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Kim, Bichseam,Kim, Nahui,Kim, Jun Young,Kim, Byung Sup,Jung, Hee-Jeong,Hwang, Indoek,Noua, Ill-Sup,Sim, Sung-Chur,Park, Younghoon,Belzile, F. Canadian Science Publishing 2016 Genome Vol.59 No.3
<P> Fusarium crown and root rot is a severe fungal disease of tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In this study, the genomic location of the FORL-resistance locus was determined using a set of molecular markers on chromosome 9 and an F2 population derived from FORL-resistant inbred ‘AV107-4’ (Solanum lycopersicum) × susceptible ‘L3708’ (Solanum pimpinellifolium). Bioassay performed using Korean FORL strain KACC 40031 showed single dominant inheritance of FORL resistance in the F2 population. In all, 13 polymerase chain reaction-based markers encompassing approximately 3.6-72.0 Mb of chromosome 9 were developed based on the Tomato-EXPEN 2000 map and SolCAP Tomato single nucleotide polymorphism array analysis. These markers were genotyped on 345 F2 plants, and the FORL-resistance locus was found to be present on a pericentromeric region of suppressed chromosomal recombination in chromosome 9. The location of the FORL-resistance locus was further confirmed by testing these markers against diverse commercial tomato and stock cultivars resistant to FORL. A restriction fragment length polymorphism marker, PNU-D4, located at approximately 6.1 Mb of chromosome 9 showed the highest match with the resistance locus and was used for conducting high-resolution melting analysis for marker-assisted selection of FORL resistance. </P>
Genome Sequence of the Hemolytic-Uremic Syndrome-Causing Strain Escherichia coli NCCP15647
Jeong, H.,Zhao, F.,Igori, D.,Oh, K.-H.,Kim, S.-Y.,Kang, S. G.,Kim, B. K.,Kwon, S.-K.,Lee, C. H.,Song, J. Y.,Yu, D. S.,Park, M.-S.,Cho, S.-H.,Kim, J. F. American Society for Microbiology 2012 Journal of Bacteriology Vol.194 No.14
Hazardous materials in buildings
Kim, Jeong Tai,Yu, Chuck W. F. Sage Publications 2014 Indoor and Built Environment Vol.23 No.1
<P>The purpose of this paper is to review the types of building materials that could present a hazardous risk to health of building occupants. The review is necessary as many countries including Korea and the UK have a policy target to make building sustainable and air-tight; therefore a strategy and guide is needed to address the possible hazards that could be found in existing structures of many buildings. For new buildings, the assessment should be at the beginning of building conception, which should be extended to all stages of construction, and the potential hazard should be registered in record to inform the future refurbishment procedures and end-of-life management of the building, for disposal and re-use of materials. The assessment of hazardous materials should be an important aspect of the green building certification such as those being developed in Korea. Various types of hazardous building materials are described. Guidance is provided to encourage precaution and remediation of risks when handling these materials during construction or refurbishment or with materials already in place in existing buildings. The good practice should include a checklist procedure including: survey, assess condition, assess presence, identify and analyse, record, evaluate, and finally develop a plan strategy for prevention and possible remediation.</P>
Song, Insil,Kim, Eun-Jin,Kim, In-Hyeok,Park, Eun-Mi,Lee, Kyung Eun,Shin, Joo-Ho,Guengerich, F. Peter,Choi, Jeong-Yun American Chemical Society 2014 Chemical research in toxicology Vol.27 No.5
