The clonality of all picked cells was further verified by microscopy, prior to transfer into the DNA extraction mixture. As a control, FITC-labeled cysts, purified from patient fecal material were transferred to 12-well microscope Compound C research buy slides (ntot = 44 cysts) and fixed by desiccation, followed by the addition of mounting buffer to each well individually. The analysis was performed without the addition of cover slips in order to avoid cross contamination between the wells. The slides were analyzed using a fluorescence microscope and single cysts were present in

all 44 wells. Also, all negative controls indicated the absence of Giardia cysts. Evaluation of different methods for DNA extraction and efficiency of PCR of single Giardia cells Two different methods were set up and evaluated in their efficiency of generating DNA from single trophozoites (GS/M-H7) that would yield sequences of high enough quality for the discrimination of ASH. PCR products could efficiently be produced using both protocols, however, the generation

of sequences with double peaks in the expected positions showed complete efficiency only when applying the DNAreleasy protocol, as indicated in Table 1. Since the DNAreleasy Small molecule library solubility dmso protocol showed to be the most efficient for the extraction of high quality DNA from single trophozoites, it was subsequently also applied to the LY2606368 in vivo single cysts. Both

the long and the short extraction protocols provided by the manufacturer were assayed. Applying the long extraction protocol yielded a higher number of positive results in subsequent PCR reactions (data not shown). Table 1 Comparative sequence analysis of single GS/M trophozoites Protirelin at the tpi locus Isolate Material DNAreleasy GenBank acc no Nucleotide position from start of gene         39* 45 264 GS/M Cloned sequence   EF688030 A T G   Cloned sequence   EF688028 G C A   Crude isolate   FJ560571 R Y R GS/M Crude isolate   N/A R Y R GS/M_3 Single trophozoites Not used N/A G C A GS/M_5       G C A GS/M_7       G C A GS/M_8 Single trophozoite Not used N/A A T G GS/M_6 Single trophozoite Not used N/A R Y R GS/M_71 Single trophozoites Used JN579671 R Y R GS/M_72       R Y R GS/M_73       R Y R GS/M_74       R Y R GS/M_76       R Y R GS/M_77       R Y R GS/M_78       R Y R GS/M_79       R Y R GS/M_80       R Y R * This nucleotide position is a substitution pattern proposed as a marker for different B sub-assemblages [25]. Sequencing of Giardia from culture and at the single cell level Double peaks were stringently validated in the chromatograms of all sequences generated in this study.