Showing papers by "Technical University of Denmark published in 1998"

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

Abstract: Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation.

A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences

Abstract: A novel method to model and predict the location and orientation of alpha helices in membrane- spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core, helix caps on either side, loop on the cytoplasmic side, two loops for the non-cytoplasmic side, and a globular domain state in the middle of each loop. The two loop paths on the non-cytoplasmic side are used to model short and long loops separately, which corresponds biologically to the two known different membrane insertions mechanisms. The close mapping between the biological and computational states allows us to infer which parts of the model architecture are important to capture the information that encodes the membrane topology, and to gain a better understanding of the mechanisms and constraints involved. Models were estimated both by maximum likelihood and a discriminative method, and a method for reassignment of the membrane helix boundaries were developed. In a cross validated test on single sequences, our transmembrane HMM, TMHMM, correctly predicts the entire topology for 77% of the sequences in a standard dataset of 83 proteins with known topology. The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods.

Effect of Strain on the Reactivity of Metal Surfaces

Abstract: Self-consistent density functional calculations for the adsorption of O and CO, and the dissociation of CO on strained and unstrained Ru(0001) surfaces are used to show how strained metal surfaces have chemical properties that are significantly different from those of unstrained surfaces. Surface reactivity increases with lattice expansion, following a concurrent up-shift of the metal $d$ states. Consequences for the catalytic activity of thin metal overlayers are discussed.

Numerical instabilities in topology optimization: A survey on procedures dealing with checkerboards, mesh-dependencies and local minima

Abstract: In this paper we seek to summarize the current knowledge about numerical instabilities such as checkerboards, mesh-dependence and local minima occurring in applications of the topology optimization method. The checkerboard problem refers to the formation of regions of alternating solid and void elements ordered in a checkerboard-like fashion. The mesh-dependence problem refers to obtaining qualitatively different solutions for different mesh-sizes or discretizations. Local minima refers to the problem of obtaining different solutions to the same discretized problem when choosing different algorithmic parameters. We review the current knowledge on why and when these problems appear, and we list the methods with which they can be avoided and discuss their advantages and disadvantages.

Softening of nanocrystalline metals at very small grain sizes

Abstract: Nanocrystalline solids, in which the grain size is in the nanometre range, often have technologically interesting properties such as increased hardness and ductility. Nanocrystalline metals can be produced in several ways, among the most common of which are high-pressure compaction of nanometre-sized clusters and high-energy ball-milling1,2,3,4. The result is a polycrystalline metal with the grains randomly orientated. The hardness and yield stress ofthe material typically increase with decreasing grain size, a phenomenon known as the Hall–Petch effect5,6. Here we present computer simulations of the deformation of nanocrystalline copper, which show a softening with grain size (a reverse Hall–Petch effect3,7) for the smallest sizes. Most of the plastic deformation is due to a large number of small ‘sliding’ events of atomic planes at the grain boundaries, with only a minor part being caused by dislocation activity in the grains; the softening that we see at small grain sizes is therefore due to the larger fraction of atoms at grain boundaries. This softening will ultimately impose a limit on how strong nanocrystalline metals may become.

New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria

Abstract: Use of the green fluorescent protein (Gfp) from the jellyfish Aequorea victoria is a powerful method for nondestructive in situ monitoring, since expression of green fluorescence does not require any substrate addition. To expand the use of Gfp as a reporter protein, new variants have been constructed by the addition of short peptide sequences to the C-terminal end of intact Gfp. This rendered the Gfp susceptible to the action of indigenous housekeeping proteases, resulting in protein variants with half-lives ranging from 40 min to a few hours when synthesized in Escherichia coli and Pseudomonas putida. The new Gfp variants should be useful for in situ studies of temporal gene expression.

Bioinformatics: The Machine Learning Approach

Abstract: In this book Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed both at biologists and biochemists who need to understand new data-driven algorithms and at those with a primary background in physics, mathematics, statistics, or computer science who need to know more about applications in molecular biology.

Topology optimization of continuum structures with local stress constraints

Abstract: We introduce an extension of current technologies for topology optimization of continuum structures which allows for treating local stress criteria. We first consider relevant stress criteria for porous composite materials, initially by studying the stress states of the so-called rank 2 layered materials. Then, on the basis of the theoretical study of the rank 2 microstructures, we propose an empirical model that extends the power penalized stiffness model (also called SIMP for Solid Isotropic Microstructure with Penalization for inter-mediate densities). In a second part, solution aspects of topology problems are considered. To deal with the so-called ‘singularity’ phenomenon of stress constraints in topology design, an ϵ-constraint relaxation of the stress constraints is used. We describe the mathematical programming approach that is used to solve the numerical optimization problems, and show results for a number of example applications. © 1998 John Wiley & Sons, Ltd.

Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model

Abstract: A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region, and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our data, the length distributions for the three regions are significantly different from expectations. For instance, the assigned hydrophobic region is between 8 and 12 residues long in almost all eukaryotic signal peptides. This analysis also makes obvious the difference between eukaryotes, Gram-positive bacteria, and Gram-negative bacteria. The model can be used to predict the location of the cleavage site, which it finds correctly in nearly 70% of signal peptides in a cross-validated test—almost the same accuracy as the best previous method. One of the problems for existing prediction methods is the poor discrimination between signal peptides and uncleaved signal anchors, but this is substantially improved by the hidden Markov model when expanding it with a very simple signal anchor model.

A full genome screen for autism with evidence for linkage to a region on chromosome 7q International Molecular Genetic Study of Autism Consortium

Abstract: Autism is characterized by impairments in reciprocal social interaction and communication, and restricted and stereotyped patterns of interests and activities. Developmental difficulties are apparent before 3 years of age and there is evidence for strong genetic influences most likely involving more than one susceptibility gene. A two-stage genome search for susceptibility loci in autism was performed on 87 affected sib pairs plus 12 non-sib affected relativepairs, from a total of 99 families identified by an international consortium. Regions on six chromosomes (4, 7, 10, 16, 19 and 22) were identified which generated a multipoint maximum lod score (MLS) > 1. A region on chromosome 7q was the most significant with an MLS of 3.55 near markers D7S530 and D7S684 in the subset of 56 UK affected sib-pair families, and an MLS of 2.53 in all 87 affected sib-pair families. An area on chromosome 16p near the telomere was the next most significant, with an MLS of 1.97 in the UK families, and 1.51 in all families. These results are an important step towards identifying genes predisposing to autism; establishing their general applicability requires further study.

Impact of temperature and humidity on the perception of indoor air quality

Abstract: Sensory responses to clean air and air polluted by five building materials under different combinations of temperature and humidity in the ranges 18-28°C and 30-70%RH were studied in the laboratory. A specially designed test system was built and a set of experiments was designed to observe separately the impact of temperature and humidity on the perception of air quality/odour intensity, and on the emission of pollutants from the materials. This paper reports on the impact on perception. The odour intensity of air did not change significantly with temperature and humidity; however, a strong and significant impact of temperature and humidity on the perception of air quality was found. The air was perceived as less acceptable with increasing temperature and humidity. This impact decreased with an increasing level of air pollution. Significant linear correlations were found between acceptability and enthalpy of the air at all pollution levels tested, and a linear model was established to describe the dependence of perceived air quality on temperature and humidity at different pollution levels.

NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility.

Abstract: The specificities of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases which link the carbohydrate GalNAc to the side-chain of certain serine and threonine residues in mucin type glycoproteins, are presently unknown. The specificity seems to be modulated by sequence context, secondary structure and surface accessibility. The sequence context of glycosylated threonines was found to differ from that of serine, and the sites were found to cluster. Non-clustered sites had a sequence context different from that of clustered sites. Charged residues were disfavoured at position – 1 and +3. A jury of artificial neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83% of the glycosylated and 90% of the non-glycosylated serine and threonine residues in independent test sets, thus proving more accurate than matrix statistics and vector projection methods. Predictions of O-glycosylation sites in the envelope glycoprotein gp120 from the primate lentiviruses HIV-1, HIV-2 and SIV are presented. The most conserved O-glycosylation signals in these evolutionary-related glycoproteins were found in their first hypervariable loop, V1. However, the strain variation for HIV-1 gp120 was significant. A computer server, available through WWW or E-mail, has been developed for prediction of mucin type O-glycosylation sites in proteins based on the amino acid sequence. The server addresses are http://www.cbs.dtu.dk/services/NetOGlyc/ and netOglyc@cbs.dtu.dk.

Transparent optical packet switching: the European ACTS KEOPS project approach

Abstract: This paper reviews the work carried out under the European ACTS KEOPS (KEys to Optical Packet Switching) project, centering on the definition, development and assessment of optical packet switching and routing networks capable of providing transparency to the payload bit rate. The adopted approach uses optical packets of fixed duration with low bit rate headers to facilitate processing at the network/node interfaces. The paper concentrates on the networking concepts developed in the KEOPS project through a description of the implementation issues pertinent to optical packet switching nodes and network/node interfacing blocks, and consideration of the network functionalities provided within the optical packet layer. The implementation, from necessity, relies on advanced optoelectronic components specifically developed within the project, which are also briefly described.

