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Biomedical subjects

P Schuster

Publications and source records attributed to P Schuster.

At least 19 recordsLinked to original sources
PubMed1995

How to search for RNA structures. Theoretical concepts in evolutionary biotechnology.

The relation between RNA sequences and minimum free energy secondary structures is viewed as a mapping from sequence space into shape space. The properties of such mappings depend strongly on the ratios of the numbers of sequences and structures and, hence, substantial differences are observed between samples of structures derived from AUGC, pure AU or pure GC sequences. Statistical analysis of large samples is used to demonstrate that structures from AUGC sequences are much less sensitive to point mutations than those from sequences containing exclusively AU or GC. The frequency with which a structure is realized in sequence space is inversely proportional to some power c > 1 of the structure's frequency rank, thus following a (generalized) Zipf law. For long sequences the exponent approaches c = 1. An inverse folding algorithm is used to compute samples of sequences folding into the same secondary structure. These sequences are distributed randomly in sequence space. Common structures form extended neutral networks along which populations can migrate through the entire sequence space without changing structure. In this migration, moves of Hamming distance d = 1 and d = 2 are accepted in order to allow for base and base pair exchanges, respectively. Around any arbitrarily chosen sequence a ball that contains sequences folding into all common structures can be drawn. This ball has a diameter that is much smaller than the diameter of sequence space. Hence, only a small fraction of sequence space needs to be searched in order to find a given structure. The results derived from the mapping of sequences into structures are used to suggest a rationale for evolutionary searches on RNA structures: selection cycles with high and low mutation rates applied in alternation. Generalizations of the results to RNA 3-D structures and protein structures are discussed.

Algorithms↗
PubMed1994

From sequences to shapes and back: a case study in RNA secondary structures.

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that sequences sharing the same structure are distributed randomly over sequence space. All common structures can be accessed from an arbitrary sequence by a number of mutations much smaller than the chain length. The sequence space is percolated by extensive neutral networks connecting nearest neighbours folding into identical structures. Implications for evolutionary adaptation and for applied molecular evolution are evident: finding a particular structure by mutation and selection is much simpler than expected and, even if catalytic activity should turn out to be sparse of RNA structures, it can hardly be missed by evolutionary processes.

Base Composition↗
PubMed1994

Immune networks modeled by replicator equations.

In order to evaluate the role of idiotypic networks in the operation of the immune system a number of mathematical models have been formulated. Here we examine a class of B-cell models in which cell proliferation is governed by a non-negative, unimodal, symmetric response function f (h), where the field h summarizes the effect of the network on a single clone. We show that by transforming into relative concentrations, the B-cell network equations can be brought into a form that closely resembles the replicator equation. We then show that when the total number of clones in a network is conserved, the dynamics of the network can be represented by the dynamics of a replicator equation. The number of equilibria and their stability are then characterized using methods developed for the study of second-order replicator equations. Analogies with standard Lotka-Volterra equations are also indicated. A particularly interesting result of our analysis is the fact that even though the immune network equations are not second-order, the number and stability of their equilibria can be obtained by a superposition of second-order replicator systems. As a consequence, the problem of finding all of the equilibrium points of the nonlinear network equations can be reduced to solving linear equations.

Animals↗
PubMed1994

Statistics of RNA melting kinetics.

We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a "landscape" of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies.

Base Sequence↗
PubMed1994

Landscapes: complex optimization problems and biopolymer structures.

