title: 5.8S rRNA Sequence and Secondary Structure inParabronema skrjabiniand Related Habronematidae Species.
abstract: BACKGROUND
  Genomic DNA was isolated fromParabronema skrjabini. rRNA region was amplified and sequenced.
  
  
  METHODS
  The RNA secondary structure was predicted using mfold software ( http://mfold.rit.albany.edu ). The secondary structure with bulge, hairpins, helices, interior, external and multi loops was predicted for 5.8srDNA of our sequence ofP. skrjabiniand a sequenceof P. skrjabiniand two species ofHabronema(H. microstomaandH. muscae) in GenBank. RNA motifs were predicted by MEME program version 4.10.2.
  
  
  RESULTS
  The length of 5.8S rRNA sequence forP. skrjabini#1,P. skrjabini#2,H. microstomaandH. muscaewas 158, 156, 127 and 127bp, and the DG required for the formation of the secondary structure was -70.50, -56.40, -41.50 and -41.40 kcal/Mol, respectively. Common structural elements were initially recognized with the help of mfold by screening for thermodynamically optimal and suboptimal secondary structures (default settings, with T = 37 °C). The energy levels of the presumptive secondary structures were then calculated with mfold at the DNA level. Both motifs and the sequence ofP. skrjabini#1were completely different from the other analyzed samples. This difference might be due to the differences in host and geographical area.
  
  
  CONCLUSIONS
  This is the first molecular study ofP. skrjabiniin sheep, which could be further used in the structure modeling across Habronematidae.
authors.affiliation: Dept. of Parasitology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
authors.forename: Seyed Sajjad
authors.initials: SS
authors.lastname: Hasheminasab
keywords: Parabronema skrjabini; Secondary structure