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Lee, Jungeun,He, Kun,Stolc, Viktor,Lee, Horim,Figueroa, Pablo,Gao, Ying,Tongprasit, Waraporn,Zhao, Hongyu,Lee, Ilha,Deng, Xing Wang American Society of Plant Physiologists 2007 The Plant cell Vol.19 No.3
<P>The transcription factor LONG HYPOCOTYL5 (HY5) acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here, we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using a high-density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis thaliana genome, we mapped genome-wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed >3000 chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light-responsive genes and transcription factor genes. Our data thus support a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis.</P>
Spatiotemporal genomic architecture informs precision oncology in glioblastoma
Lee, Jin-Ku,Wang, Jiguang,Sa, Jason K,Ladewig, Erik,Lee, Hae-Ock,Lee, In-Hee,Kang, Hyun Ju,Rosenbloom, Daniel S,Camara, Pablo G,Liu, Zhaoqi,van Nieuwenhuizen, Patrick,Jung, Sang Won,Choi, Seung Won,Ki Nature Pub. Co 2017 Nature genetics Vol.49 No.4
<P>Precision medicine in cancer proposes that genomic characterization of tumors can inform personalized targeted therapies1-5. However, this proposition is complicated by spatial and temporal heterogeneity6-14. Here we study genomic and expression profiles across 127 multisector or longitudinal specimens from 52 individuals with glioblastoma (GBM). Using bulk and single-cell data, we find that samples from the same tumor mass share genomic and expression signatures, whereas geographically separated, multifocal tumors and/or long-term recurrent tumors are seeded from different clones. Chemical screening of patient-derived glioma cells (PDCs) shows that therapeutic response is associated with genetic similarity, and multifocal tumors that are enriched with PIK3CA mutations have a heterogeneous drug-response pattern. We show that targeting truncal events is more efficacious than targeting private events in reducing the tumor burden. In summary, this work demonstrates that evolutionary inference from integrated genomic analysis in multisector biopsies can inform targeted therapeutic interventions for patients with GBM.</P>
Loss of glucocerebrosidase 1 activity causes lysosomal dysfunction and α-synuclein aggregation
Bae, Eun-Jin,Yang, Na Young,Lee, Cheolsoon,Lee, He-Jin,Kim, Seokjoong,Sardi, Sergio Pablo,Lee, Seung-Jae Nature Publishing Group 2015 Experimental and molecular medicine Vol.47 No.3
<P>Lysosomal dysfunction is a common pathological feature of neurodegenerative diseases. GTP-binding protein type A1 (<I>GBA1</I>) encodes β-glucocerebrosidase 1 (GCase 1), a lysosomal hydrolase. Homozygous mutations in <I>GBA1</I> cause Gaucher disease, the most common lysosomal storage disease, while heterozygous mutations are strong risk factors for Parkinson's disease. However, whether loss of GCase 1 activity is sufficient for lysosomal dysfunction has not been clearly determined. Here, we generated human neuroblastoma cell lines with nonsense mutations in the <I>GBA1</I> gene using zinc-finger nucleases. Depending on the site of mutation, GCase 1 activity was lost or maintained. The cell line with GCase 1 deficiency showed indications of lysosomal dysfunction, such as accumulation of lysosomal substrates, reduced dextran degradation and accumulation of enlarged vacuolar structures. In contrast, the cell line with C-terminal truncation of GCase 1 but with intact GCase 1 activity showed normal lysosomal function. When α-synuclein was overexpressed, accumulation and secretion of insoluble aggregates increased in cells with GCase 1 deficiency but did not change in mutant cells with normal GCase 1 activity. These results demonstrate that loss of GCase 1 activity is sufficient to cause lysosomal dysfunction and accumulation of α-synuclein aggregates.</P>
