Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay

Kim, Jungho,Wang, Hye-young,Kim, Seoyong,Park, Soon Deok,Yu, Kwangmin,Kim, Hyo Youl,Uh, Young,Lee, Hyeyoung Elsevier Biomedical 2016 Journal of microbiological methods Vol.128 No.-

<P><B>Abstract</B></P> <P>DNA extraction efficiency affects the success of PCR-based method applications. The Punch-it™ NA-Sample kit for extracting DNA by using paper chromatography is technically easy to use and requires just two reagents and only 10min to complete. The Punch-it™ NA-Sample kit could be offered as a rapid, accurate, and convenient method for extracting bacterial and fungal DNA from blood culture bottles. We compared the efficiencies of the commercial kit (Punch-it™ NA-Sample kit) and an in-house conventional boiling method with Chelex-100 resin for DNA extraction from blood culture bottles. The efficiency of the two DNA extraction methods was assessed by PCR-reverse blot hybridization assay (PCR-REBA, REBA Sepsis-ID) for detecting Gram positive (GP) bacteria, Gram negative (GN) bacteria, and <I>Candida</I> species with 196 positive and 200 negative blood culture bottles. The detection limits of the two DNA extraction methods were 10<SUP>3</SUP> CFU/mL for GP bacteria, 10<SUP>3</SUP> CFU/mL for GN bacteria, and 10<SUP>4</SUP> CFU/mL for <I>Candida</I>. The sensitivity and specificity of the Punch-it™ NA-Sample kit by REBA Sepsis-ID were 95.4% (187/196) and 100% (200/200), respectively. The overall agreement of the two DNA extraction methods was 98.9% (392/396). Three of four samples showing discrepant results between the two extraction methods were more accurately matched up with the Punch-it™ NA-Sample kit based on conventional culture methods. The results indicated that the Punch-it™ NA-Sample kit extracted bacterial and fungal DNA in blood culture bottles and allowed extracted DNA to be used in molecular assay.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Punch-it™ NA-Sample kit and boiling method for DNA extraction were compared. </LI> <LI> Punch-it™ NA-Sample kit extracted bacterial and fungal DNA in blood culture bottles. </LI> <LI> The Punch-it™ NA-Sample kit does not require enzyme to digest cell walls. </LI> </UL> </P>

Study on nanoparticle production process characteristics in transferred arc plasma system using heat and mass balance

Kim, Byungkwon,Song, Jungho,Kim, Jeong-Yeol,Hwang, Jungho,Park, Dongho Elsevier 2018 Advanced powder technology Vol.29 No.12

<P><B>Abstract</B></P> <P>The nanoparticle production process in a transferred arc plasma system was studied. The plasma temperature, particle heating time, and particle residence time in plasma were calculated using heat and mass balance with a lumped capacitance method. We analyzed the nanoparticle production characteristics based on different operating conditions by comparing the particle vaporization time with the particle residence time in the plasma. The limit size for particle vaporization was derived. With higher plasma power, the nanoparticle production rate increased and the energy consumption rate decreased. It was confirmed that the energy consumption rate reaches an optimal point according to the plasma power. Experiments to determine the nanoparticle production rate according to plasma power were also conducted and the experimental data were compared with numerical values. The results show that the error rate between the numerical values and experimental data was approximately ±18%. Therefore, the developed model which was studied could be useful for designing nanoparticle production process using a transferred arc plasma system because of its simple approach.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Nanoparticle production process in a transferred arc plasma system was studied. </LI> <LI> Nanoparticle production characteristics were analyzed for varying conditions. </LI> <LI> Numerical values agreed well with experimental results. </LI> <LI> The method can be useful for design of large-scale nanoparticle production systems. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Novel SIRT1 activator MHY2233 improves glucose tolerance and reduces hepatic lipid accumulation in db/db mice

Kim, Min Jo,An, Hye Jin,Kim, Dae Hyun,Lee, Bonggi,Lee, Hye Jin,Ullah, Sultan,Kim, Su Jeong,Jeong, Hyoung Oh,Moon, Kyoung Mi,Lee, Eun Kyeong,Yang, Jungho,Akter, Jinia,Chun, Pusoon,Moon, Hyung Ryong,Chu Elsevier 2018 Bioorganic & medicinal chemistry letters Vol.28 No.4

