Effects of the interface roughness in metal-adhesive-metal structure on the propagation of shear horizontal waves.

The influence of the interface roughness in a three-layer metal-adhesive-metal structure on the propagation of shear horizontal waves and more particularly on the transmission coefficient versus the frequency is studied in the particular case of a periodic grating of triangular grooves. For given phonon frequencies, the interaction of an incident shear horizontal mode with the periodical grating gives rise to a retro-converted mode. A numerical finite element simulation permits us to predict the existence of the phonon mode in the three-layer structure and to obtain the evolution of the transmission coefficient around the phonon frequency. An experimental study, based on a generation of waves by a piezocomposite contact transducer and a reception by a laser vibrometer, then confirms these predictions. Finally, a parametric numerical study is performed: the influence of the depth of the roughness and of the number of spatial periods of the grooves on the transmission coefficient is studied.

Use of shear horizontal waves to distinguish adhesive thickness variation from reduction in bonding strength.

The capability of shear horizontal (SH) guided waves, to evaluate geometrical imperfections in a bonding layer, is investigated. SH waves are used in a three-layer structure in which the adhesive layer has variable thickness. It is proven that the SH waves are adapting to the local thickness of the adhesive layer (adiabatic waves). This is particularly useful in case of small thickness variations, which is of technical interest. The influence of thickness and stiffness of the adhesive layer on the wavenumbers are investigated. The selected SH2 mode is proven to be very sensitive to the adhesive layer thickness variation in the given frequency range and considerably less sensitive to the adhesive stiffness variation. This property is due to its specific displacement field and is important in practical applications, such as inspection techniques based on SH waves, in order to avoid false alarms.

The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites.

Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S-C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur-like proteins, the crystal structure of HpFur reveals a unique structured N-terminal extension and an unusual C-terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS4 site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site-directed mutagenesis and spectroscopy analyses of purified wild-type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site.

Coupled amino acid deamidase-transport systems essential for Helicobacter pylori colonization.

In addition to their classical roles as carbon or nitrogen sources, amino acids can be used for bacterial virulence, colonization, or stress resistance. We found that original deamidase-transport systems impact colonization by Helicobacter pylori, a human pathogen associated with gastric pathologies, including adenocarcinoma. We demonstrated that l-asparaginase (Hp-AnsB) and gamma-glutamyltranspeptidase (Hp-gammaGT) are highly active periplasmic deamidases in H. pylori, producing ammonia and aspartate or glutamate from asparagine and glutamine, respectively. Hp-GltS was identified as a sole and specialized transporter for glutamate, while aspartate was exclusively imported by Hp-DcuA. Uptake of Gln and Asn strictly relies on indirect pathways following prior periplasmic deamidation into Glu and Asp. Hence, in H. pylori, the coupled action of periplasmic deamidases with their respective transporters enables the acquisition of Glu and Asp from Gln and Asn, respectively. These systems were active at neutral rather than acidic pH, suggesting their function near the host epithelial cells. We showed that Hp-DcuA, the fourth component of these novel deamidase-transport systems, was as crucial as Hp-gammaGT, Hp-AnsB, and Hp-GltS for animal model colonization. In conclusion, the pH-regulated coupled amino acid deamidase-uptake system represents an original optimized system that is essential for in vivo colonization of the stomach environment by H. pylori. We propose a model in which these two nonredundant systems participate in H. pylori virulence by depleting gastric or immune cells from protective amino acids such as Gln and producing toxic ammonia close to the host cells.

Flavin-dependent thymidylate synthase ThyX activity: implications for the folate cycle in bacteria.

Although flavin-dependent ThyX proteins show thymidylate synthase activity in vitro and functionally complement thyA defects in heterologous systems, direct proof of their cellular functions is missing. Using insertional mutagenesis of Rhodobacter capsulatus thyX, we constructed the first defined thyX inactivation mutant. Phenotypic analyses of the obtained mutant strain confirmed that R. capsulatus ThyX is required for de novo thymidylate synthesis. Full complementation of the R. capsulatus thyX::spec strain to thymidine prototrophy required not only the canonical thymidylate synthase ThyA but also the dihydrofolate reductase FolA. Strikingly, we also found that addition of exogenous methylenetetrahydrofolate transiently inhibited the growth of the different Rhodobacter strains used in this work. To rationalize these experimental results, we used a mathematical model of bacterial folate metabolism. This model suggests that a very low dihydrofolate reductase activity is enough to rescue significant thymidylate synthesis in the presence of ThyX proteins and is in agreement with the notion that intracellular accumulation of folates results in growth inhibition. In addition, our observations suggest that the presence of flavin-dependent thymidylate synthase X provides growth benefits under conditions in which the level of reduced folate derivatives is compromised.

Ultrasonic Measurements on ß Cyclodextrin/Hydroxyapatite Composites for Potential Water Depollution.

This paper presents structural, morphological and preliminary ultrasonic characterizations of the ß-Cyclodextrin/hydroxyapatite (CD-HAp) composites synthesized by an adapted co-precipitation method. The structural and morphological properties were evaluated by Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDX). The specific surface area, pore size and pore volume were determined using the methods of Brunauer-Emmett-Teller (BET) and Barrett-Joyner-Halenda (BJH), respectively. The novelty of our study consists in preliminary ultrasonic measurements conducted on CD-HAp composite, uniformly dispersed in distilled water. The benefit of this non-destructive method was to facilitate and simplify the characterization techniques of nanoparticles. Our experiments proved that the efficiency of lead ion removal by CD-HAp composites depended on the initial concentration of lead. The maximum adsorption capacity of the solid phase, for Pb2+ indicated a higher rate of removal by the CD-HAp_2. These adsorption results bring valuable insight into the beneficial contribution of our compounds, for the removal of heavy metal ions from aqueous solutions. Furthermore, in the present study, was evaluated the toxic effect of lead ions adsorbed by hydroxyapatite from contaminated water on HeLa cells.

