microRNAs calibrate T cell responses by regulating mTOR.

International audienc

Genome Assembly Techniques

Since the publication of the human genome in 2001, the price and the time of DNA sequencing have dropped dramatically. The genome of many more species have since been sequenced, and genome sequencing is an ever more important tool for biologists. This trend will likely revolutionize biology and medicine in the near future where the genome sequence of each individual person, instead of a model genome for the human, becomes readily accessible. Nevertheless, genome assembly remains a challenging computational problem, even more so with second generation sequencing technologies which generate a greater amount of data and make the assembly process more complex. Research to quickly, cheaply and accurately assemble the increasing amount of DNA sequenced is of great practical importance. In the first part of this thesis, we present two software developed to improve genome assemblies. First, Jellyfish is a fast k-mer counter, capable of handling large data sets. k-mer frequencies are central to many tasks in genome assembly (e.g. for error correction, finding read overlaps) and other study of the genome (e.g. finding highly repeated sequences such as transposons). Second, Chromosome Builder is a scaffolder and contig placement software. It aims at improving the accuracy of genome assembly. In the second part of this thesis we explore several problems dealing with graphs. The theory of graphs can be used to solve many computational problems. For example, the genome assembly problem can be represented as finding an Eulerian path in a de Bruijn graph. The physical interactions between proteins (PPI network), or between transcription factors and genes (regulatory networks), are naturally expressed as graphs. First, we introduce the concept of "exactly 3-edge-connected" graphs. These graphs have only a remote biological motivation but are interesting in their own right. Second, we study the reconstruction of ancestral network which aims at inferring the state of ancestral species' biological networks based on the networks of current species

Impact of Erysiphe alphitoides on transpiration and photosynthesis in Quercus robur leaves

International audienceOak powdery mildew, (Erysiphe alphitoides) causes one of the most common diseases of oaks. We assessed the impact of this pathogen on photosynthesis and water relations of infected leaves using greenhouse grown oak seedlings. Transpiration of seedling infected by oak powdery mildew was also investigated. Altogether, E. alphitoides had a low impact on host gas exchange whether at leaf or whole plant scale. Maximal stomatal conductance of infected leaves was reduced by 20-30% as compared to healthy controls. Severely infected seedlings did not experience any detectable change of whole plant transpiration. The reduction in net CO 2 assimilation, A n , was less than proportional to the fraction infected leaf area. Powdery mildew reduced both the maximal light driven electron flux (J max) and the apparent maximal carboxylation velocity (Vc max) although Vc max was slightly more impacted than J max. No compensation of the infection occurred in healthy leaves of partly infected seedlings as the reduced photosynthesis in the infected leaves was not paralleled by increased A n levels in the healthy leaves of the seedlings. However, E. alphitoides had a strong impact on leaf lifespan of infected leaves. It is concluded that the moderate effect of E. alphitoides on oak might be related to the small impact on net CO 2 assimilation rates and on tree transpiration; nevertheless, the severe reduction in leaf lifespan of heavily infected leaves may lead to decreased carbon uptake over the growth season

Influence of site and stand factors on Hymenoscyphus fraxineus-induced basal lesions

Hymenoscyphus fraxineus is an invasive fungus in Europe and causes a severe decline affecting ash, which began in the late 1990s. One of the symptoms associated with the disease is lesions in the outer bark of the collar area. However, the aetiology of these basal lesions, and in particular the relative roles of H.fraxineus and Armillaria species, is still controversial; moreover, little is known about the influence of environmental factors on the disease epidemiology.This study therefore surveyed 42 plots located in northeastern France, in an area affected by ash decline since 2008, in order to determine which environmental factors condition the severity of lesions associated with H.fraxineus on ash collar. The spatial pattern that is a consequence of the invasive spread of the disease was taken into account in the analysis, using a spatial hierarchical Bayesian model fitted by integrated nested laplace approximation (INLA).Results show that while basal lesions are tightly associated with H.fraxineus, their severity is influenced by the Armillaria species present in the plot. Sites with vegetation indicating moist conditions, or more humid topographical positions, were associated with more developed basal lesions

Lagged rejuvenation of groundwater indicates internal flow structures and hydrological connectivity

