Serial analysis of gene expression (SAGE) in Plasmodium falciparum: application of the technique to A-T rich genomes.

The advent of high-throughput methods for the analysis of global gene expression, together with the Malaria Genome Project open up new opportunities for furthering our understanding of the fundamental biology and virulence of the malaria parasite. Serial analysis of gene expression (SAGE) is particularly well suited for malarial systems, as the genomes of Plasmodium species remain to be fully annotated. By simultaneously and quantitatively analyzing mRNA transcript profiles from a given cell population, SAGE allows for the discovery of new genes. In this study, one reports the successful application of SAGE in Plasmodium falciparum, 3D7 strain parasites, from which a preliminary library of 6880 tags corresponding to 4146 different genes was generated. It was demonstrated that P. falciparum is amenable to this technique, despite the remarkably high A-T content of its genome. SAGE tags as short as 10 nucleotides were sufficient to uniquely identify parasite transcripts from both nuclear and mitochondrial genomes. Moreover, the skewed A-T content of parasite sequence did not preclude the use of enzymes that are crucial for generating representative SAGE libraries. Finally, a few modifications to DNA extraction and cloning steps of the SAGE protocol proved useful for circumventing specific problems presented by A-T rich genomes.

A call for respect and equality for indigenous scholarship in Hawaiian health.

In the State of Hawai'i, there has been steady interest on the part of Western scholarly communities in studies of indigenous Hawaiian intellectual properties. There exists an academic desire to appropriate new fields of knowledge from Hawaiian sources. This pursuit of knowledge runs the risk of increasing the sense of cultural violation already felt by many indigenous populations. If conducted using the means of colonialist intellectualism common to the academy of the dominant culture, this quest for new information will likely contribute to a legacy of spiritual and cultural violation felt by the Hawaiian people. This effort will then likely lead to a further decline in feelings of cultural integrity on the part of native populations. This endeavor will then increase the basis for the psycho-spiritual malaise that underpins the negative health statistics evidenced in Native Hawaiian populations. If present day researchers are to gain greater insight into the lexicon of knowledge available from Native Hawaiians, they will have to employ methods that provide for indigenous scholars to serve as co-researchers in this quest. If Western scholars are to gain access to Native Hawaiian knowledge, such information will more likely come as a result of healing this social wound by developing a new relationship of respect for Native Hawaiian cosmology, epistemology, and pedagogy--one wherein all parties are accepted as co-equals in the scholarly process.

Combining serial analysis of gene expression and array technologies to identify genes differentially expressed in breast cancer.

Several methods have been used recently to determine gene expression profiles of cell populations. Here we demonstrate the strength of combining two approaches, serial analysis of gene expression (SAGE) and DNA arrays, to help elucidate pathways in breast cancer progression by finding genes consistently expressed at different levels in primary breast cancers, metastatic breast cancers, and normal mammary epithelial cells. SAGE profiles of 21PT and 21MT, two well-characterized breast tumor cell lines, were compared with SAGE profiles of normal breast epithelial cells to identify differentially expressed genes. A subset of these candidates was then placed on an array and screened with clinical breast tumor samples to find genes and expressed sequence tags that are consistently expressed at different levels in diseased and normal tissues. In addition to finding the predicted overexpression of known breast cancer markers HER-2/neu and MUC-1, the powerful coupling of SAGE and DNA arrays resulted in the identification of genes and potential pathways not implicated previously in breast cancer. Moreover, these techniques also generated information about the differences and similarities of expression profiles in primary and metastatic breast tumors. Thus, combining SAGE and custom array technology allowed for the rapid identification and validation of the clinical relevance of many genes potentially involved in breast cancer progression. These differentially expressed genes may be useful as tumor markers and prognostic indicators and may be suitable targets for various forms of therapeutic intervention.