• Title/Summary/Keyword: Genetic test

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Microsatellite Alterations of Plasma DNA in Non Small Cell Lung Cancer (비소세포폐암 환자의 혈장 DNA를 이용한 Microsatellite 분석)

  • Kim, Kyu-Sik;Kim, Eun-Jung;Kim, Soo-Ock;Oh, In-Jae;Park, Chang-Min;Jeong, Ju-Yeon;Kim, Yu-Il;Lim, Sung-Chul;Park, Jong-Tae;Kim, Young-Chul
    • Tuberculosis and Respiratory Diseases
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    • v.58 no.4
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    • pp.352-358
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    • 2005
  • Microsatellites are short tandem repeated nucleotide sequences that are present throughout the human genome. Variations in the repeat number or a loss of heterozygosity around the microsatellites have been termed a microsatellite alteration (MA). A MA reflects the genetic instability caused by an impairment in the DNA mismatch repair system and is suggested to be a novel tumorigenic mechanism. A number of studies have reported that MA in the DNA extracted from the plasma occurs at varying frequencies among patients with a non-small cell lung carcinoma (NSCLC). The genomic DNA from 9 subjects with a non-small cell lung cancer (squamous cell cancer 6, adenocarcinoma 2, non-small cell lung cancer1) and 9 age matched non-cancer control subjects (AMC: tuberculosis 3, other inflammatory lung disease 6) and 12 normal control subjects (NC) were extracted from the peripheral blood leukocytes and plasma. Three microsatellite loci were amplified with the primers targeting the Gene Bank sequence D21S1245, D3S1300, and D3S1234. MA in the form of an allelic loss or a band shift was examined with 6% polyacrylamide gel electrophoresis and silver staining. None (0/12) of the NC subjects less than 40 years of age showed a MA in any of the three markers, while 88.9%(8/9) of the AMC above 40 showed a MA in at least one of the three markers (p<0.05). Sixty percent(6/10) of the control subjects with a smoking history showed a MA in one of the three markers, while 9.1%(1/11) of the control subjects without smoking history showed a MA (p<0.05). However, not only did 66.7%(6/9) of lung cancer patients show a MA in at least one of the three markers but so did 88.9%(8/21) of the AMC patients (p>0.05). In conclusion, a MA in the D21S1245, D3S1300, and D3S1234 loci using DNA extracted from the plasma was detected in 66.7% of lung cancer while no MA was found in the young non-smoking control subjects. However, many of the non-cancer control subjects (aged smokers) also showed a MA, which compromised the specificity of the MA analysis as a screening test. Therefore, a further study with a larger sample size will be needed.

Improving Corsican pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology and germination

