Browsing by Author "Chen, Yu-Ching"

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Colorimetric detection of Al3+ ions using triazole-ether functionalized gold nanoparticles
(2013-12-15)
Chen, Yu-Ching
;
Lee, I-Lin
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Sung, Yi-Ming
;
Wu, Shu-Pao
;
應用化學系
A sensitive, selective colorimetric Al3+ detection method has been developed by using triazole-ether functionalized gold nanoparticles (TTP-AuNPs). Gold nanoparticles were prepared by reducing HAuCl4 with sodium borohydride in the presence of 5-(1,2-dithiolan-3-yl)-N-(prop-2-yn-1-yl)pentanamide (TP). The azide part of 2-[2-(2-azidoethoxy)ethoxy]ethanol and the acetylene part of TP were combined to form a triazole structure through a click reaction. Aggregation of TTP-AuNPs was induced immediately in the presence of Al3+ ions, yielding a color change from red to blue. This Al3+-induced aggregation of TTP-AuNPs was monitored first with the naked eye and then UV-vis spectroscopy with a detection limit of 18.0 nM. The TTP-AuNPs showed excellent selectivity for Al3+, compared to other metal ions (Ag+, Ca2+, Cd2+, Co2+, Cu2+, Cr3+, Fe2+, Fe3+, Hg2+, Mg2+, Mn2+, Ni2+, Pb2+, and Zn2+). In addition, TTP-AuNPs were used to detect Al3+ in sea water samples, with low interference. (C) 2013 Elsevier B.V. All rights reserved.
Decentralized stabilization of H-infinity fuzzy control for nonlinear multiple time-delay interconnected systems
(2007-03-01)
Hsiao, Feng-Hsiag
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Xu, Sheng-Dong
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Lin, Chia-Yen
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Chou, Yu-Jun
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Chen, Yu-Ching
A robustness design of H infinity fuzzy control is proposed in this paper to overcome the effect of modeling errors between nonlinear multiple time-delay systems and fuzzy models. In terms of Lyapunov's direct method, a stability criterion is derived to guarantee the UUB (uniformly ultimately bounded) stability of nonlinear multiple time-delay interconnected systems with disturbances. Based on this criterion and the decentralized control scheme, a set of fuzzy controllers is then synthesized via the technique of parallel distributed compensation (PDC) to stabilize the nonlinear multiple time-delay interconnected systems and the H infinity control performance is achieved in the mean time.
Decentralized stabilization of Nonlinear multiple time-delay interconnected systems via h-infinity fuzzy control
(2006)
Hsiao, Feng-Hsiag
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Xu, Sheng-Dong
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Lin, Chia-Yen
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Chou, Yu-Jun
;
Chen, Yu-Ching
A robustness design of H-infinity fuzzy control is proposed in this paper to overcome the effect of modeling error between nonlinear multiple time-delay systems and fuzzy models. In terms of Lyapunov\'s direct method, a stability criterion is hence derived to guarantee the UUB (uniformly ultimately bounded) stability of nonlinear multiple time-delay interconnected systems with disturbances. Based on this criterion and the decentralized control scheme, a set of fuzzy controllers is then synthesized via the technique of parallel distributed compensation (PDC) to stabilize the nonlinear multiple time-delay interconnected systems and the H-infinity control performance is achieved in the mean time.
Integration of Refined Composite Multiscale Cross-Sample Entropy and Backpropagation Neural Networks for Structural Health Monitoring
(2020-02-01)
Lin, Tzu-Kang
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Chen, Yu-Ching
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土木工程學系
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Department of Civil Engineering
This study developed a structural health monitoring (SHM) system based on refined composite multiscale cross-sample entropy (RCMCSE) and an artificial neural network for monitoring structures under ambient vibrations. RCMCSE was applied to enhance the reliability of entropy estimations. First, RCMCSE was implemented to extract damage features, and finite element analysis software was then used to generate training samples, which included stiffness reductions to achieve various damage patterns. A neural network model was constructed and trained using entropy values for these damage patterns. An experiment was conducted on a seven-story steel benchmark structure to validate the performance of the proposed system. Additionally, a confusion matrix was established to evaluate the performance of the proposed system. The results obtained for a scaled-down benchmark structure indicated that 89.8% of the floors were accurately classified, and 90% of the practical damaged floors were correctly diagnosed. The performance evaluation demonstrated that the proposed SHM system exhibited increased damage location accuracy.
Predicting disulfide connectivity patterns
(2007-05-01)
Lu, Chih-Hao
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Chen, Yu-Ching
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Yu, Chin-Sheng
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Hwang, Jenn-Kang
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生物資訊及系統生物研究所
Disulfide bonds play an important role in stabilizing protein structure and regulating protein function. Therefore, the ability to infer disulfide connectivity from protein sequences will be valuable in structural modeling and functional analysis. However, to predict disulfide connectivity directly from sequences presents a challenge to computational biologists due to the nonlocal nature of disulfide bonds, i.e., the close spatial proximity of the cysteine pair that forms the disulfide bond does not necessarily imply the short sequence separation of the cysteine residues. Recently, Chen and Hwang (Proteins 2005;61:507-512) treated this problem as a multiple class classification by defining each distinct disulfide pattern as a class. They used multiple support vector machines based on a variety of sequence features to predict the disulfide patterns. Their results compare favorably with those in the literature for a benchmark dataset sharing less than 30% sequence identity. However, since the number of disulfide patterns grows rapidly when the number of disulfide bonds increases, their method performs unsatisfactorily for the cases of large number of disulfide bonds. In this work, we propose a novel method to represent disulfide connectivity in terms of cysteine pairs, instead of disulfide patterns. Since the number of bonding states of the cysteine pairs is independent of that of disulfide bonds, the problem of class explosion is avoided. The bonding states of the cysteine pairs are predicted using the support vector machines together with the genetic algorithm optimization for feature selection. The complete disulfide patterns are then determined from the connectivity matrices that are constructed from the predicted bonding states of the cysteine pairs. Our approach outperforms the current approaches in the literature.
Prediction of protein subcellular localization
(2006-08-15)
Yu, Chin-Sheng
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Chen, Yu-Ching
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Lu, Chih-Hao
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Hwang, Jenn-Kang
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生物科技學系
Because the protein's function is usually related to its subcellular localization, the ability to predict subcellular localization directly from protein sequences will be useful for inferring protein functions. Recent years have seen a surging interest in the development of novel computational tools to predict subcellular localization. At present, these approaches, based on a wide range of algorithms, have achieved varying degrees of success for specific organisms and for certain localization categories. A number of authors have noticed that sequence similarity is useful in predicting subcellular localization. For example, Nair and Rost (Protein Sci 2002;11:2836-2847) have carried out extensive analysis of the relation between sequence similarity and identity in subcellular localization, and have found a close relationship between them above a certain similarity threshold. However, many existing benchmark data sets used for the prediction accuracy assessment contain highly homologous sequences-some data sets comprising sequences up to 80-90% sequence identity. Using these benchmark test data will surely lead to overestimation of the performance of the methods considered. Here, we develop an approach based on a two-level support vector machine (SVM) system: the first level comprises a number of SVM classifiers, each based on a specific type of feature vectors derived from sequences; the second level SVM classifier functions as the jury machine to generate the probability distribution of decisions for possible localizations. We compare our approach with a global sequence alignment approach and other existing approaches for two benchmark data sets-one comprising prokaryotic sequences and the other eukaryotic sequences. Furthermore, we carried out all-against-all sequence alignment for several data sets to investigate the relationship between sequence homology and subcellular localization. Our results, which are consistent with previous studies, indicate that the homology search approach performs well down to 30% sequence identity, although its performance deteriorates considerably for sequences sharing lower sequence identity. A data set of high homology levels will undoubtedly lead to biased assessment of the performances of the predictive approaches-especially those relying on homology search or sequence annotations. Our two-level classification system based on SVM does not rely on homology search; therefore, its performance remains relatively unaffected by sequence homology. When compared with other approaches, our approach performed significantly better. Furthermore, we also develop a practical hybrid method, which combines the two-level SVM classifier and the homology search method, as a general tool for the sequence annotation of subcellular localization.
Purification, crystallization and preliminary X-ray analysis of a thermostable direct haemolysin from Grimontia hollisae
(2011-02-01)
Wang, Yu-Kuo
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Huang, Sheng-Cih
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Wu, Yi-Fang
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Chen, Yu-Ching
;
Chen, Wen-Hung
Vibrio hollisae, a halophilic species recently reclassified as Grimontia hollisae, is a causative agent of gastroenteritis and septicaemia. One important pathogenic Vibrio factor, thermostable direct haemolysin (TDH), has been purified and crystallized in two crystal forms using the vapour-diffusion method. The crystals belonged to an orthorhombic space group, with unit-cell parameters a = 104.8, b = 112.4, c = 61.3 angstrom and a = 122.9, b = 123.3, c = 89.8 angstrom. The crystals contained either four or eight molecules per asymmetric unit, with predicted solvent contents of 49.4 and 46.3% and Matthews coefficients (V(M)) of 2.4 and 2.3 angstrom(3) Da(-1), respectively. These crystals were suitable for structure determination, which would yield structural details related to the cytotoxicity and oligomeric structure of this pore-forming toxin.
Purification, crystallization and preliminary X-ray crystallographic analysis of xylose reductase from Candida tropicalis
(2009-04-01)
Chen, Li-Chun
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Huang, Sheng-Cih
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Chuankhayan, Phimonphan
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Chen, Chung-Der
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Huang, Yen-Chieh
Xylose reductase (XR), which requires NADPH as a co-substrate, catalyzes the reduction of D-xylose to xylitol, which is the first step in the metabolism of D-xylose. The detailed three-dimensional structure of XR will provide a better understanding of the biological significance of XR in the efficient production of xylitol from biomass. XR of molecular mass 36.6 kDa from Candida tropicalis was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data from C. tropicalis XR crystals at 2.91 angstrom resolution, the unit cell belongs to space group P3(1) or P3(2). Preliminary analysis indicated the presence of four XR molecules in the asymmetric unit, with 68.0% solvent content.
