Showing papers by "Université catholique de Louvain published in 1992"

The complete DNA sequence of yeast chromosome III.

Abstract: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

Stability of the Astronomical Frequencies Over the Earth's History for Paleoclimate Studies

Abstract: The expected changes over the past 500 million years in the principal astronomical frequencies influencing the Earth's climate may be strong enough to be detectable in the geological records, and such effects have been inferred in several cases. Calculations suggest that the shortening of the Earth-moon distance and of the length of the day back in time induced a shortening of the fundamental periods for the obliquity and climatic precession, from 54 to 35, 41 to 29, 23 to 19, and 19 to 16 thousand years over the last half-billion years. At the same time, the precessional constant increased from 50 to 61 arc seconds per year. The changes in the frequencies of the planetary system due to its chaotic motion are much smaller; their influence on the changes of the periods of climatic precession, obliquity, and eccentricity of the Earth's orbit around the sun can be neglected. Eccentricity periods used for Quaternary climate studies may therefore be considered to have been more or less constant for pre-Quaternary times.

Direct simulation of fluid particle motions

Abstract: Continuum models of two-phase flows of solids and liquids use constitutive assumptions to close the equations. A more fundamental approach is a “molecular dynamic” simulation of flowing “big” particles based on reliable macroscopic equations for both solid and liquid. We developed a package that simulates the unsteady two-dimensional solid-liquid two-phase flows using the Navier-Stokes equations for the liquid and Newton's equations of motion for the solid particles. The Navier-Stokes equations are solved using a finite-element formulation and Newton's equations of motion are solved using an explicit-implicit scheme. We show that the simplest fully explicit scheme to update the particle motion using Newton's equations is unstable. To correct this instability we propose and implement and Explicit-Implicit Scheme in which, at each time step, the positions of the particles are updated explicitly, the computational domain is remeshed, the solution at the previous time is mapped onto the new mesh, and finally the nonlinear Navier-Stokes equation and the implicitly discretized Newton's equations for particle velocities are solved on the new mesh iteratively. The numerical simulation reveals the effect of vortex shedding on the motion of the cylinders and reproduces the drafting, kissing, and tumbling scenario which is the dominant rearrangement mechanism in two-phase flow of solids and liquids in beds of spheres which are constrained to move in only two dimensions.

Dielectric tensor, effective charges, and phonons in alpha -quartz by variational density-functional perturbation theory.

Abstract: A new method is introduced to calculate response functions within density-functional theory. It uses a conjugate-gradient algorithm applied to a variational expression from perturbation theory. The dielectric tensor, effective charges, and TO and LO phonons at q=0 in alpha-quartz are obtained. A one-parameter scissors operator gives the dielectric tensor within 0.5% of the experimental value. The anisotropy of the effective charge tensor is shown to be crucial for reproducing the LO-TO splittings.

The Greenhouse-effect

Abstract: The greenhouse effect on the Earth is identified by the difference between the effective radiating temperature of the planet and its surface temperature. The difference between the energy emitted by the surface and that emitted upward to space by the upper atmosphere quantifies it; it can therefore be defined as the long wave energy trapped in the atmosphere. Climate forcing and the response of the climate system within which climate feedback mechanisms are contained, will be defined in this review. Quantitative examples will illustrate what could happen if the greenhouse effect is perturbed by the human activities, in particular if atmospheric CO2 concentrations would double in the future. Recent measurements by satellites of the greenhouse effect will be given. The net cooling effect of clouds on the Earth and whether or not there will be less cooling by clouds as the planet warms, are discussed following a series of papers recently published by Ramanathan and his collaborators.

Transfection and expression of a gene coding for a human melanoma antigen recognized by autologous cytolytic T lymphocytes.

Abstract: Human melanoma line MZ2-MEL expresses several antigens recognized by autologous cytolytic T lymphocytes (CTL). As a first step towards the cloning of the gene coding for one of these antigens, we tried to obtain transfectants expressing the antigen. The DNA recipient cell was a variant of MZ2-MEL which had been selected with a CTL clone for the loss of antigen E. It was cotransfected with genomic DNA of the original melanoma line and with selective plasmid pSVtkneo beta. Geneticin-resistant transfectants were obtained at a frequency of 2 x 10(-4). These transfectants were then screened for their ability to stimulate the production of tumor necrosis factor by the anti-E CTL clone. One transfectant expressing antigen E was identified among 70,000 drug-resistant transfectants. Its sensitivity to lysis by the anti-E CTL was equal to that of the original melanoma cell line. When this transfectant was submitted to immunoselection with the anti-E CTL clone, the resulting antigen-loss variants were found to have lost several of the transfected pSVtkneo beta sequences. This indicated that the gene coding for the antigen had been integrated in the vicinity of pSVtkneo beta sequences, as expected for cotransfected DNA.

