Showing papers by "Centre national de la recherche scientifique published in 1999"

Swarm intelligence: from natural to artificial systems

Abstract: 1. Introduction 2. Ant Foraging Behavior, Combinatorial Optimization, and Routing in Communications Networks 3. Division of Labor and Task Allocation 4. Cemetery Organization, Brood Sorting, Data Analysis, and Graph Partitioning 5. Self-Organization and Templates: Application to Data Analysis and Graph Partitioning 6. Nest Building and Self-Assembling 7. Cooperative Transport by Insects and Robots 8. Epilogue

Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica

Abstract: The recent completion of drilling at Vostok station in East Antarctica has allowed the extension of the ice record of atmospheric composition and climate to the past four glacial–interglacial cycles. The succession of changes through each climate cycle and termination was similar, and atmospheric and climate properties oscillated between stable bounds. Interglacial periods differed in temporal evolution and duration. Atmospheric concentrations of carbon dioxide and methane correlate well with Antarctic air-temperature throughout the record. Present-day atmospheric burdens of these two important greenhouse gases seem to have been unprecedented during the past 420,000 years.

Molecular characterization of mitochondrial apoptosis-inducing factor

Abstract: Mitochondria play a key part in the regulation of apoptosis (cell death). Their intermembrane space contains several proteins that are liberated through the outer membrane in order to participate in the degradation phase of apoptosis. Here we report the identification and cloning of an apoptosis-inducing factor, AIF, which is sufficient to induce apoptosis of isolated nuclei. AIF is a flavoprotein of relative molecular mass 57,000 which shares homology with the bacterial oxidoreductases; it is normally confined to mitochondria but translocates to the nucleus when apoptosis is induced. Recombinant AIF causes chromatin condensation in isolated nuclei and large-scale fragmentation of DNA. It induces purified mitochondria to release the apoptogenic proteins cytochrome c and caspase-9. Microinjection of AIF into the cytoplasm of intact cells induces condensation of chromatin, dissipation of the mitochondrial transmembrane potential, and exposure of phosphatidylserine in the plasma membrane. None of these effects is prevented by the wide-ranging caspase inhibitor known as Z-VAD.fmk. Overexpression of Bcl-2, which controls the opening of mitochondrial permeability transition pores, prevents the release of AIF from the mitochondrion but does not affect its apoptogenic activity. These results indicate that AIF is a mitochondrial effector of apoptotic cell death.

Measuring phase synchrony in brain signals

Abstract: This article presents, for the first time, a practical method for the direct quantification of frequency-specific synchronization (i.e., transient phase-locking) between two neuroelectric signals. The motivation for its development is to be able to examine the role of neural synchronies as a putative mechanism for long-range neural integration during cognitive tasks. The method, called phase-locking statistics (PLS), measures the significance of the phase covariance between two signals with a reasonable time-resolution (,100 ms). Unlike the more traditional method of spectral coherence, PLS separates the phase and amplitude components and can be directly interpreted in the framework of neural integration. To validate synchrony values against background fluctuations, PLS uses surrogate data and thus makes no a priori assumptions on the nature of the experimental data. We also apply PLS to investigate intracortical recordings from an epileptic patient performing a visual discrimination task. We find large-scale synchronies in the gamma band (45 Hz), e.g., between hippocampus and frontal gyrus, and local synchronies, within a limbic region, a few cm apart. We argue that whereas long-scale effects do reflect cognitive processing, short-scale synchronies are likely to be due to volume conduction. We discuss ways to separate such conduction effects from true signal synchrony. Hum Brain Mapping 8:194-208, 1999. r 1999 Wiley-Liss, Inc.

Phylogenetic Perspectives in Innate Immunity

Abstract: The concept of innate immunity refers to the first-line host defense that serves to limit infection in the early hours after exposure to microorganisms. Recent data have highlighted similarities between pathogen recognition, signaling pathways, and effector mechanisms of innate immunity in Drosophila and mammals, pointing to a common ancestry of these defenses. In addition to its role in the early phase of defense, innate immunity in mammals appears to play a key role in stimulating the subsequent, clonal response of adaptive immunity.

Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes

Abstract: The human AIDS viruses human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) represent cross-species (zoonotic) infections. Although the primate reservoir of HIV-2 has been clearly identified as the sooty mangabey (Cercocebus atys), the origin of HIV-1 remains uncertain. Viruses related to HIV-1 have been isolated from the common chimpanzee (Pan troglodytes), but only three such SIVcpz infections have been documented, one of which involved a virus so divergent that it might represent a different primate lentiviral lineage. In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. We find that two chimpanzee subspecies in Africa, the central P. t. troglodytes and the eastern P. t. schweinfurthii, harbour SIVcpz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. All HIV-1 strains known to infect man, including HIV-1 groups M, N and O, are closely related to just one of these SIVcpz lineages, that found in P. t. troglodytes. Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. These results, together with the observation that the natural range of P. t. troglodytes coincides uniquely with areas of HIV-1 group M, N and O endemicity, indicate that P. t. troglodytes is the primary reservoir for HIV-1 and has been the source of at least three independent introductions of SIVcpz into the human population.

