DNA CODING FOR IMAGE STORAGE USING IMAGE COMPRESSION TECHNIQUES

International audienceLiving in the age of the digital media explosion the urge for finding new efficient methods of data storage increases significantly. Existing storage devices such as hard disks, flash, tape or even optical storage have limited durability in the range of 5 to 20 years. Recent studies have proven that the method of DNA data storage introduces a strong candidate to achieve data longevity. The DNA's biological properties permit the compression of a great amount of information into an extraordinary small volume while also promising efficient data storage for millions of years with no loss of information. This work proposes a new encoding scheme especially designed for the encoding of still images, extending the existing algorithms of DNA data storage by introducing image compression techniques

KTA : a framework for integrating expert knowledge and experiment memory in transcriptome analysis

International audienceThis paper addresses the problem of the integration of expert knowledge in a data mining process. We present the KTA ( integrating expert Knowledge in Transcriptome analysis) framework which allows the mining process to be driven by prior knowledge on the application domain. KTA is embedded in the MEDIANTE project for evaluating and using DNA microarrays, the CORESE semantic search engine and the ANNOT module which annotates scientific publications.Cet article propose une solution au problème de l’intégration de la connaissance experte dans le processus de data mining. Nous présentons KTA (integrating expert Knowledge in Transcriptome Analysis) qui permet au processus de data mining d’être conduit par des connaissances à priori sur le domaine d’application. KTA est une composante du projet MEDIANTE dont le but est d’évaluer et utiliser des biopuces à ADN

Mining Biomedical Texts to Generate Semantic Annotations

This report focuses on text mining in the biomedical domain for the generation of semantic annotations based on a formal model which is ontology. We start by exposing the generic methodology for the generation of annotations from texts. Then, we present a state of the art on different knowledge extraction techniques used on biomedical texts. We propose our approach based on Semantic Web Technologies and Natural Language Processing (NLP): it relies on formal ontologies to generate semantic annotations on scientific articles and on other knowledge sources (databases, experiment sheets). This approach can be extended to other do-mains requiring experiments and massive data analyses. Finally, we conclude with a discussion about our work and we present some learnt lessons

Mining Biomedical Texts to Generate Semantic Annotations

This report focuses on text mining in the biomedical domain for the generation of semantic annotations based on a formal model which is ontology. We start by exposing the generic methodology for the generation of annotations from texts. Then, we present a state of the art on different knowledge extraction techniques used on biomedical texts. We propose our approach based on Semantic Web Technologies and Natural Language Processing (NLP): it relies on formal ontologies to generate semantic annotations on scientific articles and on other knowledge sources (databases, experiment sheets). This approach can be extended to other do-mains requiring experiments and massive data analyses. Finally, we conclude with a discussion about our work and we present some learnt lessons

Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis

International audienceABSTRACT: BACKGROUND: In severe obesity, as well as in normal development, the growth of adipose tissue is the result of an increase in adipocyte size and numbers, which is underlain by the stimulation of adipogenic differentiation of precursor cells. A better knowledge of the pathways that regulate adipogenesis is therefore essential for an improved understanding of adipose tissue expansion. As microRNAs (miRNAs) have a critical role in many differentiation processes, our study aimed to identify the role of miRNA-mediated gene silencing in the regulation of adipogenic differentiation. RESULTS: We used deep sequencing to identify small RNAs that are differentially expressed during adipogenesis of adipose tissue-derived stem cells. This approach revealed the un-annotated miR-642a-3p as a highly adipocyte-specific miRNA. We then focused our study on the miR-30 family, which was also up-regulated during adipogenic differentiation and for which the role in adipogenesis had not yet been elucidated. Inhibition of the miR-30 family blocked adipogenesis, whilst over-expression of miR-30a and miR-30d stimulated this process. We additionally showed that both miR-30a and miR-30d target the transcription factor RUNX2, and stimulate adipogenesis via the modulation of this major regulator of osteogenesis. CONCLUSIONS: Overall, our data suggest that the miR-30 family plays a central role in adipocyte development. Moreover, as adipose tissue-derived stem cells can differentiate into either adipocytes or osteoblasts, the down-regulation of the osteogenesis regulator RUNX2 represents a plausible mechanism by which miR-30 miRNAs may contribute to adipogenic differentiation of adipose tissue-derived stem cells

Innovative approach for transcriptomic analysis of obligate intracellular pathogen: selective capture of transcribed sequences of Ehrlichia ruminantium

