• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.844-854
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• 2005

We constructed a defined physical and genetic map of H. pylori strain 51, previously isolated from a Korean patient with a duodenal ulcer, by combining a restriction analysis by pulse-field gel electrophoresis with the construction of a BAC library. A Notl-digest of H. pylori strain 51 genome yielded seven fragments, from which the genomic size was estimated to be 1,698$\pm$24 kb. The BAC library was constructed from 50 to 200 kb fragments of HindIII-digested genomic DNA. From 700 BAC clones, an ordered overlapping maxi-set of 82 BAC clones was assembled that covered the entire genome. The positions of 15 genes were localized in the strain 51 genome with 4-22 kb of resolution and were compared with their orthologues in strain 26695 and strain J99. The arrangement of the 15 genes was identical in strain 51 and strain J99, except for flaA and hpaA. The plasticity zone of strain 51, like that of strain J99, was located in the single region, and was shorter than those of strain 26695 and strain J99. The strain 51 plasticity zone consisted of ORFs common only to strain 51 and J99 or to strain 51 and 26695, as well as strain 51-specific ORFs. Three genetic translocations and/or inversions were found between orthologue ORFs in strain 51 and strain J99. These results show that the chromosomal organization of strain 51 differs from Western strains such as strain 26695 and strain J99.

• Applied Biological Chemistry
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• v.28 no.1
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• pp.19-27
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• 1985

The physicochemical properties of starch isolated from Yullmoo (Coix lachrymajobi var. mayuen stapf.) and Yeomjoo (Coix lachryma-jobi L.) were investigated. The average diameters of starch granules of Yullmoo and Yeomjoo were 12.0 microns, both of all, and the shape of these starch granules were hexagon, octagon and round. X-ray diffraction patterns of two samples were A-types and amylose contents of Yullmoo and Yeomjoo starch were 0% and 23%, respectively, iodine affinities of these were 0.08% and 4.2%, respectively, blue values and alkali numbers of these were 0.13 and 0.43, 2.4 and 7.2, and raising power of these were 280 and 20, respectively. Yullmoo starch had higher swelling power than Yeomjoo starch. The increase in optical transmittance of 0.1% suspensions of Yullmoo and Yeomjoo starches occurred at $60^{\circ}C$ and continued up to $75^{\circ}C$ for Yullmoo, $85^{\circ}C$ for Yeomjoo. Amylogram data on 5% of Yullmoo and Yeomjoo starch suspensions showed that gelatinization temperatures and maximum peak heights of Yullmoo and Yeomjoo were $68.5^{\circ}C\;and\;78^{\circ}C$, 920 and 310 B.U., respectiyely. Intrinsic viscosities of Yullmoo and Yeomjoo starches were 1.49 and 1.77, respectively, and interaction coefficients of the two starches were 0.57 and 0.56, respectively The extent of retrogradation determined at $2^{\circ}C$ showed that retrogradation occurred slowly with Yullmoo starch paste tut little with Yullmoo.

• Journal of Microbiology and Biotechnology
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• v.28 no.4
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• pp.588-596
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• 2018

An endo-${\beta}$-1,4-glucanase gene, cel9K, was cloned using the shot-gun method from Paenibacillus sp. X4, which was isolated from alpine soil. The gene was 2,994 bp in length, encoding a protein of 997 amino acid residues with a predicted signal peptide composed of 32 amino acid residues. Cel9K was a multimodular enzyme, and the molecular mass and theoretical pI of the mature Cel9K were 103.5 kDa and 4.81, respectively. Cel9K contains the GGxxDAGD, PHHR, GAxxGG, YxDDI, and EVxxDYN motifs found in most glycoside hydrolase family 9 (GH9) members. The protein sequence showed the highest similarity (88%) with the cellulase of Bacillus sp. BP23 in comparison with the enzymes with reported properties. The enzyme was purified by chromatography using HiTrap Q, CHT-II, and HiTrap Butyl HP. Using SDS-PAGE/activity staining, the molecular mass of Cel9K was estimated to be 93 kDa, which is a truncated form produced by the proteolytic cleavage of its C-terminus. Cel9K was optimally active at pH 5.5 and $50^{\circ}C$ and showed a half-life of 59.2 min at $50^{\circ}C$. The CMCase activity was increased to more than 150% in the presence of 2 mM $Na^+$, $K^+$, and $Ba^{2+}$, but decreased significantly to less than 50% by $Mn^{2+}$ and $Co^{2+}$. The addition of Cel9K to a commercial enzyme set (Celluclast 1.5L + Novozym 188) increased the saccharification of the pretreated reed and rice straw powders by 30.4% and 15.9%, respectively. The results suggest that Cel9K can be used to enhance the enzymatic conversion of lignocellulosic biomass to reducing sugars as an additive.

