Activity Report 2012. Project-Team RMOD. Analyses and Languages Constructs for Object-Oriented Application Evolution

Activity Report 2012 Project-Team RMOD Analyses and Languages Constructs for Object-Oriented Application Evolutio

An ontology for Xenopus anatomy and development

YesFunding provided by the Open Access Authors Fund

Identification of post-transcriptionally regulated Xenopus tropicalis maternal mRNAs by microarray

Cytoplasmic control of the adenylation state of mRNAs is a critical post-transcriptional process involved in the regulation of mRNAs stability and translational efficiency. The early development of Xenopus laevis has been a major model for the study of such regulations. We describe here a microarray analysis to identify mRNAs that are regulated by changes in their adenylation state during oogenesis and early development of the diploid frog Xenopus tropicalis. The microarray data were validated using qRT–PCR and direct analysis of the adenylation state of endogenous maternal mRNAs during the period studied. We identified more than 500 mRNAs regulated at the post-transcriptional level among the 3000 mRNAs potentially detected by the microarray. The mRNAs were classified into nine different adenylation behavior categories. The various adenylation profiles observed during oocyte maturation and early development and the analyses of 3′-untranslated region sequences suggest that previously uncharacterized sequence elements control the adenylation behavior of the newly identified mRNAs. These data should prove useful in identifying mRNAs with important functions during oocyte maturation and early development

Project-Team RMoD 2013 Activity Report

Activity Report 2013 Project-Team RMOD Analyses and Languages Constructs for Object-Oriented Application Evolutio

Introduction

En 2006, Jacques Commaille, Pierre Rouillard et Serge Wolikow écrivaient : « La politique nationale de développement des MSH est une réalité et un projet ». Aujourd’hui, comme ils le souhaitaient, ce projet est « totalement inscrit dans la réalité » nationale de la recherche en sciences humaines et sociales. Si nous avons fait le choix, en 2020, de rééditer l’ouvrage de 2006 consacré aux Maisons des sciences de l’homme, c’est avec la dou..

Evaluation of time profile reconstruction from complex two-color microarray designs

<p>Abstract</p> <p>Background</p> <p>As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (more replicates of the conditions of interest for the same number of arrays). However, the interpretation of the measurements is less straightforward and a reconstruction method is needed to convert the observed ratios into the genuine profile of interest (e.g. a time profile). The potential advantages of using these alternative designs thus largely depend on the success of the profile reconstruction. Therefore, we compared to what extent different linear models agree with each other in reconstructing expression ratios and corresponding time profiles from a complex design.</p> <p>Results</p> <p>On average the correlation between the estimated ratios was high, and all methods agreed with each other in predicting the same profile, especially for genes of which the expression profile showed a large variance across the different time points. Assessing the similarity in profile shape, it appears that, the more similar the underlying principles of the methods (model and input data), the more similar their results. Methods with a dye effect seemed more robust against array failure. The influence of a different normalization was not drastic and independent of the method used.</p> <p>Conclusion</p> <p>Including a dye effect such as in the methods lmbr_dye, anovaFix and anovaMix compensates for residual dye related inconsistencies in the data and renders the results more robust against array failure. Including random effects requires more parameters to be estimated and is only advised when a design is used with a sufficient number of replicates. Because of this, we believe lmbr_dye, anovaFix and anovaMix are most appropriate for practical use.</p

Project-Team RMoD (Analyses and Language Constructs for Object-Oriented Application Evolution) 2011 Activity Report

This is the yearly report of the RMOD team (http://rmod.lille.inria.fr/). A good way to understand what we are doing