Many-body Green's function GW and Bethe-Salpeter study of the optical excitations in a paradigmatic model dipeptide.

We study within the many-body Green's function GW and Bethe-Salpeter formalisms the excitation energies of a paradigmatic model dipeptide, focusing on the four lowest-lying local and charge-transfer excitations. Our GW calculations are performed at the self-consistent level, updating first the quasiparticle energies, and further the single-particle wavefunctions within the static Coulomb-hole plus screened-exchange approximation to the GW self-energy operator. Important level crossings, as compared to the starting Kohn-Sham LDA spectrum, are identified. Our final Bethe-Salpeter singlet excitation energies are found to agree, within 0.07 eV, with CASPT2 reference data, except for one charge-transfer state where the discrepancy can be as large as 0.5 eV. Our results agree best with LC-BLYP and CAM-B3LYP calculations with enhanced long-range exchange, with a 0.1 eV mean absolute error. This has been achieved employing a parameter-free formalism applicable to metallic or insulating extended or finite systems.

Is the in vitro ejection of bacteriophage DNA quasistatic? A bulk to single virus study.

Bacteriophage T5 DNA ejection is a complex process that occurs on several timescales in vitro. By using a combination of bulk and single phage measurements, we quantitatively study the three steps of the ejection-binding to the host receptor, channel-opening, and DNA release. Each step is separately addressed and its kinetics parameters evaluated. We reconstruct the bulk kinetics from the distribution of single phage events by following individual DNA molecules with unprecedented time resolution. We show that, at the single phage level, the ejection kinetics of the DNA happens by rapid transient bursts that are not correlated to any genome sequence defects. We speculate that these transient pauses are due to local phase transitions of the DNA inside the capsid. We predict that such pauses should be seen for other phages with similar DNA packing ratios.

Influence of chimeric human-bovine fibers on adenoviral uptake by liver cells and the antiviral immune response.

Human adenoviruses (HAdV) are widely used for in vitro and in vivo gene transfer. Viral hepatotropism, inflammatory responses and neutralization by pre-existing antibodies (NAbs) are obstacles for clinical applications of HAdV vectors. Although the multifactorial events leading to innate HAdV toxicity are far from being elucidated, there is a consensus that the majority of intravenously injected-HAdV vectors is sequestered by Kuppfer cells, probably independently of coagulation factors. In this study, we show that the adenoviral-associated humoral and innate cytokine immune responses are significantly reduced when HAdV-5 vector carrying human bovine chimeric fibers (HAdV-5-F2/BAdV-4) is intravenously injected into mice. Fiber pseudotyping modified its interaction with blood coagulation factors, as FIX and FX no longer mediate the infection of liver cells by HAdV-5-F2/BAdV-4. As a consequence, at early time points post-infection, several cytokines and chemokines (IFN-gamma, IL-6, IP-10, MCP-1, RANTES and MP1beta) were found to be present at lower levels in the plasma of mice that had been intravenously injected with HAdV-5-F2/BAdV-4 compared with mice injected with the parental vector HAdV-5. Moreover, genetic modification of the fiber allowed HAdV-5-F2/BAdV-4 to partially escape neutralization by NAbs.

A method to evaluate skill transfer and acquisition of obstetric gestures based on the curvatures analysis of the position and the orientation.

This paper focuses on the gesture analysis in order to compare two human gestures. The orientations and the positions of the gestures are both taken into account and the similarity rate between two gestures is calculated. In our case, the application is in obstetrics and the aim is to evaluate forceps blade placement. The method is based on the curvature analysis of the paths during the gesture. The 3-D position paths are expressed according to their cumulated chord length and the orientation paths in the quaternion unit space. These parameterizations lead to analyze data in space independently to time as requested by physicians. After filtering data in order to minimize sensor noises, the gestures are then compared by calculating the correlation between the position and the orientation curvatures of a novice gesture and an expert one. The results clearly show that novice skills in handling forceps increase in becoming smoother and closer to the reference placement. A childbirth simulator allows novices to acquire experience without any risks, however the training have to be completed with the extraction gesture evaluation and a compulsory training period in the delivery ward.

Adenovirus 5 vector genetically re-targeted by an Affibody molecule with specificity for tumor antigen HER2/neu.

