Genome-wide computational prediction of tandem gene arrays: application in yeasts

<p>Abstract</p> <p>Background</p> <p>This paper describes an efficient <it>in silico </it>method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality.</p> <p>Results</p> <p>Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs.</p> <p>Conclusion</p> <p>The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.</p

Somatostatin and Neuropeptide Y in Cerebrospinal Fluid: Correlations With Amyloid Peptides Aβ1–42 and Tau Proteins in Elderly Patients With Mild Cognitive Impairment

A combination of low cerebrospinal fluid (CSF) Amyloid β1–42 (Aβ1–42) and high Total-Tau (T-Tau) and Phosphorylated-Tau (P-Tau) occurs at a prodromal stage of Alzheimer’s disease (AD) and recent findings suggest that network abnormalities and interneurons dysfunction contribute to cognitive deficits. Somatostatin (SOM) and Neuropeptide Y (NPY) are two neuropeptides which are expressed in GABAergic interneurons with different fates in AD the former only being markedly affected. The aim of this study was to analyze CSF SOM, NPY and CSF Aβ1–42; T-Tau, P-Tau relationships in 43 elderly mild cognitively impairment (MCI) participants from the Biomarker of AmyLoïd pepTide and AlZheimer’s disease Risk (BALTAZAR) cohort. In these samples, CSF SOM and CSF Aβ1–42 on the one hand, and CSF NPY and CSF T-Tau and P-Tau on the other hand are positively correlated. CSF SOM and NPY concentrations should be further investigated to determine if they can stand for early AD biomarkers.Clinical Trial Registration: www.ClinicalTrials.gov, identifier #NCT01315639

Transitions de phase dans les monocouches de lécithines aux interfaces eau-air : un modèle thermodynamique

En s’appuyant sur de récents travaux expérimentaux, nous proposons un modèle visant à décrire le comportement des monocouches de lécithine déposées sur une interface eau-air. Une des principales caractéristiques de ces molécules est leur cosurface anisotrope dans le plan de l’interface. De plus, elles possèdent une tête polaire interagissant fortement avec l’eau. Ces deux propriétés sont prises en compte dans notre modèle où nous représentons les molécules par des rectangles (munis d’une tête polaire) distribués sur un réseau carré. Nous obtenons différentes phases dont une phase nématique bidimensionnelle et une phase où les têtes polaires s’ordonnent, donnant alors une structure hexagonale pour les chaînes. Ces différentes phases sont analogues à celles trouvées par les expérimentateurs en référence

Modèle de transition de phase dans les monocouches de molécules amphiphiles

Nous proposons un modèle de monocouches de molécules amphiphiles déposées sur un support aqueux. Le substrat est représenté par un réseau à mailles carrées, les projections des molécules sur le plan de l'interface eau-air par des rectangles. On fait ainsi apparaître un paramètre d’ordre lié à l'existence d'une direction privilégiée au sein de la monocouche. Nous mettons en évidence deux transitions :

Comparative genomics of protoploid Saccharomycetaceae.

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified

Varia

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Les agglomérations secondaires

Ce dossier consacré aux agglomérations secondaires lémovices et limousines a été envisagé sur la longue durée, du second âge du fer au Moyen Âge. La réflexion a débuté par un réexamen des sources à disposition de l’historien et de l’archéologue travaillant sur cette question. Ensuite, plusieurs chantiers de recherche suffisamment avancés ont donné lieu à des premières synthèses, consacrées aux aspects religieux des agglomérations secondaires antiques de la cité des Lémovices et à la question des « lieux centraux » du Limousin médiéval. Enfin, la présentation de plusieurs études de cas très bien documentées par des études archéologiques récentes a permis de mettre en résonance les cas observés chez les Lémovices et la réflexion globale sur le concept d’agglomération secondaire. This issue is devoted to the Lemovice and Limousin small towns as situated in longue durée history, from the Second Iron Age to the Middle Ages. Investigation beginswith a re-examination of the sources available to historians and archeologists of this topic. Next, several fields of research have been sufficiently explored to develop preliminary syntheses, devoted to the religious aspects of the small towns of Lemovice city in antiquity and the question of the “central sites” of medieval Limousin. Finally, the presentation of several well document case studies in recent archeological research has allowed scholars to situate the observations of Lemovice antiquity with an overall assessment of the concept of small towns. Translation : Marie Bolto