• Korean Journal of Biological Psychiatry
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• v.8 no.2
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• The Korean Journal of Mycology
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• v.49 no.1
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• pp.11-19
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• 2021

In 2017, Talaromyces variabilis was isolated during a survey of fungal diversity in field soils in Korea. This isolate was described based on its morphological and molecular characteristics and it was identified molecularly using the partial 18S-ITS1-5.8S-ITS2-28S rDNA region and calmodulin (CaM)-encoding gene sequence data. Thus, this study reported morphological and multigene sequence characterization of T. variabilis.

• Korean Journal of Microbiology
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• v.44 no.1
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• pp.1-9
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• 2008

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight on rice. In this paper, current status on molecular genetic study of major virulence genes, hypersensitive response and pathogenicity (hrp), productions of extracellular polysaccharide (EPS), extracellular enzymes and lipopolysaccharides (LPS), avr genes were reviewed. The IS elements with 611 copies including 133 ORF IS were inserted in various regions of the Xoo genome and in expecially regions franking virulence genes. Whole genome sequence of X. oryzae pv. oryzae KACC10331 were used for defining genetic organization of the virulence genes. Futhermore, the virulence genes in Xoo genome were compared to those of other Xanthomonas species in Blast GenBank data base.

• Development and Reproduction
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• v.18 no.4
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• pp.275-286
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• 2014

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.743-750
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• 2016

Mus musculus (Rodentia: Muridae) has generally been infected with a rodent hookworm Nippostrongylus brasiliensis. In this report, we present morphological and molecular identification of N. brasiliensis by light and scanning electron microscopy and PCR amplification of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the protein sequences encoded by cox1 gene, respectively. Despite the use of N. brasiliensis in many biochemistry studies from India, their taxonomic identification was not fully understood, especially at the species level, and no molecular data is available in GenBank from India. Sequence analysis of cox1 gene in this study revealed that the present specimen showed close identity with the same species available in GenBank, confirming that the species is N. brasiliensis. This study represents the first record of molecular identification of N. brasiliensis from India and the protein structure to better understand the comparative phylogenetic characteristics.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• BMB Reports
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• v.31 no.6
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• pp.525-535
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• 1998

A critical step in the faithful translation of genetic information is specific tRNA recognition by aminoacyl-tRNA synthetases. These enzymes catalyze the covalent attachment of particular amino acids to the terminal adenosine of cognate tRNA substrates. In general, there is one synthetase for each of the twenty amino acids and each enzyme must discriminate against all of the cellular tRNAs that are specific for the nineteen noncognate amino acids. Primary sequence information combined with structural data have resulted in the division of the twenty synthetases into two classes. In recent years, several high-resolution co-crystal structures along with biochemical data have led to an increased understanding of tRNA recognition by synthetases of both classes. The anticodon sequence and the amino acid acceptor stem are the most common locations for critical recognition elements. This review will focus on acceptor stem discrimination by class II synthetases. In particular, the results of in vitro aminoacylation assays and site-directed and atomic group mutagenesis studies will be discussed. These studies have revealed that even subtle atomic determinants can provide signals for specific tRNA aminoacylation.

• ALGAE
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• v.21 no.2
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• pp.169-174
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• 2006

We have cultured more than 100 Arctic and Antarctic cryophilic microalgal strains in KOPRI culture collections of polar microorganisms (KCCPM). Among them, we tried to identify an Antarctic strain, KOPRI AnM0008 by morphological and molecular analysis. Nuclear SSU rDNA and plastid rbcL sequences were used to identify the strain. It was identified as Porosira pseudodenticulata based on SSU sequence data showing 99% identity with GenBank X85398. This result was supported by morphological features like solitary labiate process, external foramina and internal cribra by optical and scanning electron microscope. Morphological identification and molecular analysis on polar cryophilic microalgae will be accomplished to construct the databases for KCCPM.

• Korean Journal of Ichthyology
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• v.18 no.1
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• pp.12-19
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• 2006

To examine the relationship of geological distribution and phylogenetic tree of O. latipes in the Far East, we analyzed cytochrome b (cyt b) gene in the mitochondrial genome. In this study we employed the entire sequence of cyt b of 53 samples collected from nine Korean locations and 117 cyt b data retrieved from the GenBank. From 170 Oryzias latipes cyt b sequence data, 142 different haplotypes were identified and phylogenetic relationship was reconstructed based on the dataset. According to the phylogeny, haplotypes were divided into three major haplogroups A, B and C, and their relationships were well correlated to their distributional patterns. Haplogroup A which is widely distribute in the southern part of Korea is separated in the geographical distribution from the haplogroup B which is found from China to the western part of Korea. Haplogroup C is only found in Japan.

• The Bulletin of The Korean Astronomical Society
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• v.37 no.2
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• pp.85.2-85.2
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• 2012

The interstellar medium (ISM) of galaxies in the galaxy cluster can well be affected by the intracluster medium (ICM). Among many suggested environmental processes, ram pressure stripping can effectively remove gas through the interaction with the ICM. In fact, Cluster galaxies are lower in HI gas mass compared to their field counterparts, and in recent high resolution HI imaging studies, many galaxies in dense environments have been found to be ram pressure stripped in HI. However, it is still under debate whether the ICM pressure can also remove dense molecular gas from the galactic disk, which plays more important role in star formation and hence galaxy evolution. To answer this question, we have obtained high resolution 12/13 CO (2-1) data from the Sub Millimeter Array (SMA) of four galaxies at various HI stripping stages to study how the molecular gas properties change as the galaxy experiences the ICM pressure. We investigate the physical properties of molecular gas with 12/13 CO images. By comparing with other wavelength data, i.e. data(optical, HI, $H{\alpha}$, etc), we discuss how and in which timescale galaxies can migrate from the blue cloud to the red sequence due to ram pressure stripping.