Perception's shadow: long-distance synchronization of human brain activity.

Abstract: Transient periods of synchronization of oscillating neuronal discharges in the frequency range 30-80 Hz (gamma oscillations) have been proposed to act as an integrative mechanism that may bring a widely distributed set of neurons together into a coherent ensemble that underlies a cognitive act. Results of several experiments in animals provide support for this idea. In humans, gamma oscillations have been described both on the scalp (measured by electroencephalography and magnetoencephalography) and in intracortical recordings, but no direct participation of synchrony in a cognitive task has been demonstrated so far. Here we record electrical brain activity from subjects who are viewing ambiguous visual stimuli (perceived either as faces or as meaningless shapes). We show for the first time, to our knowledge, that only face perception induces a long-distance pattern of synchronization, corresponding to the moment of perception itself and to the ensuing motor response. A period of strong desynchronization marks the transition between the moment of perception and the motor response. We suggest that this desynchronization reflects a process of active uncoupling of the underlying neural ensembles that is necessary to proceed from one cognitive state to another.

Molecular tinkering of G protein‐coupled receptors: an evolutionary success

Abstract: Among membrane‐bound receptors, the G protein‐coupled receptors (GPCRs) are certainly the most diverse. They have been very successful during evolution, being capable of transducing messages as different as photons, organic odorants, nucleotides, nucleosides, peptides, lipids and proteins. Indirect studies, as well as two‐dimensional crystallization of rhodopsin, have led to a useful model of a common ‘central core’, composed of seven transmembrane helical domains, and its structural modifications during activation. There are at least six families of GPCRs showing no sequence similarity. They use an amazing number of different domains both to bind their ligands and to activate G proteins. The fine‐tuning of their coupling to G proteins is regulated by splicing, RNA editing and phosphorylation. Some GPCRs have been found to form either homo‐ or heterodimers with a structurally different GPCR, but also with membrane‐bound proteins having one transmembrane domain such as nina‐A, odr‐4 or RAMP, the latter being involved in their targeting, function and pharmacology. Finally, some GPCRs are unfaithful to G proteins and interact directly, via their C‐terminal domain, with proteins containing PDZ and Enabled/VASP homology (EVH)‐like domains.

The uncontrolled manifold concept: identifying control variables for a functional task

Abstract: The degrees of freedom problem is often posed by asking which of the many possible degrees of freedom does the nervous system control? By implication, other degrees of freedom are not controlled. We give an operational meaning to "controlled" and "uncontrolled" and describe a method of analysis through which hypotheses about controlled and uncontrolled degrees of freedom can be tested. In this conception, control refers to stabilization, so that lack of control implies reduced stability. The method was used to analyze an experiment on the sit-to-stand transition. By testing different hypotheses about the controlled variables, we systematically approximated the structure of control in joint space. We found that, for the task of sit-to-stand, the position of the center of mass in the sagittal plane was controlled. The horizontal head position and the position of the hand were controlled less stably, while vertical head position appears to be no more controlled than joint motions.

Geochemical Consequences of Increased Atmospheric Carbon Dioxide on Coral Reefs

Abstract: A coral reef represents the net accumulation of calcium carbonate (CaCO3) produced by corals and other calcifying organisms. If calcification declines, then reef-building capacity also declines. Coral reef calcification depends on the saturation state of the carbonate mineral aragonite of surface waters. By the middle of the next century, an increased concentration of carbon dioxide will decrease the aragonite saturation state in the tropics by 30 percent and biogenic aragonite precipitation by 14 to 30 percent. Coral reefs are particularly threatened, because reef-building organisms secrete metastable forms of CaCO3, but the biogeochemical consequences on other calcifying marine ecosystems may be equally severe.

New Methods Employing Multilocus Genotypes to Select or Exclude Populations as Origins of Individuals

Abstract: A new method for assigning individuals of unknown origin to populations, based on the genetic distance between individuals and populations, was compared to two existing methods based on the likelihood of multilocus genotypes. The distribution of the assignment criterion (genetic distance or genotype likelihood) for individuals of a given population was used to define the probability that an individual belongs to the population. Using this definition, it becomes possible to exclude a population as the origin of an individual, a useful extension of the currently available assignment methods. Using simulated data based on the coalescent process, the different methods were evaluated, varying the time of divergence of populations, the mutation model, the sample size, and the number of loci. Likelihood-based methods (especially the Bayesian method) always performed better than distance methods. Other things being equal, genetic markers were always more efficient when evolving under the infinite allele model than under the stepwise mutation model, even for equal values of the differentiation parameter F(st). Using the Bayesian method, a 100% correct assignment rate can be achieved by scoring ca. 10 microsatellite loci (H approximately 0.6) on 30-50 individuals from each of 10 populations when the F(st) is near 0.1.

