• The Korea Genome Conference
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• 2003.09a
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• pp.49.1-49.1
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• 2003

• BMB Reports
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• v.41 no.3
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• pp.184-193
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• 2008

Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.

• Journal of Environmental Impact Assessment
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• v.32 no.2
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• pp.94-111
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• 2023

In order to establish an effective management strategy for invasive species early detection and regular monitoring are required to assess their introduction or dispersal. Environmental DNA (eDNA) is actively applied to evaluate the fauna including the presence of invasive species as it has high detection sensitivity and can detect multiple species simultaneously. In Korea, the applicability evaluation of metabarcoding is being conducted mainly on fish, and research on other taxa is insufficient. Therefore, this study identified the feasibility of detecting invasive species in Korea using eDNA metabarcoding. In addition, to confirm the possibility of detection by taxa, the detection of target species was evaluated using four universal primers (MiFish, MiMammal, Mibird, Amp16S) designed for fish, mammals, birds, and amphibians. As a result, target species (Trachemys scripta, 3 sites; Cervus nippon, 3 sites; Micropterus salmoides, 7 sites; Rana catesbeiana, 4 sites) were detected in 17 of the total 55 sites. Even in the selection of dense sampling sites within the study area, there was a difference in the detection result by reflecting the ecological characteristics of the target species. A comparison of community structures (species richness, abundance and diversity) based on the presence of invasive species focused on M.salmoides and T.scripta, showed higher diversity at the point where invasive species were detected. Also, 1 to 4 more species were detected and abundance was also up to 1.7 times higher. The results of invasive species detection through metabarcoding and the comparison of community structures indicate that the accumulation of large amounts of monitoring data through eDNA can be efficiently utilized for multidimensional ecosystem evaluation. In addition, it suggested that eDNA can be used as major data for evaluation and prediction, such as tracking biological changes caused by artificial and natural factors and environmental impact assessment.

• Korean Journal of Plant Taxonomy
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• v.47 no.2
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• pp.161-169
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• 2017

The genome size is one of the basic characters of an organism, and it is widely applied in various fields of biology, such as systematics, breeding biology, population biology, and evolutionary biology. This factor was recently highlighted in genome studies because choosing a representative of a plant group having the smallest genome size is important for the efficiency of a genome project. For the estimation of the genome size, flow cytometry has recently been highlighted because it is a convenient, fast, and reliable method. In this study, we report the genome sizes of 15 taxa of Lamiaceae from nine genera distributed in Korea using flow cytometry. Data pertaining to the genome size for all of our species have not been reported thus far, and the data from Agastache, Clinopodium, Elsholtzia, and Isodon are the first reported for each genus. The genome sizes of 15 genera and 39 species were reported to the Plant DNA C-values Database (http://data.kew.org/cvalues/). Scutellaria indica L. has a genome size of 0.37 pg (1C). This is the fourth smallest value among the 98 Lamiaceae taxa in the Angiosperm DNA C-value Database, indicating that this taxon can be used as a reference species in the genome studies in Lamiaceae as a native Korean species. The largest genome size observed in this study is in Phlomis umbrosa Turcz. (1C=2.60 pg), representing the possible polyploidy origin of this species in the family.

• The Korean Journal of Ecology
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• v.24 no.6
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• pp.359-364
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• 2001

Regional variations of Dictyostelid cellular slime molds were examined using molecular data. The intertranscribed spacer regions including the 5.8S ribosomal DNA of 2 species(D. purpureum, P. violaceum) of Cellular Slime Molds were sequenced and analyzed. Among 13 strains of D. purpureum and 12 strains of P. violaceum analyzed, each two strains were obtained from ATCC and the others were isolated from the forest soils in Korea. The sequences of the 5.8S ribosomal DNA were conserved among the strains of the same species, but unexpectedly highly variable among species. A high level of genetic diversity was found which was best resolved at the genus/species level as well as the family level by sequence data from the ITS 1 and ITS 2 regions. According to the sequence alignments by CLUSTAL X and the phylogeographic analyses by PAUP, 12 strains of P. violaceum were divided into three groups among which there were no difference of the morphological characteristics. Among 13 strains of D. purpureum, genetic variations were related to two morphological types, the temperate and subtropical type. There was no variation pattern according to geography in Korea, but there were some variations between Korea and other countries.

• Journal of Microbiology
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• v.40 no.4
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• pp.254-259
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• 2002

The Phytophthora infestans requires two mating types for sexual reproduction. Amplified fragment length polymorphism (AFLP) was used to specifically detect different mating types of P. infestans. The AFLP primers E+AA (5'-GACTGCGTACCAATTCAA-3') and M+CAA (5'-GATGAGTCCTGAG-TAAC AA-3') detected a fragment that is specific in the A2 mating type of P. infestans. This fragment was cloned and sequenced. Based on the sequence data, PHYB-1 and PHYB-2 primer were designed to detect the A2 mating type of P. infestans. A single 347 bp segment was observed in the A2 mating type of P. infestans, but not in the A1 mating type of P. infestans or other Phytophthora spp. Identification of mating type was performed with phenotype (sexual reproduction) and genotype (CAPs marker) methods. Two factors, the annealing temperature and template DNA quantity, were investigated to determine the optimal conditions. Using mating type-specific primers, a unique band was obtained within annealing temperatures of 57$^{\circ}C$-62$^{\circ}C$ and DNA levels of 10pg-100 ng (data not shown).

