PubMed Health⌕ Search

Biomedical subjects

E Yeramian

Publications and source records attributed to E Yeramian.

11 recordsLinked to original sources
PubMed2000

The physics of DNA and the annotation of the Plasmodium falciparum genome.

A gene identification procedure is formulated, based on large-scale structural analyses of genomic sequences. The structural property is the physical - thermal - stability of the DNA double-helix, as described by the classical helix-coil model. The analyses are detailed for the Plasmodium falciparum genome, which represents one of the most difficult cases for the gene identification problem (notably because of the extreme AT-richness of the genome). In this genome, the coding domains (either uninterrupted genes or exons in split genes) are accurately identified as regions of high thermal stability. The conclusion is based on the study of the available cloned genes, of which 17 examples are described in detail. These examples demonstrate that the physical criterion is valid for the detection of coding regions whose lengths extend from a few base pairs up to several thousand base pairs. Accordingly, the structural analyses can provide a powerful and convenient tool for the identification of complex genes in the P. falciparum genome. The limits of such a scheme are discussed. The gene identification procedure is applied to the completely sequenced chromosomes (2 and 3), and the results are compared with the database annotations. The structural analyses suggest more or less extensive revision to the annotations, and also allow new putative genes to be identified in the chromosome sequences. Several examples of such new genes are described in detail.

Animals↗
PubMed2000

Genes and the physics of the DNA double-helix.

The processing of the genetic information stored in the double-helical DNA implies the separation of the two strands, the physics of which is described by the helix-coil transition model. Is there a relationship between genetic maps and DNA physical stability maps that plot the sequence-specific propensity for the thermal disruption of the double-helix? Here, with appropriate methodological formulations, such maps are derived for a large set of sequences, including complete genomes. The superposition of the two maps leads to a contrasted picture with correlations ranging between two extremes: from almost perfect (with the genes precisely delineated as stable regions) to more or less complete unrelatedness. The simplest explanation for the results is that the observed striking correlations correspond to the relics of a primeval organisation of the genetic message, with the physics of DNA playing a role in the delimitation of coding regions. In order to trace the evolutionary fate of this signal further, a detailed study of the yeast complete genome is performed. In this study, the superposition of the genetic and physical stability maps is examined in the light of information concerning gene duplication. On the basis of this analysis it is concluded that the 'signature' associated with the supposed archaic signal is in the process of being erased, most probably because the underlying feature is no longer under selective pressure. There are many evolutionary implications for the results presented and for their proposed interpretations, notably concerning models of mutational dynamics in relation to erasure processes.

Algorithms↗
PubMed1999

Comparative sequence analysis of human minisatellites showing meiotic repeat instability.

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.

CpG Islands↗
PubMed1994

CRP fixes the rotational orientation of covalently closed DNA molecules.

Five minicircles of 284 bp were constructed with a reporter sequence located approximately opposite a CRP binding site. The spacing between the center of the CRP site and this sequence is varied within 1.2 helical turns. The reactivity of the reference sequence to DNAse I was determined on the minicircles and on the corresponding fragments, in both the absence and presence of CRP. A rigorous mathematical analysis of the data shows that in the absence of CRP no preferred rotational orientation of the DNA is observed. In contrast, binding of CRP fixes, in a phase-dependent manner, the rotational orientation of the reporter sequence in the minicircles. This result illustrates the transmission at a distance along the DNA molecule of a structural modification. Such effects modulate the extent of synergy between activators and polymerases during the initiation of transcription.

Binding Sites↗
PubMed1989

Long-range structural effects in supercoiled DNA: statistical thermodynamics reveals a correlation between calculated cooperative melting and contextual influence on cruciform extrusion.

We have previously described [K. M. Sullivan and D. M. J. Lilley (1986) Cell 47, 817-827] a set of sequences, called C-type inducing sequences, which cause cruciform extrusion by adjacent inverted repeats to occur by an abnormal kinetic pathway involving a large denatured region of DNA. In this paper we apply statistical thermodynamic DNA helix melting theory to these sequences. We find a marked correlation between the ability of sequences to confer C-type cruciform character experimentally and their calculated propensity to undergo cooperative melting, and no exceptions have been found. The correlations are both qualitative and quantitative. Thus the ColE1 flanking sequences behave as single melting units, while the DNA of the S-type plasmid pIRbke8 exhibits no propensity to melt in the region of the bke cruciform. The results of the calculations are also fully consistent with the following experimental observations: 1. the ability of the isolated colL and colR fragments of the ColE1 flanking sequences, as well as the short sequence col30, to confer C-type character; 2. C-type induction by an A + T rich Drosophila sequence; 3. low-temperature cruciform extrusion by an (AT)34 sequence; 4. the effect of changing sequences at a site 90 base pairs (bp) removed from the inverted repeat; 5. the effects of systematic deletion of the colL sequence; and 6. the effects of insertion of various sequences in between the colL sequence and the xke inverted repeat. These studies show that telestability effects on thermal denaturation as predicted from equilibrium helix melting theory of linear DNA molecules may explain all the features that are revealed by studying the extrusion of cruciforms in circular DNA molecules subjected to superhelical stress.

Base Composition↗
PubMed1989

A rigorous mathematical treatment for the excluded volume effect in Monte Carlo simulations of polymeric chains.

