Browsing by Author "Chen, Chih-Chieh"

Now showing 1 - 17 of 17

Characteristics and prevalence of KRAS, BRAF, and PIK3CA mutations in colorectal cancer by high-resolution melting analysis in Taiwanese population
(2012-10-09)
Hsieh, Li-Ling
;
Er, Tze-Kiong
;
Chen, Chih-Chieh
;
Hsieh, Jan-Sing
;
Chang, Jan-Gowth
Background: The identification of KRAS, BRAF, and PIK3CA mutations before the administration of anti-epidermal growth factor receptor therapy of colorectal cancer has become important The aim of the present study was to investigate the occurrence of KRAS, BRAF, and PIK3CA mutations in the Taiwanese population with colorectal cancer. This study was undertaken to identify BRAF and PIK3CA mutations in patients with colorectal cancer by high-resolution melting (HRM) analysis. HRM analysis is a new gene scan tool that quickly performs the PCR and identifies sequence alterations without requiring post-PCR treatment Methods: In the present study, DNAs were extracted from 182 cases of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer samples for clinical KRAS mutational analysis by direct sequencing. All the samples were also tested for mutations within BRAF V600E and PIK3CA (exons 9 and 20) by HRM analysis. Results: The results were confirmed by direct sequencing. The frequency of BRAF and PIK3CA mutations is 1.1%, and 7.1%, respectively. Intriguingly, we found that nine patients (4.9%) with the KRAS mutation were coexistent with the PIK3CA mutation. Four patients (22%) without the KRAS mutation were existent with the PIK3CA mutation. Two patients (1.1%) without the KRAS mutation were existent with the BRAF mutation. Conclusions: In the current study, we suppose that HRM analysis is rapid, feasible, and powerful diagnostic tool for the detection of BRAF and PIK3CA mutations in a clinical setting. Additionally, our results indicated the prevalence of KRAS. BRAF, and PIK3C4 mutational status in the Taiwanese population. (C) 2012 Elsevier B.V. All rights reserved.
Clinical relevance of KRAS mutations in codon 13: Where are we?
(2014-02-01)
Er, Tze-Kiong
;
Chen, Chih-Chieh
;
Bujanda, Luis
;
Herreros-Villanueva, Marta
;
生物資訊及系統生物研究所
Recent advances in molecular diagnosis and the trend towards personalized medicine have made colorectal cancer one of the tumors where therapies have significantly improved patient survival after metastasis development. KRAS mutations in codon 12 and 13 are recognized biomarkers that are analyzed in clinic previously for anti-EGFR therapies administration. Since originally mutations in both codons were considered as a predictor of lack of response to cetuximab or panitumumab, the European Medicines Agency and the US Food and Drug Administration suggested that patients harboring any of those mutations should be excluded from the treatment. However, subsequent retrospective analysis has shown that mutations in codon 12 and codon 13 of KRAS gene could be different in their biological characteristics and as a result could confer variable effects in patients. In addition and increasing and sometimes contradictory number of solutions have been published demonstrating that patients with mutations in codon 13 could have worse outcome but could obtain a significant clinical benefit from anti-EGFR therapies. Here, we review and update the latest data on the biological role leading to a predictive outcome and benefit from anti-EGFR antibodies in patients with specific KRAS mutations in codon 13. (C) 2013 Elsevier Ireland Ltd. All rights reserved.
