Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets

<p>Abstract</p> <p>Background</p> <p>The function and significance of the widespread expression of natural antisense transcripts (NATs) is largely unknown. The ability to quantitatively assess changes in NAT expression for many different transcripts in multiple samples would facilitate our understanding of this relatively new class of RNA molecules.</p> <p>Results</p> <p>Here, we demonstrate that standard expression analysis Affymetrix MOE430 and HG-U133 GeneChips contain hundreds of probe sets that detect NATs. Probe sets carrying a "Negative Strand Matching Probes" annotation in NetAffx were validated using Ensembl by manual and automated approaches. More than 50 % of the 1,113 probe sets with "Negative Strand Matching Probes" on the MOE430 2.0 GeneChip were confirmed as detecting NATs. Expression of selected antisense transcripts as indicated by Affymetrix data was confirmed using strand-specific RT-PCR. Thus, Affymetrix datasets can be mined to reveal information about the regulated expression of a considerable number of NATs. In a correlation analysis of 179 sense-antisense (SAS) probe set pairs using publicly available data from 1637 MOE430 2.0 GeneChips a significant number of SAS transcript pairs were found to be positively correlated.</p> <p>Conclusion</p> <p>Standard expression analysis Affymetrix GeneChips can be used to measure many different NATs. The large amount of samples deposited in microarray databases represents a valuable resource for a quantitative analysis of NAT expression and regulation in different cells, tissues and biological conditions.</p

Serum-Kupfer-Analysen mit Hilfe der Absorptions-Flammenphotometrie

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Stat6-Dependent Inhibition of Mincle Expression in Mouse and Human Antigen-Presenting Cells by the Th2 Cytokine IL-4

The C-type lectin receptors (CLR) Mincle, Mcl and Dectin-2 bind mycobacterial and fungal cell wall glycolipids and carbohydrates. Recently, we described that expression of these CLR is down-regulated during differentiation of human monocytes to dendritic cells (DC) in the presence of GM-CSF and IL-4. Here, we demonstrate that the Th2 cytokine IL-4 specifically inhibits expression of Mincle, Mcl and Dectin-2in human APC. This inhibitory effect of IL-4 was observed across species, as murine macrophages and DC treated with IL-4 also down-regulated these receptors. IL-4 blocked up-regulation of Mincle and Mcl mRNA expression and cell surface protein by murine macrophages in response to the Mincle ligand Trehalose-6,6-dibehenate (TDB), whereas the TLR4 ligand LPS overcame inhibition by IL-4. Functionally, down-regulation of Mincle expression by IL-4 was accompanied by reduced cytokine production upon stimulation with TDB. These inhibitory effects of IL-4 were dependent on the transcription factor Stat6. Together, our results show that the key Th2 cytokine IL-4 exerts a negative effect on the expression of Mincle and other Dectin-2 cluster CLR in mouse and human macrophages and DC, which may render these sentinel cells less vigilant for sensing mycobacterial and fungal ligands

Novel role of the SIRT4-OPA1 axis in mitochondrial quality control

Mammalian sirtuins are fundamental regulators of a plethora of cellular functions, including gene expression, proliferation, metabolism, and ultimatively cellular aging and organismal life-span. The mitochondrial sirtuin SIRT4 acts as metabolic tumor suppressor and is down-regulated in many cancer types. We showed that SIRT4 expression was up-regulated during replicative senescence and by different anti-proliferative and senescence inducing stressors, including UVB and ionizing radiation, due to inhibition of its negative regulator, microRNA miR-15b. In our recent studies we addressed the molecular consequences of increased SIRT4 expression for mitochondrial function and quality control. We demonstrated that SIRT4 reduces O2 consumption and decreases mitochondrial membrane potential in line with an increased generation of mitochondrial reactive oxygen species (mtROS). This led to the accumulation of dysfunctional mitochondria and a more fused mitochondrial network associated with a decreased mitophagic clearance. Mechanistically, our data indicate that SIRT4 promotes mitochondrial fusion in an enzymatically dependent manner through interaction with and stabilization of the dynamin-related GTPase L-OPA1, thereby opposing fission and mitophagy. Our findings provide novel insight in the role of SIRT4 as stress triggered factor that causes mitochondrial dysfunction and impaired mitochondrial quality control through decreased mitophagy, a major hallmark of aging

First-principles study of electron transport through C20C_{20} cages

Electron transport properties of C$_{20}$ molecules suspended between gold electrodes are investigated using first-principles calculations. Our study reveals that the conductances are quite sensitive to the number of C$_{20}$ molecules between electrodes: the conductances of C$_{20}$ monomers are near 1 G$_{0}$, while those of dimers are markedly smaller, since incident electrons easily pass the C$_{20}$ molecules and are predominantly scattered at the C$_{20}$-C$_{20}$ junctions. Moreover, we find both channel currents locally circulating the outermost carbon atoms.Comment: 8 pages and 3 figure