Adsorption and temperature-dependent decomposition of SO₂ on Cu(100) and Cu(111): A fast and high-resolution core-level spectroscopy study

The adsorption and temperature-dependent decomposition of SO2 on Cu(100) and Cu(111) have been studied by fast and high-resolution core-level photoemission. The analysis of the S 2p and O 1s data shows that molecular SO2 adsorption dominates at 170 K. On heating the SO2-covered surfaces to about room temperature, SO2 decomposes into SO+O+S. On further heating SO+O recombine to form SO2, which is the only species detected in corresponding temperature-programmed desorption (TPD) experiments. From the temperature- (time-) dependent S and O coverages a ‘‘TPD curve’’ can be constructed

Atomic contributions to the valence band photoelectron spectra of metal-free, iron and manganese phthalocyanines

The present work reports a photoelectron spectroscopy study of the low-energy region of the valence band of metal-free phthalocyanine (H2Pc) compared with those of iron phthalocyanine (FePc) and manganese phthalocyanine (MnPc). Density Functional Theory calculations have been used to resolve the atomic orbital composition of the valence spectra of all the phthalocyanines (Pcs) analyzed in this study. Moreover we show how the atomic character of the Highest Occupied Molecular Orbital (HOMO) is reflected on the outermost valence band binding energy region. The intensity related to the C 2p contributions, resulting in the HOMO for H2Pc and FePc and in the HOMO-1 for MnPc as described by the theoretical predictions is in very good agreement with the experimental results. The DFT simulations, discerning the atomic contribution to the density of states, indicate how the central metal atom interacts with the C and N atoms of the molecule, giving rise to different partial and total density of states for these three different Pc molecules

m-MTDATA on Au(111): Spectroscopic Evidence of Molecule-Substrate Interactions

The starburst π-conjugated molecule based on triphenylamine (TPA) building blocks, 4,4′,4″-tris(N-3-ethylphenyl-N-phenylamino)triphenylamine (C57H48N4, m-MTDATA), is widely used in optoelectronic devices due to its electron-donating properties. The electronic structure of m-MTDATA adsorbed on an Au(111) surface was investigated by means of photoelectron spectroscopy (PES) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results were further compared to gas-phase measurements and DFT calculations. Our results clearly indicate a significant molecule-substrate interaction that induces considerable modifications on the electronic structure of the adsorbate compared to the isolated molecule. The energy level alignment analysis shows that the HOMO-LUMO gap is filled by new interface states

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands

DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The method used for these predictions is also validated on another external whole-genome dataset. Our results reveal features correlated to DNA methylation and confirm or disprove various hypotheses of DNA methylation related features. This study confirms correlations between DNA methylation and histone modifications, DNA structure, DNA sequence, genomic attributes and CpG island properties. Furthermore, the method has been validated on a genome-wide dataset from the ENCODE consortium. The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

<p>Abstract</p> <p>Background</p> <p>In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low <it>p</it>-value. However, the interpretation of each single <it>p</it>-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, <it>game theory </it>has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions.</p> <p>Results</p> <p>In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called <it>Comparative Analysis of Shapley value </it>(shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability.</p> <p>Conclusion</p> <p>CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways.</p

Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma

<p>Abstract</p> <p>Background</p> <p>The ubiquitin carboxyl-terminal hydrolase 1 (UCHL1) gene involved in the regulation of cellular ubiquitin levels plays an important role in different cellular processes including cell growth and differentiation. Aberrant expression of UCHL1 has been found in a number of human solid tumors including renal cell carcinoma (RCC). In RCC, UCHL1 overexpression is associated with tumor progression and an altered von Hippel Lindau gene expression.</p> <p>Methods</p> <p>To determine the underlying mechanisms for the heterogeneous UCHL1 expression pattern in RCC the UCHL1 promoter DNA methylation status was determined in 17 RCC cell lines as well as in 32 RCC lesions and corresponding tumor adjacent kidney epithelium using combined bisulfite restriction analysis as well as bisulfite DNA sequencing.</p> <p>Results</p> <p>UCHL1 expression was found in all 32 tumor adjacent kidney epithelium samples. However, the lack of or reduced UCHL1 mRNA and/or protein expression was detected in 13/32 RCC biopsies and 7/17 RCC cell lines and due to either a total or partial methylation of the UCHL1 promoter DNA. Upon 2'-deoxy-5-azacytidine treatment an induction of UCHL1 mRNA and protein expression was found in 9/17 RCC cell lines, which was linked to the demethylation degree of the UCHL1 promoter DNA.</p> <p>Conclusion</p> <p>Promoter hypermethylation represents a mechanism for the silencing of the UCHL1 gene expression in RCC and supports the concept of an epigenetic control for the expression of UCHL1 during disease progression.</p