Showing papers by "Technical University of Denmark published in 1999"

Improved adsorption energetics within density-functional theory using revised Perdew-Burke-Ernzerhof functionals

Abstract: A simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE) [Phys. Rev. Lett. 77, 3865 (1996)]. Subsequently Zhang and Yang [Phys. Rev. Lett. 80, 890 (1998)] have shown that a slight revision of the PBE functional systematically improves the atomization energies for a large database of small molecules. In the present work, we show that the Zhang and Yang functional (revPBE) also improves the chemisorption energetics of atoms and molecules on transition-metal surfaces. Our test systems comprise atomic and molecular adsorption of oxygen, CO, and NO on Ni(100), Ni(111), Rh(100), Pd(100), and Pd(111) surfaces. As the revPBE functional may locally violate the Lieb-Oxford criterion, we further develop an alternative revision of the PBE functional, RPBE, which gives the same improvement of the chemisorption energies as the revPBE functional at the same time as it fulfills the Lieb-Oxford criterion locally.

Material interpolation schemes in topology optimization

Abstract: In topology optimization of structures, materials and mechanisms, parametrization of geometry is often performed by a grey-scale density-like interpolation function. In this paper we analyze and compare the various approaches to this concept in the light of variational bounds on effective properties of composite materials. This allows us to derive simple necessary conditions for the possible realization of grey-scale via composites, leading to a physical interpretation of all feasible designs as well as the optimal design. Thus it is shown that the so-called artificial interpolation model in many circumstances actually falls within the framework of microstructurally based models. Single material and multi-material structural design in elasticity as well as in multi-physics problems is discussed.

ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.

Abstract: We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http://www.cbs.dtu.dk/services/ChloroP/.

The Infinite Gaussian Mixture Model

Abstract: In a Bayesian mixture model it is not necessary a priori to limit the number of components to be finite. In this paper an infinite Gaussian mixture model is presented which neatly sidesteps the difficult problem of finding the "right" number of mixture components. Inference in the model is done using an efficient parameter-free Markov Chain that relies entirely on Gibbs sampling.

Surface segregation energies in transition-metal alloys

Abstract: We present a database of $24\ifmmode\times\else\texttimes\fi{}24$ surface segregation energies of single transition metal impurities in transition-metal hosts obtained by a Green's-function linear-muffin-tin-orbitals method in conjunction with the coherent potential and atomic sphere approximations including a multipole correction to the electrostatic potential and energy. We use the database to establish the major factors which govern surface segregation in transition metal alloys. We find that the calculated trends are well described by Friedel's rectangular state density model and that the few but significant deviations from the simple trends are caused by crystal structure effects.

Role of Steps in N 2 Activation on Ru(0001)

Abstract: Using adsorption experiments and density functional calculations we show that ${\mathrm{N}}_{2}$ dissociation on the Ru(0001) surface is totally dominated by steps. The measured adsorption rate at the steps is at least 9 orders of magnitude higher than on the terraces at 500 K, and the corresponding calculated difference in activation energy is 1.5 eV. The low barrier at the step is shown to be due to a combination of electronic and geometrical effects. The consequences for Ru as a catalyst for ammonia synthesis are discussed.

Potential of biobased materials for food packaging

Abstract: During the last decade, joint efforts by the packaging and the food industries have reduced the amount of food packaging materials. Nonetheless, used packaging materials are still very visible to the consumer in the context of disposal. Environmental issues are becoming increasingly important to the European consumer. Consequently, consumer pressure may trigger the use of biobased packaging materials as an alternative to materials produced from non-renewable resources. Biologically based packaging is defined as packaging containing raw materials originating from agricultural sources, i. e. produced from renewable, biological raw materials such as starch and bioderived monomers. These materials are not necessarily biodegradable. Consequently, this review is not limited to biodegradable packaging. To date, biodegradable packaging has commanded great attention, and numerous projects are under way in this field. One important reason for this attention is the marketing of environmentally friendly packaging materials. Furthermore, use of biodegradable packaging materials has the greatest potential in countries where landfill is the main waste management tool. Biobased packaging materials include both edible films and edible coatings along with primary and secondary packaging materials. Excellent in-depth reviews on edible films and coatings are already available 1 , 2 , 3 . Therefore, this review focuses on biobased primary packaging materials for foods. Several concerns must be addressed prior to commercial use of biobased primary food packaging materials. These concerns include degradation rates under various conditions, changes in mechanical properties during storage, potential for microbial growth, and release of harmful compounds into the packaged food product. Furthermore, the biopackaging must function as food packaging and meet the requirements of the individual food product. This review evaluates the suitability of biobased packaging for foods. Additionally, it identifies the challenges involved when using biobased packaging for different foods.