Quantum Phase Interference and Parity Effects in Magnetic Molecular Clusters

Abstract: An experimental method based on the Landau-Zener model was developed to measure very small tunnel splittings in molecular clusters of eight iron atoms, which at low temperature behave like a nanomagnet with a spin ground state of S = 10. The observed oscillations of the tunnel splittings as a function of the magnetic field applied along the hard anisotropy axis are due to topological quantum interference of two tunnel paths of opposite windings. Transitions between quantum numbers M = -S and (S - n), with n even or odd, revealed a parity effect that is analogous to the suppression of tunneling predicted for half-integer spins. This observation is direct evidence of the topological part of the quantum spin phase (Berry phase) in a magnetic system.

Chemical reactivity indexes in density functional theory

Abstract: The theoretical description of charge distribution, and related properties, such as chemical reactivity descriptors of chemical compounds, has greatly benefited from the development of density functional theory (DFT) methods. Indeed, most concepts stemmed from DFT but, up to now, they have been used mostly within semiempirical MO methods, Hartree–Fock, or post-Hartree–Fock methods. During the last decade, however, DFT has enabled theoretical chemistry to predict accurately structures and energetics of clusters and molecules. Therefore, more attention should also now be paid to these reactivity descriptors determined directly from DFT calculations. In this work, chemical reactivity is explored in DFT through a functional Taylor expansion of energy that introduces various energy derivatives of chemical significance. This review summarizes their main features and examines the limitations of some indexes presently used for the characterization of reactivity. Also, several perspectives are given. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 129–154, 1999

Molecular characterization of dendritic cell-derived exosomes. Selective accumulation of the heat shock protein hsc73.

Abstract: Exosomes are membrane vesicles secreted by hematopoietic cells upon fusion of late multivesicular endosomes with the plasma membrane. Dendritic cell (DC)-derived exosomes induce potent antitumor immune responses in mice, resulting in the regression of established tumors (Zitvogel, L., A. Regnault, A. Lozier, J. Wolfers, C. Flament, D. Tenza, P. Ricciardi-Castagnoli, G. Raposo, and S. Amigorena. 1998. Nat. Med. 4:594–600). To unravel the molecular basis of exosome-induced immune stimulation, we now analyze the regulation of their production during DC maturation and characterize extensively their protein composition by peptide mass mapping. Exosomes contain several cytosolic proteins (including annexin II, heat shock cognate protein hsc73, and heteromeric G protein Gi2α), as well as different integral or peripherally associated membrane proteins (major histocompatiblity complex class II, Mac-1 integrin, CD9, milk fat globule-EGF-factor VIII [MFG-E8]). MFG-E8, the major exosomal component, binds integrins expressed by DCs and macrophages, suggesting that it may be involved in exosome targeting to these professional antigen-presenting cells. Another exosome component is hsc73, a cytosolic heat shock protein (hsp) also present in DC endocytic compartments. hsc73 was shown to induce antitumor immune responses in vivo, and therefore could be involved in the exosome's potent antitumor effects. Finally, exosome production is downregulated upon DC maturation, indicating that in vivo, exosomes are produced by immature DCs in peripheral tissues. Thus, DC-derived exosomes accumulate a defined subset of cellular proteins reflecting their endosomal biogenesis and accounting for their biological function.

Antimicrobial peptides in insects; structure and function

Abstract: Antimicrobial peptides appear to be ubiquitous and multipotent components of the innate immune defense arsenal used by both prokaryotic and eukaryotic organisms. During the past 15 years a multitude of these peptides have been isolated largely from insects. In spite of great differences in size, amino acid composition and structure, most of the antimicrobial peptides from insects can be grouped into one of three categories. The largest category in number contains peptides with intramolecular disulfide bonds forming hairpin-like β-sheets or α-helical–β-sheet mixed structures. The second most important group is composed of peptides forming amphipathic α-helices. The third group comprises peptides with an overrepresentation in proline and/or glycine residues. In general, the insect antimicrobial peptides have a broad range of activity and are not cytotoxic. Despite a wealth of information on structural requirements for their antimicrobial activity, the mode of action of these peptides is not yet fully understood. However, some data suggest the existence of two types of mode of action: 1. through peptide–lipid interaction or 2. through receptor-mediated recognition processes. This review presents the main results obtained during the last four years in the field of antimicrobial peptides from insects with a special focus on the proline-rich and cysteine-rich peptides.

