Annotation-based meta-analysis of microarray experiments

We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments

Quantum Dot in Z-shaped Graphene Nanoribbon

Stimulated by recent advances in isolating graphene, we discovered that quantum dot can be trapped in Z-shaped graphene nanoribbon junciton. The topological structure of the junction can confine electronic states completely. By varying junction length, we can alter the spatial confinement and the number of discrete levels within the junction. In addition, quantum dot can be realized regardless of substrate induced static disorder or irregular edges of the junction. This device can be used to easily design quantum dot devices. This platform can also be used to design zero-dimensional functional nanoscale electronic devices using graphene ribbons.Comment: 4 pages, 3 figure

Structure-based Discovery of Novel Small Molecule Wnt Signaling Inhibitors by Targeting the Cysteine-rich Domain of Frizzled.

Frizzled is the earliest discovered glycosylated Wnt protein receptor and is critical for the initiation of Wnt signaling. Antagonizing Frizzled is effective in inhibiting the growth of multiple tumor types. The extracellular N terminus of Frizzled contains a conserved cysteine-rich domain that directly interacts with Wnt ligands. Structure-based virtual screening and cell-based assays were used to identify five small molecules that can inhibit canonical Wnt signaling and have low IC50 values in the micromolar range. NMR experiments confirmed that these compounds specifically bind to the Wnt binding site on the Frizzled8 cysteine-rich domain with submicromolar dissociation constants. Our study confirms the feasibility of targeting the Frizzled cysteine-rich domain as an effective way of regulating canonical Wnt signaling. These small molecules can be further optimized into more potent therapeutic agents for regulating abnormal Wnt signaling by targeting Frizzled