In order to use adenovirus (Ad) type 5 (Ad5) for cancer gene therapy, Ad needs to be de-targeted from its native receptors and re-targeted to a tumor antigen. A limiting factor for this has been to find a ligand that (i) binds a relevant target, (ii) is able to fold correctly in the reducing environment of the cytoplasm and (iii) when incorporated at an optimal position on the virion results in a virus with a low physical particle to plaque-forming units ratio to diminish the viral load to be administered to a future patient. Here, we present a solution to these problems by producing a genetically re-targeted Ad with a tandem repeat of the HER2/neu reactive Affibody molecule (ZH) in the HI-loop of a Coxsackie B virus and Ad receptor (CAR) binding ablated fiber genetically modified to contain sequences for flexible linkers between the ZH and the knob sequences. ZH is an Affibody molecule specific for the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu) that is overexpressed in inter alia breast and ovarian carcinomas. The virus presented here exhibits near wild-type growth characteristics, infects cells via HER2/neu instead of CAR and represents an important step toward the development of genetically re-targeted adenoviruses with clinical relevance.

Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships.

Evolutionary relationships between viruses may be obscure by protein sequence but unmasked by structure. Analysis of bacteriophage T5 by cryo-electron microscopy and protein sequence analysis reveals analogies with HK97 and T4 that suggest a mosaic of such connections. The T5 capsid is consistent with the HK97 capsid protein fold but has a different geometry, incorporating three additional hexamers on each icosahedral facet. Similarly to HK97, the T5 major capsid protein has an N-terminal extension, or Delta-domain that is missing in the mature capsid, and by analogy with HK97, may function as an assembly or scaffold domain. This Delta-domain is predicted to be largely coiled-coil, as for that of HK97, but is approximately 70% longer correlating with the larger capsid. Thus, capsid architecture appears likely to be specified by the Delta-domain. Unlike HK97, the T5 capsid binds a decoration protein in the center of each hexamer similarly to the "hoc" protein of phage T4, suggesting a common role for these molecules. The tail-tube has unusual trimeric symmetry that may aid in the unique two-stage DNA-ejection process, and joins the tail-tip at a disk where tail fibers attach. This intriguing mix of characteristics embodied by phage T5 offers insights into virus assembly, subunit function, and the evolutionary connections between related viruses.

Recovery of homogeneous and functional beta 2-adrenergic receptors from extracellular baculovirus particles.

Expression in baculovirus-infected insect cells allows sufficient production of G-protein coupled receptor for structural studies. An important drawback of this expression system comes from the presence of unprocessed and biologically inactive receptors that have to be eliminated during receptor purification steps. We show that viral particles released from Sf9 cells infected with a recombinant baculovirus coding for the human beta 2-adrenergic receptor (beta 2AR) cDNA contain glycosylated and biologically active beta 2AR. In addition, post-translational modifications known to modulate receptor activity were found to occur in these particles.

Preparation and in vitro/in vivo evaluation of nano-sized crystals for dissolution rate enhancement of ucb-35440-3, a highly dosed poorly water-soluble weak base.

Ucb-35440-3 is a new drug entity under investigation at UCB S.A. Due to its physicochemical characteristics, the drug, a poorly water-soluble weak base, shows poor solubility and dissolution characteristics. In rat, the low oral bioavailability (F < 10%) is largely due to poor absorption. In order to enhance the solubility and dissolution characteristics, formulation of ucb-35440-3 as nanocrystals has been achieved in this study. Nanoparticles were prepared using high pressure homogenization and were characterized in terms of size and morphology. In vitro dissolution characteristics were investigated and compared to the un-milled drug in order to verify the theoretical hypothesis on the benefit of increased surface area. In vivo pharmacokinetic evaluation of ucb-35440-3 nanoparticles was also carried out on rats. Crystalline state evaluation before and following particle size reduction was conducted through polarized light microscopy and PXRD to denote any possible transformation to an amorphous state during the homogenization process. Drug chemical stability was also assessed following homogenization. The dissolution rate increased significantly at pH 3.0, 5.0 and 6.5 for ucb-35440-3 nanoparticles. However, the pharmacokinetic profile obtained yielded lower systemic exposure than the un-milled compound (in fed state), this although being thought to be the consequence of the drug and formulation characteristics.

[Oxidatif-stress and COPD. Role of infection. Prevention]. / Stress oxydatif et BPCO. Rôle des infections. Prévention.

