A measure of semantic similarity between gene ontology terms based on semantic pathway covering

Semantic similarity between Gene Ontology (GO) terms is critical in resolving semantic heterogeneousness when integrating heterogeneous biological databases. Traditionally, distance based and information content based measures are two major methods. In this paper, a new method based on semantic pathway covering is proposed and an algorithm, COMBINE algorithm, is presented, which considers information contents of two given nodes and those of all nodes included in the two nodes’ pathways. Experiments show that COMBINE algorithm obtains the highest correlation index compared with those distance based and information content based algorithms.     

Molecular diversity and evolution of cystine knot toxins of the tarantula Chilobrachys jingzhao

Cystine knot toxins (CKTs) in spider venoms represent a rich source of novel ligands for varied ion channels. Here, we identified 95 novel putative CKT precursors by analyzing expressed sequence tags of the tarantula Chilobrachys jingzhao venom gland. Phylogenetics analyses revealed one orphan family and six families with sequence similarity to known toxins. To further investigate the relationships of their structures, functions and evolution, we assayed 10 representative toxins for their effect on ion channels, and performed structure model comparisons, evolution analysis and toxin distribution analysis. This study revealed two major types of CKTs: pore-blocking toxins and gating modifier toxins. A few blockers were observed with relatively high abundance and wide distribution, which may be a category of original toxins that block channels conserved in various preys with relatively high specificity. The gating modifier families contain advanced toxins, usually have many members and interact with diverse regulatory components of channels.     

Size-controlled synthesis of Fe3O4 and Fe3O4@SiO2 nanoparticles and their superparamagnetic properties tailoring

Superparamagnetic properties and fine-tuning of colloidal Fe₃O₄nanoparticles are important for their widespread biomedical applications. Herein, colloidal Fe₃O₄nanoparticles(NPs) of different sizes(8–20 nm) were prepared,and their hydrophilization with SiO₂shell coating to be Fe₃O₄@SiO₂core-shell had been realized successively.The size of Fe₃O₄NPs was controlled by different heating rate...