  • Wtpsk, Senarath;Shaw, D.S.;Lee, Kui-Jae;Lee, Wang-Hyu
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2003.04a
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    • pp.61-62
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    • 2003
  • Clonal propagation of high-value forest trees through somatic embryogenesis (SE) has the potential to rapidly capture the benefits of breeding or genetic engineering programs and to improve raw material uniformity and quality. A major barrier to the commercialization of this technology is the low quality of the resulting embryos. Several factors limit commercialization of SE for Corsican pine, including low initiation rates, low culture survival, culture decline causing low or no embryo production, and inability of somatic embryos to fully mature, resulting in low germination and reduced vigour of somatic seedlings. The objective was to develop a Corsican pine maturation medium that would produce cotyledonary embryos capable of germination. Treatments were arranged in a completely randomized design. Data were analyzed by analysis of variance, and significant differences between treatments determined by multiple range test at P=0.05. Corsican pine (Pinus nigra var. maritima) cultures were initiated on modified !P6 medium. Modifications of the same media were used for culture multiplication and maintenance. Embryogenic cultures were maintained on the same medium semi solidified with 2.5 g/l Gelrite. A maturation medium, capable of promoting the development of Corsican pine somatic embryos that can germinate, is a combination of iP6 modified salts, 2% maltose, 13% polyethylene glycol (PEG), 5 mg!l abscisic acid (ABA), and 2.5 g/l Gelrite. After initiation and once enough tissue developed they were grown in liquid medium. Embryogenic cell suspensions were established by adding 0.951.05 g of 10- to 14-day-old semisolid-grown embryogenic tissue to 9 ml of liquid maintenance media in a 250ml Erlenmeyer flask. Cultures were then incubated in the dark at 2022$^{\circ}$C and rotated at 120 rpm. After 2.53 months on maturation medium, somatic embryos were selected that exhibited normal embryo shape. Ten embryos were placed horizontally on 20 ml of either germination medium ($\frac{2}{1}$strength Murashige and Skoog (1962) salts with 2.5 g/l activated charcoal) or same medium with copper sulphate adjusted to 0.25 mg/1 to compensate for copper adsorption by activated carbon. 2% and 4% maltose was substituted by 7.5% and 13% PEG respectively to improve the yield of the embryos. Substitution of' maltose with PEG was clearly beneficial to embryo development. When 2% of the maltose was replaced with 7.5% PEG, many embryos developed to large bullet-shaped embryos. At latter stages of development most embryos callused and stopped development. A few short, barrel-shaped cotyledonary embryos formed that were covered by callus on the sides and base. When 4% of the maltose was removed and substituted with 13% PEG, the embryos developed further, emerging from the callus and increasing yield slightly. Microscopic examination of the cultures showed differing morphologies, varying from mostly single cells or clumps to well-formed somatic embryos that resembled early zygotic embryos only liquid cultures with organized early-stag. A procedure for converting and acclimating germinants to growth in soil and greenhouse conditions is also tested. Seedling conversion and growth were highly related to the quality of the germinant at the time of planting. Germinants with larger shoots, longer, straighter hypocotyls and longer roots performed best. When mature zygotic embryos germinate the root emerges, before or coincident with the shoot. In contrast, somatic embryos germinate in reverse sequence, with the cotyledons greening first, then shoot emergence and then, much later, if at all, the appearance of the root. Somatic seedlings, produced from the maturation medium, showed 100% survival when planted in a field setting. Somatic seedlings showed normal yearly growth relative to standard seedlings from natural seed.

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Validation of QF-PCR for Rapid Prenatal Diagnosis of Common Chromosomal Aneuploidies in Korea

  • Han, Sung-Hee;Ryu, Jae-Song;An, Jeong-Wook;Park, Ok-Kyoung;Yoon, Hye-Ryoung;Yang, Young-Ho;Lee, Kyoung-Ryul
    • Journal of Genetic Medicine
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    • v.7 no.1
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    • pp.59-66
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    • 2010
  • Purpose: Quantitative fluorescent polymerase chain reaction (QF-PCR) allows for the rapid prenatal diagnosis of common aneuploidies. The main advantages of this assay are its low cost, speed, and automation, allowing for large-scale application. However, despite these advantages, it is not a routine method for prenatal aneuploidy screening in Korea. Our objective in the present study was to validate the performance of QF-PCR using short tandem repeat (STR) markers in a Korean population as a means for rapid prenatal diagnosis. Material and Methods: A QF-PCR assay using an Elucigene kit (Gen-Probe, Abingdon, UK), containing 20 STR markers located on chromosomes 13, 18, 21, X and Y, was performed on 847 amniotic fluid (AF) samples for prenatal aneuploidy screening referred for prenatal aneuploidy screening from 2007 to 2009. The results were then compared to those obtained using conventional cytogenetic analysis. To evaluate the informativity of STR markers, the heterozygosity index of each marker was determined in all the samples. Results: Three autosomes (13, 18, and 21) and X and Y chromosome aneuploidies were detected in 19 cases (2.2%, 19/847) after QF-PCR analysis of the 847 AF samples. Their results are identical to those of conventional cytogenetic analysis, with 100% positive predictive value. However, after cytogenetic analysis, 7 cases (0.8%, 7/847) were found to have 5 balanced and 2 unbalanced chromosomal abnormalities that were not detected by QF-PCR. The STR markers had a slightly low heterozygosity index (average: 0.76) compared to those reported in Caucasians (average: 0.80). Submicroscopic duplication of D13S634 marker, which might be a unique finding in Koreans, was detected in 1.4% (12/847) of the samples in the present study. Conclusion: A QF-PCR assay for prenatal aneuploidy screening was validated in our institution and proved to be efficient and reliable. However, we suggest that each laboratory must perform an independent validation test for each STR marker in order to develop interpretation guidelines of the results and must integrate QF-PCR into the routine cytogenetic laboratory workflow.

