• Journal of Microbiology and Biotechnology
• /
• v.22 no.9
• /
• pp.1301-1306
• /
• 2012

We combined real-time RT-PCR and real-time PCR (R/P) assays using a hydrolysis probe to detect Mycobacterium tuberculosis complex (MTBC)-specific 16S rRNA and its rRNA gene (rDNA). The assay was applied to 28 non-respiratory and 207 respiratory specimens from 218 patients. Total nucleic acids (including RNA and DNA) were extracted from samples, and results were considered positive if the repeat RT-PCR threshold cycle was ${\leq}35$ and the ratio of real-time RT-PCR and real-time PCR load was ${\geq}1.51$. The results were compared with those from existing methods, including smear, culture, and real-time PCR. Following resolution of the discrepant results between R/P assay and culture, the overall sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) of all samples (including non-respiratory and respiratory specimens) were 98.2%, 97.2%, 91.7%, and 99.4%, respectively, for R/P assay, and 83.9%, 89.9%, 72.3%, and 94.7%, respectively, for real-time PCR. Furthermore, the R/P assay of four patient samples showed a higher ratio before treatment than after several days of treatment. We conclude that the R/P assay is a rapid and accurate method for direct detection of MTBC, which can distinguish viable and nonviable MTBC, and thus may guide patient therapy and public health decisions.

• Journal of Aquaculture
• /
• v.17 no.1
• /
• pp.1-7
• /
• 2004

A rainbow trout uncoupling protein 3 (UCP3) cDNA clone, encoding a 310 amino acid protein, was cloned and sequenced from a liver cDNA library. Two different splice variants designated UCP3-vl and UCP3-v2, were identified through liver cDNA library screening using rainbow trout UCP3 cDNA clone as a probe. UCP3-vl has 3 insertions in the UCP3 cDNA: the first insertion (133 bp), the second (141 bp), and the third (370 bp) were located 126 bp, 334 bp and 532 bp downstream from the start codon, respectively. UCP3-v2 contained a single insertion, identical in sequence and location to the second insertion of UCP3-vl. UCP3, a mitochondrial protein, functions to modulate the efficiency of oxidative phosphorylation. UCP3 has been detected from heart, testis, spinal cord, eye, retina, colon, muscle, brown adipose tissue and white adipose tissue in mammalian animals. Human and rodent UCP3s are highly expressed in skeletal muscle and brown adipose tissue, while they show weak expression of UCP3 in heart and white adipose tissue. In contrast to mammalian studies, RT-PCR and Southern blot analysis of the rainbow trout demonstrated that UCP3 is strongly expressed in liver and heart. UCP3, UCP3-vl, and UCP3-v2 all contain an Ava III short interspersed element (SINE), located in the 3'untraslated region (UTR). PCR using primers from the Ava III SINE and the UCP3 3'UTR region indicates that the UCP3 cDNA is structurally conserved among salmonids and that these primers may be useful for salmonid species genotyping.

• THE JOURNAL OF KOREAN ORIENTAL ONCOLOGY
• /
• v.6 no.1
• /
• pp.67-79
• /
• 2000

Objective : Hedyotis diffusa has been used as an anticancer agent for several decades in oriental medicine. We test whether the methanol extract of the herb affects transcriptional activation factors including $NF-{\kappa}B$ and AP-1. Methods : 1. HL-60 cells were treated with various concentrations(from 200 to $50{\mu}g/ml$) of methanol extract and $H_2O$ extract($200{\mu}g/ml$)of hedyotis diffusa, After 48h later, the cells were tested for viability by MTT assay. 2. The HL-60 cells were treated with $200{\mu}g/ml$ of methanol extract for the indicated periods. First. Nuclear extracts were isolated and incubated with oligonucleotide probe of $NF-{\kappa}B$ and AP-1. Second. Nuclear extracts were isolated and reacted with p50, p65. c-rel pan-Jun, c-Jun, JunB. JunD antibody on ice for 30min. Finally The cell lysates were prepared and analyzed by western blotting using anti-Fas, anti-FasL and anti-p53 antibody. Results : 1. The methanol extract decreases the viability of human lymphoid origin leukemia HL-60 cells in a dose-dependent manner. 2. $NF-{\kappa}B$ is rapidly activated by the addition of the methanol extract, reaches a peak at 30min and gradually returns to resting level. We confirm that $NF-{\kappa}B$ is a heterodimer mainly composed of p65 subunit with c-Rel. 3. Transcriptional activation of AP-1 is detected at 30min and reaches a maximum at 1hr after stimulation of the cells with the methanol extract. AP-1 is mainly composed with Jur-D and partially Jug-B proteins. 4. the methanol extract of Hedyotis diffusa induces the expression of Fas, Fas ligand and p53 proteins of HL-60 cells in a time dependent fashion. Conclusions : These results suggest that the methanol extract of Hedyotis diffusa exerts anticancer effects to induce the death of human leukomic HL-60 cells via activation of trascriptional factors such as $NF-{\kappa}B$ and AP-1, increase in expression of Fas mediated signalling proteins, and induction of tumor suppressor gene. p53.

