• 가정과삶의질연구
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• 제26권4호
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• pp.41-54
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• 2008

The purpose of this study was to investigate predictors concerning preschoolers' ability to read words, in terms of their sub-skills of alphabet knowledge, phonological awareness, and phonological processing. Fourteen literacy sub-tests and three types of reading tasks were administered to 289 kindergartners aged 4 to 6 in Busan. The main results are as follows. Sub-skills that predicted reading ability varied with children's age. Irrespective of children's age groups, knowledge of consonant names and digit naming speed commonly explained the reading of real words. In contrast, skills of syllable deletion and phoneme substitution and knowledge of alphabet composition principles were related to only 4-year-olds' reading skills. Exclusively included was digit memory in predicting 5-year-olds' reading abilities, and knowledge of vowel sounds in 6-year-olds' reading skills. The type of reading task also influenced reading ability. A few common variables such as knowledge of consonant names and vowel sounds, digit naming speed, and phoneme substitution skill explained all types of word reading. Syllable counting skills, however, had predictive value only for the reading of real words. Phoneme insertion skills and digit memory had predictive value for the reading of pseudo words and low frequency letters. Likewise, knowledge of consonant sounds and vowel stroke-adding principles were significant only for the reading of low frequency letters.

• 한국연초학회지
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• 제30권2호
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• pp.85-93
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• 2008

This report describes a set of seven informative single-nucleotide polymorphisms (SNPs) and one insertion-deletion (INDEL) distributed over 24 cultivars that can be used for tobacco (Nicotiana tabacum L.) cultivar identification. We analyzed 163,000 genomic DNA sequences downloaded from Tobacco Genome Initiative database and assembled 31,370 contigs and 60,000 singletons. Using relatively long contigs, we designed primer sets for PCR amplification. We amplified 61 loci from 24 cultivars and sequenced the PCR products. We found seven significant SNPs and one INDEL among the sequences and we classified the 24 cultivars into 10 groups. SNP frequency of tobacco, 1/8,380 bp, was very low in comparison with those of other plant species, between 1/46 bp and 1/336 bp. For exact identification of tobacco cultivars, many more SNP markers should be developed. This study is the first attempt to identify tobacco cultivars using SNP markers.

• Asian-Australasian Journal of Animal Sciences
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• 제25권7호
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• pp.927-934
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• 2012

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island.

• Asian-Australasian Journal of Animal Sciences
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• 제28권1호
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• pp.14-19
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• 2015

The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities ($H_O$) and expected heterozygosities ($H_E$) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei's genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

• Molecules and Cells
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• 제27권1호
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• pp.119-123
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• 2009

Porcine endogenous retroviruses (PERVs) gamma1 in the pig genome have the potential to act as harmful factors in xenotransplantation (pig-to-human). Long terminal repeats (LTRs) are known to be strong promoter elements that could control the transcription activity of PERV elements and the adjacent functional genes. To investigate the transcribed PERV gamma1 LTR elements in pig tissues, bioinformatic and experimental approaches were conducted. Using RT-PCR amplification and sequencing approaches, 69 different transcribed LTR elements were identified. And 69 LTR elements could be divided into six groups (15 subgroups) by internal variation including tandem repeated sequences, insertion and deletion (INDEL). Remarkably, all internal variations were indentified in U3 region of LTR elements. Taken together, the identification and characterization of various PERV LTR transcripts allow us to extend our knowledge of PERV and its transcriptional study.

• 대한의생명과학회지
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• 제18권4호
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• pp.406-412
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• 2012

The polymorphism (insertion, I or deletion, D) of angiotensin converting enzyme (ACE) gene is designated as the presence of a 287 bp Alu repeat. The D/D homozygote carrier is associated with high ACE activity, and this high activity has been implicated with hypertension, coronary artery disease, or diabetic nephropathy. We studied the clinical candidate marker in ACE gene polymorphism using chemical and hematological analysis. The subjects are divided into normotensive and hypertensive groups and ACE genotype in the group was confirmed by PCR method. Chemical analysis was preceded with Hitachi7060, and hematological analysis was performed using Mythic 22. In 116 targeted people, 17 (38.64%) of 44 I/I genotype group are hypertension, 15 (34.09%) in 44 with D/I, but, D/D type in the 28 cases is 15 patients (53.57%) in hypertension. In hypertension group, biochemical analysis (triglyceride, and alkaline phosphatase) and hematological analysis (white blood cell, platelet) are showed high value in D/D genotype of ACE gene. The relationship between hypertension and ACE genotype is the same results as previously reported and we thought that the high laboratory value of white blood cell, platelet, triglycerides, and alkaline phosphatase are also indicator of hypertension in D/D type of ACE.

