Genomic profiling: cDNA arrays and oligoarrays.

The introduction of microarray technology, which is a multiplexed hybridization-based process, allows simultaneous analysis of a large number of nucleic acid transcripts. This massively parallel analysis of a cellular genome will become essential for guiding disease diagnosis and molecular profiling of an individual patient's tumor. Nucleic acid based microarrays can be used for: gene expression profiling, single-nucleotide polymorphisms (SNPs) detection, array-comparative genomic hybridizations, comparisons of DNA-methylation status, and microRNA evaluation.

Characterization of the last step of the aerobic phenylacetic acid degradation pathway.

Phenylacetic acid (PA) degradation in bacteria involves an aerobic hybrid pathway encoded by the paa gene cluster. It is shown here that succinyl-CoA is one of the final products of this pathway in Pseudomonas putida and Escherichia coli. Moreover, in vivo and in vitro studies revealed that the paaE gene encodes the beta-ketoadipyl-CoA thiolase that catalyses the last step of the PA catabolic pathway, i.

Identification of thioredoxin reductase 1-regulated genes using small interference RNA and cDNA microarray.

Thioredoxin reductase 1 (TrxR1) is a cytosolic enzyme that plays a central role in controlling cellular redox homeostasis. TrxR1 can transduce regulatory redox signals through NADPH-dependent reduction of thioredoxin (Trx), which is able to reduce a broad spectrum of target enzymes and regulate the activity of several transcription factors (e.g.

Use of surface-enhanced laser desorption/ionization -time of flight to explore bacterial proteomes.

Surface-enhanced laser desorption/ionization (SELDI)-time of flight is a recent technology that allows proteomic analysis with limited material requirements. This characteristic makes it a valuable technique for microbiologists handling problematic samples, such as low cell number cultures. We compared three simple procedures for protein extraction from bacteria for compatibility with the ProteinChip Array; we also determined the amount of protein required for each analysis.

Development of a new reference standard for microarray experiments.

Often microarray studies require a reference to indirectly compare the samples under observation. References based on pooled RNA from different cell lines have already been described (here referred to as RNA-R), but they usually do not exhaustively represent the set of genes printed on a chip, thus requiring many adjustments during the analyses. A reference could also be generated in vitro transcribing the collection of cDNA clones printed on the microarray in use (here referred to as T3-R).