• Title/Summary/Keyword: Genome Analysis

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Development of a Window Program for Searching CpG Island (CpG Island 검색용 윈도우 프로그램 개발)

  • Kim, Ki-Bong
    • Journal of Life Science
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    • v.18 no.8
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    • pp.1132-1139
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    • 2008
  • A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

Construction of a Transgenic Tobacco Expressing a Polydnaviral Cystatin (폴리드나바이러스 유래 시스타틴 유전자 발현 형질전환 담배 제작)

  • Kim, Yeongtae;Kim, Eunsung;Park, Youngjin;Kim, Yonggyun
    • Korean journal of applied entomology
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    • v.54 no.1
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    • pp.7-15
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    • 2015
  • CpBV (Cotesia plutellae bracovirus) is a polydnavirus and encodes a cystatin (CpBV-CST1) gene. Its overexpression suppresses insect immunity and alters insect developmental processes. This study aimed to construct a genetically modified (GM) tobacco to further explore the physiological function of the viral cystatin and to apply to control insect pests. To this end, the transgenic tobacco lines were screened in expression of the target gene and assessed in insecticidal activity. A recombinant vector (pBI121-CST) was prepared and used to transform a bacterium, Agrobacterium tumefasciens. The transformed bacteria were used to generate transgenic tobacco lines, which were induced to grow callus and resulted in about 92% of shoot regeneration. The regenerated plants were screened by PCR analysis to confirm the insertion of the target gene in the plant genome. In addition, the expression of the target gene was assessed in the regenerated plants by quantitative real-time PCR (qRT-PCR). The qRT-PCR analysis showed that the transgenic line plant expressed the target gene about 17 times more than the control tobacco, indicating a stable insertion and expression of the target gene in the transgenic tobacco line. The insecticidal activity was then analyzed using the screened transgenic tobacco lines against the teneral 1st instar larvae of the oriental tobacco budworm, Helicoverpa assulta. Though there was a variation in the insecticidal efficacy among transgenic lines, T9 and T12 lines exhibited more than 95% mortality at 7 days after feeding treatment. These results suggest that CpBV-CST1 is a useful genetic resource to be used to generate GM crop against insect pests.

Development of dry milling suitable rice cultivar to invigorate rice processing products

  • Jeung, Ji-Ung
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.10-10
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    • 2017
  • Rice consumption has been continuously decreasing as the eating habits of Koreans have become westernized and diversified. The per capita annual rice consumption in Korea has dropped sharply from 136.4 kg in 1970 to 61.9 kg in 2016. The Korean government, therefore, has been trying to promote rice consumption by invigorating the processed food industry using rice flour. To facilitate the market for processed rice foods, it is essential to develop proper milling technology in terms of flour particle size and damaged starch content to produce high quality rice flour at competitive cost. Dry milling and wet milling are the two major processes used to produce rice flour. Although the dry milling process is relatively simple with a lower production cost, damaged starch content increases because of the high grain hardness of rice. In wet milling, the quality of rice flour is improved by reducing flour particle size as well as damaged starch content through soaking procedures. However, the production costs are high because of the additional expenses associated with the disposal of waste water, sterilization and drying of the wet flour. Recently developed technologies such as jet milling and cryogenic milling also require expensive investment and production. Therefore, developing new rice cultivars with dry milling adaptability as well as good processing properties is an important goal of rice breeding in Korea. 'Suweon 542' is a floury endosperm mutant line derived from sodium azide treatment on a high-yield, early maturing, and non-glutinous japonica rice cultivar, 'Namil'. Compared with the wild type, after dry milling process, the grain hardness of 'Suweon 542' was significantly lower because of its round and loosely packed starch granules. Also, the flour of 'Suweon 542' had significantly smaller particles and less damaged starch than 'Namil' and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Recently, through collaborations with nine universities and food companies, a total of 21 kinds of processed prototypes, using the dry milling flour of 'Suweon 542', were evaluated. In the production of major rice processing products, there was no significant quality difference between the flours prepared by wet milling and dry milling. Although the amount of water added to the dough was slightly increased, it was confirmed that the recipe applying the wet flour could be used without significant change. To efficiently transfer the floury endosperm characteristics of 'Suweon 542' to other commercial rice cultivars, it is essential to develop DNA marker tightly linked to the target gene. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from 'Suweon 542'/'Milyang 23' showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of 'Suweon 542' was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population. Through further physical mapping, a co-segregate and co-dominant DNA marker with the locus, flo7(t) was successfully developed, by which, thereby, breeding efficiency of rice cultivars having proper dry milling adaptability with high yield potential or useful functional materials would be improved. 'Suweon 542' maintained the early maturity of the wild type, Namil, which can be used in rice-wheat double cropping systems in Korea not only for improved arable land but also for sharing flour production facilities. In addition to the high susceptibility against major rice diseases, nevertheless, another possible drawback of 'Suweon 542' is the high rate of viviparous under prolonged rainfall during the harvesting season. To overcome susceptibility and vivipary of 'Suweon 542', the progeny lines, derived from the crosses 'Suweon 542' and 'Jopyeong', an early maturing rice cultivar with multiple resistance against rice blast, bacterial blight, and rice strip virus, and 'Heugjinju', a anthocyanin pigment containing black rice cultivar, were intensively evaluated. As the outputs, three dry milling suitable rice elite lines, 'Jeonju614', 'Jeonju615', and 'Jeonju616' were developed.

