• Journal of Genetic Medicine
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• v.2 no.2
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• pp.53-57
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• 1998

Spinal muscular atrophy (SMA) type I is a common severe autosomal recessive inherited neuromuscular disorder that has been mapped to chromosome 5q11.2-13.3. The survival motor neuron (SMN) gene, a candidate gene, is known to be deleted in 96% of patients with SMA type I. Presently, PCR and single strand conformation polymorphism (PCR-SSCP) analyses have been made possible for application to both archival slides and paraffin-embedded tissues. Archival materials represent valuable DNA resources for genetic diagnosis. We applied these methods for the identification of SMN gene of SMA type I in archival specimens for the prenatal diagnosis. In this study, we performed the prenatal diagnosis with chorionic villus sampling (CVS) cells on two women who had experienced neonatal death of SMA type I. DNA extraction was done from archival slide and tissue materials and PEP-PCR was performed using CVS cells. In order to identify common deletion region of SMN and neuronal apoptosis-inhibitory protein (NAIP) genes, cold PCR-SSCP and PCR-restriction site assay were carried out. Case 1 had deletions of the exons 7 and 8, and case 2 had exon 7 only on the telomeric SMN gene. Both cases were found to be normal on NAIP gene. These results were the same for both CVS and archival biopsied specimens. In both cases, the fetuses were, therefore, predicted to be at very high risk of being affected and the pregnancy were terminated. These data clearly demonstrate that archival slide and paraffin-embedded tissues can be a valuable source of DNA when the prenatal genetic diagnosis is needed in case any source for genetic analysis is not readily available due to previous death of the fetus or neonate.

• The KIPS Transactions:PartD
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• v.13D no.4 s.107
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• pp.463-476
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• 2006

R-trees have been traditionally optimized for the I/O performance with the disk page as the tree node. Recently, researchers have proposed cache-conscious variations of R-trees optimized for the CPU cache performance in main memory environments, where the node size is several cache lines wide and more entries are packed in a node by compressing MBR keys. However, because there is a big difference between the node sizes of two types of R-trees, disk-optimized R-trees show poor cache performance while cache-optimized R-trees exhibit poor disk performance. In this paper, we propose a cache and disk optimized R-tree, called the PR-tree (Prefetching R-tree). For the cache performance, the node size of the PR-tree is wider than a cache line, and the prefetch instruction is used to reduce the number of cache misses. For the I/O performance, the nodes of the PR-tree are fitted into one disk page. We represent the detailed analysis of cache misses for range queries, and enumerate all the reasonable in-page leaf and nonleaf node sizes, and heights of in-page trees to figure out tree parameters for best cache and I/O performance. The PR-tree that we propose achieves better cache performance than the disk-optimized R-tree: a factor of 3.5-15.1 improvement for one-by-one insertions, 6.5-15.1 improvement for deletions, 1.3-1.9 improvement for range queries, and 2.7-9.7 improvement for k-nearest neighbor queries. All experimental results do not show notable declines of the I/O performance.

• The Korean Journal of Financial Management
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• v.26 no.1
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• pp.65-94
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• 2009

The event of change in KOSPI 200 Index composition is one of the main subjects for the test of EMH. According to EMH, when a certain event is not related with firm's fundamental value, stock price should not change after the announcement of news. This hypothesis leads us to the conclusion of horizontal demand curve of stock. This logic was questioned by Shleifer(1986) and argued that downward sloping demand curve hypothesis was supported. But Harris and Gruel(1986) found a different empirical evidence that price reversal occurs in the long run, which is called price pressure hypothesis. They argued that short term price effect by large block trading (price pressure) is offset in the long run because these event is unrelated to fundamental value. Therefor, they argued that EMH can not be rejected in the long run. Until now, there are two empirical studies with Korean market data in this area. Using a data with same time period of $1996{\sim}1999$, Kweon and Park(2000) and Ahn and Park(2005) showed that stock price or beta is not significantly affected by change in index composition. This study retested this event expanding sample period from 1996 to 2006, and analyzed why this event was considered an uninformative events in the preceding studies. We analyzed a market impact by separating samples according to firm size and market condition. In case of newly enlisted firm, we found the evidence supporting price pressure hypothesis on average. However, we found the long run price effect in the sample of large firms under bearish markets. At the same time, we know that the number of samples under the category of large firms under bearish markets is relatively small, which drives the same result of supporting the hypothesis that change in index composition is a non-informative event on average. Also, the long run price effect of large size firms under bearish markets was supported by the analyses using trading volumes. On the other hand, in case of delisting from the index, we found the long run price effect but that was not supported by trading volume analyses.

