• IMMUNE NETWORK
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• v.7 no.3
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• pp.149-157
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• 2007

Background: The microsatellites within human leukocyte antigen (HLA) region show considerable polymorphism and strong linkage disequilibrium (LD) with HLA alleles. These microsatellites have been used for genetic analysis including disease mapping to understand susceptibility to autoimmune and infectious diseases. Also, use of microsatellites has recently been proposed as an approach for identifying non-HLA markers within the HLA region that could function as transplantation determinants and for the selection of potential donors for transplantation. Methods: To analyse the frequency of five microsatellites in the Korean population, genotyping for polymorphisms at five microsatellites markers (BAT2, MIB, DQCAR, D6S105 and TNFd) within HLA region was performed on 143 healthy Korean controls. Results: The most frequent genotype shown in healthy Korean controls were BAT2 8 (153 bp, 42.7%), MIB 1 (326 bp, 40.6%), DQCAR 3 (188 bp, 38.5%), D6S105 7 (126 bp, 58.0%) and TNFd 3 (128 bp, 58.0%). And common two-loci haplotypes were found as MIB 1-HLA-B*62 (HF: 10.6%), MIB 6-HLA-B*44 (HF: 7.8%), DQCAR 3-HLA-DRB1*13 (HF: 8.5%), TNFd 5-HLA-B*62 (HF: 7.8%) and D6S105 7-HLA-A*02 (HF: 16.2%). Conclusion: These data might provide useful information on the microsatellites markers with HLA region in Korean population and be helpful in further defining the clinical impact of these microsatellites.

• Journal of Life Science
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• v.13 no.3
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• pp.291-297
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• 2003

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. Two pol fragments (HWP-FB10 and HWP-FBl2) of HERV-W family were identified and analysed by the PCR approach with cDNA library of human fetal brain. They showed 89 percent nucleotide sequence similarity with that of the HERV-W (accession no. AF009668). Deletion/insertion or point mutation in the coding region of the pol fragments from human fetal brain resulted in amino acid frameshift that induced a mutated protein. Phylogenetic analysis of the HERV-W family from GenBank database indicates that the HWP-FB10 is very closely related to the AC000064 derived from human chromosome 7q21-q22. Further studies on the genetic relationship with neighbouring genes and functional role of these new HERV-W pol sequences are indicated.

• Journal of Life Science
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• v.17 no.6 s.86
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• pp.741-747
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• 2007

In the azoospermic patients, there are many of undiagnosed factors related to genetic bases. Among them, Klinefelter's syndrome (47,XXY; KS) and Y-chromosomal microdeletion with normal karyotype(46,XY; YMNK) are the most frequent causes of male infertility. This research focused on the comparative analysis of YMNK (n = 66) and K5 (n = 30) patients suffered from male infertility in Korean population. We used the polymerase chain reaction (PCR) approach including 19 pairs of sequence-tagged site (STS) primers for detecting the Y-chromosomal microdeletion on AZFa, b, c regions, indicating that Y chromosomal microdeletions were almost evenly occurred in AZF all regions in Korean population. Comparative analysis indicated that 34.9% YMNK and 73.4% KS patients harbored the microdeleted Y-chromosome. It seems to be high instability of Y-chromosome in KS patients than that of YMNK infertility patients. Taken together, genome instability containing microdeletion could bring male infertility with the disturbance of normal spermatogenesis.

