Molecular characterization and in silico analysis of RNA polymerase alpha subunit gene (rpoA) in Date Palm (Phoenix dactylifera L.) cv. Deglet Nour

The rpoA gene coding for the ??-subunit of DNA-dependent RNA polymerase located in the chloroplastic genome of date palm has been characterized from the elite cultivar Deglet Nour by cloning and sequencing of the PCR amplification product. The full length of rpoA-Pd (Phoenix dactylifera) gene was 1014 bp. The comparison in Genbank showed that the rpoA gene has a 100% homology with the Khalas cultivar of date palm and a strong homology with Oil Palm (99%). The deduced protein full length is 337 amino acid corresponding to 38,692 Da polypeptide. It contained an Alpha N-terminal domain (alpha-NTD) between 1 to 233 (aa) and Alpha C-terminal domain (alpha-CTD) between 266 to 337 (aa). Initially, we have compared the sequences of the full-length DNA rpoA gene from Date Palm and Oil palm, 15 mutations have been detected, 4 do not affect amino acid sequences. A multiple alignment of protein sequences of Date Palm and other plants shows 6 mutations specific for palms family and one is specific to monocots species. A multiple alignment of 35 nucleotide sequences from different plant species shows 3 SNPs specific to Date Palm, 6 SNPs specific to Palms family and 6 other to monocot species. The phylogenetic analysis performed in this work shows a strong similarity between Pd-rpoA and rpoA genes from other plant species, but it shows a great divergence with the rpoA of E. coli. To explain whether the separation of the two clades was due to selection pressure. We calculate the ratio Ka/Ks for different species. A synteny analyses of rpoA genes was effected, a high genomic synteny is observed for the ropA in all the species included in this study.     

VEGF-C promotes immune tolerance in B16 melanomas and cross-presentation of tumor antigen by lymph node lymphatics

Tumor expression of the lymphangiogenic factor VEGF-C is correlated with metastasis and poor prognosis, and although VEGF-C enhances transport to the draining lymph node (dLN) and antigen exposure to the adaptive immune system, its role in tumor immunity remains unexplored. Here, we demonstrate that VEGF-C promotes immune tolerance in murine melanoma. In B16 F10 melanomas expressing a foreign antigen (OVA), VEGF-C protected tumors against preexisting antitumor immunity and promoted local deletion of OVA-specific CD8(+) T cells. Naive OVA-specific CD8(+) T cells, transferred into tumor-bearing mice, were dysfunctionally activated and apoptotic. Lymphatic endothelial cells (LECs) in dLNs cross-presented OVA, and naive LECs scavenge and cross-present OVA in vitro. Cross-presenting LECs drove the proliferation and apoptosis of OVA-specific CD8(+) T cells ex vivo. Our findings introduce a tumor-promoting role for lymphatics in the tumor and dLN and suggest that lymphatic endothelium in the local microenvironment may be a target for immunomodulation.     

Effects of nasal continuous positive-airway pressure on nutritive swallowing in lambs

Current knowledge suggests that, to be successful, oral feeding in preterm infants should be initiated as soon as possible, often at an age where immature respiration still requires ventilatory support in the form of nasal continuous positive airway pressure (nCPAP). While some neonatologist teams claim great success with initiation of oral feeding in immature infants with nCPAP, others strictly wait for this ventilatory support to be no longer necessary before any attempt at oral feeding, fearing laryngeal penetration and tracheal aspiration. Therefore, the aim of the present study was to provide a first assessment of the effect of various levels of nCPAP on bottle-feeding in a neonatal ovine model, including feeding safety, feeding efficiency, and nutritive swallowing-breathing coordination. Eight lambs born at term were surgically instrumented 48 h after birth to collect recordings of electrical activity of laryngeal constrictor muscle, electrocardiography, and arterial blood gases. Two days after surgery, lambs were bottle-fed under five randomized nCPAP conditions, including without any nCPAP or nasal mask and nCPAP of 0, 4, 7, and 10 cmH(2)O. Results revealed that application of nCPAP in the full-term lamb had no deleterious effect on feeding safety and efficiency or on nutritive swallowing-breathing coordination. The present study provides a first and unique insight on the effect of nCPAP on oral feeding, demonstrating its safety in newborn lambs born at term. These results open the way for further research in preterm lambs to better mimic the problems encountered in neonatology.     

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.