• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.67-72
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• 2006

The aim of this paper is to discuss the effect of missing values in detecting differentially expressed genes in a cDNA microarray experiment in the context of a one sample problem. We conducted a cDNA micro array experiment to detect differentially expressed genes for the metastasis of colorectal cancer based on twenty patients who underwent liver resection due to liver metastasis from colorectal cancer. Total RNAs from metastatic liver tumor and adjacent normal liver tissue from a single patient were labeled with cy5 and cy3, respectively, and competitively hybridized to a cDNA microarray with 7775 human genes. We used $M=log_2(R/G)$ for the signal evaluation, where Rand G denoted the fluorescent intensities of Cy5 and Cy3 dyes, respectively. The statistical problem comprises a one sample test of testing E(M)=0 for each gene and involves multiple tests. The twenty cDNA microarray data would comprise a matrix of dimension 7775 by 20, if there were no missing values. However, missing values occur for various reasons. For each gene, the no missing proportion (NMP) was defined to be the proportion of non-missing values out of twenty. In detecting differentially expressed (DE) genes, we used the genes whose NMP is greater than or equal to 0.4 and then sequentially increased NMP by 0.1 for investigating its effect on the detection of DE genes. For each fixed NMP, we imputed the missing values with K-nearest neighbor method (K=10) and applied the nonparametric t-test of Dudoit et al. (2002), SAM by Tusher et al. (2001) and empirical Bayes procedure by $L\ddot{o}nnstedt$ and Speed (2002) to find out the effect of missing values in the final outcome. These three procedures yielded substantially agreeable result in detecting DE genes. Of these three procedures we used SAM for exploring the acceptable NMP level. The result showed that the optimum no missing proportion (NMP) found in this data set turned out to be 80%. It is more desirable to find the optimum level of NMP for each data set by applying the method described in this note, when the plot of (NMP, Number of overlapping genes) shows a turning point.

• Korean Journal of Medicinal Crop Science
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• v.26 no.1
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• pp.26-31
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• 2018

Background: Angelica gigas, A. sinensis, and A. acutiloba are commercially important in the herbal medicine market, and among them, A. gigas has the highest economic value and price. However, their similar morphological traits are often used for fraud. Despite their importance in herbal medicine, recognition of the differences between Angelica species is currently inadequate. Methods and Results: A multiplex polymerase chain reaction (PCR) method was developed for direct detection and identification of A. gigas, A. sinensis, and A. acutiloba. The gene for the distinction of species was targeted at ITS in the nucleus and trnC-petN gene in chloroplasts. The optimized multiplex PCR in the present study utilized each Angelica species-specific primer pairs. Each primer pair yielded products of 229 base pairs (bp) for A. gigas, 53 bp for A. sinensis, 170 bp for A. acutiloba. Additionally non-specific PCR products were not detected in similar species by species-specific primers. Conclusions: In the present study, a multiplex-PCR assay, successfully assessed the authenticity of Angelica species (A. gigas, A. sinensis, and A. acutiloba). and whole genome amplification (WGA) was performed after DNA extraction to identify, the species in the product. The detection method of raw materials developed in the present study could be applied to herbal medicine and health functional food management.

• The Korean Journal of Mycology
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• v.44 no.2
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• pp.103-107
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• 2016

To establish a rapid and accurate detection of Phytophthora pinifolia, which is a quarantine pathogenic fungus in Korea, a species-specific primer was developed based on the ras-related protein (Ypt1) gene. Species-specific primer based on the DNA sequences of Ypt1 gene amplified 193 bp polymerase chain reaction (PCR) product for P. pinifolia. The primer pair yielded the predicted PCR product size exactly in testing with target pathogen DNAs, but not from the other 10 species of Phytophthora and 14 species of other phytopathogenic fungi. The primer pair also showed only the species-specific amplification curve on realtime PCR on target pathogen DNA. The detection sensitivity of real time PCR using species-specific primer pair was 10 to 100 times higher than conventional PCR, with 1 to $10pg/{\mu}L$.

• Clinical and Experimental Pediatrics
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• v.53 no.8
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• pp.809-813
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• 2010

Bartter syndrome (BS) is an autosomal recessively inherited rare renal tubular disorder characterized by hypokalemic metabolic alkalosis and hyperreninemic hyperaldosteronism with normal to low blood pressure due to a renal loss of sodium. Genetically, BS is classified into 5 subtypes according to the underlying genetic defects, and BS is clinically categorized into antenatal BS and classical BS according to onset age. BS type I is caused by loss-of-function mutations in the $SLC12A1$ gene and usually manifests as antenatal BS. This report concerns a male patient with compound heterozygous missense mutations on $SLC12A1$ (p.C436Y and p.L560P) and atypical clinical and laboratory features. The patient had low urinary sodium and chloride levels without definite metabolic alkalosis until the age of 32 months, which led to confusion between BS and nephrogenic diabetes insipidus (NDI). In addition, the clinical onset of the patient was far beyond the neonatal period. Genetic study eventually led to the diagnosis of BS type I. The low urinary sodium and chloride concentrations may be caused by secondary NDI, and the later onset may suggest the existence of a genotype-phenotype correlation. In summary, BS type I may have phenotype variability including low urine sodium and chloride levels and later onset. A definitive diagnosis can be confirmed by genetic testing.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.12
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• pp.5055-5061
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• 2014

