Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

BACKGROUND: Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data. RESULTS: To provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface. CONCLUSIONS: YeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/.     

HCV NS5B蛋白对HCV RNA的模板特异性研究

在大肠杆菌菌株BL21(DE3)中表达并纯化HCV的依赖于RNA的RNA多聚酶(RNA-dependent RNA polymerase,RdRp,NS5B蛋白).以HCV正、负链RNA 3′末端的序列为模板,体外研究NS5B蛋白催化的RNA合成.结果显示,正链RNA在体外不能指导RNA合成,而负链RNA模板可以产生一条全长的正链RNA产物,表明NS5B对负链RNA具有模板特异性.NS5B对负链RNA的特异性在模板竞争性实验中得到进一步证实,正链RNA的存在和竞争对以负链为模板的RNA合成没有影响.这样,就合理解释了在HCV RNA复制时正链RNA的数量远比负链RNA多这一问题.同时,本实验的结果也为进一步研究病毒或其它细胞因子参与以正链RNA为模板进行的RNA合成,以及有关负链RNA模板特性的研究奠定了基础.     

Nox1-dependent superoxide production controls colon adenocarcinoma cell migration

Reactive oxygen species are well-known mediators of various biological responses. Recently, new homologues of the catalytic subunit of NADPH oxidase have been discovered in non-phagocytic cells. These new homologues (Nox1-Nox5) produce low levels of superoxides compared to the phagocytic homologue Nox2/gp91phox. Using Nox1 siRNA, we show that Nox1-dependent superoxide production affects the migration of HT29-D4 colonic adenocarcinoma cells on collagen-I. Nox1 inhibition or down-regulation led to a decrease of superoxide production and alpha 2 beta 1 integrin membrane availability. An addition of arachidonic acid stimulated Nox1-dependent superoxide production and HT29-D4 cell migration. Pharmacological evidences using phospholipase A2, lipoxygenases and protein kinase C inhibitors show that upstream regulation of Nox1 relies on arachidonic acid metabolism. Inhibition of 12-lipoxygenase decreased basal and arachidonic acid induced Nox1-dependent superoxide production and cell migration. Migration and ROS production inhibited by a 12-lipoxygenase inhibitor were restored by the addition of 12(S)-HETE, a downstream product of 12-lipoxygenase. Protein kinase C delta inhibition by rottlerin (and also GO6983) prevented Nox1-dependent superoxide production and inhibited cell migration, while other protein kinase C inhibitors were ineffective. We conclude that Nox1 activation by arachidonic acid metabolism occurs through 12-lipoxygenase and protein kinase C delta, and controls cell migration by affecting integrin alpha 2 subunit turn-over.     

Description de deux nouvelles espèces de Lamellodiscus Johnston & Tiegs, 1922 (Monogenea: Diplectanidae) du groupe morphologique ‘ignoratus’, parasites de Diplodus sargus et D. vulgaris (Teleostei: Sparidae)

The study of the diplectanid gill parasites of Diplodus Rafinesque (Teleostei: Sparidae) from off the Algerian coast revealed the presence of several species of Lamellodiscus Johnston & Tiegs, 1922 on D. sargus (Linnaeus) and D. vulgaris (Geoffroy Saint-Hilaire). Some of these species differ from the others by having a copulatory organ "en lyre" and lamellodiscs of the morphological group 'ignoratus' of Oliver (1987). In Lamellodiscus, the subgroup 'ignoratus', proposed by Amine & Euzet (2005), characterised by a simple lateral dorsal bar, includes L. ignoratus Palombi, 1943 and L. fraternus Bychowsky, 1957. Two new species, L. falcus n. sp. and L. neifari n. sp. form part of the 'ignoratus' subgroup. These species are distinguished by the morphology and the size of the sclerotised parts of the haptor and copulatory organ.     