Correlation Analyses on Growth Traits, Body Size Traits and Carcass Traits in Hanwoo Steers (한우 후대검정우 체중, 체척 및 도체형질간 상관분석)

  • Lee, Jae-Gu;Choy, Yun-Ho;Park, Byung-Ho;Choi, Jae-Kwan;Lee, Seung-Su;Na, Jong-Sam;Roh, Seung-Hee;Choi, Tae-Jeong
    • Journal of agriculture & life science
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    • v.46 no.1
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    • pp.123-131
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    • 2012
  • This study was conducted to estimate correlation structure between Hanwoo steer growth traits - body weights at 6 month, 12 month, 18 month and 24 month of age, average daily gain, carcass traits, body size traits at 18 months of age. Hanwoo progeny test data(body weight, body size traits) collected from 2004 to 2008 on a total of 1,838 steers at Hanwoo Improvement Main Center(NACF) were analyzed. Carcass traits were used to score the 24 months of age and slaughter. Correlation analyses were performed with observed scales of the traits and with residuals considering fixed effects in generalized linear models. The correlated coefficient estimated between live weight at slaughter(24 months of age) and cold carcass weight was high at 0.92. Correlation between beef yield index values and backfat thickness was estimated to be high and negative at -0.92. Hip height and wither height was found to be highly correlated(0.89). Chest width and chest depth also was found to be highly correlated at 0.73. Rump width was highly correlated with chest depth(0.75) and chest width(0.74). Correlation between pelvic width and rump width was estimated to be 0.74. Hipbone width was shown to be highly correlated with chest depth(0.73), chest width(0.70), rump width(0.75), or pelvic width(0.75). Correlation between wither height and carcass weight was 0.48 in observed scale. Chest girth was phenotyically (residual correlation) correlated with carcass weight (0.51), the estimates of which were some higher than than with the other carcass traits. This study will be utilized for Hanwoo Steers genetic evaluation.

The Effect of Data Size on the k-NN Predictability: Application to Samsung Electronics Stock Market Prediction (데이터 크기에 따른 k-NN의 예측력 연구: 삼성전자주가를 사례로)

  • Chun, Se-Hak
    • Journal of Intelligence and Information Systems
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    • v.25 no.3
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    • pp.239-251
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    • 2019
  • Statistical methods such as moving averages, Kalman filtering, exponential smoothing, regression analysis, and ARIMA (autoregressive integrated moving average) have been used for stock market predictions. However, these statistical methods have not produced superior performances. In recent years, machine learning techniques have been widely used in stock market predictions, including artificial neural network, SVM, and genetic algorithm. In particular, a case-based reasoning method, known as k-nearest neighbor is also widely used for stock price prediction. Case based reasoning retrieves several similar cases from previous cases when a new problem occurs, and combines the class labels of similar cases to create a classification for the new problem. However, case based reasoning has some problems. First, case based reasoning has a tendency to search for a fixed number of neighbors in the observation space and always selects the same number of neighbors rather than the best similar neighbors for the target case. So, case based reasoning may have to take into account more cases even when there are fewer cases applicable depending on the subject. Second, case based reasoning may select neighbors that are far away from the target case. Thus, case based reasoning does not guarantee an optimal pseudo-neighborhood for various target cases, and the predictability can be degraded due to a deviation from the desired similar neighbor. This paper examines how the size of learning data affects stock price predictability through k-nearest neighbor and compares the predictability of k-nearest neighbor with the random walk model according to the size of the learning data and the number of neighbors. In this study, Samsung electronics stock prices were predicted by dividing the learning dataset into two types. For the prediction of next day's closing price, we used four variables: opening value, daily high, daily low, and daily close. In the first experiment, data from January 1, 2000 to December 31, 2017 were used for the learning process. In the second experiment, data from January 1, 2015 to December 31, 2017 were used for the learning process. The test data is from January 1, 2018 to August 31, 2018 for both experiments. We compared the performance of k-NN with the random walk model using the two learning dataset. The mean absolute percentage error (MAPE) was 1.3497 for the random walk model and 1.3570 for the k-NN for the first experiment when the learning data was small. However, the mean absolute percentage error (MAPE) for the random walk model was 1.3497 and the k-NN was 1.2928 for the second experiment when the learning data was large. These results show that the prediction power when more learning data are used is higher than when less learning data are used. Also, this paper shows that k-NN generally produces a better predictive power than random walk model for larger learning datasets and does not when the learning dataset is relatively small. Future studies need to consider macroeconomic variables related to stock price forecasting including opening price, low price, high price, and closing price. Also, to produce better results, it is recommended that the k-nearest neighbor needs to find nearest neighbors using the second step filtering method considering fundamental economic variables as well as a sufficient amount of learning data.