Machine learning approaches for the prediction of signal peptides and other protein sorting signals.

Abstract: Prediction of protein sorting signals from the sequence of amino acids has great importance in the field of proteomics today. Recently, the growth of protein databases, combined with machine learning approaches, such as neural networks and hidden Markov models, have made it possible to achieve a level of reliability where practical use in, for example automatic database annotation is feasible. In this review, we concentrate on the present status and future perspectives of SignalP, our neural network-based method for prediction of the most well-known sorting signal: the secretory signal peptide. We discuss the problems associated with the use of SignalP on genomic sequences, showing that signal peptide prediction will improve further if integrated with predictions of start codons and transmembrane helices. As a step towards this goal, a hidden Markov model version of SignalP has been developed, making it possible to discriminate between cleaved signal peptides and uncleaved signal anchors. Furthermore, we show how SignalP can be used to characterize putative signal peptides from an archaeon, Methanococcus jannaschii. Finally, we briefly review a few methods for predicting other protein sorting signals and discuss the future of protein sorting prediction in general.

Evidence that halogenated furanones from Delisea pulchra inhibit acylated homoserine lactone (AHL)-mediated gene expression by displacing the AHL signal from its receptor protein.

Abstract: Summary: Acylated homoserine lactone (AHL)-mediated gene expression controls phenotypes involved in colonization, often specifically of higher organisms, in both marine and terrestrial environments. The marine red alga Delisea pulchra produces halogenated furanones which resemble AHLs structurally and show inhibitory activity at ecologically realistic concentrations in AHL bioassays. Evidence is presented that halogenated furanones displace tritiated OHHL [N-3- (oxohexanoy1)-L-homoserine lactone] from Escherichia coli cells overproducing LuxR with potencies corresponding to their respective inhibitory activities in an AHL-regulated bioluminescence assay, indicating that this is the mechanism by which furanones inhibit AHL-dependent phenotypes. Alternative mechanisms for this phenomenon are also addressed. General metabolic disruption was assessed with two-dimensional PAGE, revealing limited non- AHL-related effects. A direct chemical interaction between the algal compounds and AHLs, as monitored by 1H NMR spectroscopy, was shown not to occur in vitro. These results support the contention that furanones, at the concentrations produced by the alga, can control bacterial colonization of surfaces by specifically interfering with AHL-mediated gene expression at the level of the LuxR protein.

Atomic-scale simulations of the mechanical deformation of nanocrystalline metals

Abstract: Nanocrystalline metals, ie, metals in which the grain size is in the nanometer range, have a range of technologically interesting properties including increased hardness and yield strength We present atomic-scale simulations of the plastic behavior of nanocrystalline copper The simulations show that the main deformation mode is sliding in the grain boundaries through a large number of uncorrelated events, where a few atoms (or a few tens of atoms) slide with respect to each other Little dislocation activity is seen in the grain interiors The localization of the deformation to the grain boundaries leads to a hardening as the grain size is increased (reverse Hall-Petch effect), implying a maximum in hardness for a grain size above the ones studied here We investigate the effects of varying temperature, strain rate, and porosity, and discuss the relation to recent experiments At increasing temperatures the material becomes softer in both the plastic and elastic regime Porosity in the samples result in a softening of the material; this may be a significant effect in many experiments

An outbreak of multidrug-resistant, quinolone-resistant Salmonella enterica serotype typhimurium DT104

Abstract: Background Food-borne salmonella infections have become a major problem in industrialized countries. The strain of Salmonella enterica serotype typhimurium known as definitive phage type 104 (DT104) is usually resistant to five drugs: ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline. An increasing proportion of DT104 isolates also have reduced susceptibility to fluoroquinolones. Methods The Danish salmonella surveillance program determines the phage types of all typhimurium strains from the food chain, and in the case of suspected outbreaks, five-drug–resistant strains are characterized by molecular methods. All patients infected with five-drug–resistant typhimurium are interviewed to obtain clinical and epidemiologic data. In 1998, an outbreak of salmonella occurred, in which the strain of typhimurium DT104 was new to Denmark. We investigated this outbreak and report our findings here. Results Until 1997, DT104 infections made up less than 1 percent of all human salmonella infect...