First-principles study of the electronic properties of simple hexagonal graphite

Abstract: The electronic properties of simple hexagonal graphite have been studied in the framework of the density-functional technique, using nonlocal ionic pseudopotentials and a large number of plane waves. This work leads to a first-step qualitative understanding of the electronic properties of nonperiodic structures such as pregraphitic and disordered carbons (turbostratic graphite), which are composed of periodic regions of simple hexagonal graphite surrounded by domains of the usual (Bernal) form of graphite. Particular attention has been paid to the comparison with the properties of the Bernal graphite. The valence charge density, the density of states, the band structure, as well as a description of the electronic energies at the Fermi level are provided. The latter is parametrized by a tight-binding model, and compared to the Slonczewski-Weiss-McClure model of Bernal graphite electronic energies. The Fermi surface is calculated and an exchange of hole and electron pockets between these two forms of graphite is observed. The behavior of electronic energies under pressure, and the associated deformation potentials, are also studied.

Location on networks

Abstract: Facility location analysis deals with the problem of locating one or several facilities with regard to existing facilities and clients in order to optimize some economic criterion. In this survey, we consider specifically the problem of selecting one or several points of a network in order to optimize a function which is distance-dependent with respect to given points of the network. Minisum and minimax problems, where the objectives are to minimize respectively the sum or the maximum of different functions of distances, are reviewed. We also discuss models integrating more economic variables, such as prices, and putting more emphasis on the decision making context, particularly the competitive location models. Discrete models, for which the set of possible locations is finite and which have received the most attention of practionners, are presented as well.

Impairment of renal function with increasing blood lead concentrations in the general population. The Cadmibel Study Group.

Abstract: Background. Nephropathy is known to occur in persons with heavy exposure to lead. Whether exposure to lead in the general population leads to impaired renal function is not known. Methods. We studied renal function and indexes of lead exposure in a random population sample of 965 men and 1016 women (age range, 20 to 88 years). In all the subjects we measured creatinine clearance and blood concentrations of lead and zinc protoporphyrin (an indirect measure of blood lead level). Results. The mean (±SD) creatinine clearance rate was 99±30 ml per minute in the men and 80±25 ml per minute in the women. In the men the geometric mean blood lead concentration was 114 μg per liter (0.55 μmol per liter) (range, 23 to 725 μg per liter [0.11 to 3.5 μmol per liter]), and in the women 75 μg per liter (0.36 μmol per liter) (range, 17 to 603 μg per liter [0.08 to 2.9 μmol per liter]); the zinc protoporphyrin values in blood averaged 1.0 and 1.1 μg per gram of hemoglobin, respectively. The creatinine clearance ra...

A CMOS 13-b cyclic RSD A/D converter

Abstract: A 13-b CMOS cyclic A/D converter that does not need trimming nor digital calibration is presented. The effects associated with the error on the gain factor 2 as well as the offset errors are corrected by taking full advantage of the redundant signed digit (RSD) principle. The gain error resulting from mismatches among switched capacitors is corrected by a novel strategy that implements an exact multiplication by four after two cycles. As a result, offset errors do not affect the integral or the differential linearities from the RSD algorithm. The remaining overall shift caused by offsets is reduced under the LSB level by a proper choice of capacitor switching sequence. The converter achieves 1/2 LSB integral and differential linearity at 25 kS/s; harmonic distortion is less than -83 dB. Chip area is 2.9 mm2 in a standard CMOS 3-mu-m technology, including control logic and the serial-to-parallel output shift register. Power consumption is 45 mW under +/-5-V supplies.

Role of the transcriptional activator, VirF, and temperature in the expression of the pYV plasmid genes of Yersinia enterocolitica.

