Showing papers by "Humboldt University of Berlin published in 1991"

Mathematical analysis of enzymic reaction systems using optimization principles.

Abstract: Mathematical modelling of metabolic networks is nowadays an important subject of theoretical biology. Most studies in this field concern (a) the development of models for the simulation of stationary and time dependent states of metabolic pathways; (b) the analysis of complex dynamic phenomena such as transitions between multiple stationary states, oscillations and even chaotic behaviour; and (c) the quantitative characterization of control properties of metabolic pathways.

Entropy of symbolic sequences: the role of correlations

Abstract: The role of correlations in the a priori probability of occurrence of a symbolic sequence is analysed, on the basis of the scaling behaviour of the entropy as a function of the sequence length. It is shown that sporadic systems give rise to peculiar scaling properties as a result of long-range correlations. The potential implications of this possibility in the structure of natural languages are explored.

Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences.

Abstract: The existence of hypervariable DNA sequences in nuclear genomes, and the use of appropriate “fingerprinting” probes to detect them, has gained widespread scientific interest, and also led to multiple applications in diverse areas. Two years ago, the new technique of “DNA fingerprinting” was also introduced into the analysis and characterization of plant genomes, initially by using human or M 13 minisatellites as probes. In the present article, we demonstrate the applicability for plant DNA fingerprinting of oligonucleotide probes specific for simple repetitive DNA sequences. We show that various levels of intra- and interspecific polymorphisms can be detected; the information to be gained depends on the optimal combination of probe and species. Variety-specific patterns were obtained in several cases. Some probes revealed variability between individuals. Somatic variability was not observed. Different DNA isolation and purification procedures were tested in order to introduce a fast and easy-to-perform isolation method suitable for a large variety of plant species. Nonradioactive fingerprinting was performed using digoxigenated oligonucleotides as probes. Banding patterns obtained with radioactive and digoxigenin-based labeling techniques proved to be of similar quality.

Polynomial-time inference of arbitrary pattern languages

Abstract: A pattern is a finite string of constants and variables (cf. [1]). The language of a pattern is the set of all strings which can be obtained by substituting non-null strings of constants for the variables of the pattern. In the present paper, we consider the problem of learning pattern languages from examples. As a main result we present an inconsistent polynomial-time algorithm which identifies every pattern language in the limit. Furthermore, we investigate inference of arbitrary pattern languages within the framework of learning from good examples. Finally, we show that every pattern language can be identified in polynomial time from polynomially many disjointness queries, only.

The Tetrazolium-Formazan System: Design and Histochemistry

Abstract: Our increasing knowledge about the chemistry and the correlations between chemical structure and histochemical properties of the tetrazolium/formazan system is resulting in: a better understanding of existing histochemical tetrazolium techniques; the selection of optimal tetrazolium salts for qualified use in histochemistry, cytochemistry and biochemistry; both qualitative and quantitative improvements in histochemical techniques for purposes demonstrating the activities of various dehydrogenating enzymes; an extended insight into the "state" of the tested biological object by means of tetrazolium indicators with special properties; and the combination of histochemical enzyme determination with further morphological techniques. This article has attempted to illustrate the progress in the use of the tetrazolium/formazan-system for histochemical purposes.

Chemical sensitivity of an ISFET with Ta2O5 membrane in strong acid and alkaline solutions

Abstract: A detailed study concerning the chemical sensitivity of an ISFET with a Ta 2 O 5 membrane is presented The results indicate that in the absence of alkali ions, the Ta 2 O 5 -ISFET has practically an ideal Nernstian pH response in a wide pH range from −7 to 137 A deviation from Nernstian response has been observed in electrolyte solutions containing lithium (at pH>7), sodium and potassium (at pH>12) ions Lithium ions have the most significant effect, giving rise to a change from pH response to pLi response

Oligonucleotide fingerprinting using simple repeat motifs: a convenient, ubiquitously applicable method to detect hypervariability for multiple purposes.

