Bozdech, Z. et al. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 4, R9

Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA.
Genome biology (Impact Factor: 10.81). 02/2003; 4(2):R9. DOI: 10.1186/gb-2003-4-2-r9
Source: PubMed


The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development.
We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages.
DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.

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    • "Some, such as OligoArray (Rouillard et al., 2003), OligoPicker (Wang and Seed, 2003), PICKY (Chou et al., 2004b) and YODA (Nordberg, 2005), perform optimization calculations by adapting some parameters, such as the probe length, to select probes in the expected T m range. For some programmes, such as ArrayOligoSelector (Bozdech et al., 2003) and ProbeSelect (Li and Stormo, 2001), T m is not considered and selection is based solely on the similar T m values of probes with uniform lengths and GC content. Finally, all of the available formulas calculate the T m for oligonucleotides that are free in solution, and not oligonucleotide probes bound to a glass surface. "

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    • "In the intra erythrocytic developmental stage/cycle (IDC), Plasmodium infects the red blood cells (RBCs), morphs through ring, trophozoite and schizont stages and emerges by rupturing the RBCs (Llinas and DeRisi, 2004). Microarray and proteomics based data has revealed significant regulation of transcripts and protein expression profiles associated with these morphological and developmental changes during the various stages of its life cycle (Bozdech et al., 2003a,b; Le Roch et al., 2004; Le Roch et al., 2003). Remarkable changes in the transcript abundance of the P. falciparum transcriptome were observed when subjected to different perturbed conditions (Natalang et al., 2008; Oakley et al., 2007; Tamez et al., 2008). "
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    ABSTRACT: Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how the parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which are best suited for better survival. With the discovery of natural antisense transcripts (NATs) in this parasite and considering the various proposed mechanisms by which NATs might regulate gene expression, it has been speculated that these might be playing a critical role in gene regulation. We report here the diversity of NATs in this parasite, using isolates taken directly from patients with differing clinical symptoms caused by malaria infection. Using a custom designed strand specific whole genome microarray, a total of 797 NATs targeted against annotated loci have been detected. Out of these, 545 NATs are unique to this study. The majority of NATs were positively correlated with the expression pattern of the sense transcript. However, 96 genes showed a change in sense/antisense ratio on comparison between uncomplicated and complicated disease conditions. The antisense transcripts map to a broad range of biochemical/ metabolic pathways, especially pathways pertaining to the central carbon metabolism and stress related pathways. Our data strongly suggests that a large group of NATs detected here are unannotated transcription units antisense to annotated gene models. The results reveal a previously unknown set of NATs that prevails in this parasite, their differential regulation in disease conditions and mapping to functionally well annotated genes. The results detailed here call for studies to deduce the possible mechanism of action of NATs, which would further help in understanding the in vivo pathological adaptations of these parasites.
    Full-text · Article · Mar 2014 · Experimental Parasitology
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    • "ND: not determined. contents during invasion [5] [21] in accordance with rhoptry proteins' expression during schizont stage [8] [9]. The rhoptry proteins characterized to date include the reticulocyte binding-like (RBL) family, i.e. "
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    ABSTRACT: Plasmodium falciparum malaria parasite invasion of erythrocytes is an essential step in host infection and the proteins involved in such invasion are the main target in developing an antimalarial vaccine. Secretory organelle-derived proteins (micronemal AMA1 protein and the RON2, 4, and 5 rhoptry neck proteins) have been recently described as components of moving junction complex formation allowing merozoites to move into a newly-created parasitophorous vacuole. This study led to identifying RON5 regions involved in binding to human erythrocytes by using a highly robust, sensitive and specific receptor-ligand interaction assay; it is further shown that the RON5 protein remains highly conserved throughout different parasite strains. It is shown that the binding peptide-erythrocyte interaction is saturable and sensitive to chymotrypsin and trypsin. Invasion inhibition assays using erythrocyte binding peptides showed that the RON5-erythrocyte interaction could be critical for merozoite invasion of erythrocytes. This work provides evidence (for the first time) suggesting a fundamental role for RON5 in erythrocyte invasion.
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