Biomedical subjects

A Dress

Publications and source records attributed to A Dress.

11 recordsLinked to original sources

PubMed1999

An error limit for the evolution of language.

On the evolutionary trajectory that led to human language there must have been a transition from a fairly limited to an essentially unlimited communication system. The structure of modern human languages reveals at least two steps that are required for such a transition: in all languages (i) a small number of phonemes are used to generate a large number of words; and (ii) a large number of words are used to a produce an unlimited number of sentences. The first (and simpler) step is the topic of the current paper. We study the evolution of communication in the presence of errors and show that this limits the number of objects (or concepts) that can be described by a simple communication system. The evolutionary optimum is achieved by using only a small number of signals to describe a few valuable concepts. Adding more signals does not increase the fitness of a language. This represents an error limit for the evolution of communication. We show that this error limit can be overcome by combining signals (phonemes) into words. The transition from an analogue to a digital system was a necessary step toward the evolution of human language.

Biological Evolution↗

PubMed1999

Positional dependence, cliques, and predictive motifs in the bHLH protein domain.

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.

Amino Acid Sequence↗

PubMed1998

DIALIGN: finding local similarities by multiple sequence alignment.

MOTIVATION: DIALIGN is a new method for pairwise as well as multiple alignment of nucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families. RESULTS: Using four different data sets, we show that DIALIGN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs. AVAILABILITY: DIALIGN is available to the scientific community free of charge for non-commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html CONTACT: werner, morgenstern@gsf.de

Algorithms↗

PubMed1998

Segment-based scores for pairwise and multiple sequence alignments.

In this paper, we discuss a novel scoring scheme for sequence alignments. The score of an alignment is defined as the sum of so-called weights of aligned segment pairs. A simple modification of the weight function used by the original version of the DIALIGN alignment program turns out to have a crucial advantage: it can be applied to both, global and local alignment problems without the need to specify a threshold parameter.

Amino Acid Sequence↗

PubMed1996

Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues. Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicity, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested. As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease H proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters.

Algorithms↗

PubMed1995

A divide and conquer approach to multiple alignment.

We present a report on work in progress on a divide and conquer approach to multiple alignment. The algorithm makes use of the costs calculated from applying the standard dynamic programming scheme to all pairs of sequences. The resulting cost matrices for pairwise alignment give rise to secondary matrices containing the additional costs imposed by fixing the path through the dynamic programming graph at a particular vertex. Such a constraint corresponds to a division of the problem obtained by slicing both sequences between two particular positions, and aligning the two sequences on the left and the two sequences on the right, charging for gaps introduced at the slicing point. To obtain an estimate for the additional cost imposed by forcing the multiple alignment through a particular vertex in the whole hypercube, we will take a (weighted) sum of secondary costs over all pairwise projections of the division of the problem, as defined by this vertex, that is, by slicing all sequences at the points suggested by the vertex. We then use that partition of every single sequence under consideration into two 'halfs' which imposes a minimal (weighted) sum of pairwise additional costs, making sure that one of the sequences is divided somewhere close to its midpoint. Hence, each iteration can cut the problem size in half. As the enumeration of all possible partitions may restrict this approach to small-size problems, we eliminate futile partitions, and organize their enumeration in a way that starts with the most promising ones.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed1993

Split decomposition: a technique to analyze viral evolution.

A clustering technique allowing a restricted amount of overlapping and based on an abstract theory of coherent decompositions of finite metrics is used to analyze the evolution of foot-and-mouth disease viruses. The emerging picture is compatible with the existence of viral populations with a quasispecies structure and illustrates various forms of evolution of this virus family. In addition, it allows the correlation of these forms with geographic occurrence.

Animals↗

PubMed1993

Formation of morphological differentiation patterns in the ascomycete Neurospora crassa.