Abstract: A panel of simple repetitive oligonucleotide probes has been designed and tested for multilocus DNA fingerprinting in some 200 fungal, plant and animal species as well as man. To date at least one of the probes has been found to be informative in each species. The human genome, however, has been the major target of many fingerprinting studies. Using the probe (CAC)5 or (GTG)5, individualization of all humans is possible except for monozygotic twins. Paternity analyses are now performed on a routine basis by the use of multilocus fingerprints, including also cases of deficiency, i.e. where one of the parents is not available for analysis. In forensic science stain analysis is feasible in all tissue remains containing nucleated cells. Depending on the degree of DNA degradation a variety of oligonucleotides are informative, and they have been proven useful in actual case work. Advantages in comparison to other methods including enzymatic DNA amplification techniques (PCR) are evident. Fingerprint patterns of tumors may be changed due to the gain or loss of chromosomes and/or intrachromosomal deletion and amplification events. Locus-specific probes were isolated from the human (CAC)5/(GTG)5 fingerprint with a varying degree of informativeness (monomorphic versus truly hypervariable markers). The feasibility of three different approaches for the isolation of hypervariable mono-locus probes was evaluated. Finally, one particular mixed simple (gt)n(ga)m repeat locus in the second intron of the HLA-DRB genes has been scrutinized to allow comparison of the extent of exon-encoded (protein-) polymorphisms versus intronic hypervariability of simple repeats: adjacent to a single gene sequence (e.g. HLA-DRB1*0401) many different length alleles were found. Group-specific structures of basic repeats were identified within the evolutionarily related DRB alleles. As a further application it is suggested here that due to the ubiquitous interspersion of their targets, short probes for simple repeat sequences are especially useful tools for ordering genomic cosmid, yeast artificial chromosome and phage banks.

Differentiation of species and strains among filamentous fungi by DNA fingerprinting.

Abstract: We have analyzed 11 strains and clones, representing five species (Penicillium janthinellum, P. citrioviridae, P. chrysogenum, Aspergillus niger, Trichoderma harzianum) and three genera of filamentous fungi, for the presence of hypervariable loci in their genomes by hybridization with simple repeat oligonucleotides and the DNA of phage M13. The oligonucleotide probes (CT)8, (GTG)5 and (GACA)4, as well as M13 DNA, are informative probes for fingerprinting in all genera and species tested. The probe (GATA)4 produced informative fingerprints only with the genomic DNA of A. niger. There was no similarity between the fingerprints originating from fungi of different genera and also little similarity between the fingerprints of different species belonging to the same genus. Fingerprints of strains of the same species differed only slightly from each other. Fingerprints of clones originating from one strain were identical. The results indicate that DNA fingerprinting is a powerful method to differentiate species and strains of filamentous fungi.

Stability analysis for stochastic programs

Abstract: For stochastic programs with recourse and with (several joint) probabilistic constraints, respectively, we derive quantitative continuity properties of the relevant expectation functionals and constraint set mappings. This leads to qualitative and quantitative stability results for optimal values and optimal solutions with respect to perturbations of the underlying probability distributions. Earlier stability results for stochastic programs with recourse and for those with probabilistic constraints are refined and extended, respectively. Emphasis is placed on equipping sets of probability measures with metrics that one can handle in specific situations. To illustrate the general stability results we present possible consequences when estimating the original probability measure via empirical ones.

Hybrid Bacillus (1-3,1-4)-beta-glucanases: engineering thermostable enzymes by construction of hybrid genes.

