• Journal of the Institute of Convergence Signal Processing
• /
• v.6 no.2
• /
• pp.95-99
• /
• 2005

This paper presents an accurate recovery method of the reference clock which is needed for network synchronization in two-way satellite multimedia systems compliant with DVB-RCS specification and which use closed loop method for burst synchronization. In these systems, the remote station transmits TDMA burst via return link. For burst synchronization, it obtains reference clock from program clock reference (PCR) defined by MPEG-2 system specification. The PCR is generated periodically at the hub system by sampling system clock which runs at 27MHz $\pm$ 30ppm. Since the reference clock is recovered by means of digital PLL(DPLL) using imprecise PCR values due to variable random jitter, the recovered clock frequency of remote station doesn't exactly match reference clock of hub station. We propose a robust recovery method of reference clock against random delay jitter The simulation results show that the recovery error is remarkably decreased from 5 clocks to 1 clock of 27MHz relative to the general DPLL recovery method.

• BMB Reports
• /
• v.37 no.3
• /
• pp.356-361
• /
• 2004

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

• Food Science and Biotechnology
• /
• v.18 no.5
• /
• pp.1150-1154
• /
• 2009

Low levels of virus contamination and naturally occurring reverse transcription-polymerase chain reaction (RT-PCR) inhibitors restrain virus detection in oysters. A rapid and efficient oyster-processing procedure that can be used for sensitive virus detection in oysters was developed. Poliovirus type 1 Sabin strain was used to evaluate the efficacy of virus recovery. The procedure included (a) acid-adsorption and elution with buffers (0.25M glycine-0.14 M NaCl, pH 7.5; 0.25M threonine-0.14M NaCl, pH 7.5); (b) polyethylene glycol (PEG) precipitation; (c) resuspension in Tween 80/Tris solution and chloroform extraction; (d) the second PEG precipitation; (e) viral RNA extraction with TRIzol and isopropanol precipitation; and (f) RT-PCR combined with semi-nested PCR. The overall recovery of elution/concentration was 19.5% with poliovirus. The whole procedure usually takes 19 hr. The overall detection sensitivity was 4 RT-PCR units of genogroup I norovirus (NoV) and 6.4 RT-PCR units of genogroup II Nov/25 g of oysters initially seeded. The virus-detecting method developed in this study should facilitate the detection of low levels of NoV in oysters.

• Development and Reproduction
• /
• v.13 no.3
• /
• pp.199-205
• /
• 2009

HSP70 has widely been induced in in vivo hyperthermia conditions in various organisms to study gene regulation and recently neuroprotectve roles of the induced gene expression under varying conditions. We investigated different responses among various tissues in zebrafish under heat shock to evaluate whether spatial and temporal expression pattern of zebrafish (z) hsp70 in transcriptional and translational level under heat shock stress in different brain regions. Heat shock groups were given for 1 h at $37^{\circ}C$ after recovery by transferring the treated animals back to $28^{\circ}C$ for 1, 2 and 24 h for recovery, respectively. Control (CTRL) group was kept at $28^{\circ}C$. At the end of treatments, five animals were collected and used for isolation of total RNAs and peptides from the corresponding tissues. Expression of zhsp70 mRNA showed different patterns in recovery periods in the tissues including the brain, eye, intestines, muscles, heart and testis by RT-PCR. Unlike the RT-PCR analysis, Northern blot analysis demonstrated nearly 30-fold increase in zhsp70 at 1 h heat shock, suggesting that RT-PCR may not be appropriate in unmasking regulation of the time-dependent zhsp70 expression. In the experiment involving different brain regions, the cerebellum showed gradual activation at 1 h to R1h and decreases in R2h and R24h, while the medulla oblongata and optic tectum showed gradual increase at R1h and decrease at R24h, indicating that different brain tissues respond specifically to heat shock in inducing zhsp70 and recovering from the heat shock status. Western blot analysis also demonstrated that the intracellular levels of zHSP70 in three different brain regions including the cerebellum, medulla oblongata and optic tectum are differently induced and recovered to normal state. These results clearly demonstrate that different regions of the body and the brain tissues are responding differently to heat shock in the aspects of its level of expression and speed of recovery.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.42 no.3
• /
• pp.238-242
• /
• 2009

Recently coastal seawater has been contaminated by enteric viruses such as the norovirus via untreated groundwater globally. Accordingly, the consumption of molluscan shellfish from seawater that has been contaminated with fecal material has become an important issues. The levels of enteric viruses in seawater are low and recovery and concentration of the virus from large volumes of water is difficult. We compared the effectiveness of two representative method of concentrating virus using negatively and positively charged filters. The mean retention of seeded FCV by HAMF and NCCF was 48% and 78%, respectively. Overall, the recovery of NCCF was 43.3$\pm$11% better than that of HAMF. However, the eluate obtained by using beef extract solution in the NCCF procedure caused an inhibitory effect on the RT-PCR; therefore, it was necessary to employ a PCR inhibitor removal procedure. The HAMF eluate contained no PCR inhibitors, but HAMF was not an effective method of concentrating the virus from large volumes of natural seawater due to clogging.