For the next decade, COPD will become the third cause of mortality in the world. COPD is mainly due to cigarette smoking and presents different levels of severity according to people, probably linked to environmental and genetic factors, which are not well documented. Recent publications pointed out bacterial bronchial colonization and exacerbations of infectious origin as worsening factors through a pro-inflammatory effect and oxidative stress. This should lead to a comprehensive review of anti-infectious prevention tools and to discuss the role of prophylactic antibiotherapy and antioxidants.

[The fate of alpha and epsilon lysine amino groups in rat liver in vitro (author's transl)]. / La destinée des groupements aminés alpha et epsilon de la lysine dans le foie de rat in vitro

The fate of alpha and epsilon lysine amino groups has been explored in rat liver homogenate by means of L-lysine labelled selectively in the two positions. alpha-15NH2 and epsilon-15NH2 are rapidly incorporated into the amino group of glutamic acid and it seems at first that both transaminations occur simultaneously. But the reversible transfer of the amino group between alpha-aminoadipic acid and glutamic acid, determined by means of labelled alpha-aminoadipic acid, proceeds swiftly, and the incorporation of alpha-15NH2 from the corresponding labelled lysine in glutamic acid may be easily explained by epsilon-transamination and saccharopine formation. The direct transamination of the alpha-amino group of L-lysine is most improbable and might be limited to some microorganisms and to epsilon-N-substituted lysine derivatives.

Functional and structural effects of an Ala to Val mutation in the adenovirus serotype 2 fibre.

H2ts125 is a fibre-defective, temperature-sensitive mutant of adenovirus serotype 2. H2ts125 fibre is unstable at the non-permissive temperature (ts phenotype), and does not migrate in the same way as the wild-type fibre in an SDS/polyacrylamide gel (elm phenotype). Sequence analysis has shown that H2ts125 carries two mutations on the fibre gene: Leu105 to Phe, and Ala434 to Val. Analysis of the structural modifications occurring in H2ts125 fibre was performed using peptide finger-printing and antipeptide sera as immunological probes. We found that all the detectable structural alterations in the mutant fibre were due to the substitution on codon 434. In addition, the ts phenotype was rescued by a wild-type DNA fragment containing the 3' moiety of the fibre gene and overlapping the 434th codon. Morphological analysis of fibre molecules observed under the electron microscope showed minor but statistically significant differences in the fibre length between mutant and wild-type. The mutant fibre was found to be slightly longer (308.8 +/- 1.9 A) than the wild-type fibre (300.1 +/- 2.1 A). Thus both ts and elm phenotypes were carried by the same Ala434 to Val mutation which probably resulted from a change in the three-dimensional structure of the fibre protein, and not from some proteolytic cleavage.

Crystal packing and stoichiometry of the fibre protein of adenovirus type 2.

Crystals of the fibre protein of adenovirus type 2 have been grown and studied by electron microscopy and X-ray powder diffraction. The molecular packing and density of the crystals suggest that the fibre is dimeric.

Characterization of a high-affinity complex between the bacterial outer membrane protein FhuA and the phage T5 protein pb5.

Binding of bacteriophage T5 to Escherichia coli cells is mediated by specific interactions between the receptor-binding protein pb5 (67.8 kDa) and the outer membrane iron-transporter FhuA. A histidine-tagged form of pb5 was overproduced and purified. Isolated pb5 is monomeric and organized mostly as beta-sheets (51%). pb5 functionality was attested in vivo by its ability to impair infection of E. coli cells by phage T5 and Phi80, and to prevent growth of bacteria on iron-ferrichrome as unique iron source. pb5 was functional in vitro, since addition of an equimolar concentration of pb5 to purified FhuA prevented DNA release from phage T5. However, pb5 alone was not sufficient for the conversion of FhuA into an open channel. Direct interaction of pb5 with FhuA was demonstrated by isolating a pb5/FhuA complex using size-exclusion chromatography. The stoichiometry, 1 mol of pb5/1 mol of FhuA, was deduced from its molecular mass, established by analytical ultracentrifugation after determination of the amount of bound detergent. SDS-PAGE and differential scanning calorimetry experiments highlighted the great stability of the complex: (i) it was not dissociated by 2% SDS even when the temperature was raised to 70 degrees C; (ii) thermal denaturation of the complex occurred at 85 degrees C, while pb5 and FhuA were denatured at 45 degrees C and 74 degrees C, respectively. The stability of the complex renders it suitable for high-resolution structural studies, allowing future analysis of conformational changes into both FhuA and pb5 upon adsorption of the virus to its host.

