• Journal of Life Science
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• v.26 no.5
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• pp.620-631
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• 2016

Viroids are about 250-400 base pair of short single strand RNA fragments have been associated with economically important plant diseases. Due to the lack of protein expression capacity associated with replication, it is very difficult to diagnosis viroid diseases in serological methods. For detecting viroid at plants, molecular-based techniques such as agarose gel electrophoresis, polyacrylamide gel electrophoresis (PAGE), DNA-hybridization, blotting analysis and conventional RT-PCR are reliable. Real-time RT-PCR methods that grafted on RT-PCR methods with improved confirmation methods have been also utilized. However, they are still labor-intensive, time-consuming, and require personnel with expertise. Loop-mediated Isothermal Amplification (LAMP) method is a nucleic acid amplification method under the isothermal condition. The LAMP methodology has been reported to be simple, rapid, sensitive and field applicable in detecting a variety of pathogens. The results of LAMP method can be colorized by adding a visible material such as SYBR green I, Evagreen, Calcein, Berberine and Hydroxy naphthol blue (HNB) with simple equipment or naked eyes. The combination of LAMP method and nucleic pathogens, viroids, can be used to realize simple diagnosis platform for the genetic point-of care testing system. The aim at this review is to summary viroid-caused diseases and the simple visible approach for diagnosing viroids using Loop-mediated Isothermal Amplification (LAMP) method.

• The Korean Journal of Pesticide Science
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• v.18 no.4
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• pp.396-403
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• 2014

Ginseng (Panax ginseng C. A. Meyer) is an economically valuable pharmaceutical crop in Korea. In order to find promising biocontrol agents for soil-borne fungal pathogens which infect ginseng roots, we have isolated actinomycete, BK185 from soil. The isolate was investigated for the antifungal activity against to ginseng rot pathogens prior to testing genetic and chemical properties. The strain was identified as Streptomyces sp. using phylogenetic analysis based on 16S rRNA gene sequence. The most closely related species was S. sporoclivatus and S. geldanamycininus with high similarities (>99%). The isolate, BK185 showed positive reaction for PCR detection targeting biosynthetic gene clusters of PKS (Type-I polyketide synthase) and NRPS (Non-ribosomal polypeptide synthetase) genes. Major metabolite from the BK185 was analyzed by The LC/MS and identified to geldamycin, which was known to contained broad antibacterial, antifungal or anticancer activities. The results provide evidences that the strain, BK185 can be promising biocontrol agent for ginseng organic farming.

• Clinical and Experimental Pediatrics
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• v.55 no.11
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• pp.438-444
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• 2012

Mucolipidosis II (ML II) or inclusion cell disease (I-cell disease) is a rarely occurring autosomal recessive lysosomal enzyme-targeting disease. This disease is usually found to occur in individuals aged between 6 and 12 months, with a clinical phenotype resembling that of Hurler syndrome and radiological findings resembling those of dysostosis multiplex. However, we encountered a rare case of an infant with ML II who presented with prenatal skeletal dysplasia and typical clinical features of severe secondary hyperparathyroidism at birth. A female infant was born at $37^{+1}$ weeks of gestation with a birth weight of 1,690 g (<3rd percentile). Prenatal ultrasonographic findings revealed intrauterine growth retardation and skeletal dysplasia. At birth, the patient had characteristic features of ML II, and skeletal radiographs revealed dysostosis multiplex, similar to rickets. In addition, the patient had high levels of alkaline phosphatase and parathyroid hormone, consistent with severe secondary neonatal hyperparathyroidism. The activities of ${\beta}$-D-hexosaminidase and ${\alpha}$-N-acetylglucosaminidase were moderately decreased in the leukocytes but were 5- to 10-fold higher in the plasma. Examination of a placental biopsy specimen showed foamy vacuolar changes in trophoblasts and syncytiotrophoblasts. The diagnosis of ML II was confirmed via GNPTAB genetic testing, which revealed compound heterozygosity of c.3091C>T (p.Arg1031X) and c.3456_3459dupCAAC (p.Ile1154GlnfsX3), the latter being a novel mutation. The infant was treated with vitamin D supplements but expired because of asphyxia at the age of 2 months.

