• Journal of KIISE:Software and Applications
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• v.34 no.12
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• pp.1056-1064
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• 2007

Biomolecular computing is a new computing paradigm that uses biomolecules such as DNA for information representation and processing. The huge number of molecules in a small volume and the innate massive parallelism inspired a novel computation method, and various computation models and molecular algorithms were developed for problem solving. In the meantime, the use of biomolecules for information processing supports the possibility of DNA computing as an application for biological problems. It has the potential as an analysis tool for biochemical information such as gene expression patterns. In this context, a DNA computing-based model of a biomolecular perceptron has been proposed and the result of its experimental implementation was presented previously. The weight encoding and weighted sum operation, which are the main components of a biomolecular perceptron, are based on the competitive hybridization reactions between the input molecules and weight-encoding probe molecules. However, thermodynamic symmetry in the competitive hybridizations is assumed, so there can be some error in the weight representation depending on the probe species in use. Here we suggest a generalized model of hybridization reactions considering the asymmetric thermodynamics in competitive hybridizations and present a weight encoding method for the reliable implementation of a biomolecular perceptron based on this model. We compare the accuracy of our weight encoding method with that of the previous one via computer simulations and present the condition of probe composition to satisfy the error limit.

• Korean Journal of Ecology and Environment
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• v.55 no.3
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• pp.212-220
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• 2022

An estuary is a water ecosystem with a high abundance of the species diversity, due to a variety of complex physicochemical factors of the area where freshwater and ocean mixed. The identification of Corbicula species in the estuary environments is difficult because of various morphological characteristics. In this study, we provide taxonomic information on Corbicula species with taxonomic difficulties using morphological and genetic analysis. This study was conducted on clams from the Seomjin River-Gwangyang Bay, one of the major production area of marsh clam in Korea. As a result, we characterized Cytocrome C Oxidase subunit I (COI) sequences of the Corbicula. The 636 bp nucleotide sequences of COI have 98% homology among Corbicula species collected from 2 sites of Seomjin River-Gwangyang Bay. The phylogenetic analysis with 17 species of Corbicula indicated that most of the species collected from Seomjin River-Gwangyang Bay were brackish water clam (Corbicula japonica), and only one Asian clam (Corbicula fluminea). The evolutionary distance between C. japonica and C. fluminea was less than 0.003. Therefore, it was confirmed that C. japonica is phylogenetically closely related to C. fluminea. In 9 species of Cyrenidae, phylogenetic tree was classified into three lineages. These results will be used as an important data for an identification of clam species by providing genetic information for Corbicula species with a morphological diversity.

• Korean Journal of Medicinal Crop Science
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• v.23 no.6
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• pp.439-445
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• 2015

Background : Correct identification of Panax species is important to ensure food quality, safety, authenticity and health for consumers. This paper describes a high resolution melting (HRM) analysis based method using internal transcribed spacer (ITS) and 5.8S ribosomal DNA barcoding regions as target (Bar-HRM) to obtain barcoding information for the major Panax species and to identify the origin of ginseng plant. Methods and Results : A PCR-based approach, Bar-HRM was developed to discriminate among Panax species. In this study, the ITS1, ITS2, and 5.8S rDNA genes were targeted for testing, since these have been identified as suitable genes for use in the identification of Panax species. The HRM analysis generated cluster patterns that were specific and sensitive enough to detect small sequence differences among the tested Panax species. Conclusion : The results of this study show that the HRM curve analysis of the ITS regions and 5.8S rDNA sequences is a simple, quick, and reproducible method. It can simultaneously identify three Panax species and screen for variants. Thus, ITS1HRM and 5.8SHRM primer sets can be used to distinguish among Panax species.

• Proceedings of KOSOMES biannual meeting
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• 2017.11a
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• pp.209-209
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• 2017

• Ocean and Polar Research
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• v.43 no.1
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• pp.45-51
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• 2021

Studies on marine zooplankton diversity and ecology are important for understanding marine ecosystem, as well as environmental conservation and fisheries management. DNA metabarcoding is known as a useful tool to reveal and understand diversity among animals, but a comparative evaluation with classical microscopy is still required in order to properly use it for marine zooplankton research. This study compared crustacean mesozooplankton taxa revealed by morphological analysis and metabarcoding of the cytochrome oxidase I (COI). A total of 17 crustacean species were identified by morphological analysis, and 18 species by metabarcoding. Copepods made up the highest proportion of taxa, accounting for more than 50% of the total number of species delineated by both methods. Cladocerans were not found by morphological analysis, whereas amphipods and mysids were not detected by metabarcoding. Unlike morphological analysis, metabarcoding was able to identify decapods down to the species level. There were some discrepancies in copepod species, which could be due to a lack of genetic database, or biases during DNA extraction, amplification, pooling and bioinformatics. Morphological analysis will be useful for ecological studies as it can classify and quantify the life history stages of marine zooplankton that metabarcoding cannot detect. Metabarcoding can be a powerful tool for determining marine zooplankton diversity, if its methods or database are further supplemented.