<P><B>Abstract</B></P> <P>The NAD<SUP>+</SUP>-dependent deacetylase SIRT1, which is associated with the improvement of metabolic syndromes, such as type 2 diabetes, is a well-known longevity-related gene. Several <I>in vitro</I> and <I>in vivo</I> studies have shown the known protective effects of SIRT1 activators, such as resveratrol and SRT1720, on diabetes- or obesity-induced fatty liver and insulin resistance. Here, we newly synthesized 18 benzoxazole hydrochloride derivatives based on the structure of resveratrol and SRT1720. We performed an <I>in vitro</I> SIRT1 activity assay to identify the strongest SIRT1 activator. The assay confirmed MHY2233 to be the strongest SIRT1 activator (1.5-fold more potent than resveratrol), and docking simulation showed that the binding affinity of MHY2233 was higher than that of resveratrol and SRT1720. To investigate its beneficial effects, db/db mice were orally administered MHY2233 for 1 month, and various metabolic parameters were assessed in the serum and liver tissues. MHY2233 markedly ameliorated insulin signaling without affecting body weight in db/db mice. In particular, the mRNA expression of lipogenic genes, such as acetyl CoA carboxylase, fatty acid synthase, and sterol regulatory element-binding protein, which increased in db/db mice, decreased following oral treatment with MHY2233.</P> <P>In conclusion, the novel SIRT1 activator MHY2233 reduced lipid accumulation and improved insulin resistance. This finding may contribute toward therapeutic approaches for fatty liver disease and glucose tolerance.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

The control of particle size distribution for fabricated alumina nanoparticles using a thermophoretic separator

Kim, Byungkwon,Song, Jungho,Kim, Jeong-Yeol,Hwang, Jungho,Park, Dongho VSP 2019 Advanced powder technology Vol.30 No.10

<P><B>Abstract</B></P> <P>Control of the particle size distribution of fabricated alumina nanoparticles from general alumina powder with a large geometric standard deviation (GSD) was studied. A thermophoretic separator was used to control the GSD of the nanoparticles, and unevaporated and primary particles were separated to yield a small GSD. The fabricated nanoparticles were characterized by field emission scanning electron microscopy (FESEM) and a scanning mobility particle sizer (SMPS). We confirmed that the GSD of the nanoparticles was controlled by the thermophoretic separator. A temperature difference between 79 K and 151 K was applied to the thermophoretic separator for control of the nanoparticle GSD. The GSD of the fabricated alumina nanoparticles was improved from 1.74 to 1.44.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Alumina nanoparticles were fabricated using a plasma torch and thermophoretic separator. </LI> <LI> The method allowed separation of primary nanoparticles and control of their size distribution. </LI> <LI> Controlled particle size will enhance applications employing alumina nanoparticles. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Control of Charge Dynamics via Use of Nonionic Phosphonate Chains and Their Effectiveness for Inverted Structure Solar Cells

Kim, Gyoungsik,Song, Seyeong,Lee, Jungho,Kim, Taehyo,Lee, Tack Ho,Walker, Bright,Kim, Jin Young,Yang, Changduk Wiley Blackwell (John Wiley Sons) 2015 ADVANCED ENERGY MATERIALS Vol.5 No.18

Infrared study of giant dielectric constant in Li- and Ti-doped NiO

Kim, Jungho,Lee, Youngwoo,Kim, M. G.,Souchkov, A.,Lee, J. S.,Drew, H. D.,Oh, S.-J.,Nan, C. W.,Choi, E. J. American Physical Society 2004 Physical review. B, Condensed matter and materials Vol.70 No.17

Small RNA Transcriptome of Hibiscus Syriacus Provides Insights into the Potential Influence of microRNAs in Flower Development and Terpene Synthesis

Kim, Taewook,Park, June Hyun,Lee, Sang-gil,Kim, Soyoung,Kim, Jihyun,Lee, Jungho,Shin, Chanseok Korean Society for Molecular and Cellular Biology 2017 Molecules and cells Vol.40 No.8

MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. We employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissuespecific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in H. syriacus. Collectively, this study provides the first reliable draft of the H. syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in H. syriacus.

