The ancient bone DNA analysis essentially requires PCR amplification of the targeting genes of study due to the limitation of the ancient bone sample and DNA amounts. In contrast to the fresh living human DNA, it is common to face failing in amplifying the poorly preserved ancient DNA after death. Therefore, the optimized PCR methods appropriate for ancient DNA are required. However, there is no report to date that a systemic investigation of enhanced PCR amplification methods suitable for ancient samples has been conducted Approximately 500~3,300-year-old Korean and Mongolian ancient bones that are resistant to PCR were selected and an extensive number of PCR conditions were systematically investigated for the comparison of PCR success rates. For the PCR analysis, a mitochondrial DNA fragment as a multicopy DNA and a M175 Y chromosome biallelic marker DNA fragment as a single copy DNA that is the marker of the prevalent Y haplogroup (haplogroup O) in Korea were targeted. The identity of the amplified products were confirmed by DNA sequencing. Through this study, we established the optimized PCR conditions for the highly successful amplification of ancient bone DNAs. This estabilished method allowed for the successful amplification of mitochondrial DNAs from all the ancient bone samples tested and the amplification by 50% success rates in the amplification of M175 Y chromosome biallelic marker DNA but with the highest success rates. These results demonstrate that the optimized PCR condition will be useful for the promising ancient DNA analysis in the fields of molecular genetic anthropological studies.
Coat Protein Complex I ; DNA ; DNA, Mitochondrial ; Humans ; Korea ; Mitochondria ; Molecular Biology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Y Chromosome

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.
Coat Protein Complex I ; DNA Copy Number Variations ; Genetic Variation ; Humans ; Polymerase Chain Reaction

As characterization of mitochondrial DNA (mtDNA) shows maternal inheritance and exists as more than thousands copies per cell, it is widely used for population genetics and forensic scientific field. However, mitochondrial DNA study has difficulties because heteroplasmy of mtDNA is being reported from coding and control region. In this study, we have analyzed 200 samples to examine heteroplasmy in mitochondrial DNA of Korean and Mongolian. The control region and coding region in mtDNA of blood from Koreans and Mongolians were analyzed with PCR amplication and sequencing. As a result, several heteroplasmy was observed from total 10 positions including 5 positions in coding region and 5 positions in control region, respectively. Moreover, it showed more than one heteroplasmy in coding region from 6 samples in Korean and 17 samples in Mongolian. Interestingly, heteroplasmy at 5178 position was shown in 6 samples among 23 samples. Considering that the position is important for deciding haplogroup D, we suggest that additional analysis on 4883 position needs for correct haplogrouping. Beside, we also found heteroplasmy in the other positions of 204, 4853, or 16249. Therefore, we suggest that it is required of combinatory analysis on several key nucleotide positions to obtain good results when determining mitochondrial haplogroups.
Clinical Coding ; Coat Protein Complex I ; DNA, Mitochondrial ; Genetics, Population ; Polymerase Chain Reaction ; Wills

OBJECTIVE: The individual cascades of the insulin-like growth factor-1 (IGF-1) signaling pathway and the molecular mechanism of aging have not been fully clarified. In the current study, we explored the effect of DNA polymerase delta 1 (POLD1) on the IGF-1 signaling pathway in cell aging. METHODS: First, we analyzed the relationship between IGF-1 and POLD1 expression in aging. To investigate the effect of IGF-1 on POLD1 expression and aging, the 2BS cells were incubated with young-age or old-age human serum, IGF-1 protein, or linsitinib. Next, the effect of IGF-1 on aging was examined in the 2BS cells with increased or decreased POLD1 expression to clarify the molecular mechanism. RESULTS: In this study, we found that IGF-1 expression increased and POLD1 expression decreased with aging in human serum and hippocampal tissues of SAMP8 mice, and a negative relationship between IGF-1 and POLD1 expression was observed. Furthermore, the cells cultured with old-age human serum or IGF-1 showed lower POLD1 expression and more pronounced senescence characteristics, and the effect could be reversed by treatment with linsitinib or overexpression of POLD1, while the effect of linsitinib on cell aging could be reversed with the knockdown of POLD1. CONCLUSION Taken collectively, our findings demonstrate that IGF-1 promotes aging by binding to IGF-1R and inhibiting the expression of POLD1. These findings offer a new target for anti-aging strategies.
Humans ; Animals ; Mice ; Insulin-Like Growth Factor I/pharmacology* ; Cellular Senescence ; Aging ; Hippocampus ; DNA Polymerase III