• KSBB Journal
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• v.21 no.2
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• pp.144-150
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• 2006

The exploitation of metagenome, the access to the natural extant of enormous potential resources, is the way for elucidating the functions of organism in environmental communities, for genomic analyses of uncultured microorganism, and also for the recovery of entirely novel natural products from microbial communities. The major breakthrough in metagenomics is opened by the construction of libraries with total DNAs directly isolated from environmental samples and screening of these libraries by activity and sequence-based approaches. Screening with activity-based approach is presumed as a plausible route for finding new catabolic genes under designed conditions without any prior sequence information. The main limitation of these approaches, however, is the very low positive hits in a single round of screening because transcription, translation and appropriate folding are not always possible in E. coli, a typical surrogate host. Thus, to obtain information about these obstacles, we studied the genetic organization of individual URF's(unidentified open reading frame from metagenome sequenced and deposited in GenBank), especially on the expression factors such as codon usage, promoter region and ribosome binding site(rbs), based on DNA sequence analyses using bioinformatics tools. And then we also investigated the above-mentioned properties for 4100 ORFs(Open Reading Frames) of E. coli K-12 generally used as a host cell for the screening of noble genes from metagenome. Finally, we analyzed the differences between the properties of URFs of metagenome and ORFs of E. coli. Information derived from these comparative metagenomic analyses can provide some specific features or environmental blueprint available to screen a novel biocatalyst efficiently.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.1 no.1
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• pp.28-44
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• 1998

This study was conducted to suggest the ecological restoration strategies for the disturbed landscapes by theoretical study. Especially, it is aimed to suggest three objectives for restoration by using native plants ; (1) prevention or reduction of wind and water erosion, (2) provision of food and cover for variety of animal species, (3) improvement of the visual or aesthetic quality of disturbed sites. The main results were summarized as follows. 1. Cooperation between restoration ecologists and restoration practitioners is needed to delineate a scientific approach to restoration ; (1) Being aware of published literature that describes similar work and/or establish general principles. (2) Preparedness to carry out proper experiments to test ideas. (3) Preparedness to monitor fundamental parameters in a restoration scheme. (4) Providing information about the behavior of species. (5) Publish results. 2. There are three models of succession in theories of plant succession. The tolerance and facilitation models were recommended to ecological restoration. The inhibition model applies in most secondary succession, but the actual species which are introduced first may inhibit the germination and growth of slower-growing species, or they may prevent the growth of other species whose propagules arrive later. 3. The objectives of erosion control, wildlife habitat provision, and visual quality improvement are not mutually exclusive. However, many revegetation practices in the past have emphasized one of these aspects at the expense of the others. 4. A native plant community can be the model of ecological restoration. By stylization/abstraction of native plant community, trying to learn the most essential characteristics of community types - environmental factors ; dominant, prevalent, and "visual essence" species composition - in order to use such information in restoration. 5. After developing mass/spaces plan, match plant communities to the mass/space plan. In utilizing community grouping, there needs aesthetic ability to understand design elements. 6. Several hydrophytes such as Pennisetum saccharifluous, Themeda triandra, Cirsium pendulum show relatively good germination rates. In case of mesophytes and xerophytes, Arundinella hina, Artemisia princeps, Oenothera odorata and legumes seem to have quick-germinating abilities at barren sites. Pinus thunbergii, Rhus chinensis, Evodia daniellii, Alnus firma and Albizzia julibrissin can be considered as "late succession" woody plants because they show low germinating rates and slow growing habitat. 7. The seeds used for restoration should be collected within a certain radius of where it will be planted. Consideration in genetic issues in the collection and use of germplasm can increase the odds for successful restoration efforts. 8. The useful model in the "drift" pattern occurs so abundantly in naturally evolving landscapes. As one species diminishes in density, a second or third species are increased. Thus, dynamic interactions between species are created. Careful using of "drift phenomenon" in planting was recommended. 9. Virtually no stand of vegetation today is immune from the introduction and/or spreading of exotic species. Therefore, the perpetuation of a restored sites requires conscious monitoring and management. Thus, management would be the most important process in ecological restoration. 10. In order to keep the sites "natural", alternative management strategies would be applied in management ; Atenative management strategies are decelerating successional process, accelerating successional processes or modifying species composition. As management tools, mechanical, chemical, biological or environmental factor manipulation, e.g., fire could be used.

