• Animal cells and systems
• /
• v.5 no.2
• /
• pp.153-156
• /
• 2001

A key aspect of genomic research in the “post-genome era”is to associate sequence variations with heritable phenotypes. The most common variations in the human genome are single nucleotide polymorphisms (SNPs) that occur approximately once in every 500 to 1,000 bases. Although analyzing the phenotypic outcome of these SNPs is crucial to facilitate large-scale association studies of genetic diseases, detection of SNPs from an extended number of human DNA samples is often difficult, labor-intensive and time-consuming. Recent development in SNP detection methods using DNA microarrays and mass spectrophotometry has allowed automated high throughput analyses, but such equipments are not accessible to many scientists. In this study, we demonstrate that a simple PCR-based method using primers with a mismatched base at the 3'-end provides a fast and easy tool to identify known SNPs from human genomic DNA in a regular molecular biology laboratory. Results from this PCR amplification of specific alleles (PASA) analysis efficiently and accurately typed the Q576R polymorphism of human IL4 receptor from the genomic DNAs of 29 Koreans, including 9 samples whose genotype could not be discerned by the conventiona1 PCR-SSCP (single strand conformation polymorphism) method. Given the increasing attention to disease-associated polymorphisms in genomic research, this alternative technique will be very useful to identify SNPs in large-scale population studies.

• Korean Journal of Environment and Ecology
• /
• v.32 no.6
• /
• pp.566-574
• /
• 2018

The purpose of this study was to identify the phylogenetic relationships of the plants in the Korean genus Suaeda and to find out the molecular markers that could confirm the interspecies relationships in the family tree through molecular phylogenetic studies. We used the nuclear ribosomal DNA ITS and the chloroplast DNA matK, psbA-trnH, and trnL-trnF as the molecular markers. We could not distinguish between S. japonica and S. maritima and between S. maritima and S. australis in the ITS region and could not distinguish between S. japonica and S. australis with the base sequence in the psbA-trnH and trnL-trnF region. However, we analyzed the combinations of four molecular marker regions and confirmed that each of five plant species of the genus Suaeda formed the independent line. Therefore, it is considered that combinations of molecular markers would be useful for the analysis of phylogenetic relationships in the genus Suaeda. Further investigations of the ecological and morphological characteristics would be needed to understand the phylogenetic relationship and lineage diversification in the genus Suaeda.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• v.13 no.4
• /
• pp.1765-1794
• /
• 2019

Genetic Programming (GP) is an intelligence technique whereby computer programs are encoded as a set of genes which are evolved utilizing a Genetic Algorithm (GA). In other words, the GP employs novel optimization techniques to modify computer programs; imitating the way humans develop programs by progressively re-writing them for solving problems automatically. Trial programs are frequently altered in the search for obtaining superior solutions due to the base is GA. These are evolutionary search techniques inspired by biological evolution such as mutation, reproduction, natural selection, recombination, and survival of the fittest. The power of GAs is being represented by an advancing range of applications; vector processing, quantum computing, VLSI circuit layout, and so on. But one of the most significant uses of GAs is the automatic generation of programs. Technically, the GP solves problems automatically without having to tell the computer specifically how to process it. To meet this requirement, the GP utilizes GAs to a "population" of trial programs, traditionally encoded in memory as tree-structures. Trial programs are estimated using a "fitness function" and the suited solutions picked for re-evaluation and modification such that this sequence is replicated until a "correct" program is generated. GP has represented its power by modifying a simple program for categorizing news stories, executing optical character recognition, medical signal filters, and for target identification, etc. This paper reviews existing literature regarding the GPs and their applications in different scientific fields and aims to provide an easy understanding of various types of GPs for beginners.

