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Search Results: 1 - 10 of 24373 matches for " Jeongsik Yong "
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Pseudophosphorylated αB-Crystallin Is a Nuclear Chaperone Imported into the Nucleus with Help of the SMN Complex
John den Engelsman, Chantal van de Schootbrugge, Jeongsik Yong, Ger J. M. Pruijn, Wilbert C. Boelens
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073489
Abstract: The human small heat shock protein αB-crystallin (HspB5) is a molecular chaperone which is mainly localized in the cytoplasm. A small fraction can also be found in nuclear speckles, of which the localization is mediated by successional phosphorylation at Ser-59 and Ser-45. αB-crystallin does not contain a canonical nuclear localization signal sequence and the mechanism by which αB-crystallin is imported into the nucleus is not known. Here we show that after heat shock pseudophosphorylated αB-crystallin mutant αB-STD, in which all three phosphorylatable serine residues (Ser-19, Ser-45 and Ser-59) were replaced by negatively charged aspartate residues, is released from the nuclear speckles. This allows αB-crystallin to chaperone proteins in the nucleoplasm, as shown by the ability of αB-STD to restore nuclear firefly luciferase activity after a heat shock. With the help of a yeast two-hybrid screen we found that αB-crystallin can interact with the C-terminal part of Gemin3 and confirmed this interaction by co-immunoprecipitation. Gemin3 is a component of the SMN complex, which is involved in the assembly and nuclear import of U-snRNPs. Knockdown of Gemin3 in an in situ nuclear import assay strongly reduced the accumulation of αB-STD in nuclear speckles. Furthermore, depletion of SMN inhibited nuclear import of fluorescently labeled recombinant αB-STD in an in vitro nuclear import assay, which could be restored by the addition of purified SMN complex. These results show that the SMN-complex facilitates the accumulation of hyperphosphorylated αB-crystallin in nuclear speckles, thereby creating a chaperone depot enabling a rapid chaperone function in the nucleus in response to stress.
Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
Wei Zhang,Jae-Woong Chang,Lilong Lin,Kay Minn,Baolin Wu,Jeremy Chien,Jeongsik Yong,Hui Zheng,Rui Kuang
Computer Science , 2014,
Abstract: High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
Wei Zhang?,Jae-Woong Chang?,Lilong Lin?,Kay Minn?,Baolin Wu?,Jeremy Chien?,Jeongsik Yong,Hui Zheng?,Rui Kuang
PLOS Computational Biology , 2015, DOI: 10.1371/journal.pcbi.1004465
Abstract: High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification. Net-RSTQ toolbox is available at http://compbio.cs.umn.edu/Net-RSTQ/.
Instrumentation and Software for Analysis of Arabidopsis Circadian Leaf Movement
Jeongsik Kim,Hong Gil Nam
Interdisciplinary Bio Central , 2009,
Abstract: This article is an addendum to the authors’ previous article (Kim, J. et al. (2008) Plant Cell 20, 307-319). The instrumentation and software described in this article were used to analyze the circadian leaf movement in the previous article. Here, we provide detailed and practical information on the instrumentation and the software. The source code of the LMA program is freely available from the authors.The circadian clock regulates a wide range of cyclic physiological responses with a 24 hour period in most organisms. Rhythmic leaf movement in plants is a typical robust manifestation of rhythms controlled by the circadian clock and has been used to monitor endogenous circadian clock activity. Here, we introduce a relatively easy, inexpensive, and simple approach for measuring leaf movement circadian rhythms using a USB-based web camera, public domain software and a Leaf Movement Assay (LMA) program. The LMA program is a semi-automated tool that enables the user to measure leaf lengths of individual Arabidopsis seedlings from a set of time-series images and generates a wave-form output for leaf rhythm. This is a useful and convenient tool for monitoring the status of a plant’s circadian clock without an expensive commercial instrumentation and software.
Research on Plane 2-D Sediment Model of a Watercourse on Yangtze River  [PDF]
Yong FAN
Journal of Water Resource and Protection (JWARP) , 2009, DOI: 10.4236/jwarp.2009.14032
Abstract: To provide basis for sand excavation of hydraulic fill and land forming in Daohukou region in a watercourse (Wuhan reach) on Yangtze River, a 2-D water-sand mathematic model of this river reach is established. The variation of water levels of this reach and the back silting of watercourse after sand excavation are calculated. The rationality of the results calculated by this model and the measured data are validated and analyzed. The results show that, this model is reasonable and reliable.
