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AUTO-GUIDING SYSTEM FOR CQUEAN (CAMERA FOR QUASARS IN EARLY UNIVERSE)
Kim, Eun-Bin,Park, Won-Kee,Jeong, Hyeon-Ju,Kim, Jin-Young,Kuehne, John,Kim, Dong-Han,Kim, Han-Geun,Odoms, Peter S.,Chang, Seung-Hyuk,Im, Myung-Shin,Pak, Soo-Jong The Korean Astronomical Society 2011 Journal of The Korean Astronomical Society Vol.44 No.4
To perform imaging observations of optically red objects such as high redshift quasars and brown dwarfs, the Center for the Exploration of the Origin of the Universe (CEOU) recently developed an optical CCD camera, Camera for QUasars in EArly uNiverse (CQUEAN), which is sensitive at 0.7-1.1 ${\mu}m$. To enable observations with long exposures, we develop an auto-guiding system for CQUEAN. This system consists of an off-axis mirror, a baffle, a CCD camera, a motor and a differential decelerator. To increase the number of available guiding stars, we design a rotating mechanism for the off-axis guiding camera. The guiding field can be scanned along the 10 arcmin ring offset from the optical axis of the telescope. Combined with the auto-guiding software of the McDonald Observatory, we confirm that a stable image can be obtained with an exposure time as long as 1200 seconds.
Kim, Eun‐,Mi,Kim, Jaehi,Kim, Yun‐,Gon,Lee, Peter,Shin, Dong‐,Sik,Kim, Mira,Hahn, Ji‐,Sook,Lee, Yoon‐,Sik,Kim, Byung‐,Gee John Wiley Sons, Ltd. 2011 Journal of peptide science Vol.17 No.5
<P><B>Abstract</B></P><P>Identification of substrate specificity of kinases is crucial to understand the roles of the kinases in cellular signal transduction pathways. Here, we present an approach applicable for the discovery of substrate specificity of Ser/Thr kinases. The method, which is named as the ‘high‐throughput phosphorylation profiling (HTPP)’ method was developed on the basis of a fully randomized one‐bead one‐compound (OBOC) combinatorial ladder type peptide library and MALDI‐TOF MS. The OBOC ladder peptide library was constructed by the ‘split and pool’ method on a HiCore resin. The peptide library sequence was Ac‐Ala‐X‐X‐X‐Ser‐X‐X‐Ala‐BEBE‐PLL resin. The substrate specificity of murine PKA (cAMP‐dependent protein kinase A) and yeast Yak1 kinase was identified using this method. On the basis of the result, we identified Ifh1, which is a co‐activator for the transcription of ribosomal protein genes, as a novel substrate of Yak1 kinase. The putative Yak1‐dependent phosphorylation site of Ifh1 was verified by <I>in vitro</I> kinase assay. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.</P>
Caspase-8 controls the secretion of inflammatory lysyl-tRNA synthetase in exosomes from cancer cells
Kim, Sang Bum,Kim, Hye Rim,Park, Min Chul,Cho, Seongmin,Goughnour, Peter C.,Han, Daeyoung,Yoon, Ina,Kim, YounHa,Kang, Taehee,Song, Eunjoo,Kim, Pilhan,Choi, Hyosun,Mun, Ji Young,Song, Chihong,Lee, Sang Rockefeller University Press 2017 The Journal of cell biology Vol.216 No.7
<P>Aminoacyl-tRNA synthetases (ARSs), enzymes that normally control protein synthesis, can be secreted and have different activities in the extracellular space, but the mechanism of their secretion is not understood. This study describes the secretion route of the ARS lysyl-tRNA synthetase (KRS) and how this process is regulated by caspase activity, which has been implicated in the unconventional secretion of other proteins. We show that KRS is secreted from colorectal carcinoma cells within the lumen of exosomes that can trigger an inflammatory response. Caspase-8 cleaved the N-terminal of KRS, thus exposing a PDZ-binding motif located in the C terminus of KRS. Syntenin bound to the exposed PDZ-binding motif of KRS and facilitated the exosomic secretion of KRS dissociated from the multi-tRNA synthetase complex. KRS-containing exosomes released by cancer cells induced macrophage migration, and their secretion of TNF-α and cleaved KRS made a significant contribution to these activities, which suggests a novel mechanism by which caspase-8 may promote inflammation.</P>
Kim, Seung Tae,Kim, Kyoung‐,Mee,Kim, Nayoung K.D.,Park, Joon Oh,Ahn, Soomin,Yun, Jae‐,Won,Kim, Kyu‐,Tae,Park, Se Hoon,Park, Peter J.,Kim, Hee Cheol,Sohn, Tae Sung,Choi, Dong Il,Cho, AlphaMed Press 2017 The oncologist Vol.22 No.10
