Showing papers by "Bielefeld University published in 1999"

Coding theorem and strong converse for quantum channels

Abstract: We present a new proof of Holevo's (1973, 1977) coding theorem for transmitting classical information through quantum channels, and its strong converse. The technique is largely inspired by Wolfwitz's (1964) combinatorial approach using types of sequences. As a byproduct of our approach which is independent of previous ones, both in the coding theorem and the converse, we can give a new proof of Holevo's information bound.

Scientific expertise and political accountability: paradoxes of science in politics

Abstract: Two paradoxes form the nucleus of the problems of scientific expertise and policy-making. The first is the simultaneous scientification of politics and the politicisation of science. This has destructive effects: the increased use of scientific expertise by policy-makers has not increased the degree of certainty, in fact it becomes delegitimating. This gives rise to the second paradox: despite the loss of authority of scientific expertise, policy-makers do not abandon their reliance on existing advisory arrangements, nor do the scholars adapt their ideas on science and its relation to politics. How can this stability be achieved? How can science-politics be institutionalised? Copyright , Beech Tree Publishing.

REPuter: fast computation of maximal repeats in complete genomes.

Abstract: Summary A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently. Availability Via the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rep uter/).

Molecular growth from a Mo 176 to a Mo 248 cluster

Abstract: In polyoxometalate chemistry a large variety of compounds, clusters and solid-state structures can be formed by the linking together of well-defined metal–oxygen building blocks1, 2. These species exhibit unusual topological and electronic properties, andfind applications ranging from medicine3 to industrial processes4. The recently reported ring-shaped mixed-valence polyoxomolybdates of the type {Mo154} (refs 5, 6) and {Mo176} (refs 7, 8) represent a new class of giant clusters with nanometre-sized cavities and interesting properties for host–guest chemistry. Here we describe the formation of related clusters of the type {Mo248} formed by addition of further units to the inner surface of the {Mo176} ‘wheel’. The additional units arrange themselves into two {Mo36} ‘hub-caps’ on the initial wheel—clusters that are not stable in isolation. These findings reveal a new pathway to the development of complex coordination clusters.

Reducing the space requirement of suffix trees

Abstract: SUMMARY We show that suffix trees store various kinds of redundant information. We exploit these redundancies to obtain more space efficient representations. The most space efficient of our representations requires 20 bytes per input character in the worst case, and 10.1 bytes per input character on average for a collection of 42 files of different type. This is an advantage of more than 8 bytes per input character over previous work. Our representations can be constructed without extra space, and as fast as previous representations. The asymptotic running times of suffix tree applications are retained. Copyright © 1999 John Wiley & Sons, Ltd.

Structural properties of matrix metalloproteinases

Abstract: Matrix metalloproteinases (MMPs) are involved in extracellular matrix degradation. Their proteolytic activity must be precisely regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance results in serious diseases such as arthritis, tumour growth and metastasis. Knowledge of the tertiary structures of the proteins involved is crucial for understanding their functional properties and interference with associated dysfunctions. Within the last few years, several three-dimensional MMP and MMP-TIMP structures became available, showing the domain organization, polypeptide fold and main specificity determinants. Complexes of the catalytic MMP domains with various synthetic inhibitors enabled the structure-based design and improvement of high-affinity ligands, which might be elaborated into drugs. A multitude of reviews surveying work done on all aspects of MMPs have appeared in recent years, but none of them has focused on the three-dimensional structures. This review was written to close the gap.

Positional Dependence, Cliques, and Predictive Motifs in the bHLH Protein Domain

Abstract: Quantitative analyses were carried out on a large number of proteins that contain the highly conserved basic helix–loop–helix domain. Measures derived from information theory were used to examine the extent of conservation at amino acid sites within the bHLH domain as well as the extent of mutual information among sites within the domain. Using the Boltzmann entropy measure, we described the extent of amino acid conservation throughout the bHLH domain. We used position association (pa) statistics that reflect the joint probability of occurrence of events to estimate the ``mutual information content'' among distinct amino acid sites. Further, we used pa statistics to estimate the extent of association in amino acid composition at each site in the domain and between amino acid composition and variables reflecting clade and group membership, loop length, and the presence of a leucine zipper. The pa values were also used to describe groups of amino acid sites called ``cliques'' that were highly associated with each other. Finally, a predictive motif was constructed that accurately identifies bHLH domain-containing proteins that belong to Groups A and B.