NORs are loops of DNA which occur in nucleoli and which posses ribosomal DNA genes. Ribosomal DNA genes transcribe to ribosomal RNA by RNA polymerase I and are of vital significance in the ultimate synthesis of protein. Proteins associated with the NORs are stained with silver nitrate (Ag-NORs). Ag-NORs were studied in various tumors and might reflect the activity of cells and might be an indicator of the degree of malignancy in tumors. Specimens of prostate obtained by transurethral resection or fine needle biopsy were examined with regard to the number and area of NORs in order to find out whether the above mentioned two parameters reflect proliferative activity in 23 cases of prostatic adenocarcinoma and 10 cases of benign prostatic hyperplasia as controls. The mean number of Ag-NORs in BPH, well, moderate and poorly differentiated adenocarcinoma was 1.24+/-0.10 (mean+/-SD; n=10), 1.87+/-0.23 (n=6). 2.08 J=0.28 (n=10). 4.02+/-0.22 (n=7). respectively. In each group, significant difference was found statistically (p<0.05) except between well and moderate differentiated adenocarcinoma. The mean area of Ag-NORs calculated by morphometry in BPH, well, moderate and poorly differentiated adenocarcinoma was 5.40+/-1.8 um2, 7.84+/-3.68 um2. 14.02+/-4.95 um2, 23.99+/-6.94 um2, respectively and significant difference was found statistically in each group (p<0.05). We concluded that the number and area of NORs increased with degree of malignancy and may reflect proliferative activity of cells in prostatic adenocarcinoma. Further investigations may be needed to confirm whether the number or area of Ag-NORs may be available as a prognostic factor for patient`s survival.
Adenocarcinoma* ; Biopsy, Fine-Needle ; DNA ; DNA, Ribosomal ; Nucleolus Organizer Region* ; Prostate ; Prostatic Hyperplasia ; RNA Polymerase I ; RNA, Ribosomal ; Silver Nitrate

An aphidicolin is a chemical agent which selectively inhibits DNA polymerase alpha in S phase of cell cycle. The purpose of this study is toinvestigate of chromosomal abnormalities including fragile sites induced by 0.2 microgram/ml and 0.4 ng/ml aphidicolin in lymphocyte cultures of six healthy individuals. The results were follows. 1. A significant decreasing in mitotic indexes in respect to control culture was observed with both aphidicolin concentrations used. 2. The cells showing chromosome aberrations and the total number of cytogeneticic alterations were significantly increased both aphidicolin treated cultures than control cultures. 3. The total numbers of chromosomal aberrations were increased in the concentration of 0.4 microgram/ml aphidicolin compared to 0.2 microgram/ml treated groups. 4. The most frequent type of chromosomal aberration is a gap. 5. A site showing a gap or break was defined as common fragile sites (c-fra) if it appeared more than 1% of cells analyzed and in at least three of six individuals studied with the same culture treatment. Using these criteria, 3p14, 4q12, 5p13, 6q16, 9p13, and 16q23 were induced in different proportions by different concentration of aphidicolin and four of these c-fras, 4q12, 5p13, 6q16, 9p13 have not been reported so far. This results support that aphidicolin induced fragile sites differently according to cultured cell or cultured conditions, and also suggest the mechanism that common fragile sites caused be closely related with the defect of DNA synthesis in the S phase of cell cycle.
Aphidicolin* ; Cell Cycle ; Cells, Cultured ; Chromosome Aberrations ; Cytogenetics ; DNA ; DNA Polymerase I ; Humans* ; Lymphocytes* ; Mitotic Index ; S Phase