Abstract: Hybrid (1-3,1-4)-β-glucanase genes were constructed by extension of overlapping segments of the (1-3,1-4)-β-glucanase genes from Bacillus amyloliquefaciens and B. macerans generated by the polymerase chain reaction (PCR). Four hybrid genes were expressed in Escherichia coli cells. The mature hybrid enzymes contain a 16, 36, 78, or 152 amino acid N-terminal sequence derived from B. amyloliquefaciens (1-3,1-4)-β-glucanase followed by a C-terminal segment derived from B. macerans (1-3,1-4)-β-glucanase. Biochemical characterization of parental and hybrid enzymes shows a significant increase in thermostability of three of the hybrid enzymes when exposed to an acidic environment thus combining two important enzyme characteristics within the same molecule. At pH 4.1, 85%-95% of the initial activity was retained after 1 h at 65° C in contrast to 5% and 0% for the parental enzymes from B. amyloliquefaciens and B. macerans. After 60 min incubation at 70° C, pH 6.0, the parental enzymes retained 5% or less of the initial activity whilst one of the hybrids still exhibited 90% of the initial activity. Of the parental enzymes B. macerans (1-3,1-4)-β-glucanase had the lower specific activity while the hybrid enzymes exhibited specific activities that were 1.5- to 3-fold higher. These experimental results demonstrate that exchange of homologous gene segments from different species may be a useful technique for obtaining new and improved versions of biologically active proteins.

Lipschitzian inverse functions, directional derivatives, and applications in C 1,1 optimization

Abstract: The paper shows that Thibault's limit sets allow an iff-characterization of local Lipschitzian invertibility in finite dimension. We consider these sets as directional derivatives and extend the calculus in a way that can be used to clarify whether critical points are strongly stable inC 1,1 optimization problems.

Laser‐induced birefringence in homeotropic films of photochromic comb‐shaped liquid‐crystalline copolymers with azobenzene moieties at different temperatures

Abstract: Comb-shaped liquid-crystalline copolymers (LCP) containing azobenzene moieties have attracted much attention in the last few This particular interest in ordered photochromic polymer films is predominantly caused by their unique combination of optically anisotropic and polymer properties, which allows different types of laser-addressed, reversible optical data storage. The use of linearly polarized light offers a fundamentally new approach to induce optical anisotropy by rotational diffusion in amorphous photochromic polymers 1 3 , 14) as well as in LCP’s’s2). Recent publications6-12) were aimed at showing that azo moieties undergo E-Z photoisomerization and reorientation, in such a way that optically anisotropic properties such as birefringence and dichroism of homeotropically and planary oriented films of LCP’s are modified in the glassy as well as in the visco-elastic state. It had been shown that the photoinduced rotational diffusion of azo-chromophores does not disturb the other surrounding mesogenic side groups in the glassy state of LCP’s9s10). In contrast to these conclusions, our results from conoscopic studies of LCP’s, which differ concerning the mesogenic moieties, suggest that even in the glassy state the photoinduced reorientation of a minority of azo-chromophores triggers the physical reorientation of other mesogenic groups in the same direction, i.e. perpendicular to the plane of polarization of the incident light ’7 12) . Up to now, there is no information about the influence of temperature, type of mesophase and content of azo moieties on the kinetics of this type of photorecording. The main concern of this paper is to present quantitative results of photoinduced birefringence at different temperatures, using homeotropic films of smectic as well as nematic LCP’s with different structures and different contents of azo-chromophores.

Pentoxifylline Prevents Murine Cerebral Malaria

Abstract: Pentoxifylline, a widely used methylxanthine, was tested for its capacity to prevent cerebral malaria (CM) in Plasmodium berghei ANKA-infected CBA/Ca mice. Nine of 12 control mice developed neurologic signs and died from CM approximately 2 weeks after infection. All 12 mice treated with daily intraperitoneal pentoxifylline (1 mg) for 10 days after infection did not develop CM. All surviving mice developed high parasitemia and severe anemia and died 2 weeks later without neurologic signs. In pentoxifylline-treated mice, serum tumor necrosis factor (TNF) bioactivity was nondetectable, whereas control mice had high TNF levels on day 6 after infection. These findings were supported by in vitro investigations of malaria antigen-induced TNF synthesis. Northern blot analysis of TNF mRNA from stimulated macrophages showed that pentoxifylline inhibited TNF expression at the transcription level, and TNF bioactivity in supernatants was strongly depressed. These findings make pentoxifylline a potential candidate for study as a supportive agent in human CM.