Protective Function of Chloroplast 2-Cysteine Peroxiredoxin in Photosynthesis. Evidence from Transgenic Arabidopsis

Abstract: 2-Cysteine peroxiredoxins (2-CPs) constitute a ubiquitous group of peroxidases that reduce cell-toxic alkyl hydroperoxides to their corresponding alcohols. Recently, we cloned 2-CP cDNAs from plants and characterized them as chloroplast proteins. To elucidate the physiological function of the 2-CP in plant metabolism, we generated antisense mutants in Arabidopsis. In the mutant lines a 2-CP deficiency developed during early leaf and plant development and eventually the protein accumulated to wild-type levels. In young mutants with reduced amounts of 2-CP, photosynthesis was impaired and the levels of D1 protein, the light-harvesting protein complex associated with photosystem II, chloroplast ATP synthase, and ribulose-1,5-bisphosphate carboxylase/oxygenase were decreased. Photoinhibition was particularly pronounced after the application of the protein synthesis inhibitor, lincomycin. We concluded that the photosynthetic machinery needs high levels of 2-CP during leaf development to protect it from oxidative damage and that the damage is reduced by the accumulation of 2-CP protein, by the de novo synthesis and replacement of damaged proteins, and by the induction of other antioxidant defenses in 2-CP mutants.

Insights into MMP-TIMP interactions.

Abstract: The proteolytic activity of the matrix metalloproteinases (MMPs) involved in extracellular matrix degradation must be precisely regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance can result in serious diseases such as arthritis and tumor growth and metastasis. Knowledge of the tertiary structures of the proteins involved in such processes is crucial for understanding their functional properties and to interfere with associated dysfunctions. Within the last few years, several three-dimensional structures have been determined showing the domain organization, the polypeptide fold, and the main specificity determinants of the MMPs. Complexes of the catalytic MMP domains with various synthetic inhibitors enabled the structure-based design and improvement of high-affinity ligands, which might be elaborated into drugs. Very recently, structural information also became available for some TIMP structures and MMP-TIMP complexes, and these new data elucidated important structural features that govern the enzyme-inhibitor interaction.

Two different strategies of Mediterranean macchia plants to avoid photoinhibitory damage by excessive radiation levels during summer drought

Abstract: The adaptive strategies to high radiation and water stress of the drought tolerant evergreen sclerophylls Quercus coccifera and Arbutus unedo are compared to those of the semi-deciduous Cistus spp. (C. albidus and C. monspeliensis). Cistus spp. partially avoided drought by a marked reduction of their transpirational surface through leaf abscission during summer, when predawn water potential declined below -5.5 MPa. Chlorophyll fluorescence measurements revealed a reversible diurnal decrease of maximum photochemical efficiency of PSII (F-v/F-m), which became more accentuated during summer drought in all species. An important strategy to avoid damage by excessive radiation levels in Cistus spp. was the structural regulation of light interception through leaf angle changes, from a more horizontal orientation in spring ( 70 degrees). Horizontal orientated leaves were highly susceptible to photoinhibition, and excessive radiation often resulted in irreversible photodamage followed by leaf abscission during summer, whereas vertical leaf orientation appeared to protect the leaf from severe photoinhibition. Still, these mechanisms were not fully successful in avoiding chronic photoinhibition, and predawn F-v/F-m values remained low in Cistus spp. during summer (only exhibiting a partial overnight recovery). Evergreen sclerophylls were less susceptible to photoinhibition, and the diurnal decline in F-v/F-m remained fully reversible during drought. Structural regulation of light interception was not found to be an important strategy in these species, and only small, though significant changes in leaf angle occurred. The ecological importance of the adaptive strategies of each functional group is discussed. (C) Elsevier, Paris.

Listen to your Data: Model-Based Sonification for Data Analysis

Abstract: Sonification is the use of non-speech audio to convey information. We are developing tools for interactive data exploration, which make use of sonification for data presentation. In this paper, model-based sonification is presented as a concept to design auditory displays. Two designs are described: (1) particle trajectories in a "data potential" is a sonification model to reveal information about the clustering of vectorial data and (2) "data-sonograms" is a sonification for data from a classification problem to reveal information about the mixing of distinct classes.

