Toward the blood-borne miRNome of human diseases.

In a multicenter study, we determined the expression profiles of 863 microRNAs by array analysis of 454 blood samples from human individuals with different cancers or noncancer diseases, and validated this 'miRNome' by quantitative real-time PCR. We detected consistently deregulated profiles for all tested diseases; pathway analysis confirmed disease association of the respective microRNAs. We observed significant correlations (P = 0.004) between the genomic location of disease-associated genetic variants and deregulated microRNAs.

Genome-wide transcriptome profile of the human osteosarcoma Sa OS and U-2 OS cell lines.

With the use of genome-wide cDNA microarrays, we investigated the transcriptome profile of the human osteosarcoma Sa OS and U-2 OS cell lines. In all, 1,098 chip entries were differentially regulated in the two cell lines; of these, 796 entries corresponded to characterized mRNAs. The identified genes are mostly expressed in epithelial tissues and localize on chromosomes 1, 10, and 20. Furthermore, signaling cascades for cell cycle, glycolysis, and gluconeogenesis, the p53 pathway, cell communication, and focal adhesion were found to be differently regulated in the two cell lines. The transcriptome profiles reported here provide novel information about the considerable molecular differences between these two widely used human osteosarcoma cell lines.

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development.

Nk-2 proteins are essential developmental regulators from flies to humans. In Drosophila, the family member tinman is the major regulator of cell fate within the dorsal mesoderm, including heart, visceral, and dorsal somatic muscle. To decipher Tinman's direct regulatory role, we performed a time course of ChIP-on-chip experiments, revealing a more prominent role in somatic muscle specification than previously anticipated. Through the combination of transgenic enhancer-reporter assays, colocalization studies, and phenotypic analyses, we uncovered two additional factors within this myogenic network: by activating eyes absent, Tinman's regulatory network extends beyond developmental stages and tissues where it is expressed; by regulating stat92E expression, Tinman modulates the transcriptional readout of JAK/STAT signaling. We show that this pathway is essential for somatic muscle development in Drosophila and for myotome morphogenesis in zebrafish. Taken together, these data uncover a conserved requirement for JAK/STAT signaling and an important component of the transcriptional network driving myogenesis.

Regulation of translation initiation in mussels (Mytilus galloprovincialis, lam.) following contamination stress.

The use of mussels (Mytilus sp.) as bioindicators of the aquatic environment is a valuable approach to monitor environmental contamination. Applying batteries of biomarkers is an essential prerequisite, since the complexity of environmental contaminants can induce in mussels a variety of structural and functional responses, which are not necessarily correlated. In an attempt to correlate translation responses to contamination stress, the sedimentation profiles of runoff ribosomes isolated from digestive gland cells of control or contaminated Mediterranean mussels (Mytilus galloprovincialis, Lam.) were examined and the efficiency of these ribosomes to accomplish protein synthesis was determined. While the major species of ribosomal material was 80S monomers, native 60S and 40S ribosomal subunits were also detected independently of the contamination level in the surrounding waters. However, concomitant with the increase of contamination stress, the level of 80S ribosomes was reduced in favor of free ribosomal subunits. In addition, ribosomes isolated from contaminated mussels and programmed with poly(U) were less efficient to enzymatically bind AcPhe-tRNA, compared with ribosomes from control samples. These results suggest that the contamination stress causes stoichiometric aberrations in the ribosomal particle pool and reduction of translation machinery capability to initate protein synthesis. Data support the notion that downregulation of translation is an important component of the cellular stress response and may be exploited as a biomarker of environmental contamination.

The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.

A photoreactive analogue of spermine, N1-azidobenzamidino (ABA)-spermine, was covalently attached after irradiation to Escherichia coli 30S ribosomal subunits or naked 16S rRNA. By means of RNase H digestion and primer extension, the cross-linking sites of ABA-spermine in naked 16S rRNA were characterised and compared with those identified in 30S subunits. The 5' domain, the internal and terminal loops of helix H24, as well as the upper part of helix H44 in naked 16S rRNA, were found to be preferable binding sites for polyamines. Association of 16S rRNA with ribosomal proteins facilitated its interaction with photoprobe, except for 530 stem-loop nt, whose modification by ABA-spermine was abolished. Association of 30S with 50S subunits, poly(U) and AcPhe-tRNA (complex C) further altered the susceptibility of ABA-spermine cross-linking to 16S rRNA. Complex C, modified in its 30S subunit by ABA-spermine, reacted with puromycin similarly to non-photolabelled complex. On the contrary, poly(U)-programmed 70S ribosomes reconstituted from photolabelled 30S subunits and untreated 50S subunits bound AcPhe-tRNA more efficiently than untreated ribosomes, but were less able to recognise and reject near cognate aminoacyl-tRNA. The above can be interpreted in terms of conformational changes in 16S rRNA, induced by the incorporation of ABA-spermine.