• Molecules and Cells
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• v.41 no.12
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• pp.1061-1071
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• 2018

From Xenopus embryo studies, the BMP4/Smad1-targeted gene circuit is a key signaling pathway for specifying the cell fate between the ectoderm and neuro-ectoderm as well as the ventral and dorsal mesoderm. In this context, several BMP4/Smad1 target transcriptional factors have been identified as repressors of the neuro-ectoderm. However, none of these direct target transcription factors in this pathway, including GATA1b, Msx1 and Ventx1.1 have yet been proven as direct repressors of early neuro-ectodermal gene expression. In order to demonstrate that Ventx1.1 is a direct repressor of neuro-ectoderm genes, a genome-wide Xenopus ChIP-Seq of Ventx1.1 was performed. In this study, we demonstrated that Ventx1.1 bound to the Ventx1.1 response cis-acting element 1 and 2 (VRE1 and VRE2) on the promoter for zic3, which is a key early neuro-ectoderm gene, and this Ventx1.1 binding led to repression of zic3 transcription. Site-directed mutagenesis of VRE1 and VRE2 within zic3 promoter completely abolished the repression caused by Ventx1.1. In addition, we found both the positive and negative regulation of zic3 promoter activity by FoxD5b and Xcad2, respectively, and that these occur through the VREs and via modulation of Ventx1.1 levels. Taken together, the results demonstrate that the BMP4/Smad1 target gene, Ventx1.1, is a direct repressor of neuro-ectodermal gene zic3 during early Xenopus embryogenesis.

• Design & Manufacturing
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• v.17 no.1
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• pp.20-26
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• 2023

Lab-on-a-disc is a circular disc shape of cartridge that can be used for blood-based liquid biopsy to diagnose an early stage of cancer. Currently, liquid biopsies are regarded as a time-consuming process, and require sophisticated skills to precisely separate cell-free DNA (cfDNA) and circulating tumor cells (CTCs) floating in the bloodstream for accurate diagnosis. However, by applying the lab-on-a-disc to liquid biopsy, the entire process can be operated automatically. To do so, the lab-on-a-disc should be designed to prevent blood leakage during the centrifugation, transport, and dilution of blood inside the lab-on-a-disc in the process of liquid biopsy. In this study, the main components of lab-on-a-disc for liquid biopsy are fabricated by injection molding for mass production, and ultrasonic welding is employed to ensure the bonding strength between the components. To guarantee accurate ultrasonic welding, the flatness of the components is optimized numerically by using the response surface methodology with four main injection molding processing parameters, including the mold & resin temperatures, the injection speed, and the packing pressure. The 27 times finite element analyses using Moldflow® reveal that the injection time and the packing pressure are the critical factors affecting the flatness of the components with an optimal set of values for all four processing parameters. To further improve the flatness of the lab-on-a-disc components for stable mass production, a quarter-disc shape of lab-on-a-disc with a radius of 75 mm is used instead of a full circular shape of the disc, and this significantly decreases the standard deviation of flatness to 30% due to the reduced overall length of the injection molded components by one-half. Moreover, it is also beneficial to use a quarter disc shape to manage the deviation of flatness under 3 sigma limits.

• International Journal of Stem Cells
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• v.16 no.2
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• pp.215-233
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• 2023

Background and Objectives: MYC, also known as an oncogenic reprogramming factor, is a multifunctional transcription factor that maintains induced pluripotent stem cells (iPSCs). Although MYC is frequently upregulated in various cancers and is correlated with a poor prognosis, MYC is downregulated and correlated with a good prognosis in lung adenocarcinoma. MYC and two other MYC family genes, MYCN and MYCL, have similar structures and could contribute to tumorigenic conversion both in vitro and in vivo. Methods and Results: We systematically investigated whether MYC family genes act as prognostic factors in various human cancers. We first evaluated alterations in the expression of MYC family genes in various cancers using the Oncomine and The Cancer Genome Atlas (TCGA) database and their mutation and copy number alterations using the TCGA database with cBioPortal. Then, we investigated the association between the expression of MYC family genes and the prognosis of cancer patients using various prognosis databases. Multivariate analysis also confirmed that co-expression of MYC/MYCL/MYCN was significantly associated with the prognosis of lung, gastric, liver, and breast cancers. Conclusions: Taken together, our results demonstrate that the MYC family can function not only as an oncogene but also as a tumor suppressor gene in various cancers, which could be used to develop a novel approach to cancer treatment.