[Oxidative stress in bronchopulmonary disease: contribution of N-acetylcysteine (NAC)]. / Le stress oxydatif en pathologie broncho-pulmonaire: apport de la N-acétyl-cystéine (NAC).

Oxidative stress is a frequent mechanism involved in the pathogenesis of bronchopulmonary disease. The cause can be exogenous, in particular related to to atmospheric pollution and tobacco smoke, or endogenous, related to mobilization of inflammatory cells (macrophages and polymorphonuclear neutrophils). In this general review, we present work demonstrating this oxidative stress and activation of inflammatory cells. We discuss the effect of oxidative stress on the bronchial tree and the need to maintain an adequate balance between oxidants and anti-oxidants. This reviews focuses on experimental studies proving the anti-oxidant effect of NAC on glutathione synthesis and on different pharmacological models. We then discuss human trials, initially experimental then in different bronchopulmonary pathologies related to oxidative stress. Acetaminophen intoxication and pulmonary fibrosis are models for use of NAC. Recent work on COPD appears to show a decrease in exacerbations, improvement in symptoms and quality-of-life, and perhaps a reduction in the alteration of ventilatory function.

Enhancement of adenovirus-mediated gene delivery by use of an oligopeptide with dual binding specificity.

The efficiency of human adenovirus serotype 5 (Ad5) transgene delivery was tested on several human and animal cell lines in vitro, by using a bimodular 35-mer oligopeptide carrying two peptide domains with different ligand specificities. One domain mimicked the fiber knob-binding region of the alpha2 domain of human MHC-1 molecules (MH20), and the other corresponded to the gastrin-releasing peptide (GRP). Two synthetic peptides with different configurations were analyzed in Ad-mediated gene transfer assays using Ad5Luc3 vector carrying the luciferase reporter gene. One peptide (GRP-MH20) had the GRP domain on the N-terminal side of MH20, while the other (MH20-GRP), the C-terminally amidified GRP, was on the C-terminal side of MH20. The GRP-MH20 peptide, but not MH20-GRP, was capable of enhancing luciferase gene delivery to Ad-susceptible cells in a GRP receptor-dependent manner. More importantly, GRP-MH20 could also confer susceptibility to Ad infection to normal or cancer cells that lack fiber receptors for the virus. Our data suggested that GRP receptors could function efficiently as alternative attachment receptors for Ad5, but that Ad5 bound to GRP receptors still depended, at least partially, on the penton base-mediated endocytotic pathway for subsequent cell entry. Gene delivery by a human adenovirus serotype 5 (Ad5) vector was assayed with a bimodular oligopeptide carrying two peptide domains of different binding specificities. One domain was a high-affinity peptide ligand of the Ad5 fiber knob (MH20), and the other corresponded to the gastrin-releasing peptide (GRP). The synthetic peptide GRP-MH20 was found to be capable of enhancing Ad-mediated gene transfer to Ad-susceptible cells in a GRP receptor-dependent manner. More importantly, GRP-MH20 could also confer susceptibility to Ad infection to normal or cancer cells that lack fiber receptors. Our data suggested that GRP receptors could function efficiently as alternative attachment receptors for Ad5, but virus bound to GRP receptors still depended partially on the penton base-mediated pathway for cell entry.

Genetic modification of adenovirus 5 tropism by a novel class of ligands based on a three-helix bundle scaffold derived from staphylococcal protein A.