The evolution of RNA molecules in replication assays, viroids and RNA viruses can be viewed as an adaptation process on a 'fitness' landscape. The dynamics of evolution is hence tightly linked to the structure of the underlying landscape. Global features of landscapes can be described by statistical measures like number of optima, lengths of walks and correlation functions. The evolution of a quasispecies on such landscapes exhibits three dynamical regimes depending on the replication fidelity: Above the "localization threshold" the population is centered around a (local) optimum. Between localization and "dispersion threshold" the population is still centered around a consensus sequence, which, however, changes in time. For very large mutation rates the population spreads in sequence space like a gas. The critical mutation rates separating the three domains depend strongly on characteristics properties of the fitness landscapes. Statistical characteristics of RNA landscapes are accessible by mathematical analysis and computer calculations on the level of secondary structures: these RNA landscapes belong to the same class as well known optimization problems and simple spin glass models. The notion of a landscape is extended to combinatory maps, thereby allowing for a direct statistical investigation of the sequence structure relationships of RNA at the level of secondary structures. Frequencies of structures are highly non-uniform: we find relatively few common and many rare ones, as expressed by a generalized form of Zipf's law. Using an algorithm for inverse folding we show that sequences sharing the same structure are distributed randomly over sequence space. Together with calculations of structure correlations and a survey of neutral mutations this provides convincing evidence that RNA landscapes are as simple as they could possibly be for evolutionary adaptation: Any desired secondary structure can be found close to an arbitrary initial sequence and at the same time almost all bases can be substituted sequentially without ever changing the shape of the molecule. Consequences of these results for evolutionary optimization, the early stages of life, and molecular biotechnology are discussed.

Adaptation, Biological↗
PubMed1993

Statistics of RNA secondary structures.

A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and free ends. Statistical properties of these elements are computed for small RNA molecules of chain lengths up to 100. The results of RNA structure statistics depend strongly on the particular alphabet chosen. The statistical reference is compared with the data derived from natural RNA molecules with similar base frequencies. Secondary structures are represented as trees. Tree editing provides a quantitative measure for the distance dt, between two structures. We compute a structure density surface as the conditional probability of two structures having distance t given that their sequences have distance h. This surface indicates that the vast majority of possible minimum free energy secondary structures occur within a fairly small neighborhood of any typical (random) sequence. Correlation lengths for secondary structures in their tree representations are computed from probability densities. They are appropriate measures for the complexity of the sequence-structure relation. The correlation length also provides a quantitative estimate for the mean sensitivity of structures to point mutations.

Base Sequence↗
PubMed1993

RNA multi-structure landscapes. A study based on temperature dependent partition functions.

Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest, in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced and pair correlations at the level of the structures themselves are computed. Just as with landscapes based on most stable secondary structure prediction, the landscapes defined on the full biophysical GCAU alphabet are much smoother than the landscapes restricted to pure GC sequences and the correlation lengths are almost constant fractions of the chain lengths. Correlation functions for multi-structure landscape exhibit an increased correlation length, especially near the melting temperature. However, the main effect on evolution is rather an effective increase in sampling for finite populations where each sequence explores multiple structures.

Base Composition↗
PubMed1993

RNA based evolutionary optimization.

The notion of an RNA world has been introduced for a prebiotic scenario that is dominated by RNA molecules and their properties, in particular their capabilities to act as templates for reproduction and as catalysts for several cleavage and ligation reactions of polynucleotides and polypeptides. This notion is used here also for simple experimental assays which are well suited to study evolution in the test tube. In molecular evolution experiments fitness is determined in essence by the molecular structures of RNA molecules. Evidence is presented for adaptation to environment in cell-free media. RNA based molecular evolution experiments have led to interesting spin-offs in biotechnology, commonly called 'applied molecular evolution', which make use of Darwinian trial-and-error strategies in order to synthesize new pharmacological compounds and other advanced materials on a biological basis. Error-propagation in RNA replication leads to formation of mutant spectra called 'quasispecies'. An increase in the error rate broadens the mutant spectrum. There exists a sharply defined threshold beyond which heredity breaks down and evolutionary adaptation becomes impossible. Almost all RNA viruses studied so far operate at conditions close to this error threshold. Quasispecies and error thresholds are important for an understanding of RNA virus evolution, and they may help to develop novel antiviral strategies. Evolution of RNA molecules can be studied and interpreted by considering secondary structures. The notion of sequence space introduces a distance between pairs of RNA sequences which is tantamount to counting the minimal number of point mutations required to convert the sequences into each other. The mean sensitivity of RNA secondary structures to mutation depends strongly on the base pairing alphabet: structures from sequences which contain only one base pair (GC or AU are much less stable against mutation than those derived from the natural (AUGC) sequences. Evolutionary optimization of two-letter sequences in thus more difficult than optimization in the world of natural RNA sequences with four bases. This fact might explain the usage of four bases in the genetic language of nature. Finally we study the mapping from RNA sequences into secondary structures and explore the topology of RNA shape space. We find that 'neutral paths' connecting neighbouring sequences with identical structures go very frequently through entire sequence space. Sequences folding into common structures are found everywhere in sequence space.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Physiological↗
PubMed1992

Mutation in autocatalytic reaction networks. An analysis based on perturbation theory.

