Biomedical subjects

Cosmin Deciu

Publications and source records attributed to Cosmin Deciu.

3 recordsLinked to original sources

PubMed2003

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae.

The mRNA and protein expression in Saccharomyces cerevisiae cultured in rich or minimal media was analyzed by oligonucleotide arrays and quantitative multidimensional protein identification technology. The overall correlation between mRNA and protein expression was weakly positive with a Spearman rank correlation coefficient of 0.45 for 678 loci. To place the data sets in a proper biological context, a clustering approach based on protein pathways and protein complexes was implemented. Protein expression levels were transcriptionally controlled for not only single loci but for entire protein pathways (e.g., Met, Arg, and Leu biosynthetic pathways). In contrast, the protein expression of loci in several protein complexes (e.g., SPT, COPI, and ribosome) was posttranscriptionally controlled. The coupling of the methods described provided insight into the biology of S. cerevisiae and a clustering strategy by which future studies should be based.

Amino Acid Sequence↗

PubMed2002

Proteomic survey of metabolic pathways in rice.

A systematic proteomic analysis of rice (Oryza sativa) leaf, root, and seed tissue using two independent technologies, two-dimensional gel electrophoresis followed by tandem mass spectrometry and multidimensional protein identification technology, allowed the detection and identification of 2,528 unique proteins, which represents the most comprehensive proteome exploration to date. A comparative display of the expression patterns indicated that enzymes involved in central metabolic pathways are present in all tissues, whereas metabolic specialization is reflected in the occurrence of a tissue-specific enzyme complement. For example, tissue-specific and subcellular compartment-specific isoforms of ADP-glucose pyrophosphorylase were detected, thus providing proteomic confirmation of the presence of distinct regulatory mechanisms involved in the biosynthesis and breakdown of separate starch pools in different tissues. In addition, several previously characterized allergenic proteins were identified in the seed sample, indicating the potential of proteomic approaches to survey food samples with regard to the occurrence of allergens.

Amino Acid Sequence↗

PubMed2002

Analysis of quantitative proteomic data generated via multidimensional protein identification technology.

We describe the analysis of quantitative proteomic samples via multidimensional protein identification technology (MudPIT). Ratio amounts of the soluble portion of the S. cerevisiae proteome from cultures of S. cerevisiae strain S288C grown in either 14N minimal media or 15N-enriched minimal media were mixed and digested into a complex peptide mixture. A 1 x 14N/1 x 15N complex peptide mixture was analyzed by single-dimensional reversed-phase chromatography and electrospray ionization quadrapole time-of-flight mass spectrometry in order to demonstrate the replacement of 14N by 15N under the growth conditions used. After conformation of the incorporation of 15N into the labeled sample, three separate samples consisting of a 1 x 14N/1 x 15N complex peptide mixture, a 5 x 14N/1 x 15N complex peptide mixture, and a 10 x 14N/1 x 15N complex peptide mixture were analyzed via MudPIT. We demonstrate the dynamic range of the system by analyzing a 1:1, 5:1, and 10:1 data set using the soluble portion from S. cerevisiae grown in either 14N or 15N-enriched minimal media. The method described provides an accurate way to undertake a large-scale quantitative proteomic study.

Chromatography, High Pressure Liquid↗