Comparison of the Efficacy of Disinfectants to Control Caseous Lymphadenitis in Korean Black Goat Farms (흑염소의 건락성 림프절염 제어를 위한 소독제 효능 비교)

  • Cho, Hyeunwoo;Kim, Yeona;Jang, Beomsoon;Kim, Chan-Lan;Park, Kun Taek
    • Journal of Food Hygiene and Safety
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    • v.37 no.5
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    • pp.317-322
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    • 2022
  • Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis (CLA), a chronic contagious disease in small ruminants. The prevalence of CLA has been reported to be >50% in Korean black goats. CLA is difficult to control due to a lack of efficient vaccines and treatment methods. Effective disinfection of the farm environment may be an alternative strategy for reducing the spread of C. pseudotuberculosis. The objective of this study was to evaluate the efficacy of commercial disinfectants against CLA. The six commercial disinfectants, largely composed of sodium dichloroisocyanurate, sodium hypochlorite, potassium monopersulfate triple salt, quaternary ammonium, citric acid, and copper sulfate, were tested against five different genotypes of C. pseudotuberculosis isolated from goat farms in Korea. Efficacy tests were performed in accordance with the disinfectant efficacy test guidelines recommended by the Animal and Plant Quarantine Agency of Korea with slight modifications. All disinfectants except for copper sulfate exhibited >99.99% killing efficacy under hard water conditions following 30 min of incubation, which is the recommended standard treatment time according to guidelines. The minimum bactericidal treatment time was evaluated by employing treatments for durations of 1, 5, and 15 min. The most effective compounds under hard water conditions were sodium dichloroisocyanurate, potassium monopersulfate triple salt, and sodium hypochlorite, exhibiting >99.99% killing efficacy after 1 min of treatment. In the aqueous solution forms, citric acid and the quaternary ammonium compound were the most effective, but required at least 5 min to kill >99.99% of the bacteria. The current study characterizes the killing efficacy of six commercial disinfectant active compounds against C. pseudotuberculosis. Thus, this study provides essential information regarding the efficacy of the disinfectants used to control CLA in goat farms.

Development of Rapid-cycling Brassica rapa Plant Program based on Cognitive Apprenticeship Model and its Application Effects (인지적 도제 모델 기반의 Rapid-cycling Brassica rapa 식물 프로그램의 개발 및 적용 효과)