A class of kinetic equations describing catalysed and template induced replication, and mutation is introduced. This ODE in its most general form is split into two vector fields, a replication and a mutation field. The mutation field is considered as a perturbation of the replicator equation. The perturbation expansion is a Taylor series in a mutation parameter lambda. First, second and higher order contributions are computed by means of the conventional Rayleigh-Schrödinger approach. Qualitative shift in the positions of rest points and limit cycles on the boundary of the physically meaningful part of concentration space are predicted from flow topologies. The results of the topological analysis are summarized in two theorems which turned out to be useful in applications: the rest point migration theorem (RPM) and the limit cycle migration theorem (LCM). Quantitative expressions for the shifts of rest points are computed directly from the perturbation expansion. The concept is applied to a collection of selected examples from biophysical chemistry and biology.

Catalysis↗
PubMed1990

[Noninvasive studies of the left ventricular systolic function in patients over 65 years old].

Left ventricular functions were assessed in 96 patients (26 men, 70 women aged over 65 years; mean age 74.6 +/- 6.3 years) with various cardiovascular diseases (arterial hypertension, coronary heart disease, cardiomyopathy, various cardiac defects) by comparing various left-ventricular time intervals obtained from resting ECGs, apex cardiograms, carotid-pulse curves and phonocardiograms with left-ventricular ejection fractions by echocardiography. The correlations were strongest with the Weissler index (ratio of pre-ejection and left-ventricular ejection times), PEP/LVET (r = -0.76; P less than 0.001), with PEP itself (r = -0.65; P less than 0.001), as well as with rate-corrected PEP (r = -0.71; P less than 0.001). The plain chest X-ray did not make it possible to assess quantitatively patients with diminished cardiac pump function, despite radiological signs of congestion.

Age Factors↗
PubMed1990

Dynamics of small autocatalytic reaction networks--I. Bifurcations, permanence and exclusion.

Catalysis in replication networks has become an important issue in biophysics and other areas of biology. Examples are RNA catalysis, idiotype recognition in the immune response and dynamical models of Maynard-Smith games in sociobiology. Chemical reaction networks describing catalysed, template-induced reproduction of three species are analysed in full generality. The nine-dimensional parameter space is reduced to three relevant angular coordinates which determine completely the phase portraits (PPs) and the bifurcation patterns. All cases are classified and all generic as well as most of the non-generic transitions are listed and described.

Catalysis↗
PubMed1990

Psychometric assessment of DSM-III personality disorders: another facet of the problem.

An empirical study with the Personality Diagnostic Questionnaire, which in substance follows exactly the criteria of personality disorders described in the DSM-III, is used to highlight a number of problems connected with the DSM-III. Criticisms of the DSM-III previously expressed by other authors, e.g. concerning multiple choice between characteristics and equal weighting of different symptoms, are supported by this empirical study.

Cluster Analysis↗
PubMed1990

[Comments on the diagnostic principles of DSM-III exemplified by the borderline personality disorder].

The first disputes around the DSM-III, which were charged with emotion and cathected by ideologies, are now followed by criticisms based on practical experience with the criteria used in the diagnostic approach of the DSM-III. The present paper is an attempt to show for the area of personality disorders, (and here in particular for borderline personality disorders) that the specific formulation of individual diagnostic questions is a contributory factor to the diagnostic assessment in this field, despite the descriptive approach of the DSM-III. By comparing different item formulations for the same criterion we try to illustrate the problems involved in a purely quantitative registration of characteristics. When criteria, such as identity, interhuman relationship, etc. are concerned, subjective variables will always contribute to the diagnostic assessment.

Borderline Personality Disorder↗
PubMed1989

Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet.