• Journal of Life Science
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• v.20 no.11
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• pp.1697-1703
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• 2010

Asarum consists of low-growing herbs and is a genus in the Aristolochiaceae family with species found in the north temperate zones with most species in Asia. We evaluated the nine taxa with the trnL - trnT region of the chloroplast genome to estimate phenotypic relationships within genus Asarum in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within the Asarum was mostly due to nucleotide inserts/deletions, although several indels and inserts were found. Another source of sequence divergence was length variation due to stretches of short repeats that occur at the trnL - trnT region in all the Asarum. A + T content for nine Korean species of genus Asarum ranged between 74.7% and 78.3%. These values were higher than those for the angiosperm alignments of the total trnL and trnT region (64.5~67.1%). Within genus Asarum, A. patens was strikingly different from the others in the three phylogenetic analyses (MP, ML, and NJ). However, some internal nodes were poorly supported. Within Korean Asarum, four species were unsolved portions. Possible reasons for the striking non-congruence between the previous morphological traits and the trnL - trnT based on phylogeny were discussed.

• The Korean Journal of Zoology
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• v.23 no.4
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• pp.203-218
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• 1980

Unscheduled DNA synthesis, chromosome aberrations, sister chromatid exchanges and DNA replication inhibition induced by the combined treatments with ara-C and UV-light or MMS in $HF_1$, CHO and $HelaS_3$ cells were studied, and the results obtained were as follows: (1) Ara-C was found to inhibit UV-or MMS-induced unscheduled DNA synthesis and the inhibitory effect of ara-C was more remarkable in its post-treatment. (2) Ara-C enhanced the rate of chromosome aberrations induced by MMS or UV-light. Post-treatment with ara-C exhibited the synergistic effect on MMS-induced chromosome aberrations mainly by increases of chromatid deletions. (3) Contrarily, ara-C did not increase the rate of sister chromatid exchanges, particularly in the pre-treatment with MMS, although it was found to induce sister chromatid exchanges. (4) The rate of DNA synthesis was declined immediately after are-C treatment and then recovered. The combined treatments with ara-C and UV-light or MMS showed that the initial response on replication inhibition was similar to that of ara-C, but later responses were similar to that of UV-light or MMS treated group.

• Molecules and Cells
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• v.24 no.2
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• pp.200-209
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• 2007

We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).

• Journal of Microbiology and Biotechnology
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• v.23 no.7
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• pp.905-912
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• 2013

A novel species, Metschnikowia cibodasensis, is proposed to accommodate eight strains (ID03-$0093^T$, ID03-0094, ID03-0095, ID03-0096, ID03-0097, ID03-0098, ID03-0099, and ID03-0109) isolated from flowers of Saurauia pendula, Berberis nepalensis, and Brunfelsia americana in Cibodas Botanical Garden, West Java, Indonesia. The type strain of M. cibodasensis is ID03-$0093^T$ (= NBRC $101693^T$ =UICC $Y-335^T$ = BTCC-$Y25^T$). The common features of M. cibodasensis are a spherical to ellipsoidopedunculate shaped ascus, which contains one or two needle-shaped ascospores, and lyse at maturity. Asci generally develop directly from vegetative cells but sometimes from chlamydospores. The neighbor-joining tree based on the D1/D2 domain of nuclear large subunit (nLSU) ribosomal DNA sequences strongly supports that M. cibodasensis (eight strains) and its closest teleomorphic species, M. reukaufii, are different species by a 100% bootstrap value. The type strain of M. cibodasensis, ID03-$0093^T$, differed from M. reukaufii NBRC $1679^T$ by six nt (five substitutions and one deletion) in their D1/D2 region of nLSU rDNA, and by 18 nt (five deletions, four insertions, and nine substitutions) in their internal transcribed spacer regions of rDNA, respectively. Four strains representative of M. cibodasensis (ID03-$0093^T$, ID03-0095, ID03-0096, and ID03-0099) showed a mol% G+C content of $44.05{\pm}0.25%$, whereas that of M. reukaufii NBRC $1679^T$ was 41.3%. The low value of DNA-DNA homology (5-16%) in four strains of M. cibodasensis and M. reukaufii NBRC $1679^T$ strongly supported that these strains represent a distinct species.