Abstract: Upon incubation at 37°C in the absence of Ca2+ ions, pathogenic yersiniae release high amounts of pYV plasmid-encoded proteins called Yops, involved in pathogenesis. Yersinia enterocolitica also express two outer membrane proteins, an adhesin called YadA and a lipoprotein called YIpA. The production of the Yops is co-ordinately regulated by a 20kb region of the plasmid referred to as the 'Ca2+ dependence region' and containing at least four loci called virA, virB, virC, and virF. The 8.5kb virC region, involved in the specific transport of the Yops, is a single operon containing 13 open reading frames called yscA to yscM. Gene virF encodes a key transcriptional activator of the yop, yadA and ylpA genes. It is only transcribed at 37°C and its expression is modulated by a chromosome-encoded histone-like protein called YmoA. We show here that virF also controls the virC operon. By contrast, VirF is not essential for the induction of virA and virB. The VirF protein binds specifically to yop promoters. In particular, it protects the region spanning nucleotides -64 to -34 of yopH. In order to analyse the role of temperature in the induction of the yop regulon, we constructed Y. enterocolitica strains expressing virF from the tac promoter. In spite of the fact that virF was transcribed at 25°C, neither the Yops nor YadA were expressed at that temperature. This poor response to VirF at 25°C was at least partially due to a weak and slow transcription of the genes controlled by virF. Surprisingly, when cloned on pACYC184, gene yadA was expressed even in absence of VirF, but remained thermodependent. Hence temperature and virF are both required for the induction of the yop regulon. Among other possible roles, temperature could modify the structure of either the activator itself or the yop promoter. The fact that VirF binds in vitro to yop promoters at 25°C rules out the first hypothesis. In order to test the second hypothesis, we studied, in vivo, the activity of the yopH promoter in ymoA mutants. The yopH promoter became active in the absence of VirF, indicating that yop promoter activity depends upon chromatin structure. We conclude from these two observations that, in vivo, temperature is required to modify the DNA structure of the yop promoters in order to allow the action of the transcriptional activator.

Kernel regression smoothing of time series

Abstract: . A class of non-parametric regression smoothers for times series is defined by the kernel method. The kernel approach allows flexible modelling of a time series without reference to a specific parametric class. The technique is applicable to detection of non-linear dependences in time series and to prediction in smooth regression models with serially correlated observations. In practice these estimators are to be tuned by a smoothing parameter. A data-driven selector for this smoothing parameter is presented that asymptotically minimizes a squared error measure. We prove asymptotic optimality of this selector. We illustrate the technique with a simulated example and by constructing a smooth prediction curve for the variation of gold prices. In both cases the non-parametric method proves to be useful in uncovering non-linear structure.

Phase Cooperation and Remote-control Effects in Selective Oxidation Catalysts

Abstract: This review paper concerns allylic oxidations and oxidative dehydrogenations. The corresponding catalysts often contain two or several oxide phases. The objective is to discuss the possible reasons why these phases cooperate (act synergetically). Different interpretations are reviewed. The authors discuss in detail the evidence showing that the synergy is often due to remote control. In such a mechanism, one phase, the donor, dissociates oxygen to form a surface mobile species which spills over to the other phase, or acceptor. The acceptor is the potentially active phase. This phase needs to be irrigated by spill-over oxygen to exhibit maximum activity and selectivity. The various modifications of the acceptor brought about by spill-over oxygen are discussed: maintaining the acceptor at a high oxidation state, preventing the destruction of the structure of the acceptor, and inhibiting the formation of carbonaceous deposits or coke precursors. Parallel experiments with the same two-phase catalysts catalysing an oxygen aided dehydration suggest that the role of spill-over oxygen is to protect some Bronsted acidity of the acceptor. This interpretation of the cooperation between phases permits definite roles to be attributed to the oxide phases present in multicomponent catalysts and to measure approximately their ability to act as donors or acceptors.

A single-stranded DNA binding protein required for mitochondrial DNA replication in S. cerevisiae is homologous to E. coli SSB.

Abstract: It has previously been shown that the mitochondrial DNA (mtDNA) of Saccharomyces cerevisiae becomes thermosensitive due to the inactivation of the mitochondrial DNA helicase gene, PIF1 A suppressor of this thermosensitive phenotype was isolated from a wild-type plasmid library by transforming a pif1 null strain to growth on glycerol at the non-permissive temperature This suppressor is a nuclear gene encoding a 135 amino acid protein that is itself essential for mtDNA replication; cells lacking this gene are totally devoid of mtDNA We therefore named this gene RIM1 for replication in mitochondria The primary structure of the RIM1 protein is homologous to the single-stranded DNA binding protein (SSB) from Escherichia coli and to the mitochondrial SSB from Xenopus laevis The mature RIM1 gene product has been purified from yeast extracts using a DNA unwinding assay dependent upon the DNA helicase activity of SV40 T-antigen Direct amino acid sequencing of the protein reveals that RIM1 is a previously uncharacterized SSB Antibodies against this purified protein localize RIM1 to mitochondria The SSB encoded by RIM1 is therefore an essential component of the yeast mtDNA replication apparatus

