Article

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray

Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA.
Genome biology (Impact Factor: 10.47). 02/2003; 4(2):R9. DOI: 10.1186/gb-2003-4-2-r9
Source: PubMed

ABSTRACT 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.

Full-text

Available from: Fred E Cohen, May 30, 2015
0 Followers
 · 
115 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract The goal of the present research was to identify the genes that are differentially expressed between two lineages of Pacific white shrimp Litopenaeus vannamei displaying different susceptibilities to Taura syndrome virus (TSV) and to understand the molecular pathways involved in resistance to the disease. An oligonucleotide microarray was constructed and used to identify several genes that were differentially expressed in the two L. vannamei lineages following infection with TSV. Individual L. vannamei from either resistant or susceptible lineages were exposed via injection to TSV. Individuals were removed at 6 and 24 h postinfection, and gene expression was assessed with the in-house microarray. The microarray data resulted in the selection of a set of 397 genes that were altered by TSV exposure between the different lineages. Significantly differentially expressed genes were subjected to hierarchical clustering and revealed a lineage-dependent clustering at 24 h postinoculation, but not at 6 h postinoculation. Discriminant analysis resulted in the identification of a set of 11 genes that were able to correctly classify Pacific white shrimp as resistant or susceptible based on gene expression data. Received June 21, 2013; accepted October 24, 2013.
    Journal of Aquatic Animal Health 09/2014; 26(3):137-143. DOI:10.1080/08997659.2013.860058 · 0.97 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: 1 Abstract. The binding of transcriptional regulators to DNA can induce or repress gene expression in a cell-specific manner in different physiological conditions. To help understand this mechanism on a genome-wide scale, we developed a series of microarrays for chromatin immunoprecipitation (ChIP chips) for human and mouse. To assay DNA binding that occurs near to transcriptional start sites (TSSs), we first created gene-centric ChIP chips to reflect activity in transcriptional units' proximal promoters. To select TSS data of high confidence for human and mouse, we merged mapping data from at least three gene sets (such as RefSeq, Ensembl, and MGC), selecting TSSs (n = 18k for human; 16k for mouse) consistent across at least two databases. Promoters (-8 kb to +2 kb relative to the TSS) were extracted from the genome after processing with RepeatMasker 1 . To assay transcriptional regulators, including those that bind far from known transcriptional units, we also designed a much larger chipset based on the entire RepeatMasked genome. These genome-scale oligonucleotide ChIP chips required the selection of sequences that can optimally represent a region of the genome of at least 300 nt. To help minimize false positive signals, representative probes were designed close enough that adjacent probes could measure any binding event. On the other hand, probes were selected far enough apart so a minimal number could represent large regions or all of the genome. Finally, to ensure that we could identify binding events near the edge of repetitive genomic regions, we selected probes near the distal ends of each non-repetitive region. 2 Results.