Linear motion of dielectric particles and living cells in microfabricated structures induced by traveling electric fields

Abstract: Arrangements of microelectrodes as obtained by a microfabrication technique are found to be well suited for a linear transfer of microscopic particles such as biological cells and other objects of microscopic dimensions The conditions for an effective manipulation of the particles are electrode geometries which correspond to the dimensions of the particle and adapted electrical excitation of the electrodes (traveling high-frequency waves) The motion of particles was found to be a super-position of dielectrophoresis and charge relaxation processes as they are dominant, eg in dielectric induction motors Microparticle velocities of some hundreds mu /s could be achieved by applying phase-shifted rectangular pulses with amplitudes between 5 and 15 volts >

Structure and importance of logspace-MOD-classes

Abstract: We refine the techniques of Beigel, Gill, Hertrampf [BGH90] who investigated polynomial time counting classes, in order to make them applicable to the case of logarithmic space. We define the complexity classes MODkL and demonstrate their significance by proving that all standard problems of linear algebra over the finite rings Z/kZ are complete for these classes. We then define new complexity classes LogFew and LogFewNL and identify them as adequate logspace versions of Few and LogFew and FewP. We show that LogFew and LogFewNL is contained in MODZkL and that LogFew is contained in MODkL for all k. Also an upper bound for L #L in terms of computation of integer determinants is given from which we conclude that all logspace counting classes are contained in NC2.

Distribution sensitivity in stochastic programming

Abstract: In this paper, stochastic programming problems are viewed as parametric programs with respect to the probability distributions of the random coefficients. General results on quantitative stability in parametric optimization are used to study distribution sensitivity of stochastic programs. For recourse and chance constrained models quantitative continuity results for optimal values and optimal solution sets are proved (with respect to suitable metrics on the space of probability distributions). The results are useful to study the effect of approximations and of incomplete information in stochastic programming.

Photoreaction in mesogenic media, 5. Photoinduced optical anisotropy of liquid‐crystalline sidechain polymers with azochromophores by linearly polarized light of low intensity

Abstract: A novel process of photo-induced orientation and optical anisotropy in the whole matrix of a photochromic liquid-crystalline polymer (LCP) in the glassy state via angular-dependent photoselection by the absorption of linearly polarized light with low intensity is presented Spectroscopical and conoscopical studies give information about the interaction between azochromophores and the mesogenic side chains in homeotropic and homogeneous LCP monodomain films as a result of the photoselection process Novel variations of erasable optical storage are described using photochromic LCPs in combination with polarized light

The Newtonian Limit of Fourth and Higher Order Gravity

Abstract: We consider the Newtonian limit of the theory based on the Lagrangian . The gravitational potential of a point mass turns out to be a combination of Newtonian and Yukawa terms. For sixth-order gravity (p = 1) the coefficients are calculated explicitly. For general p one gets . Therefore, the potential is always unbounded near. The origin. Wir betrachten den Newtonschen Grenzwert der durch den Lagrangian beschriebenen Theorie. Das Gravitationspotential einer Punktmasse hat die Gestalt von Kombinationen von Newton- und Yukawa-Termen. Fur Gravitationsgleichungen sechster Ordnung (p = 1) wird das Fernfeld von Punktmassen explizit angegeben. Fur allgemeine p wird die Summe der Koeffizienten vor den Yukawa-Termen durch beschrieben. Also ist das Potential stets unbeschrarkt.