• The Korean Journal of Mycology
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• v.38 no.1
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• pp.34-39
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• 2010

We have attempted to verify 30 strains of Hypsizigus marmoreus from various mushroom stocks in Korea using random amplified polymorphic DNA (RAPD) methodology. Chromosomal DNAs of them were extracted and subjected to PCR analyses with 3 random primers. Each PCR produced approximately 30 distinct PCR bands with the size from 200 bp to 3000 bp. A dendrogram was acquired using the unweighted pair-group method with arithmetic average (UPGMA) clustering methodology on the basis of the DNA band pattern. The analysis revealed that 30 strains of H. marmoreus were clustered into two distinct clusters. Cluster 1 contained 3 subgroups while the cluster 2 consisted of rather diverse strains. Interestingly, Hm3-10, a wild strain collected from Deog-Yu mountain, was not included in either clusters, indicative of uniqueness of this strain. We nextly attempted to develop strain-specific DNA markers to verify a specific strain. A unique band in the RAPD gel lane of Hm0-4 was extracted and its sequence was determined. PCR with a primer set from the determined sequence revealed that the primer set gave a 250 bp DNA band only for Hm0-4, indicating that this approach works well for the strain-specific identification of H. marmoreus.

• Clinical and Experimental Pediatrics
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• v.64 no.10
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• pp.504-510
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• 2021

Population screening of newborns is an extremely important and informative diagnostic approach that allows early identification of babies who are predisposed to the development of a number of serious diseases. Some of these diseases are known and have effective treatment methods. Neonatal screening enables the early diagnosis and subsequent timely initiation of therapy. This helps to prevent serious complications and reduce the percentage of disability and deaths among newborns and young children. Primary immunodeficiency diseases and primary immunodeficiency syndrome (PIDS) are a heterogeneous group of diseases and conditions based on impaired immune system function associated with developmental defects and characterized by various combinations of recurrent infections, development of autoimmune and lymphoproliferative syndromes (genetic defects in apoptosis, gene mutation Fas receptor or ligand), granulomatous process, and malignant neoplasms. Most of these diseases manifest in infancy and lead to serious illness, disability, and high mortality rates. Until recently, it was impossible to identify children with PIDS before the onset of the first clinical symptoms, which are usually accompanied by complications in the form of severe coinfections of a viral-bacterial-fungal etiology. Modern advances in medical laboratory technology have allowed the identification of children with severe PIDS, manifested by T- and/or B-cell lymphopenia and other disorders of the immune system. This review discusses the main existing strategies and directions used in PIDS screening programs for newborns, including approaches to screening based on excision of T-cell receptors and kappa-recombination excision circles, as well as the potential role and place of next-generation sequencing technology to increase the diagnostic accuracy of these diseases.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.9
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• pp.1349-1354
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• 2019

Objective: The objective of this study was to determine the best approach for handling missing records of first to successful insemination (FS) in Japanese Black heifers. Methods: Of a total of 2,367 records of heifers born between 2003 and 2015 used, 206 (8.7%) of open heifers were missing. Four penalty methods based on the number of inseminations were set as follows: C1, FS average according to the number of inseminations; C2, constant number of days, 359; C3, maximum number of FS days to each insemination; and C4, average of FS at the last insemination and FS of C2. C5 was generated by adding a constant number (21 d) to the highest number of FS days in each contemporary group. The bootstrap method was used to compare among the 5 methods in terms of bias, mean squared error (MSE) and coefficient of correlation between estimated breeding value (EBV) of non-censored data and censored data. Three percentages (5%, 10%, and 15%) were investigated using the random censoring scheme. The univariate animal model was used to conduct genetic analysis. Results: Heritability of FS in non-censored data was $0.012{\pm}0.016$, slightly lower than the average estimate from the five penalty methods. C1, C2, and C3 showed lower standard errors of estimated heritability but demonstrated inconsistent results for different percentages of missing records. C4 showed moderate standard errors but more stable ones for all percentages of the missing records, whereas C5 showed the highest standard errors compared with noncensored data. The MSE in C4 heritability was $0.633{\times}10^{-4}$, $0.879{\times}10^{-4}$, $0.876{\times}10^{-4}$ and $0.866{\times}10^{-4}$ for 5%, 8.7%, 10%, and 15%, respectively, of the missing records. Thus, C4 showed the lowest and the most stable MSE of heritability; the coefficient of correlation for EBV was 0.88; 0.93 and 0.90 for heifer, sire and dam, respectively. Conclusion: C4 demonstrated the highest positive correlation with the non-censored data set and was consistent within different percentages of the missing records. We concluded that C4 was the best penalty method for missing records due to the stable value of estimated parameters and the highest coefficient of correlation.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.7
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• pp.913-921
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• 2019