Expression of the Corynebacterium glutamicum panD Gene Encoding l-Aspartate-α-Decarboxylase Leads to Pantothenate Overproduction in Escherichia coli

Abstract: The Corynebacterium glutamicum panD gene was identified by functional complementation of an Escherichia coli panD mutant strain. Sequence analysis revealed that the coding region of panD comprises 411 bp and specifies a protein of 136 amino acid residues with a deduced molecular mass of 14.1 kDa. A defined C. glutamicum panD mutant completely lacked L-aspartate-alpha-decarboxylase activity and exhibited beta-alanine auxotrophy. The C. glutamicum panD (panDC. g.) as well as the E. coli panD (panDE.c.) genes were cloned into a bifunctional expression plasmid to allow gene analysis in C. glutamicum as well as in E. coli. The enhanced expression of panDC.g. in C. glutamicum resulted in the formation of two distinct proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, leading to the assumption that the panDC.g. gene product is proteolytically processed into two subunits. By increased expression of panDC.g. in C. glutamicum, the activity of L-aspartate-alpha-decarboxylase was 288-fold increased, whereas the panDE.c. gene resulted only in a 4-fold enhancement. The similar experiment performed in E. coli revealed that panDC.g. achieved a 41-fold increase and that panDE.c. achieved a 3-fold increase of enzyme activity. The effect of the panDC.g. and panDE.c. gene expression in E. coli was studied with a view to pantothenate accumulation. Only by expression of the panDC.g. gene was sufficient beta-alanine produced to abolish its limiting effect on pantothenate production. In cultures expressing the panDE.c. gene, the maximal pantothenate production was still dependent on external beta-alanine supplementation. The enhanced expression of panDC.g. in E. coli yielded the highest amount of pantothenate in the culture medium, with a specific productivity of 140 ng of pantothenate mg (dry weight)-1 h-1.

Molecular dissection of the role of histidine in nickel hyperaccumulation in Thlaspi goesingense (Halacsy)

Abstract: To understand the role of free histidine (His) in Ni hyperaccumulation in Thlaspi goesingense, we investigated the regulation of His biosynthesis at both the molecular and biochemical levels. Three T. goesingense cDNAs encoding the following His biosynthetic enzymes, ATP phosphoribosyltransferase (THG1, GenBank accession no. AF003347), imidazoleglycerol phosphate dehydratase (THB1, GenBank accession no. AF023140), and histidinol dehydrogenase (THD1, GenBank accession no. AF023141) were isolated by functional complementation of Escherichia coli His auxotrophs. Northern analysis of THG1, THD1, and THB1 gene expression revealed that each gene is expressed in both roots and shoots, but at the concentrations and dosage times of Ni treatment used in this study, these genes failed to show any regulation by Ni. We were also unable to observe any increases in the concentration of free His in root, shoot, or xylem sap of T. goesingense in response to Ni exposure. X-ray absorption spectroscopy of root and shoot tissue from T. goesingense and the non-accumulator species Thlaspi arvense revealed no major differences in the coordination of Ni by His in these tissues. We therefore conclude that the Ni hyperaccumulation phenotype in T. goesingense is not determined by the overproduction of His in response to Ni.

Top-quark condensation.

Abstract: Top quark condensation, in particular the minimal framework where the neutral Higgs scalar is (predominantly) an effective ¯ tt condensate of the stan- dard model, is reviewed. Computational approaches are compared and sim- ilarities, differences and deficiencies pointed out. Extensions of the minimal framework, including scenarios with two composite Higgs doublets, additional neutrino condensates, andcondensation arising from four-fermion interac- tions with enlarged symmetries, are described. Possible renormalizable mod- els of underlying physics potentially responsible for the condensation, includ- ing topcolor assisted technicolor frameworks, are discussed. Phenomenological implications of top condensate models are outlined. Outstanding theoretical issues and problems for future investigation are pointed out. Progress in the field after this article was accepted has been briefly covered in a Note added at the end.

From embryo to adult: persistent neurogenesis and apoptotic cell death shape the lobster deutocerebrum.