Signal-adapted multiresolution transform for image coding

Abstract: The authors consider the problem of designing multiresolution transforms that are adapted to the given image signal, in the sense that they maximize the coding gain at each resolution level. A simple alternating optimization algorithm is derived for solving this problem in the framework of the lattice realization of para-unitary quadrature mirror filters. The resulting large coding scheme is discussed in some detail, and its performance is compared with that of the discrete cosine transform (JPEG) technique and with that of some nonadapted multiresolution transforms. >

Factorial kriging analysis: a useful tool for exploring the structure of multivariate spatial soil information

Abstract: Most studies of relations between soil properties fail to take account of their regionalized nature because of the lack of appropriate methods. This paper describes a geostatistical technique, factorial kriging analysis, that bridges the gap between classical multivariate analysis and a univariate geostatistical approach. The basic feature of the method is the fitting of a linear model of coregionalization, i.e. all experimental simple and cross-variograms are modelled with a linear combination of basic variogram functions. A particular variance covariance matrix, the coregionalization matrix, can then be associated with each spatial scale defined by the range of the basic variogram function. Each coregionalization matrix describes relationships between variables at given spatial scale. A principal component analysis of these matrices produces a set of components, the regionalized factors, that reflect the main features of the multivariate information for each spatial scale and whose scores are estimated by cokriging. The technique is described and illustrated with three case studies based on a simulated data set and soil survey data. The results are compared with those of the principal component analysis of the variance-covariance matrix and the variogram matrices.

Dynamic feedback linearization of nonholonomic wheeled mobile robots

Abstract: Smooth time-varying laws can solve the stabilization problem of nonholonomic mechanical systems. The authors show that by means of dynamic state feedback, it is possible for three-wheeled mobile robots to track arbitrary fast trajectories not reduced to equilibrium points. Dynamical modeling of nonholonomic mechanical systems for the case of three-wheeled mobile robots is considered. Dynamic feedback allows solution of the tracking problem for an omnidirectional mobile robot with less motors than degrees of freedom. This is possible by choosing output functions depending on the mass repartition of the robot. >

Yeast mitochondrial DNA mutators with deficient proofreading exonucleolytic activity

Abstract: The MIP1 gene which encodes yeast mitochondrial DNA polymerase possesses in its N-terminal region the three motifs (Exo1, Exo2 and Exo3) which characterize the 3'-5' exonucleolytic domain of many DNA polymerases. By site directed mutagenesis we have substituted alanine or glycine residues for conserved aspartate residues in each consensus sequence. Yeast mutants were therefore generated that are capable of replicating mitochondrial DNA (mtDNA) and exhibit a mutator phenotype, as estimated by the several hundred-fold increase in the frequency of spontaneous mitochondrial erythromycin resistant mutants. By overexpressing the mtDNA polymerase from the GAL1 promoter as a major 140 kDa polypeptide, we showed that the wild-type enzyme possesses a mismatch-specific 3'-5' exonuclease activity. This activity was decreased by approximately 500-fold in the mutant D347A; in contrast, the extent of DNA synthesis was only slightly decreased. The wild-type mtDNA polymerase efficiently catalyses elongation of singly-primed M13 DNA to the full-length product. However, the mutant preferentially accumulates low molecular weight products. These data were extended to the two other mutators D171G and D230A. Glycine substitution for the Cys344 residue which is present in the Exo3 site of several polymerases generates a mutant with a slightly higher mtDNA mutation rate and a slightly lower 3'-5' exonucleolytic activity. We conclude that proofreading is an important determinant of accuracy in the replication of yeast mtDNA.

Interaction of the yeast pleiotropic drug resistance genes PDR1 and PDR5.