<p>Abstract</p> <p>Background</p> <p>Whole genome transcriptomic analysis is a powerful approach to elucidate the molecular mechanisms controlling the pathogenesis of obligate intracellular bacteria. However, the major hurdle resides in the low quantity of prokaryotic mRNAs extracted from host cells. Our model <it>Ehrlichia ruminantium (ER</it>), the causative agent of heartwater, is transmitted by tick <it>Amblyomma variegatum</it>. This bacterium affects wild and domestic ruminants and is present in Sub-Saharan Africa and the Caribbean islands. Because of its strictly intracellular location, which constitutes a limitation for its extensive study, the molecular mechanisms involved in its pathogenicity are still poorly understood.</p> <p>Results</p> <p>We successfully adapted the SCOTS method (Selective Capture of Transcribed Sequences) on the model Rickettsiales <it>ER </it>to capture mRNAs. Southern Blots and RT-PCR revealed an enrichment of <it>ER</it>'s cDNAs and a diminution of ribosomal contaminants after three rounds of capture. qRT-PCR and whole-genome <it>ER </it>microarrays hybridizations demonstrated that SCOTS method introduced only a limited bias on gene expression. Indeed, we confirmed the differential gene expression between poorly and highly expressed genes before and after SCOTS captures. The comparative gene expression obtained from <it>ER </it>microarrays data, on samples before and after SCOTS at 96 hpi was significantly correlated (R²= 0.7). Moreover, SCOTS method is crucial for microarrays analysis of <it>ER</it>, especially for early time points post-infection. There was low detection of transcripts for untreated samples whereas 24% and 70.7% were revealed for SCOTS samples at 24 and 96 hpi respectively.</p> <p>Conclusions</p> <p>We conclude that this SCOTS method has a key importance for the transcriptomic analysis of <it>ER </it>and can be potentially used for other Rickettsiales. This study constitutes the first step for further gene expression analyses that will lead to a better understanding of both <it>ER </it>pathogenicity and the adaptation of obligate intracellular bacteria to their environment.</p

In Utero Exposure to Maternal Diabetes Impairs Vascular Expression of Prostacyclin Receptor in Rat Offspring

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RNY-derived small RNAs as a signature of coronary artery disease

International audienceBackgroundData from next generation sequencing technologies uncovered the existence of many classes of small RNAs. Recent studies reported that small RNAs are released by cells and can be detected in the blood. In this report, we aimed to discover the occurrence of novel circulating small RNAs in coronary artery disease (CAD).MethodsWe used high-throughput sequencing of small RNAs from human and mouse apoptotic primary macrophages, and analyzed the data by empirical Bayes moderated t-statistics to assess differential expression and the Benjamini and Hochberg method to control the false discovery rate. Results were then confirmed by Northern blot and RT-qPCR in foam cells and in two animal models for atherosclerosis, namely ApoE −/− and Ldlr −/− mouse lines. Quantitative RT-PCR to detect identified small RNAs, the RNY-derived small RNAs, was performed using sera of 263 patients with CAD compared to 514 matched healthy controls; the Student t-test was applied to statistically assess differences. Associations of small RNAs with clinical characteristics and biological markers were tested using Spearman’s rank correlations, while multivariate logistic regressions were performed to test the statistical association of small RNA levels with CAD.ResultsHere, we report that, in macrophages stimulated with pro-apoptotic or pro-atherogenic stimuli, the Ro-associated non-coding RNAs, called RNYs or Y-RNAs, are processed into small RNAs (~24–34 nt) referred to as small-RNYs (s-RNYs), including s-RNY1-5p processed from RNY1. A significant upregulation of s-RNY expression was found in aortic arches and blood plasma from ApoE −/− and Ldlr −/− mice and in serum from CAD patients (P <0.001). Biostatistical analysis revealed a positive association of s-RNY1-5p with hs-CRP and ApoB levels; however, no statistical interaction was found between either of these two markers and s-RNY1-5p in relation to the CAD status. Levels of s-RNY1-5p were also independent from statin and fibrate therapies.ConclusionOur results position the s-RNY1-5p as a relevant novel independent diagnostic biomarker for atherosclerosis-related diseases. Measurement of circulating s-RNY expression would be a valuable companion diagnostic to monitor foam cell apoptosis during atherosclerosis pathogenesis and to evaluate patient’s responsiveness to future therapeutic strategies aiming to attenuate apoptosis in foam cells in advanced atherosclerotic lesions

Hypoxia-inducible factor 1α is a new target of microphthalmia-associated transcription factor (MITF) in melanoma cells

In melanocytes and melanoma cells α-melanocyte stimulating hormone (α-MSH), via the cAMP pathway, elicits a large array of biological responses that control melanocyte differentiation and influence melanoma development or susceptibility. In this work, we show that cAMP transcriptionally activates Hif1a gene in a melanocyte cell–specific manner and increases the expression of a functional hypoxia-inducible factor 1α (HIF1α) protein resulting in a stimulation of Vegf expression. Interestingly, we report that the melanocyte-specific transcription factor, microphthalmia-associated transcription factor (MITF), binds to the Hif1a promoter and strongly stimulates its transcriptional activity. Further, MITF “silencing” abrogates the cAMP effect on Hif1a expression, and overexpression of MITF in human melanoma cells is sufficient to stimulate HIF1A mRNA. Our data demonstrate that Hif1a is a new MITF target gene and that MITF mediates the cAMP stimulation of Hif1a in melanocytes and melanoma cells. Importantly, we provide results demonstrating that HIF1 plays a pro-survival role in this cell system. We therefore conclude that the α-MSH/cAMP pathway, using MITF as a signal transducer and HIF1α as a target, might contribute to melanoma progression