BACKGROUND AND OBJECTIVES: Vasospastic angina (VA) is a specific type of coronary artery disease and develops as a result of coronary artery spasm. Recently, a few studies have revealed that VA caused by coronary artery spasm is related to genetic traits. The objective of this study was to use the recently developed technique of array comparative genomic hybridization (CGH) to screen the genetic aberrations of VA. SUBJECTS AND METHODS: To identify candidate genes that might be causally involved in the pathogenesis of VA, genomic deoxyribonucleic acids were extracted from whole blood of 28 patients with VA who presented at Department of Cardiology at Seoul St. Mary's Hospital, Seoul, Korea. The copy number profiles of these patients was then analyzed using array CGH and reverse transcriptase (RT) quantitative polymerase chain reaction (PCR). RESULTS: Array CGH revealed gains in 31 different regions, with losses in the 4q35.2, 7q22.1, 10q26.3, 15q11.2, 16p13.11, 17p11.2 and 19q13.3 regions (more than 32% aberration in these regions). Several loci were found to be frequently including gains of 5p and 11q (50% of samples). The most common losses were found in 7q (54% of samples). Copy number aberrations in chromosomal regions were detected and corresponding genes were confirmed by RT quantitative PCR. The fold change levels were highest in the CTDP1 (18q23), HDAC10 (22q13.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), NOTCH2 (1p12-p11.2), PCSK6 (15q26.3), SDHA (5p15.33), and MUC17 (7q22.1) genes. CONCLUSION: Many candidate chromosomal regions that might be related to the pathogenesis of VA were detected by array CGH and should be systematically investigated to establish the causative and specific genes for VA.
Cardiology ; Coat Protein Complex I ; Comparative Genomic Hybridization ; Coronary Artery Disease ; Coronary Vessels ; DNA ; Humans ; Korea ; Polymerase Chain Reaction ; RNA-Directed DNA Polymerase ; Spasm

BACKGROUND: Target point mutation of DNA topoisomerase, which is the typical mode of quinolone resistance, cannot explain high level resistance to quinolones. Therefore, many authors looked into over expression of efflux pump as the possibility. After quantificating the arcA mRNA, which controls AcrAB- TolC, the authors tried to find out the difference in the expression of arcA mRNA according to MIC of ciprofloxacin. The authors also tried to determine the usefulness of real time PCR, which is more reproducible and takes less time than preexisting immunoblot assay, through quantification of acrA. MATERIAL AND METHODS: Mutations in topoisomerase (GyrA, ParC) of 20 quinolone resistant E. coli isolates were identified by PCR and direct DNA sequencing. AcrA level was measured by real time PCR. GAPDH of E.coli was used as endogenous control. The expression of acrA was confirmed through northern hybridization method, the results obtained by real time PCR were compared. RESULTS: 1) Topoisomerase mutations were found in all quinolone resistant E. coli strains. 2) AcrA expression in fluoroquinolone-resistant E. coli was quantified by using real time PCR. There was no relationship between the ratio of acrA expression to GAPDH and MIC of ciprofloxacin. 3) With Northern hybridization, we compared the band of acrA to that of GAPDH in compactness and area. No difference in the expression according to MIC could be found. 4) The results of AcrA/GAPDH were significantly correlated between the real-time PCR and northern blot (P<0.05, correlation coefficiency 0.98). CONCLUSION: In this study, no relationship between overexpression of AcrA gene and high level fluoroquinolone resistance. Therefore, we assume that mechanism other than AcrAB efflux pump is involved in and contribute to high-level fluoroquinolone resistance. However, the degree of efflux pump expression could be confirmed with real time PCR using acrA mRNA. Therefore, real time PCR could be used in the molecular biologic study on the mechanism of resistance to antibiotics.
Anti-Bacterial Agents ; Blotting, Northern ; Ciprofloxacin ; DNA Topoisomerases, Type I ; Escherichia* ; Fluoroquinolones* ; Point Mutation ; Polymerase Chain Reaction ; Quinolones ; Real-Time Polymerase Chain Reaction* ; RNA, Messenger ; Sequence Analysis, DNA

