Biomedical subjects

A Ehrenfeucht

Publications and source records attributed to A Ehrenfeucht.

6 recordsLinked to original sources

PubMed2006

A model for the origin of internal eliminated segments (IESs) and gene rearrangement in stichotrichous ciliates.

A characteristic feature of ciliates (ciliated protozoans) is their nuclear dimorphism: the presence of two kinds of functionally different nuclei in the same cell--a micronucleus (MIC) and the macronucleus (MAC). In the stichotrichous group of ciliates the organization of DNA in the MIC is dramatically different from that in the MAC. Genes in the MIC consist of the sequence of segments, called MDSs, which are separated by short noncoding pieces of DNA, called IESs. Moreover, the order of MDSs in the MIC may be scrambled compared to their order in the MAC, and also some MDSs may be inverted with respect to each other. In this paper, we consider the evolutionary origin of this bizarre form of MIC genes, and in particular we postulate that the insertion of IESs as well as possible scramblings/inversions have resulted from a repair of one or more breaks in a DNA molecule. We propose a specific repair scheme, and postulate that this repair scheme applied to a coiled structure of a DNA molecule that has undergone multiple breaks can produce IES insertions and/or scrambled/inverted MIC gene patterns. All experimentally demonstrated as well as theoretical MIC gene patterns can be produced in this way.

Animals↗

PubMed2003

Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates.

The micronuclear versions of genes in stichotrichous ciliates are interrupted by multiple, short, non-coding DNA segments called internal eliminated segments, or IESs. IESs divide a gene into macronuclear destined segments, or MDSs. In some micronuclear genes MDSs are in a scrambled disorder. During development of a micronucleus into a macronucleus after cell mating the IESs are excised from micronuclear genes and the MDSs are spliced in the sequentially correct order. Pairs of short repeat sequences in the ends of MDSs undergo homologous recombination to excise IESs and splice MDSs. However, the repeat sequences are too short to guide unambiguously their own alignment in preparation for recombination. Based on experiments by others on the distantly related ciliate, Paramecium, we propose a molecular model of template-guided recombination to explain the excision of the 100,000-150,000 IESs and splicing of MDSs, including unscrambling, in the genome of stichotrichous ciliates. The model solves the problem of correct pairing of pointers, precisely identifies MDS-IES junctions, and provides for irreversible recombination.

Animals↗

PubMed1986

Information content of binding sites on nucleotide sequences.

Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (R sequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (R frequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between R sequence and R frequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome.

Bacterial Proteins↗

PubMed1982

Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.

We have used a "Perceptron" algorithm to find a weighting function which distinguishes E. coli translational initiation sites from all other sites in a library of over 78,000 nucleotides of mRNA sequence. The "Perceptron" examined sequences as linear representations. The "Perceptron" is more successful at finding gene beginnings than our previous searches using "rules" (see previous paper). We note that the weighting function can find translational initiation sites within sequences that were not included in the training set.

Base Sequence↗

PubMed1982

How an unfamiliar thing should be called.

An empirical method is described to derive good names for unfamiliar objects. It is based on three principles: (1) The names should be within users' linguistic capacities; (2) names should be informationally efficient; (3) names should form a classification system. The principles lead to a three-step method: (1) Subjects generate names for the objects; (2) a subset of the names, which fulfills the principles, is selected; (3) how good the names are is tested by matching and recall tasks. Steps 2 and 3 are iterated to improve the names. The names that result are natural, short, easily matched with their physical referents, and well recalled. The method is generalizable and ought to be useful in a large variety of situations where names for unfamiliar objects are needed.

Form Perception↗

PubMed1973

Organization of memory.

A new learning algorithm is presented that may have applications in the theory of natural and artificial intelligence.

Brain↗