In this study, an anti-oxidant and anti-tumor protein Latcripin-3 of Lentinula edodes C91-3 was expressed in Escherichia coli. for the first time. According to the cDNA library, the full-length gene of Latcripin-3 was cloned by the methods of 3'-full rapid amplification of cDNA Ends (RACE) and 5'-full RACE. The structural domain gene of Latcripin-3 was inserted into the pET32 a(+). The functional protein of Latcripin-3 was expressed in Rosetta-gami (DE3) E. coli, evaluated by Western blotting and mass spectrometry. DPPH testing showed that the protein Latcripin-3 can scavenge free radicals remarkably well. The activity of functional protein Latcripin-3 on A549 cells was studied with flow cytometry and the MTT method. The MTT assay results showed that there was a decreases in cell viability in a dose-dependent and time-dependent manner in protein Latcripin-3 treated groups. Flow cytometry demonstrated that Latcripin-3 can induce apoptosis and block S phase dramatically in human A549 lung cancer cells as compared to the control group. At the same time, the cell ultrastructure observed by transmission electron microscopy supported the results of flow cytometry. This research offers new insights and advantages for identifying anti-oxidant and anti-tumor proteins.

• Journal of Periodontal and Implant Science
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• v.34 no.2
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• pp.425-448
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• 2004

A bioactive and degradable poly(epsilon -caprolactone)/silica nanohybrid(PSH) was synthesized for the application as a bone substitute. PSH was manufactured by using silica and polycaprolacton. PSH was manufactured in some composition after low crystaline apatite had been formed in simulated body fluid and, was used this study. The safety of the PSH was established by test of acute, and subacute toxicity, sensitization cytotoxicity and sterility. In order to assess activity of osteoblast, the test for attaching osteoblast, proliferation test for osteoblast, differentiating gene expression test are performed in vitro. And bone substitutes were grafted in rabbit's calvarium, during 8 weeks for testing efficacy of bone substitutes. Degree of osteogenesis and absorption of substitutes were evaluated in microscopic level. In result, it was not appeared that acute and subacute toxicity, sensitization in intradermal induction phase, topical induction phase and challenge phase. It was shown that the test can not inhibit cell proliferation. adversely, it had some ability to accelerate cell proliferation. The result of sterility test described bacterial growth was not detected in most test tube. The attaching and proliferation test of osteoblast had good results. In the result of differentiating gene expression test for osteoblast, cbfa1 and, alkaline phosphatase, osteocalcin and GAPDH were detected with mRNA analysis. In the PSH bone formation test, ostgeoblastic activity would be different as material constitution but it had good new bone formation ability except group #218. futhermore, some material had been absorbed within 8 weeks. Above studies, PSH had bio-compatibility with human body, new bone formation ability and accelerate osteoblastic activity. So it would be the efficient bone substitute material with bio-active and biodegradable.

• Journal of Genetic Medicine
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• v.14 no.2
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• pp.75-79
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• 2017

Duchenne and Becker muscular dystrophies (DMD and BMD, respectively) are X-linked neuromuscular disorders characterized by progressive muscle weakness and severe skeletal muscle degeneration. BMD is a milder form with a later onset. Patients with BMD tend to survive much longer than those with DMD. The differentiation between DMD and BMD is important in the genetic counseling of affected patients and their families. Since muscle biopsies are invasive procedures, the differential diagnosis of BMD and DMD is often dependent on the mutation identified in the DMD gene in affected patients. However, when a novel DMD mutation is identified, the differential diagnosis should be based on muscle biopsy findings with other clinical findings. Here we describe two Korean patients with BMD confirmed by muscle biopsy and genetic testing. Two novel exonic deletions in the DMD gene were identified.

• Korean Journal of Agricultural Science
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• v.43 no.2
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• pp.205-214
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• 2016

A drought-tolerant transgenic rice (Agb0103) was developed using a pepper methionine sulfoxide reductase (CaMsrB2) under the control of rice Rab21 promoter with a selection marker, the phosphinothricin acetyltransferase (PAT) gene. Commercialization of genetically modified (GM) crops will require the evaluation of risks associated with the release of GM crops. With the potential problems associated to GM crops safety testing, the investigation of their effects on non-target organisms is necessary for environmental risk research. This study was carried out to assess acute toxicity of a GM crop using the water flea (Daphnia magna) for non-target organism risk evaluation. The effect of acute toxicity on Daphnia magna of Agb0103 rice and a non-GM rice, Ilmibyeo, were investigated at different concentrations (0, 625, 1,250, 2,500, 5,000, and 10,000 mg/L). The Agb0103 rice used for the test was confirmed to express the CaMsrB2/PAT gene by the PCR and ELISA. Daphnia magna feeding tests showed no significant differences in cumulative immobility or abnormal response with either Agb0103 rice or non-GM rice. The 48hr-EC50 values showed no difference between Agb0103 rice (2243 mg/L) and non-GM rice (2694 mg/L). These results suggest that there is no significant difference in toxicity to Daphnia magna between Agb0103 rice and its non-GM counterpart.

• Korean Journal of Veterinary Research
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• v.55 no.1
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• pp.31-39
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• 2015

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1487-1492
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• 2014

This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.