• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.9 no.2
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• pp.83-89
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• 2005

In this paper a new algorithm of learning and evolving artificial neural networks using gene expression programming (GEP) is presented. Compared with other traditional algorithms, this new algorithm has more advantages in self-learning and self-organizing, and can find optimal solutions of artificial neural networks more efficiently and elegantly. Simulation experiments show that the algorithm of evolving weights or thresholds can easily find the perfect architecture of artificial neural networks, and obviously improves previous traditional evolving methods of artificial neural networks because the GEP algorithm imitates the evolution of the natural neural system of biology according to genotype schemes of biology to crossover and mutate the genes or chromosomes to generate the next generation, and the optimal architecture of artificial neural networks with evolved weights or thresholds is finally achieved.

• Journal of Institute of Control, Robotics and Systems
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• v.10 no.12
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• pp.1189-1195
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• 2004

This paper investigates construction of gene (interaction) networks from gene expression time-series data based on evolutionary computation. To illustrate the proposed approach in a comprehensive way, we first assume an artificial gene network and then compare it with the reconstructed network from the gene expression time-series data generated by the artificial network. Next, we employ real gene expression time-series data (Spellman's yeast data) to construct a gene network by applying the proposed approach. From these experiments, we find that the proposed approach can be used as a useful tool for discovering the structure of a gene network as well as the corresponding relations among genes. The constructed gene network can further provide biologists with information to generate/test new hypotheses and ultimately to unravel the gene functions.

• Molecules and Cells
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• v.21 no.3
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• pp.376-380
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• 2006

Gene expression is regulated in large part at the level of transcription under the control of sequence-specific transcriptional regulatory proteins. Therefore, the ability to affect gene expression at will using sequencespecific artificial transcription factors would provide researchers with a powerful tool for biotechnology research and drug discovery. Previously, we isolated 56 novel sequence-specific DNA-binding domains from the human genome by in vivo selection. We hypothesized that these domains might be more useful for regulating gene expression in higher eukaryotic cells than those selected in vitro using phage display. However, an unpredictable factor, termed the "context effect", is associated with the construction of novel zinc finger transcription factors--- DNA-binding proteins that bind specifically to 9-base pair target sequences. In this study, we directly selected active artificial zinc finger proteins from a zinc finger protein library. Direct in vivo selection of constituents of a zinc finger protein library may be an efficient method for isolating multi-finger DNA binding proteins while avoiding the context effect.

• Journal of Microbiology and Biotechnology
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• v.2 no.1
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• pp.1-6
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• 1992

The aspartame, $\alpha$-L-aspartyl-L-phenylalanine methylester, is an artificial sweetener. Taking advantage of the fact that the aspartame is a derivative of dipeptide, synthesis of aspartame from the artificial polypeptide made by an artificial gene has been attempted. The artificial polypeptide (LAP32), a polymer of tripeptide (aspartyl-phenylalanyl-lysine), was purified from the E. coli cells harboring a recombinant plasmid containing the artificial gene. This polypeptide was then digested with trypsin and carboxypeptidase B to produce dipeptide (Asp-Phe). Using the esterase activity of $\alpha$-chymotrypsin, the dipeptide was directly converted into Asp-Phe methylester in a water-methanol system. When the methanol concentration in reaction mixture was 25%, 50% of dipeptide was converted to the dipeptide methylester without producing any by-products.

• Proceedings of the Korean Society of Crop Science Conference
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• 2021.04a
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• pp.119-119
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• 2021

• KSBB Journal
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• v.25 no.3
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• pp.215-222
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• 2010

Monogenic diseases are resulted from modifications in a single gene of human cells. Because their treatment with pharmacological medicine have a temporary effect, continuous nursing care and retreatment are required. Gene therapy, gene targeting and induced pluripotent stem cell (iPSC) are considered permanent treatment methods of them. In gene therapy, however, retroviral vectors that have potential toxicity caused by random insertion of harmful virus are used as vehicles for transferring genetic materials. On the other hand, gene targeting could replace and remove the modified gene though homologous recombination (HR) induced by site-specific endonucleases. This short review provides a brief overview on the recently tailored endonucleses with high selectivity for HR.