<P>Molecular profiling of actionable mutations in refractory cancer patients has the potential to enable 'precision medicine,' wherein individualized therapies are guided based on genomic profiling. The molecular-screening program was intended to route participants to different candidate drugs in trials based on clinical-sequencing reports. In this screening program, we used a custom target-enrichment panel consisting of cancer-related genes to interrogate single-nucleotide variants, insertions and deletions, copy number variants, and a subset of gene fusions. From August 2014 through April 2015, 654 patients consented to participate in the program at Samsung Medical Center. Of these patients, 588 passed the quality control process for the 381-gene cancer-panel test, and 418 patients were included in the final analysis as being eligible for any anticancer treatment (127 gastric cancer, 122 colorectal cancer, 62 pancreatic/biliary tract cancer, 67 sarcoma/other cancer, and 40 genitourinary cancer patients). Of the 418 patients, 55 (12%) harbored a biomarker that guided them to a biomarker-selected clinical trial, and 184 (44%) patients harbored at least one genomic alteration that was potentially targetable. This study demonstrated that the panel-based sequencing program resulted in an increased rate of trial enrollment of metastatic cancer patients into biomarker-selected clinical trials. Given the expanding list of biomarker-selected trials, the guidance percentage to matched trials is anticipated to increase.</P>
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
Sona, Peter,Hong, Jong Hui,Lee, Sunho,Kim, Byong Joon,Hong, Woon-Young,Jung, Jongcheol,Kim, Han-Na,Kim, Hyung-Lae,Christopher, David,Herviou, Laurent,Im, Young Hwan,Lee, Kwee-Yum,Kim, Tae Soon,Jung, J BioMed Central 2018 BMC bioinformatics Vol.19 No.1
<P><B>Background</B></P><P>The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts.</P><P><B>Results</B></P><P>IGS was integrated on Maha-Fs (HPC) system, to provide the parallelization required to analyze 2504 whole genomes. Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and SGI-UV300 (solid state drive memory). It was observed that SGI-UV300 was faster, having 32.5 mins of process time, while that of the Maha-Fs was 55.2 mins.</P><P><B>Conclusions</B></P><P>The implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this approach will accelerate research advancement in personalized genomic medicine. Our method is comparable to the fastest methods for sequence alignment.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-018-2499-1) contains supplementary material, which is available to authorized users.</P>
Kim, In Ah,No, Mina,Lee, Jang Mi,Shin, Jin Hee,Oh, Jee Sun,Choi, Eun Jung,Kim, Il Han,Atadja, Peter,Bernhard, Eric J. Elsevier 2009 Radiotherapy and oncology Vol.92 No.1
<P><B>Abstract</B></P><P><B>Background and purpose</B></P><P>Histone deacetylase inhibitors (HDIs) are prototypes of agents targeting epigenetic modifications and have received considerable attention for their promise as targeted anticancer drugs. We examined the effects and potential mechanism(s) of combining LBH589 and irradiation in human cancer cells having activated EGFR or HER-2 signaling, focusing on the role of HDAC6.</P><P><B>Methods and materials</B></P><P>We evaluated whether the HDI, LBH589, would radiosensitize a panel of human tumor cell lines having activated EGFR or HER-2 signaling. A mechanistic role for the HDAC6 isotype was investigated using RNA interference and ectopic overexpression HDAC6.</P><P><B>Results</B></P><P>The HDI, LBH589, enhanced the radiosensitivity of the human carcinoma cell lines we tested. Radiosensitization was accompanied by abrogation of radiation-induced G2/M arrest and was associated with aberrant mitotic features and prolonged γH2AX foci. Radiation-induced apoptosis was also increased. LBH589 radiosensitized cells with activated EGFR or HER-2 signaling to a greater degree than the HDIs SK7041 or TSA. However radiosensitization by the three HDI was equivalent in cells without activation of this signaling. LBH589 led acetylation of histone H3 and HSP90. This was associated with down-regulation of the client oncoproteins EGFR, HER-2, and decreased phosphorylation of Akt and ERK. Specific inhibition of HDAC6 by RNAi increased radiosensitivity as well as increasing acetylation of HSP90 and reducing the association of HSP90 with its client proteins. Conversely, ectopic overexpression of HDAC6 isotype increased the levels of p-EGFR and p-AKT expression, and reduced LBH589-mediated radiosensitization.</P><P><B>Conclusions</B></P><P>These findings define a unique mechanism for counteracting pro-survival signaling from EGFR or HER-2 that is present in many tumor cells.</P>