• Smart Structures and Systems
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• v.25 no.4
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• pp.487-499
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• 2020

This paper proposes a novel approach to model updating for a large-scale cable-stayed bridge based on ambient vibration tests coupled with a hybrid metaheuristic search algorithm. Vibration measurements are carried out under excitation sources of passing vehicles and wind. Based on the measured structural dynamic characteristics, a finite element (FE) model is updated. For long-span bridges, ambient vibration test (AVT) is the most effective vibration testing technique because ambient excitation is freely available, whereas a forced vibration test (FVT) requires considerable efforts to install actuators such as shakers to produce measurable responses. Particle swarm optimization (PSO) is a famous metaheuristic algorithm applied successfully in numerous fields over the last decades. However, PSO has big drawbacks that may decrease its efficiency in tackling the optimization problems. A possible drawback of PSO is premature convergence leading to low convergence level, particularly in complicated multi-peak search issues. On the other hand, PSO not only depends crucially on the quality of initial populations, but also it is impossible to improve the quality of new generations. If the positions of initial particles are far from the global best, it may be difficult to seek the best solution. To overcome the drawbacks of PSO, we propose a hybrid algorithm combining GA with an improved PSO (HGAIPSO). Two striking characteristics of HGAIPSO are briefly described as follows: (1) because of possessing crossover and mutation operators, GA is applied to generate the initial elite populations and (2) those populations are then employed to seek the best solution based on the global search capacity of IPSO that can tackle the problem of premature convergence of PSO. The results show that HGAIPSO not only identifies uncertain parameters of the considered bridge accurately, but also outperforms than PSO, improved PSO (IPSO), and a combination of GA and PSO (HGAPSO) in terms of convergence level and accuracy.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.11
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• pp.1537-1544
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• 2015

Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

• Journal of Intelligence and Information Systems
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• v.12 no.3
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• pp.67-82
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• 2006

We propose the HBEM(Hybrid Behavior Evolution Model) composed of rule classification and evolutionary neural network using rule descriptor and link descriptor for evolutionary behavior of virtual robots. In our model, two levels of the knowledge of behaviors were represented. In the upper level, the representation was improved using rule and link descriptors together. And then in the lower level, behavior knowledge was represented in form of bit string and learned adapting their chromosomes by the genetic operators. A virtual robot was composed by the learned chromosome which had the best fitness. The composed virtual robot perceives the surrounding situations and they were classifying the pattern through rules and processing the result in neural network and behaving. To evaluate our proposed model, we developed HBES(Hybrid Behavior Evolution System) and adapted the problem of gathering food of the virtual robots. In the results of testing our system, the learning time was fewer than the evolution neural network of the condition which was same. And then, to evaluate the effect improving the fitness by the rules we respectively measured the fitness adapted or not about the chromosomes where the learning was completed. In the results of evaluating, if the rules were not adapted the fitness was lowered. It showed that our proposed model was better in the learning performance and more regular than the evolutionary neural network in the behavior evolution of the virtual robots.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.2
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• pp.689-692
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• 2015

Background: Incorporation of molecular analysis of the epidermal growth factor receptor (EGFR) gene into routine clinical practice has shown great promise to provide personalized therapy of the non-small cell lung cancer (NSCLC) in the developed world. However, the genetic testing of EGFR mutations has not yet become routine clinical practice in territories remote from the central regions of Russia. Therefore, we aimed to study the frequency of major types of activating mutations of the EGFR gene in NSCLC patients residing in West Siberia. Materials and Methods: We examined EGFR mutations in exons 19 and 21 in 147 NSCLC patients (excluding squamous cell lung carcinomas) by real time polymerase chain reaction. Results: EGFR mutations were detected in 28 of the 147 (19%) patients. There were 19 (13%) cases with mutations in exon 19 and 9 cases (6%) in exon 21. Mutations were more frequently observed in women (42%, p=0.000) than in men (1%). A significantly higher incidence of EGFR mutations was observed in bronchioloalveolar carcinomas (28%, p=0.019) and in adenocarcinomas (21%, p=0.024) than in large cell carcinomas, mixed adenocarcinomas, and NOS (4%). The EGFR mutation rate was much higher in never-smokers than in smokers: 38% vs. 3% (p=0.000). The frequency of EGFR mutations in the Kemerovo and Tomsk regions was 19%. Conclusions: The incorporation of molecular analysis of the EGFR gene into routine clinical practice will allow clinicians to provide personalised therapy, resulting in a significant increase in survival rates and improvement in life quality of advanced NSCLC patients.

