Background: Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.

Oxidative stress may initiate lipid peroxidation that generates ethane. Ethane, at low concentrations, is eliminated by pulmonary exhalation. Previous methods have not allowed frequent sampling, thus ethane kinetics has not been studied in man. A validated method over the range 3.8-100,000 ppb with a limit of quantitation of 3.8 ppb (CV 9.3%) based on cryofocusing technique of a 60 ml breath sample allowed frequent sampling. Due to a rapid analytical procedure batches of more than 100 samples may be analyzed. In human volunteers (24-55 years) uptake was studied for up to 23 min (n = 9), elimination was studied for 210 min (n = 9). Ethane was inhaled (concentrations varied from 16 to 29 ppm (parts per million)) through a non-rebreathing system; sampling was performed with short intervals from the expiratory limb. Samples were also drawn from the inhalatory limb. Ninety-five percent of steady state (inspired) concentration was reached within 1.75 min. Five percent of the initially inhaled concentrations was found in exhaled air 1.5 min after termination of inhalation. A terminal mean half life of 31 min for ethane was also observed. The data indicate that frequent sampling will be necessary to capture relevant changes in breath ethane.

Background: The measurement of gene expression using microarray technology is a complicated process in which a large number of factors can be varied. Due to the lack of standard calibration samples such as are used in traditional chemical analysis it may be a problem to evaluate whether changes done to the microarray procedure actually improve the identification of truly differentially expressed genes. The purpose of the present work is to report the optimization of several steps in the microarray process both in laboratory practices and in data processing using criteria that do not rely on external standards.

Background: RNA dot blot hybridization is a commonly used technique for gene expression assays. However, membrane based RNA dot/slot blot hybridization is time consuming, requires large amounts of RNA, and is less suited for parallel assays of more than one gene at a time. Here, we describe a glass-slide based miniaturized RNA dot blot (RNA array) procedure for rapid and parallel gene expression analysis using fluorescently labeled probes.

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