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Articles Online (Volume 7, Issue 3)

Review Article

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe grisea from Horizontal Gene Transfer Hypothesis

Chunyang Li, Ying Wang, Hao Peng, Hejiao Bian, Mingwei Min, Longfei Chen, Qian Liu, Jinku Bao

Horizontal gene transfer (HGT) has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes (corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136) were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan's corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.

Page 77–86

Review Article

Computational Analysis of Cysteine Proteases (Clan CA, Family Cl) of Leishmania major to Find Potential Epitopic Regions

Babak Saffari, Hassan Mohabatkar

Leishmania is associated with a broad spectrum of diseases, ranging from simple cutaneous to invasive visceral leishmaniasis. Here, the sequences of ten cysteine proteases of types A, B and C of Leishmania major were obtained from GeneDB database. Prediction of MHC class I epitopes of these cysteine proteases was performed by NetCTL program version 1.2. In addition, by using BcePred server, different structural properties of the proteins were predicted to find out their potential B cell epitopes. According to this computational analysis, nine regions were predicted as B cell epitopes. The results provide useful information for designing peptide-based vaccines.

Page 87–95

Review Article

Evolutionary Implication of Outer Membrane Lipoprotein-Encoding Genes ompL1, lipL32 and lipL41 of Pathogenic Leptospira Species

K. Vedhagiri, K. Natarajaseenivasan, P. Chellapandi, S.G. Prabhakaran, Joseph Selvin, S. Sharmac, P. Vijayachari

Leptospirosis is recognized as the most widespread zoonosis with a global distribution. In this study, the antigenic variation in Leptospira interrogans and Leptospira borgpetersenii isolated from human urine and field rat kidney was preliminarily confirmed by microscopic agglutination test using monoclonal antibodies, and was further subjected to amplification and identification of outer membrane lipoproteins with structural gene variation. Sequence similarity analysis revealed that these protein sequences, namely OmpL1, LipL32 and LipL41, showed no more homologies to outer membrane lipoproteins of non-pathogenic Leptospira and other closely related Spirochetes, but showed a strong identity within L. interrogans, suggesting intra-specific phylogenetic lineages that might be originated from a common pathogenic leptospiral origin. Moreover, the ompL1 gene showed more antigenic variation than UpL32 and lipL41 due to less conservation in secondary structural evolution within closely related species. Phylogenetically, ompLl and lipL41 of these strains gave a considerable proximity to L. weilii and L. santaro-sai. The ompLl gene of L. interrogans clustered distinctly from other pathogenic and non-pathogenic leptospiral species. The diversity of ompL genes has been analyzed and it envisaged that sequence-specific variations at antigenic determinant sites would result in slow evolutionary changes along with new serovar origination within closely related species. Thus, a crucial work on effective recombinant vaccine development and engineered antibodies will hopefully meet to solve the therapeutic challenges.

Page 96–106

Review Article

Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees

Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu

Purified protein derivative (PPD) skin tests often yield poor specificity, so that to develop new serological antigens for distinguishing between Mycobacterium tuberculosis infection and Bacille Calmette-Guerin (BCG) vaccination is a priority, especially for developing countries like China. We predicted the antigenicity for selected open reading frames (ORFs) based on the genome sequences of M. tuberculosis H37Rv and M. bovis BCG, as well as their functions and differences of expression under different stimulus. The candidate ORFs were cloned from H37Rv sequences and expressed as recombinant proteins in Escherichia coli. We studied the serodiagnostic potential of 11 purified recombinants by using enzyme-linked immunosorbent assay (ELISA) and involving a cohort composed of 58 TB patients (34 males and 24 females), 8 healthy volunteers and 50 PPD-negative individuals before and after BCG vaccination. For all the 11 antigens, the median OD values for the sera from TB patients were statistically significantly higher than those for PPD-negative individuals before or after BCG vaccination (P<0.01). They had at least 92% specificity in healthy controls and six seroantigens (Rv0251c, Rvl973, Rv2376c, Rv2537c, Rv2785c and Rv3873A) were never reported with seroantigenicities previously. Thus the approach combining comparative genomics, bioinformatics and ELISA techniques can be employed to identify new seroantigens distinguishing M. tuberculosis infection from BCG vaccination.

Page 107–115

Review Article

How Do Variable Substitution Rates Influence Ka and Ks Calculations?

Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu

The ratio of nonsynonymous substitution rate (Ka) to synonymous substitution rate (Ks) is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new γ-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and YN methods based on an introduction of gamma distribution to illustrate the variation of raw mutation rate over sites. The novelty comes in two ways: (1) we incorporate an optimal gamma distribution shape parameter a into γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, and γ-YN methods; (2) we investigate how variable substitution rates affect the methods that adopt different models as well as the interplay among four evolutional features with respect to Ka/Ks computations. Our results suggest that variable substitution rates over sites under negative selection exhibit an opposite effect on ω estimates compared with those under positive selection. We believe that the sensitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka/Ks computation.

Page 116–127

Review Article

How Many 3D Structures Do We Need to Train a Predictor?

Pantelis G. Bagos, Georgios N. Tsaousis, Stavros J. Hamodrakas

It has been shown that the progress in the determination of membrane protein structure grows exponentially, with approximately the same growth rate as that of the water-soluble proteins. In order to investigate the effect of this, on the performance of prediction algorithms for both α-helical and β-barrel membrane proteins, we conducted a prospective study based on historical records. We trained separate hidden Markov models with different sized training sets and evaluated their performance on topology prediction for the two classes of transmembrane proteins. We show that the existing top-scoring algorithms for predicting the transmembrane segments of α-helical membrane proteins perform slightly better than that of β-barrel outer membrane proteins in all measures of accuracy. With the same rationale, a meta-analysis of the performance of the secondary structure prediction algorithms indicates that existing algorithmic techniques cannot be further improved by just adding more non-homologous sequences to the training sets. The upper limit for secondary structure prediction is estimated to be no more than 70% and 80% of correctly predicted residues for single sequence based methods and multiple sequence based ones, respectively. Therefore, we should concentrate our efforts on utilizing new techniques for the development of even better scoring predictors.

Page 128–137

Application Note

PBOND: Web Server for the Prediction of Proline and Non-Proline cis I trans Isomerization

Konstantinos P. Exarchos, Themis P. Exarchos, Costas Papaloukas, Anastassios N. Troganis, Dimitrios I. Fotiadis

PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages: (1) feature extraction, (2) feature selection and (3) peptide bond classification. PBOND can handle both single sequences as well as multiple sequences for batch processing. The predictions can either be directly downloaded from the web site or returned via e-mail. The PBOND web server is freely available at http://195.251.198.21/pbond.html.

Page 138–142

Application Note

3D Genome Tuner: Compare Multiple Circular Genomes in a 3D Context

Qi Wang, Qun Liang, Xiuqing Zhang

Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner, a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available (under an LGPL licence) at http://sourceforge.net/projects/dgenometuner.

Page 143–146