• Genomics & Informatics
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• 제11권4호
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• pp.164-173
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• 2013

Genomic instability, which occurs through both genetic mechanisms (underlying inheritable phenotypic variations caused by DNA sequence-dependent alterations, such as mutation, deletion, insertion, inversion, translocation, and chromosomal aneuploidy) and epigenomic aberrations (underlying inheritable phenotypic variations caused by DNA sequence-independent alterations caused by a change of chromatin structure, such as DNA methylation and histone modifications), is known to promote tumorigenesis and tumor progression. Mechanisms involve both genomic instability and epigenomic aberrations that lose or gain the function of genes that impinge on tumor suppression/prevention or oncogenesis. Growing evidence points to an epigenome-wide disruption that involves large-scale DNA hypomethylation but specific hyper-methylation of tumor suppressor genes, large blocks of aberrant histone modifications, and abnormal miRNA expression profile. Emerging molecular details regarding the modulation of these epigenetic events in cancer are used to illustrate the alterations of epigenetic molecules, and their consequent malfunctions could contribute to cancer biology. More recently, intriguing evidence supporting that genetic and epigenetic mechanisms are not separate events in cancer has been emerging; they intertwine and take advantage of each other during tumorigenesis. In addition, we discuss the collusion between epigenetics and genetics mediated by heterochromatin protein 1, a major component of heterochromatin, in order to maintain genome integrity.

• 한국작물학회지
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• 제60권2호
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• pp.224-230
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• 2015

Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.

• Asian Pacific Journal of Cancer Prevention
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• 제14권12호
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• pp.7271-7275
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• 2013

Objective: To investigate the association between the gene polymorphisms of angiotensin-converting enzyme (ACE) and digestive system cancer risk. Method: A search was performed in Pubmed, Medline, ISI Web of Science and Chinese Biomedical (CBM) databases, covering all studies until Sep 1st, 2013. Statistical analysis was performed by using Revman5.2 and STATA 12.0. Results: A total of 15 case-control studies comprising 2,390 digestive system cancer patients and 9,706 controls were identified. No significant association was found between the I/D polymorphism and digestive cancer risk (OR=0.93, 95%CI = (0.75, 1.16), P=0.53 for DD+DI vs. II). In the subgroup analysis by ethnicity and cancer type, no significant associations were found for the comparison of DD+DI vs. II. Results from other comparative genetic models also indicated a lack of associations between this polymorphism and digestive system cancer risks. Conclusions: This meta-analysis suggested that the ACE D/I polymorphism might not contribute to the risk of digestive system cancer.

• 대한수의학회지
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• 제60권3호
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• pp.109-116
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• 2020

This study aimed to develop a semi-nested polymerase chain reaction assay for the direct detection of Mycoplasma synoviae (M. synoviae) from clinical samples using three newly designed oligonucleotide primers specific to the variable lipoprotein haemagglutinin (vlhA) gene and differentiate M. synoviae field strains based on a nucleotide deletion or the insertion of the proline-rich repeat (PRR) region of the vlhA gene. The developed semi-nested polymerase chain reaction (PCR) assay revealed positive results in 12 out of 100 clinical samples collected from chickens showing lameness and joint swelling. Six positive samples were selected randomly for sequencing, and sequence analysis revealed 96.3-100% nucleotide identities compared to the reference sequences. Phylogenetic analysis showed that sequences of the strains in this study were closely related to WVU1853 (Spain), CK.MS.UDL.PK.2014.2 (Pakistan), and F10-2AS (USA) strains, but they were distinct from the M. synoviae-H vaccine strain sequence. M. synoviae obtained from these samples were identified as types A and C with a length of 38 and 32 amino acids, respectively. These results indicated that the specific and sensitive semi-nested PCR could be a useful diagnostic tool for the direct identification of clinical samples, and the sequence analysis of the partial vlhA gene can be useful for typing M. Synoviae.