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Comparative analysis of chloroplast genomes and 45S nuclear ribosomal DNAs within 9 perilla species
Seon-Hwa Bae,In-Seon Jeong,Ye-Ji Lee,Myoung-Hee Lee,Jeong-Hee Lee,Ung-Han Yoon,Jang-Ho Hahn,Tae-Ho Kim 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Perilla is a annual herb plant of the mint family, Laminaceae and mainly cultivated in eastern Asia, i.e. Korea, China and Japan. In response to an increased interest for healthy supplement food from the public, people are focusing on the properties of perilla. The applicable parts of perilla plants are the leaves and seeds. Perilla has been cultivated as a source of unsaturated fatty acid oil. But in spite of advantage of the important nutritional traits the genome or molecular studies on perilla remains largely unknown. Sequence comparisons of chloroplast (cp) genomes or nuclear ribosomal DNA (nrDNA) are of great important to provide a evidence for taxonomic studies or species identification or understanding mechanisms that underlie the evolution of perilla species. So, we tried to study a structural analysis of perilla genome and 45s nrDNA using 9 species (3 Diploid; Perilla B-17, P. hirtella, P. setoyensis / 6 Tetraploid; YCPL 285, YCPL 170, YCPL 205-1, YCPL 181-1, YCPL 177-1, YCPL 207-1). The complete cp genome and nrDNA of 9 perilla species were determined using Illumina sequencing technology and analyzed on the variance in base level between perilla B-17 and salvia miltiorrhiza. Total chloroplast genome size of perilla B-17 as a reference was 152,589 bp in length. We also identified an slightly overlapped intergenic regions between salvia miltiorrhiza and B-17. The results above will contribute to growing of molecular or genome structure and functional genomics of perilla available in studying perilla biology. For further study, we will look for genetic diversity of perilla species.
2017 Thyroid Radiofrequency Ablation Guideline: Korean Society of Thyroid Radiology
Kim, Ji-hoon,Baek, Jung Hwan,Lim, Hyun Kyung,Ahn, Hye Shin,Baek, Seon Mi,Choi, Yoon Jung,Choi, Young Jun,Chung, Sae Rom,Ha, Eun Ju,Hahn, Soo Yeon,Jung, So Lyung,Kim, Dae Sik,Kim, Soo Jin,Kim, Yeo Koon The Korean Society of Radiology 2018 KOREAN JOURNAL OF RADIOLOGY Vol.19 No.4
<P>Thermal ablation using radiofrequency is a new, minimally invasive modality employed as an alternative to surgery in patients with benign thyroid nodules and recurrent thyroid cancers. The Task Force Committee of the Korean Society of Thyroid Radiology (KSThR) developed recommendations for the optimal use of radiofrequency ablation for thyroid tumors in 2012. As new meaningful evidences have accumulated, KSThR decided to revise the guidelines. The revised guideline is based on a comprehensive analysis of the current literature and expert consensus.</P>
Hahn, Soojung,Kim, Mi Sun,Choi, Seon Young,Jeong, Sukin,Jee, JooHyun,Kim, Han Kyung,Jeong, Sang Yun,Shin, Hyunsoo,Kim, Hyoung Sun,Park, Joon Seong,Yoo, Jongman Elsevier 2019 Biochemical and biophysical research communication Vol.508 No.2
<P><B>Abstract</B></P> <P>An organoid is a complex, multi-cell three-dimensional (3D) structure that contains tissue-specific cells. Epithelial stem cells, which are marked by leucine-rich repeat-containing G-protein coupled receptor 5 (Lgr5), have the potential for self-renewal and expansion as organoids. However, in the case of intestinal organoids from Lgr5-EGFP-IRES-CreERT2 transgenic mice, <I>in vitro</I> expansion of the Lgr5 expression is limited in a culture condition supplemented with essential proteins, such as epidermal growth factor (E), noggin (N), and R-spondin 1 (R). In this study, we hypothesized