• The Journal of the Korean Society for Microbiology
• /
• v.22 no.4
• /
• pp.463-471
• /
• 1987

The genomes of leptospiral field isolates from Korea belonging to serogroup Icterohaemorrhagiae (21 strains) and serogroup Canicola (1 strain) were analysed and compared by restriction enzyme analysis with EcoRI and HindIII as digesting enzymes. One isolate belonging to serogroup Canicola showed the same pattern as serovar portlandvere. All 21 isolates belonging to serogroup Icterohaemorrhagiae showed almost same patterns as Leptospira serovar lai from China, But with very slight differences 21 isolates could be classified into 8 subtypes and these grouping seems to reflect the differences in epidemiological niche. And also the geographical data consisted with the grouping into 8 subtypes. According to our results, we concluded that the restriction endonuclease analysis of chromosomal DNA will be an accurate and reliable method to compare and classify pathogenic leptospires.

• Journal of Nutrition and Health
• /
• v.9 no.2
• /
• pp.40-53
• /
• 1976

This study was designed to comparse the metabolic effects of Korean diet pattern which contained all-polished rice and 70% polished rice, and to compare dietary restriction. The results were as follows. 1. Food intake survey to catch the Korean diet pattern The calory intake showed women took much more than men and farm village was higher than city, However, protein intake showed men were higher than women and decrease gradually from city, fishing village, and farm village. Calcium intake showed Seoul was the first rank of all, but was merely 70% of recommended quantities. Fe intake was greatly short especially in women and vitamin C also showed same situation. In the view of food group intake, grains and potatoes were 70.06%, vegetables and fruits 13.05%, meats fishes and beans 11.99%, respectivelly. Oil and fat intake showed lowest percentage as 0.77%. 2. Nutritional experiments albino rats have been fed for 7 weeks with three different diet: all-polished rice diet, 70% polished rice diet, and the standard diet for contral group. Dietary restriction were at 4 levels: 5% , 10%, 15%, 20% in 70% polished rice det. Body weight of 70% polished rice group gained value compare to all polished rice group. In the final organ weight all-polished rice group and 70% polished rice group and 70% polished rice group revealed similar results, but organ weight almost decreased dued to dietary restriction and statistical data showed significant differences between dietary restriction group and none-restriction group. In the femur length, 70% polished rice group was longer than all polished rice group but there was no significant differences. The nitrogen content of liver and muscle of 70% polished rice group was higher than all-polished rice group. Furthermone there was significant differences in the female (P<0.1). In the 10% restriction group(female) and 15% restriction group(male), nitrogen retention was higher than 0% restriction group. The other biochemical analysis such as liver lipid, serum cholesterol, glucose of urine, feces and serum were not revealed any significant differences. As a result of studying, it seems clear that 70% polished rice intake influenced much nourshment to white rat growth than all-porished rice intake, and there is no significant influence to animal growth and metabolic effect even if it was restricted $5{\sim}10%$ of diet.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2002.10a
• /
• pp.15-21
• /
• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

• Journal of Microbiology
• /
• v.41 no.4
• /
• pp.327-334
• /
• 2003

This study employed two PCR-based 16S rDNA approaches, amplified rDNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis (DGGE), to characterize the bacterial community structure in groundwater. Samples were collected from groundwater for the use by private residences, as well as for industrial and agricultural purposes, in Ansan City. Each PCR product was obtained by PCR with eubacteria 16S rDNA and variable V3 region specific primer sets. After amplification, the 16S rDNA PCR products were digested with 4-base site specific restriction endonucleases, and the restriction pattern analyzed. The genetic diversity and similarity of the groundwater bacterial community was analyzed by eubacteria universal primer sets for the amplification of variable V3 regions of the bacterial 16S rDNA. The result of the bacterial community analysis, by ARDRA and DGGE, revealed the same pattern. The highest diversity was found in groundwater from site G1, which was used in residences. In the DGGE profile, a high intensity band was sequenced, and revealed to be Pseudomonas sp. strain P51.

• Korean Journal of Veterinary Research
• /
• v.50 no.3
• /
• pp.239-246
• /
• 2010

Among 203 avian pathogenic Escherichia coli (APEC) isolated from poultry with colibacillosis in korea, 14 isolates were selected from total 68 isolates transferred R plasmid and classified into 5 groups on the basis of antimicrobial minimal inhibitory concentration (MIC) pattern, farm source and O serotype. An association between clonal origin and R plasmid of them was investigated by R plasmid profile, restriction endonuclease analysis and pulsed-field gel electrophoresis (PFGE). The strains that showed the same or very similar antimicrobial MIC pattern, but different farm source and O serotype, revealed different PFGE pattern, which seemed to be different clonal origin. And the strains that showed the same MIC pattern and O serotype, revealed different PFGE pattern, seemed to be originated from different clone. Also the strains showing the same MIC pattern and farm source, but different O serotype, revealed to be different clonal origin. The strains that showed the same or similar MIC pattern, farm source, and O serotype, revealed identical or similar PFGE pattern, which seemed to belong to be one clone. Meanwhile, horizontal transfer of R plasmid seems to be common in APEC with regardless of O serotype and clone of the strains. These results indicate that rapid and accurate epidemiological survey of APEC can be possible by the combination of O serotyping, plasmid profiling and PFGE analysis following the classification of them into groups of antimicrobial drug resistance pattern.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
• /
• 2010.10a
• /
• pp.663-665
• /
• 2010

