NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm

BACKGROUND: Protein palmitoylation, an essential and reversible post-translational modification (PTM), has been implicated in cellular dynamics and plasticity. Although numerous experimental studies have been performed to explore the molecular mechanisms underlying palmitoylation processes, the intrinsic feature of substrate specificity has remained elusive. Thus, computational approaches for palmitoylation prediction are much desirable for further experimental design. RESULTS: In this work, we present NBA-Palm, a novel computational method based on Naïve Bayes algorithm for prediction of palmitoylation site. The training data is curated from scientific literature (PubMed) and includes 245 palmitoylated sites from 105 distinct proteins after redundancy elimination. The proper window length for a potential palmitoylated peptide is optimized as six. To evaluate the prediction performance of NBA-Palm, 3-fold cross-validation, 8-fold cross-validation and Jack-Knife validation have been carried out. Prediction accuracies reach 85.79% for 3-fold cross-validation, 86.72% for 8-fold cross-validation and 86.74% for Jack-Knife validation. Two more algorithms, RBF network and support vector machine (SVM), also have been employed and compared with NBA-Palm. CONCLUSION: Taken together, our analyses demonstrate that NBA-Palm is a useful computational program that provides insights for further experimentation. The accuracy of NBA-Palm is comparable with our previously described tool CSS-Palm. The NBA-Palm is freely accessible from:

Early life perfluorooctanesulphonic acid (PFOS) exposure impairs zebrafish organogenesis

Additional authors (Zengxin Gai and Xue Ma) appear and the author order is revised on the published version of this article.As a persistent organic contaminant, perfluorooctanesulphonic acid (PFOS) has been widely detected in the environment, wildlife, and humans. The present study revealed that zebrafish embryos exposed to 16 µM PFOS during a sensitive window of 48-96 hour post-fertilization (hpf) disrupted larval morphology at 120 hpf. Malformed zebrafish larvae were characterized by uninflated swim bladder, less developed gut, and curved spine. Histological and ultrastructural examination of PFOS-exposed larvae showed structural alterations in swim bladder and gut. Whole genome microarray was used to identify the early transcripts dysregulated following exposure to 16 µM PFOS at 96 hpf. In total, 1,278 transcripts were significantly misexpressed (p < 0.05) and 211 genes were changed at least two-fold upon PFOS exposure in comparison to the vehicle exposed control group. A PFOS-induced network of perturbed transcripts relating to swim bladder and gut development revealed that misexpression of genes were involved in organogenesis. Taken together, early life stage exposure to PFOS perturbs various molecular pathways potentially resulting in observed defects in swim bladder and gut development.This is an author's peer-reviewed manuscript. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/aquatic-toxicology/.Keywords: Perfluorooctanesulfonic acid, Zebrafish embryo, Developmental toxicity, Swim bladder, GutKeywords: Perfluorooctanesulfonic acid, Zebrafish embryo, Developmental toxicity, Swim bladder, Gu

Phase portraits and optical soliton solutions of coupled Sasa–Satsuma model in birefringent fibers

The main purpose of this paper is to discuss the optical soliton solutions and phase portraits of the coupled Sasa–Satsuma model in nonlinear optics. This model is usually used to describe the propagation of femtosecond pulses in optical fibers. By using traveling wave transformation, the coupled Sasa–Satsuma model is simplified into the coupled nonlinear ordinary differential equations. After that, the coupled nonlinear ordinary differential equations are transformed into two-dimensional planar dynamic system with the Hamiltonian system. According to the bifurcation theory of planar dynamical system, the phase portrait of two-dimensional dynamical system is drawn. What is more, some very important optical soliton solutions are also constructed. In order to explain the propagation of optical solitons, three-dimensional diagrams, two-dimensional diagrams and the contour plots of the obtained solutions are drawn by using Maple software

GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm.

As one of the most important and ubiquitous post-translational modifications (PTMs) of proteins, S-nitrosylation plays important roles in a variety of biological processes, including the regulation of cellular dynamics and plasticity. Identification of S-nitrosylated substrates with their exact sites is crucial for understanding the molecular mechanisms of S-nitrosylation. In contrast with labor-intensive and time-consuming experimental approaches, prediction of S-nitrosylation sites using computational methods could provide convenience and increased speed. In this work, we developed a novel software of GPS-SNO 1.0 for the prediction of S-nitrosylation sites. We greatly improved our previously developed algorithm and released the GPS 3.0 algorithm for GPS-SNO. By comparison, the prediction performance of GPS 3.0 algorithm was better than other methods, with an accuracy of 75.80%, a sensitivity of 53.57% and a specificity of 80.14%. As an application of GPS-SNO 1.0, we predicted putative S-nitrosylation sites for hundreds of potentially S-nitrosylated substrates for which the exact S-nitrosylation sites had not been experimentally determined. In this regard, GPS-SNO 1.0 should prove to be a useful tool for experimentalists. The online service and local packages of GPS-SNO were implemented in JAVA and are freely available at: http://sno.biocuckoo.org/

A Modified Shape Model Incorporating Continuous Accumulated Growing Degree Days for Phenology Detection of Early Rice

Using a shape model (SM) is a typical method to determine the phenological phases of crops with long-time-series satellite remote sensing data. The average AGDD-based shape model (AAGDD-SM) takes temperature into account compared to SM, however, the commonly used daily average temperature is not sufficient to determine the exact AGDD owing to the possibly significant changes in temperatures throughout the day. In this paper, a modified shape model was proposed for the better estimation of phenological dates and it is incorporated into the continuous AGDD (CAGDD) which was calculated based on temperatures from a continuous 24 h within a day, different from the calendar day or the average AGDD indicators. In this study, the CAGDD replaced the abscissa of the NDVI growth curve over a 5-year period (2014 to 2018, excluding 2015) for a test site of early rice in Jiangxi province of China. Four key phenological phases, including the reviving, tillering, heading and anthesis phases, were selected and determined with reference to the field-observed phenological data. The results show that compared with the AAGDD-SM, the method proposed in this paper has basically improved the prediction of each phenological period. For those cases where the average temperature is lower than the minimum temperatures (K1) but the effective accumulated temperature is not zero, more accurate AGDD can be calculated according to the method in this paper