Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

BACKGROUND: The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin. RESULTS: Using a technique for analysis of auto-correlations based on linear projection, we identified the sequences responsible for the bias. Prokaryotic and lower eukaryotic genomes are covered with ubiquitous patterns that we termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50 bp in length. They belong to what we named the "flexible pattern" type, in that there is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11 bp periodic bias. CONCLUSION: Judging from the structure of the patterns, we suggest that they may define a dense network of protein interaction sites in chromosomes

Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

BACKGROUND: Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes) but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability. RESULTS: We report 11 gene families conserved throughout eukaryotes from yeasts (such as Saccharomyces cerevisiae) to bilaterian animals (such as Drosophila melanogaster or Caenorhabditis elegans). This evolutionarily wide conservation suggests they were present in the last common ancestors of fungi and metazoan animals. None of these 11 gene families are found in human nor mouse genomes, and their absence generally extends to all vertebrates. A total of 8 out of these 11 gene families have orthologs in plants, suggesting they were present in the Last Eukaryotic Common Ancestor (LECA). We investigated known functional information for these 11 gene families. This allowed us to correlate some of the lost gene families to loss of capabilities. CONCLUSION: Mammalian and vertebrate genomes lost evolutionary conserved ancestral genes that are probably otherwise not dispensable in eukaryotes. Hence, the human genome, which is generally viewed as being the result of increased complexity and gene-content, has also evolved through simplification and gene losses. This acknowledgement confirms, as already suggested, that the genome of our far ancestor was probably more complex than ever considered

Where do animal α-amylases come from? An interkingdom trip

AbstractAlpha-amylases are widely found in eukaryotes and prokaryotes. Few amino acids are conserved among these organisms, but at an intra-kingdom level, conserved protein domains exist. In animals, numerous conserved stretches are considered as typical of animal α-amylases. Searching databases, we found no animal-type α-amylases outside the Bilateria. Instead, we found in the sponge Reniera sp. and in the sea anemone Nematostella vectensis, α-amylases whose most similar cognate was that of the amoeba Dictyostelium discoideum. We found that this “Dictyo-type” α-amylase was shared not only by these non-Bilaterian animals, but also by other Amoebozoa, Choanoflagellates, and Fungi. This suggested that the Dictyo-type α-amylase was present in the last common ancestor of Unikonts. The additional presence of the Dictyo-type in some Ciliates and Excavates, suggests that horizontal gene transfers may have occurred among Eukaryotes. We have also detected putative interkingdom transfers of amylase genes, which obscured the historical reconstitution. Several alternative scenarii are discussed

Evolution de la prise en charge et du pronostic des syndromes coronariens aigus en France entre 1995 et 2010

Dans les pays développés , les syndromes coronariens aigus (SCA) représentent une pathologie fréquente et grave et les maladies cardiovasculaires restent la première cause de mortalité en Europe. Au cours de la dernière décennie, pourtant, plusieurs travaux épidémiologiques ont suggéré une baisse sensible de l'incidence des infarctus et la mortalité cardiovasculaire est dorénavant en recul dans de très nombreux pays, dont la France. La cardiologie est une des disciplines médicales qui a connu les plus grands bouleversements au cours des 25 dernières années et la prise en charge des SCA ainsi que le profil des patients ont considérablement évolué. Dans ce contexte, il nous a paru intéressant d'étudier la manière dont le devenir des patients présentant un infarctus aigu pouvait participer à cette baisse générale de la mortalité cardio-vasculaire. A partir de quatre enquêtes longitudinales successives répertoriant les SCA (USIK 1995, USIC 2000, FAST-MI 2005, FAST-MI 2010) et de l observatoire national des actes de cardiologie interventionnelle (ONACI), nous avons observé, après standardisation sur les caractéristiques initiales des différentes cohortes, une baisse spectaculaire de la mortalité quel que soit le type de SCA (avec sus-décalage ST [SCA ST+] ou ST-elevation myocardial infarction [STEMI] ; sans sus-décalage ST [SCA ST-] ou non-ST-elevation myocardial infarction [NSTEMI]). Cette évolution peut être expliquée par plusieurs paramètres : amélioration de la prise en charge globale, meilleur suivi des recommandations, changement de profils des patients (pour les STEMI), développement de la stratégie invasive et utilisation de nouvelles thérapeutiques, évolution des techniques de cardiologie interventionnelle Ainsi, il apparaît que l'amélioration du pronostic des patients atteints d'infarctus est bien un des éléments ayant pu contribuer à la baisse de la mortalité cardiovasculaire. L enjeu aujourd hui est de maintenir ces résultats, de renforcer les mesures de prévention et d améliorer le pronostic à long terme en développant notamment les programmes d éducation thérapeutique.In developed countries, acute coronary syndromes (ACS) represent a common and serious disease, and cardiovascular disease remains the leading cause of death in Europe. During the last decade, however, several epidemiological studies have suggested a significant reduction in the incidence of myocardial infarction and cardiovascular mortality in many countries, including France. Over the past 25 years, Cardiology has dramatically evolved and the management of ACS, as well as patient risk profile have substantially changed. In this context, we aimed to evaluate how the outcomes of patients with acute myocardial infarction could participate in the general decline in cardiovascular mortality. From four successive longitudinal surveys including ACS (USIK 1995, USIC 2000, FAST-MI 2005, FAST-MI 2010) and the national observatory of interventional cardiology (ONACI) we observed, after standardization of the cohorts on baseline clinical characteristics, a dramatic decline in mortality regardless of the type of ACS (STEMI, ST-elevation myocardial infarction, NSTEMI, non-ST-elevation myocardial infarction). This evolution can be explained by several factors: overall improvement in organization of care, better implementation of recommendations, substantial change in the patient risk profile (for STEMI), increasing use of invasive strategy and adjunctive therapies, improved technique for Interventional Cardiology ... Therefore, the improved prognosis of patients with myocardial infarction appears to be one of the factors that have contributed to the decline in cardiovascular mortality. For the future, the challenge will be to maintain these results, strengthen preventive measures and improve long-term prognosis in particular by developing the therapeutic education programs.PARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