• Journal of Microbiology and Biotechnology
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• v.34 no.7
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• pp.1475-1483
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• 2024

Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11^T, SW19^T, and YR1^T, were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11^T, SW19^T, and YR1^T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11^T was closely affiliated with Agromyces cavernae SYSU K20354^T (98.1%), strain SW19^T showed the closest affiliation with Rathayibacter rubneri ZW T2_19^T (97.0%), and strain YR1^T was most closely related to Nocardioides marmorisolisilvae KIS18-7^T (98.0%). The genome sizes of strains W11^T, SW19^T, and YR1^T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA-DNA hybridization values of W11^T, SW19^T, and YR1^T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11^T were anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0. In strain SW19^T, they were summed feature 9 (C_16:0 10-methyl and/or iso-C_17:1ω 9c), anteiso-C_17:0, and anteiso-C_15:0. Strain YR1^T exhibited C_18:1ω 9c, C_18:0 10-methyl, TBSA, and anteiso-C_15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11^T, SW19^T, and YR1^T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11^T (=KCTC 49818^T =NBRC 115999^T), Rathayibacter soli sp. nov., with the type strain SW19^T (=KCTC 49860^T =NBRC 116108^T), and Nocardioides terrisoli sp. nov., with the type strain YR1^T (=KCTC 49863^T =NBRC 116165^T).

• Journal of Life Science
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• v.28 no.3
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• pp.369-375
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• 2018

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

• The Journal of the Convergence on Culture Technology
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• v.3 no.4
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• pp.1-19
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• 2017

Death culture continues to lead human history with complementarity in the sense that it is half of life culture. The three sacred gates and the two tombs are connected to the olegil space. In this space, the principle of complementarity in which coexistence exist between life and death is hidden in Jeju culture. It is a question and wait. Contrarily, the opposite is complementary. (Contraria Sunt Complementa Latin) This refers to the relationship of each other in relation to one another and in a mutually dependent relationship. The Jong Nang is used as basic logic in DNA codon of human body as well as communication principle. In addition, there is a pattern of similarity of the linkage between the square oval ear of the grave, the Korean Taegeukguk and 卦, the genome (DNA) 卦. The Jong Nang 'Batdam' and 'Sandam' are conneted like 'black dragon ten thousand', and stone walls are connected to each other as the stone network, which is called as the 'Goendam' (and conventionally is told as the 'Goendang') and is related to the Family networks. The relationship between the Tomb of the ancestors and their offspring is believed to be "Soul Synchronizing the Ancestor to Offspring" and becomes "Change in Future", and Genetic factors in the physical blood are transmitted directly to the children. The DNA RNA was represented by the determinant.

• Journal of Plant Biotechnology
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• v.44 no.1
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• pp.89-96
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• 2017

The CRISPR/Cas9 is a core technology that can result in a paradigm for breeding new varieties. This study describes in detail the sgRNA design, vector construction, and the development of a transgenic plant and its molecular analysis, and demonstrates how gene editing technology through the CRISPR/Cas9 system can be applied easily and accurately. CRISPR/Cas9 facilitates targeted gene editing through RNA-guided DNA cleavage, followed by cellular DNA repair mechanisms that introduce sequence changes at the site of cleavage. It also allows the generation of heritable-targeted gene mutations and corrections. Here, we present detailed procedures involved in the CRISPR/Cas9 system to acquire faster, easier and more cost-efficient gene edited transgenic rice. The protocol described here establishes the strategies and steps for the selection of targets, design of sgRNA, vector construction, and analysis of the transgenic lines. The same principles can be used to customize the versatile CRISPR/Cas9 system, for application to other plant species.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.454-458
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• 2006