• Journal of the Korean Institute of Landscape Architecture
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• v.18 no.4
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• pp.45-71
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• 1991

The landscape systems in Korean island settlements can be recognized as results of ingabitants' ecological adptation to the isolated environment with the limited natural resources. Both the fishery dominant industry in island society and ecological nature of its environments seem to have influenced on inhabitants' environmental cognition as well as the physical landscape of island villages such as its location, spatial pattern in each village, housing form and so on. This study was done mainly by both refering to the related documents and direct observations in case study areas, and results of the study can be summarized as follows. 1. In general, the landscape of an individual island seems to take more innate characteristics of island's own, corresponding to the degree of isolation from mainland. That is, while the landscape of island in neighboring waters takes both inland-like and island-innate landscape character at the same time, the one in the open sea far from land takes more innate landscape character of all island's own in the aspects of village location, land use and housing density etc. 2. The convex landform of most islands brings about more centrifugal village allocation than centripetal allocation in most inland villages. And thus most villages in each island face extremely diverse directions different from the south facing preference in most inland rural villages. 3. Most island villages tend to be located along the ecologically transitional strip between land and sea, so called 'line of life', rather than between hilly slope and flat land as being in most inland village locations. So they are located with marine ecology bounded fishing ground ahead and land ecology bounded agricultural site at the back of them. 4. The settlement pattern of the island fishing villages shows more compact spatial structure than that of inland agricultural villages, due to the absolute limits of usable land resources and the adaptation to the marine environment with severe sea winds and waves or for the easy accessability to the fishing grounds. And also the managerial patterns of public owned sea weed catching ground, which take each family as the unit of usership rather than an individual, seem to make the villagescape more compact and the size of Individual residence smaller than that of inland agricultural village. 5. The folk shrine('Dand') systems, in persrective of villagescape, represent innate environmental cognition of island inhabitants above all other cultural landscape elements in the island. Usually the kinds and the meanings of island's communal shrine and its allocative patternsin island villagescape are composed of set with binary opposition, for example 'Upper shrine(representing 'earth', 'mountain' or 'fire')' and 'Lower Shrine(representing 'sea', 'dragon' or 'water') are those. They are usually located at contrary positions in villagescape each other. That is, they are located at 'the virtical center or visual terminus(Upper shrine at hillside behind the village)' and 'the border or entrance(Lower Shrine at seashore in front of the village)'. Each of these shirines' divinity coincides with each subsystem of island's natural eco-system(earth sphere vs marine sphere) and they also contribute to ecological conservation, bonded with the 'Sacred Forest(usually with another function of windbreak)' or 'Sacred Natural Fountain' nearby them, which are representatives of island's natural resources.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.73-73
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• 2018