Clinical relevance of KRAS mutations in codon 13: Where are we? (vol 343, pg 1, 2013)
(2014-07-10)
Er, Tze-Kiong
;
Chen, Chih-Chieh
;
Bujanda, Luis
;
Herreros-Villanueva, Marta
;
生物資訊及系統生物研究所
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif
(2011-10-21)
Er, Tze-Kiong
;
Chen, Chih-Chieh
;
Liu, Yen-Yi
;
Chang, Hui-Chiu
;
Chien, Yin-Hsiu
Background: Multiple acyl-coenzyme A dehydrogenase deficiency (MADD) is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene, encoding electron transfer flavoprotein: ubiquinone oxidoreductase (ETF:QO) have been reported to be the major causes of riboflavin-responsive MADD. To date, no studies have been performed to explore the functional impact of these mutations or their mechanism of disrupting enzyme activity. Results: High resolution melting (HRM) analysis and sequencing of the entire ETFDH gene revealed a novel mutation (p.Phe128Ser) and the hotspot mutation (p.Ala84Thr) from a patient with MADD. According to the predicted 3D structure of ETF: QO, the two mutations are located within the flavin adenine dinucleotide (FAD) binding domain; however, the two residues do not have direct interactions with the FAD ligand. Using molecular dynamics (MD) simulations and normal mode analysis (NMA), we found that the p. Ala84Thr and p.Phe128Ser mutations are most likely to alter the protein structure near the FAD binding site as well as disrupt the stability of the FAD binding required for the activation of ETF: QO. Intriguingly, NMA revealed that several reported disease-causing mutations in the ETF: QO protein show highly correlated motions with the FAD-binding site. Conclusions: Based on the present findings, we conclude that the changes made to the amino acids in ETF: QO are likely to influence the FAD-binding stability.
Computational Analysis of KRAS Mutations: Implications for Different Effects on the KRAS p.G12D and p.G13D Mutations
(2013-02-20)
Chen, Chih-Chieh
;
Er, Tze-Kiong
;
Liu, Yen-Yi
;
Hwang, Jenn-Kang
;
Jesus Barrio, Maria
Background: The issue of whether patients diagnosed with metastatic colorectal cancer who harbor KRAS codon 13 mutations could benefit from the addition of anti-epidermal growth factor receptor therapy remains under debate. The aim of the current study was to perform computational analysis to investigate the structural implications of the underlying mutations caused by c.38G>A (p.G13D) on protein conformation. Methods: Molecular dynamics (MD) simulations were performed to understand the plausible structural and dynamical implications caused by c.35G>A (p.G12D) and c.38G>A (p.G13D). The potential of mean force (PMF) simulations were carried out to determine the free energy profiles of the binding processes of GTP interacting with wild-type (WT) KRAS and its mutants (MT). Results: Using MD simulations, we observed that the root mean square deviation (RMSD) increased as a function of time for the MT c.35G>A (p.G12D) and MT c.38G>A (p.G13D) when compared with the WT. We also observed that the GTP-binding pocket in the c.35G>A (p.G12D) mutant is more open than that of the WT and the c.38G>A (p.G13D) proteins. Intriguingly, the analysis of atomic fluctuations and free energy profiles revealed that the mutation of c.35G>A (p.G12D) may induce additional fluctuations in the sensitive sites (P-loop, switch I and II regions). Such fluctuations may promote instability in these protein regions and hamper GTP binding. Conclusions: Taken together with the results obtained from MD and PMF simulations, the present findings implicate fluctuations at the sensitive sites (P-loop, switch I and II regions). Our findings revealed that KRAS mutations in codon 13 have similar behavior as KRAS WT. To gain a better insight into why patients with metastatic colorectal cancer (mCRC) and the KRAS c.38G>A (p.G13D) mutation appear to benefit from anti-EGFR therapy, the role of the KRAS c.38G>A (p.G13D) mutation in mCRC needs to be further investigated.
Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters
(2013-04-10)
Liu, Yen-Yi
;
Shih, Chien-Hua
;
Hwang, Jenn-Kang
;
Chen, Chih-Chieh
;
生物資訊及系統生物研究所
Dynamic information in proteins may provide valuable information for understanding allosteric regulation of protein complexes or long-range effects of the mutations on enzyme activity. Experimental data such as X-ray B-factors or NMR order parameters provide a convenient estimate of atomic fluctuations (or atomic auto-correlated motions) in proteins. However, it is not as straightforward to obtain atomic cross-correlated motions in proteins - one usually resorts to more sophisticated computational methods such as Molecular Dynamics, normal mode analysis or atomic network models. In this report, we show that atomic cross-correlations can be reliably obtained directly from protein structure using X-ray refinement data. We have derived an analytic form of atomic correlated motions in terms of the original MS parameters used to refine the B-factors of X-ray structures. The correlated maps computed using this equation are well correlated with those of the method based on a mechanical model (the correlation coefficient is 0.75) for a non-homologous dataset comprising 100 structures. We have developed an approach to compute atomic cross-correlations directly from X-ray protein structure. Being in analytic form, it is fast and provides a feasible way to compute correlated motions in proteins in a high throughput way. In addition, avoiding sophisticated computational operations; it provides a quick, reliable way, especially for non-computational biologists, to obtain dynamics information directly from protein structure relevant to its function. (c) 2012 Elsevier B.V. All rights reserved.
Detecting Amplification Attacks with Software Defined Networking
(2017-01-01)
Chen, Chih-Chieh
;
Chen, Yi-Ren
;
Lu, Wei-Chih
;
Tsai, Shi-Chun
;
Yang, Ming-Chuan
Distributed denial of service (DDoS) is an attack that attempts to disrupt network service for various malicious purposes. It makes use of public services as reflectors to amplify the traffic, and thus called distributed reflection denial of service attacks. This type of attack forges source IP address, and makes it hard to filter the problematic packets. With Software Defined Networking (SDN) and machine learning techniques, we implement a system to detect DRDoS packets and block the amplification attacks automatically. DNS and NTP amplifications are two typical attacks of DDoS. By analyzing the traffic features, although our classifier is trained only for the DNS amplification attack, our system can identify and then block both DNS and NTP amplification attacks with great accuracy.
Development of a feasible assay for the detection of GAA mutations in patients with Pompe disease
(2014-02-15)
Er, Tze-Kiong
;
Chen, Chih-Chieh
;
Chien, Yin-Hsiu
;
Liang, Wen-Chen
;
Kan, Tzu-Min
Background: Pompe disease is an inherited autosomal recessive deficiency of acid alpha-glucosidase (GAA) and is due to pathogenic sequence variants in the corresponding GM gene. While the analysis of enzyme activity remains the diagnostic test of choice for individuals with Pompe disease, mutation analysis remains for establishing a definitive diagnosis. Methods: High resolution melting (HRM) analysis was performed to screen GM mutations. Genomic DNA was extracted from peripheral blood samples of the two patients with Pompe disease and 250 normal controls. Exons 2 through 20 of the GM gene were screened by the HEM analysis. The results were subsequently confirmed by direct sequencing. Results: This assay proved to be feasible in detecting seven known (c2T>C, c.1726G>A, c.1845G>A, c.1935C>A, c.1958C>A, c.2238G>C, and c2815_2816del) GM mutations. Each mutation could be readily and accurately identified in the difference plot curves. We estimated the carrier frequency of the most common mutation, c.1935G>A (p.D645E), in the Taiwanese population to be 02%. Conclusions: In clinical practice, we suggest that HEM analysis is assumed as a fast and reliable method for screening GM gene mutations especially the most common mutations which are responsible for Pompe disease among the Taiwanese populations. (C) 2013 Elsevier B.V. All rights reserved.
Forwarding Path Discovery with Software Defined Networking
(2017-01-01)
Chen, Chih-Chieh
;
Chen, Yi-Ren
;
Tsai, Shi-Chun
;
Yang, Ming-Chuan
;
資訊工程學系
Without STP and LLDP, we propose a new approach to find faster paths between the source and the destination and fully utilize the links between switches under the Software Defined Network paradigm. To find round-trip path with lighter load, we design a mechanism to compose special ARP packets for exploring the routing path and avoid broadcast storm by dropping late or duplicate packets. Meanwhile, the controller can carefully regulate other packets without affecting the behavior of the special packets. The evaluation results with the Clos-like network topology show that our approach can be used to improve the performance of transmission throughput. We believe our method is very suitable, especially, for a dynamic network environment, where links are up and down frequently. Our implementation can be seen as an instance showing the flexibility of SDN.