Role of the cAMP-Dependent Carbon Catabolite Repression in Capsular Polysaccharide Biosynthesis in Klebsiella pneumoniae
(2013-02-11)
Lin, Ching-Ting
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Chen, Yu-Ching
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Jinn, Tzyy-Rong
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Wu, Chien-Chen
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Hong, Yi-Ming
K. pneumoniae is the predominant pathogen isolated from liver abscesses of diabetic patients in Asian countries. Although elevated blood glucose levels cause various immune problems, its effects on K. pneumoniae virulence are unknown. This study investigated the regulation of capsular polysaccharide (CPS) biosynthesis, a major determinant for K. pneumoniae virulence, in response to exogenous glucose. We found that K. pneumoniae produce more CPS in glucose-rich medium via reduction in cyclic AMP (cAMP) levels. Individual deletion of cyaA or crp, which respectively encode adenylate cyclase and cAMP receptor protein in K. pneumoniae, markedly increased CPS production, while deletion of cpdA, which encodes cAMP phosphodiesterase, decreased CPS production. These results indicate that K. pneumoniae CPS biosynthesis is controlled by the cAMP-dependent carbon catabolite repression (CCR). To investigate the underlying mechanism, quantitative real-time PCR and promoter-reporter assays were used to verify that the transcription of CPS biosynthesis genes, which are organized into 3 transcription units (orf1-2, orf3-15, and orf16-17), were activated by the deletion of crp. Sequence analysis revealed putative CRP binding sites located on Porf3-15 and Porf16-17, suggesting direct CRP-cAMP regulation on the promoters. These results were then confirmed by electrophoretic mobility shift assay. In addition, we found putative CRP binding sites located in the promoter region of rcsA, which encodes a cps transcriptional activator, demonstrating a direct repression of CRP-cAMP and P-rcsA. The deletion of rcsA in mutation of crp partially reduced CPS biosynthesis and the transcription of orf1-2 but not of orf3-15 or orf16-17. These results suggest that RcsA participates in the CRP-cAMP regulation of orf1-2 transcription and influences CPS biosynthesis. Finally, the effect of glucose and CCR proteins on CPS biosynthesis also reflects bacterial resistance to serum killing. We here provide evidence that K. pneumoniae increases CPS biosynthesis for successful infection in response to exogenous glucose via cAMP-dependent CCR.
Site-Directed Mutations of Thermostable Direct Hemolysin from Grimontia hollisae Alter Its Arrhenius Effect and Biophysical Properties
(2011)
Wang, Yu-Kuo
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Huang, Sheng-Cih
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Wu, Yi-Fang
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Chen, Yu-Ching
;
Lin, Yen-Ling
Recombinant thermostable direct hemolysin from Grimontia hollisae (Gh-rTDH) exhibits paradoxical Arrhenius effect, where the hemolytic activity is inactivated by heating at 60 degrees C but is reactivated by additional heating above 80 degrees C. This study investigated individual or collective mutational effect of Tyr53, Thr59, and Ser63 positions of Gh-rTDH on hemolytic activity, Arrhenius effect, and biophysical properties. In contrast to the Gh-rTDH wild-type (Gh-rTDH(WT)) protein, a 2-fold decrease of hemolytic activity and alteration of Arrhenius effect could be detected from the Gh-rTDH(Y53H/T59I) and Gh-rTDH(T59I/S63T) double-mutants and the Gh-rTDH(Y53H/T59I/S63T) triple-mutant. Differential scanning calorimetry results showed that the Arrhenius effect-loss and -retaining mutants consistently exhibited higher and lower endothermic transition temperatures, respectively, than that of the Gh-rTDHWT. Circular dichroism measurements of Gh-rTDH(WT) and Gh-rTDH(mut) showed a conspicuous change from a beta-sheet to alpha-helix structure around the endothermic transition temperature. Consistent with the observation is the conformational change of the proteins from native globular form into fibrillar form, as determined by Congo red experiments and transmission electron microscopy.
Triazole functionalized gold nanoparticles for colorimetric Cr+ sensing
(2013-11-01)
Chen, Yu-Ching
;
Lee, I-Lin
;
Sung, Yi-Ming
;
Wu, Shu-Pao
;
應用化學系
Triazole functionalized gold nanoparticles (NTP@AuNPs) were synthesized through a click reaction and have been developed for sensitive and selective colorimetric Cr3+ detection. Gold nanoparticles were prepared by reducing HAuCl4 with sodium citrate and then using 4-(prop-2-ynyloxy)pyridine (PP) as the capping agent. The acetylene part of PP and the azide part of 1-(azidomethyl)-4-nitrobenzene were combined to form a triazole structure through a click reaction. Aggregation of NTP@AuNPs was induced immediately in the presence of Cr3+ ions, yielding a color change from red to purple. This Cr3+-induced aggregation of NTP@AuNPs was first monitored using the naked eye and then UV-vis spectroscopy with a detection limit of 1.4 mu M. In addition, NTP@AuNPs were also used to detect Cr3+ in lake water samples, with low interference. (C) 2013 Elsevier B.V. All rights reserved.