BACKGROUND: Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. RESULTS: Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. CONCLUSION: The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest

CASSIOPE: An expert system for conserved regions searches

<p>Abstract</p> <p>Background</p> <p>Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in genome evolution and their implications for the study of biological systems. Detection of conserved regions (descending from a common ancestor) not only helps clarify genome evolution but also makes it possible to identify quantitative trait loci (QTLs) and investigate gene function.</p> <p>The identification and comparison of conserved regions on a genome scale is computationally intensive, making process automation essential. Three key requirements are necessary: consideration of phylogeny to identify orthologs between multiple species, frequent updating of the annotation and panel of compared genomes and computation of statistical tests to assess the significance of identified conserved gene clusters.</p> <p>Results</p> <p>We developed a modular system superimposed on a multi-agent framework, called CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution). CASSIOPE automatically identifies statistically significant conserved regions between multiple genomes based on automated phylogenies and statistical testing. Conserved regions were searched for in 19 species and 1,561 hits were found. To our knowledge, CASSIOPE is the first system to date that integrates evolutionary biology-based concepts and fulfills all three key requirements stated above. All results are available at <url>http://194.57.197.245/cassiopeWeb/displayCluster?clusterId=1</url></p> <p>Conclusion</p> <p>CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions.</p> <p><b>Source code </b>is freely available, please contact: <email>[email protected]</email></p

Dopamine and Serotonin Are Both Required for Mate-Copying in Drosophila melanogaster

Mate-copying is a form of social learning in which the mate-choice decision of an individual (often a female) is influenced by the mate-choice of conspecifics. Drosophila melanogaster females are known to perform such social learning, and in particular, to mate-copy after a single observation of one conspecific female mating with a male of one phenotype, while the other male phenotype is rejected. Here, we show that this form of social learning is dependent on serotonin and dopamine. Using a pharmacological approach, we reduced dopamine or serotonin synthesis in adult virgin females with 3-iodotyrosine (3-IY) and DL-para-chlorophenylalanine (PCPA), respectively, and then tested their mate-copying performance. We found that, while control females without drug treatment copied the choice of the demonstrator, drug-treated females with reduced dopamine or serotonin chose randomly. To ensure the specificity of the drugs, the direct precursors of the neurotransmitters, either the dopamine precursor L-3,4-dihydroxyphenylalanine (L-DOPA) or the serotonin precursor 5-L-hydroxytryptophan (5-HTP) were given together with the drug, (respectively 3-IY and PCPA) resulting in a full rescue of the mate-copying defects. This indicates that dopamine and serotonin are both required for mate-copying. These results give a first insight into the mechanistic pathway underlying this form of social learning in D. melanogaster

Impact of the use of cryobank samples in a selected cattle breed: a simulation study

<p>Abstract</p> <p>Background</p> <p>High selection pressure on domestic cattle has led to an undesirable increase in inbreeding, as well as to the deterioration of some functional traits which are indirectly selected. Semen stored in a cryobank may be a useful way to redirect selection or limit the loss of genetic diversity in a selected breed. The purpose of this study was to analyse the efficiency of current cryobank sampling methods, by investigating the benefits of using cryopreserved semen in a selection scheme several generations after the semen was collected.</p> <p>Methods</p> <p>The theoretical impact of using cryopreserved semen in a selection scheme of a dairy cattle breed was investigated by simulating various scenarios involving two negatively correlated traits and a change in genetic variability of the breed.</p> <p>Results</p> <p>Our results indicate that using cryopreserved semen to redirect selection will have an impact on negatively selected traits only if it is combined with major changes in selection objectives or practices. If the purpose is to increase genetic diversity in the breed, it can be a viable option.</p> <p>Conclusions</p> <p>Using cryopreserved semen to redirect selection or to improve genetic diversity should be carried out with caution, by considering the pros and cons of prospective changes in genetic diversity and the value of the selected traits. However, the use of genomic information should lead to more interesting perspectives to choose which animals to store in a cryobank and to increase the value of cryobank collections for selected breeds.</p