Bacterial leaf blight(BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a collection of 192 accessions was used in the genome-wide association study (GWAS) for BLB resistance loci against four Korean races of Xoo that were represented by the prevailing BLB isolates under Xoo differential system. A total of 192 accessions of rice germplasm were selected on the basis of the bioassay using four isolated races of Xoo such as K1, K2, K3 and K3a. The selected accessions was used to prepare 384-plex genotyping by sequencing (GBS) libraries and Illumina HiSeq 2000 paired- end read was used for GBS sequencing. GWAS was conducted using T ASSEL 5.0. The T ASSEL program uses a mixed linear model (MLM). T he results of the bioassay using a selected set of 192 accessions showed that a large number of accessions (93.75%) were resistant to K1 race, while the least number of accessions (34.37%) resisted K3a race. For races K2 and K3, the resistant germplasm proportion remained between 66.67 to 70.83%. T he genotypic data produced SNP matrix for a total of 293,379 SNPs. After imputation the missing data was removed, which exhibited 34,724 SNPs for association analysis. GWAS results showed strong signals of association at a threshold of [-log10(P-value)] more than5 (K1 and K2) and more than4 (K3 and K3a) for nine of the 39 SNPs, which are plausible candidate loci of resistance genes. T hese SNP loci were positioned on rice chromosome 2, 9, and 11 for K1 and K2 races, whereas on chromosome 4, 6, 11, and 12 for K3 and K3a races. The significant loci detected have also been illustrated, NBS-LRR type disease resistance protein, SNARE domain containing protein, Histone deacetylase 19, NADP-dependent oxidoreductase, and other expressed and unknown proteins. Our results provide a better understanding of the distribution of genetic variation of BLB resistance to Korean pathogen races and breeding of resistant rice.

• Ocean and Polar Research
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• v.35 no.4
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• pp.407-414
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• 2013

One of the most important challenges facing the Spirulina mass cultivation industry is to find a way to reduce the high production costs involved in production. Although the most commercial medium (Zarrouk's medium) for Spirulina cultivation is too expensive to use, it contains higher amount of $NaHCO_3$ (16.80 g $L^{-1}$), trace metals and vitamin solutions. The purpose of this study was to increase the efficiency of Spirulina platensis biomass production by developing a low-cost culture medium at an isolated tropical island such as Chuuk State, Federated States of Micronesia (FSM). This study set out to formulate a lowcost medium for the culture of S. platensis, by substituting nutrients of Zarrouk's medium using fertilizer- grade urea and soil extract with a different concentration of carbon source under natural weather condition. In order to select a low-cost culture medium of S. platensis, 10 culture media were prepared with different concentrations of nitrogen (urea and $NaNO_3$) and $NaHCO_3$. The highest maximum specific growth rate (${\mu}max$) and mass production were 0.50 $day^{-1}$ and 1.05 g $L^{-1}$ in modified medium ($NaHCO_3$ 7.50 g $L^{-1}$, urea 2.00 g $L^{-1}$ without $NaNO_3$) among all the synthesized media. Protein (56.14%) and carbohydrate (16.21%) concentrations of the lyophilized standard samples were estimated with highest concentration of glutamic acid (14.93%). This study revealed that the use of a low concentration of urea and $NaHCO_3$ with soil extract was an affordable medium for natural mass cultivation in the FSM.

• Research in Plant Disease
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• v.22 no.4
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• pp.269-275
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• 2016

Black shoot blight disease caused by Erwinia pyrifoliae have damaged economic loss to apple and pear growers until now since it was firstly reported in 1995 in Korea. This study was performed to reduce economic loss by mandatory eradication of all infected trees in case of more 10% disease incidence per orchard as official control. It also aims to set up effective management protocol for this disease by examining how far bacterial pathogen is present from the border of symptomatic and asymptomatic regions in infected apple twigs. Colony-PCR using isolated bacterial cells instead of genomic DNA was used to identify bacterial pathogen, EpSPF/EpSPR primer designed in enterobacterial repetitive intergenic consensus (ERIC) region was selected as specific for E. pyrifoliae. As results of monitoring of this disease during April to October in 2014-2015 by colony-PCR, occurrence of this disease was frequent from mid-May to early-July, when daily average temperature was around $25^{\circ}C$. Moreover, bacterial cells were continuously detected only in symptomatic regions and also asymptomatic regions of less than 20 cm from symptomatic regions. Therefore, we concluded that pruning of infected twigs at the region of more than 20 cm from symptomatic regions might be effective to manage black shoot blight disease in apple trees.