Abstract: The network of genes which mediates multiple drug resistance in yeast includes, among others, the PDR1 gene, which encodes a putative regulator of gene expression, and PDR5, a locus whose amplification leads to resistance. We demonstrate that disruption of PDR5 causes marked hypersensitivity not only to cycloheximide but also to sulphometuron methyl and the mitochondrial inhibitors chloramphenicol, lincomycin, erythromycin and antimycin. Genetic analysis of double mutants containing an insertion in PDR5 (pdr5:Tn5), which renders cells hypersensitive to cycloheximide, and a pdr1 mutation, which confers resistance to this inhibitor, indicates that the expression of resistance requires a functional PDR5 gene. The same interdependency is observed for chloramphenicol, but not for oligomycin, lincomycin, crythromycin or sulphometuron methyl. Northern analysis of PDR1 and PDR5 transcripts reveals that the 5.2 kbp PDR5 transcript is overexpressed in pdr1 (resistant) mutants, but underexpressed in a disruption of PDR1. These observations provide strong experimental support for our former proposal that the PDR5 gene is a target for regulation by the PDR1 gene product.

Precursor frequency analysis of human cytolytic T lymphocytes directed against autologous melanoma cells

Abstract: Limiting numbers of peripheral-blood mononuclear cells (PBMC) from melanoma patients were stimulated with irradiated autologous tumor cells in the presence of interleukins-2 and -4 and in the absence of feeder cells. The responder cells were restimulated every week. After 2 to 4 weeks, the microcultures were tested for their lytic activity against the autologous tumor cells. Significant lysis of the tumor cells was observed with a fraction of these microcultures, whereas no lysis was observed with control microcultures seeded without stimulator melanoma cells. Because our aim was to measure the precursor frequency of CTL showing specificity for the tumor, and not that of NK-like effectors that were also capable of lysing the melanoma cells, we used cold-target inhibition with an excess of NK target K562 to inhibit the NK-like activity. Microcultures whose lysis on the tumor cells was not abolished by K562 competition were observed. The specificity of these CTL clones was confirmed by the absence of lytic activity on autologous T-cell blasts. The numbers of microcultures with anti-tumor CTL activity fitted the zero-order of the Poisson distribution equation, indicating that they resulted from the activity of single T-cell clones. The frequency of anti-tumor CTL precursor cells (CTL-P) of 7 melanoma patients ranged from 1/900 to 1/33,000. Frequencies of anti-tumoral CTL-P were higher and NK-like effectors were less frequent when sorted CD8+ T lymphocytes were used as responder cells.

Global ischaemia induces a biphasic response of the mitochondrial respiratory chain. Anoxic pre-perfusion protects against ischaemic damage.

Abstract: Studies of Langendorff-perfused rat hearts have revealed a biphasic response of the mitochondrial respiratory chain to global ischaemia. The initial effect is a 30-40% increase in the rate of glutamate/malate oxidation after 10 min of ischaemia, owing to an increase in the capacity for NADH oxidation. This effect is followed by a progressive decrease in these oxidative activities as the ischaemia is prolonged, apparently owing to damage to Complex I at a site subsequent to the NADH dehydrogenase component. This damage is exacerbated by reperfusion, which causes a further decrease in Complex I activity and also decreases the activities of the other complexes, most notably of Complex III. Perfusion for up to 1 h with anoxic buffer produced only the increase in NADH oxidase activity, and neither anoxia alone, nor anoxia and reperfusion, caused loss of Complex I activity. Perfusing for 3-10 min with anoxic buffer before 1 h of global ischaemia had a significant protective effect against the ischaemia-induced damage to Complex I.

Short-chain and medium-chain aliphatic-ester synthesis in Saccharomyces cerevisiae.

Abstract: In the yeast Saccharomyces cerevisiae, the enzymes which catalyse the synthesis of ethyl acetate, ethyl n-hexanoate and isoamyl acetate were partly resolved from a fraction containing slowly sedimenting lipoproteins released during cell disruption with glass beads. Solubilization with detergents and fractionation by affinity chromatography have demonstrated the presence of at least three, and probably four, ester synthases which differ in their catalytic properties. Isoamyl-acetate synthase was solubilized and extensively purified to apparent homogeneity by successive chromatographies on various columns. On the basis of its specific activity in cell-free extracts, the enzyme was purified 19,000-fold with a 5% activity yield. As judged by SDS/PAGE, it consists of a single polypeptide chain with a molecular mass of 57 +/- 3 kDa and its apparent pI is 5.5. The enzyme acetylates isoamyl alcohol, ethanol and 12-DL-hydroxystearic acid from acetyl-CoA but is unable to use n-hexanoyl-CoA as a cosubstrate. This enzyme, defined as an acetyl-CoA: O-alcohol acetyltransferase, could be the product of one of the anaerobically induced genes in S. cerevisiae.