Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain...Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific lterative-Basic Local Alignment Search Tool （PSI-BLAST） has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and lst-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network （PSP-WNN）. The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.展开更多
Signal transducers and activators of transcription 3 (STAT3) play an important role in various autoimmune disorders including inflammatory bowel disease (IBD). Recent studies have revealed that STAT3 activation plays ...Signal transducers and activators of transcription 3 (STAT3) play an important role in various autoimmune disorders including inflammatory bowel disease (IBD). Recent studies have revealed that STAT3 activation plays distinctly different roles between innate immune responses and acquired immune responses in colitis. STAT3-mediated activation of acquired immune re-sponses plays a pathogenic role in colitis by enhancing the survival of pathogenic T cells. In contrast, STAT3-mediated activation of innate responses contributes to the suppression of colitis. This review will summarize the current understanding of the roles of STAT3 in IBD and the potential of targeting STAT3 for the treatment of IBD, emphasizing recent observations.展开更多
AIM:To investigate the potential role of Active Chinese mistletoe lectin-55 (ACML-55) in tumor immune surveillance. METHODS: In this study, an experimental model was established by hypodermic inoculating the colon can...AIM:To investigate the potential role of Active Chinese mistletoe lectin-55 (ACML-55) in tumor immune surveillance. METHODS: In this study, an experimental model was established by hypodermic inoculating the colon cancer cell line CT26 (5 × 105 cells) into BALB/c mice. The experimental treatment was orally administered with ACML-55 or PBS, followed by the inoculation of colon cancer cell line CT26. Intracellular cytokine staining was used to detect IFN-γ production by tumor antigen specific CD8+ T cells. FACS analysis was employed to profi le composition and activation of CD4+, CD8+, γδ T and NK cells. RESULTS: Our results showed, compared to PBS treated mice, ACML-55 treatment signifi cantly delayed colon cancer development in colon cancer -bearingBalb/c mice in vivo. Treatment with ACML-55 enhanced both Ag specifi c activation and proliferation of CD4+ and CD8+ T cells, and increased the number of tumor Ag specific CD8+ T cells. It was more important to increase the frequency of tumor Ag specific IFN-γ producing-CD8+ T cells. Interestingly, ACML-55 treatment also showed increased cell number of NK, and γδT cells, indicating the role of ACML-55 in activation of innate lymphocytes. CONCLUSION: Our results demonstrate that ACML-55 therapy can enhance function in immune surveillance in colon cancer-bearing mice through regulating both innate and adaptive immune responses.展开更多
基金the National Natural Science Foundation of China (No. 60471003).
文摘Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific lterative-Basic Local Alignment Search Tool （PSI-BLAST） has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and lst-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network （PSP-WNN）. The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.
文摘Signal transducers and activators of transcription 3 (STAT3) play an important role in various autoimmune disorders including inflammatory bowel disease (IBD). Recent studies have revealed that STAT3 activation plays distinctly different roles between innate immune responses and acquired immune responses in colitis. STAT3-mediated activation of acquired immune re-sponses plays a pathogenic role in colitis by enhancing the survival of pathogenic T cells. In contrast, STAT3-mediated activation of innate responses contributes to the suppression of colitis. This review will summarize the current understanding of the roles of STAT3 in IBD and the potential of targeting STAT3 for the treatment of IBD, emphasizing recent observations.
基金The National Natural Science Foundation of China,No.30471593 and No. 30670939the Shanghai Leading Academic Discipline Project,No.T0206+1 种基金the Shanghai Commission of Science and Technology,No.07JC14033the Shanghai Institute of Immunology Project,No.07-A02
文摘AIM:To investigate the potential role of Active Chinese mistletoe lectin-55 (ACML-55) in tumor immune surveillance. METHODS: In this study, an experimental model was established by hypodermic inoculating the colon cancer cell line CT26 (5 × 105 cells) into BALB/c mice. The experimental treatment was orally administered with ACML-55 or PBS, followed by the inoculation of colon cancer cell line CT26. Intracellular cytokine staining was used to detect IFN-γ production by tumor antigen specific CD8+ T cells. FACS analysis was employed to profi le composition and activation of CD4+, CD8+, γδ T and NK cells. RESULTS: Our results showed, compared to PBS treated mice, ACML-55 treatment signifi cantly delayed colon cancer development in colon cancer -bearingBalb/c mice in vivo. Treatment with ACML-55 enhanced both Ag specifi c activation and proliferation of CD4+ and CD8+ T cells, and increased the number of tumor Ag specific CD8+ T cells. It was more important to increase the frequency of tumor Ag specific IFN-γ producing-CD8+ T cells. Interestingly, ACML-55 treatment also showed increased cell number of NK, and γδT cells, indicating the role of ACML-55 in activation of innate lymphocytes. CONCLUSION: Our results demonstrate that ACML-55 therapy can enhance function in immune surveillance in colon cancer-bearing mice through regulating both innate and adaptive immune responses.