Objective: The objectives of this study were to compare identified informative regions through two genome-wide association study (GWAS) approaches and determine the accuracy and bias of the direct genomic value (DGV) for milk production traits in Korean Holstein cattle, using two genomic prediction approaches: single-step genomic best linear unbiased prediction (ss-GBLUP) and Bayesian Bayes-B. Methods: Records on production traits such as adjusted 305-day milk (MY305), fat (FY305), and protein (PY305) yields were collected from 265,271 first parity cows. After quality control, 50,765 single-nucleotide polymorphic genotypes were available for analysis. In GWAS for ss-GBLUP (ssGWAS) and Bayes-B (BayesGWAS), the proportion of genetic variance for each 1-Mb genomic window was calculated and used to identify informative genomic regions. Accuracy of the DGV was estimated by a five-fold cross-validation with random clustering. As a measure of accuracy for DGV, we also assessed the correlation between DGV and deregressed-estimated breeding value (DEBV). The bias of DGV for each method was obtained by determining regression coefficients. Results: A total of nine and five significant windows (1 Mb) were identified for MY305 using ssGWAS and BayesGWAS, respectively. Using ssGWAS and BayesGWAS, we also detected multiple significant regions for FY305 (12 and 7) and PY305 (14 and 2), respectively. Both single-step DGV and Bayes DGV also showed somewhat moderate accuracy ranges for MY305 (0.32 to 0.34), FY305 (0.37 to 0.39), and PY305 (0.35 to 0.36) traits, respectively. The mean biases of DGVs determined using the single-step and Bayesian methods were $1.50{\pm}0.21$ and $1.18{\pm}0.26$ for MY305, $1.75{\pm}0.33$ and $1.14{\pm}0.20$ for FY305, and $1.59{\pm}0.20$ and $1.14{\pm}0.15$ for PY305, respectively. Conclusion: From the bias perspective, we believe that genomic selection based on the application of Bayesian approaches would be more suitable than application of ss-GBLUP in Korean Holstein populations.

• Journal of Korean Society of Forest Science
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• v.100 no.3
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• pp.367-373
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• 2011

The demand for Japanese larch (Larix kaempferi) seeds has increased in Korea but their supply has been limited due to sporadic natural seed production. To enhance seed production, stem girdling was applied to 42-yearold Japanese larches, resulting in remarkable enhancement of strobilus production in terms of the rate of strobilusbearing tree and the number of strobilus per tree. Metabolic alterations in the girdled and the control trees were interrogated through GC/MS analysis. In the girdled tree, the contents of 14 individual metabolites including polar and non-polar compounds were significantly increased compared to the control. In the cambium and phloem tissues of girdled trees, the contents of pimaric acid, phosphoric acid, sucrose, and two different unknown compounds were enhanced, while the levels of malic acid, inositol, two different disaccharide, 11-trans-Octadecenoic acid and 4 different unknown compounds were decreased compared to the control. The girdled trees showed to be contained significantly higher amount of total nitrogen in the cambium and phloem tissues than that of control trees. Although the role of individual metabolites on enhanced strobilus production remains unclear, the approach presented in this study might provide useful information in elucidating metabolic network modulation induced by girdling and will be further applied for enhanced strobilus production in Japanese larch trees.