Morphological differentiation patterns--among them concentric rings and radial zonations--can be induced in the band-mutant of Neurospora crassa by appropriate experimental conditions, in particular by a mere shift of certain salt concentrations in the medium. The role of initial experimental conditions is examined and, furthermore, the influences of artificially induced phase differences are analyzed with respect to pattern formation. While the concentric ring pattern is due to some (endogenous) circadian rhythmicity within every hypha, nothing is known about the underlying mechanism of radial zonation development. Various hypotheses were tested with the help of a cellular automaton model which mimics growth, branching and differentiation of a fungal mycelium. In particular, sufficient conditions are provided which imply the formation of radial spore zonations. These conditions postulate a rather homogeneous microscopic hyphal branching pattern and induction of spore differentiation by means of an activator-inhibitor system. Furthermore, a working hypothesis for the formation of spore patterns in Neurospora crassa is suggested which is based on an extracellular control of fungal differentiation.

Cell Differentiation↗

PubMed1990

On the cost functions for the control of the human arm movement.

The aim of our investigation is to understand the mechanisms which control the movement of the human arm. The arm is here considered as a redundant system: the shoulder, elbow and wrist joints, which provide three degrees of freedom, combine to move the hand in a horizontal plane, i.e. a two dimensional space. Thus the system has one extra degree of freedom. Earlier investigations of the static situation led to the hypothesis that independent cost functions were attached to each of the three joints and that the configuration chosen for a given target position is that which provides the minimum total cost (Cruse 1986). The aim of the current investigation was to look for measurable values corresponding to the hypothetical cost functions. Experiments using pointers of different lengths attached to the hand showed that the strategy in choosing the joint angles are independent of the limb length. The muscle force necessary to reach a given angle is increased by a spring mounted across a joint. In this situation the angles of the loaded joint are changed for a given target point to give way to the force effect. This leads to the conclusion that the hypothetical cost functions are not independent of the physiological costs necessary to hold the joint at a given angle. The cost functions seem to depend on joint angle and on the force which is necessary to hold the joint in a given position. Cost functions are measured by psychophysical methods. The results show U-shaped curves which can be approximated by parabolas. The position of minimum cost (maximum comfort) for one joint showed no or weak dependency on the angles of the other joints. For each subject these "psychophysical" cost functions are compared with the hypothetical cost functions. The comparison showed reasonable agreement. This supports the assumption that the psychophysically measured "comfort functions" provide a measure for the hypothetical cost functions postulated to explain the targeting movements. Targeting experiments using a four joint arm which has two extra degrees of freedom showed a much larger scatter compared to the three joint arm. Nevertheless, the results still conform to the hypothesis that also in this case the minimum cost principle is applied to solve the redundancy problem. As the cost function for the whole arm shows a large minimum valley, quite a large range of arm positions is possible of about equal total costs.(ABSTRACT TRUNCATED AT 400 WORDS)

Arm↗

PubMed1989

How old is the genetic code? Statistical geometry of tRNA provides an answer.

The age of the molecular organization of life as expressed in the genetic code can be estimated from experimental data. Comparative sequence analysis of transfer RNA by the method of statistical geometry in sequence space suggests that about one-third of the present transfer RNA sequence divergence was present at the urkingdom level about the time when archaebacteria separated from eubacteria. It is concluded that the genetic code is not older than, but almost as old as our planet. While this result may not be unexpected, it was not clear until now that interpretable data exist that permit inferences about such early stages of life as the establishment of the genetic code.

Anticodon↗

PubMed1988

Statistical geometry in sequence space: a method of quantitative comparative sequence analysis.

A statistical method of comparative sequence analysis that combines horizontal and vertical correlations among aligned sequences is introduced. It is based on the analysis mainly of quartet combinations of sequences considered as geometric configurations in sequence space. Numerical invariants related to relative internal segment lengths are assigned to each such configuration and statistical averages of these invariants are established. They are used for internal calibration of the topology of divergence and for quantitative determination of the noise level. Comparison of computer simulations with experimental data reveals the high sensitivity of assignment of basic topologies even if much randomized. In addition, these procedures are checked by vertical analysis of the aligned sequences to allow the study of divergences with positionally varying substitution probabilities.

Base Sequence↗