• Genomics & Informatics
• /
• v.17 no.1
• /
• pp.5.1-5.9
• /
• 2019

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the $Ad{\acute{e}}lie$ (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins' transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.7
• /
• pp.939-948
• /
• 2019

Objective: Extension and Agouti loci play a key role for proportions of eumelanin and pheomelanin in determining coat color in several species, including goat. Mongolian goats exhibit diverse types of coat color phenotypes. In this study, investigation of the melanocortin 1 receptor (MC1R) coding region in different coat colors in Mongolian goats was performed to ascertain the presence of the extension allele. Methods: A total of 105 goat samples representing three goat breeds were collected for this study from middle Mongolia. A 938 base pair (bp) long coding region of the MC1R gene was sequenced for three different breeds with different coat colors (Gobi Gurwan Saikhan: complete black, Zalaa Jinstiin Tsagaan: complete white, Mongolian native goat: admixture of different of coat colors). The genotypes of these goats were obtained from analyzing and comparing the sequencing results. Results: A total of seven haplotypes defined by five substitution were identified. The five single nucleotide polymorphisms included two synonymous mutations (c.183C>T and c.489G>A) and three missense (non-synonymous) mutations (c.676A>G, c.748T>G, and c.770T>A). Comparison of genotypes frequencies of two common missense mutions using chi-sqaure ($x^2$) test revealed significant differences between coat color groups (p<0.001). A logistic regression analysis additionally suggested highly significant association between genotypes and variation of black versus white uniform combination. Alternatively, most investigated goats (60.4%) belonged to H2 (TGAGT) haplotype. Conclusion: According to the findings obtained in this study on the investigated coat colors, mutations in MC1R gene may have the crucial role for determining eumelanin and pheomelanin phenotypes. Due to the complication of coat color phenotype, more detailed investigation needed.

• Korean Journal of Environmental Agriculture
• /
• v.40 no.3
• /
• pp.186-193
• /
• 2021

BACKGROUND: Before generating transgenic plant using the CRISPR-Cas9 system, the efficiency test of sgRNAs is recommended to reduce the time and effort for plant transformation and regeneration process. The efficiency of the sgRNA can be measured through the transient expression of sgRNA and Cas9 gene in tomato cotyledon; however, we found that the calculated efficiency showed a large variation. It is necessary to increase the precision of the experiment to obtain reliable sgRNA efficiency data from transient expression. METHODS AND RESULTS: The cotyledon of 11^th, 15^th, 19^th, and 23^rd-day-old tomato (Solanum lycopersicum cv. Micro-Tom) were used for expressing CRISPR-Cas9 transiently. The agrobacterium harboring sgRNA for targeting ALS2 gene of tomato was injected through the stomata of leaf adaxial side and the genomic DNA was extracted in 5 days after injection. The target gene edition was identified by amplifying DNA fragment of target region and analyzing with Illumina sequencing method. The target gene editing efficiency was calculated by counting base deletion and insertion events from total target sequence read. CONCLUSION: The CRISPR-Cas9 editing efficiency varied with tomato cotyledon age. The highest efficiency was observed at the 19-day-old cotyledons. Both the median and mean were the highest at this stage and the sample variability was also minimized. We found that the transgene of CRISPR-Cas9 system was strongly correlated with plant leaf development and suggested the optimum cotyledon leaf age for Agrobacterium-mediated transfection in tomato.

• Journal of Korean Society on Water Environment
• /
• v.27 no.3
• /
• pp.334-341
• /
• 2011

The free residual chlorine of tap water samples, collected from 266 faucets on the water pipe network in Daegu City, was between 0.1 and 0.79 mg/L. On microorganic tests, general bacteria and the coliform goup were not detected and thus the tap water was turned out to be fit to drink. In particular, samples of which free residual chlorine was 0.1 mg/L and over were cultured in R2A agar media at $25^{\circ}C$ for 7 days, and as a result heterotrophic bacteria were detected in 65.9% of samples; (1). The closer tap water got to the faucet from the stilling basin, the lower residual chlorine concentration became but the more the bacterial count became. And, more bacteria were detected in the R2A agar medium than in the PCA medium. (2). In the case of separated strains, most colonies were reddish or yellowish. 16S rRNA sequence was identified as Methylobacterium sp. and Williamsia sp., and yellow strain was identified as Sphingomonas sp., Sphingobium sp., Novosphingobium sp., Blastomonas sp., Rhodococcus sp. and Microbacterium sp. White strain was identified as Staphylococcus sp. (3). Sterilized tap water in polyethylene bottles was inoculated with separated strain and was left as it was for 2 months. As a result, bio-film was observed in tap water inoculated with Methylobacterium sp. and Sphingomonas sp. It was found that heterotrophic bacteria increased when free residual chlorine was removed from tap water in the water pipe network. Thus, there is a need to determine a base value for heterotrophic bacteria in order to check the cleanliness of tap water in the water pipe network.