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Association Analysis between (AAT)n Repeats in the Cannabinoid Receptor 1 Gene and Schizophrenia in a Korean Population (한국인에서 조현병과 Cannabinoid Receptor 1 유전자의 삼핵산 반복서열의 연합에 대한 연구)

  • Kim, Ji-Won;Roh, Yang-Ho;Kim, Min-Jea;Kim, Chea-Ri;Park, Byung-Lae;Bae, Joon Seol;Shin, Hyoung Doo;Choi, Ihn-Geun;Han, Sang-Woo;Hwang, Jaeuk;Woo, Sung-Il
    • Korean Journal of Biological Psychiatry
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    • v.21 no.3
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    • pp.99-106
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    • 2014
  • Objectives Previous studies suggest that the cannabinoid receptor 1 (CNR1) gene could be an important candidate gene for schizophrenia. According to linkage studies, this gene is located on chromosome 6q14-q15, which is known to harbor the schizophrenia susceptibility locus (locus 5, SCZ5, OMIM 803175). The pharmacological agent delta-9-tetrahydrocannabinol (${\Delta}$-9-THC) seems to elicit the symptoms of schizophrenia. The association between CNR1 polymorphisms and schizophrenia is actively being investigated, and some studies have linked the AAT-trinucleotide repeats in CNR1 to the onset of schizophrenia. In this study, we have investigated the association between the AAT-trinucleotide repeats in CNR1 and schizophrenia by studying schizophrenia patients and healthy individuals from Korea. Methods DNA was extracted from the blood samples of 394 control subjects and 337 patients diagnosed with schizophrenia (as per the Diagnostic and Statistical Manual of Mental Disorders, fourth edition criteria). After polymerase chain reaction amplification, a logistic regression analysis, with age and gender as the covariates, was performed to study the variations in the AAT-repeat polymorphisms between the two groups. Results In total, 8 types of trinucleotide repeats were identified, each containing 7, 8, 10, 11, 12, 13, 14, and 15 repeats, respectively. $(AAT)_{13}$ allele was most frequently observed, with a frequency of 33.6% and 31.6% in the patient and control groups, respectively. The frequency of the other repeat alleles in the patient group (in the decreasing order) was as follows : $(AAT)_{13}$ 33.6%, $(AAT)_{14}$ 21.6%, $(AAT)_{12}$ 18.5%, and $(AAT)_{7}$ 11.1%. The frequency of the repeat alleles in the control group (in the decreasing order) was as follows : $(AAT)_{13}$ 31.6%, $(AAT)_{14}$ 24.5%, $(AAT)_{12}$ 17.2%, and $(AAT)_{7}$ 11.6%. However, there were no significant differences in the AAT-repeat polymorphisms of the CNR1 gene between the patient group and the control group. Conclusions Although our study revealed no significant association of the AAT-repeat polymorphism of the CNR1 gene with schizophrenia, it will serve as a good reference for future studies designed to examine the cannabinoid hypothesis of schizophrenia.