From electrostatic precipitation to nanoparticle generation
(2012-09-01)
Lin, Chih-Wei
;
Huang, Sheng-Hsiu
;
Kuo, Yu-Mei
;
Chang, Kuang-Nan
;
Wu, Chong-Sin
This work demonstrated that an electrostatic precipitator (ESP), originally designed for dust collection, could become a nanoparticle generator under specific operating conditions. A lab-scale wire-plate positive ESP was built for measuring aerosol penetration and generation rate. The carrier air was filtered by activated charcoal, silica gel and HEPA filters to remove potential contaminants. The data, obtained in both power-on and power-off modes, were utilized to calculate penetration and generation rate of aerosol. The results showed that air temperature appeared to have a strong effect on ESP nanoparticle generation. At temperature above 37 C and flow rate below 9 L/min, the nanoparticle penetration of ESP exceeded 100%, indicating that the ESP was generating aerosol particles. Sputtering on the corona discharger appeared to be the key mechanism of aerosol generation. The ozone concentration increased with increasing corona current. The ESP reached a maximum number concentration at the electric field strength of 4.8 kV/cm when the air flow and temperature were fixed at 6 L/min and 40 C, respectively. The particle size ranged from 5 to 40 nm, with a mode around 12 nm. Elementary components of the discharge wire were detected on the filter samples collected downstream the ESP and ground plates, indicating that nanoparticles were generated from the discharge wire. (C) 2012 Elsevier Ltd. All rights reserved.
From electrostatic precipitation to nanoparticle generation (vol 51, pg 57, 2012)
(2012-10-01)
Lin, Chih-Wei
;
Huang, Sheng-Hsiu
;
Kuo, Yu-Mei
;
Chang, Kuang-Nan
;
Wu, Chong-Sin
ID-Free Multigroup Cardinality Estimation for Massive RFID Tags in IoT
(2019-01-01)
Lee, Tsu-Kuang
;
Chen, Chih-Chieh
;
Ren, Yi
;
Lin, Cheng-Kuan
;
Tseng, Yu-Chee
The Internet of Things (IoT) has become the hottest in both the research community and industry. Among them, Radio Frequency Identification (RFID) plays a key role in IoT. On the RFID tags estimation problem, most existing researches are trying to identifying tags' ID rather than counting the number of tags. But the number of tags is useful information in many applications such as stock management and traffic flow management. Massive tags cause taking a lot of cost and time in the estimate. So an essential problem is how to quickly and accurately estimate the number of massive tags. In order to solve this problem, this paper proposes an accuracy and efficiency hybrid scheme by decreasing time and space complexity. The results of simulation conducted to test the effectiveness of the proposed approach, which matches well with the theoretical analytical model.
IDENTIFICATION A NOVEL MISSENSE MUTATION P.F128S IN A TAIWANESE PATIENT WITH RIBOFLAVIN-RESPONSIVE MULTIPLE ACYL-COA DEHYDROGENASE DEFIENCY
(2011-05-01)
Er, Tze-Kiong
;
Liang, Wen-Chen
;
Chen, Chih-Chieh
;
Liu, Ta-Chi
;
Chang, Jan-Gowth
pKNOT v.2: the protein KNOT web server
(2012-07-01)
Lai, Yan-Long
;
Chen, Chih-Chieh
;
Hwang, Jenn-Kang
;
生物資訊及系統生物研究所
;
Institude of Bioinformatics and Systems Biology
"Knotted proteins have recently received lots of attention due to their interesting topological novelty as well as its puzzling folding mechanisms. We previously published a pKNOT server, which provides a structural database of knotted proteins, analysis tools for detecting and analyzing knotted regions from structures as well as a Java-based 3D graphics viewer for visualizing knotted structures. However, there lacks a convenient platform performing similar tasks directly from 'protein sequences'. In the current version of the web server, referred to as pKNOT v.2, we implement a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or Protein Data Bank (PDB) IDs and return knot analysis. In addition, we have updated the database of knotted proteins from the current PDB with a combination of automatic and manual procedure. We believe that the updated pKNOT server with its extended functionalities will provide better service to biologists interested in the research of knotted proteins. The pKNOT v.2 is available from http://pknot.life.nctu.edu.tw/."
