Memetic algorithms for the unconstrained binary quadratic programming problem

This paper presents a memetic algorithm, a highly effective evolutionary algorithm incorporating local search for solving the unconstrained binary quadratic programming problem (BQP). To justify the approach, a fitness landscape analysis is conducted experimentally for several instances of the BQP. The results of the analysis show that recombination-based variation operators are well suited for the evolutionary algorithms with local search. Therefore, the proposed approach includes--besides a highly effective randomized k-opt local search--a new variation operator that has been tailored specially for the application in the hybrid evolutionary framework. The operator is called innovative variation and is fundamentally different from traditional crossover operators, since new genetic material is included in the offspring which is not contained in one of the parents. The evolutionary heuristic is tested on 35 publicly available BQP instances, and it is shown experimentally that the algorithm is capable of finding best-known solutions to large BQPs in a short time and with a high frequency. In comparison to other approaches for the BQP, the approach appears to be much more effective, particularly for large instances of 1000 or 2500 binary variables.     

Antifungal activity of oosporein from an antagonistic fungus against Phytophthora infestans

An antifungal metabolite, oosporein, was isolated from the culture of Verticillium psalliotae that produced the antagonistic effects on Phytophthora infestans. Oosporein exhibited a significant growth-inhibitory effect on P. infestans in comparison with other phytopathogenic fungi.     

Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces

Protein-DNA interactions play an essential role in the genetic activities of life. Many structures of protein-DNA complexes are already known, but the common rules on how and where proteins bind to DNA have not emerged. Many attempts have been made to predict protein-DNA interactions using structural information, but the success rate is still about 80%. We analyzed 63 protein-DNA complexes by focusing our attention on the shape of the molecular surface of the protein and DNA, along with the electrostatic potential on the surface, and constructed a new statistical evaluation function to make predictions of DNA interaction sites on protein molecular surfaces. The shape of the molecular surface was described by a combination of local and global average curvature, which are intended to describe the small convex and concave and the large-scale concave curvatures of the protein surface preferentially appearing at DNA-binding sites. Using these structural features, along with the electrostatic potential obtained by solving the Poisson-Boltzmann equation numerically, we have developed prediction schemes with 86% and 96% accuracy for DNA-binding and non-DNA-binding proteins, respectively.     

In vivo MR detection of vascular endothelial injury using a new class of MRI contrast agent

A new class of dye-based MRI contrast agents, EB-DTPA-Gd, was designed and synthesized. The contrast agent was found to accumulate at the site of endothelial injury when the reagent was applied to isolated porcine blood vessels or in an ex vivo experiment using rat. In vivo MR detection of vascular endothelial injury was also successful in rat with its common carotid artery injured by balloon treatment. These results indicate that EB-DTPA-Gd is potentially useful for the diagnosis of vascular diseases.     

Structure-activity relationships of epolactaene analogs as DNA polymerases inhibitors

Epolactaene, a neuritogenic compound in human neuroblastoma cells, showed inhibitory activities against DNA polymerases alpha and beta. The synthesis and inhibitory activities of epolactaene analogs are described. The alpha,beta-epoxy-gamma-lactam moiety in the core and the length of the side chain greatly influenced the activities. Compound 5 was the strongest inhibitor of DNA polymerase alpha and beta of all synthesized compounds with IC(50) values of 13 and 78 microM, respectively. N- and O-alkyl derivatives that had modified core moieties showed moderate inhibition.     

eF-site and PDBjViewer: database and viewer for protein functional sites

The electrostatic-surface of functional site (eF-site) is a database for the molecular surfaces of protein functional sites. To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program. AVAILABILITY: The eF-site database and PDBjViewer are freely available from http://www.pdbj.org/eF-site/     

YSL16 Is a Phloem-Localized Transporter of the Copper-Nicotianamine Complex That Is Responsible for Copper Distribution in Rice

Cu is an essential element for plant growth, but the molecular mechanisms of its distribution and redistribution within the plants are unknown. Here, we report that Yellow stripe-like16 (YSL16) is involved in Cu distribution and redistribution in rice (Oryza sativa). Rice YSL16 was expressed in the roots, leaves, and unelongated nodes at the vegetative growth stage and highly expressed in the upper nodes at the reproductive stage. YSL16 was expressed at the phloem of nodes and vascular tissues of leaves. Knockout of this gene resulted in a higher Cu concentration in the older leaves but a lower concentration in the younger leaves at the vegetative stage. At the reproductive stage, a higher Cu concentration was found in the flag leaf and husk, but less Cu was present in the brown rice, resulting in a significant reduction in fertility in the knockout line. Isotope labeling experiments with ⁶⁵Cu showed that the mutant lost the ability to transport Cu-nicotianamine from older to younger leaves and from the flag leaf to the panicle. Rice YSL16 transported the Cu-nicotianamine complex in yeast. Taken together, our results indicate that Os-YSL16 is a Cu-nicotianamine transporter that is required for delivering Cu to the developing young tissues and seeds through phloem transport.     

Olprinone and colforsin daropate alleviate septic lung inflammation and apoptosis through CREB-independent activation of the Akt pathway

Olprinone, a specific phosphodiesterase III inhibitor, and corforsin daropate, a direct adenylate cyclase activator, are now being used in critical conditions. We investigated whether their therapeutic use provides protection against septic acute lung injury (ALI) and mortality. Polymicrobial sepsis was induced by cecal ligation and puncture (CLP) in BALB/c mice. Olprinone or colforsin daropate was continuously given through an osmotic pump that was implanted into the peritoneal cavity immediately following CLP. These treatments prevented the ALI development in CLP mice, as indicated by the findings that severe hypoxemia, increased pulmonary vascular permeability, and histological lung damage were strikingly remedied. Furthermore, continued administration of olprinone or colforsin daropate suppressed apoptosis induction in septic lungs and improved the survival of CLP mice. Olprinone and corforsin daropate enhanced Akt phosphorylation in septic lungs. Wortmannin, which inhibits the Akt upstream regulator phosphatidylinositol 3-kinase, abrogated the protective effects of olprinone and corforsin daropate on sepsis-associated lung inflammation and apoptosis. In vivo transfection of cyclic AMP response element binding protein (CREB) decoy oligodeoxynucleotide failed to negate the abilities of these agents to increase Akt phosphorylation and to inhibit IκBα degradation in septic lungs. These results demonstrate for the first time that CREB-independent Akt-mediated signaling is a critical mechanism contributing to the therapeutic effects of olprinone and corforsin daropate on septic ALI. Moreover, our data also suggest that these cyclic AMP-related agents, by blocking both nuclear factor-κB activation and apoptosis induction, may represent an effective therapeutic approach to the treatment of the septic syndrome.