Detecting strictly detailed balanced subnetworks in open chemical reaction networks

Abstract: The notion “strictly detailed balanced subnetwork” is introduced, for chemical reaction networks which are open and spatially homogeneous, to refer to any set of reactions the net rates of which vanish in each asymptotically stable steady state, regardless of the kinetic parameters of any reaction in the whole network. Necessary and sufficient conditions for sets of reactions to be strictly detailed balanced subnetworks are derived. An algorithm for detecting all reactions belonging to such subnetworks in systems of arbitrary stoichiometry is given, justified and applied to a realistic biochemical system. A computer program in PASCAL, performing the essential parts of this algorithm, is added.

Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks. II. Time hierarchy, enzymatic rate laws, and erythrocyte metabolism.

Abstract: The multiobjective problem of minimizing all intermediate concentrations is solved for a model of glycolysis, the pentose monophosphate shunt and the glutathione system in human erythrocytes. It turns out that one solution out of four obtained corresponds qualitatively to the real system. Furthermore, it is shown that for any reaction system, the mentioned optimality principle implies distinct time hierarchy in that some reactions are infinitely fast and subsist in quasi-equilibrium. Finally, the relationships to the standard method of deriving enzymatic rate laws are discussed.

Changes of neuron-specific enolase concentration in plasma after cardiac arrest and resuscitation.

Abstract: The concentration of neuron-specific enolase (NSE) was measured in plasma of 18 patients after cardiac arrest and resuscitation (14 nonsurvivors and 4 survivors). In all patients, the NSE concentration was significantly higher in comparison to reference values. The highest concentration was measured in nonsurvivors. Time-course investigation in the first 24 h after cardiac arrest was performed in five patients. Two nonsurvivors and one survivor of the five patients showed a significant rise, and a NSE peak concentration of 42.7 μg/L, 13.6 μg/L, and 10.5 μg/L, respectively, was found 10–19 h after cardiac arrest.

Thyrotropin-releasing hormone induces opposite effects on Ca2+ channel currents in pituitary cells by two pathways

Abstract: Thyrotropin-releasing hormone (TRH) stimulates pituitary secretion by steps involving a cytosolic Ca2+ rise. We examined various pathways of Ca2+ elevation in pituitary GH3 cells. By using the patch clamp technique in the whole-cell configuration and Ba2+ as divalent charge carrier through Ca2+ channels, TRH (1 microM) reversibly reduced the current by about 55%. This hormonal effect was prevented by infusing guanine 5'-[beta-thio]diphosphate (GDP[beta S]) intracellularly but not by pretreating the cell with pertussis toxin (PT). Since PT-insensitive guanine nucleotide-binding regulatory (G) proteins are known to mediate a hormone-stimulated inositol trisphosphate-mediated Ca2+ release from intracellular stores, we assume that the inhibitory effect of TRH on Ba2+ currents through Ca2+ channels is caused by the increased intracellular Ca2+. To prevent a Ca(2+)-release-dependent inhibition of Ca2+ channels, we preincubated GH3 cells in a medium free of divalent charge carriers and measured the Na+ current through Ca2+ channels. When fura-2 was used as indicator for the cytosolic Ca2+, TRH induced a release from intracellular stores only once and had no effect on the intracellular Ca2+ concentration during further applications. In line with this observation, TRH initially reduced the Na+ current through Ca2+ channels but stimulated it during subsequent applications. The stimulation was sensitive to GDP[beta S] and was abolished by pretreatment with PT, suggesting that the stimulatory action of TRH is mediated by a G protein different from the one that functionally couples the receptor to phosphatidylinositol 4,5-bisphosphate hydrolysis. In conclusion, the present data suggest that TRH increases the intracellular Ca2+ concentration by two interacting pathways, that release from intracellular stores causes a secondary blockage of Ca2+ channels, and that, especially with empty intracellular Ca2+ stores, Ca2+ channels are stimulated by a PT-sensitive G protein.

Linear skorohod stochastic differential equations

Abstract: Let σ ∈ C 4 b(R1). We provide assumptions on the random variable G and the process b = (b t (x)) possibly anticipating the driving Wiener process (W t ) under which the anticipative stochastic differential equation with Skorohod integral 21-1