A simple method for classifying genes and a bootstrap test for classifications

Molecular Characterization and Phylogenetic Analysis of Theileria spp. and Babesia spp. Isolated from Various Ticks in Southeastern and Northwestern Regions of Iran

INTRODUCTION

Piroplasms are hemoprotozoa comprising heterogeneous tick-borne parasites, which are differentiated into three genera, namely Babesia, Theileria, and Cytauxzoon. The aim of this study was to determine the prevalence, molecular identification, and phylogenetic relationship of both Theileria spp. and Babesia spp. in tick species isolated from different domestic animals from two different geographical locations of Iran.

MATERIALS AND METHODS

A total of 930 ticks collected from goats, sheep, and cattle were examined for the presence of Theileria spp. and Babesia spp. using PCR targeting 18S rRNA gene followed by sequencing. Sequence analysis was performed based on the data published in the GenBank on Theileria spp. and Babesia spp. isolates using bioinformatic tools, such as the standard nucleotide BLAST.

RESULTS

A 390 or 430 base pair fragment of 18S rRNA gene of Theileria and Babesia species was successfully amplified in 17.2% of the examined ticks (16of 93). Genome of Theileria or Babesia species was detected in 4 ticks collected in Heris, including 3 Dermacentor marginatus and 1 Rhipicephalus sanguineus, and also in 12 ticks collected in Chabahar, including 10 R. sanguineus and 2 D. marginatus. Partial analysis of 18S rRNA gene sequence of the four D. marginatus, collected from goats and sheep in Heris, showed that they were infected with Theileria spp. that were 95-97% identical to Iranian Theileria ovis present in the GenBank database (GenBank acc. no. KP019206.1). While the five R. sanguineus, collected from sheep and goats in Chabahar, were infected with Babesia spp. that were 91-97% identical to Iranian Babesia ovis present in the GenBank database (GenBank acc. no. AY362829.1: KT587794.1).

CONCLUSION

The prevalence of Babesia and Theileria is different in southeastern and northwestern parts of Iran, with higher prevalence of babesiosis in the southeastern region and that of theileriosis in the northwestern region. Sequence analysis of 18S rRNA gene revealed that T. ovis and B. ovis are genetically polymorphic in these regions.

Correlation of Genetic Heterogeneity with Cytopathological and Epidemiological Findings of Leishmania major Isolated from Cutaneous Leishmaniasis in Southern Iran

OBJECTIVE

Cutaneous leishmaniasis (CL) has recently grown into a major public health problem in 88 countries of the world, including Iran. It is a polymorphic disease which may show various clinicopathological features. Although the effect of the genetic diversity of the parasite has been demonstrated as one of the factors influencing clinical manifestations in CL, no data exist regarding the genetic variation of Leishmania major and its microscopical features.

STUDY DESIGN

Fine-needle aspiration, touch smears and the histological sections of 100 patients were examined for Leishmania amastigotes, using Giemsa and hematoxylin and eosin. Diverse types of inflammatory cells in the 40 positive and 5 negative smears were differentiated. Kinetoplast DNA (kDNA) was amplified using nested PCR and subsequently sequenced. Sequencing analysis of the amplified kDNA was used to investigate the genetic variations among L. major isolates and to correlate the findings with microscopical features and geographical origins.

RESULTS

The quantified amastigote density in the 40 positive touch smears was blindly classified by 3 observers. Grade I, II, III and IV had 7, 13, 9 and 11 cases, respectively. The microscopical features, the mean percentage of neutrophils, lymphocytes and other inflammatory cells, and the leishmanial density of the grades and negative cytopathological samples were contrasting. kDNA amplification of L. major was detected from the cutaneous lesion, and 21 of these amplicons were successfully sequenced.

CONCLUSIONS

These results indicate that L. major strains causing CL in southern Iran are genetically diverse; furthermore, a correlation between the genetic heterogeneity of the parasite, the microscopical manifestation and the geographical regions of the disease in humans was found.

Standardizing and simplifying analysis of peptide library data

Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, we describe a set of algorithms which allow quick, efficient, and standard analysis of peptide libraries. Four main techniques are described: (1) choice of the number of motifs present in a peptide library; (2) separation of the peptides into groups of similar sequences; (3) fitting of a model to the peptides to extract motifs; (4) analysis of the library using quantitative structure-property relationships if no clear motifs are present. The application of five previously published data sets shows these techniques can automatically repeat the work of experts quickly and allow much more flexibility in analysis. A new way of visually presenting peptide libraries is also described, which allows visual inspection of the grouping and spread of sequences. The algorithms have been implemented in an open-source plug-in called "peplib" and an online web application.

New weighting methods for phylogenetic tree reconstruction using multiple loci

Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima–Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima–Takezaki and by the modified least-squares method.