In Monte Carlo simulations of polymeric chains, the chains are most often represented as spheres, or cylinders with flat ends. In this methodological paper, we adopt a representation of the chains as spherocylinders (continuous cylinders ending in semispheres). With such a representation the testing for chain overlap, which is the crucial step for the inclusion of the excluded volume effect in the simulations, can be defined in a rigorous geometrical framework. The treatment we then derive fulfills the following features: it allows a very simple, automatic, and exhaustive classification of all the possible configurations; and it provides a physical representation for steric hindrance effects more natural than the flat-ended cylinders. Notably, this representation avoids the introduction of artificial anisotropies in the treatments. This spherocylindrical representation is also well suited for several types of calculations that can be involved in elaborate Monte Carlo simulations.

Biopolymers↗
PubMed1986

Acetylcholine receptors are not functionally independent.

Analysis of current recordings from acetylcholine-activated channels has largely rested so far on the hypothesis of independence, which states that the opening of one channel does not influence that of its neighbors. We have submitted this assumption to several tests, using as experimental material single channel currents from rat myotubes. We found that, even though the distribution of multiple channel openings may be approximated by the Poisson law, openings are strongly coupled. This conclusion is derived from the analysis of two-time properties associated with patch-clamp data. We show how these properties, which contain more detailed information than the stationary probabilities, can be calculated in practice and why a Poisson analysis is misleading in the present case. The implications of our findings are finally discussed in terms of channel structure and function.

Animals↗
PubMed1985

Actions of betahistine at histamine receptors in the brain.

The actions of betahistine (N alpha-methyl-2-pyridylethylamine) on brain histamine receptors were investigated in a series of biological models. [3H]Mepyramine binding to H1-receptors in membranes from guinea-pig cerebellum was inhibited by betahistine with a Ki value of 31 microM. The binding of [3H]mepyramine in brain of the living mouse was inhibited by betahistine in high dosages (150-300 mg/kg). In slices from mouse cerebral cortex, betahistine induced [3H]glycogen hydrolysis in a concentration-dependent manner with an EC50 value of 9.0 microM with a maximal effect 57% that of histamine. Mepyramine and triprolidine, two H1-receptor antagonists, inhibited the betahistine-induced glycogenolysis with Ki values of 28 nM and 7 nM respectively. In slices from guinea-pig hippocampus, betahistine stimulated the accumulation of cyclic AMP in the presence of 5 microM impromidine, a H2-receptor agonist. The maximal effect represented 22% of that elicited by histamine at the H1-receptor and the EC50 value was 32.4 microM. Mepyramine at 0.1 microM partially blocked the response to betahistine. Together these various observations indicate that betahistine is a partial agonist at cerebral H1-receptors. Finally, betahistine was not an agonist at histamine H3-autoreceptors but was a rather potent antagonist of the inhibitory effect of exogenous histamine on [3H]histamine release elicited by K+ depolarisation in slices from rat cerebral cortex (Ki = 6.9 microM).

Animals↗
PubMed1985

N-ethylmaleimide-induced changes in agonist affinity for histamine H1-receptors in the guinea pig brain.

The effect of the thiol-alkylating agent, N-ethylmaleimide (NEM), on histamine (HA) H1-receptors from guinea pig cerebellum, labeled with [3H]mepyramine, was investigated. The properties of [3H]mepyramine binding (apparent dissociation constant and maximal number of sites) were not modified by prior treatment of the membranes with 2 or 5 mM NEM. This treatment did not change either the inhibition curves of d-chlorpheniramine or mianserin, two H1-receptor antagonists. In contrast, treatments of membranes with NEM significantly decreased the IC50 values of HA and the slope indexes (pseudo Hill coefficients) of HA inhibition curves, which became inferior to unity. These effects were irreversible, and their extent related to the NEM treatment duration and the NEM concentration. A computer analysis of the data indicated that part of the H1-receptors were converted from a state of low affinity for the amine (IC50 value of 75 microM) into a high agonist affinity state (IC50 value of 2 microM). The change was less marked for partial agonists than for HA. The NEM-induced change was observed in the presence and in the absence of Na+ ions, known to decrease the affinity of HA for H1-receptors. Agonists or antagonists did not protect against the modification of HA affinity induced by NEM. The digitonin-solubilized receptors retained their sensitivity to NEM. Among other thiol reagents, iodoacetamide and iodoacetic acid were ineffective, and organic mercurial agents strongly reduced the number of [3H]mepyramine-binding sites. NEM treatment might alkylate a critical thiol group located outside the ligand-binding domain of the H1 receptor and thereby stabilize the latter in a conformation distinct from that of the activated state.

Animals↗
PubMedDate not supplied

Tandem repeats in complete bacterial genome sequences: sequence and structural analyses for comparative studies.

A series of complete bacterial genome sequences have recently become available and powerful methods have been developed for the identification of tandem repeats on a very large scale. It is thus possible to derive extensive comparative descriptions of such repeats at the level of complete genomes, as illustrated here for three different bacterial genomes: Escherichia coli, Haemophilus influenzae, and Mycobacterium tuberculosis. Such sequence analyses can be usefully complemented by structural characterisations of the repeats.

Bacteria↗