Universal Expression of the Optical Power Dissipation in Multilayer Structures with Complex Permittivity and Permeability

Kim, Jungho,Kim, Kyoung-Youm,Kim, Sungchul IOP Publishing 2012 Japanese journal of applied physics Vol.51 No.r2

Reference thermal neutron field at KRISS for calibration of neutron detectors

Kim, Yun Ho,Park, Hyeonseo,Kim, Yong Kyun,Kim, Jungho,Kang, Jeongsoo Elsevier 2017 Radiation measurements Vol.107 No.-

<P><B>Abstract</B></P> <P>A reference thermal neutron field has been established at the Korea Research Institute of Standards and Science (KRISS) by using a <SUP>241</SUP>Am-Be neutron source and a high-purity graphite pile constructed by stacking graphite blocks. The properties of the graphite blocks such as impurities, density, and dimensions were studied thoroughly to understand the characteristics of the generated field. The energy spectrum and thermal neutron fractions were simulated with the Monte Carlo N-Particle eXtended code using measured physical parameters. The neutron effective temperature was 308 K, and the fraction of thermal neutrons was approximately 95% at the reference position of the thermal neutron field. The thermal neutron fluence rate was determined by adopting the Westcott convention method based on neutron activation analysis using a gold foil. The Westcott fluence rate for thermal neutron at the reference position was (2326.7 ± 8.4) cm<SUP>−2</SUP>s<SUP>−1</SUP>. The true thermal neutron fluence rate at the reference position in the KRISS thermal neutron field was (2700 ± 29) cm<SUP>−2</SUP>s<SUP>−1</SUP> (at the reference date of June 30, 2014). The response of a spherical proportional counter with He-3 (SP9 neutron detector) was evaluated in the newly established field as (3.083 ± 0.045) cm<SUP>2</SUP> for the reference calibration condition (a parallel neutron beam with a Maxwellian energy distribution having a most probable energy of 0.025 eV).</P> <P><B>Highlights</B></P> <P> <UL> <LI> Thermal neutron field was developed for the calibration of neutron detectors. </LI> <LI> A <SUP>241</SUP>Am-Be neutron source and a pure graphite pile were used for the construction. </LI> <LI> Monte Carlo simulation was performed to understand characteristics of the field. </LI> <LI> Thermal neutron fluence rate was determined based on neutron activation analysis. </LI> <LI> The sensitivity of the SP9 detector was calibrated with an uncertainty of ∼3%. </LI> </UL> </P>

Evidence showing duplication and recombination of cel genes in tandem from hyperthermophilic Thermotoga sp.

Kim, Min Keun,Kang, Tae Ho,Kim, Jungho,Kim, Hoon,Yun, Han Dae Humana Press 2012 Applied biochemistry and biotechnology Vol.168 No.7

<P>This study was conducted to assess the gene duplication and diversification of tandem cellulase genes in thermophilic bacteria. The tandem cellulase genes cel5C and cel5D were cloned from Thermotoga maritima MSB8, and a survey of the thermophilic bacterial genome for tandem cel genes from the databases was carried out. A clone having 2.3 kb fragment from T. maritima MSB8 showed cellulase activity, which had two open reading frames in tandem (cel5C and cel5D). The cel5C gene has 954 bp, which encodes a protein of 317 amino acid residues with a signal peptide of 23 amino acids, and the other gene cel5D consisting of 990 bp encoding a protein of 329 amino acid residues. These two proteins have similarity with the enzymes of glycosyl hydrolase family 5. From the enzyme assay, it was observed that Cel5C was extracellular and Cel5D was intracellular cellulase. Phylogenetic and homology matrix analyses of DNA and protein sequences revealed that family 12 cellulase enzymes Cel12A and Cel12B displayed higher homology (>50 %), but Cel5C and Cel5D enzymes belong to family 5 displayed lower homology (<30 %). In addition, repeated and mirror sequences in tandem genes are supposed to show the existence of gene duplication and recombination.</P>