The use of adenovirus (Ad) as an efficient and versatile vector for in vivo tumor therapy requires the modulation of its cellular tropism. We previously developed a method to genetically alter the tropism of Ad5 fibers by replacing the fiber knob domain by an extrinsic trimerization motif and a new cellular ligand. However, fibers carrying complex ligands such as single-chain antibody fragments did not assemble into functional pentons in vitro in the presence of penton base, and failed to be rescued into infectious virions because of their inability to fold correctly within the cytoplasm of Ad-infected cells. Here we show that the coding sequence for a disulfide bond-independent three-helix bundle scaffold Z, derived from domain B of Staphylococcal protein A and capable of binding to the Fc portion of immunoglobulin (Ig) G1, could be incorporated into modified knobless Ad fiber gene constructs with seven shaft repeats. These fiber gene constructs could be rescued into viable virions that were demonstrated to enter 293 cells engineered for IgG Fc surface expression but not unmodified 293 cells, via a mechanism that could be specifically blocked with soluble Fc target protein. However, the tropism modified viruses showed a slightly impaired cellular entry and a lower infectivity than wildtype (WT) virus. In addition, we generated recombinant fibers containing an IgA binding Affibody ligand, derived from combinatorial specificity-engineering of the Z domain scaffold. Such fiber constructs also showed the expected target specific binding, indicating that the affibody protein class is ideally suited for genetic engineering of Ad tropism.

Metabolism of sex steroids in the human and canine vas deferens.

The contribution of the vas deferens to the metabolism of steroids was investigated in the human and in the dog by perfusion experiments and in vitro incubation. Perfusion of testosterone or androstenedione through the canine vas deferens resulted in the formation of dihydrotestosterone; no significant formation of estrogens could be detected. When dihydrotestosterone was perfused, 3alpha- and 3beta-androstanediols were isolated. In vitro incubation experiments with human was deferencs have shown an active metabolism of androgens by this time and, therefore, confer a new role to the vas deferens in the male.

Restriction maps of human adenovirus types 2, 5 and 3 for BclI, ClaI, pvul and SphI endonucleases.

The sites of cleavage by BclI, ClaI, PvuI and SphI in the DNA from adenovirus (Ad) serotypes 2, 5 and 3 have been located. Certain site coordinates were in accord with nucleotide sequences already published. A small difference in size between the PvuI-E fragments from Ad2 and Ad5 confirmed the existence of a deletion in the N-terminal moiety of Ad5 hexon gene, as previously implied by interserotypic recombinants (Boursnell and Mautner, Virology 112 (1981) 198-209) and more recently by amino acid sequencing (Von Bahr-Lindström et al., Virology 118 (1982) 352-362).

Involvement of ion channels in the transport of phage DNA through the cytoplasmic membrane of E. coli.

Upon infection, phage DNA is transported through the bacterial cytoplasmic membrane. This crossing is accompanied by a transient increase in the permeability of the cytoplasmic membrane toward ions and small solutes. This has led several authors to propose that DNA might cross the cytoplasmic membrane through channels. In the first part of the review we present data that we obtained with phage T4 and that strongly support this proposal. We then present the structural and ionic characteristics of these channels. In the second part, we summarize data obtained by several authors concerning the permeability changes induced by different phages and show that these results are compatible with a model of phage DNA transfer through channels. Finally, we discuss the possible origin of these channels.

FhuA, an Escherichia coli outer membrane protein with a dual function of transporter and channel which mediates the transport of phage DNA.

FhuA (M(r) = 78,900) is an Escherichia coli outer membrane protein which transports the ferric siderophore ferrichrome and is the receptor for phage T5, phi 80 and T1 and for colicin M. FhuA was purified chromatographically in non-ionic detergent (octyl glucoside). The circular dichroism spectrum indicates that FhuA is essentially organized in beta-strands like the majority of proteins of the outer membrane of Gram-negative bacteria. The structural parameters of FhuA were assessed from size exclusion chromatography, sedimention equilibrium and velocity experiments. FhuA is monomeric in solution and functional since binding of phage T5 causes the release of the phage genome, a double-stranded DNA of 121,000 base pairs, into the surrounding medium. Planar lipid bilayer experiments showed that the FhuA transporter is converted into a high conductance channel upon binding of phage T5. FhuA was reconstituted into large unilamellar vesicles (mean diameter 125 nm). Cryo-electron microscopy and fluorescence experiments, using a DNA intercalant YO-PRO 1, showed that binding of T5 to FhuA triggers the transfer of the phage genome into the proteoliposomes without altering their morphology. Two models can account for these observations, which apply both to in vitro and in vivo DNA transport. The simplest model supposes that the naked DNA is transported through the FhuA channel. Alternatively transfer of DNA might be mediated by pb2, the protein forming the phage straight fiber. pb2 would insert either directly in the membrane or inside the FhuA channel.