• Korean Journal of Microbiology
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• v.40 no.3
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• pp.189-198
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• 2004

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size ($60{\pm}2$) bp-($667{\pm}2$) bp) appeared evenly at the surface sediments but two T-RFs with 60(${\pm}2$)bp and 93 (${\pm}2$)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (${\geq}similarity$ 98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to $\alpha$-, $\gamma$-, and $\delta$-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth). $\gamma$-Proteobacteria and $\delta$-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.

• The Korean Journal of Zoology
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• v.31 no.1
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• pp.49-55
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• 1988

A few SV4O-transformed human cells such as SV8O are potentially tumorigenic but rejected by athymic hosts. However, one cell line in this group (W118IVA-2) is known to be fully tumorigenic. Two clones were obtained after the injection of W118IVA-2, of which NW1SC1-1 was tumorigenic but NW18C1-2 was not in nude mice. As examined by Southern blot analysis, NW18C1-1 appears to contain more copy number of SV40 sequences than NW18C1-2 does. However, it was unable to demonstrate that this difference elicits the tumorigenicity in NW18C1-1 but not in NW18C1-2. Therefore, the latter clone was tested if it expresses SV40 early genes to produce large T as well as small t antigens using indirect immunofluorescent assay and immunoprecipitation. In addition, mouse NIH3T3 cells were transfected with the cellular DNA of NW1SC1-2 as well as that of NW18C1-1 to examine if the viral genomes in the clones can make the nontransformed cells to acquire malignant growth potential in vivo. The transformed cells expressed large T antigen and became tumorigenic. Thus, the transforming functions of NW1SC1-2 cell appers to be intact. These results clearly suggest that the inability of NW18C1-2 cell to form tumor in nude mice is not because they are inherently nontumorigenic. However, the possibility that the interaction of SV40 with its host differs in these clones can not he ruled out.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.

• Journal of Korean Society of Forest Science
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• v.90 no.6
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• pp.734-741
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• 2001

The two-month-old rooted-cuttings of Populus alba ${\times}$ glandulosa, P. euramericana and P. nigra ${\times}$ maximowiczii clones were exposed to livestock waste water - one of major water pollutants, and ground water in order to determine the effects of livestock waste water on growth response and absorption capacity of the species. For this purpose, 5 clones of each species were used. In all the species, the height growth of rooted-cuttings was better in livestock waste water treatment than in ground water. Of all the poplar species compared, the height growth was best in P. alba ${\times}$ glandulosa. In the cases of P. euramericana and P. nigra ${\times}$ maximowiczii, the height growth in the livestock waste water treatment was statistically different among clones, whereas there was no significant difference among P. alba ${\times}$ glandulosa clones. Aboveground biomass such as leaf and shoot dry weight of all the species increased in the livestock waste water treatment, while root dry weight decreased. In addition, chlorophyll contents in leaf of all the poplar species increased in the livestock waste water treatment. All the poplar trees showed temporal variation in the absorption amount of livestock waste water during the experimental period. In all the poplar species, the absorption amount of livestock waste water was less than that of ground water. Of 3 poplar species, P. alba ${\times}$ glandulosa was best in the absorption capacity of livestock waste water. Of all 15 poplar clones compared in this study, the 72-16 clone of P. alba ${\times}$ glandulosa showed the best absorption capacity.

• Journal of Korean Society of Forest Science
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• v.90 no.1
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• pp.10-18
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• 2001

Experiments were conducted to compare ozone sensitivity among clones. Ten clones of Papulus deltoides Marsh. were exposured in walk-in type chambers to charcoal-filtered air, 50ppb, 100ppb, and 150ppb ozone for 8h $day^{-1}$ for 21 consecutive days. Occurrence of premature leaf-fall, and visible foliar injury expressed as adaxial stipple were measured after termination of ozone exposure for 3 weeks. Rate of premature leaf-fall increased progressively according to ozone exposure levels. As a result, rate of premature leaf-fall was estimated over 50% at 150ppb ozone. In the charcoal-filtered air and 50ppb ozone treatments, visible foliar injury was not found. But injury was estimated as LA; 17.3%, AA; 6.5%, and LAA; 1.6% to 100ppb ozone treatment and LA; 34.1%, AA; 17.5%, and LAA; 7.4% to 150ppb ozone treatment. Clonal differences of sensitivity within the species were manifested by significant clone differences of adaxial stipple(LAA) in 100ppb and 150ppb ozone treatments.

• Journal of Korean Society of Forest Science
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• v.90 no.6
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• pp.717-724
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• 2001

This study was conducted in an attempt to quantify some traits that may be involved in the reproductive process of Pinus thunbergii. During the past 6 years (1995-2000), we surveyed flowering patterns of 60 P. thunbergii clones in a seed orchard which was established in Anmyon-do, 1979. From this survey, we estimated clonal contributions of male and female flowers and sexual asymmetry. Among 60 clones, 18 clones (30%) accounted for 0.37 (1999)~0.46 (1995) of clonal contribution in female flowers and 0.44 (1999)~0.57 (1995) of clonal contribution in male flowers. As compared with the previous reports in other pine species, more clones made contributions to reproductive process in P. thunbergii seed orchard. The relative effective population numbers for females (v♀) varied from 0.59 (1995) to 0.91 (1999) and those for males ( v♂) were between 0.56 (1995) and 0.83 (1998) at gamete level. This showed that the female gametes effectively contribute to the reproductive process more than did the male gametes. The relative effective population numbers at clonal level ($v_b$) were in the range of 0.72 (1995) and 0.93 (1999). More than 73% of the total clones showed values of 0.4~0.6 ($0.5{\pm}0.1$) in maleness index. The values averaged over all the clones were temporally variable with the range of 73% in 1996 and 100% in 2000. The degree of sexual asymmetry ($A_s$) ranged from 0.09 to 0.26. These values were relatively low when compared with those of other trees, suggesting that P. thunbergii seed orchard remains a high level of homogeneity in the number of male and female. All of the various types of effective population numbers were positively correlated with each other while they were negatively correlated with the degree of sexual asymmetry.