• Tuberculosis and Respiratory Diseases
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• v.45 no.5
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• pp.975-983
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• 1998

Purpose: Frequent deletion of 3p in numerous cancer including lung cancer suggests the presence of tumor suppressor gene. 3p has been analysed by RFLP and PCR-LOH of microsatellite locus. In this study, we observed the deletion of 3p in Korean NSCLC by PCR-LOH of 4 microsatellite loci and investigated the clinical significance. Method: 62 surgically resected NSCLC DNA and normal lung DNA have been analysed by PCR-LOH at three dinucleotide[D3S1228 (3p14.1-14.3), D3S1067 (3p14.3-21.1), D3S1029 (3p21.1-21.3)] and one tetranucleotide[D3S1537 (3p 22-24.2)] repeat microsatellite loci. Results: Among 59 informative cases, 3p deletion by PCR-LOH at four microsatellite loci was found in 31 patients(52.5%). 3p deletion were found in 55% of squamous cell lung cancer and 47% of adenocarcinoma patients. No significant difference has been found in clinical parameters such as staging, smoking and survival according to the status of 3p deletion. Conclusion: Deletions in 3p have played an important role in Korean NSCLC though no clinical significance was detected.

• Journal of Life Science
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• v.25 no.4
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• pp.481-485
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• 2015

Retroviruses genes have been inserted into the human genome for millions of years. These retroviruses are now inactive due to mutations such as deletions or nonsense mutations. After mutation, retroviruses eventually became fixed in the genome in their endogenous forms and existed as traces of ancient viruses. These retroviruses are called endogenous retroviruses (ERVs), with the human form known as human endogenous retrovirus. HERV cannot become a fully active virus, but a number of viral proteins or even virus particles are expressed under various conditions. Compared to endogenous retroviruses, some exogenous retroviruses are still infectious and can threaten human life. Among these, human immunodeficiency virus (HIV) is one of the most well-known and best-studied. Recent studies have shown some elements of HERV were activated by HIV infection and interact with HIV-derived proteins. In addition, many studies have attempted to use HERV as vaccination against HIV infection. This review will describe the regulation and interaction between HERV and HIV infection and mention the development of vaccines and therapeutic agents against HIV infection by using HERV elements.

• Korean Journal of Microbiology
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• v.34 no.4
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• pp.248-253
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• 1998

Bacteriophage N4, a lytic phage specific for Esherichia coli K12 strain encodes single-stranded DNA-binding protein, N4SSB (bacteriophage N4-coded single-stranded DNA-binding protein). N4SSB protein is originally identified as a protein required for N4 DNA replication. N4SSB protein is also required for N4 late transcription, which is catalyzed by E. coli ${\sigma}^{70}$ RNA polymerase. N4 late transcription does not occur until N4SSB protein is synthesized. Recently it is reported that N4SSB protein is essential for N4 DNA recombination. Therefore N 4SSB protein is a multifunctional protein required for N4 DNA replication, late transcription, and N4 DNA recombination. In this study, a variety of mutant N4SSB proteins containing internal deletions or substitutions were constructed to define and characterize domains important for N4 DNA replication, late transcription, and N4 DNA recombination. Test for the ill vivo activity of these mutant N4SSBs for N4 DNA replication, late transcription, and N4 DNA recombination was examined. The results suggest that C-terminal 7 amino acid residues are important for the activity of N4SSB. Three lysine residues, which are contained in this region play important roles on N4SSB activity.