Bio-Medical Materials and Engineering - Volume 24, issue 6

Authors: Wu, Xiaohui | Zhao, Chuang | Su, Yaru

Article Type: Research Article

Abstract: Polyadenylation [poly(A)] of mRNA is a critical step during gene expression, which plays an important role in the termination of transcription. Prediction of poly(A) sites can help identify 3' ends of genes and improve genome annotation. Due to the limited knowledge of poly(A) signals in plants, predictive modeling of poly(A) sites in agricultural crops remains challenging. Recent studies have uncovered widespread occurrences of alternative poly(A) (APA) sites in intron and coding sequence (CDS), whereas the study on the prediction of these APA sites is scarce. In this study, four feature representation methods, involving a position weight matrix, the k-gram frequency, …core hexamers, and a transition matrix, were adopted to characterize poly(A) signals surrounding APA sites. The classification model was built to predict each group of APA sites. Experimental results showed that this model was effective in the identification of APA sites located in different genomic regions, with a compromise between sensitivity and specificity higher than 87%. Compared with previous model PASS rice, accuracies for the prediction of APA sites in 3'-UTR, intron and CDS were enhanced by 5%, 7%, and 27%, respectively. This model will contribute to genetic engineering by enabling researchers to control poly(A) site selection. Show more

Keywords: Rice, polyadenylation, alternative polyadenylation, prediction, classification model

DOI: 10.3233/BME-141207

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3779-3785, 2014

Authors: Wang, Gongming | Xu, Fan

Article Type: Research Article

Abstract: The output of icosahedral symmetry-adapted functions (ISAF) reconstruction algorithm is a virus capsid, where the density function of every outside point is theoretically zero. However, original ISAF algorithm takes reconstructed map as a solid sphere and density function of every point in the whole sphere is calculated. The density functions outside virus capsid may not be always zero, which may sometimes produce noise. In this study, Fourier shell correlation (FSC) is used for proving that density function calculation of original ISAF algorithm can reduce reconstruction precision. Subsequently, the range of virus capsid is determined with radial density function curve and …the original ISAF algorithm is improved by calculating density function inside virus capsid. The experimental results on Cryo-electron microscopy (Cryo-EM) data of cytoplasmic polyhedrosis virus (CPV) indicate that the improved ISAF algorithm can generate more details of virus capsid and achieve a higher resolution. Show more

Keywords: Single-particle reconstruction, icosahedral symmetry-adapted functions, virus capsid, density function, Fourier shell correlation

DOI: 10.3233/BME-141208

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3787-3795, 2014

Authors: Bao, Wenzheng | Chen, Yuehui | Wang, Dong

Article Type: Research Article

Abstract: Prediction of protein structural classes is of great significance to better understand protein folding patterns. An array of methods has been proposed to predict these structures based on sequences. However, the accuracy is strongly affected by the homology of sequences. In the present study, the features based on correlation coefficient of sequence and amino acid composition are extracted. Flexible neutral tree is employed as the classification model. To examine the performance of this method, four benchmark datasets are selected. Altogether, the results show that a higher prediction accuracy of alpha/beta can be achieved by the method compared to others.

Keywords: Protein structural classification, flexible neural tree, correlation coefficient

DOI: 10.3233/BME-141209

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3797-3806, 2014

Authors: Lee, Nung Kion | Fong, Pui Kwan | Abdullah, Mohd Tajuddin

Article Type: Research Article

Abstract: Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature …improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features. Show more

Keywords: Genetic algorithm, tree-based feature, histone feature

DOI: 10.3233/BME-141210

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3807-3814, 2014

Authors: Zheng, Shichao | Ren, Zhenzhen | Zhang, Yanling | Qiao, Yanjiang

Article Type: Research Article

Abstract: Tanshinone IIA (Tan IIA) is one of the major fat-soluble ingredients in Salvia miltiorrhiza which has been widely used for various inflammatory conditions associated with cardiovascular and cerebrovascular disorders. However, the underlying anti-inflammatory mechanisms of Tan IIA are incompletely understood. The purpose of this study was to illuminate the anti-inflammatory mechanism of Tan IIA based on the protein interaction network (PIN) analysis. A PIN of Tan IIA was constructed with 281 nodes and 814 interactions and analyzed by gene ontology (GO) enrichment analysis based on Markov Cluster algorithm (MCL). Three modules were associated with anti-inflammatory actions. The most interesting finding …of this study was that the anti-inflammatory effect of Tan IIA may be partly attributable to the mediate activation of TRAF2, TRAF3 and TRAF6, to inhibit the toll-like receptor signaling pathway and combine with AGER. Therefore, the module-based network analysis approach will be a new method for better understanding the anti-inflammatory mechanism of Tan IIA. Show more

Keywords: Protein interaction network, module, anti-inflammatory actions, Tanshinone IIA, GO enrichment analysis

DOI: 10.3233/BME-141211

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3815-3824, 2014

Authors: Fernández-Granero, M.A. | Sánchez-Morillo, D. | León-Jiménez, A. | Crespo, L.F.