<P>DNA polymerase (pol) κ, one of the Y-family polymerases, has been shown to function in error-free translesion DNA synthesis (TLS) opposite the bulky <I>N</I><SUP>2</SUP>-guanyl DNA lesions induced by many carcinogens such as polycyclic aromatic hydrocarbons. We analyzed the biochemical properties of eight reported human pol κ variants positioned in the polymerase core domain, using the recombinant pol κ (residues 1–526) protein and the DNA template containing an <I>N</I><SUP>2</SUP>-CH<SUB>2</SUB>(9-anthracenyl)G (<I>N</I><SUP>2</SUP>-AnthG). The truncation R219X was devoid of polymerase activity, and the E419G and Y432S variants showed much lower polymerase activity than wild-type pol κ. In steady-state kinetic analyses, E419G and Y432S displayed 20- to 34-fold decreases in <I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB> for dCTP insertion opposite G and <I>N</I><SUP>2</SUP>-AnthG compared to that of wild-type pol κ. The L21F, I39T, and D189G variants, as well as E419G and Y432S, displayed 6- to 22-fold decreases in <I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB> for next-base extension from C paired with <I>N</I><SUP>2</SUP>-AnthG, compared to that of wild-type pol κ. The defective Y432S variant had 4- to 5-fold lower DNA-binding affinity than wild-type, while a slightly more efficient S423R variant possessed 2- to 3-fold higher DNA-binding affinity. These results suggest that R219X abolishes and the E419G, Y432S, L21F, I39T, and D189G variations substantially impair the TLS ability of pol κ opposite bulky <I>N</I><SUP>2</SUP>-G lesions in the insertion step opposite the lesion and/or the subsequent extension step, raising the possibility that certain nonsynonymous pol κ genetic variations translate into individual differences in susceptibility to genotoxic carcinogens.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/crtoec/2014/crtoec.2014.27.issue-5/tx500072m/production/images/medium/tx-2014-00072m_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/tx500072m'>ACS Electronic Supporting Info</A></P>
Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657
Kim, B. K.,Song, G. C.,Hong, G. H.,Seong, W.-K.,Kim, S.-Y.,Jeong, H.,Kang, S. G.,Kwon, S.-K.,Lee, C. H.,Song, J. Y.,Yu, D. S.,Park, M.-S.,Cho, S.-H.,Kim, J. F. American Society for Microbiology 2012 Journal of Bacteriology Vol.194 No.14
Genome Sequence of the Probiotic Bacterium Bifidobacterium animalis subsp. lactis AD011
Kim, Jihyun F.,Jeong, Haeyoung,Yu, Dong Su,Choi, Sang-Haeng,Hur, Cheol-Goo,Park, Myeong-Soo,Yoon, Sung Ho,Kim, Dae-Won,Ji, Geun Eog,Park, Hong-Seog,Oh, Tae Kwang American Society for Microbiology 2009 Journal of Bacteriology Vol.191 No.2
<B>ABSTRACT</B><P><I>Bifidobacterium animalis</I> subsp. <I>lactis</I> is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of <I>B. animalis</I> subsp. <I>lactis</I> AD011 that was isolated from an infant fecal sample. Biological functions encoded in a single circular chromosome of 1,933,695 bp, smallest among the completely sequenced bifidobacterial genomes, are suggestive of their probiotic functions, such as utilization of bifidogenic factors and a variety of glycosidic enzymes and biosynthesis of polysaccharides.</P>
Ferromagnetism in single crystal and nanocomposite Sr(Ti,Fe)O<sub>3</sub> epitaxial films
Kim, Hyun-Suk,Bi, Lei,Kim, Dong Hun,Yang, Dae-Jin,Choi, Yoon Jeong,Lee, Jung Woo,Kang, Jeung Ku,Chang Park, Yun,Dionne, Gerald F.,Ross, Caroline A. Royal Society of Chemistry 2011 Journal of materials chemistry Vol.21 No.28
<P>The ferromagnetic properties and electrical leakage current of single-phase SrTi<SUB>1−<I>x</I></SUB>Fe<SUB><I>x</I></SUB>O<SUB>3</SUB> (STF) perovskite films are compared for two different samples: a single-crystal film with a (100) orientation, and a ‘doubly oriented’ nanocomposite film consisting of (110)-oriented nanopillars embedded homoepitaxially in a (100)-oriented matrix. The STF films contain mixed valence Fe ions, with a lower average valence state present in the single crystal film. The films are under an in-plane compressive strain, and exhibit an out-of-plane magnetic easy axis due to magnetoelastic effects. The nanopillars in the double-epitaxial STF films act as single ferromagnetic domains, whereas the single-crystal films show a maze-like domain structure. Composition fluctuations seen in single-crystal films are suppressed in the double-epitaxial structure, which has a lower electrical leakage current. First-principles modeling supports a tendency for Fe ions to occupy adjacent sites. The correlations between the valence state and distribution of the Fe ions, the microstructure, and the magnetic and electrical properties provide a general method of tailoring the properties of perovskite films, which have immense technological value in a range of multiferroic, ferromagnetic, optical, spintronic and hybrid devices.