Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

<p>Abstract</p> <p>Background</p> <p>Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp) and highly compact (~1 gene/kb) genome of the human parasite <it>Encephalitozoon cuniculi </it>has been fully sequenced. The aim of this study was to characterize noncoding motifs that could be involved in regulation of gene expression in <it>E. cuniculi </it>and to show whether these motifs are conserved among the phylum Microsporidia.</p> <p>Results</p> <p>To identify such signals, 5' and 3'RACE-PCR experiments were performed on different E. cuniculi mRNAs. This analysis confirmed that transcription overrun occurs in E. cuniculi and may result from stochastic recognition of the AAUAAA polyadenylation signal. Such experiments also showed highly reduced 5'UTR's (<7 nts). Most of the <it>E. cuniculi </it>genes presented a CCC-like motif immediately upstream from the coding start. To characterize other signals involved in differential transcriptional regulation, we then focused our attention on the gene family coding for ribosomal proteins. An AAATTT-like signal was identified upstream from the CCC-like motif. In rare cases the cytosine triplet was shown to be substituted by a GGG-like motif. Comparative genomic studies confirmed that these different signals are also located upstream from genes encoding ribosomal proteins in other microsporidian species including <it>Antonospora locustae</it>, <it>Enterocytozoon bieneusi</it>, <it>Anncaliia algerae </it>(syn. <it>Brachiola algerae</it>) and <it>Nosema ceranae</it>. Based on these results a systematic analysis of the ~2000 E. cuniculi coding DNA sequences was then performed and brings to highlight that 364 translation initiation codons (18.29% of total CDSs) had been badly predicted.</p> <p>Conclusion</p> <p>We identified various signals involved in the maturation of E. cuniculi mRNAs. Presence of such signals, in phylogenetically distant microsporidian species, suggests that a common regulatory mechanism exists among the microsporidia. Furthermore, 5'UTRs being strongly reduced, these signals can be used to ensure the accurate prediction of translation initiation codons for microsporidian genes and to improve microsporidian genome annotation.</p

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

<p>Abstract</p> <p>Background</p> <p>Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.</p> <p>Results</p> <p>First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain <it>Sphingomonas paucimobilis </it>sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.</p> <p>Conclusions</p> <p>We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.</p

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

BACKGROUND: A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, “Candidatus Methanomethylophilus alvus", “Candidatus Methanomassiliicoccus intestinalis” and Methanomassiliicoccus luminyensis. RESULTS: Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, “Ca. M. alvus” and “Ca. M. intestinalis” do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS: This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmat

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Approche autonome pour la localisation et la surveillance de l'intégrité d'un véhicule automobile en environnement complexe

COMPIEGNE-BU (601592101) / SudocSudocFranceF

Comparison of estimation methods to quantify methane plume concentration at high spatial resolution from hyperspectral images

International audienceThe detection and the quantification of greenhouse gases is essential to climate change studies, avoid leakages in industrial site, prevent accidental explosions. Because of these properties, methane (CH 4) is an important target gas in remote sensing quantification. We focused on industrial plume quantification with data obtained during airborne campaign with HySpex-Neo hyperspectral camera. The 1.4 m of spatial resolution allows comparing quantification methods on real data combined with full or semi-synthetic plume case. A linear method largely used in the literature is compared with a quantification method based on the rebuilt background image and the estimation of plume transmission (PTE method). We have developed a hybrid approach using intermediate results of two previous methods. The hybrid method is based on the optimal estimation (OE) formalism and is providing uncertainty estimates. We show that the linear method underestimates the concentration of plumes for concentration above 5000 ppm.m. For low reflectance pixels, the hybrid method is more robust than the PTE method. The uncertainty of the hybrid method is about 30% for pixels with concentrations above 5000 ppm.m. For a HySpex-Neo image, the total mass of the plume is underestimated by 30% with the linear method compared to the hybrid method.La détection et la quantification des gaz à effet de serre sont essentielles pour étudier le changement climatique, éviter les fuites sur les sites industriels et prévenir les explosions accidentelles. En raison de ces propriétés, le méthane (CH4) est un gaz cible important pour la quantification par télédétection. Nous nous sommes concentrés sur la quantification des panaches industriels avec les données obtenues lors de la campagne aéroportée avec la caméra hyperspectrale HySpex-Neo. La résolution spatiale de 1,4 m permet de comparer les méthodes de quantification sur des données réelles combinées à un cas de panache complet ou semi-synthétique. Une méthode linéaire largement utilisée dans la littérature est comparée à une méthode de quantification basée sur la reconstruction de l'image de fond et l'estimation de la transmission du panache (méthode PTE). Une méthode hybride, utilisant les résultats intermédiaires des deux méthodes précédentes, est basée sur une estimation optimale et fournit une étude de la propagation des erreurs. Nous montrons que la méthode linéaire sous-estime la concentration des panaches pour une concentration supérieure à 15 000 ppm.m. Les méthodes PTE et hybride retrouvent une concentration en bon accord avec la concentration synthétique. Pour les pixels de faible réflectance, la méthode hybride est plus robuste que la méthode PTE

Performance Evaluation of Fault Detection Algorithms as Applied to Automotive Localisation

A very important parameter to measure the quality of localisation systems is integrity in Global Navigation Satellite System (GNSS). Within this perspective, Integrity first considers the removal of outliers at the receiver level. It is typically monitored applying Fault Detection and Exclusion (FDE) algorithms. Then, integrity ensures a high probability bounded position error by computing protection levels. However, their performance depends very much on the faults characteristics and data redundancy which reflect the environment in which location estimates are made, and thus differ from scenario to scenario. After analyzing the specificities of GNSS based positioning in the automotive context, and the mechanism of the Receiver Autonomous Integrity Monitoring (RAIM) algorithm, a novel Kalman Filter based FDE algorithm is proposed in this paper. This is validated using hybrid simulation techniques based on real data from vehicle proprioceptive sensors and partially simulated GNSS data, where satellite configuration and faults characteristics can be controlled. The chosen scenario is that found in urban environments, representative of areas where localisation systems suffer many difficulties when mounted on land platforms. A comparison between the RAIM and the new algorithm is included