BACKGROUND: Target point mutation of DNA topoisomerase, which is the typical mode of quinolone resistance, cannot explain high level resistance to quinolones. Therefore, many authors looked into over expression of efflux pump as the possibility. After quantificating the arcA mRNA, which controls AcrAB- TolC, the authors tried to find out the difference in the expression of arcA mRNA according to MIC of ciprofloxacin. The authors also tried to determine the usefulness of real time PCR, which is more reproducible and takes less time than preexisting immunoblot assay, through quantification of acrA. MATERIAL AND METHODS: Mutations in topoisomerase (GyrA, ParC) of 20 quinolone resistant E. coli isolates were identified by PCR and direct DNA sequencing. AcrA level was measured by real time PCR. GAPDH of E.coli was used as endogenous control. The expression of acrA was confirmed through northern hybridization method, the results obtained by real time PCR were compared. RESULTS: 1) Topoisomerase mutations were found in all quinolone resistant E. coli strains. 2) AcrA expression in fluoroquinolone-resistant E. coli was quantified by using real time PCR. There was no relationship between the ratio of acrA expression to GAPDH and MIC of ciprofloxacin. 3) With Northern hybridization, we compared the band of acrA to that of GAPDH in compactness and area. No difference in the expression according to MIC could be found. 4) The results of AcrA/GAPDH were significantly correlated between the real-time PCR and northern blot (P<0.05, correlation coefficiency 0.98). CONCLUSION: In this study, no relationship between overexpression of AcrA gene and high level fluoroquinolone resistance. Therefore, we assume that mechanism other than AcrAB efflux pump is involved in and contribute to high-level fluoroquinolone resistance. However, the degree of efflux pump expression could be confirmed with real time PCR using acrA mRNA. Therefore, real time PCR could be used in the molecular biologic study on the mechanism of resistance to antibiotics.
Anti-Bacterial Agents ; Blotting, Northern ; Ciprofloxacin ; DNA Topoisomerases, Type I ; Escherichia* ; Fluoroquinolones* ; Point Mutation ; Polymerase Chain Reaction ; Quinolones ; Real-Time Polymerase Chain Reaction* ; RNA, Messenger ; Sequence Analysis, DNA

Chromosome microdissection has become a very powerful approach to generate chromosome band-specific library and painting probes for physical mapping or cytogenetic analysis. Here we have constructed the band-specific painting probe for human chromosome 18p11.1-p11.2 by microdissec-tion and polymerase chain reaction (PCR). We pretreated the microdissected fragments with Topoisomerase I (Topo I) which catalyzes the relaxation of supercoiled DNA, and performed two initial rounds of DNA synthesis with T7 DNA polymerase followed by conventional PCR to enable the reliable preparation of fluorescent in situ hybridization (FISH) probe from a single microdissected chromosome. With this method, it was possible to construct region-specific painting probe for 18p11.1-p11.2. The probe has been used successfully to determine the trisomy 18. Thus this painting probe can be applied to detect the related marker chromosomes in various solid tumors, and the band specific probe pools may be used to analyse the genes.
Chromosomes, Human ; Cytogenetic Analysis ; DNA ; DNA Topoisomerases, Type I ; DNA, Superhelical ; Humans ; In Situ Hybridization, Fluorescence ; Microdissection ; Paint* ; Paintings* ; Polymerase Chain Reaction ; Relaxation ; Trisomy