Isoprene Polymerization on Iron Nanoparticles Confined in Carbon Nanotubes.

The confinement of air-protected metallic magnetic nanoparticles in the inner cavity of carbon nanotubes (CNTs) should offer an interesting perspective for biomedical applications or for controlling CNT alignment in composites. Because the direct confinement of polymer-precoated nanoparticles in CNTs could be restricted by diffusion limitations, we developed a process based on: 1) the confinement of iron nanoparticles surface-modified with an iron polymerization catalyst in the cavity of CNTs and 2) the polymerization of isoprene on the confined nanoparticles. The resulting material consists in CNT-confined iron nanoparticles coated with a polyisoprene air barrier. This approach constitutes a proof of concept for the development of smart materials for use in medicine or composites.

Comparative mapping in the Fagaceae and beyond with EST-SSRs.

BACKGROUND: Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS: We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS: This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.

Theoretical and experimental studies on the carbon-nanotube surface oxidation by nitric acid: interplay between functionalization and vacancy enlargement.

The nitric acid oxidation of multiwalled carbon nanotubes leading to surface carboxylic groups has been investigated both experimentally and theoretically. The experimental results show that such a reaction involves the initial rapid formation of carbonyl groups, which are then transformed into phenol or carboxylic groups. At room temperature, this reaction takes place on the most reactive carbon atoms. At higher temperatures a different mechanism would operate, as evidenced by the difference in activation energies. Experimental data can be partially related to first-principles calculations, showing a multistep functionalization mechanism. The theoretical aspects of the present article have led us to propose the most efficient pathway leading to carboxylic acid functional groups on the surface. Starting from mono-vacancies, it ends up with the synergistic formation of dangling -COOH groups and the enlargement of the vacancies.

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.

BACKGROUND: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). RESULTS: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. CONCLUSION: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.

Metabolic control through ornithine and uracil of epithelial cell invasion by Shigella flexneri.

This paper shows that compounds in defined growth media strongly influence the expression of the effectors of virulence in the human invasive pathogen Shigella flexneri. Ornithine in conjunction with uracil reduces the haemolytic ability of wild-type cultures more than 20-fold and the expression of the type III secretion system more than 8-fold, as monitored by an mxiC : : lacZ transcriptional reporter. mxiC gene expression is further decreased by the presence of methionine or branched-chain amino acids (15-fold or 25-fold at least, respectively). Lysine and a few other aminated metabolites (cadaverine, homoserine and diaminopimelate) counteract the ornithine-mediated inhibition of haemolytic activity and of the expression of a transcriptional activator virF reporter. The complete abolition of invasion of HeLa cells by wild-type bacteria by ornithine, uracil, methionine or branched-chain amino acids establishes that these metabolites are powerful effectors of virulence. These findings provide a direct connection between metabolism and virulence in S. flexneri. The inhibitory potential exhibited by the nutritional environment is stronger than temperature, the classical environmental effector of virulence. The implications and practical application of this finding in prophylaxis and treatment of shigellosis are discussed.

DOSY technique applied to palladium nanoparticles in ionic liquids.

Multinuclear ((1)H, (31)P, (19)F and (11)B) diffusion ordered spectroscopy (DOSY) technique has been applied to palladium nanoparticles systems dispersed in ionic liquids (ILs). Even if the nanoparticles themselves cannot be detected through NMR, observation of the solvent (methanol) and the IL ([BMI][PF(6)] or [BMI][NTf(2)]), their diffusion coefficients and their changes in the presence of nanoparticles allow us to draw significant assumptions about the organisation of palladium nanoparticles in the IL. For comparison, the corresponding molecular precursors ([PdCl(2)(cod)] or [Pd(2)(dba)(3)]) have been also studied.

New atropisomeric N-N ligands for CO/vinyl arene copolymerization reaction.