Mucoid conversion of Pseudomonas aeruginosa by hydrogen peroxide: a mechanism for virulence activation in the cystic fibrosis lung.

Abstract: The leading cause of mortality in patients with cystic fibrosis (CF) is respiratoy failure due in large part to chronic lung infection with Pseudomonas aeruginosa strains that undergo mucoid conversion, display a biofilm mode of growth in vivo and resist the infiltration of polymorphonuclear leukocytes (PMNs), which release free oxygen radicals such as H2O2. The mucoid phenotype among the strains infecting CF patients indicates overproduction of a linear polysaccharide called alginate. To mimic the inflammatory environment of the CF lung, P. aeruginosa PAO1, a typical non-mucoid strain, was grown in a biofilm. This was treated with low levels of H2O2, as if released by the PMNs, and the formation of mucoid variants was observed. These mucoid variants had mutations in mucA, which encodes an anti-σ factor; this leads to the deregulation of an alternative σ factor (σ22, AlgT or AlgU) required for expression of the alginate biosynthetic operon. All of the mucoid variants tested showed the same mutation, the mucA22 allele, a common allele seen in CF isolates. The mucoid mucA22 variants, when compared to the smooth parent strain PA01, produced 2--6-fold higher levels of alginate|ii) exhibited no detectable differences in growth rate|iii) showed an unaltered LPS profile|iv) were ~72% reduced in the amount of inducible-β-lactamase and (v) secreted little no LasA protease and only showed 44% elastase activity. A characteristic ~54 kDa protein associated with alginate overproducing strains was identified as AlgE (Alg76) by N-terminal sequence analysis. Thus, the common phenotype of the mucoid variants, which included a genetically engineered mucA22 mutant, suggested that the only mutation incurred as a result of H2O2 treatment was in mucA. When a P. aeruginosa biofilm was repeatedly expose to activated PMNs in vitro, mucoid variants were also observed, mimicking in vivo observations. Thus, PMNs and their oxygen by-products may cause P. aeruginosa to undergo the typical adaptation to the intractable mu- coid form in the CF lung. These findings indicate that gene activation in bacteria by toxic oxygen radicals, similar to that found in plants and mammalian cells, may serve as a defence mechanism for the bacteria. This suggests that mucoid conversion is a response to oxygen radical exposure and that this response is mechanism of defence by the bacteria. This is the first report to show that PMNs and their oxygen radicals can cause this phenotypic and genotypic change which is so typical of the intractable form of P. aeruginosa in the CF lung. These findings may provide a basis for the development of anti-oxidant and anti-inflammatory therapy for the early stages of infection in CF patients

Perceived air quality, sick building syndrome (SBS) symptoms and productivity in an office with two different pollution loads.

Abstract: Perceived air quality, Sick Building Syndrome (SBS) symptoms and productivity were studied in an existing office in which the air pollution level could be modified by introducing or removing a pollution source. This reversible intervention allowed the space to be classified as either non-low-polluting or low-polluting, as specified in the new European design criteria for the indoor environment CEN CR 1752 (1998). The pollution source was a 20-year-old used carpet which was introduced on a rack behind a screen so that it was invisible to the occupants. Five groups of six female subjects each were exposed to the conditions in the office twice, once with the pollution source present and once with the pollution source absent, each exposure being 265 min in the afternoon, one group at a time. They assessed the perceived air quality and SBS symptoms while performing simulated office work. The subject-rated acceptability of the perceived air quality in the office corresponded to 22% dissatisfied when the pollution source was present, and to 15% dissatisfied when the pollution source was absent. In the former condition there was a significantly increased prevalence of headaches (P = 0.04) and significantly lower levels of reported effort (p = 0.02) during the text typing and calculation tasks, both of which required a sustained level of concentration. In the text typing task, subjects worked significantly more slowly when the pollution source was present in the office (P = 0.003), typing 6.5% less text than when the pollution source was absent from the office Reducing the pollution load on indoor air proved to be an effective means of improving the comfort, health and productivity of building occupants.

Inhibition of vibrio anguillarum by Pseudomonas fluorescens AH2, a possible probiotic treatment of fish.