Tailoring the specificity of a plant cystatin toward herbivorous insect digestive cysteine proteases by single mutations at positively selected amino acid sites

Plant cystatins, similar to other defense proteins, include hypervariable, positively selected amino acid sites presumably impacting their biological activity. Using 29 single mutants of the eighth domain of tomato (Solanum lycopersicum) multicystatin, SlCYS8, we assessed here the potential of site-directed mutagenesis at positively selected amino acid sites to generate cystatin variants with improved inhibitory potency and specificity toward herbivorous insect digestive cysteine (Cys) proteases. Compared to SlCYS8, several mutants (22 out of 29) exhibited either improved or lowered potency against different model Cys proteases, strongly suggesting the potential of positively selected amino acids as target sites to modulate the inhibitory specificity of the cystatin toward Cys proteases of agronomic significance. Accordingly, mutations at positively selected sites strongly influenced the inhibitory potency of SlCYS8 against digestive Cys proteases of the insect herbivore Colorado potato beetle (Leptinotarsa decemlineata). In particular, several variants exhibited improved potency against both cystatin-sensitive and cystatin-insensitive digestive Cys proteases of this insect. Of these, some variants also showed weaker activity against leaf Cys proteases of the host plant (potato [Solanum tuberosum]) and against a major digestive Cys protease of the two-spotted stinkbug Perillus bioculatus, an insect predator of Colorado potato beetle showing potential for biological control. Overall, these observations suggest the usefulness of site-directed mutagenesis at positively selected amino acid sites for the engineering of recombinant cystatins with both improved inhibitory potency toward the digestive proteases of target herbivores and weaker potency against nontarget Cys proteases in the host plant or the environment.     

In Situ Probing and Synthetic Control of Cationic Ordering in Ni‐Rich Layered Oxide Cathodes

Ni‐rich layered oxides (LiNi_1–x M_x O₂; M = Co, Mn, …) are appealing alternatives to conventional LiCoO₂ as cathodes in Li‐ion batteries for automobile and other large‐scale applications due to their high theoretical capacity and low cost. However, preparing stoichiometric LiNi_1–x M_x O₂ with ordered layer structure and high reversible capacity, has proven difficult due to cation mixing in octahedral sites. Herein, in situ studies of synthesis reactions and the associated structural ordering in preparing LiNiO₂ and the Co‐substituted variant, LiNi_0.8Co_0.2O₂, are made, to gain insights into synthetic control of the structure and electrochemical properties of Ni‐rich layered oxides. Results from this study indicate a direct transformation of the intermediate from the rock salt structure into hexagonal phase, and during the process, Co substitution facilities the nucleation of a Co‐rich layered phase at low temperatures and subsequent growth and stabilization of solid solution Li(Ni, Co)O₂ upon further heat treatment. Optimal conditions are identified from the in situ studies and utilized to obtain stoichiometric LiNi_0.8Co_0.2O₂ that exhibits high capacity (up to 200 mA h g^?1 ) with excellent retention. The findings shed light on designing high performance Ni‐rich layered oxide cathodes through synthetic control of the structural ordering in the materials.     

Phytoremediation of palm oil mill secondary effluent (POMSE) by Chrysopogon zizanioides (L.) using artificial neural networks

Artificial neural networks (ANNs) have been widely used to solve the problems because of their reliable, robust, and salient characteristics in capturing the nonlinear relationships between variables in complex systems. In this study, ANN was applied for modeling of Chemical Oxygen Demand (COD) and biodegradable organic matter (BOD) removal from palm oil mill secondary effluent (POMSE) by vetiver system. The independent variable, including POMSE concentration, vetiver slips density, and removal time, has been considered as input parameters to optimize the network, while the removal percentage of COD and BOD were selected as output. To determine the number of hidden layer nodes, the root mean squared error of testing set was minimized, and the topologies of the algorithms were compared by coefficient of determination and absolute average deviation. The comparison indicated that the quick propagation (QP) algorithm had minimum root mean squared error and absolute average deviation, and maximum coefficient of determination. The importance values of the variables was included vetiver slips density with 42.41%, time with 29.8%, and the POMSE concentration with 27.79%, which showed none of them, is negligible. Results show that the ANN has great potential ability in prediction of COD and BOD removal from POMSE with residual standard error (RSE) of less than 0.45%.     

Copper(II)/H(2)O(2)-mediated DNA cleavage: involvement of a copper(III) species in H-atom abstraction of deoxyribose units.

A new bis-amido-copper(II) complex 2 has been prepared. In the presence of reducing agents (ascorbate or DTT) under air atmosphere or hydrogen peroxide, complex 2 exhibited interesting nuclease activities in the 1-10 microM concentration range. For explaining the activity observed with hydrogen peroxide, we propose the occurrence of a bis-amido-copper(III) intermediate and an oxidation mechanism involving a H-atom abstraction of deoxyribose moieties of DNA.