• Geomechanics and Engineering
• /
• v.27 no.6
• /
• pp.561-571
• /
• 2021

Cofferdams made of teel sheet piles are commonly utilized as support structures for excavation of sea-crossing bridge foundations. As cofferdams are often subject to tide variation, it is imperative to consider potential effects of tide on stability and serviceability of sheet piles, particularly, ultralong steel sheet piles (USSPs). In this study, a real USSP cofferdam constructed using new construction technology in Nanxi River was reported. The design of key parts of USSP cofferdam in the presence of tidal action was first introduced followed by the description of entire construction technology and associated monitoring results. Subsequently, a three-dimensional finite-element model corresponding to all construction steps was established to back-analyze measured deflection of USSPs. Finally, a series of parametric studies was carried out to investigate effects of tide level, soil parameters, support stiffness and construction sequence on lateral deflection of USSPs. Monitoring results indicate that the maximum deflection during construction occurred near the riverbed. In addition, measured stress of USSPs showed that stability of USSP cofferdam strengthened as construction stages proceeded. Moreover, the numerical back-analysis demonstrated that the USSP cofferdam fulfilled the safety requirements for construction under tidal action. The maximum deflection of USSPs subject to high tide was only 13.57 mm at a depth of -4 m. Sensitivity analyses results showed that the design of USSP cofferdam system must be further improved for construction in cohesionless soils. Furthermore, the 5th strut level before concreting played an indispensable role in controlling lateral deflection of USSPs. It was also observed that pumping out water before concreting base slab could greatly simplify and benefit construction program. On the other hand, the simplification in construction procedures could induce seepage inside the cofferdam, which additionally increased the deflection of USSPs by 10 mm on average.

• The Korea Journal of Herbology
• /
• v.28 no.6
• /
• pp.9-14
• /
• 2013

Objectives : Cnidii Fructus is prescribed as the fruit of Cnidium monnieri (L.) Cusson or Torilis japonica (Houtt.) DC. in Korea pharmacopoeia. Although there are differences in the composition of useful components, two species have been used without distinction. In order to discriminate them, DNA sequencing and taste pattern analysis were used in this study. Methods : Primers ITS 1 and ITS 4 were used to amplify the intergenic transcribed spacer(ITS) region of nuclear ribosomal DNA from seven T. japonica and six C. monnieri samples. Taste pattern of samples were measured by using taste-sensing system SA402B equipped with five foodstuff sensors(CT0, C00, AAE, CA0, and AE1). The five initial taste(sourness, bitterness, astringency, umami, and saltiness) and three aftertaste(aftertaste of bitterness, astringency, and umami) of two species were compared. Results : According to the results of ITS region sequence analysis, two species showed 94 base pairs differences. The similarity of two sequences was 85%. From the taste pattern analysis, sourness, bitterness, aftertaste of bitterness(aftertaste-B), and umami showed a different pattern. Especially, bitterness and aftertaste-B of C. monnieri were significantly higher than T. japonica. In addition, two species were shown to have two markedly different clustering by these two flavors. Conclusion : T. japonica and C. monnieri were effectively discriminated using DNA sequencing and taste pattern analysis. These methods can be used to identify the origin of traditional medicine in order to maintain therapeutic efficacy.

• Investigative Magnetic Resonance Imaging
• /
• v.5 no.1
• /
• pp.38-42
• /
• 2001

Dark band artifacts are often observed in angiograms of arteries obtained by 2D time-of-flight (TOF) angiography with saturation of veins by presaturation RF pulses. At some arteries the arterial blood velocity varies in a triphasic pattern during a cardiac cycle. The arterial blood, that is saturated by presaturation RF pulses in the saturation band, can flow back into the imaging slice during the retrograde flow phase of the triphasic variation. When such saturated retrograde flow occurs during the acquisition of the central part of the K space, a signal void can result in base images and consequently dark band artifacts can appear in angiograms. This phenomenon is experimentally demonstrated by varying the gap between the imaging slice and the saturation band. Furthermore, a new pulse sequence is proposed to eliminate the dark band artifacts by changing the profile of the saturation band front a rectangle to a ramp.