• Journal of Genetic Medicine
• /
• v.10 no.1
• /
• pp.33-37
• /
• 2013

Purpose: Myotonic dystrophy 1 (DM1, OMIM 160900) is an autosomal-dominant muscular disorder caused by an expansion of CTG repeats in the 3' UTR of the DMPK gene. Variable expansions of CTG repeats preclude the accurate determination of repeat size. We tried to show the clinical and analytical validity of the application of Southern blotting after long-range PCR was demonstrated in Korean DM1 patients. Materials and Methods: The Southern blotting of long-range PCR was applied to 1,231 cases with clinical suspicion of DM1, between 2000 and 2011. PCR was performed using genomic DNA with forward 5'-CAGTTCACAACCGCTCCGAGC-3' and reverse 5'-CGTGGAGGATGGAACACGGAC-3' primers. Subsequently, the PCR fragments were subjected to gel electrophoresis, capillary transfer to a nylon membrane, hybridization with a labeled (CAG)10 probe. The correlation between clinical manifestations and the CTG repeat expansions were analyzed. Results: Among a total of 1,231 tested cases, 642 individuals were diagnosed with DM1 and the range of the detected expansion was 50 to 2,500 repeats; fourteen cases with mild DM1 ($75{\pm}14$ repeats), 602 cases with classical DM1 ($314{\pm}143$ repeats), and 26 cases with congenital DM1 ($1,219{\pm}402$ repeats). The positive and negative predictive values were 100%. The age at test requested and the CTG repeat numbers were inversely correlated (R=-0.444, P<0.01). Conclusion: This study indicates that Southern blotting after long-range PCR is a reliable diagnostic method DM1.

• Journal of Genetic Medicine
• /
• v.14 no.2
• /
• pp.56-61
• /
• 2017

Purpose: Neurofibromatosis type 2 (NF2) is characterized by multiple tumors, including vestibular schwannoma (VS) and others affecting cranial and peripheral nerves. NF2 is caused by mutation of the NF2 gene. The mutation spectrum of NF2 has not been characterized in Korean patients. In the current study, the clinical and genetic characteristics of Korean NF2 patients were analyzed. Materials and Methods: Twenty-five unrelated Korean families were enrolled according to the Manchester criteria. Genetic analysis was performed by direct sequencing and multiplex ligation-dependent probe amplification methods using genomic DNA from peripheral lymphocytes or tumor tissues. Results: All patients had bilateral/unilateral VS and/or other cranial and peripheral nerve tumors. Two patients were familial cases and the other 24 patients were sporadic. Germline NF2 mutations were detected in peripheral lymphocytes from both familial cases, but only in 26.1% of the 23 sporadic families. Somatic mutations were also found in tumor tissues from two of the sporadic families. These somatic mutations were not found in peripheral lymphocytes. A total of 10 different mutations including 2 novel mutations were found in 40.0% of studied families. Five mutations (50.0%) were located in exon 6 of NF2, the FERM domain coding region. Conclusion: Family history was an important factor in identifying germline NF2 mutations. Further study is required to investigate whether exon 6 is a mutation hotspot in Korean NF2 patients and its correlation to phenotypic severity.

• Biomedical Science Letters
• /
• v.6 no.1
• /
• pp.65-72
• /
• 2000

In order to improve the early diagnosis of Johne's disease in ruminants, duplex polymerase chain reaction system for the detection of the etiologic agent of M. paratuberculosis and for the differentiation of other mycobacterial animal pathogens, such as M. bovis and M. avium, was applied. Genomic DNAs were purified from peripheral blood monocytes or milk macrophages and were used as templates in the duplex PCR. Detection of Mycobacterium spp. in the specimen was carried out by PCR using primer set specific to the mycobacterial 16S rDNA. And then, mycobacterial DNA-positive specimens were further differentiated with duplex PCR system which was composed of primer sets specific to 16S rDNA of M. avium complex and Is900 gene of M. paratuberculosis. The results were re-confirmed by Southern blot hybridization with oligonucleotide specific to the internal sequence of IS900 PCR amplicons. The applicability of this duplex PCR system was evaluated with DNAs extracted from clinical specimens of peripheral blood monocytes and milk macrophages. In summary, the duplex PCR amplification system described in this experiment is promising molecular technique for the early diagnosis of Johne's disease in ruminants.