</P> <P>Graphic Abstract</P><P>The ferromagnetic and electrical properties of SrTi<SUB>1−<I>x</I></SUB>Fe<SUB><I>x</I></SUB>O<SUB>3</SUB> films grown on buffered Si are characterized for both (100)-oriented single crystal films and double-epitaxial films consisting of (110)-oriented nanopillars embedded homoepitaxially in a (100)-oriented matrix. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c1jm11286d'> </P>
Ogata, Alana F.,Song, Seok-Won,Cho, Su-Ho,Koo, Won-Tae,Jang, Ji-Soo,Jeong, Yong Jin,Kim, Min-Hyeok,Cheong, Jun Young,Penner, Reginald M.,Kim, Il-Doo American Chemical Society 2018 ANALYTICAL CHEMISTRY - Vol.90 No.15
<P>A new type of chemiresistor, the impedance-transduced chemiresistor (ITCR), is described for the rapid analysis of glucose. The ITCR exploits porous, high surface area, fluorine-doped carbon nanofibers prepared by electrospinning of fluorinated polymer nanofibers followed by pyrolysis. These nanofibers are functionalized with a boronic acid receptor and stabilized by Nafion to form the ITCR channel for glucose detection. The recognition and binding of glucose by the ITCR is detected by measuring its electrical impedance at a single frequency. The analysis frequency is selected by measuring the signal-to-noise (<I>S</I>/<I>N</I>) for glucose detection across 5 orders of magnitude, evaluating both the imaginary and real components of the complex impedance. On the basis of this analysis, an optimal frequency of 13 kHz is selected for glucose detection, yielding an <I>S</I>/<I>N</I> ratio of 60-100 for [glucose] = 5 mM using the change in the total impedance, Δ<I>Z</I>. The resulting ITCR glucose sensor shows a rapid analysis time (<8 s), low coefficient of variation for a series of sensors (<10%), an analysis range of 50 μM to 5 mM, and excellent specificity versus fructose, ascorbic acid, and uric acid. These metrics for the ITCR are obtained using a sample size as small as 5 μL.</P> [FIG OMISSION]</BR>
Park, Su-Hyun,Jeong, Jin Seo,Redillas, Mark C.F.R.,Jung, Harin,Bang, Seung Woon,Kim, Youn Shic,Kim, Ju-Kon 한국식물생명공학회 2013 Plant biotechnology reports Vol.7 No.1
Gene regulation at the post-transcriptional level is a well-organized process to adjust plants in response to environmental changes. Here, we identified a novel RNA-binding protein (RBP) possessing a CBS (cystathionine-${\beta}$-synthase) domain through yeast three-hybrid screening. This RBP, 3'-UTR-interacting protein 1 (UIP1), interacts with 3' untranslated region of the Rubisco small subunit mRNA (3' RbcS)-the major mRNA element that mediates the stress-induced mRNA decay (SMD) under drought and salt stress conditions. Six deletion constructs were made to delineate the binding domain of the UIP1 protein. Co-transformation of yeast with these constructs together with three different hybrid RNAs in various combinations showed that deletion of 51 N-terminal amino acids resulted in a loss of sequence-specific binding affinity. Further deletion at the region between 52 and 212 amino acids revealed that the CBS domain of UIP1 is necessary for binding to 3' RbcS. Transgenic overexpression of UIP1 in rice resulted in an increase in tolerance to drought stress at the vegetative stage of growth. Under drought, high salt and low temperature conditions, the maximum photochemical efficiency of photosystem II ($F_v/F_m$) of UIP1 plants was higher than those of the nontransgenic plants. Interestingly, the effect of UIP1 overexpression on tolerance to stress was much more pronounced under drought than under high salt and low temperature conditions. Taken together, our results demonstrate that UIP1 interacts with 3' untranslated region of RbcS1 mRNA and increases tolerance of transgenic overexpressors to drought stress.