• KIPS Transactions on Software and Data Engineering
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• v.12 no.1
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• pp.1-18
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• 2023

Similar software is often developed with the Clone-And-Own (CAO) approach that copies and modifies existing artifacts. The CAO approach is considered as a bad practice because it makes maintenance difficult as the number of cloned products increases. Software product line engineering is a methodology that can solve the issue of the CAO approach by developing a product family through systematic reuse. Migrating product families that have been developed with the CAO approach to the product line engineering begins with finding, integrating, and building them as reusable assets. However, cloning occurs at various levels from directories to code lines, and their structures can be changed. This makes it difficult to build product line code base simply by finding clones. Successful migration thus requires unifying the source code's file path, class name, and method signature. This paper proposes a clustering method that identifies a set of similar codes scattered across product variants and some of their method full paths are different, so path unification is necessary. In order to show the effectiveness of the proposed method, we conducted an experiment using the Apo Games product line, which has evolved with the CAO approach. As a result, the average precision of clustering performed without preprocessing was 0.91 and the number of identified common clusters was 0, whereas our method showed 0.98 and 15 respectively.

• The korean journal of orthodontics
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• v.36 no.4
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• pp.251-262
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• 2006

Objective: The purpose of this study was to compare the bacterial flora at the peri-implant sulcus of the orthodontic mini-implant placed in the alveolar mucosa with the bacterial flora at the adjacent healthy gingival sulcus. Methods: Two plaque samples from 7 patients were collected by inserting paper points into the sulcus between the mini-implant and ligature wire connected to the mini-implant head and inflamed alveolar mucosa, and from the gingival sulcus of a healthy tooth adjacent to the mini-implant. Results: Using 16S rDNA clone library, the 24 kinds of bacteria including Haemophilus aphrophilus, Sphingomonas species, Capnocytophaga species, Prevotella melaninogenica, Lachnospiraceae species, Porphyromonas species, Neisseria flava were identified only from the sulcus around the mini-implant. These bacteria constituted only 9.2% of total clones, and the bacteria identified from both the sulcus around mini-implants and the gingival sulcus constituted 80.4% of total clones. Of these bacteria, clones of Prevotella species, Atopobium rimae, Veillonella species, Streptococcus intermedius/constellatus, Streptococcus salivarius were more frequently isolated from the peri-implant sulcus. Conclusion: This study suggests that a broad epidemiological study is needed to find causative bacteria which induce inflammation from the peri-implant sulcus.

• Applied Biological Chemistry
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• v.50 no.4
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• pp.268-275
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• 2007

Diversity of the mud flat microbial population in Suncheon Bay was investigated by studying extracellular enzyme activities and 16S rDNA sequences. Four culturable bacterial strains with CMCase, xylanase and protease activities were isolated from the wetland and the mud flat. All the strains produced more xylanase activity than CMCase or protease activity, and the properties of the isolate enzymes from the wetland were similar to those from the mud flat. About 2,000 clones were obtained with the 16S rDNA amplified from the metagenomic DNA isolated from the mud samples. Based on the restriction pattern(s), seventeen clones were selected for base sequence analysis. Of the 17 clones, only 35% (6 clones) were found to be cultured strains and 65% (11 clones) to be uncultured strains. The similarities in the base sequences of the clones ranged from 91.0% to 99.9% with an average similarity of 97.3%. The clones could be divided into 7 groups, Proteobacteria (9 clones, 52.9%), Firmicutes (3 clones, 17.6%), Bacteroidetes (1 clone), Flavobacteria (1 clone), Verrucomicrobia (1 clone), Acidobacteria (1 clone), and Chloroflexi (1 clone). Most of the Proteobacteria clones were gamma Proteobacteria associated with oxidation-reduction of sulfur.

• Radiation Oncology Journal
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• v.19 no.4
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• pp.389-396
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• 2001

Purpose : To detect differentially expressed genes in the patients with uterine cervical cancer during the radiation therapy. Materials and Methods : In patients with biopsy proven uterine cervical cancer, we took tumor tissue just before radiation therapy and at 40 minutes after external irradiation of 1.8 Gy. Total RNAs isolated from non-irradiated and irradiated tumor tissue samples were analyzed using the differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs(mRNAs) were eluted, and cloned. The differential expression of the corresponding mRNAs was confirmed by reverse northern blot. Differentially expressed cDNA bands were sequenced. Nucleotide sequence data were analyzed in the Gene Bank and EMBL databases via the BLAST network sewer to identify homologies to known genes or cDNA fragments. Expression pattern of down-regulated clone was examined using RT-PCR in S patients undergoing radiotherapy. Results : We identified 18 differentially expressed bands by DDRT-PCR, which were eluted and cloned. There were 10 up-regulated clones and 1 down-regulated clone in reverse northern blot. One cDNA fragment had homology to chemokine receptor CXCR4, four were identified as Human ESTs in the EMBL database in EST clones. Down-regulated CxCa-11 was also down regulated in all patients. Conclusion : Using the DDRT-PCR, we have identified 10 up-regulated and 1 down-regulated clone(s) in the patients with uterine cervical cancer during the radiation therapy. The clinical relevance and the functions of these genes will be further investigated.