RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina

<p>Abstract</p> <p>Background</p> <p>The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including age-related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina.</p> <p>Description</p> <p>RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression meta-data and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed in 5 different model systems: drosophila, zebrafish, rat, mouse and human. The database is supported by a platform that is designed to easily integrate new functionalities and is also frequently updated.</p> <p>Conclusion</p> <p>The results obtained from various biological scenarios can be visualized, compared and downloaded. The results of a case study are presented that highlight the utility of RETINOBASE. Overall, RETINOBASE provides efficient access to the global expression profiling of retinal genes from different organisms under various conditions.</p

Increased dietary protein in the second trimester of gestation increases live weight gain and carcass composition in weaner calves to 6 months of age

Genetically similar nulliparous Polled Hereford heifers from a closed pedigree herd were used to evaluate the effects of dietary protein during the first and second trimester of gestation upon fetal, placental and postnatal growth. Heifers were randomly allocated into two groups at 35d post AI (35dpc) to a single bull and fed High (15.7%CP) or Low (5.9%CP) protein in the first trimester (T1). At 90dpc, half of each nutritional treatment group changed to a High or Low protein diet for the second trimester until 180dpc (T2). High protein intake in the second trimester increased birthweight in females (P = 0.05) but there was no effect of treatment upon birthweight when taken over both sexes. Biparietal diameter was significantly increased by high protein in the second trimester with the effect being greater in the female (P = 0.02) but also significant overall (P = 0.05). Placental weight was positively correlated with birth weight, fibroblast volume, and relative blood vessel volume (P < 0.05). Placental fibroblast density was increased and trophoblast volume decreased in the high protein first trimester treatment group (P <0.05). There was a trend for placental weight to be increased by high protein in the second trimester (P = 0.06). Calves from heifers fed the high protein treatment in the second trimester weighed significantly more on all occasions preweaning (at one month (P = 0.0004), 2 mths (P = 0.006), 3 mths (P = 0.002), 4 mths (P = 0.01), 5 mths (P = 41 0.03), 6 mths (P = 0.001)), and grew at a faster rate over the 6 month period. By 6 mths of age the calves from heifers fed high nutrition in the second trimester weighed 33kg heavier than those fed the low diet in the second trimester. These results suggest that dietary protein in early pregnancy alters the development of the bovine placenta and calf growth to weaning

Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae

The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular “dialogue” between the partners that includes interactions between the host’s innate immune system and the symbiont

Comment inciter les régulations métacognitives pour favoriser la résolution de problèmes mal structurés?

Parvenir à inciter les processus métacognitifs à l'oeuvre dans des résolutions de problèmes mal structurés constitue un enjeu important. Ces processus sont en effet requis mais rarement mobilisés de façon spontanée. Trois études ont été proposées, afin de vérifier les effets positifs de différents types d'incitations métacognitives sur l'émergence de régulations métacognitives et sur les performances à des problèmes peu structurés. Les résultats ont permis d'une part, de clarifier la nature et le fonctionnement des régulations métacognitives, exprimées sous la forme d'expériences et de prises de décisions métacognitives. D'autre part, il a été possible de circonscrire certaines conditions d'efficacité des incitations métacognitives proposées. Sur la base de ces constats empiriques, des réponses aux points encore en suspens du concept de métacognition ont été proposées