Life without dihydrofolate reductase FolA.

Reduced folate derivatives participate in numerous reactions of bacterial intermediary metabolism. Consequently, the well-characterized enzyme implicated in the formation of tetrahydrofolate--dihydrofolate reductase FolA--was considered to be essential for bacterial growth. However, comparative genomics has revealed several bacterial genome sequences that appear to lack the folA gene. Here, we provide in silico evidence indicating that folA-lacking bacteria use a recently discovered class of flavin-dependent thymidylate synthases for deoxythymidine-5'-monophosphate synthesis, and propose that many bacteria must contain uncharacterized sources for reduced folate molecules that are still waiting to be discovered.

The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB.

In response to iron limitation, the siderophore enterobactin is synthesized and secreted by Escherichia coli. Its biosynthesis is performed by a series of enzymes encoded by the Ent gene cluster. Among the genes of this cluster, ybdB has not been implicated in enterobactin production to date. We demonstrate here an in vivo role for the hotdog protein EntH (YbdB) in the optimal production of enterobactin. Indeed, we showed that EntH is a thioesterase specifically produced under iron limitation conditions. Furthermore, EntH interacts specifically with the aryl carrier protein (ArCP) domain of EntB, a crucial bifunctional enzyme of the enterobactin biosynthesis pathway and a potential target of EntH thioesterase activity. A strain devoid of EntH is impaired for growth under iron limitation associated with the presence of the salicylate inhibitor, correlating with the diminution of enterobactin production under these conditions. Normal growth and enterobactin production are restored upon expression of entH in trans. Inversely, unnecessary overproduction of EntH provokes a fall of the quantity of siderophore produced under iron starvation conditions. Our findings point to a proofreading role for EntH during biosynthesis of enterobactin in vivo. EntH thioesterase activity could be required for cleaving wrongly charged molecules on the carrier protein EntB. This is the first description of such a role in the optimization of a nonribosomal biosynthesis pathway for a protein of the hotdog superfamily.

An alternative flavin-dependent mechanism for thymidylate synthesis.

Although deoxythymidylate cannot be provided directly by ribonucleotide reductase, the gene encoding thymidylate synthase ThyA is absent from the genomes of a large number of nonsymbiotic microbes. We show that ThyX (Thy1) proteins of previously unknown function form a large and distinct class of thymidylate synthases. ThyX has a wide but sporadic phylogenetic distribution, almost exclusively limited to microbial genomes lacking thyA. ThyX and ThyA use different reductive mechanisms, because ThyX activity is dependent on reduced flavin nucleotides. Our findings reveal complexity in the evolution of thymidine in present-day DNA. Because ThyX proteins are found in many pathogenic microbes, they present a previously uncharacterized target for antimicrobial compounds.

Functional evidence for active site location of tetrameric thymidylate synthase X at the interphase of three monomers.

Little is known about the catalytic mechanism of the recently discovered ThyX family of flavin-dependent thymidylate synthases that are required for thymidylate (deoxythymidine 5'-monophosphate) synthesis in a large number of microbial species. Using a combination of site-directed mutagenesis and biochemical measurements, we have identified several residues of the Helicobacter pylori ThyX protein with crucial roles in ThyX catalysis. By providing functional evidence that the active site(s) of homotetrameric ThyX proteins is formed by three different subunits, our findings suggest that ThyX proteins have evolved through multimerization of inactive monomers. Moreover, because the active-site configurations of ThyX proteins, present in many human pathogenic bacteria, and of human thymidylate synthase ThyA are different, our results will aid in the identification of compounds specifically inhibiting microbial growth.

Functional analysis of FAD-dependent thymidylate synthase ThyX from Paramecium bursaria Chlorella virus-1.

Sequence analysis of the 330-kb double-stranded DNA genome of Paramecium bursaria chlorella virus-1 revealed an open reading frame A674R that encodes a protein with up to 53% amino acid identity to a recently discovered new class of thymidylate synthases, called ThyX. Unlike the traditional thymidylate synthase, ThyA, that uses methylenetetrahydrofolate (CH(2)H(4)folate) as both a source of the methylene group and the reductant, CH(2)H(4)folate only supplies the methylene group in ThyX-catalyzed reactions. Furthermore, ThyX only catalyzes thymidylate (dTMP) formation in the presence of reduced pyridine nucleotides and oxidized FAD. The distribution and transcription patterns of the a674r gene in Chlorella viruses were examined. The a674r gene was cloned, and the protein was expressed in Escherichia coli. Biochemical characterization of the P. bursaria chlorella virus-1 recombinant ThyX protein indicates that it is more efficient at converting dUMP to dTMP than previously studied ThyX enzymes, thus allowing more detailed mechanistic studies of the enzyme. The ThyX-dUMP complexes with bound FAD function as efficient NAD(P)H oxidases, indicating that dUMP binds to the enzyme prior to NAD(P)H. This oxidation activity is directly linked to FAD reduction. Our results indicate that ThyX-specific inhibitors can be designed that do not affect ThyA enzymes. Finally, a model is proposed for the early stages of ThyX catalysis.