• Korean Journal of Microbiology
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• v.35 no.1
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• pp.28-34
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• 1999

Fragmentation vectors are used to analyze function and genomic structure of a gene of interest by creating deletion derivatives of large fragments of genomic DNA cloned as yeast artificial chromosomes (YACs). Herein, we developed a new hicistronic fragmentation vector that contains internal ribosomal entry sile (IRES) of encephalomyocarditis vin~s (EMCV) and $\beta$-galactosidase as a reporter gene. This vector system provides a novcl loo1 to analyze expression patterns of a gene of interest due to simultaneous expression of a target gene as well as $\beta$-galactosidase driven from a single message. In addition, the bicistronic fragmentation vector contains four rare-cutting restriction enzyme sites in the polycloning sites which can be used to conveniently insert any kinds of genes and therefore facilitates targeting DNA scgments into YAC by means of homologous recombination. This approach establishes a paradigm for manipulation of mammalian DNA segments and characterization of expression and regulatory regions of mammalian gene cloned as YAC.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.885-891
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• 2004

To evaluate the feasibility of using sperm-mediated gene transfer (SMGT) for carrying foreign gene into chicken oocyte, a reporter gene, CX-EGFP, was used in this study. The reporter gene was first mixed with liposome or liposome-like compound and the mixtures were further combined with ejaculated cock spermatozoa. The spermatozoa treated with liposome and CX-EGFP mixture was subsequently coincubated with DNaseI to remove the extra DNA which insured the authenticity of positive signals. The treated sperms were then subjected to transgene (reporter gene) existence analysis and artificial insemination of laying hens. Obtained results indicated that the spermatozoa were able to take-in the foreign DNA; which was confirmed by polymerase chain reaction and Southern blot analysis. In the following experiment, fresh ejaculated sperms were mixed with CX-EGFP-liposome or CX-EGFP-liposome-like complex then used for artificial insemination of each of six laying hens. Eggs laid between day-3 and day-7 post insemination were collected. Newly hatched chicks, two out of 53 from CX-EGFP/liposome treated group and two out of 21 from CXEGFP/liposome-like treated group, were proven to be transgenic. This study suggests that SMGT is a powerful method for generating transgenic chickens.

• BMB Reports
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• v.35 no.5
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• pp.459-464
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• 2002

Fusogenic liposomes that incorporate Sendai virus envelope proteins, so-called Sendai virosomes, have been developed for in vitro and in vivo genetic modification of animal cells. In this study, several different virosomes of varying lipid compositions were formulated and their in vitro gene-transfer efficiencies compared. The virosomes were prepared by quantitative reconstitution of the Sendai envelope, fusion (F) and hemagglutinin-neuraminidase (HN) proteins into liposomal vesicles. Virosomes that contained luciferase reporter genes were tested in 293 transformed human kidney cells. F/HN-virosomes that were prepared with an artificial Sendai viral envelope (ASVE-virosomes) or phosphatidylserine (PS-virosomes) exhibited an 8- or 6-fold higher gene-transfer efficiency than cationic liposomes that were made with 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP). F/HN-virosomes that were prepared with phosphatidic acid (PA-virosomes) instead of PS were less efficient in gene transfer than either ASVE- or PS-virosomes. In addition, the genetransfer capability of ASVE- and PS-virosomes was maximal at a $Ca^{2+}$ concentration of 510 mM. These results suggest that the incorporated lipid components significantly affect the in vitro gene transfer that is mediated by Sendai F/HN-virosomes.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.365-368
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• 2006

Yeast mitochondrial transformation has been confirmed by cell death and CFP expression (CDF: cell death factor gene). Expression vector containing CDF and CFP driven by one TPI (Triose-phosphate isomerase) promoter (called artificial operon type) was bombarded to Yeast. Interestingly, yeast cells were progressively deformed into unusual shapes and lysed inner cytoplasm resulting in ell death after all after bombarding with expression vector (CDC and GFP). Since there is no report about more than one gene expression simultaneously in a single mitochondria, this report is very important to novel type of eukaryotic gene expression. Successful yeast cell transformation in this report implies possible eukaryotic mitochodrial transformation including plants and animals and moreover two or more gene expression which can be excellent applicable protocols to pharmaceutical field including antibody production.