The Processing of Dui-construction in Chinese  [PDF]
Yong Zhai
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.26086
Abstract: In the present study, I examined the Dui-construction from a psycholinguistic perspective. Two experiments on the processing of Dui-constructions have been carried out to reexamine the findings of previous experiments on empty subjects in English and Japanese. There are two advantages of using the Chinese Dui-construction over English and Japanese. Firstly, Chinese is similar to English in that the verb is located before the empty subject of an infinitival clause. It is therefore possible to verify whether the verb control information is delayed or not in this case. Secondly, Chinese is similar to Japanese in that they both allow scrambling of arguments. As such, I can examine whether the recency hypothesis applies to Chinese or not. The results indicated that 1) The control information of the verb is accessed immediately; 2) The recency hypothesis is not supported in the processing of Duii-constructions. In other words, there exists a language-specific processing system independent of the general recency strategy.
Elucidation and Identification of Double-Tip Effects in Atomic Force Microscopy Studies of Biological Structures  [PDF]
Yong Chen
Journal of Surface Engineered Materials and Advanced Technology (JSEMAT) , 2012, DOI: 10.4236/jsemat.2012.223037
Abstract: While atomic force microscopy (AFM) has been increasingly applied to life science, artifactual measurements or images can occur during nanoscale analyses of cell components and biomolecules. Tip-sample convolution effect is the most common mechanism responsible for causing artifacts. Some deconvolution-based methods or algorithms have been developed to reconstruct the specimen surface or the tip geometry. Double-tip or double-probe effect can also induce artifactual images by a different mechanism from that of convolution effect. However, an objective method for identifying the double-tip/probe-induced artifactual images is still absent. To fill this important gap, we made use of our expertise of AFM to analyze artifactual double-tip images of cell structures and biomolecules, such as linear DNA, during AFM scanning and imaging. Mathematical models were then generated to elucidate the artifactual double-tip effects and images develop during AFM imaging of cell structures and biomolecules. Based on these models, computational formulas were created to measure and identify potential double-tip AFM images. Such formulas proved to be useful for identification of double-tip images of cell structures and DNA molecules. The present studies provide a useful methodology to evaluate double-tip effects and images. Our results can serve as a foundation to design computer-based automatic detection of double-tip AFM images during nanoscale measuring and imaging of biomolecules and even non-biological materials or structures, and then personal experience is not needed any longer to evaluate artifactual images induced by the double-tip/probe effect.
Towards Capability Maturity Model of e-Learning Process  [PDF]
Yong Zhou
Intelligent Information Management (IIM) , 2012, DOI: 10.4236/iim.2012.44015
Abstract: ePCMM (e-Learning Process Capability Maturity Model) is used for evaluating the capability and maturity of an institution engaged in e-Learning based on e-Learning key process areas. It is a stepwise process improvement which can be implemented by both staged model and continues model.
Knowledge Transferring Features in Traditional Construction Project Team in China: Based on SNA  [PDF]
Yong Tang
Technology and Investment (TI) , 2012, DOI: 10.4236/ti.2012.34032
Abstract: For the uniqueness and one-time feature, construction project is urgently needed in knowledge transferring to acquire its high performance. This paper focuses in the exploration of knowledge transferring features from the network perspective. Based on the data from a real construction project team of 40 members, we find that all members have knowledge transferring behavior, while the knowledge transferring density is comparatively low and distance is long; from cluster analysis we find that 89 different clusters in the whole network, and some members (especially the managers) repeated appear in different clusters and assume the responsibilities in coordinating knowledge transferring.
Uniqueness of Radial Solutions for Elliptic Equation Involving the Pucci Operator  [PDF]
Yong Liu
Advances in Pure Mathematics (APM) , 2012, DOI: 10.4236/apm.2012.26061
Abstract: The solution of a nonlinear elliptic equation involving Pucci maximal operator and super linear nonlinearity is studied. Uniqueness results of positive radial solutions in the annulus with Dirichlet boundary condition are obtained. The main tool is Lane-Emden transformation and Koffman type analysis. This is a generalization of the corresponding classical results involving Laplace operator.
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