Subgraph spotting in graph representations of comic book images

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record Graph-based representations are the most powerful data structures for extracting, representing and preserving the structural information of underlying data. Subgraph spotting is an interesting research problem, especially for studying and investigating the structural information based content-based image retrieval (CBIR) and query by example (QBE) in image databases. In this paper we address the problem of lack of freely available ground-truthed datasets for subgraph spotting and present a new dataset for subgraph spotting in graph representations of comic book images (SSGCI) with its ground-truth and evaluation protocol. Experimental results of two state-of-the-art methods of subgraph spotting are presented on the new SSGCI dataset.University of La Rochelle (France

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5′TOP sequence

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5′TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5′ UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5′TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signaling to ribosome biogenesis

Development of an efficient cis-trans-cis ribozyme cassette to inactivate plant genes

Summary Inactivation of a targeted gene is one of the main strategies used to understand their precise cellular role. In plants, apart from chemical or physical mutagenesis and random insertions of DNA elements followed by screening for a desired phenotype, the most common strategy to inhibit the expression of a given gene involves RNA silencing. This can be achieved either through antisense suppression, sense over-expression leading to co-suppression, or expression of double-stranded DNA constructs (dsRNA). The use of ribozymes to inhibit gene product accumulation has only been occasionally attempted, mainly because of the more complex genetic engineering procedure involved, although the specificity of ribozymes can be an important factor when targeting close members of a gene family. We report here the development of a new cis -acting ribozyme cassette for the production of RNAs with desired termini. Attention to many details has been brought in order to provide a powerful procedure for plant application. For example, ultrastable GNRA tetraloops were substituted for both loops II and III of cis -acting hammerhead sequences, thereby favouring folding into the catalytically active structure that results in the self-cleavage of all transcripts. We demonstrate the usefulness of this cassette by producing a ribozyme that cleaves in trans , originally embedded in the cis -acting self-cleaving cassette. The activity of the cistrans-cis construct, was demonstrated both in vitro and in vivo , in transgenic plants with the specific cleavage of an mRNA encoding a 2-oxo-glutarate-dependant dioxygenase predominantly expressed in pistils tissues and in leaves, from the wild potato Solanum chacoense

Clustering of Unhealthy Behaviors in the Aerobics Center Longitudinal Study

Background Clustering of unhealthy behaviors has been reported in previous studies; however the link with all-cause mortality and differences between those with and without chronic disease requires further investigation. Objectives To observe the clustering effects of unhealthy diet, fitness, smoking, and excessive alcohol consumption in adults with and without chronic disease and to assess all-cause mortality risk according to the clustering of unhealthy behaviors. Methods Participants were 13,621 adults (aged 20–84) from the Aerobics Center Longitudinal Study. Four health behaviors were observed (diet, fitness, smoking, and drinking). Baseline characteristics of the study population and bivariate relations between pairs of the health behaviors were evaluated separately for those with and without chronic disease using cross-tabulation and a chi-square test. The odds of partaking in unhealthy behaviors were also calculated. Latent class analysis (LCA) was used to assess clustering. Cox regression was used to assess the relationship between the behaviors and mortality. Results The four health behaviors were related to each other. LCA results suggested that two classes existed. Participants in class 1 had a higher probability of partaking in each of the four unhealthy behaviors than participants in class 2. No differences in health behavior clustering were found between participants with and without chronic disease. Mortality risk increased relative to the number of unhealthy behaviors participants engaged in. Conclusion Unhealthy behaviors cluster together irrespective of chronic disease status. Such findings suggest that multi-behavioral intervention strategies can be similar in those with and without chronic disease

Lettre de P. Héroux à Joseph Masson

3 page

Transcription et étude du Roman d'Eledus et Serene : la question du roman idyllique médiéval

Ce mémoire s’articule en deux parties. En ce qui concerne la première, il s’agit de fournir une nouvelle transcription ponctuée du manuscrit BnF NAF 1943, unique témoin, datant de la fin du XIVe siècle, du Roman d’Eledus et Serene. Ce manuscrit n’a été édité qu’une seule fois, en 1923, dans une thèse de John Revell Reinhard comportant plusieurs lacunes et présentant un apparat critique restreint. La seconde partie consiste en une étude générique du Roman d’Eledus et Serene. Bien que ce texte figure traditionnellement dans les listes de romans idylliques médiévaux, aucune étude ne s’est encore employée à statuer sur la légitimité de ce classement. Le genre même du roman idyllique est peu connu, même au sein de la communauté médiéviste, et est encore mal défini. Une première définition, que les critiques s’accordent à qualifier de « dépassée », a été établie en 1913 par Myrrha Lot-Borodine dans son ouvrage Le roman idyllique au Moyen Âge. Depuis lors, bien que plusieurs altérations ponctuelles aient été apportées à cette définition d’origine, aucun travail critique ne s’est encore penché sur l’élaboration d’une nouvelle définition du genre. Ce mémoire s’emploie donc à compiler les caractéristiques génériques qui ont été associées au roman idyllique médiéval par la critique, en diachronie, pour en établir une nouvelle définition, aussi complète et opératoire que possible. Finalement, une analyse du Roman d’Eledus et Serene à la lumière de cette définition et en fonction d’autres témoins du corpus idyllique vise à légitimer son appartenance au genre

Improvement Of The Crystallizability And Expression Of An Rna Crystallization Chaperone

Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex. The Authors 2011. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved2011 © The Authors 2011. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved