Identification of Plant Messenger RNA Polyadenylation Sites Using Length-Variable Second Order Markov Model

In this paper we adopted a length-variable second order Markov model to identify plant messenger RNA poly(A) sites, and provided a common method that only relies on the experimental sequences. The efficacy of our model is showed up to 92% sensitivity and 79% specificity. This method is particularly suitable for the prediction of the poly(A) site which is lack of biological priori knowledge and has poor conservative signal characteristic, as well as for the identification of the alternative poly(A) sites in different genetic regions. Compared with other algorithms, generalized hidden Markov model needed the signal distributions and AdaBoost required the construction of signal features around the sites, our model is more versatile

Identification of plant messenger RNA polyadenylation sites using length-variable second order Markov model

Conference Name:2011 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2011. Conference Address: Anchorage, AK, United states. Time:October 9, 2011 - October 12, 2011.In this paper we adopted a length-variable second order Markov model to identify plant messenger RNA poly(A) sites, and provided a common method that only relies on the experimental sequences. The efficacy of our model is showed up to 92% sensitivity and 79% specificity. This method is particularly suitable for the prediction of the poly(A) site which is lack of biological priori knowledge and has poor conservative signal characteristic, as well as for the identification of the alternative poly(A) sites in different genetic regions. Compared with other algorithms, generalized hidden Markov model needed the signal distributions and AdaBoost required the construction of signal features around the sites, our model is more versatile. ? 2011 IEEE

Identification of mRNA poly(A) signal patterns

Conference Name:2011 International Symposium on INnovations in Intelligent SysTems and Applications, INISTA 2011. Conference Address: Istanbul-Kadikoy, Turkey. Time:June 15, 2011 - June 18, 2011.TUBITAK; IEEEThe poly(A) signal patterns surrounding the poly(A) site in model plant Arabidopsis thaliana were generated, selected and verified. First, candidate nucleotide patterns of different signal regions were generated based on their conservatism, using the TFxIDF index of vector space model that is widely used in text categorization. Then, effective features were selected through a genetic algorithm based wrapper feature selection method. Finally, a boosting method called Adaboost.M1 was adopted to verify the feature subset by identifying poly(A) sites. The results showed that our feature selection method could significantly reduce the dimension of feature space to enhance the classifier performance to a large extent. Moreover, the selected features could be used to improve the parameters of the poly(A) site recognition model, thus enhanced the prediction accuracy greatly. This study will not only enhance our understanding of poly(A) signals, but also concisely show a poly(A) site recognition model by applying classifier on the feature space. ? 2011 IEEE

Egress of sperm autoantigen from seminiferous tubules maintains systemic tolerance

Autoimmune responses to meiotic germ cell antigens (MGCA) that are expressed on sperm and testis occur in human infertility and after vasectomy. Many MGCA are also expressed as cancer/testis antigens (CTA) in human cancers, but the tolerance status of MGCA has not been investigated. MGCA are considered to be uniformly immunogenic and nontolerogenic, and the prevailing view posits that MGCA are sequestered behind the Sertoli cell barrier in seminiferous tubules. Here, we have shown that only some murine MGCA are sequestered. Nonsequestered MCGA (NS-MGCA) egressed from normal tubules, as evidenced by their ability to interact with systemically injected antibodies and form localized immune complexes outside the Sertoli cell barrier. NS-MGCA derived from cell fragments that were discarded by spermatids during spermiation. They egressed as cargo in residual bodies and maintained Treg-dependent physiological tolerance. In contrast, sequestered MGCA (S-MGCA) were undetectable in residual bodies and were nontolerogenic. Unlike postvasectomy autoantibodies, which have been shown to mainly target S-MGCA, autoantibodies produced by normal mice with transient Treg depletion that developed autoimmune orchitis exclusively targeted NS-MGCA. We conclude that spermiation, a physiological checkpoint in spermatogenesis, determines the egress and tolerogenicity of MGCA. Our findings will affect target antigen selection in testis and sperm autoimmunity and the immune responses to CTA in male cancer patients