• Journal of Microbiology
• /
• v.35 no.4
• /
• pp.354-359
• /
• 1997

Methods for the extraction of DNA from water sample were approximated. Four different procedures of DNA extraction were carried out with pellets obtained from centrifugation of 4 liter water samples. The recovery efficiency and purity of DNA extracted by each method from different sources were compared. DNA yield varied with extraction methods, Method I, which involves enzymatic and freeze-thaw lysis steps and phenol and phenol-chloroform purification of extracted nucleic acid, showed a significantly higher yield and purity than the other methods. The use of glass beads in the DNA extraction methods improved the purity of DNA suitable for PCR. Bovine serum albumin in the PCR reaction mixture was useful in reducing inhibitory effects of contaminants. The efficiency of an extraction method was determined by the detection of the aer of Aeromonas hydrophila with PCR. The lower limit of detection of A. hydrophila from seeded tap water was 2 CFU/ml in PCR when method I was used for DNA preparation.

• Food Science and Biotechnology
• /
• v.18 no.2
• /
• pp.407-412
• /
• 2009

In this study, a rapid and efficient concentrating procedure that can be used for detecting viruses in vegetables was developed. The Sabin strain of poliovirus type 1 was used to evaluate the efficiency of virus recovery. The procedure included: (a) elution with 0.25 M threonine-0.3 M NaCl pH 9.5; (b) polyethylene glycol (PEG) 8000 precipitation; (c) chloroform extraction; (d) 2$^{nd}$ PEG precipitation; (f) RNA extraction; (g) reverse transcription-polymerase chain reaction (RT-PCR) combined with semi-nested PCR. The overall recoveries by elution/concentration were 29.0% from cabbage and 13.7% from lettuce. The whole procedure usually takes 18 hr. The overall detection sensitivity was 100 RT-PCR units of genogroup II norovirus (GII NoV)/25 g cabbage and 100 RT-PCR units of GII NoV/10 g lettuce. The virus detecting method developed in this study should facilitate the detection of low levels of NoV in cabbage and lettuce.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.8
• /
• pp.1453-1458
• /
• 2008

For quantitative PCR assay of Salmonella enterica serovar Typhimurium in food samples, a real-time PCR method was developed, based on DNA genome equivalent. Specific primers and probe designed based on the STM4497 gene of S. Typhimurium LT2 showed the specificity to S. Typhimurium. Threshold cycle (Ct) values of real-time PCR were obtained from a quantitative standard curve with genomic DNA of Salmonella Typhimurium. In addition, the recovery of S. Typhimurium inoculated artificially to chicken samples with $4.5{\times}10^5$ to 4.5 CFU/ml was evaluated by using real-time PCR and plate-count methods. Result showed that the number of cells calculated from the real-time PCR method had good correlation with that of the plate-count method. This real-time PCR method could be applicable to the detection and quantification of S. Typhimurium in food samples.

• Korean Journal of Veterinary Research
• /
• v.44 no.2
• /
• pp.163-169
• /
• 2004

To elucidate the molecular mechanisms of autoimmune inflammation in the central nervous system, we examined the expression and localization of STAT1, STAT3, STAT4 and STAT6 molecules during experimental autoimmune encephalomyelitis (EAE) by competitive PCR. In the present study, we quantitated IL-4 and IL-12 p40 mRNA by competitive PCR in the CNS during EAE. IL-4 mRNA was found at early and peak stages. On the other hand, the IL-12 p40 mRNA level reached maximal levels at the peak stage and still found at the recovery stage of the disease. We examined the kinetics of STAT mRNA in the CNS during EAE and demonstrated that STAT1 and STAT4 mRNA reached a maximal level at the peak stage of EAE, whereas STAT3 mRNA level increased gradually to the recovery stage. STAT6 mRNA increased rapidly at the early stage followed by gradual decrease till the recovery stage. Taken together, these findings suggest that STAT4 which was probably activated by IL-12 plays a pro-inflammatory role and that STAT3 which was activated throughout the disease course seems to serve as a transducer of anti-inflammatory signals.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.3
• /
• pp.423-427
• /
• 2004

Seventy-six animals including cattle, sheep, horses, 6 species of zoo animals were employed for collection of fresh feces in order to detect verotoxigenic Esherichia coli (VTEC) by safe, quick and sensitive PCR-based molecular methods. Bacterial cell disruption with bead-beating followed by bacterial DNA purification with hydroxyapatide chromatography and gel filtration allowed DNA preparation from animal feces with high recovery and purity. A mountain goat was firstly shown by PCR and sequencing to shed verotoxin 2 gene (vt2) that was used to generate vt2 probe and second primer set for nested PCR to attempt more sensitive detection. Most sensitive nested PCR revealed that 45% of tested cattle and 47% of tested zoo animals were VTEC-positive, while least sensitive normal PCR detected VTEC from none of these animals except a mountain goat. Moderately sensitive detection by PCR in combination with hybridization suggested that the VTEC density varied between the VTEC-positive cattle.