Abstract: Neuronal plasticity and synaptic remodeling play important roles during the development of the invertebrate nervous system. In addition, structural neuroplasticity as a result of long-term environmental changes, behavioral modifications, age, and experience have been demonstrated in the brains of sexually mature insects. In adult vertebrates, persistent neurogenesis is found in the granule cell layer of the mammalian hippocampus and the subventricular zone, as well as in the telencephalon of songbirds, indicating that persistent neurogenesis, which is presumably related to plasticity and learning, may be an integral part of the normal biology of the mature brain. In decapod crustaceans, persistent neurogenesis among olfactory projection neurons is a common principle that shapes the adult brain, indicating a remarkable degree of life-long structural plasticity. The present study closes a gap in our knowledge of this phenomenon by describing the continuous cell proliferation and gradual displacement of proliferation domains in the central olfactory pathway of the American lobster Homarus americanus from early embryonic through larval and juvenile stages into adult life. Neurogenesis in the deutocerebrum was examined by the in vivo incorporation of bromodeoxyuridine, and development and structural maturation of the deutocerebral neuropils were studied using immunohistochemistry against Drosophila synapsin. The role of apoptotic cell death in shaping the developing deutocerebrum was studied using the terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling method, combined with immunolabeling using an antiphospho histone H3 mitosis marker. Our results indicate that, in juvenile and adult lobsters, birth and death of olfactory interneurons occur in parallel, suggesting a turnover of these cells. When the persistent neurogenesis and concurrent death of interneurons in the central olfactory pathway of the crustacean brain are taken into account with the life-long turnover of olfactory receptor cells in crustacean antennules, a new, highly dynamic picture of olfaction in crustaceans emerges.

Self-Organizing Maps on non-euclidean Spaces

Abstract: Publisher Summary This chapter proposes a new type of self-organizing map (SOM) that is based on discretizations of curved, non-euclidean spaces. As an introductory example, it briefly discusses “spherical SOMs” on tesselations of the sphere for the display of directional data. It describes the construction of “hyperbolic SOMs” using regular tesselations of the hyperbolic plane, which is a non-euclidean space characterized by constant negative gaussian curvature. While the applications of the SOM are extremely wide-spread, the majority of uses still follow the original motivation of the SOM to create dimension-reduced “feature maps” for various uses, most prominently the data visualization. The approach is motivated by the recent observation that the geometry of hyperbolic spaces possesses very favorable properties for the mapping of hierarchical data. The chapter concludes with some initial simulation results illustrating some properties of the hyperbolic SOM and discusses a number of issues for future research.

Developing HMM-Based Recognizers with ESMERALDA

Abstract: ESMERALDA is an integrated environment for the development of speech recognition systems. It provides a powerful selection of methods for building statistical models together with an efficient incremental recognizer. In this paper the approaches adopted for estimating mixture densities, Hidden Markov Models, and n-gram language models are described as well as the algorithms applied during recognition. Evaluation results on a speaker independent spontaneous speech recognition task demonstrate the capabilities of ESMERALDA.

Efficient Implementation of Lazy Suffix Trees

Abstract: We present an efficient implementation of a write-only top-down construction for suffix trees. Our implementation is based on a new, space-efficient representation of suffix trees which requires only 12 bytes per input character in the worst case, and 8:5 bytes per input character on average for a collection of files of different type. We show how to efficiently implement the lazy evaluation of suffix trees such that a subtree is evaluated not before it is traversed for the first time. Our experiments show that for the problem of searching many exact patterns in a fixed input string, the lazy top-down construction is often faster and more space efficient than other methods.

Stable homotopical algebra and Γ-spaces

Abstract: In this paper we advertise the category of Γ-spaces as a convenient framework for doing ‘algebra’ over ‘rings’ in stable homotopy theory. Γ-spaces were introduced by Segal [Se] who showed that they give rise to a homotopy category equivalent to the usual homotopy category of connective (i.e. (−1)-connected) spectra. Bousfield and Friedlander [BF] later provided model category structures for Γ-spaces. The study of ‘rings, modules and algebras’ based on Γ-spaces became possible when Lydakis [Ly] introduced a symmetric monoidal smash product with good homotopical properties. Here we develop model category structures for modules and algebras, set up (derived) smash products and associated spectral sequences and compare simplicial modules and algebras to their Eilenberg–MacLane spectra counterparts.