Large proportions of rainwater and snowmelt infiltrate into the subsurface before contributing to stream flow and stream water quality. Subsurface flow dynamics steer the transport and transformation of contaminants, carbon, weathering products and other biogeochemistry. The distribution of groundwater ages with depth is a key feature of these flow dynamics. Predicting these ages are a strong test of hypotheses about subsurface structures and time-varying processes. Chlorofluorocarbon (CFC)-based groundwater ages revealed an unexpected groundwater age stratification in a 0.47 km(2) forested catchment called Svartberget in northern Sweden. An overall groundwater age stratification, representative for the Svartberget site, was derived by measuring CFCs from nine different wells with depths of 2-18 m close to the stream network. Immediately below the water table, CFC-based groundwater ages of already 30 years that increased with depth were found. Using complementary groundwater flow models, we could reproduce the observed groundwater age stratification and show that the 30 year lag in rejuvenation comes from return flow of groundwater at a subsurface discharge zone that evolves along the interface between two soil types. By comparing the observed groundwater age stratification with a simple analytical approximation, we show that the observed lag in rejuvenation can be a powerful indicator of the extent and structure of the subsurface discharge zone, while the vertical gradient of the age-depth-relationship can still be used as a proxy of the overall aquifer recharge even when sampled in the discharge zone. The single age stratification profile measured in the discharge zone, close to the aquifer outlet, can reveal the main structure of the groundwater flow pattern from recharge to discharge. This groundwater flow pattern provides information on the participation of groundwater in the hydrological cycle and indicates the lower boundary of hydrological connectivity

Relationships between Oak powdery mildew incidence and severity and commensal fungi

Oak (Quercus robur) powdery mildew is a common and damaging fungal disease. In a local survey at Reading, UK, oak powdery mildew was common on trees of all height classes but was most common on trees of 3-9m. A variety of other fungal species were commonly found growing in association with oak powdery mildew colonies. The abundance of such fungi was estimated through stratified sample surveys for 2.5 years. The taxa most commonly associated with oak powdery mildew were Acremonium sp., Trichoderma sp., Ampelomyces/Phoma sp. and Leptosphaerulina australis. Nearly 90% of mildew colonies were associated with L. australis, which is not generally considered as a mycoparasite or antagonist, in contrast with the other three fungi. Abundance varied between June and October surveys. Acremonium sp. abundance was greater in summer samplings whereas L. australis and Trichoderma sp. abundances were greater in autumn samplings. Ampelomyces/Phoma sp. was never observed in the absence of powdery mildew. Relationships between the mildew-associated fungi and oak powdery mildew appeared curved and differed significantly between sampling years. L. australis was positively correlated with the other three associated fungi studied when powdery mildew was also present. The variety and high population densities of the mildew associated fungi suggest that they may be important in determining the final density of oak mildew and the damage caused by it

Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe

Dothistroma needle blight (DNB) is an important disease of Pinus species that can be caused by one of two distinct but closely related pathogens; Dothistroma septosporum and Dothistroma pini. Dothistroma septosporum has a wide geographic distribution and is relatively well-known. In contrast, D. pini is known only from the United States and Europe, and there is a distinct lack of knowledge regarding its population structure and genetic diversity. The recent development of 16 microsatellite markers for D. pini provided an opportunity to investigate the diversity, structure, and mode of reproduction for populations collected over a period of 12 years, on eight different hosts in Europe. In total, 345 isolates from Belgium, the Czech Republic, France, Hungary, Romania, Western Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, and Ukraine were screened using microsatellite and species-specific mating type markers. A total of 109 unique multilocus haplotypes were identified and structure analyses suggested that the populations are influenced by location rather than host species. Populations from France and Spain displayed the highest levels of genetic diversity followed by the population in Ukraine. Both mating types were detected in most countries, with the exception of Hungary, Russia and Slovenia. Evidence for sexual recombination was supported only in the population from Spain. The observed population structure and several shared haplotypes between non-bordering countries provides good evidence that the movement of D. pini in Europe has been strongly influenced by human activity in Europe

microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes

The development and homeostasis of multicellular organisms relies on gene regulation within individual constituent cells. Gene regulatory circuits that increase the robustness of gene expression frequently incorporate microRNAs as post-transcriptional regulators. Computational approaches, synthetic gene circuits and observations in model organisms predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell variability in the expression of target genes. However, whether microRNAs directly regulate variability of endogenous gene expression remains to be tested in mammalian cells. Here we use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variability of protein expression in developing mouse thymocytes. We find two distinct mechanisms that control variation in the activation-induced expression of the microRNA target CD69. First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is coregulated with the target mRNA Cd69 to form an activation-induced incoherent feed-forward loop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69 to modulate cellular responses to activation. The ability of microRNAs to render gene expression more uniform across mammalian cell populations may be important for normal development and for disease

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.

Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation