Browsing by Author "Chang, Cheng-Wei"

Now showing 1 - 4 of 4

A Human DNA methylation site predictor base on SVM
(2009)
Sun, Yi-Ming
;
Liu, Baw-Jhiune
;
Liao, Wei-Li
;
Chang, Cheng-Wei
;
Huang, Hsien-Da
During gene expression, transcription factors are unable to bind to a transcription binding site (TFBS) involved in regulation if DNA methylation has occurred at the TFBS. Methyl-CpG-binding proteins may also occupy the TFBS and prevent the functioning of a transcription factor. Thus, the methylation status of CpG sites is an important issue when trying to understand gene regulation and shows strong correlation with the TFBS involved. In addition, CpG islands would seem to undergo cell-specific and tissue-specific methylation. Such differential methylation is presented at numerous genetic loci that are essential for development. Current DNA methylation site prediction tools need to be improved so that they include TFBS features and have greater accuracy in terms of the DNA region that is involved in methylation. We developed models that compare the differences across these regions and tissues. The TFBSs, DNA properties and DNA distribution were used as features for this classification. From the results, we found some TFBSs that were able to discriminate whether a sequence was methylated or not. The sensitivity, specificity and accuracy estimated using 10-fold cross validation were 90.8%, 80.54%, and 86.07%, respectively. Thus, for these four regions and twelve tissues, the performance levels (ACC) were all greater than 80%. We propose that the differential features or methylations vary between the different regions because the features common to each DNA region made up only 50% of the top 70 features. An online predictor based on EpiMeP is available at http://140.115.51.41/EpiMeP/. Supplementary file is available at http://140.115.51.41/EpiMeP/supplementary.doc.
MgO nanoparticles confined in ZIF-8 as acid-base bifunctional catalysts for enhanced glycerol carbonate production from transesterification of glycerol and dimethyl carbonate
(2020-07-01)
Chang, Cheng-Wei
;
Gong, Zi-Jie
;
Huang, Nai-Chieh
;
Wang, Cheng-Yu
;
Yu, Wen-Yueh
MgO-loaded ZIF-8 catalysts (MgO@ZIF-8) with various MgO loadings were prepared and characterized using atomic absorption spectroscopy (AAS), powder X-ray diffraction (PXRD), Fourier-transform infrared spectroscopy (FT-IR), N-2 sorption isotherms, field-emission transmission electron microscopy (FE-TEM), and thermogravimetric analysis (TGA). Our results indicate that MgO nanoparticles could deposit onto the ZIF-8 surface with high atom efficiency while maintaining the ZIF-8 structure through a wet-impregnation and calcination process. It is suggested that the surface sites and microporosity of ZIF-8 support provide an adequate environment for the initial deposition of Mg precursor and subsequent growth of MgO nanoparticles through a nanoconfinement effect. MgO@ZIF-8 catalysts were tested for catalytic transesterification of glycerol and dimethyl carbonate to yield glycerol carbonate. It is found that the 50 wt% MgO@ZIF-8 catalyst display an improved catalytic activity than those of MgO and ZIF-8. Furthermore, the MgO@ZIF-8 catalysts showed higher catalytic activities than their physically-mixed counterparts, indicative of a synergistic effect between MgO and ZIF-8, which is explained by a proposed mechanism based on acid-base bifunctional sites on the surface.
Observation and simulation of hydrogen storage via spillover
(2018-09-01)
Wang, Cheng-Yu
;
Chang, Cheng-Wei
;
Wu, Yi-Ju
;
Lueking, Angela D.
;
材料科學與工程學系
Hydrogen spillover refers to catalytic dissociation of hydrogen molecules followed by surface diffusion to the catalytic support. This mechanism has been proposed as a means to initiate hydrogen storage at ambient temperature. When catalytic dissociation of hydrogen is used to initiate room temperature hydrogen storage, this initiates weak chemisorption. High variations in experimental uptake, combined with theoretical calculations that are inconsistent with this mechanism, have made this concept controversial. Here, we review hydrogen uptake in porous carbon and metal-organic frameworks (MOFs), with emphasis on spectroscopic evidence of atomic hydrogen bound to the surface and resolution of discrepancies between experimental and theoretical studies. We conclude with a perspective of hydrogen spillover for future material design, hydrogen storage, and fundamental understanding of a process that is crucial for adsorption and catalysis.
RiboSW - a web server for identifying RNA riboswitches
(2009)
Chang, Tzu-Hao
;
Wu, Li-Ching
;
Yeh, Chi-Ta
;
Chang, Cheng-Wei
;
Liu, Baw-Jhiune
Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://bioinfo.csie.ncu.edu.tw/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence. The supplementary data is available on the web at http://bioinfo.csie.ncu.edu.tw/RiboSW/sup.pdf.