Article Type: Research Article

Abstract: Chronic Obstructive Pulmonary Disease (COPD) is a progressive disease of the lung with a great prevalence and a remarkable socio-economic impact on patients and health systems. Early detection of exacerbations could diminish the adverse effects on patients' health and cut down costs burdened on patients with COPD. A group of 16 patients were telemonitored at home using a novel electronic daily symptoms questionnaire during a 6-months field trial. Recorded data were used to train and validate a Probabilistic Neural Network (PNN) classifier in order to enable the automatic prediction of exacerbations. The proposed system was able to predict COPD exacerbations …early with a margin of 4.8±1.8 days (average ± SD). Detection accuracy was 80.5% (33 out of 41 exacerbations were early detected); 78.8% (26 out of 33) of theses detected events were reported exacerbation and 87.5% (7 out of 8) were unreported episodes. The proposed questionnaire and the designed automatic classifier could support the early detection of COPD exacerbations of benefit to both physicians and patients. Show more

Keywords: Chronic Obstructive Pulmonary Disease, exacerbation, telehealth, symptoms, questionnaire, early detection, Probabilistic Neural Network, telemonitoring

DOI: 10.3233/BME-141212

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3825-3832, 2014

Authors: Wang, Yong-Tang | Lu, Xiu-Min | Shu, Ya-Hai | Xiao, Lan | Chen, Kai-Ting

Article Type: Research Article

Abstract: To select tag single nucleotide polymorphisms (SNPs) within and around human p75 neurotrophin receptor (p75NTR) gene in Chinese Han population, the sequence involving p75NTR gene as well as the upstream and downstream of the gene was identified according to the data from National Center for Biotechnology Information (NCBI) GenBank database, and the SNP genotype data involving 63 SNPs in the regions were obtained from Chinese Han Beijing (CHB) population of HapMap database. Then, Haploview (version 4.2) was used to calculate linkage disequilibrium (LD) statistics for the selected 32 common SNPs with a minor allele frequence (MAF) more than 0.05. Haplotype …blocks were constructed throughout the p75NTR gene according to the upper and the lower 95% confidence bound of D' value, and the tag SNPs were selected based on the r2 and LOD values between SNPs as well as the results of bioinformatics analysis. The results indicated that five haplotype blocks were constructed within and around p75NTR gene and 12 tag SNPs including rs2537710, rs603769, rs614455, rs2537706, rs534561, rs2072445, rs2072446, rs7219709, rs734194, rs741071, rs741073 and rs2671641 were selected to represent the other 51 SNPs in p75NTR gene. Therefore, the 12 selected SNPs may act as tag SNPs for the entire p75NTR gene in Chinese Han population, which will provide an effective way to select tag SNPs in a whole gene, and its biological significance is to further guide the clinical association studies between the candidate gene and disease susceptibility. Show more

Keywords: p75NTR, haplotype block, tag SNP, haplotype, bioinformatics analysis

DOI: 10.3233/BME-141213

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3833-3839, 2014

Authors: Zhang, Jinping | Zhang, Leijia | Liu, Xuehong | Zhou, Fuqun

Article Type: Research Article

Abstract: To study the expression and roles of Connexin43 (Cx43) and Paired-box3 (Pax3) proteins in the human Chorionic villi and decidua during early pregnancy, Cx43 and Pax3 protein expression in the human placental villi and decidua at 5–7 weeks of early pregnancy was studied by immunohistochemistry (SABC). Integrated optical density (IOD) of Cx43 and Pax3 protein expression was obtained by using special image analysis software. Cx43 and Pax3 proteins were expressed in all trophoblastic cells, cells of villi central axis and decidual cells. IOD of Cx43 and Pax3 proteins expressed in the syncytiotrophoblast decreased from 5 to 7 weeks, while Cx43 …and Pax3 expressed in cytotrophoblast cells and decidual cells showed increased IOD during the same period. The differences between any two groups were statistically significant (P<0.05). Cx43 and Pax3 proteins were expressed during differentiation and development of placental villous cells in early phases of pregnancy. We propose that Cx43 and Pax3 may participate in endometrial decidualization and the regulation of trophoblastic invasion and differentiation. It is likely that Cx43 and Pax3 play critical roles in cell proliferation and differentiation during the processes of chorionic villi initiation/development and placental morphogenesis. Show more

Keywords: Connexin43, pax3, Chorionic villi, decidua, Immunohistochemistry

DOI: 10.3233/BME-141214

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3841-3847, 2014

Authors: Wang, Chenyin | Avdeef, Alex | Zhang, Wen | Tam, Kin Y.

Article Type: Research Article

Abstract: The purpose of this study is to predict human jejunal permeability (Peff ) and fraction absorbed in human (%Fa) for a group of antibacterial fluoroquinolones (FQs), by using a biophysical model based on measured Caco-2 permeability. The predicted Peff (in 10−4 cm·s−1 units) ranged from 0.7 (norfloxacin) to 4.5 (pefloxacin). The calculated %Fa for norfloxacin = 51% (lit. 35%) and for ciprofloxacin = 76% (lit. 81%). Most of the FQs showed calculated %Fa >90%, and are expected to be well-absorbed. Estimates of Peff can be predicted by the biophysical model. From these values, the human absorption may …be calculated. Where absorption comparisons were possible, the agreement was acceptably good. Show more

Keywords: permeability, fraction absorbed, fluoroquinolones, human intestine, Caco-2

DOI: 10.3233/BME-141215

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3849-3854, 2014

Authors: Xue, Dan | Na, Ri | Guo, Jiu Feng | Liu, Teng

Article Type: Research Article

Abstract: With a goal of obtaining the engineering probiotics that can produce both lactic acid and laccase, Pleurotus eryngii was selected as the test material. First, the laccase gene (Lacc1) was cloned by using RT-PCR (the length of which is 1596bp), and then, the gene was ligated to the food-grade vector pMG36e from Lactobacillus buchneri. The recombinant expression vector pMG36e-Lacc1 was constructed by transforming it into Lactobacillus buchneri via an electroporation method. The recombinant plasmid was constructed successfully as confirmed by gel electrophoresis. Then, the optimum conditions for electroporation were determined. The research revealed that when the electric field intensity is …1.75 kV with an SMRS medium recovery for 1.5 h, the electroporation translation efficiency reaches its maximum level. Show more

Keywords: Laccase, Lactobacillus buchneri, expression vector system

DOI: 10.3233/BME-141216

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3855-3861, 2014