Prediction of protein-protein interaction types using association rule based classification

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2009 Park et alBackground: Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches. Results: This work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification. We incorporated domain information from protein complexes in SCOP proteins and identified 354 domain-interaction sites. 14 interface properties were calculated from amino acid and secondary structure composition and then used to generate a set of association rules characterizing these domain-interaction sites employing the APRIORI algorithm. Our results regarding the classification of PPI types based on a set of discovered association rules shows that the discriminative ability of association rules can significantly impact on the prediction power of classification models. We also showed that the accuracy of the classification can be improved through the use of structural domain information and also the use of secondary structure content. Conclusion: The advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/SHP was supported by the Korea Research Foundation Grant funded by the Korean Government(KRF-2005-214-E00050). JAR has been supported by the Programme Alβan, the European Union Programme of High level Scholarships for Latin America, scholarship E04D034854CL. SK was supported by Soongsil University Research Fund

Electronic transport in a two-dimensional superlattice engineered via self-assembled nanostructures

Nanoscience offers a unique opportunity to design modern materials from the bottom up, via low-cost, solution processed assembly of nanoscale building blocks. These systems promise electronic band structure engineering using not only the nanoscale structural modulation, but also the mesoscale spatial patterning, although experimental realization of the latter has been challenging. Here we design and fabricate a new type of artificial solid by stacking graphene on a self-assembled, nearly periodic array of nanospheres, and experimentally observe superlattice miniband effects. We find conductance dips at commensurate fillings of charge carriers per superlattice unit cell, which are key features of minibands that are induced by the quasi-periodic deformation of the graphene lattice. These dips become stronger when the lattice strain is larger. Using a tight-binding model, we simulate the effect of lattice deformation as a parameter affecting the inter-atomic hopping integral, and confirm the superlattice transport behavior. This 2D material-nanoparticle heterostructure enables facile band structure engineering via self-assembly, promising for large area electronics and optoelectronics applications

Effect of hydrostatic pressure on anelastic stress relaxation in a mixed-alkali silicate glass

The effect of hydrostatic pressure on the anelastic stress relaxation of a mixed-alkali silicate glass (0.05 Na₂O, 0.95 K₂O, 3 SiO₂) was studied at 75°C between ambient pressure and 6 kbar. The activation volume of diffusion was found to be - 4.2 cm³/mole. It is proposed that a reequilibration of the defect population at pressure gives rise to the negative activation volume of diffusion --Abstract, page ii

Stability of Glutamate-Aspartate Cardioplegia Additive Solution in Polyolefin IV Bags

Objective: Glutamate-aspartate cardioplegia additive solution (GACAS) is used to enhance myocardial preservation and left ventricular function during some cardiac surgeries. This study was designed to evaluate the stability of compounded GACAS stored in sterile polyolefin intravenous (IV) bags. The goal is to extend the default USP beyond-use date (BUD) and reduce unnecessary inventory waste. Methods: GACAS was compounded and packaged in sterile polyolefin 250 mL IV bags. The concentration was 232 mM for each amino acid. The samples were stored under refrigeration (2°C-8°C) and analyzed at 0, 1, and 2 months. At each time point, the samples were evaluated by pH measurement and visual inspection for color, clarity, and particulates. The samples were also analyzed by high-performance liquid chromatography (HPLC) for potency and degradation products. Due to the lack of ultraviolet (UV) chromophores of glutamate and aspartate, the samples were derivatized by ortho-phthalaldehyde prior to HPLC analysis. Results: The time zero samples of GACAS passed the physical, chemical, and microbiological tests. Over 2 months of storage, there was no significant change in pH or visual appearance for any of the stability samples. The HPLC results also indicated that the samples retained 101% to 103% of the label claim strengths for both amino acids. Conclusion: The physical and chemical stability of extemporaneously prepared GACAS has been confirmed for up to 2 months in polyolefin IV bags stored under refrigeration. With proper sterile compounding practice and microbiology testing, the BUD of this product can be extended to 2 months

Daphnia Halloween genes that encode cytochrome P450s mediating the synthesis of the arthropod molting hormone: Evolutionary implications

<p>Abstract</p> <p>Background</p> <p>In crustaceans and insects, development and reproduction are controlled by the steroid hormone, 20-hydroxyecdysone (20E). Like other steroids, 20E, is synthesized from cholesterol through reactions involving cytochrome P450s (CYPs). In insects, the CYP enzymes mediating 20E biosynthesis have been identified, but evidence of their probable presence in crustaceans is indirect, relying solely on the ability of crustaceans to synthesize 20E.</p> <p>Results</p> <p>To investigate the presence of these genes in crustaceans, the genome of <it>Daphnia pulex </it>was examined for orthologs of these genes, the Halloween genes, encoding those biosynthetic CYP enzymes. Single homologs of <it>spook-CYP307A1</it>, <it>phantom-CYP306A1</it>, <it>disembodied-CYP302A1</it>, <it>shadow-CYP315A1 </it>and <it>shade-CYP314A1 </it>were identified in the <it>Daphnia </it>data base. Phylogenetic analysis indicates an orthologous relationship between the insect and <it>Daphnia </it>genes. Conserved intron/exon structures and microsynteny further support the conclusion that these steroidogenic CYPs have been conserved in insects and crustaceans through some 400 million years of evolution.</p> <p>Conclusion</p> <p>Although these arthropod steroidogenic CYPs are related to steroidogenic CYPs in <it>Caenorhabditis elegans </it>and vertebrates, the data suggest that the arthropod steroidogenic CYPs became functionally specialized in a common ancestor of arthropods and are unique to these animals.</p