• Korean journal of applied entomology
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• v.55 no.4
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• pp.471-475
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• 2016

The dark-winged fungus gnats are one of the most serious fly pests attacking the mushroom cultivation in Korea. They cause severe damage to the artificial sawdust beds used to cultivate mushroom, and reduce the production of button mushroom, Agaricus bisporus, in greenhouses. In this study, we collected nine species of the mushroom flies in order to identify the dominant species of the dark-winged fungus gnat attacking the A. bisporus plantation using the yellow sticky trap in Buyeo-gun, Boryeong-gun, Yongin-si and Chilgok-gun from April to June 2015. The collected samples were used to determine the DNA sequence of the cytochrome c oxidase subunit I (COI) of the nine different species by DNA barcoding. The sequencing results showed that Lycoriella ingenua was the dominant dark-winged fungus gnat species destroying A. bisporus cultivated on the artificial sawdust beds in Korea.

• Journal of Life Science
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• v.27 no.8
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• pp.857-863
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• 2017

The FBJ murine osteosarcoma viral oncogene homolog B (FosB) gene is located at chromosome 19, and encodes 43 Kda protein. Functionally, the FosB gene is important for differentiation, development, and pathogenesis. Furthermore, the FosB gene is suggested as possible biomarker for tracing disease prognosis. In this study, we constructed plasmid containing a FosB promoter region and evaluate its promoter activity. We analyzed the putative promoter region in FosB genomic DNA using bioinformatics program, and we found important regulatory elements in 1 Kb upstream from transcription start site (TSS). Therefore, we performed polymerase chain reaction (PCR) amplification on region from-1,555 upstream to +73 of the FosB genomic DNA, and PCR product was inserted into TA vector to create the $TA-1^{st}FosBp$ plasmid. We then prepared the primer sets, which contain a restriction enzyme site for Kpn1 and Nhe1, in order to reinsert into the TA vector to prepare $TA-2^{nd}FosBp$ plasmid. It was finally subcloned into pGL3-luc vector after enzyme cutting. To evaluate whether the cloned plasmid is useful in cell based experiment, we performed luciferase assay with pGL3-FosBp-luctransfection. FosB promoter activity was increased compared to empty vector, and this activity was significantly increased by treatment of doxorubicin and taxol. We obtained consistent data on regulation of FosB gene expression after anticancer drug treatment using Western blot analysis. The results suggest that promoter cloning of the human FosB gene is very useful for studying gene expression and analyzing biomarkers.

• Journal of Life Science
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• v.19 no.4
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• pp.449-456
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• 2009

Murine Neuro-2a (N2a) cells have been widely used for the investigation of neuronal differentiation, trophic interaction and neurotoxic effects of various compounds and their associated mechanisms. N2a cells have many genomic variations such as gains or losses in DNA copy number, similar to other neuroblastoma cells, and no systematic or high-resolution studies of their genome-wide chromosomal aberrations have been reported. Presently, we conducted a systematic genome-wide determination of chromosomal aberrations in N2a cells using a high-throughput, oligonucleotide array-based comparative genomic hybridization (oaCGH) technique. A hidden Markov Model was employed to assign each genomic oligonucleotide to a DNA copy number state: double loss, single loss, normal, gain, double gain and amplification. Unlike most neuroblastoma cells, Mycn amplification was not observed in N2a cells. In addition, these cells showed gain only in the neuron-derived neurotrophic factor (NF), while other neurotrophic factors such as glial line-derived NF and brain-derived NF presented normal copy numbers. Chromosomes 4, 8, 10, 11 and 15 displayed more than 1000 aberrational oligonucleotides, while chromosomes 3, 17, 18 and 19 displayed less than 20. The largest region of gain was located on chromosome 8 and its size was no less than 26.7 Mb (Chr8:8427841-35162415), while chromosome 4 had the longest region of single deletion, with a size of 15.1 Mb (Chr4:73265785-88374165).

• Korean Journal of Microbiology
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• v.26 no.4
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• pp.283-290
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• 1988

A spontaneous revertant of mutation rbsB103 that is ribose taxis-positive was characterized. This revertant was found to be export-competent in the export of ribose-binding protein shown by the disappearance of accumulated mutant precursor protein and the export of mature ribose-binding protein to the periplasm. The reversional change was shown to be in the region of risB gene that codes for the amino terminal portion of ribose-binding protein. Analysis by high-performance liquid chromatography of peptide patterns of ribose-binding proteins confirmed the relationship between the wild-type and the revertant proteins as shown for the mutant previously (Iida et al., 1985). When the processing rate of presursor proteins from the wild type and the revertant strain in vivo was compared by pulse-chase experiment, it was found that processing is less efficient than normal in the revertant. Purified mature proteins from both wild-type and revertant were subjected to amino acid sequencing. The results confirmed the amino acid changes deduced from the DNA sequencing and showed that processing of the revertant precursor occured in the correct position even though there are two different amino acids present in the signal sequence.