(PS)(2)-v2: template-based protein structure prediction server
(2009-10-31)
Chen, Chih-Chieh
;
Hwang, Jenn-Kang
;
Yang, Jinn-Moon
;
生物科技學系
;
生物資訊及系統生物研究所
Background: Template selection and target-template alignment are critical steps for template-based modeling (TBM) methods. To identify the template for the twilight zone of 15 similar to 25% sequence similarity between targets and templates is still difficulty for template-based protein structure prediction. This study presents the (PS)(2)-v2 server, based on our original server with numerous enhancements and modifications, to improve reliability and applicability. Results: To detect homologous proteins with remote similarity, the (PS)(2)-v2 server utilizes the S2A2 matrix, which is a 60 x 60 substitution matrix using the secondary structure propensities of 20 amino acids, and the position-specific sequence profile (PSSM) generated by PSI-BLAST. In addition, our server uses multiple templates and multiple models to build and assess models. Our method was evaluated on the Lindahl benchmark for fold recognition and ProSup benchmark for sequence alignment. Evaluation results indicated that our method outperforms sequence-profile approaches, and had comparable performance to that of structure-based methods on these benchmarks. Finally, we tested our method using the 154 TBM targets of the CASP8 (Critical Assessment of Techniques for Protein Structure Prediction) dataset. Experimental results show that (PS)(2)-v2 is ranked 6(th) among 72 severs and is faster than the top-rank five serves, which utilize ab initio methods. Conclusion: Experimental results demonstrate that (PS)(2)-v2 with the S2A2 matrix is useful for template selections and target-template alignments by blending the amino acid and structural propensities. The multiple-template and multiple-model strategies are able to significantly improve the accuracies for target-template alignments in the twilight zone. We believe that this server is useful in structure prediction and modeling, especially in detecting homologous templates with sequence similarity in the twilight zone.
(PS)(2): protein structure prediction server
(2006-07-01)
Chen, Chih-Chieh
;
Hwang, Jenn-Kang
;
Yang, Jinn-Moon
;
生物科技學系
;
生物資訊及系統生物研究所
Protein structure prediction provides valuable insights into function, and comparative modeling is one of the most reliable methods to predict 3D structures directly from amino acid sequences. However, critical problems arise during the selection of the correct templates and the alignment of query sequences therewith. We have developed an automatic protein structure prediction server, (PS)(2), which uses an effective consensus strategy both in template selection, which combines PSI-BLAST and IMPALA, and target-template alignment integrating PSI-BLAST, IMPALA and T-Coffee. (PS)(2) was evaluated for 47 comparative modeling targets in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction). For the benchmark dataset, the predictive performance of (PS)(2), based on the mean GTD_TS score, was superior to 10 other automatic servers. Our method is based solely on the consensus sequence and thus is considerably faster than other methods that rely on the additional structural consensus of templates. Our results show that (PS)(2), coupled with suitable consensus strategies and anew similarity score, can significantly improve structure prediction. Our approach should be useful in structure prediction and modeling. The (PS)(2) is available through the website at http://ps2.life.nctu.edu.tw/.
(PS)(2): protein structure prediction server version 3.0
(2015-07-01)
Huang, Tsun-Tsao
;
Hwang, Jenn-Kang
;
Chen, Chu-Huang
;
Chu, Chih-Sheng
;
Lee, Chi-Wen
Protein complexes are involved in many biological processes. Examining coupling between subunits of a complexwould be useful to understand themolecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/.