A new method for estimation of velocity vectors

Abstract: The paper describes a new method for determining the velocity vector of a remotely sensed object using either sound or electromagnetic radiation. The movement of the object is determined from a field with spatial oscillations in both the axial direction of the transducer and in one or two directions transverse to the axial direction. By using a number of pulse emissions, the inter-pulse movement can be estimated and the velocity found from the estimated movement and the time between pulses. The method is based on the principle of using transverse spatial modulation for making the received signal influenced by transverse motion. Such a transverse modulation can be generated by using apodization on individual transducer array elements together with a special focusing scheme. A method for making such a field is presented along with a suitable two-dimensional velocity estimator. An implementation usable in medical ultrasound is described, and simulated results are presented. Simulation results for a flow of 1 m/s in a tube rotated in the image plane at specific angles (0, 15, 35, 55, 75, and 90 degrees) are made and characterized by the estimated mean value, estimated angle, and the standard deviation in the lateral and longitudinal direction. The average performance of the estimates for all angles is: mean velocity 0.99 m/s, longitudinal S.D. 0.015 m/s, and lateral S.D. 0.196 m/s. For flow parallel to the transducer the results are: mean velocity 0.95 m/s, angle 0.10, longitudinal S.D. 0.020 m/s, and lateral S.D. 0.172 m/s.

Transparent optical packet switching: network architecture and demonstrators in the KEOPS project

Abstract: This paper reviews the work carried out in the ACTS KEOPS (Keys to Optical Packet Switching) project, describing the results obtained to date. The main objective of the project is the definition, development, and assessment of optical packet switching and routing networks, capable of providing transparency to the payload bit rate, using optical packets of fixed duration and low bit rate headers in order to enable easier processing at the network/node interfaces. The feasibility of the KEOPS concept is assessed by modeling, laboratory experiments, and testbed implementation of optical packet switching nodes and network/node interfacing blocks, including a fully equipped demonstrator. The demonstration relies on advanced optoelectronic components, developed within the project, which are described.

In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members

Abstract: Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.

The Sequence of Spacers between the Consensus Sequences Modulates the Strength of Prokaryotic Promoters

Abstract: We constructed a library of synthetic promoters for Lactococcus lactis in which the known consensus sequences were kept constant while the sequences of the separating spacers were randomized. The library consists of 38 promoters which differ in strength from 0.3 up to more than 2,000 relative units, the latter among the strongest promoters known for this organism. The ranking of the promoter activities was somewhat different when assayed in Escherichia coli, but the promoters are efficient for modulating gene expression in this bacterium as well. DNA sequencing revealed that the weaker promoters (which had activities below 5 relative units) all had changes either in the consensus sequences or in the length of the spacer between the -35 and -10 sequences. The promoters in which those features were conserved had activities from 5 to 2,050 U, which shows that by randomizing the spacers, at least a 400-fold change in activity can be obtained. Interestingly, the entire range of promoter activities is covered in small steps of activity increase, which makes these promoters very suitable for quantitative physiological studies and for fine-tuning of gene expression in industrial bioreactors and cell factories.

Establishment of new genetic traits in a microbial biofilm community.

Abstract: Conjugational transfer of the TOL plasmid (pWWO) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. The community consisted of three species, Pseudomonas putida RI, Acinetobacter sp. strain C6, and an unidentified isolate, D8. Only P. putida RI could act as a recipient for the TOL plasmid. Cells carrying a chromosomally integrated lacIq gene and a lacp-gfp-tagged version of the TOL plasmid were introduced as donor strains in the biofilm community after its formation. The occurrence of plasmid-carrying cells was analyzed by viable-count-based enumeration of donors and transconjugants. Upon transfer of the plasmids to the recipient cells, expression of green fluorescence was activated as a result of zygotic induction of the gfp gene. This allowed a direct in situ identification of cells receiving the gfp-tagged version of the TOL plasmid. Our data suggest that the frequency of horizontal plasmid transfer was low, and growth (vertical transfer) of the recipient strain was the major cause of plasmid establishment in the biofilm community. Employment of scanning confocal laser microscopy on fixed biofilms, combined with simultaneous identification of P. putida cells and transconjugants by 16S rRNA hybridization and expression of green fluorescence, showed that transconjugants were always associated with noninfected P. putida RI recipient microcolonies. Pure colonies of transconjugants were never observed, indicating that proliferation of transconjugant cells preferentially took place on preexisting P. putida RI microcolonies in the biofilm.

A Markovian approach for modeling packet traffic with long-range dependence

Abstract: We present a simple Markovian framework for modeling packet traffic with variability over several time scales. We present a fitting procedure for matching second-order properties of counts to that of a second-order self-similar process. Our models essentially consist of superpositions of two-state Markov modulated Poisson processes (MMPPs). We illustrate that a superposition of four two-state MMPPs suffices to model second-order self-similar behavior over several time scales. Our modeling approach allows us to fit to additional descriptors while maintaining the second-order behavior of the counting process. We use this to match interarrival time correlations.