Transcriptome analysis of antigenic variation in Plasmodium falciparum - var silencing is not dependent on antisense RNA

BACKGROUND: Plasmodium falciparum, the causative agent of the most severe form of malaria, undergoes antigenic variation through successive presentation of a family of antigens on the surface of parasitized erythrocytes. These antigens, known as Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) proteins, are subject to a mutually exclusive expression system, and are encoded by the multigene var family. The mechanism whereby inactive var genes are silenced is poorly understood. To investigate transcriptional features of this mechanism, we conducted a microarray analysis of parasites that were selected to express different var genes by adhesion to chondroitin sulfate A (CSA) or CD36. RESULTS: In addition to oligonucleotides for all predicted protein-coding genes, oligonucleotide probes specific to each known var gene of the FCR3 background were designed and added to the microarray, as well as tiled sense and antisense probes for a subset of var genes. In parasites selected for adhesion to CSA, one full-length var gene (var2csa) was strongly upregulated, as were sense RNA molecules emanating from the 3' end of a limited subset of other var genes. No global relationship between sense and antisense production of var genes was observed, but notably, some var genes had coincident high levels of both antisense and sense transcript. CONCLUSION: Mutually exclusive expression of PfEMP1 proteins results from transcriptional silencing of non-expressed var genes. The distribution of steady-state sense and antisense RNA at var loci are not consistent with a silencing mechanism based on antisense silencing of inactive var genes. Silencing of var loci is also associated with altered regulation of genes distal to var loci

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

Background: Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III). Results: Microarrays were designed to compare gene transcription profiles under a temporal As(III) exposure. Transcriptome kinetic analysis demonstrated the existence of two phases in arsenic response. The expression of approximatively 14% of the whole genome was significantly affected by an As(III) early stress and 4% by an As(III) late exposure. The early response was characterized by arsenic resistance, oxidative stress, chaperone synthesis and sulfur metabolism. The late response was characterized by arsenic metabolism and associated mechanisms such as phosphate transport and motility. The major metabolic changes were confirmed by chemical, transcriptional, physiological and biochemical experiments. These early and late responses were defined as general stress response and specific response to As(III), respectively. Conclusion: Gene expression patterns suggest that the exposure to As(III) induces an acute response to rapidly minimize the immediate effects of As(III). Upon a longer arsenic exposure, a broad metabolic response was induced. These data allowed to propose for the first time a kinetic model of the As(III) response in bacteria

Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica

Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alternative usage of splicing and polyadenylation sites in Entamoeba histolytica using RNA-Seq. First, we identified a large number of rarely spliced alternative junctions and then showed that the occurrence of these alternative splicing events is correlated with splicing site sequence, occurrence of constitutive splicing events and messenger RNA abundance. Our results implied the majority of these alternative splicing events are likely to be stochastic error of splicing machineries, and we estimated the corresponding error rates. Second, we observed extensive microheterogeneity of polyadenylation cleavage sites, and the extent of such microheterogeneity is correlated with the occurrence of constitutive cleavage events, suggesting most of such microheterogeneity is likely to be stochastic. Overall, we only observed a small fraction of alternative splicing and polyadenylation isoforms that are unlikely to be solely stochastic, implying the functional relevance of alternative splicing and polyadenylation in E. histolytica is limited. Lastly, we revised the gene models and annotated their 3′UTR in AmoebaDB, providing valuable resources to the community

Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability

Cryptochromes are conserved flavoprotein receptors found throughout the biological kingdom with diversified roles in plant development and entrainment of the circadian clock in animals. Light perception is proposed to occur through flavin radical formation that correlates with biological activity in vivo in both plants and Drosophila. By contrast, mammalian (Type II) cryptochromes regulate the circadian clock independently of light, raising the fundamental question of whether mammalian cryptochromes have evolved entirely distinct signaling mechanisms. Here we show by developmental and transcriptome analysis that Homo sapiens cryptochrome - 1 (HsCRY1) confers biological activity in transgenic expressing Drosophila in darkness, that can in some cases be further stimulated by light. In contrast to all other cryptochromes, purified recombinant HsCRY1 protein was stably isolated in the anionic radical flavin state, containing only a small proportion of oxidized flavin which could be reduced by illumination. We conclude that animal Type I and Type II cryptochromes may both have signaling mechanisms involving formation of a flavin radical signaling state, and that light independent activity of Type II cryptochromes is a consequence of dark accumulation of this redox form in vivo rather than of a fundamental difference in signaling mechanism

High resolution mapping of population change in breeding birds in Wallonia (Southern Belgium)

Patterns of fine-scale change in bird abundance across different landscapes may inform about the driving forces behind bird communities evolution. We compare km²-resolution map of breeding birds in Wallonia (Southern Belgium) at 10 years interval. The maps are based on repeated sampling transects conducted inside a km²-grid. Spatial modelling techniques were applied on these two dataset using environmental variables produced by the LifeWatch-WB Project. Variables are issued from pixel-based land cover classification of orthophoto mapping and satellite images, with a resolution of 2 meters and are available for the two periods corresponding to bird data. Others variables included in the model are climatic, topographic or soil attributes. For each bird species, spatial models built with data from the first period are projected with the value of the environmental variables for the more recent period, and viceversa. Moreover, another method is to compare models built independently on the two periods. Modelling methods mainly are of two types: Generalized Additive Model (GAM) and RandomForest. Comparison between prediction and real data at the km² level offers insight about the causes of change in bird populations

High resolution mapping of population change in breeding birds in Wallonia (Southern Belgium)

