Transduction motif analysis of gastric cancer based on a human signaling network

To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

Epipolythiodioxopiperazines from fungi: chemistry and bioactivities.

Epipolythiodioxopiperazines (ETPs), characterized by a unique bridged disulfide or polysulfide dioxopiperazine six-membered ring, occur in many fungi. Due to its broad spectra of bioactivities, ETPs have drawn wide attention in recent years. This review covers diverse natural sources that produce ETPs, the synthetic chemistry of ETPs and an overview of promising bioactivities exhibited by some well studied ETPs. The plausible biosynthetic hypotheses of ETPs and some new results on antitumor activity of ETPs are also reviewed.

Microelectrical characterizations of junctions in solar cell devices by scanning Kelvin probe force microscopy.

Scanning Kelvin probe force microscopy was applied to the microelectrical characterizations of junctions in solar cell devices. Surface Fermi-level pinning effects on the surface potential measurement were avoided by applying a bias voltage (V(b)) to the device and taking the V(b)-induced potential and electric field changes. Two characterizations are presented: the first is a direct measurement of Bi-induced junction shift in GaInNAs(Bi) cells; the second is a junction-uniformity measurement in a-Si:H devices. In the first characterization, using Bi as a surfactant during the molecular beam epitaxy growth of GaInNAs(Bi) makes the epitaxial layer smoother. However, the electrical potential measurement exhibits a clear Bi-induced junction shift to the back side of the absorber layer, which results in significant device degradation. In the second characterization, the potential measurement reveals highly non-uniform electric field distributions across the n-i-p junction of a-Si:H devices; the electric field concentrates much more at both n/i and i/p interfaces than in the middle of the i-layer. This non-uniform electric field is due possibly to high defect concentrations at the interfaces. The potential measurements further showed a significant improvement in the electric field uniformity by depositing buffer layers at the interfaces, and this indeed improved the device performance.

Electrically benign behavior of grain boundaries in polycrystalline CuInSe2 films.

The classic grain-boundary (GB) model concludes that GBs in polycrystalline semiconductors create deep levels that are extremely harmful to optoelectronic applications. However, our first-principles density-functional theory calculations reveal that, surprisingly, GBs in CuInSe2 (CIS) do not follow the classic GB model: GBs in CIS do not create deep levels due to the large atomic relaxation in GB regions. Thus, unlike the classic GB model, GBs in CIS are electrically benign, which explains the long-standing puzzling fact that polycrystalline CIS solar cells with remarkable efficiency can be achieved without deliberate GB passivation. This benign electrical character of GBs in CIS is confirmed by our scanning Kelvin probe microscopy measurements on Cu(In,Ga)Se2 chalcopyrite films.

Scanning tunneling spectroscopy of Ag films: the effect of periodic versus quasiperiodic modulation.

By using scanning tunneling spectroscopy to probe a silver thin film that contains both periodic and quasiperiodic modulation, and by using Fourier analysis, we unravel the influences of individual Fourier components of the scattering potential (periodic versus quasiperiodic) on the electronic structure of a one-dimensional quasiperiodically modulated thin Ag film. Along the periodically modulated direction, a Bragg reflection-induced energy gap is observed in k space. On the other hand, the exotic E vs k spectrum with many minigaps was observed along the quasiperiodic direction.

Building Pb nanomesas with atomic-layer precision.

We demonstrate a novel scheme for manipulating metallic nanostructures involving a macroscopic number of atoms, yet with precise control in their local structures. The scheme entails a two-step process: (a) a triggering step using a scanning tunneling microscope, followed by (b) self-driven and self-limiting mass-transfer process. By using this scheme, we construct Pb nanomesas on Si(111) substrates whose thickness can be controlled with atomic-layer precision. The kinetic barrier for the mass transfer and the underlying mechanism behind this novel manipulation are determined.