HSF1 is the heat shock transcription factor in Saccharomyces cerevisiae. S. cerevisiae KNU5377 can ferment at high temperature such as $40^{\b{o}}C$. We have been the subjects of intense study because Hsf1p mediates gene expression not only to heat shock, but to a variety of cellular and environmental stress challenges. Basing these facts, we firstly tried to construct the hsf1 gene-deleted mutant. PCR-method for fast production of gene disruption cassette was introduced in a thermotolerant yeast S. cerevisiae KNU5377, which allowed the addition of short flanking homology region as short as 45 bp suffice to mediate homologous recombination to kanMX module. Such a cassette is composed of linking genomic DNA of target gene to the selectable marker kanMX4 that confers geneticin (G418) resistance in yeast. That module is extensively used for PCR-based gene replacement of target gene in the laboratory strains. We describe here the generation of hsf1 gene disruption construction using PCR product of selectable marker with primers that provide homology to the hsf1 gene following separation of haploid strain in wild type yeast S. cerevisiae KNU5377. Yeast deletion overview containing replace cassette module, deletion mutant construction and strain confirmation in this study used Saccharomyces Genome Deletion Project (http:://www-sequence.standard.edu/group/yeast_deletion_project). This mutant by genetic manipulation of wild type yeast KNU5377 strain will provide a good system for analyzing the research of the molecular biology underlying their physiology and metabolic process under fermentation and improvement of their fermentative properties.

• Journal of Life Science
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• v.20 no.12
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• pp.1859-1866
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• 2010

It is reported that about 80% of deer antlers (Cervi Pantotricuhum Cornu) produced in the world are consumed in Korea. Fraudulent replacement or mislabeling of costly deer antlers with cheaper ones, however, is one of the most common problems in the Korean deer antler market. Therefore, there is a continuous need for the development of genetic markers to discriminate between genuine and fraudulent deer antlers. This study was performed to develop a method for the identification and authentication of deer antlers using nucleotide sequence analysis against displacement loop of mitochondrial genome among four deer antlers, Cervus eleaphus sibericus, Cervus eleaphus bactrianus, Cervus eleaphus Canadensis, and Cervus eleaphus, originated from Russia, China, North America and New Zealand, respectively. As a result, multiple-alignment of mitochondrial displacement (D) loop region in 1.2 kb showed that, among the four deer antlers, a deleted sequence of about 70 bps was only found in Cervus elaphus bactrianus from China. Finally, Cervus elaphus bactrianus among nine samples of deer antlers were successfully identified by PCR using primer amplifying deleted D-loop. Cervus elaphus bactrianus was also confirmed from cloning the PCR products and their nucleotide sequence analyses were confirmed. However, no marker to identify Cervus eleaphus sibericus, Cervus eleaphus canadensis and Cervus eleaphus were found in the nucleotide sequences of mitochondrial D-loop. Our results suggest that PCR for deleted D-loop region of mitochondrial DNA are useful for identification and authentication of deer antlers of Cervus elaphus bactrianus originating from China.

• Journal of Plant Biotechnology
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• v.33 no.1
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• pp.27-32
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• 2006

To clarify the roles of bromelain in plants, we isolated BL1 gene encoding bromelain from pineapple stem tissues and sequenced. The full length cDNA is 933 bp and encodes a polypeptide of 311 amino acid residues. The cDNA is most similar 94% at the amino acid level to bromelain previously isolated from pineapple (BAA21929). Explants of Lactuca sativa were co-cultivated with Agrobacterium tume-faciences LBA 4404 strains containing nptII and BL1 gene for transformation. Through initial selection of regenerated explants by culturing on a kanamycin and carbenicillin containing MS medium, multiple shoots were obtained after 2 months of culture. For a complementary step of selection, putative transgenic shoots were transferred to 1/2 Ms basal medium supplemented with 100 mg/L kanamycin and 500 mg/L carbenicillin. The selected shoots were obtained T1 generation seeds with emasculation, and tested with PCR analysis using 35S promoter and BL1 specific primers whether BL1 gene was introduced to genome of the plants. These results confirmed that produced the specific PCR bands in the putative transgenic lines. Additionally the Northern blot and endo protease activity showed that transcripts of BL1 gene were detected in transgenic lines. Theses results suggest that BL1 gene be successfully integrated and transcripted in the transgenic lettuce plants.