• BMB Reports
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• v.39 no.4
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• pp.464-467
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• 2006

Recently, the nucleotide sequences of entire genomes became available. This information combined with older sequencing data discloses the exact chromosomal location of millions of nucleotide markers stored in the databases at NCBI, EMBO or DDBJ. Despite having resolved the intron/exon structures of all described genes within these genomes with a stroke of a pen, the sequencing data opens up other interesting possibilities. For example, the genomic mapping of the end sequences of the human, murine and rat BAC libraries generated at The Institute for Genomic Research (TIGR), reveals now the entire encompassed sequence of the inserts for more than a million of these clones. Since these clones are individually stored, they are now an invaluable source for experiments which depend on genomic DNA. Isolation of smaller fragments from such clones with standard methods is a time consuming process. We describe here a reliable one-step cloning technique to obtain a DNA fragment with a defined size and sequence from larger genomic clones in less than 48 hours using a standard vector with a multiple cloning site, and common restriction enzymes and equipment. The only prerequisites are the sequences of ends of the insert and of the underlying genome.

• Korean Journal of Plant Taxonomy
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• v.50 no.3
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• pp.253-261
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• 2020

Carex splendentissima U. Kang & J. M. Chung, endemic to the Korean peninsula, is characterized by staminate terminal spikes and glabrous elliptic perigynia. Based on its broad leaves, androgynous spikes, and tri-stigmatic features, the species has been placed in Carex sect. Siderostictae Franch. ex Ohwi, an East Asian section and a basal group in the genus. To clarify the monophyly and phylogenetic position of the species, a molecular study using the internal transcribed spacer region of nuclear ribosomal DNA and chloroplast DNA (trnL-F) data was conducted. The DNA sequence data of ten taxa in sect. Siderostictae and closely related taxa (two taxa in sect. Surculosae) with outgroups were analyzed based on maximum parsimony and maximum likelihood (ML) criteria. In the analyses, C. splendentissima was monophyletic and placed within the Siderostictae clade (sect. Siderostictae + two species of sect. Surculosae), forming a clade with C. ciliatomarginata and C. pachygyna (endemic to Japan). The clade (C. splendentissima + C. ciliatomarginata + C. pachygyna) shows evidence of diploidy. Furthermore, C. splendentissima is a sister to C. ciliatomarginata in the ML tree, and the two taxa have staminate terminal spikes. This study also updates the distribution of C. splendentissima and provides keys to the four Korean taxa in sect. Siderostictae. To conserve the endemic species C. splendentissima, further research on its genetic and ecological features should be conducted at the population level.

• Korean Journal of Environmental Biology
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• v.31 no.3
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• pp.189-191
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• 2013

Mycotoxins such as aflatoxin B1 (AFB1), ochratoxin A (OTA) and zearalenone (ZEA) are widespread contaminants of food and feedstuffs. It is very likely, that humans and animals are always exposed to mixtures of mycotoxins rather than to individual compounds. Therefore, risk assessments should consider mixture toxicity data. In the present study the combination of AFB1, OTA and ZEA was tested for genotoxicity in rat bone marrow and blood leukocytes after 15, 30 and 60 days treatment. The level of DNA damage was determined by the comet assay. The tail intensity and Olive tail moment in leukocytes and bone marrow cells were significantly higher than in controls. At the same time, the level of DNA damage in bone marrow cells was higher than in leukocytes. The data suggests that prolonged exposure to mycotoxins combination through food consumption can induce DNA damage contributing to the harmful effects in vivo.

• Animal cells and systems
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• v.4 no.4
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• pp.319-324
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• 2000

Species boundaries among the Alcyonacean soft coral, the genus Dendronephthya, are often obscured by inter- and intraspecific morphological variations. In the present study, we attempted to infer the genetic relationships of eight dendronephthians based on their molecular characters, the internal transcribed spacer (ITS) regions of ribosomal DNA, and then compared this result together with the random amplified polymorphic DNA (RAPD) data from our previous investigation. Dendronephthya. putteri and D. suensoni formed a divaricate form - VI grade specific clade, whereas D. castanea, D. gigantea, D. aurea and D. spinifera, formed a umbellate and glomerate form - IV and III grade specific clade. Therefore, we confirmed that the main characters the growth form and the anthocodial grade and formula, are important in identification of the species in dendronephthians despite some problems. Also, the relationships of the growth form are clarified as the glomerate form is much closer to the umbellate form than to the divaricate form based on two sets of independent molecular data. However, we cannot determine the molecular markers which limit the species boundaries among this genus with ITS sequences.