Patterns of fine-scale change in bird abundance across different landscapes may inform about the driving forces behind bird communities evolution. We compare km²-resolution map of breeding birds in Wallonia (Southern Belgium) at 10 years interval. The maps are based on repeated sampling transects conducted inside a km²-grid. Spatial modelling techniques were applied on these two dataset using environmental variables produced by the LifeWatch-WB Project. Variables are issued from pixel-based land cover classification of orthophoto mapping and satellite images, with a resolution of 2 meters and are available for the two periods corresponding to bird data. Others variables included in the model are topographic and soil attributes. For each bird species, spatial models built with data from the first period are projected with the value of the environmental variables for the more recent period, and vice-versa. Moreover, another method is to compare models built independently on the two periods. GAM (Generalized Additive Models) are used for modelling. These analyses allow to study if it is possible to predict the change in bird populations thanks to the data of changes of land cover

Molecular analysis of revertants from a respiratory-deficient mutant affecting the center o domain of cytochrome b in Saccharomyces cerevisiae.

In bc complexes, cytochrome b plays a major role in electron transfer and in proton translocation across the membrane. Several inhibitor-resistant and respiratory-deficient mutants have already been used to study the structure-function relationships of this integral membrane protein. We describe here the selection and the molecular analysis of revertants from a thermo-sensitive mit-mutant of known nucleotide changes. Among 80 independent pseudo-wild type revertants screened by DNA-labelled oligonucleotide hybridization, 33 have been sequenced. Eight suppressor mutations, affecting a region critical for both the function and the binding of center o inhibitors (end of helix C) were identified. Two of them were found to be more resistant to myxothiazol

Temporal transferability of species abundance models to study the changes of breeding bird species based on land cover changes

peer reviewedAim: Species distribution models have become important tools for studying changes in biodiversity. Most studies use these models to evaluate the impact of global changes on biodiversity. For that purpose, scenarios are used that are based on changes in land use and/or land cover, or on climatic changes. However, the temporal transferability of such models depends heavily on modeling methods, environmental predictors and the ecological traits of species. Here, we evaluate the power of modeling tools to predict changes in bird species abundances based on observed changes in land cover. Location: Wallonia, Belgium Methods: To assess this temporal transferability, this research makes use of two biological and two environmental datasets, both sampled with a 10-year interval. This allows us to compare the predictions of models for another period than the period used to fit the models, with actual values for species abundance. We also analyzed the impact of ecological traits on the temporal transferability. Generalized additive models were fitted for 75 breeding birds. While a lot of studies use occurrence data, we used abundance data for fitting models. Abundance data contains more information and should allow us to better capture abundance changes in bird populations. Results: For the majority of species studied, the results show a low temporal transferability. With a few exceptions, e.g., species with softwood habitats, predicted changes do not correspond to observed changes. For certain bird species, e.g., those on arable lands, we observed an increase in predicted abundances in the future, while these species actually decreased. Few ecological traits seem to significantly impact the models’ transferability. Main conclusions: Our findings show that it is difficult to predict abundance changes of bird species based only on land cover changes. It is necessary to add other predictors into the models, e.g., predictors of habitat quality or spatial configuration

Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence.

International audienceThe bacterium Legionella pneumophila is found ubiquitously in aquatic environments and can cause a severe pneumonia in humans called Legionnaires' disease. How this bacterium switches from intracellular to extracellular life and adapts to different hosts and environmental conditions is only partly understood. Here we used RNA deep sequencing from exponentially (replicative) and post exponentially (virulent) grown L. pneumophila to analyze the transcriptional landscape of its entire genome. We established the complete operon map and defined 2561 primary transcriptional start sites (TSS). Interestingly, 187 of the 1805 TSS of protein-coding genes contained tandem promoters of which 93 show alternative usage dependent on the growth phase. Similarly, over 60% of 713 here identified ncRNAs are phase dependently regulated. Analysis of their conservation among the seven L. pneumophila genomes sequenced revealed many strain specific differences suggesting that L. pneumophila contains a highly dynamic pool of ncRNAs. Analysis of six ncRNAs exhibiting the same expression pattern as virulence genes showed that two, Lppnc0584 and Lppnc0405 are indeed involved in intracellular growth of L. pneumophila in A. castellanii. Furthermore, L. pneumophila encodes a small RNA named RsmX that functions together with RsmY and RsmZ in the LetA-CsrA regulatory pathway, crucial for the switch to the virulent phenotype. Together our data provide new insight into the transcriptional organization of the L. pneumophila genome, identified many new ncRNAs and will provide a framework for the understanding of virulence and adaptation properties of L. pneumophila

The alien's identity: consequences of taxonomic status for the international bumblebee trade regulations

International audienceThe species international trade leads to multiple non-native invasions. Besides species invasions, commercial exchanges may also contribute to translocation between closely related taxa or allopatric populations. Consequently, preserving endemic taxa and specificity of local populations require to regulate commercial translocations of species or populations. To be efficient such regulation needs a resolved taxonomy and a thorough analysis of the population structure of native taxa/populations. To provide guidelines for an efficient regulation of the trade of Bombus terrestris within its natural range, we analyzed its taxonomy and its population structure using an integrative taxonomic approach. Our results show that B. terrestris translocations involve two species, three subspecies, and several populations with weak differentiation. These different levels of differentiation imply specific and appropriate regulations of translocations with different levels of prioritization. We ultimately assess the relevance of current policies and propose potentially efficient regulations for policy-makers. Such integrative taxonomic approach should be used in other traded polytypic species