The occurrence of thresholds for error propagation in asexually replicating populations is investigated by means of a simple birth and death model as well as by numerical simulation. Previous results derived for infinite population sizes are extended to finite populations. Here, replication has to be more accurate than in infinitely large populations because the master sequence can be lost not only by accumulation of errors--similar to the loss of wildtype through the operation of Muller's ratchet--but also by natural fluctuations. An analytical expression is given which allows straight computation of highly accurate values of error thresholds. The error threshold can be expanded in a power series of the reciprocal square root of the population size and thus increases with 1 square root of N in sufficiently large populations.

Computer Simulation↗
PubMed1989

Fixation probabilities for advantageous mutants: a note on multiplication and sampling.

If the average number of gametes produced by the individual is small, as may be the case for haploid organisms, then sampling with and without replacement can lead to considerable differences in the fixation probabilities of mutant alleles. As a function of the population size N, these probabilities converge quickly to the survival probabilities given by branching processes with Poisson or Bernoulli offspring distributions.

Biological Evolution↗
PubMed1989

Psychophysiological research in psychiatry and neuropsychopharmacology. I. Methodological aspects of the Viennese Psychophysiological Test-System (VPTS).

In order to find a psychophysiological paradigm for clinical application we have developed the Viennese Psychophysiological Test-System (VPTS), which includes a special selection and combination of experimental situations, physiological measurements, behavioral measurements and data analysis. This study presents detailed information concerning these four aspects. Experimental situations are related to the human model of information processing, where short changes of stimulus-reaction-correlated processes are selected: resting conditions (eyes open, eyes closed), habituation-orienting test, psychomotor-performance test, signal-detection test and reaction-time test. Physiological measures include central and peripheral activity of the cerebrospinal and autonomic nervous system: cortical activity (spontaneous electroencephalogram, auditory evoked potentials, late positive components, slow potentials), ocular activity (eye and eyelid movements), electrodermal activity (skin conductance), cardiac activity (heart rate measurement), respiratory activity (rate of respiration) and peripheral vascular activity (finger pulse volume). Behavioral measurements extend from micro behavior to complex diagnostic systems: psychomotor measurements, self-reported mood, arousal and visceral perception, psychological and psychiatric interviews. The application of this test system in 15 elderly subjects of both sexes aged 58-77 years gives information which exceeds the sum of the singular constructing elements of the VPTS.

Electrocardiography↗
PubMed1989

Psychophysiological research in psychiatry and neuropsychopharmacology. II. The investigation of antihypoxidotic/nootropic drugs (tenilsetam and co-dergocrine-mesylate) in elderlies with the Viennese Psychophysiological Test-System (VPTS).

In a double-blind placebo-controlled study, the effects of tenilsetam, a novel antihypoxidotic/nootropic agent, on spontaneous and event-related activity of the central and autonomous nervous system were studied in 15 elderly subjects of both sexes aged 58-77 years by means of the Viennese Psychophysiological Test-System (VPTS). The VPTS includes a special selection and combination of experimental situations, physiological measurements, behavioral measurements and data analysis. At weekly intervals, the subjects received randomized single oral doses of placebo, 150 mg, 300 mg and 900 mg tenilsetam (TEN) and 5 mg co-dergocrine-mesylate (CDM) as reference drug. Psychophysiological testings were carried out before and 2 h after drug administration. Evaluation of the spontaneous EEG-activity demonstrated no significant drug effects as compared to placebo. In contrast, TEN showed a dose-dependent augmentation of the N1-P2 and N2-P300 amplitudes of the event-related potentials (ERPs) in specific experimental conditions. In reference to placebo, the increase of N2-P300 amplitude after the highest dosage of TEN, as well as after CDM, amounted to approximately 5 microV, which confirms the hypothesis that nootropic drugs may influence the P300 amplitude in the sense of an improved availability of cognitive processing resources. There was no effect on ERP latencies, on mean amplitudes of contingent negative variation and of post-imperative negative variation, on autonomous nervous system, on psychological measurements, nor on reaction time. However, specific improvements were observed in psychomotor measures, such as synchronization accuracy and rhythmicity. These findings highlight the importance of using EEG and ERP measures in different experimental situations in conjunction with behavioral, psychological and autonomous nervous system measures to study nootropic drug effects.

Aged↗