• Journal of Life Science
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• v.17 no.8 s.88
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• pp.1157-1165
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• 2007

VvMSA, a grapevine ASR which is highly inducible by sugar and abscisic acid signals was previously shown to be a transcription factor for a hexose transporter gene VvHT1. We isolated a cDNA clone, VlASR which is regulated temporally during the grape berry development by ACP RT-PCR (annealing control primer reverse transcriptase-polymerase chain reaction) and it proved identical to VvMSA. RT-PCR and real-time PCR analyses revealed that the VlASR gene was expressed in berries at fruit set and that its expression increased as berries aged but decreased at the late ripening stage. In order to understand the regulatory mechanism of the asr gene, a genomic fragment was cloned from grapevine. The genomic DNA was 1375 bp long and a sugar box (sucrose box 3 and sucrose responsive element 1) was identified in the 611 bp upstream region of the open reading frame. Analysis of the VlASR promoter::reporter gene fusion demonstrated that this promoter was expressed in transgenic Arabidopsis even without sucrose treatment. This result suggests that the ASR/VvHT1-mediated sugar/ABA signaling, previously reported in grapevine, may not function in Arabidopsis which has no ASR homologue.

• Korean Journal of Soil Science and Fertilizer
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• v.37 no.4
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• pp.266-287
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• 2004

The non infecting, plant associated bacteria have attracted increased attention for stimulating plant growth and as environmental friendly plant protecting agents. Pink-pigmented facultatively methylotrophic bacteria (PPFMs), classified as Methylobacterium spp., are persistent colonizers of plant leaf surfaces. As the leaves of most or all plants harbor PPFMs that utilize leaf methanol as their sole source of carbon and energy, which is a specific attribute of the genus Methylobacterium. Although they are not well known, these bacteria are co-evolved, interacting partners in plant metabolism. This claim is supported, for example, by the following observations: (1) PPFMs are seed-transmitted, (2) PPFMs are frequently found in putatively axenic cell cultures, (3) Low numbers of seed-borne PPFMs correlate with low germinability, (4) Plants with reduced numbers of PPFM show elevated shoot/root ratios, (5) Foliar application of PPFMs to soybean during pod fill enhances seed set and yield, (6) Liverwort tissue in culture requires PPFM-produced vitamin B12 for growth, (7) treated plants to suppress or decrease disease incidence of sheath blight caused by Rhizoctonia solani in rice, and (8) the PPFM inoculation induced number of stomata, chlorophyll concentration and malic acid content, they led to increased photosynthetic activity. Methylobacterium spp. are bacterial symbionts of plants, shown previously to participate in plant metabolism by consuming plant waste products and producing metabolites useful to the plant. There are reports that inform about the beneficial interactions between this group of bacteria and plants. Screening of such kind of bacteria having immense plant growth promoting activities like nitrogen fixation, phytohormone production, alleviating water stress to the plants can be successfully isolated and characterized and integration of such kind of organism in crop production will lead to increased productivity.

• Journal of Gastric Cancer
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• v.16 no.4
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• pp.221-229
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• 2016

Purpose: Dysregulated microRNAs (miRNAs) can contribute to cancer development by leading to abnormal proliferation of cells, apoptosis, and differentiation. Although several miRNAs that are related to gastric cancer have been identified, the reported results have been inconsistent. The aim of this study was to determine miRNA expression profiles and validate miRNAs up- and down-regulated in gastric cancer. Materials and Methods: We evaluated 34 primary gastric cancer tissues and paired adjacent nontumorous gastric tissues. Total RNA was extracted, and low-molecular-weight RNAs (<200 nucleotides) were isolated for further analysis. Two pairs of tissues were processed for GeneChip microarray analysis, and the identified up- and down-regulated miRNAs were validated by real-time quantitative polymerase chain reaction (qPCR). Results: In the set of differentially expressed miRNAs, 5 were overexpressed by more than 2 fold, and 5 were reduced by 2 fold or less in gastric cancer tissues compared with normal gastric tissues. Four of these miRNAs (miR-196b-5p, miR-375, miR-483-5p, and miR-486-5p) were then validated by qPCR, and the relative expression levels of 2 miRNAs (miR-196b-5p and miR-375) were significantly different between cancer and normal tissues. Conclusions: Our results revealed that the expression of miR-196b-5p and miR-375 significantly correlates with gastric cancer. These miRNAs could therefore serve as diagnostic biomarkers of gastric cancer.