Cattle Age Prediction by Leukocytes Telomere Quantification (혈액세포의 텔로미어 함량을 이용한 소의 연령예측)

  • Choi, Na-Eun;Kim, Hyun-Sub;Choe, Chang-Yong;Jeon, Gwang-Joo;Sohn, Sea-Hwan
    • Journal of Animal Science and Technology
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    • v.52 no.5
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    • pp.367-374
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    • 2010
  • Telomeres at the end of chromosomes consist of tandem repeats of (TTAGGG)n DNA sequence and associated proteins. Telomeres have the essential functions in chromosome stability and genome integrity and are hence related to cell senescence and cancer. This study was carried out to quantify the amount of telomeric DNA and establish age prediction equations by using the quantity of telomeric DNA for cattle. Analysis of the telomere quantity of the lymphocytes was performed at different age, across breeds and between different sexes of cattle. We quantified the amount of telomeric DNA by the Q-FISH technique using the telomeric DNA probe in 460 cattle at age of 1~166 months in Korean Cattle and Holstein breeds. In results, we found that the amount of telomeric DNA decreased gradually with age. The amount of telomeric DNA of Korean Cattle was significantly higher than that of Holstein breed (P<0.01). In addition, the amount of telomeric DNA in male was significantly higher than that in female (P<0.01). Using the relationship between age and the amount of telomeric DNA in cattle, age predicting equations were established as a result of regression analysis. Because sex and breeds influenced telomeric DNA quantity, the age prediction equations were estimated separately in Korean Cattle females and Holstein females. The regression equations were $\hat{Y}$=$38.102X^2$-220.103X + 318.309 (P<0.0001, $R^2$=0.8019) in Korean Cattle females and $\hat{Y}$ = $42.799X^2$ - 199.682X + 242.106 (P<0.0001, $R^2$ = 0.8379) in Holstein females, where the X was quantity of telomeric DNA and Y was predicted age in months. These equations predicted the age of cattle with high significance and accuracy and have high R square values. Thus, it could be possible to scientifically predict the age using the above equations for Korean Cattle and Holstein females.

Population-Based Newborn Hearing Impairment Screening Test Using GJB2 Mutation Analysis

  • Lee, Kyung-Ok;Jeong, Su-Jin;Byun, Ji-Young;Kim, Jeong-Sook;Lee, Hye-Jung;Seong, Hye-Soon;Kim, Kyung-Tae
    • Korean Journal of Clinical Laboratory Science
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    • v.39 no.2
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    • pp.113-121
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    • 2007
  • Hearing loss is a common congenital disorder that is frequently associated with mutations in the Cx26 gene (GJB2). Recently, the mutation analysis of GJB2 has been used in a newborn screening test for the detection of hearing impairment. Population-based studies should be performed before the application of genetic testing for the identification of deaf newborns. In this study, 8 positions of GJB2 mutations-including 35delG, 167delT, 235delC, V27I, V37I, M34T, E114G, and I203T-were analyzed using PCR-direct sequencing in a total of 437 healthy Korean neonates. DNAs from dried blood spots were extracted using a commercial DNA extraction kit. The PCR-amplified products (783 bps) of the GJB2 gene were detected using 2% agarose gel electrophoresis and subjected to direct sequencing. The sequences were compared with those in the GenBank database by using the BLAST program. In this study, 5 GJB2 mutations -including V27I (79G>A), V37I (109G>A), E114G (341A>G), I203T (608T>C), and 235delC- were found. Of the 437 neonate samples, 301 subjects showed GJB2 mutations (68.9%, 301/437). The V27I mutation was found in 271 subjects and was the most frequent (62.0%, 271/437). The E114G, I203T and V37I mutations were shown in 146, 17 and 14 subjects, respectively. The 235delC mutation was found in 1 subject. The E114G mutation was frequently accompanied by the V27I mutation. V27I/E114G (97.2%, 143/147) was the most common double mutation and 3 subjects had the double mutation V27I/I203T. A triple mutation, V27I/E114G/I203T, was found in 1 subject. In conclusion, PCR-direct sequencing is a convenient tool for the rapid detection of GJB2 mutations and this data might provide information for the genetic counseling of the GJB2 gene.

