The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.     

The identification and characterization of a novel splicing protein, Isy1p, of Saccharomyces cerevisiae

We have identified a novel splicing factor, Isy1p, through two-hybrid screens for interacting proteins involved in nuclear pre-mRNA splicing. Isy1p was tagged and demonstrated to be part of the splicing machinery, associated with spliceosomes throughout the splicing reactions. At least a portion of the Isy1 protein population is associated with snRNAs; low levels of U5 and U6 snRNAs are coimmunoprecipitated specifically with Isy1p. When the ISY1 gene was knocked out, no defect in vegetative growth was observed. Using a sensitive in vivo splicing assay, however, we observed lower splicing efficiency in the isy1 null mutant compared to wild-type, indicating that Isy1 p is important in the optimization of splicing.     

Bacterial counts in canine duodenal fluid after exposure to saline, sodium bicarbonate and hypertonic dextrose solutions used to maintain patency of chronically implanted catheters

Flushing of intestinal vascular access ports (VAPs) is commonly performed to prevent the problems of blockage and infection, and in this study four different flushing solutions were compared. The growth of bacteria from canine duodenal contents was compared in: 0.9% saline, 50% dextrose, 8.4% sodium bicarbonate (NaHCO3) and 0.01 M phosphate buffered saline (PBS). Duodenal contents from three laboratory beagles were serially diluted in these four solutions, spread plated onto agar at 24 h periods for 7 days and bacterial counts were performed. Immediately after the duodenal juices were added, no significant differences could be seen in bacterial counts with any of the solutions. Over the 7 day period, bacterial numbers greatly increased in saline and phosphate buffered saline, but greatly decreased in dextrose and sodium bicarbonate solutions. Dextrose and sodium bicarbonate appeared to be the most promising flushing solutions tested to minimize infections of associated intestinal VAPs.     

The GPI biosynthetic pathway as a therapeutic target for African sleeping sickness

African sleeping sickness is a debilitating and often fatal disease caused by tsetse fly transmitted African trypanosomes. These extracellular protozoan parasites survive in the human bloodstream by virtue of a dense cell surface coat made of variant surface glycoprotein. The parasites have a repertoire of several hundred immunologically distinct variant surface glycoproteins and they evade the host immune response by antigenic variation. All variant surface glycoproteins are anchored to the plasma membrane via glycosylphosphatidylinositol membrane anchors and compounds that inhibit the assembly or transfer of these anchors could have trypanocidal potential. This article compares glycosylphosphatidylinositol biosynthesis in African trypanosomes and mammalian cells and identifies several steps that could be targets for the development of parasite-specific therapeutic agents.     

Halide fluxes in epithelial cells measured with an automated cell plate reader

A method is introduced to measure chloride permeability in cultured epithelial cells using 6-methoxy-N-(3-sulfopropyl)quinolinium (SPQ) and 6-methoxy-N-ethylquinolinium iodide quinolinium (MEQ) as fluorescent chloride-sensitive probes. The method involves growing cells in multiwell plates, incubating cells with SPQ or MEQ, and then exchanging intracellular or extracellular halide ions with nitrate. The resulting time course of SPQ or MEQ fluorescence is followed by repetitive readings with a multiwell fluorescence plate reader. Exchange times are extracted by fitting the time course with a single exponential function of time. The method was validated by measuring the effect of chloride channel activators and blockers in A6 and MDCK cells. The baseline iodide/nitrate exchange time was 200-300 s. Isoproterenol (a modulator of cAMP-activated chloride channels) increased the exchange rate by a factor of 1.4+/-0.1; A23187 (a modulator of calcium-activated chloride channels) increased the rate by 3.4+/-0.4; bradykinin (also a modulator of calcium-activated chloride channels) increased the rate by 2.0+/-0.4; forskolin (a direct stimulator of adenylate cyclase) increased the rate by 2.7+/-0.3. Diphenylamine-2-carboxylate (a chloride channel blocker) decreased the rate by 0.12+/-0.03. These results indicate that our method is a valid indicator of halide-nitrate exchange in cultured epithelial cells.     

Full-thickness human foreskin transplantation onto nude rats as an in vivo model of acute human wound healing

Current wound-healing models do not fully duplicate the in vivo human environment. The feasibility of grafting human full-thickness foreskin onto nude rats, as a model of acute wound healing, was evaluated. Incisions were then created on the grafted skin, and wound healing was evaluated. Full-thickness human skin was obtained after elective circumcision and was grafted subcutaneously onto the dorsal thorax of nude rats. At 10 days after transplantation, graft beds were judged for graft viability, on the basis of gross appearance, texture, and adherence. Full-thickness wounds were then made in the foreskin. Graft wounds were left to close by secondary intention. The wounds were allowed to heal for 7 days. Wounds were excised and tested for breaking stress. Histological evaluations included proliferating cell nuclear antigen, factor VIII, hematoxylin and eosin, and trichrome staining. Twenty grafts were performed, with 100 percent viability. Upon incision, all grafts bled freely, indicating a rich vascular supply and tissue viability. Graft viability was confirmed by the presence of proliferating cells in the parabasal stratum of the epithelium. Furthermore, there was evidence of angiogenesis, as confirmed by staining for factor VIII. Breaking stress was evaluated by tensiometry, 7 days after wounding. Histological evaluations revealed viable grafts and active wound-healing events. Full-thickness human skin can be successfully transplanted onto nude rats, providing a larger, more physiological model of human wound healing. This model closely parallels the in vivo situation, providing a promising model for study of the complex biological processes of acute human wound healing, in a reproducible manner.     

What is life? Prerequisites for a definition

Biologists view life as transient while theologians see it as eternal. An unbiased definition for life would respect both views until one or both were eliminated by evidence. This paper identifies pre-requisites for such a definition. First among these is that all assumptions be made explicit. Currently "life" is surrounded by implicit assumptions, e.g., that it is what organisms lose at death or that it is eternal, that its quality is inversely related to personal distress, that it originated some four billion years ago, and that animate matter can be distinguished from inanimate matter. None of these assumptions are supported by data. It is possible therefore that "life" is as meaningless as phlogiston. If life has meaning, i.e., if it is true, it must be as permanent as buoyancy, gravity, electricity, and the other truths of nature. Any definition for life that would permit such truth to be seen must be free of unwarranted assumptions. For the moment, at least, such a definition would need to be loosely structured and broadly focused. It would need to describe the long and convoluted process by which matter and energy form organisms which then evolve to form conscious organisms which then explore nature and eventually discover truth. Such a definition would include all the reactions and interactions of matter and energy and all the aspects of conscious discovery. It would suffer from superficiality, but, by being free from bias, provide a foundation for dialogue between biologists and theologians.