For the “Ident and Sim” analysis within the DEAD-box sequences, we first performed a MUSCLE IWP-2 cell line alignment at the EBI website and then ran the

program at “The Sequence Manipulation Suite”. The structural domains and sequence patterns were first predicted at the Eukaryotic Linear Motif resource (ELM) [81], getting the DEXDc and HELICc RNA selleck chemical helicase domains and the HA2 and Sec63 domains. After that, each specific family motif was checked manually and indicated using the putative consensus motifs described in the literature [43]. For the graphical representation of the amino acid conserved motifs within each family we used the web-based application WebLogo [38], where each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, whereas the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The putative

Dicer amino acid sequence analysis was performed using the Eukaryotic Linear Motif resource (ELM) and the ExPASy – PROSITE database [82]. Phylogenetic analysis We used only the helicase domain from the RNA helicases selected to run a multiple alignment www.selleckchem.com/products/azd6738.html (MUSCLE) into the SeaView Version 4.2.12 [83–86]. Then we computed the tree using PhyML v3.0.1 as an external program [86].The design was edited using the

Adenosine triphosphate Tree Figure Drawing Tool Version 1.3.1. Cultures G. lamblia trophozoites were cultured in TYI-S-33 medium at pH7.0 with 10% adult bovine serum and bovine bile (0.5 mg/ml) [87] in anaerobiosis at 37°C. For induction of encystation, the trophozoites were cultured until confluence and then the medium was replaced with encystation medium (porcine bile 0.45%, lactic acid 0.01% and pH 7.8) [88] and grown in anaerobiosis at 37°C during 16 h. For antigenic variation experiments, a Giardia clone expressing VSP-1267 was obtained by serial dilution and selection by immunofluorescence assays using specific monoclonal antibody that recognizes only this VSP, and then cultured until 90% confluence. Induction of antigenic variation was performed according to Torri et al. (manuscript in preparation). RNA extraction and cDNA synthesis Total RNA was extracted from each sample (trophozoites and encystation induction) using Trizol reagent (Invitrogen) according with manufacturer’s instructions. Total RNA was spectrophotometrically quantified and treated with DNase I (Roche) at 37°C for 1 h. After DNase inactivation total RNA was quantified again and several PCRs were performed to check for the presence of genomic DNA.