• Journal of Genetic Medicine
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• v.5 no.2
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• pp.131-135
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• 2008

Classical galactosemia is an autosomal recessive disorder of galactose metabolism, caused by a deficiency of the enzyme galactose-1-phosphate uridyltransferase (GALT). Buildup of galactose-1-phosphate is toxic at high levels and can damage the liver, brain, eyes, and other vital organs. The case presented here was that of an 11-day-old female infant who had elevated galatose levels upon initial neonatal screening test with persistent cholestatic jaundice, coagulopathy, and hepatomegaly. The patient was transferred due to aggravation of clinical symptoms including bleeding and jaundice. She had a delayed galactose free diet because of an inappropriate diagnosis. We quickly provided her with a lactose/galactose-restricted diet as per her final diagnosis. Clinical and laboratory results were improved after a few days of treatment. For confirmatory testing for classical galactosaemia, we simultaneously analyzed for GALT enzyme activity and allele-specific PCR/fragments for seven mutations and two polymorphisms in the GALT gene. We were able to find several GALT-deficient and compound heterozygous mutations of the GALT gene.

• Journal of Genetic Medicine
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• v.5 no.1
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• pp.21-25
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• 2008

Purpose : In recent years, many countries have adopted newborn screening programs that use tandem mass spectrometry (MS/MS) to screen and the number of diseases screened has also increased. We began screening for inherited metabolic disorders using MS/MS in April, 2001. Our goal was to determine the overall prevalence of metabolic disorders and to assess the effectiveness of newborn screening by MS/MS in Korea. Methods : From April, 2001 to December, 2007, we screened newborns and high risk groups using MS/MS. Acylcarnitines and amino acids were extracted and butylated and were introduced into the inlet of MS/MS. Confirmatory testing including a repeat newborn screening, and urine organic acid and plasma amino acid analysis were performed on a case-by-case basis. Results : The total number of screened subjects 284,933 which comprised 251,799 neonates and 33,134 high risk subjects. The recall rate was 0.4% (1158 tests) and true positive cases were 117 (0.04%). Confirmed metabolic disorders (newborn/high risk group) were as follows; 78 (25/53) amino acid disorders, 27 (16/11) organic acid disorders, and 12 (5/7) fatty acid oxidation disorders. The estimated prevalence of inherited metabolic diseases in newborns was 1:5,000 and that in the total group was 1:2,000. Conclusion : Newborn screening by MS/MS improved the detection of many inherited metabolic disorders. We therefore propose that all newborns be screened by a MS/MS national program and followed-up using a systemic organization strategy.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6673-6680
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• 2013

Objective: Insulin resistance (IR) is an established risk factor for colorectal cancer (CRC). Given that CRC and IR physiologically overlap and the calpain-10 gene (CAPN10) is a candidate for IR, we explored the association between CAPN10 and CRC risk. Methods: Blood samples of 400 case-control pairs were genotyped, and the lifestyle and dietary habits of these pairs were recorded and collected. Unconditional logistic regression (LR) was used to assess the effects of CAPN10 SNP43 and SNP19, and environmental factors. Both generalized multifactor dimensionality reduction (GMDR) and the classification and regression tree (CART) were used to test gene-environment interactions for CRC risk. Results: The GA+AA genotype of SNP43 and the Del/Ins+Ins/Ins genotype of SNP19 were marginally related to CRC risk (GA+AA: OR = 1.35, 95% CI = 0.92-1.99; Del/Ins+Ins/Ins: OR = 1.31, 95% CI = 0.84-2.04). Notably, a high-order interaction was consistently identified by GMDR and CART analyses. In GMDR, the four-factor interaction model of SNP43, SNP19, red meat consumption, and smoked meat consumption was the best model, with a maximum cross-validation consistency of 10/10 and testing balance accuracy of 0.61 (P < 0.01). In LR, subjects with high red and smoked meat consumption and two risk genotypes had a 6.17-fold CRC risk (95% CI = 2.44-15.6) relative to that of subjects with low red and smoked meat consumption and null risk genotypes. In CART, individuals with high smoked and red meat consumption, SNP19 Del/Ins+Ins/Ins, and SNP43 GA+AA had higher CRC risk (OR = 4.56, 95%CI = 1.94-10.75) than those with low smoked and red meat consumption. Conclusions: Though the single loci of CAPN10 SNP43 and SNP19 are not enough to significantly increase the CRC susceptibility, the combination of SNP43, SNP19, red meat consumption, and smoked meat consumption is associated with elevated risk.