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Effects of High Stocking Density on the Expressions of Stress and Lipid Metabolism Associated Genes in the Liver of Chicken (닭의 고밀도 사양체계가 스트레스 및 지방대사 연관 유전자 발현에 미치는 영향)

  • An, Young Sook;Park, Jeong Geun;Jang, In Surk;Sohn, Sea Hwan;Moon, Yang Soo
    • Journal of Life Science
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    • v.22 no.12
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    • pp.1672-1679
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    • 2012
  • The effect of high stocking density (HSD) on the expression of stress and lipid metabolism associated genes in the liver of broiler chickens was examined by chicken genome array analysis. The chickens in a control group were randomly assigned to a $495cm^2/bird$ stocking density, whereas the chickens in a HSD group were arranged in a $245cm^2/bird$ stocking density with feeding ad libitum for 35 days. The chickens assigned to the HSD group had a significantly lower body weight, weight gain, and feed intake compared with those of the control group (p<0.05). The mortality of chickens was higher in the HSD group than in the control group. The microarray analysis indicated up-regulation of stress associated genes such as HMGCR, $HSP90{\alpha}$, HSPA5 (GRP78/Bip), DNAJC3 and ATF4, and down-regulation of interferon-${\gamma}$ and PDCD4 genes. The endoplasmic reticulum stress associated genes, HSPA5 (GRP78/Bip), DNAJC3 and ATF4, were highly expressed in the HSD group. The genes, ACSL5, TMEM195 and ELOVL6, involved in fatty acid synthesis, were elevated in the HSD group. The genes, ACAA1, ACOX1, EHHADH, LOC423347 and CPT1A, related to fatty acid oxidation, were also activated in the HSD group. These results suggest that a HSD rearing system stimulates the genes associated with fatty acid synthesis as well as fatty acid oxidation in the liver of broiler chickens.

Polymorphisms and Allele Distribution of Novel Indel Markers in Jeju Black Cattle, Hanwoo and Imported Cattle Breeds (제주흑우, 한우 및 수입 소 품종에서 새로운 indel 마커의 다형성과 대립인자 분포)

  • Han, Sang-Hyun;Kim, Jae-Hwan;Cho, In-Cheol;Cho, Sang-Rae;Cho, Won-Mo;Kim, Sang-Geum;Kim, Yoo-Kyung;Kang, Yong-Jun;Park, Yong-Sang;Kim, Young-Hoon;Park, Se-Phil;Kim, Eun-Young;Lee, Sung-Soo;Ko, Moon-Suck
    • Journal of Life Science
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    • v.22 no.12
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    • pp.1644-1650
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    • 2012
  • The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

The Studies of Activity of Retrotransposon(Tos17) according to Tissue Culture Periods in Rice(Oryza sativa L.) (벼 조직배양 기간에 따른 retrotransposon(Tos17)의 활성에 관한 연구)

  • Yang, Hee-Eun;Fang, Yilan;Shin, Young-Boum;Lee, Boung-Jin;Hong, Soon-Kwan
    • Korean Journal of Plant Resources
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    • v.20 no.5
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    • pp.389-397
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    • 2007
  • Using the active-increment of Tos17 copies in the genome of Oryza sativa L., there were many studies about induction and selection of new mutants. This study mainly focuses on the induction for retrotransposon(Tos17) activity in the callus of Ilpumbyeo(Oryza sativa L.) according to varied culture period and condition. The objectives of this study are obtaining various mutants($M_1$) through plant regeneration, identification of the mutation relation with Tos17, and subsequent phenotyping of the mutants($M_2,\;M_3$). A total of 371 $M_1$ mutants was obtained. The degree of Tos17 activity obtained regeneration plants with each different culture period was evaluated by Southern blot analysis. The result showed that control Ilpumbyeo rice has 5 numbers of copies and the band numbers obtained 7, 8, 9.5, 12, 6, 13.5, 17.5 from culture period of 1, 2, 3, 5, 6, 7, 8 month, respectively. In this study, the result showed that most effectual culture period for activity of Tos17 in Ilpumbyeo rice is 5 month. Hereafter, collections and analysis of various recombination plants will act on an important factor in multiplication and preservation of $M_2$ and $M_3$ generation. And an urgent and important subject is a development of screening method for selection of diverse mutants.