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11.
Chien-Hsun Huang Min-Gang Su Hui-Ju Kao Jhih-Hua Jhong Shun-Long Weng Tzong-Yi Lee 《BMC systems biology》2016,10(Z1):S6
Background
The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process – E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes. This ubiquitin-conjugation process typically binds the last amino acid of ubiquitin (glycine 76) to a lysine residue of a target protein. The high-throughput of mass spectrometry-based proteomics has stimulated a large-scale identification of ubiquitin-conjugated peptides. Hence, a new web resource, UbiSite, was developed to identify ubiquitin-conjugation site on lysines based on large-scale proteome dataset.Results
Given a total of 37,647 ubiquitin-conjugated proteins, including 128026 ubiquitylated peptides, obtained from various resources, this study carries out a large-scale investigation on ubiquitin-conjugation sites based on sequenced and structural characteristics. A TwoSampleLogo reveals that a significant depletion of histidine (H), arginine (R) and cysteine (C) residues around ubiquitylation sites may impact the conjugation of ubiquitins in closed three-dimensional environments. Based on the large-scale ubiquitylation dataset, a motif discovery tool, MDDLogo, has been adopted to characterize the potential substrate motifs for ubiquitin conjugation. Not only are single features such as amino acid composition (AAC), positional weighted matrix (PWM), position-specific scoring matrix (PSSM) and solvent-accessible surface area (SASA) considered, but also the effectiveness of incorporating MDDLogo-identified substrate motifs into a two-layered prediction model is taken into account. Evaluation by five-fold cross-validation showed that PSSM is the best feature in discriminating between ubiquitylation and non-ubiquitylation sites, based on support vector machine (SVM). Additionally, the two-layered SVM model integrating MDDLogo-identified substrate motifs could obtain a promising accuracy and the Matthews Correlation Coefficient (MCC) at 81.06 % and 0.586, respectively. Furthermore, the independent testing showed that the two-layered SVM model could outperform other prediction tools, reaching at 85.10 % sensitivity, 69.69 % specificity, 73.69 % accuracy and the 0.483 of MCC value.Conclusion
The independent testing result indicated the effectiveness of incorporating MDDLogo-identified motifs into the prediction of ubiquitylation sites. In order to provide meaningful assistance to researchers interested in large-scale ubiquitinome data, the two-layered SVM model has been implemented onto a web-based system (UbiSite), which is freely available at http://csb.cse.yzu.edu.tw/UbiSite/. Two cases given in the UbiSite provide a demonstration of effective identification of ubiquitylation sites with reference to substrate motifs.12.
温度对普通小球藻和鱼腥藻生长竞争的影响 总被引:1,自引:0,他引:1
通过室内实验研究了不同温度条件下主要水华藻类鱼腥藻(Anabaena sp. strain PCC)和常见淡水藻类普通小球藻(Chlorella vulgaris)的生长和种间竞争, 结果表明在单种培养和共同培养体系中, 普通小球藻的最大藻细胞浓度随着温度的升高而增加; 鱼腥藻生长最适温度为3035℃。温度对藻类种间竞争抑制参数能够产生明显影响, 鱼腥藻在温度为15℃时对普通小球藻的竞争抑制参数最大, 分别是25℃、30℃、35℃时的1.24倍、1.14倍和1.12倍; 而普通小球藻在30℃时对鱼腥藻的竞争抑制参数最大, 分别是15℃、25℃、35℃条件下的4.25倍、2.03倍和1.20倍。在4个试验温度下普通小球藻对鱼腥藻的竞争抑制参数均大于鱼腥藻对普通小球藻的竞争抑制参数。根据Lotka-Volterra竞争模型可推断, 在4个温度条件下, 普通小球藻和鱼腥藻在竞争中不稳定共存。
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13.
Shun-Long Weng Kai-Yao Huang Fergie Joanda Kaunang Chien-Hsun Huang Hui-Ju Kao Tzu-Hao Chang Hsin-Yao Wang Jang-Jih Lu Tzong-Yi Lee 《BMC bioinformatics》2017,18(3):66
Background
Protein carbonylation, an irreversible and non-enzymatic post-translational modification (PTM), is often used as a marker of oxidative stress. When reactive oxygen species (ROS) oxidized the amino acid side chains, carbonyl (CO) groups are produced especially on Lysine (K), Arginine (R), Threonine (T), and Proline (P). Nevertheless, due to the lack of information about the carbonylated substrate specificity, we were encouraged to develop a systematic method for a comprehensive investigation of protein carbonylation sites.Results
After the removal of redundant data from multipe carbonylation-related articles, totally 226 carbonylated proteins in human are regarded as training dataset, which consisted of 307, 126, 128, and 129 carbonylation sites for K, R, T and P residues, respectively. To identify the useful features in predicting carbonylation sites, the linear amino acid sequence was adopted not only to build up the predictive model from training dataset, but also to compare the effectiveness of prediction with other types of features including amino acid composition (AAC), amino acid pair composition (AAPC), position-specific scoring matrix (PSSM), positional weighted matrix (PWM), solvent-accessible surface area (ASA), and physicochemical properties. The investigation of position-specific amino acid composition revealed that the positively charged amino acids (K and R) are remarkably enriched surrounding the carbonylated sites, which may play a functional role in discriminating between carbonylation and non-carbonylation sites. A variety of predictive models were built using various features and three different machine learning methods. Based on the evaluation by five-fold cross-validation, the models trained with PWM feature could provide better sensitivity in the positive training dataset, while the models trained with AAindex feature achieved higher specificity in the negative training dataset. Additionally, the model trained using hybrid features, including PWM, AAC and AAindex, obtained best MCC values of 0.432, 0.472, 0.443 and 0.467 on K, R, T and P residues, respectively.Conclusion
When comparing to an existing prediction tool, the selected models trained with hybrid features provided a promising accuracy on an independent testing dataset. In short, this work not only characterized the carbonylated substrate preference, but also demonstrated that the proposed method could provide a feasible means for accelerating preliminary discovery of protein carbonylation.14.
Hui-Ju Kao Shun-Long Weng Kai-Yao Huang Fergie Joanda Kaunang Justin Bo-Kai Hsu Chien-Hsun Huang Tzong-Yi Lee 《BMC systems biology》2017,11(7):137