By the curing and transformation experiment, it was found thatthe genes of Pseudomonas sp.KU171(pKU19) for MCPA-degrading were located on a plasmid pKU19. Also the plasmid had degradative gens for 2,4-D, 3CB, and DCP. Molecular size of pKU19 was measured to be 31.2Kb. The restriction pattern were analyzed with Eco RI, BglII,XhoI, and the restriction map was generated.

• Korean Journal of Agricultural Science
• /
• v.44 no.3
• /
• pp.318-324
• /
• 2017

With the development of next-generation sequencing (NGS), a cutting-edge technology, genotype-by-sequencing (GBS) became available at a low cost per sample. GBS makes it possible to customize the process of library preparation to obtain high-quality single nucleotide polymorphisms (SNPs) in the most efficient way. However, a GBS library is hard to construct due to fine-tuning of concentration of each reagent and set-up. The major reason for this is the presence of undigested genomic DNA (gDNA) owing to the efficiency of different restriction enzymes for different species with unknown reasons. Therefore, this proof-concept study is to demonstrate the unpredictable patterns of enzyme digestion from various plants in order to make the reader aware of the caution needed when choosing restriction enzymes for their GBS library preparations. Indeed, no pattern was found for the digestibility of gDNA samples and restriction enzymes in the current study. We suggest that more data should be accumulated on this matter to help researchers who want to apply GBS technologies in a variety of genetic approaches.

• Proceedings of the IEEK Conference
• /
• 2002.07c
• /
• pp.1670-1673
• /
• 2002

For pattern recognition on high-dimensional data, such as images, the dimensionality reduction as a preprocessing is effective. By dimensionality reduction, we can (1) reduce storage capacity or amount of calculation, and (2) avoid "the curse of dimensionality" and improve classification performance. Popular tools for dimensionality reduction are Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Independent Component Analysis (ICA) recently. Among them, only LDA takes the class labels into consideration. Nevertheless, it, has been reported that, the classification performance with ICA is better than that with LDA because LDA has restriction on the number of dimensions after reduction. To overcome this dilemma, we propose a new dimensionality reduction technique based on an information theoretic measure for difference of distribution. It takes the class labels into consideration and still it does not, have restriction on number of dimensions after reduction. Improvement of classification performance has been confirmed experimentally.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.7
• /
• pp.910-913
• /
• 2004

Insulin-like growth factor binding protein-3 (IGFBP-3) gene is a structural gene associated with the growth and development of the animals. The present investigation was carried out to unravel nucleotide sequence and polymerase chain reactionrestriction fragment polymorphism (PCR-RFLP) of IGFBP-3 gene in buffalo. Genomic DNA was isolated from a total of 157 animals belonging to Murrah, Surti, Jaffarabadi and Nagpuri breeds of Indian riverine buffalo. A 655 bp of IGFBP-3 gene was amplified in all the breeds and amplicons were digested with Hae III, Taq I and Msp I restriction enzymes. On digestion with Hae III yielded single restriction pattern of 8 fragments of sizes 201, 165, 154, 56, 36, 19, 16 and 8 bp in all the animals studied. Similarly Taq I and Msp I also revealed single restriction pattern yielding fragments of sizes 240 and 415 bp and 145 and 510 bp, respectively. This shows nonpolymorphic nature of restriction sites in buffalo. Nucleotide sequencing of 587 bp of IGFBP-3 gene in Murrah buffalo was done and submitted to the GenBank (Accession No. AY304829). Nucleotide sequencing revealed an addition of 4 bases in the intronic region as compared to cattle.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.4
• /
• pp.346-350
• /
• 2009

Although salt is known to influence the performance of nitrification significantly, it has not been well reported on how salt affects ammonia-oxidizing bacterial(AOB) community compositions and dynamics in wastewater treatment bioreactors. In this study, these questions were evaluated in a full-scale bioreactor treating saline wastewater. Clone library analysis for the ammonia monooxygenase subunit A gene revealed that AOB belonging to the Nitrosomonas europaea and the N. oligotropha lineages inhabited in the bioreactor. Terminal restriction fragment length polymorphism analysis for monthly samples demonstrated a fluctuation pattern among AOB populations, although AOB within the N. europaea lineage were dominant during the test period. Correlation analysis between patterns of terminal restriction fragments and environmental variables suggested that sodium, chloride, and sulfate were less important; rather, temperature was the most significant factor affecting the AOB community in the bioreactor.