• Korean Journal of Clinical Laboratory Science
• /
• v.48 no.2
• /
• pp.88-93
• /
• 2016

Dirofilaria immitis is a filarial nematode parasite that causes cardiopulmonary dirofilariasis in dogs. The purpose of this study was the development of real-time PCR assays for efficient detection of D. immitis. The D. immitis-specific primers confirmed in our previous study and a newly designed TaqMan probe were used for quantitative diagnostics. First, SYBR Green real-time PCR was performed using the specific primers and serially diluted genomic DNA or plasmid DNA, and melting curve analyses were performed after amplification. The melting curve showed one specific peak in each of the genomic and plasmid DNA reactions, suggesting that the primers specifically amplify the D. immitis cytochrome c oxidase subunit I gene. Comparison of SYBR Green and TaqMan real-time PCR using serially diluted plasmid DNA showed higher efficiency and specificity with TaqMan real-time PCR. The real-time PCR assays developed in this study will provide improved diagnostic methods to overcome the limitations of conventional diagnostic tools and facilitate more rapid and accurate diagnoses.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.8
• /
• pp.2419-2424
• /
• 2013

Guanosine-5'-diphosphate 3'-diphosphate (ppGpp) serves as alarmone in bacterial stringent responses. In this study, an affinity column was constructed by immobilizing ppGpp to NHS-Sepharose for isolating ppGpp-binding proteins. A novel ppGpp-binding protein, YjgA, was isolated and characterized by MALDI-TOF MS (matrix-assisted laser desorption ionization-time-of-flight mass spectrometry) coupled with two-dimensional gel electrophoresis. YjgA and truncated forms of YjgA were cloned and over-expressed in BL21 (DE3). The binding affinity of YjgA to ppGpp was determined by equilibrium dialysis. The interaction of YjgA with ppGpp was very specific, considering that the dissociation constant of YjgA with ppGpp was measured as $5.2{\pm}2.0{\mu}M$, while the affinities to GTP and GDP were about 60 and 30 times weaker than ppGpp. Expression of yjgA gene in Escherichia coli K-12 MG1655 was examined by reverse transcription polymerase chain reaction (RT-PCR). RT-PCR results revealed that yjgA was expressed from early to late stationary phase. The yjgA deletion mutant exhibited decreased cell number at stationary phase compared to parent strain and the over-expression of YjgA increased the cell number. These results suggested that YjgA might stimulate cell division under stationary phase. In most prokaryotic genome, about half of the protein candidates are hypothetical, that are expected to be expressed but there is no experimental report on their functions. The approach utilized in this study may serve as an effective mean to probe the functions of hypothetical proteins.

• The Korean Journal of Mycology
• /
• v.31 no.3
• /
• pp.121-128
• /
• 2003

This study was carried out to identify the phylogenetic relationship of Phellinus species and to know its distribution by comparing the DNA sequences of internal transcribed spacer regions(ITS1 and IST2) and 5.8S ribosomal DNA (rDNA) repeat unit. The Phellinus species had their specific sequences in IST1 and 2 regions depending on suedes. The comparison of the ITS sequences of standard strains indicated that the sequences of ITS1 were more variable than those of ITS2. Nine strains of the commercial products of Phellinus species used in this study were identified as P. lintues, P. baumii, P. igniarius, and P. pini. Most of commercial species were P. pini and P. baumii, and P. gilvus was not found. Also, P. linteus was only found in form of mycelial culture rather than fruiting body. Moreover, the species-specific primers were designed based on ITS sequence data. Each species-specific primers were bound in P. lintues(ITSF-PL2R), P. baumii(PB1F-ITS4R), P. igniarius(IF1-IR3), P. pini(PF1-PR3), and P. gilvus(GF2-GR4), respectively. These primer sets would be useful fer the detection of specific-species among unidentified Phellinus species rapidly.

• Journal of Genetic Medicine
• /
• v.4 no.1
• /
• pp.84-87
• /
• 2007

Spinocerebellar Ataxia Type 3 (SCA 3) is a rare autosomal dominative disorder in which one of the neurodegenerative disorders is caused by a CAG repeat expansion on chromosome 14q32.1. The age at onset of disease is related to the size of the expanded CAG repeat. We present the prenatal diagnosis of SCA3 in a woman whose husband was known to carry an unstable CAG repeat expansion in the MJD gene. The diagnosis was made using PCR with a fluorescent probe for an expanded MJD allele. The normal ranges of (CAG)n of SCA3 are 14~38 repeats. The husband, who had a family history of SCA 3, has an expanded allele of 69 CAG repeats with a normal allele of 27 repeats. His wife had two normal alleles with 26 and 32 CAG repeats. The fetus had two normal alleles with 26 and 27 CAG repeats; consequently, the baby w as healthy. We report a case of prenatal diagnosis of SCA3 using a fluorescent PCR which is rapid and accurate.