Biomedical subjects

A Arneodo

Publications and source records attributed to A Arneodo.

At least 19 recordsLinked to original sources

PubMed2005

From DNA sequence analysis to modeling replication in the human genome.

We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward jumps, with a linear decreasing profile in between two successive jumps. We present a model of replication with well positioned replication origins and random terminations that accounts for the observed characteristic serrated skew profiles. We succeed in identifying 287 pairs of putative adjacent replication origins with an origin spacing approximately 1-2 Mbp that are likely to correspond to replication foci observed in interphase nuclei and recognized as stable structures that persist throughout subsequent cell generations.

DNA Replication↗

PubMed2004

Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?

We explore large-scale nucleotide compositional fluctuations of the human genome using multiresolution techniques. Analysis of the GC content and of the AT and GC skews reveals the existence of rhythms with two main periods of 110+/-20 kb and 400+/-50 kb that enlighten a remarkable cooperative gene organization. We show that the observed nonlinear oscillations are likely to display all the characteristic features of chaotic strange attractors which suggests a very attractive deterministic picture: gene orientation and location, in relation with the structure and dynamics of chromatin, might be governed by a low-dimensional nonlinear dynamical system.

AT Rich Sequence↗

PubMed2003

Transcription-coupled TA and GC strand asymmetries in the human genome.

Analysis of the whole set of human genes reveals that most of them present TA and GC skews, that these biases are correlated to each other and are specific to gene sequences, exhibiting sharp transitions between transcribed and non-transcribed regions. The GC asymmetries cannot be explained solely by a model previously proposed for (G+T) skew based on transitions measured in a small set of human genes. We propose that the GC skew results from additional transcription-coupled mutation process that would include transversions. During evolution, both processes acting on a large majority of genes in germline cells would have produced these transcription-coupled strand asymmetries.

Base Composition↗

PubMed2003

Lagrangian velocity statistics in turbulent flows: effects of dissipation.

We use the multifractal formalism to describe the effects of dissipation on Lagrangian velocity statistics in turbulent flows. We analyze high Reynolds number experiments and direct numerical simulation data. We show that this approach reproduces the shape evolution of velocity increment probability density functions from Gaussian to stretched exponentials as the time lag decreases from integral to dissipative time scales. A quantitative understanding of the departure from scaling exhibited by the magnitude cumulants, early in the inertial range, is obtained with a free parameter function D(h) which plays the role of the singularity spectrum in the asymptotic limit of infinite Reynolds number. We observe that numerical and experimental data are accurately described by a unique quadratic D(h) spectrum which is found to extend from h(min) approximately 0.18 to h(max) approximately 1.

Journal Article↗

PubMed2001

Long-range correlations in genomic DNA: a signature of the nucleosomal structure.

We use the "wavelet transform microscope" to carry out a comparative statistical analysis of DNA bending profiles and of the corresponding DNA texts. In the three kingdoms, one reveals on both signals a characteristic scale of 100-200 bp that separates two different regimes of power-law correlations (PLC). In the small-scale regime, PLC are observed in eukaryotic, in double-strand DNA viral, and in archaeal genomes, which contrasts with their total absence in the genomes of eubacteria and their viruses. This strongly suggests that small-scale PLC are related to the mechanisms underlying the wrapping of DNA in the nucleosomal structure. We further speculate that the large scale PLC are the signature of the higher-order structure and dynamics of chromatin.

Biophysical Phenomena↗

PubMed1996