  • Jae Kwon Kim;Sung-Ha Kim
    • Journal of Science Education
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    • v.47 no.2
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    • pp.192-210
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    • 2023
  • This study was intended to develop the plant molecular biology experimental program using Rapid-cycling Brassica rapa (RcBr) based on the teaching steps and teaching methods of the cognitive apprenticeship model and to determine its application effects. In order to improve a subject's cognitive function and expertise on molecular biology experiments, two themes composed of a total 8 class sessions were selected: 'Identification of DFR gene in purple RcBr and non-purple RcBr' and 'Identification of RcBr's genetic polymorphism site using the DNA profiling method'. Research subjects were 18 pre-service teaching majors in biology education of H University in Chungbuk, Korea. The effectiveness of the developed program was verified by analyzing the enhancement of 'cognitive function' related to the use of molecular biology knowledge and technology, and the enhancement of 'domain-general metacognitive abilities.' The effect of the developed program was also determined by analyzing the task flow diagram provided. The developed program was effective in improving the cognitive functions of the pre-service teachers on the use of knowledge and technology of molecular biology experiments. It was especially effective to improve the higher cognitive function of pre-service teachers who did not have the previous experience. The developed program also showed a significant improvement in the task of metacognitive knowledge and in the planning, checking, and evaluation of metacognitive regulation, which are sub-elements of domain-general metacognitive abilities. It was found that the developed program's self-test activity could help the pre-service teachers to improve their metacognitive regulation. Therefore, this developed program turned out to be helpful for pre-service teachers to develop core competencies needed for molecular biology experimental classes. If the teaching and learning materials of the developed program could be reconstructed and applied to in-service teachers or high school students, it would be expected to improve their metacognitive abilities.

The Trend and Achievements of Forest Genetics Research in Abroad (선진국(先進國)에 있어서의 임목육종연구(林木育種硏究)의 동향(動向))

  • Hyun, Sin Kyu
    • Journal of Korean Society of Forest Science
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    • v.14 no.1
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    • pp.1-20
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    • 1972
  • The trend and achievements of forest genetics research in abroad were investigated through observation tours and reference work and following facts were found to be important aspects which should be adopted in the forest genetics research program in Korea. Because of world wide recognization on the urgency of taking a measure to reserve some areas of the representative forest type on the globe before the extingtion of such forest type as the results of continuous exploitations of the natural forests to meet the timber demand all over the world, it is urgently needed to take a measure to reserve certain areas of natural stand of Pinus koraiensis, Pinus parviflora, Pinus densiflora f. erectra, Abies koreana, Quercus sp., Populus sp., etc. as gene pool to be used for the future program of forest tree improvement. And the genetic studies of those natural forest of economic tree species are also to be performed. 1. Increase of the number of selected tree for breeding purpose. Because of the fact that the number of plus tree at present is too small to carry out selection program for tree improvement, particularly for the formation of source population for recurrent selection of parent trees of the 2nd generation seed orchard it is to be strongly emphasized to increase the number of plus tree by alleviating selection criteria in order to enlarge the population size of plus trees to make the selection program more efficient. 2. Progeny testing More stress should be placed on carrying out progeny testing of selected trees with open pollinated seeds. And particular efforts are to be made for conducting studies on adult/juvenile correlation of important traits with a view to enable to predict adult performances with some traits revealed in juvenile age thus to save time for progeny testing. 3. Genotype-environment interaction Studies on genotype and environment interaction should be conducted in order to elucidate whether the plus trees selected on the good site express their superiority on the poor site or not and how the environment affect the genotype. And the justification of present classification of seed distribution area should be examined. 4. Seed orchard of broad leaf tree species. Due to the difficulty of accurate comparison of growth rate of neighbouring trees of broad leaf tree species in natural stand, it is recommended that for the improvement of broad leaf trees a seedling seed orchard is to be made by roguing the progeny test plantation planted densely with control pollinated seedlings of selected trees. 5. Breeding for insect resistant varieties. In the light of the fact that the resistant characteristics against insect such as pine gall midge (Thiecodiplosis japonensis U. et I.) and pine bark beetle (Myelophilus pinipera L.) are highly correlated with the amount and quality of resin which are known as gene controlled characteristics, breeding for insect resistance should be carried out. 6. Breeding for timber properties. With the tree species for pulp wood in particular, emphasis should be placed upon breeding for high specific gravity of timber. 7. Introduction of Cryptomeria and Japanese Cypress In the light of the fact that the major clones of Cryptomeria are originated from Yoshino source and are being planted up to considerably north and high elevation in Japan, those species should be examined on their cold resistance in Korea by planting them in further northern part of the country.

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