Abstract: To study the possible use of probiotics in fish farming, we evaluated the in vitro and in vivo antagonism of antibacterial strain Pseudomonas fluorescens strain AH2 against the fish-pathogenic bacterium Vibrio anguillarum. As iron is important in virulence and bacterial interactions, the effect of P. fluorescens AH2 was studied under iron-rich and iron-limited conditions. Sterile-filtered culture supernatants from iron-limited P. fluorescens AH2 inhibited the growth of V. anguillarum, whereas sterile-filtered supernatants from iron-replete cultures of P. fluorescens AH2 did not. P. fluorescens AH2 inhibited the growth of V. anguillarum during coculture, independently of the iron concentration, when the initial count of the antagonist was 100 to 1, 000 times greater that of the fish pathogen. These in vitro results were successfully repeated in vivo. A probiotic effect in vivo was tested by exposing rainbow trout (Oncorynchus mykiss Walbaum) to P. fluorescens AH2 at a density of 10(5) CFU/ml for 5 days before a challenge with V. anguillarum at 10(4) to 10(5) CFU/ml for 1 h. Some fish were also exposed to P. fluorescens AH2 at 10(7) CFU/ml during the 1-h infection. The combined probiotic treatment resulted in a 46% reduction of calculated accumulated mortality; accumulated mortality was 25% after 7 days at 12 degrees C in the probiotic-treated fish, whereas mortality was 47% in fish not treated with the probiont.

A comprehensive model of anaerobic bioconversion of complex substrates to biogas

Abstract: A dynamic model describing the anaerobic degradation of complex material, and codigestion of different types of wastes, was developed based on a model previously described (Angelidaki et al., 1993). In the model, the substrate is described by its composition of basic organic components, i.e., carbohydrates, lipids, and proteins, the concentration of intermediates such as volatile fatty acids and long-chain fatty acids, and important inorganic components, i.e., ammonia, phosphate, cations, and anions. This allows dynamic changes of the process during a shift of substrate composition to be simulated by changing the input substrate data. The model includes 2 enzymatic hydrolytic steps, 8 bacterial steps and involves 19 chemical compounds. The model also includes a detailed description of pH and temperature characteristics. Free ammonia, acetate, volatile fatty acids, (VFA) and long-chain fatty acids (LCFA) constitute the primary modulating factors in the model. The model was tested with success in lab-scale reactors codigesting manure with glycerol trioleate or manure with gelatin. Finally, the model was validated using results from a full-scale biogas plant codigesting manure together with a proteinous wastewater and with bentonite-bound oil, which is a waste with high content of lipids. Copyright 1999 John Wiley & Sons, Inc.

Promoter2.0: for the recognition of PolII promoter sequences.

Abstract: Motivation A new approach to the prediction of eukaryotic PolII promoters from DNA sequence takes advantage of a combination of elements similar to neural networks and genetic algorithms to recognize a set of discrete subpatterns with variable separation as one pattern: a promoter. The neural networks use as input a small window of DNA sequence, as well as the output of other neural networks. Through the use of genetic algorithms, the weights in the neural networks are optimized to discriminate maximally between promoters and non-promoters. Results After several thousand generations of optimization, the algorithm was able to discriminate between vertebrate promoter and non-promoter sequences in a test set with a correlation coefficient of 0.63. In addition, all five known transcription start sites on the plus strand of the complete adenovirus genome were within 161 bp of 35 predicted transcription start sites. On standardized test sets consisting of human genomic DNA, the performance of Promoter2.0 compares well with other software developed for the same purpose. Availability Promoter2.0 is available as a Web server at http://www.cbs.dtu. dk/services/promoter/

Developing stable fine–grain microstructures by large strain deformation

Abstract: Methods of deforming metals to large strains are reviewed and the process of equal channel angular extrusion is analysed in detail. The development of microstructure during large strain deformation is discussed, and it is concluded that the main criterion for the formation of a sub–micron grain structure is the generation of a sufficiently large fraction (> 0.7) of high–angle grain boundary during the deformation process. For aluminium alloys, it is found that a low–temperature anneal is required to convert the deformed microstructure into an equi–axed grain structure. The material, microstructural and processing factors that influence the formation of such fine–grain microstructures are discussed, and the stability of these microstructures at elevated temperatures is considered.

