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Clinical Evaluation of Human Papillomavirus DNA Genotyping Assay to Diagnose Women Cervical Cancer
Sunghyun Kim,Dongsup Lee,Yeun Kim,Geehyuk Kim,Sangjung Park,Yeonim Choi,Tae Ue Kim,Kwang Hwa Park,Hyeyoung Lee 대한의생명과학회 2012 Biomedical Science Letters Vol.18 No.2
In this study, we evaluated the human papillomavirus (HPV) genotyping test called MolecuTech REBA HPV-ID® (YD Diagnostics, Seoul, Korea) for 704 women who also had cervical cytological evaluations by Thin Prep. The infection rate of high-risk HPV genotypes was 56.6% in patients with normal cytology, 59.8% in those with benign, low-grade squamous intraepithelial lesions, 51.4% in those with atypical squamous cells of uncertain significance, 92.3% in those with high-grade squamous intraepithelial lesions, and 94.1% in those with squamous cell carcinoma or adenocarcinoma. HPV 16 was the most common genotype detected in any lesion, followed by HPV 53, 58, 33, 52, 45, 31, and 35, in order. The HPV DNA test with PCR-REBA is a very highly sensitive, but less specific, method. The infection rates and HPV genotype distribution of non-Korean people versus people from South Korea showed regional differences.
Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq
Kim, Daesik,Kim, Sojung,Kim, Sunghyun,Park, Jeongbin,Kim, Jin-Soo Cold Spring Harbor Laboratory Press 2016 Genome Research Vol.26 No.3
<P>We present multiplex Digenome-seq to profile genome-wide specificities of up to 11 CRISPR-Cas9 nucleases simultaneously, saving time and reducing cost. Cell-free human genomic DNA was digested using multiple sgRNAs combined with the Cas9 protein and then subjected to whole-genome sequencing. In vitro cleavage patterns, characteristic of on- and off-target sites, were computationally identified across the genome using a new DNA cleavage scoring system. We found that many false positive, bulge-type off-target sites were cleaved by sgRNAs transcribed from an oligonucleotide duplex but not by those transcribed from a plasmid template. Multiplex Digenome-seq captured many bona fide off-target sites, missed by other genome-wide methods, at which indels were induced at frequencies <0.1%. After analyzing 964 sites cleaved in vitro by these sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose a guideline for the choice of target sites for minimizing CRISPR-Cas9 off-target effects in the human genome.</P>
Kim, Sunghyun,Park, Jeong Won,Kim, Dongkyu,Kim, Daejin,Lee, In-Hyun,Jon, Sangyong WILEY-VCH Verlag 2009 Angewandte Chemie Vol.48 No.23
<P>Seeing is sensing: Calsequestrin (CSQ) functionalized gold nanoparticles undergo calcium-dependent CSQ polymerization, which results in a clear color change (see picture) together with precipitation. The sensing system is specific for Ca<SUP>2+</SUP> ions and the differences between normal and disease-associated abnormal (hypercalcemia) Ca<SUP>2+</SUP> ion levels in serum can be distinguished with the naked eye. <img src='wiley_img/14337851-2009-48-23-ANIE200900071-content.gif' alt='wiley_img/14337851-2009-48-23-ANIE200900071-content'> </P> <B>Graphic Abstract</B> <P>Seeing is sensing: Calsequestrin (CSQ) functionalized gold nanoparticles undergo calcium-dependent CSQ polymerization, which results in a clear color change (see picture) together with precipitation. The sensing system is specific for Ca<SUP>2+</SUP> ions and the differences between normal and disease-associated abnormal (hypercalcemia) Ca<SUP>2+</SUP> ion levels in serum can be distinguished with the naked eye. <img src='wiley_img/14337851-2009-48-23-ANIE200900071-content.gif' alt='wiley_img/14337851-2009-48-23-ANIE200900071-content'> </P>
Changes of Cytosolic Ca<SUP>2</SUP> under Metabolic Inhibition in Isolated Rat Ventricular Myocytes
Sunghyun Kang,Nari Kim,Hyun Joo,Jae Boum Youm,Won Sun Park,Mohamed Warda,Hyungkyu Kim,Dang Van Cuong,Taeho Kim,Euiyong Kim,Jin Han 대한생리학회-대한약리학회 2005 The Korean Journal of Physiology & Pharmacology Vol.9 No.5