생장조절제가 하월시아 만상(Haworthia maughanii)의 기내 대량증식에 미치는 영향
김윤희,김혜형,이지영,이재홍,정재홍,이상덕,Kim, Youn Hee,Kim, Hye Hyeong,Lee, Gee Young,Lee, Jae Hong,Jung, Jae Hong,Delgado-Sanchez, Pablo,Lee, Sang Deok 한국식물생명공학회 2018 식물생명공학회지 Vol.45 No.4
The purpose of this study was to investigate the suitable parts for callus induction and optimal concentrations of growth regulators contained in the medium affecting shoot and rooting for the in vitro mass production of Haworthia maughanii. To determine suitable parts of the plant for callus induction, the leaves, flower bloom and flower stalks were cultured in MS medium at different concentrations of $0{\sim}2mgL^{-1}$ NAA and $0{\sim}2mgL^{-1}$ TDZ, respectively. All of the parts showed 100% callus formation rate at $NAA\;1mgL^{-1}$ and $TDZ\;1mgL^{-1}$ treatment, $NAA\;2mgL^{-1}$ and $TDZ\;2mgL^{-1}$ treatment and NAA 1 to $2mgL^{-1}$, respectively. While the rate of callus formation was high in all parts, the leaves were the most efficient to obtain most culture parts. $NAA\;0.1mg\;L^{-1}$ and $BA\;0.1mg\;L^{-1}$ treatments were the most effective in shoot formation with 22.0 shoots. In addition, multiple shoot propagation showed 16.3 shoots, the highest, with $NAA\;0.1mg\;L^{-1}$ and $BA\;0.1mg\;L^{-1}$ treatments. These results led us to speculate that the optimization of culture conditions was responsible for the mass propagation for in vitro cultures of Haworthia maughanii. 하월시아(Haworthia maughanii)의 기내 식물체 대량생산을 위하여 캘러스 유도에 적합한 부위와 신초 및 발근에 영향을 미치는 생장조절제 종류 및 농도를 구명하고자 본 시험을 수행하였다. 캘러스 유도에 적합한 식물 부위를 구명 하기 위해 잎, 화뢰, 화경을 이용하여 NAA와 TDZ의 농도를 달리하여 MS배지에 치상한 결과, 잎은 $NAA\;1mgL^{-1}$와 $TDZ\;1mgL^{-1}$, 화뢰는 $NAA\;2mgL^{-1}$와 $TDZ\;2mgL^{-1}$, 화경는 $NAA\;1mgL^{-1}$이상의 단용처리에서 100% 캘러스 형성율을 보였고, 모든 부위에서 캘러스 형성율은 높았으나 가장 많은 배양절편 확보가 가능한 잎이 가장 효율적으로 판단되었다. $NAA\;0.1mgL^{-1}$와 $BA\;0.1mgL^{-1}$ 혼용처리구에서 다른 처리에 비해서 신초가 22.0개로 신초 발생에 가장 효과적이었다. 또한 신초의 대량증식은 $NAA\;0.1mgL^{-1}$와 $BA\;0.1mgL^{-1}$처리구에서 신초가 16.3개로 가장 많이 형성되었다. 이러한 결과는 최적의 기내 배양 조건을 통해 하월시아 만상의 대량생산 가능성을 보여주었다.
Lee, Jong Seok,Krause, Roland,Schreiber, Jö,rg,Mollenkopf, Hans-Joachim,Kowall, Jane,Stein, Robert,Jeon, Bo-Young,Kwak, Jeong-Yeon,Song, Min-Kyong,Patron, Juan Pablo,Jorg, Sabine,Roh, Kyoungmin,Ch Elsevier 2008 Cell host & microbe Vol.3 No.2
<P><B>Summary</B></P><P>Attenuated strains of mycobacteria can be exploited to determine genes essential for their pathogenesis and persistence. To this goal, we sequenced the genome of H37Ra, an attenuated variant of <I>Mycobacterium tuberculosis</I> H37Rv strain. Comparison with H37Rv revealed three unique coding region polymorphisms. One polymorphism was located in the DNA-binding domain of the transcriptional regulator PhoP, causing the protein's diminished DNA-binding capacity. Temporal gene expression profiles showed that several genes with reduced expression in H37Ra were also repressed in an H37Rv phoP knockout strain. At later time points, genes of the dormancy regulon, typically expressed in a state of nonreplicating persistence, were upregulated in H37Ra. Complementation of H37Ra with H37Rv <I>phoP</I> partially restored its persistence in a murine macrophage infection model. Our approach demonstrates the feasibility of identifying minute but distinct differences between isogenic strains and illustrates the consequences of single point mutations on the survival stratagem of <I>M. tuberculosis.</I></P>