Distribution of Bacterial Growth Activity in Flow-Chamber Biofilms

Abstract: In microbial communities such as those found in biofilms, individual organisms most often display heterogeneous behavior with respect to their metabolic activity, growth status, gene expression pattern, etc. In that context, a novel reporter system for monitoring of cellular growth activity has been designed. It comprises a transposon cassette carrying fusions between the growth rate-regulated Escherichia coli rrnBP1 promoter and different variant gfp genes. It is shown that the P1 promoter is regulated in the same way in E. coli and Pseudomonas putida, making it useful for monitoring of growth activity in organisms outside the group of enteric bacteria. Construction of fusions to genes encoding unstable Gfp proteins opened up the possibility of the monitoring of rates of rRNA synthesis and, in this way, allowing on-line determination of the distribution of growth activity in a complex community. With the use of these reporter tools, it is demonstrated that individual cells of a toluene-degrading P. putida strain growing in a benzyl alcohol-supplemented biofilm have different levels of growth activity which develop as the biofilm gets older. Cells that eventually grow very slowly or not at all may be stimulated to restart growth if provided with a more easily metabolizable carbon source. Thus, the dynamics of biofilm growth activity has been tracked to the level of individual cells, cell clusters, and microcolonies.

Electron Transfer in Chemistry and Biology: An Introduction to the Theory

Abstract: Some Theoretical Prerequisites. The Tunnel Effect in Physical, Chemical and Biological Processes. Elements of Dielectric Theory. Charge Transfer in Solids. The Simplest Chemical Process: Electron Transfer. Some Selected Experimental Data for Simple Electron Transfer Reactions. Towards More Precise Electron Transfer Theory. Optical Charge Transfer in Allowed and Forbidden Transitions. Elements of Proton and Other Light-Atom Transfer Theory. The Electrochemical Process. Elements of Long-Range and Multi-Level Electron Transfer. Stochastic Views in Chemical Rate Theory. Elements of Charge Transfer in Biological Systems. Perspectives and Outlook. Appendices. Index.

Competition between Sec- and TAT-dependent protein translocation in Escherichia coli.

Abstract: Recently, a new protein translocation pathway, the twin-arginine translocation (TAT) pathway, has been identified in both bacteria and chloroplasts. To study the possible competition between the TAT- and the well-characterized Sec translocon-dependent pathways in Escherichia coli, we have fused the TorA TAT-targeting signal peptide to the Sec-dependent inner membrane protein leader peptidase (Lep). We find that the soluble, periplasmic P2 domain from Lep is re-routed by the TorA signal peptide into the TAT pathway. In contrast, the full-length TorA-Lep fusion protein is not re-routed into the TAT pathway, suggesting that Sec-targeting signals in Lep can override TAT-targeting information in the TorA signal peptide. We also show that the TorA signal peptide can be converted into a Sec-targeting signal peptide by increasing the hydrophobicity of its h-region. Thus, beyond the twin-arginine motif, the overall hydrophobicity of the signal peptide plays an important role in TAT versus Sec targeting. This is consistent with statistical data showing that TAT-targeting signal peptides in general have less hydrophobic h-regions than Sec-targeting signal peptides.

PhosphoBase, a database of phosphorylation sites: release 2.0

Abstract: PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled into a common format. The current release of PhosphoBase (October 1998, version 2.0) comprises 414 phosphoprotein entries covering 1052 phosphorylatable serine, threonine and tyrosine residues. The kinetic data from peptide phosphorylation assays for approximately 330 oligopeptides is also included. The database entries are cross-referenced to the corresponding records in the Swiss-Prot protein database and literature references are linked to MedLine records. PhosphoBase is available via the WWW at http://www.cbs.dtu. dk/databases/PhosphoBase/

Molecular tools for study of biofilm physiology.

Abstract: Publisher Summary This chapter describes methods for the handling and analysis of microbial behavior of organisms in biofilm communities at both microscopic and macroscopic levels. Only methods and reporter systems that can be applied without disturbing the spatial organization of the organisms in the biofilm are presented. The in situ methods described in this chapter can be used for more than just identifying or tracing cells or genes in biofilms. By combining promoters that respond to specific environmental signals with appropriate marker genes, it may be possible to tag specific organisms and use these as monitor systems to estimate local chemical composition directly in the biofilms. Changes in environmental conditions will also have significant effects on the physiological state of the organisms. Such shifting conditions may result in several responses, such as altered growth rates, stress response, starvation, or even cell death. Most of these responses can be visualized directly using specific promoter–reporter fusions. The ribosome number is a reliable indicator of growth rate in bacteria growing in balanced growth and has been used as a standard for growth rates in biofilm-embedded bacteria as well.