Reconstitution of actin-based motility of Listeria and Shigella using pure proteins.

Abstract: Actin polymerization is essential for cell locomotion and is thought to generate the force responsible for cellular protrusions. The Arp2/3 complex is required to stimulate actin assembly at the leading edge in response to signalling. The bacteria Listeria and Shigella bypass the signalling pathway and harness the Arp2/3 complex to induce actin assembly and to propel themselves in living cells. However, the Arp2/3 complex alone is insufficient to promote movement. Here we have used pure components of the actin cytoskeleton to reconstitute sustained movement in Listeria and Shigella in vitro. Actin-based propulsion is driven by the free energy released by ATP hydrolysis linked to actin polymerization, and does not require myosin. In addition to actin and activated Arp2/3 complex, actin depolymerizing factor (ADF, or cofilin) and capping protein are also required for motility as they maintain a high steady-state level of G-actin, which controls the rate of unidirectional growth of actin filaments at the surface of the bacterium. The movement is more effective when profilin, alpha-actinin and VASP (for Listeria) are also included. These results have implications for our understanding of the mechanism of actin-based motility in cells.

High-efficiency gene transfer into skeletal muscle mediated by electric pulses

Abstract: Gene delivery to skeletal muscle is a promising strategy for the treatment of muscle disorders and for the systemic secretion of therapeutic proteins. However, present DNA delivery technologies have to be improved with regard to both the level of expression and interindividual variability. We report very efficient plasmid DNA transfer in muscle fibers by using square-wave electric pulses of low field strength (less than 300 V/cm) and of long duration (more than 1 ms). Contrary to the electropermeabilization-induced uptake of small molecules into muscle fibers, plasmid DNA has to be present in the tissue during the electric pulses, suggesting a direct effect of the electric field on DNA during electrotransfer. This i.m. electrotransfer method increases reporter and therapeutic gene expression by several orders of magnitude in various muscles in mouse, rat, rabbit, and monkey. Moreover, i.m. electrotransfer strongly decreases variability. Stability of expression was observed for at least 9 months. With a pCMV-FGF1 plasmid coding for fibroblast growth factor 1, this protein was immunodetected in the majority of muscle fibers subjected to the electric pulses. DNA electrotransfer in muscle may have broad applications in gene therapy and in physiological, pharmacological, and developmental studies.

Structure and physicochemistry of anodic oxide films on titanium and TA6V alloy

Abstract: Anodization of titanium and its alloys is an important surface treatment, especially for adhesion applications, but is not as well studied as for aluminium alloys. This paper deals with the morphological, structural and physicochemical characterization of anodic oxide films grown on titanium and Ti–6Al–4V (TA6V) in chromic acid solution without (CA) or with (CA/HF) hydrofluoric acid addition. Several investigations methods are used: high-resolution scanning electron microscopy (HR-SEM), reflection high-energy electron diffraction (RHEED), x-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), nuclear reaction analysis (NRA) and wetting angle measurements. The occurrence and morphology of the nanoporous structure for CA/HF anodization are described. The compact films grown in CA solution are amorphous and the porous films grown in the CA/HF solution are partially crystalline. The thickness and morphology of the films are described and discussed as a function of the anodizing conditions and of the composition of the underlying substrate. The composition of the film appears to be TiO2+Al2O3 (with Ti/Al atomic ratio ∽5), with incorporation of fluorine from the solution in the porous films and of small quantities of vanadium in the films that are grown. The specific role played by the Cr(VI) and F species on the film growth-and-dissolution formation process is discussed and a growth mechanism is proposed. Copyright © 1999 John Wiley & Sons, Ltd.

A penalization method to take into account obstacles in incompressible viscous flows

Abstract: From the Navier-Stokes/Brinkman model, a penalization method has been derived by several authors to compute incompressible Navier-Stokes equations around obstacles. In this paper, convergence theorems and error estimates are derived for two kinds of penalization. The first one corresponds to $L^2$ penalization inducing a Darcy equation in the solid body, the second one corresponds to a $H^1$ penalization and induces a Brinkman equation in the body. Numerical tests are performed to confirm the efficiency and accuracy of the method.

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis

Abstract: We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. In those three species, we observed a clear correlation between codon usage and gene expression levels and showed that this correlation is not due to a mutational bias. This provides direct evidence for selection on silent sites in those three distantly related multicellular eukaryotes. Surprisingly, there is a strong negative correlation between codon usage and protein length. This effect is not due to a smaller size of highly expressed proteins. Thus, for a same-expression pattern, the selective pressure on codon usage appears to be lower in genes encoding long rather than short proteins. This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms.