae GU240 showed 98-99% homologies in nucleotide sequences with other lacLM genes from L. brevis. Reverse transcription (RT)-PCR confirmed the operon structure of lacLM. The results indicated that L. zymae GU240 might be in the process of losing the ability to grow rapidly on lactose-containing medium, such as milk, due to adaptations to plant environments, including kimchi.

• Korean Journal of Microbiology
• /
• v.41 no.2
• /
• pp.152-156
• /
• 2005

In the present study, lactic acid bacterium that has antibacterial activity against Helicobacter pylori was isolated from feces of newborn baby. The selection was based on the ability to inhibit the growth of H. pylori and to withstand harsh environmental conditions such as acidic pH and high bile concentration. By biochemical test and 16S rDNA sequencing, selected strain was turned out to be an Pediococcus acidilactici, therefore designated to P. acidilactici GMB7330. In order to investigate the inhibitory effects of P. acidilactici GMB7330 on the growth of H. pylori, we have tested in vitro studies such as cell viability and urease test. These results showed that antibacterial activity of P. acidilactici GMB7330 significantly decreased the viable cell count and urease activity of H. pylori. Antibacterial activity of P. acidilactici GMB7330 against H. pylori remained after pH adjustment to neutral, and the concentration of lactate produced from P. acidilactici GMB7330 was not enough to inhibit H. pylori. On the basis of the analysis by transmission electron microscope, it demonstrated that addition of P. acidilactici GMB7330 destroyed the cell structure of H. pylori. These results strongly suggested that P. acidilactici GMB7330 produce antibacterial substances to be able to inhibit the growth of H. pylori other than lactic acid.

• Parasites, Hosts and Diseases
• /
• v.54 no.6
• /
• pp.759-768
• /
• 2016

Cystic echinococcosis (CE) treatment urgently requires a novel drug. The p38 mitogen-activated protein kinases (MAPKs) are a family of Ser/Thr protein kinases, but still have to be characterized in Echinococcus granulosus. We identified a 1,107 bp cDNA encoding a 368 amino acid MAPK protein (Egp38) in E. granulosus. Egp38 exhibits 2 distinguishing features of p38-like kinases: a highly conserved T-X-Y motif and an activation loop segment. Structural homology modeling indicated a conserved structure among Egp38, EmMPK2, and H. sapiens $p38{\alpha}$, implying a common binding mechanism for the ligand domain and downstream signal transduction processing similar to that described for $p38{\alpha}$. Egp38 and its phosphorylated form are expressed in the E. granulosus larval stages vesicle and protoscolices during intermediate host infection of an intermediate host. Treatment of in vitro cultivated protoscolices with the p38-MAPK inhibitor ML3403 effectively suppressed Egp38 activity and led to significant protoscolices death within 5 days. Treatment of in vitro-cultivated protoscolices with $TGF-{\beta}1$ effectively induced Egp38 phosphorylation. In summary, the MAPK, Egp38, was identified in E. granulosus, as an anti-CE drug target and participates in the interplay between the host and E. granulosus via human $TGF-{\beta}1$.

• Journal of Life Science
• /
• v.27 no.6
• /
• pp.708-725
• /
• 2017

Ionizing radiation is enough energy to interact with matter to remove orbital electrons, neutrons, and protons in the atom. Ionizing radiation like this leads to oxidizing metabolism that alter molecular structure through direct and indirect interactions of radiation with the deoxyribonucleic acid in the nucleus and cytoplasmic organelles or via products of cytoplasm radiolysis. These ionization can result in tissue damage and disruption of cellular function at the molecular level. Consequently, ionizing radiation-induced modifications of ion channels and transporters have been reported. When the harmful effects exceed those of homeostatic biochemical processes, induced biological changes persist and may be propagated to progeny cells. Also, Reactive oxygen species formed on the effect of ionizing radiation can get across into neighboring cells through the cell junctions that are responsible for intercellular chemical communication, and may there bring about changes characteristic to radiation damage. Depending on radiation dose, dose-rate and quality, these protective mechanisms may or may not be sufficient to cope with the stress. This paper briefly reviewed reports on ionization radiation effects on cellular level that support the concept of radiation biology. A better understanding of the biological effects of ionizing radiation will lead to better use of and better protection from radiation.

• Transactions of the Korean Society of Mechanical Engineers B
• /
• v.41 no.1
• /
• pp.63-67
• /
• 2017

In bioscience and biotechnology, the research of fundamental life mechanisms and their diseases caused by insufficiency is important. The study of a whole organism is difficult and sometimes impossible because of DNA, RNA, proteins, cellular organelles, various cells, and organs. Cell cultures can provide a simple method for researching cellular mechanisms and conditions, both in terms of physiological performance, and in response to chemical stimulation. According to conventional cell culture methodology, the flat surface is used with surface treatments for cell adhesion on the surface. Micro- and nanoscale patterns have been developed with chemical and biochemical modifications for cell immobilization. In this study, HeLa cell culture on nanostructures patterns was studied, including the 300 nm line and 150 nm pillar structures, using nanoimprint lithography and pyrrole as a biocompatible conducting polymer.