that self-renewal of Lgr5+ stem cells in a 3D culture system can be stimulated by defined compounds (CHIR99021, Valproic acid, Y-27632, and A83-01). Our results demonstrated that dissociated single cells from organoids were organized into a 3D structure in the four compounds containing the ENR culture medium in a 3D and two-dimensional (2D) culture system. Moreover, the Lgr5 expression level of organoids from the ENR- and compound-containing media increased. Furthermore, the conversion of cultured Lgr5+ stem cells from 2D to 3D was confirmed. Therefore, defined compounds promote the expansion of Lgr5+ stem cells in organoids.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Organoids are generated in 3D culture systems in defined medium containing CVYA. </LI> <LI> CVYA containing the ENR culture medium promote the expansion of Lgr5+ stem cells in organoid. </LI> <LI> The Lgr5+ enriched organoids are conversed from 2D to 3D culture system. </LI> </UL> </P>
Cloning of Notl-linked DNA Detected by Restriction Landmark Genomic Scanning of Human Genome
Kim Jeong-Hwan,Lee Kyung-Tae,Kim Hyung-Chul,Yang Jin-Ok,Hahn Yoon-Soo,Kim Sang-Soo,Kim Seon-Young,Yoo Hyang-Sook,Kim Yong-Sung Korea Genome Organization 2006 Genomics & informatics Vol.4 No.1
Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.
Kim, Jaeyoung,Kwon, Jung Hoon,Jang, Jinyoung,Lee, Hyojin,Kim, Seungki,Hahn, Young Ki,Kim, Sang Kyung,Lee, Kwan Hyi,Lee, Seok,Pyo, Heesoo,Song, Chang-Seon,Lee, Joonseok Elsevier 2018 Biosensors & Bioelectronics Vol.112 No.-
<P><B>Abstract</B></P> <P>Rapid and sensitive on-site detection of avian influenza virus (AIV) is the key for achieving near real-time surveillance of AIV and reducing the risk of dissemination. However, unlike the laboratory-prepared transparent buffer solutions containing a single type of influenza virus, distinction between real- and false- positive outputs and detection of low concentrations of AIV in stool specimens or cloacal swabs are difficult. Here, we developed a rapid and background-free lateral flow immunoassay (LFA) platform that utilizes near-infrared (NIR)-to-NIR upconversion nanoparticles (UCNPs) to yield a sensor that detects AIV nucleoproteins (NPs) from clinical samples within 20 min. Ca<SUP>2+</SUP> as a heterogeneous dopant ion in the shell enhanced the NIR-to-NIR upconversion photoluminescence (PL) emission without inducing significant changes in the morphology of the UCNPs. In a mixture of opaque stool samples and gold nanoparticles (GNPs), which are components of commercial AIV LFA, the background signal of the stool samples masked the absorption peak of GNPs. However, UCNPs dispersed in the stool samples still show strong emission centered at 800 nm when excited at 980 nm, which enables the NIR-to-NIR upconversion nanoparticle-based lateral flow immunoassay (NNLFA) platform to detect 10-times lower viral load than a commercial GNP-based AIV LFA. The detection limit of NNLFA for LPAI H5N2 and HPAI H5N6 viruses was 10<SUP>2</SUP> and 10<SUP>3.5</SUP> EID<SUB>50</SUB>/mL, respectively. Moreover, the viruses were successfully detected within dark brown-colored samples using the NNLFA but not the commercial AIV LFA. Therefore, the rapid and background-free NNLFA platform can be used for sensitive on-site detection of AIV.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Ca<SUP>2+</SUP> as a heterogeneous dopant ion enhanced the NIR-to-NIR upconversion photoluminescence. </LI> <LI> The UCNPs dispersed in opaque stool samples still show strong NIR emission when excited at 980 nm. </LI> <LI> NNLFA showed high sensitivity for AIV detection from oropharyngeal and cloacal clinical samples. </LI> </UL> </P>