Biomedical subjects

Stilianos Arhondakis

Publications and source records attributed to Stilianos Arhondakis.

3 recordsLinked to original sources

PubMed2006

Compositional properties of human cDNA libraries: practical implications.

The strikingly wide and bimodal gene distribution exhibited by the human genome has prompted us to study the correlations between EST-counts (expression levels) and base composition of genes, especially since existing data are contradictory. Here we investigate how cDNA library preparation affects the GC distributions of ESTs and/or genes found in the library, and address consequences for expression studies. We observe that strongly anomalous GC distributions often indicate experimental biases or deficits during their preparation. We propose the use of compositional distributions of raw ESTs from a cDNA library, and/or of the genes they represent, as a simple and effective tool for quality control.

Base Composition↗

PubMed2004

Base composition and expression level of human genes.

It is well known that the gene distribution is non-uniform in the human genome, reaching the highest concentration in the GC-rich isochores. Also the amino acid frequencies, and the hydrophobicity, of the corresponding encoded proteins are affected by the high GC level of the genes localized in the GC-rich isochores. It was hypothesized that the gene expression level as well is higher in GC-rich compared to GC-poor isochores [Mol. Biol. Evol. 10 (1993) 186]. Several features of human genes and proteins, namely expression level, coding and non-coding lengths, and hydrophobicity were investigated in the present paper. The results support the hypothesis reported above, since all the parameters so far studied converge to the same conclusion, that the average expression level of the GC-rich genes is significantly higher than that of the GC-poor genes.

Base Composition↗

PubMed2003

LDH-A and alpha-actin as tools to assess the effects of temperature on the vertebrate genome: some problems.

In a recent paper written with the purpose of shedding light on the question of whether genomic GC levels are related to temperature in vertebrates, Ream et al. [Mol. Biol. Evol. 20 (2003) 105] offered an analysis of two sets of homologous genes: those coding for alpha-actin and lactate dehydrogenase-A (LDH-A). The conclusion was that "there is no consistent relationship between adaptation temperature and the percentage of thermal stability-enhancing G+C base pairs in protein-coding genes". We argue here that the data presented neither prove nor suggest such a conclusion because of conceptual and methodological errors.

Actins↗