In vivo Transcriptome Profiling of Plasmodium vivax Clinical Isolates New Insights into Severe Malaria

Abstract

Among human malaria parasites, P. vivax is a geographically wide-spread malaria parasite. Long considered to cause only benign malaria is now shown to cause severe malaria, as similar to P.falciparum. As compared to P. falciparum, only very little is understood about the biology of P.vivax. This is mainly due to the absence of continuous in vitro culture system, and occurrence of less parasitemia in natural infections. The publication of the reference genome P. vivax Sal-I has provided a valuable opportunity to study this parasite. Many microarrays have been designed based on the reference strain Sal-I, and transcriptome studies performed on these microarrays has provided insights into understanding of this parasite biology. So far, only one study has performed the whole-genome transcriptome profiling of P. vivax isolates obtained directly from the patients. Moreover, available microarrays were designed based on reference Sal-I strain and do not include probes that have been experimentally verified to detect parasite transcripts from newlinefield samples. Studies reported in this PhD thesis addresses the above lacunae in the field of P. vivax transcriptomics. Attempts such as finding the transcriptional difference between P. vivax parasites causing severe and non-severe malaria are performed to understand the pathogenesis associated with severe P. vivax malaria.Initial study of this chapter deals with the designing of an experimentally optimized microarray for P. vivax field isolates causing severe or non-severe malaria. We adopted an empirical newlineapproach to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60mer) that were in-situ synthesized onto glass slide using Agilent SurePrint technology and has been developed into an 8X15K microarray format (8 identical newlinearrays on a single slide). Probes in this 15K microarray platform contains experimentally newlinevalidated probes