To characterize cytosolic Ca<SUP>2</SUP> fluctuations under metabolic inhibition, rat ventricular myocytes were exposed to 200μM 2,4-dinitrophenol (DNP), and mitochondrial Ca<SUP>2</SUP>, mitochondrial membrane potential (ΔΨ<SUB>m</SUB>), and cytosolic Ca<SUP>2</SUP> were measured, using Rhod-2 AM, TMRE, and Fluo-4 AM fluorescent dyes, respectively, by Laser Scanning Confocal Microscopy (LSCM). Furthermore, the role of sarcolemmal Na<SUP></SUP>/Ca<SUP>2</SUP> exchange (NCX) in cytosolic Ca<SUP>2</SUP> efflux was studied in KB-R7943 and Na<SUP></SUP>-free normal Tyrode s solution (143 mM LiCl ). When DNP was applied to cells loaded with Fluo-4 AM, Fluo-4 AM fluorescence intensity initially increased by 70⁑10% within 70⁑10 s, and later by 400⁑200% at 850⁑46 s. Fluorescence intensity of both Rhod-2 AM and TMRE were initially decreased by DNP, coincident with the initial increase of Fluo-4 AM fluorescence intensity. When sarcoplasmic reticulum (SR) Ca<SUP>2</SUP> was depleted by 1μM thapsigargin plus 10μM ryanodine, the initial increase of Fluo-4 AM fluorescence intensity was unaffected, however, the subsequent progressive increase was abolished. KB-R7943 delayed both the first and the second phases of cytosolic Ca<SUP>2</SUP> overload, while Na<SUP></SUP>-free solution accelerated the second. The above results suggest that: 1) the initial rise in cytosolic Ca<SUP>2</SUP> under DNP results from mitochondrial depolarization; 2) the secondary increase is caused by progressive Ca<SUP>2</SUP> release from SR; 3) NCX plays an important role in transient cytosolic Ca<SUP>2</SUP> shifts under metabolic inhibition with DNP.
Kim, Hyo Jung,Park, Ji-Hwan,Kim, Jingil,Kim, Jung Ju,Hong, Sunghyun,Kim, Jeongsik,Kim, Jin Hee,Woo, Hye Ryun,Hyeon, Changbong,Lim, Pyung Ok,Nam, Hong Gil,Hwang, Daehee National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.21
<▼1><P><B>Significance</B></P><P>Leaf senescence is regulated in a complex manner, involving time-dependent interactions with developmental and environmental signals. Genetic screens have identified key regulators of senescence, particularly late-stage senescence regulators. Recently, time-course gene-expression and network analyses, mostly analyses of static networks, have predicted many senescence regulators. However, senescence is defined by time-evolving networks, involving the temporal transition of interactions among senescence regulators. Here, we present time-evolving networks of NAM/ATAF/CUC (NAC) transcription factors, central regulators of leaf senescence in <I>Arabidopsis</I>, via time-course gene-expression analysis of NACs in their mutants. These time-evolving networks revealed a unique regulatory module of NACs that controls the timely induction of senescence-promoting processes at a presenescent stage of leaf aging.</P></▼1><▼2><P>Senescence is controlled by time-evolving networks that describe the temporal transition of interactions among senescence regulators. Here, we present time-evolving networks for NAM/ATAF/CUC (NAC) transcription factors in <I>Arabidopsis</I> during leaf aging. The most evident characteristic of these time-dependent networks was a shift from positive to negative regulation among NACs at a presenescent stage. ANAC017, ANAC082, and ANAC090, referred to as a “NAC troika,” govern the positive-to-negative regulatory shift. Knockout of the NAC troika accelerated senescence and the induction of other <I>NAC</I>s, whereas overexpression of the NAC troika had the opposite effects. Transcriptome and molecular analyses revealed shared suppression of senescence-promoting processes by the NAC troika, including salicylic acid (SA) and reactive oxygen species (ROS) responses, but with predominant regulation of SA and ROS responses by ANAC090 and ANAC017, respectively. Our time-evolving networks provide a unique regulatory module of presenescent repressors that direct the timely induction of senescence-promoting processes at the presenescent stage of leaf aging.</P></▼2>