New atropisomeric bidentate bipyridine-based ligands (3,3'-(ethylenedioxy)-2,2'-bipyridine 4; 3,3'-(propylenedioxy)-2,2'-bipyridine 4; 3,3'-(butylenedioxy)-2,2'-bipyridine 5) containing a bridge between the 3,3' positions of the aromatic rings have been prepared. Together with the previously reported analogous ligands ((R)-3,3'-(1-methylethylenedioxy)-2,2'-bipyridine) 1and ((S,S)-3,3'-(1,2-dimethylethylenedioxy)-2,2'-bipyridine) 2, they were used to synthesize the corresponding bis-chelated dicationic complexes [Pd(N-N)2][PF6]2. Crystal structures and comparison of the data obtained by X-ray analysis on four of these complexes is reported. These palladium compounds were used as precatalysts in the CO/styrene and CO/4-Me-styrene copolymerization reactions, where they showed that small variations in the ligand backbone remarkably affects the productivity of the catalytic system.

Palladium catalyzed Suzuki C-C couplings in an ionic liquid: nanoparticles responsible for the catalytic activity.

A new family of functionalized ligands derived from norborn-5-ene-2,3-dicarboxylic anhydride has been used in Suzuki C-C cross-couplings between aryl boronic acids and aryl bromide derivatives in [BMI][PF(6)] (BMI=1-n-butyl-3-methyl-imidazolium), using palladium acetate as catalytic precursor. High conversions and yields are obtained when amine ligands containing hydroxy groups are involved. TEM analyses after catalysis show the formation of small nanoparticles, in contrast to the agglomerates observed when nanoparticles are intentionally preformed, with a consequent decrease in the catalytic activity in the latter case. Some tests, including the correlation effect between solvent and ligand, are carried out to try to identify the true nature of the catalyst. All the results obtained suggest that formation of nanoparticles is required to lead to a catalytically active system.

Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL.

Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 x 'Vada' mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.

Long-lived palladium catalysts for CO/vinyl arene polyketones synthesis: a solution to deactivation problems.

A series of cationic palladium complexes of general formula [Pd(Me)(MeCN)(N-N)][PF(6)] (N-N = (phen) 1 a, 4,7-dichloro-1,10-phenanthroline (4,7-Cl(2)-phen) 2 a, 4,7-diphenyl-1,10-phenanthroline (4,7-Ph(2)-phen) 3 a, 4-methyl-1,10-phenanthroline (4-Me-phen) 4 a, 4,7-dimethyl-1,10-phenanthroline (4,7-Me(2)-phen) 5 a, 5,5,6,6-tetrafluoro-5,6-dihydro-1,10-phenanthroline (F(4)-phen) 6 a, containing different substituted phenanthroline ligands, have been prepared from the corresponding neutral chloro derivatives [Pd(Me)(Cl)(N-N)], (1 b-6 b). The X-ray crystal structure of [Pd(Cl)(2)(4,7-Cl(2)-phen)] (2 b') was determined. DFT calculations show that the electron density on the metal is tuned by the substituents on the ligands. The catalytic behavior of complexes 1 a-6 a in the CO/styrene and CO/p-Me-styrene copolymerizations was studied in detail, showing that the generated catalysts are active for at least 90 h, yielding copolymers of high molecular weight. A firm correlation between the electron density on palladium on the one hand and the catalytic activity of the complexes and the molecular weight and the stereochemistry of the polyketones synthesized on the other hand has been established: the catalyst containing the F(4)-phen is thus far the most active among those tested, yielding the syndiotactic CO/styrene copolymer with a stereoregularity of 96 % (uu triad) and with an M(w) value of 1 000 000.

Mono- and dinuclear bioxazoline-palladium complexes for the stereocontrolled synthesis of CO/styrene polyketones.

The coordination chemistry of the chiral bioxazoline ligand (4S,4'S)-2,2'-bis(4-isopropyl-4,5-dihydrooxazole) to Pd(II) provides evidence that the ligand bonding can occur either through chelation of one Pd(II) ion leading to a mononuclear species with the expected cis geometry, or by double bridging of two Pd(II) ions giving a dinuclear complex with trans geometry. The species in solution are identified by 1H NMR spectroscopy. Both the mononuclear and the dinuclear complexes promote the CO/styrene copolymerization, yielding the corresponding polyketone with a fully or a predominantly isotactic microstructure, depending on the reaction medium. The nature of the anion present in the palladium precatalysts affects the polyketone stereochemistry. MALDI-TOF analysis of the copolymers synthesized reveals the presence of p-hydroxyphenolic end-groups, thus confirming and explaining the role of 1,4-hydroquinone as a molecular weight regulator.

Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting.

Using mutants (tgt, mnmA(asuE, trmU), mnmE(trmE), miaA, miaB, miaE, truA(hisT), truB) of either Escherichia coli or Salmonella enterica serovar Typhimurium and the trm5 mutant of Saccharomyces cerevisiae, we have analyzed the influence by the modified nucleosides Q34, mnm(5)s(2)U34, ms(2)io(6)A37, Psi39, Psi55, m(1)G37, and yW37 on -1 frameshifts errors at various heptameric sequences, at which at least one codon is decoded by tRNAs having these modified nucleosides. The frequency of -1 frameshifting was the same in congenic strains only differing in the allelic state of the various tRNA modification genes. In fact, in one case (deficiency of mnm(5)s(2)U34), we observed a reduced ability of the undermodified tRNA to make a -1 frameshift error. These results are in sharp contrast to earlier observations that tRNA modification prevents +1 frameshifting suggesting that the mechanisms by which -1 and +1 frameshift errors occur are different. Possible mechanisms explaining these results are discussed.

Putrescine or a combination of methionine and arginine restores virulence gene expression in a tRNA modification-deficient mutant of Shigella flexneri: a possible role in adaptation of virulence.

The wild-type strain YSH6000 of Shigella flexneri growing in minimal medium contains the modified nucleoside epoxy-Q (oQ) in a subset of tRNAs. This nucleoside is lacking in tRNA from a tgt mutant of this bacterium. When these bacteria are growing in minimal medium, the expression of virulence genes is 10-fold lower in the tgt mutant than in the wild type, although only a twofold reduction in the expression of these virulence factors is observed in broth. Such a strong media-dependant expression of virulence genes was not observed in the wild type. Accordingly, the level of the positive regulator of virulence, VirF, is much lower in the mutant than in the wild type. However, the transcription of the virF gene in minimal medium is the same in the wild type and in the tgt mutant. As the undermodification of tRNA is not affected by the quality of the growth medium, we conclude that such an environmental change in growth conditions partly restores virulence gene expression by counteracting poor translation of the virF mRNA mediated by an oQ-deficient tRNA. Virulence gene expression is partly restored in the tgt mutant by the addition of a mixture of arginine and methionine. Addition of the polyamine putrescine, synthesis of which is metabolically related to that of arginine and methionine, has a comparable stimulatory effect on virulence gene expression. These results not only suggest a role for amino acids and polyamines in the environmental regulation of virulence gene expression in S. flexneri, but also demonstrate a strong and specific involvement of tRNA modifications, and especially oQ, in the adaptation of virulence gene expression to the nutritional quality of the growth medium.

Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri.

The modified nucleosides 2'-O-methylguanosine, present at position 18 (Gm18), 5-methyluridine, present at position 54 (m(5)U54), and pseudouridine, present at position 55 (Psi55), are located in the D and T arms of tRNAs and are close in space in the three-dimensional (3D) structure of this molecule in the bacterium Escherichia coli. The formation of these modified nucleosides is catalyzed by the products of genes trmH (Gm18), trmA (m(5)U54), and truB (Psi55). The combination of trmH, trmA, and truB mutations resulting in lack of these three modifications reduced the growth rate, especially at high temperature. Moreover, the lack of three modified nucleotides in tRNA induced defects in the translation of certain codons, sensitivity to amino acid analog 3,4-dehydro-DL-proline, and an altered oxidation of some carbon compounds. The results are consistent with the suggestion that these modified nucleosides, two of which directly interact in the 3D structure of tRNA by forming a hydrogen bond between Psi55 and Gm18, stabilize the structure of the tRNA. Moreover, lack of Psi55 in tRNA of human pathogen Shigella flexneri leads to a reduced expression of several virulence-associated genes.